data_7E4L
#
_model_server_result.job_id            ZYWy6loHOeI2cdd7MfDLbA 
_model_server_result.datetime_utc      '2024-11-29 05:38:17' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          7e4l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    7E4L 
#
_exptl.entry_id    7E4L 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              176.002 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'METHYLENEDIPHOSPHONIC ACID' 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         83.53 
_cell.angle_beta          80.43 
_cell.angle_gamma         68.57 
_cell.entry_id            7E4L 
_cell.length_a            46.205 
_cell.length_b            46.398 
_cell.length_c            66.544 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7E4L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 C O2 MDN . A MDN 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc2 C O8 MDN . A MDN 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc3 D MG MG . A MG 302 1_555 G O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc4 D MG MG . A MG 302 1_555 G O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
metalc ? metalc5 D MG MG . A MG 302 1_555 G O HOH . A HOH 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc6 D MG MG . A MG 302 1_555 G O HOH . A HOH 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc7 E O1 MDN . B MDN 301 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc8 E O6 MDN . B MDN 301 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc9 F MG MG . B MG 302 1_555 H O HOH . B HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc10 F MG MG . B MG 302 1_555 H O HOH . B HOH 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc11 F MG MG . B MG 302 1_555 H O HOH . B HOH 465 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? 
metalc ? metalc12 F MG MG . B MG 302 1_555 H O HOH . B HOH 483 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
#
_chem_comp.formula           'C H6 O6 P2' 
_chem_comp.formula_weight    176.002 
_chem_comp.id                MDN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'METHYLENEDIPHOSPHONIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
O3 P1 MDN sing 218 n n 
O3 HO3 MDN sing 219 n n 
P1 O1 MDN doub 220 n n 
P1 O2 MDN sing 221 n n 
P1 C4 MDN sing 222 n n 
O2 HO2 MDN sing 223 n n 
C4 P5 MDN sing 224 n n 
C4 H41 MDN sing 225 n n 
C4 H42 MDN sing 226 n n 
P5 O6 MDN doub 227 n n 
P5 O7 MDN sing 228 n n 
P5 O8 MDN sing 229 n n 
O7 HO7 MDN sing 230 n n 
O8 HO8 MDN sing 231 n n 
#
_atom_sites.entry_id                     7E4L 
_atom_sites.fract_transf_matrix[1][1]    0.021643 
_atom_sites.fract_transf_matrix[1][2]    -0.008496 
_atom_sites.fract_transf_matrix[1][3]    -0.003174 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023154 
_atom_sites.fract_transf_matrix[2][3]    -0.001313 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.015264 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 2 MDN A 1 301 302 MDN MDN . 
D 3 MG A 1 302 303 MG MG . 
E 2 MDN B 1 301 302 MDN MDN . 
F 3 MG B 1 302 303 MG MG . 
G 4 HOH A 1 401 565 HOH HOH . 
G 4 HOH A 2 402 409 HOH HOH . 
G 4 HOH A 3 403 410 HOH HOH . 
G 4 HOH A 4 404 403 HOH HOH . 
G 4 HOH A 5 405 411 HOH HOH . 
G 4 HOH A 6 406 580 HOH HOH . 
G 4 HOH A 7 407 652 HOH HOH . 
G 4 HOH A 8 408 587 HOH HOH . 
G 4 HOH A 9 409 506 HOH HOH . 
G 4 HOH A 10 410 625 HOH HOH . 
G 4 HOH A 11 411 669 HOH HOH . 
G 4 HOH A 12 412 576 HOH HOH . 
G 4 HOH A 13 413 564 HOH HOH . 
G 4 HOH A 14 414 539 HOH HOH . 
G 4 HOH A 15 415 617 HOH HOH . 
G 4 HOH A 16 416 529 HOH HOH . 
G 4 HOH A 17 417 406 HOH HOH . 
G 4 HOH A 18 418 657 HOH HOH . 
G 4 HOH A 19 419 560 HOH HOH . 
G 4 HOH A 20 420 532 HOH HOH . 
G 4 HOH A 21 421 629 HOH HOH . 
G 4 HOH A 22 422 524 HOH HOH . 
G 4 HOH A 23 423 515 HOH HOH . 
G 4 HOH A 24 424 660 HOH HOH . 
G 4 HOH A 25 425 602 HOH HOH . 
G 4 HOH A 26 426 658 HOH HOH . 
G 4 HOH A 27 427 557 HOH HOH . 
G 4 HOH A 28 428 574 HOH HOH . 
G 4 HOH A 29 429 408 HOH HOH . 
G 4 HOH A 30 430 575 HOH HOH . 
G 4 HOH A 31 431 405 HOH HOH . 
G 4 HOH A 32 432 655 HOH HOH . 
G 4 HOH A 33 433 582 HOH HOH . 
G 4 HOH A 34 434 597 HOH HOH . 
G 4 HOH A 35 435 598 HOH HOH . 
G 4 HOH A 36 436 626 HOH HOH . 
G 4 HOH A 37 437 401 HOH HOH . 
G 4 HOH A 38 438 501 HOH HOH . 
G 4 HOH A 39 439 523 HOH HOH . 
G 4 HOH A 40 440 513 HOH HOH . 
G 4 HOH A 41 441 646 HOH HOH . 
G 4 HOH A 42 442 593 HOH HOH . 
G 4 HOH A 43 443 517 HOH HOH . 
G 4 HOH A 44 444 404 HOH HOH . 
G 4 HOH A 45 445 654 HOH HOH . 
G 4 HOH A 46 446 601 HOH HOH . 
G 4 HOH A 47 447 556 HOH HOH . 
G 4 HOH A 48 448 610 HOH HOH . 
G 4 HOH A 49 449 527 HOH HOH . 
G 4 HOH A 50 450 616 HOH HOH . 
G 4 HOH A 51 451 577 HOH HOH . 
G 4 HOH A 52 452 502 HOH HOH . 
G 4 HOH A 53 453 572 HOH HOH . 
G 4 HOH A 54 454 514 HOH HOH . 
G 4 HOH A 55 455 569 HOH HOH . 
G 4 HOH A 56 456 639 HOH HOH . 
G 4 HOH A 57 457 599 HOH HOH . 
G 4 HOH A 58 458 546 HOH HOH . 
G 4 HOH A 59 459 603 HOH HOH . 
G 4 HOH A 60 460 518 HOH HOH . 
G 4 HOH A 61 461 647 HOH HOH . 
G 4 HOH A 62 462 670 HOH HOH . 
G 4 HOH A 63 463 590 HOH HOH . 
G 4 HOH A 64 464 623 HOH HOH . 
G 4 HOH A 65 465 548 HOH HOH . 
G 4 HOH A 66 466 536 HOH HOH . 
G 4 HOH A 67 467 588 HOH HOH . 
G 4 HOH A 68 468 543 HOH HOH . 
G 4 HOH A 69 469 594 HOH HOH . 
G 4 HOH A 70 470 622 HOH HOH . 
G 4 HOH A 71 471 619 HOH HOH . 
G 4 HOH A 72 472 561 HOH HOH . 
G 4 HOH A 73 473 592 HOH HOH . 
G 4 HOH A 74 474 640 HOH HOH . 
G 4 HOH A 75 475 551 HOH HOH . 
G 4 HOH A 76 476 407 HOH HOH . 
G 4 HOH A 77 477 632 HOH HOH . 
G 4 HOH A 78 478 614 HOH HOH . 
G 4 HOH A 79 479 534 HOH HOH . 
G 4 HOH A 80 480 402 HOH HOH . 
G 4 HOH A 81 481 573 HOH HOH . 
G 4 HOH A 82 482 581 HOH HOH . 
G 4 HOH A 83 483 542 HOH HOH . 
G 4 HOH A 84 484 653 HOH HOH . 
G 4 HOH A 85 485 558 HOH HOH . 
G 4 HOH A 86 486 567 HOH HOH . 
G 4 HOH A 87 487 649 HOH HOH . 
G 4 HOH A 88 488 656 HOH HOH . 
G 4 HOH A 89 489 613 HOH HOH . 
G 4 HOH A 90 490 651 HOH HOH . 
G 4 HOH A 91 491 659 HOH HOH . 
G 4 HOH A 92 492 618 HOH HOH . 
H 4 HOH B 1 401 606 HOH HOH . 
H 4 HOH B 2 402 661 HOH HOH . 
H 4 HOH B 3 403 596 HOH HOH . 
H 4 HOH B 4 404 644 HOH HOH . 
H 4 HOH B 5 405 407 HOH HOH . 
H 4 HOH B 6 406 511 HOH HOH . 
H 4 HOH B 7 407 645 HOH HOH . 
H 4 HOH B 8 408 579 HOH HOH . 
H 4 HOH B 9 409 533 HOH HOH . 
H 4 HOH B 10 410 635 HOH HOH . 
H 4 HOH B 11 411 505 HOH HOH . 
H 4 HOH B 12 412 607 HOH HOH . 
H 4 HOH B 13 413 403 HOH HOH . 
H 4 HOH B 14 414 544 HOH HOH . 
H 4 HOH B 15 415 621 HOH HOH . 
H 4 HOH B 16 416 552 HOH HOH . 
H 4 HOH B 17 417 664 HOH HOH . 
H 4 HOH B 18 418 405 HOH HOH . 
H 4 HOH B 19 419 538 HOH HOH . 
H 4 HOH B 20 420 512 HOH HOH . 
H 4 HOH B 21 421 637 HOH HOH . 
H 4 HOH B 22 422 541 HOH HOH . 
H 4 HOH B 23 423 547 HOH HOH . 
H 4 HOH B 24 424 401 HOH HOH . 
H 4 HOH B 25 425 571 HOH HOH . 
H 4 HOH B 26 426 589 HOH HOH . 
H 4 HOH B 27 427 549 HOH HOH . 
H 4 HOH B 28 428 504 HOH HOH . 
H 4 HOH B 29 429 408 HOH HOH . 
H 4 HOH B 30 430 535 HOH HOH . 
H 4 HOH B 31 431 628 HOH HOH . 
H 4 HOH B 32 432 521 HOH HOH . 
H 4 HOH B 33 433 672 HOH HOH . 
H 4 HOH B 34 434 562 HOH HOH . 
H 4 HOH B 35 435 636 HOH HOH . 
H 4 HOH B 36 436 627 HOH HOH . 
H 4 HOH B 37 437 633 HOH HOH . 
H 4 HOH B 38 438 584 HOH HOH . 
H 4 HOH B 39 439 503 HOH HOH . 
H 4 HOH B 40 440 510 HOH HOH . 
H 4 HOH B 41 441 586 HOH HOH . 
H 4 HOH B 42 442 648 HOH HOH . 
H 4 HOH B 43 443 583 HOH HOH . 
H 4 HOH B 44 444 671 HOH HOH . 
H 4 HOH B 45 445 604 HOH HOH . 
H 4 HOH B 46 446 600 HOH HOH . 
H 4 HOH B 47 447 550 HOH HOH . 
H 4 HOH B 48 448 559 HOH HOH . 
H 4 HOH B 49 449 540 HOH HOH . 
H 4 HOH B 50 450 522 HOH HOH . 
H 4 HOH B 51 451 563 HOH HOH . 
H 4 HOH B 52 452 520 HOH HOH . 
H 4 HOH B 53 453 620 HOH HOH . 
H 4 HOH B 54 454 508 HOH HOH . 
H 4 HOH B 55 455 663 HOH HOH . 
H 4 HOH B 56 456 516 HOH HOH . 
H 4 HOH B 57 457 406 HOH HOH . 
H 4 HOH B 58 458 410 HOH HOH . 
H 4 HOH B 59 459 545 HOH HOH . 
H 4 HOH B 60 460 667 HOH HOH . 
H 4 HOH B 61 461 566 HOH HOH . 
H 4 HOH B 62 462 631 HOH HOH . 
H 4 HOH B 63 463 509 HOH HOH . 
H 4 HOH B 64 464 568 HOH HOH . 
H 4 HOH B 65 465 404 HOH HOH . 
H 4 HOH B 66 466 519 HOH HOH . 
H 4 HOH B 67 467 609 HOH HOH . 
H 4 HOH B 68 468 634 HOH HOH . 
H 4 HOH B 69 469 595 HOH HOH . 
H 4 HOH B 70 470 608 HOH HOH . 
H 4 HOH B 71 471 537 HOH HOH . 
H 4 HOH B 72 472 570 HOH HOH . 
H 4 HOH B 73 473 507 HOH HOH . 
H 4 HOH B 74 474 409 HOH HOH . 
H 4 HOH B 75 475 668 HOH HOH . 
H 4 HOH B 76 476 553 HOH HOH . 
H 4 HOH B 77 477 578 HOH HOH . 
H 4 HOH B 78 478 624 HOH HOH . 
H 4 HOH B 79 479 611 HOH HOH . 
H 4 HOH B 80 480 585 HOH HOH . 
H 4 HOH B 81 481 531 HOH HOH . 
H 4 HOH B 82 482 630 HOH HOH . 
H 4 HOH B 83 483 402 HOH HOH . 
H 4 HOH B 84 484 591 HOH HOH . 
H 4 HOH B 85 485 526 HOH HOH . 
H 4 HOH B 86 486 638 HOH HOH . 
H 4 HOH B 87 487 554 HOH HOH . 
H 4 HOH B 88 488 525 HOH HOH . 
H 4 HOH B 89 489 615 HOH HOH . 
H 4 HOH B 90 490 528 HOH HOH . 
H 4 HOH B 91 491 666 HOH HOH . 
H 4 HOH B 92 492 530 HOH HOH . 
H 4 HOH B 93 493 650 HOH HOH . 
H 4 HOH B 94 494 642 HOH HOH . 
H 4 HOH B 95 495 662 HOH HOH . 
H 4 HOH B 96 496 555 HOH HOH . 
H 4 HOH B 97 497 641 HOH HOH . 
H 4 HOH B 98 498 665 HOH HOH . 
H 4 HOH B 99 499 643 HOH HOH . 
H 4 HOH B 100 500 612 HOH HOH . 
H 4 HOH B 101 501 605 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O3 MDN . . . C 2 -3.323 2.927 -5.604 1 12.39 ? O3 MDN 301 A 1 
HETATM 2 P P1 MDN . . . C 2 -4.436 3.843 -5.149 1 11.72 ? P1 MDN 301 A 1 
HETATM 3 O O1 MDN . . . C 2 -5.811 3.365 -5.635 1 12.43 ? O1 MDN 301 A 1 
HETATM 4 O O2 MDN . . . C 2 -4.426 4.069 -3.656 1 11.98 ? O2 MDN 301 A 1 
HETATM 5 C C4 MDN . . . C 2 -4.252 5.437 -5.993 1 11.49 ? C4 MDN 301 A 1 
HETATM 6 P P5 MDN . . . C 2 -2.885 6.547 -5.527 1 11.07 ? P5 MDN 301 A 1 
HETATM 7 O O6 MDN . . . C 2 -1.884 6.527 -6.633 1 11.52 ? O6 MDN 301 A 1 
HETATM 8 O O7 MDN . . . C 2 -3.555 7.888 -5.411 1 11.33 ? O7 MDN 301 A 1 
HETATM 9 O O8 MDN . . . C 2 -2.299 6.115 -4.228 1 10.44 ? O8 MDN 301 A 1 
#
_model_server_stats.io_time_ms              56 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           9 
#