# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Nov 22 15:42:20 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (4R,7S)-7-(N'-hydroxy-N-methylcarbamimidoyl)-1-methyl-4-[(sulfooxy)amino]-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=N/O)\[C@H]1N(C[C@H](NO[S](O)(=O)=O)c2cnn(C)c12)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 VMM  VMM  "ETX0462 (Bound form)"  ligand  40  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VMM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 VMM  C16  C  CR56  0  -0.146   4.7399  3.5181  -16.9558
 VMM  C17  C  CR15  0  -0.098   4.0000  2.4299  -16.4626
 VMM  C20  C  CH3   0  -0.527   6.8571  1.9094  -14.5320
 VMM  C21  C  CR56  0   0.511   5.9207  3.4635  -16.2521
 VMM  C22  C  C     0   0.698   6.4525  6.7588  -16.3888
 VMM  C01  C  CH3   0  -0.526   9.6297  5.8282  -16.9439
 VMM  C03  C  C     0   0.513   8.2025  3.7963  -17.2096
 VMM  C06  C  CR16  0  -0.312   7.0645  4.4118  -16.4167
 VMM  C08  C  C     0  -0.362   5.7592  5.3138  -18.2883
 VMM  C09  C  CR16  0  -0.210   4.4540  4.5691  -17.9793
 VMM  N02  N  NH1   0  -0.651   9.3745  4.4591  -17.3225
 VMM  N04  N  N     0  -0.241   7.9669  2.6346  -17.7031
 VMM  N07  N  NR6   0  -0.480   6.5342  5.5928  -17.0861
 VMM  N10  N  NH1   0  -0.343   3.4339  5.5442  -17.5828
 VMM  N18  N  N     0  -0.278   4.6763  1.7762  -15.5372
 VMM  N19  N  NR5   0  -0.337   5.8372  2.4199  -15.4138
 VMM  O05  O  OH1   0  -0.586   9.0686  2.1504  -18.3906
 VMM  O11  O  OC2   0  -0.475   2.2559  4.8198  -17.2454
 VMM  O13  O  OS    0  -0.617   0.0008  4.2824  -17.7996
 VMM  O14  O  OS    0  -0.698   0.7378  6.6590  -17.9989
 VMM  O15  O  OS    0  -0.619   1.5243  5.0889  -19.6246
 VMM  O23  O  O     0  -0.491   6.9284  6.9412  -15.2885
 VMM  S12  S  S     0   1.661   1.0577  5.1336  -18.2689
 VMM  H1   H  HCR5  0   0.258   3.0095  2.1044  -16.7426
 VMM  H2   H  HCH3  0   0.267   6.3885  1.5169  -13.6337
 VMM  H3   H  HCH3  0   0.257   7.4316  1.1202  -15.0154
 VMM  H4   H  HCH3  0   0.259   7.5342  2.7110  -14.2484
 VMM  H6   H  HCH3  0   0.257  10.7064  5.9810  -16.9479
 VMM  H7   H  HCH3  0   0.231   9.1837  6.5550  -17.6272
 VMM  H8   H  HCH3  0   0.243   9.2791  6.0396  -15.9362
 VMM  H9   H  HCR6  0   0.327   7.4458  4.7196  -15.4403
 VMM  H10  H  H     0   0.291   6.3595  4.6716  -18.9337
 VMM  H11  H  H     0   0.299   5.5679  6.2268  -18.8442
 VMM  H12  H  HCR6  0   0.281   4.1096  4.1239  -18.9155
 VMM  H13  H  HNH1  0   0.394  10.0416  4.0467  -17.9535
 VMM  H14  H  HNH1  0   0.392   3.6750  5.9765  -16.6954
 VMM  H15  H  HOH1  0   0.469   8.7740  1.2975  -18.7231
 VMM  OX   O  OH1   0  -0.612   5.7959  7.7018  -17.0630
 VMM  H5   H  H     0   0.511   0.2980  6.8101  -17.1433
 VMM  H16  H  HOH1  0   0.490   5.7800  8.5122  -16.5350

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 VMM  C08  C09  single    1.534  0.020  1.534
 VMM  C08  N07  single    1.457  0.020  1.457
 VMM  C09  N10  single    1.466  0.020  1.466
 VMM  C09  C16  single    1.495  0.020  1.495
 VMM  N10  O11  single    1.423  0.020  1.423
 VMM  O11  S12  single    1.607  0.020  1.607
 VMM  O15  S12  double    1.434  0.020  1.434
 VMM  O05  N04  single    1.386  0.020  1.386
 VMM  N07  C22  single    1.361  0.020  1.361
 VMM  N07  C06  single    1.457  0.020  1.457
 VMM  C16  C17  aromatic  1.405  0.020  1.405
 VMM  C16  C21  aromatic  1.376  0.020  1.376
 VMM  N04  C03  double    1.284  0.020  1.284
 VMM  C22  O23  double    1.213  0.020  1.213
 VMM  C17  N18  aromatic  1.319  0.020  1.319
 VMM  C03  N02  single    1.351  0.020  1.351
 VMM  C03  C06  single    1.517  0.020  1.517
 VMM  S12  O13  double    1.436  0.020  1.436
 VMM  S12  O14  single    1.582  0.020  1.582
 VMM  N02  C01  single    1.443  0.020  1.443
 VMM  C06  C21  single    1.495  0.020  1.495
 VMM  C21  N19  aromatic  1.341  0.020  1.341
 VMM  N18  N19  aromatic  1.333  0.020  1.333
 VMM  N19  C20  single    1.442  0.020  1.442
 VMM  C17  H1   single    0.930  0.020  1.080
 VMM  C20  H2   single    0.970  0.020  1.090
 VMM  C20  H3   single    0.970  0.020  1.090
 VMM  C20  H4   single    0.970  0.020  1.090
 VMM  C01  H6   single    0.970  0.020  1.090
 VMM  C01  H7   single    0.970  0.020  1.090
 VMM  C01  H8   single    0.970  0.020  1.090
 VMM  C06  H9   single    0.970  0.020  1.090
 VMM  C08  H10  single    0.970  0.020  1.090
 VMM  C08  H11  single    0.970  0.020  1.090
 VMM  C09  H12  single    0.970  0.020  1.090
 VMM  N02  H13  single    0.860  0.020  1.020
 VMM  N10  H14  single    0.890  0.020  1.040
 VMM  O05  H15  single    0.850  0.020  0.980
 VMM  C22  OX   single    1.332  0.020  1.332
 VMM  O14  H5   single    0.850  0.020  0.980
 VMM  OX   H16  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 VMM  C09  C16  C21  122.85  3.000
 VMM  C21  C16  C17  103.99  3.000
 VMM  C09  C16  C17  133.17  3.000
 VMM  H1   C17  N18  120.18  3.000
 VMM  H1   C17  C16  128.72  3.000
 VMM  N18  C17  C16  111.09  3.000
 VMM  H4   C20  H3   108.76  3.000
 VMM  H4   C20  H2   108.62  3.000
 VMM  H3   C20  H2   109.43  3.000
 VMM  H4   C20  N19  109.82  3.000
 VMM  H3   C20  N19  110.99  3.000
 VMM  H2   C20  N19  109.18  3.000
 VMM  N19  C21  C06  127.59  3.000
 VMM  N19  C21  C16  107.29  3.000
 VMM  C06  C21  C16  125.11  3.000
 VMM  OX   C22  O23  123.11  3.000
 VMM  OX   C22  N07  112.13  3.000
 VMM  O23  C22  N07  124.76  3.000
 VMM  H8   C01  H7   108.57  3.000
 VMM  H8   C01  H6   107.18  3.000
 VMM  H7   C01  H6   107.96  3.000
 VMM  H8   C01  N02  111.74  3.000
 VMM  H7   C01  N02  113.25  3.000
 VMM  H6   C01  N02  107.90  3.000
 VMM  N04  C03  N02  124.81  3.000
 VMM  N02  C03  C06  119.69  3.000
 VMM  N04  C03  C06  115.48  3.000
 VMM  H9   C06  N07  108.01  3.000
 VMM  H9   C06  C03  108.63  3.000
 VMM  N07  C06  C03  111.20  3.000
 VMM  H9   C06  C21  110.32  3.000
 VMM  C03  C06  C21  111.97  3.000
 VMM  N07  C06  C21  106.63  3.000
 VMM  H11  C08  H10  106.81  3.000
 VMM  H11  C08  N07  110.79  3.000
 VMM  H10  C08  N07  107.95  3.000
 VMM  H11  C08  C09  111.19  3.000
 VMM  H10  C08  C09  107.56  3.000
 VMM  N07  C08  C09  112.29  3.000
 VMM  H12  C09  N10  106.47  3.000
 VMM  H12  C09  C08  107.07  3.000
 VMM  N10  C09  C08  108.88  3.000
 VMM  H12  C09  C16  111.14  3.000
 VMM  N10  C09  C16  114.56  3.000
 VMM  C08  C09  C16  108.45  3.000
 VMM  H13  N02  C03  115.23  3.000
 VMM  H13  N02  C01  115.85  3.000
 VMM  C03  N02  C01  126.64  3.000
 VMM  O05  N04  C03  111.16  3.000
 VMM  C08  N07  C06  114.66  3.000
 VMM  C06  N07  C22  118.73  3.000
 VMM  C08  N07  C22  123.69  3.000
 VMM  H14  N10  O11  101.88  3.000
 VMM  H14  N10  C09  110.74  3.000
 VMM  O11  N10  C09  107.55  3.000
 VMM  N19  N18  C17  105.79  3.000
 VMM  N18  N19  C21  111.84  3.000
 VMM  N18  N19  C20  120.11  3.000
 VMM  C21  N19  C20  127.87  3.000
 VMM  H15  O05  N04  103.76  3.000
 VMM  S12  O11  N10  111.52  3.000
 VMM  H5   O14  S12  113.01  3.000
 VMM  O15  S12  O14  104.90  3.000
 VMM  O14  S12  O13  111.53  3.000
 VMM  O15  S12  O13  121.99  3.000
 VMM  O14  S12  O11  103.32  3.000
 VMM  O13  S12  O11  103.00  3.000
 VMM  O15  S12  O11  110.69  3.000
 VMM  H16  OX   C22  108.96  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 VMM  CONST_01  N19  N18  C17  C16     0.00   0.0  0
 VMM  CONST_02  N18  N19  C21  C16     0.00   0.0  0
 VMM  CONST_03  N19  C21  C16  C17     0.00   0.0  0
 VMM  CONST_04  C21  N19  N18  C17     0.00   0.0  0
 VMM  CONST_05  N18  C17  C16  C21     0.00   0.0  0
 VMM  CONST_06  C20  N19  C21  C16   180.00   0.0  0
 VMM  CONST_07  C20  N19  N18  C17   180.00   0.0  0
 VMM  CONST_08  C06  C21  N19  C20     0.00   0.0  0
 VMM  CONST_09  H1   C17  C16  C21   180.00   0.0  0
 VMM  CONST_10  H1   C17  C16  C09     0.00   0.0  0
 VMM  CONST_11  H1   C17  N18  N19   180.00   0.0  0
 VMM  CONST_12  C06  C03  N02  C01     0.00   0.0  0
 VMM  CONST_13  O05  N04  C03  C06   180.00   0.0  0
 VMM  CONST_14  H13  N02  C03  C06   180.00   0.0  0
 VMM  CONST_15  H16  OX   C22  N07   180.00   0.0  0
 VMM  CONST_16  N04  C03  N02  C01   180.00   0.0  0
 VMM  CONST_17  O05  N04  C03  N02     0.00   0.0  0
 VMM  CONST_18  H13  N02  C03  N04     0.00   0.0  0
 VMM  CONST_19  H16  OX   C22  O23     0.00   0.0  0
 VMM  Var_01    C09  C08  N07  C06    66.56  30.0  1
 VMM  Var_02    C09  C08  N07  C22   -93.82  30.0  1
 VMM  Var_03    H10  C08  N07  C06   -51.83  30.0  1
 VMM  Var_04    H11  C08  N07  C06  -168.46  30.0  1
 VMM  Var_05    O23  C22  N07  C06     8.84  30.0  2
 VMM  Var_06    OX   C22  N07  C06  -171.93  30.0  2
 VMM  Var_07    O23  C22  N07  C08   168.47  30.0  2
 VMM  Var_08    OX   C22  N07  C08   -12.31  30.0  2
 VMM  Var_09    H2   C20  N19  C21   146.68  30.0  2
 VMM  Var_10    H3   C20  N19  C21   -92.61  30.0  2
 VMM  Var_11    H4   C20  N19  C21    27.68  30.0  2
 VMM  Var_12    H10  C08  N07  C22   147.79  30.0  1
 VMM  Var_13    H11  C08  N07  C22    31.17  30.0  1
 VMM  Var_14    H2   C20  N19  N18   -38.64  30.0  2
 VMM  Var_15    H3   C20  N19  N18    82.07  30.0  2
 VMM  Var_16    H4   C20  N19  N18  -157.63  30.0  2
 VMM  Var_17    S12  O11  N10  C09  -114.37  30.0  3
 VMM  Var_18    O15  S12  O11  N10    45.79  30.0  3
 VMM  Var_19    O13  S12  O11  N10   177.73  30.0  3
 VMM  Var_20    O14  S12  O11  N10   -66.05  30.0  3
 VMM  Var_21    H6   C01  N02  C03   167.20  30.0  3
 VMM  Var_22    H7   C01  N02  C03   -73.36  30.0  3
 VMM  Var_23    H8   C01  N02  C03    49.63  30.0  3
 VMM  Var_24    H14  N10  O11  S12   129.13  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 VMM  chir_01  C06  N07  C03  C21  positiv
 VMM  chir_02  C09  N10  C08  C16  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 VMM  plan-1  C01  0.020
 VMM  plan-1  C03  0.020
 VMM  plan-1  C06  0.020
 VMM  plan-1  N02  0.020
 VMM  plan-1  N04  0.020
 VMM  plan-1  O05  0.020
 VMM  plan-1  H13  0.020
 VMM  plan-2  C16  0.020
 VMM  plan-2  C17  0.020
 VMM  plan-2  C20  0.020
 VMM  plan-2  C21  0.020
 VMM  plan-2  C06  0.020
 VMM  plan-2  C09  0.020
 VMM  plan-2  N18  0.020
 VMM  plan-2  N19  0.020
 VMM  plan-2  H1   0.020
 VMM  plan-3  C22  0.020
 VMM  plan-3  N07  0.020
 VMM  plan-3  O23  0.020
 VMM  plan-3  OX   0.020
 VMM  plan-3  H16  0.020

