# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 11:59:08 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-[(5-nitro-1H-benzimidazol-2-yl)sulfanyl]-N-(4-phenoxyphenyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc2[nH]c(SCC(=O)Nc3ccc(Oc4ccccc4)cc3)nc2c1
#
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
 CZG  CZG  2-[(5-nitro-1H-benzimidazol-2-yl)sulfanyl]-N-(4-phenoxyphenyl)acetamide  ligand  46  30  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CZG
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
 CZG  C4   C  CR6    0   0.244    7.2535   1.1732   0.0259
 CZG  C5   C  CR16   0  -0.295    7.8851  -0.0472  -0.2491
 CZG  C6   C  CR16   0  -0.291    7.1400  -1.1983  -0.4034
 CZG  C7   C  CR56   0   0.368    5.7622  -1.0808  -0.2732
 CZG  C15  C  CR6    0   0.352   -2.7798  -0.4781   0.2541
 CZG  C17  C  CR16   0  -0.333   -4.9412   0.5820  -0.0203
 CZG  C20  C  CR6    0   0.301   -7.7369   0.2918   0.0517
 CZG  C21  C  CR16   0  -0.305   -8.2251   1.1450   1.0298
 CZG  C22  C  CR16   0  -0.254   -9.0875   2.1708   0.6659
 CZG  C24  C  CR16   0  -0.254   -8.9515   1.4831  -1.6329
 CZG  C26  C  CR16   0  -0.323   -4.8056  -1.7148   0.6612
 CZG  O1   O  O     -1  -0.387    9.2739   2.2427   0.0916
 CZG  N2   N  N      1   0.328    8.0727   2.3580   0.1846
 CZG  O3   O  O      0  -0.386    7.5191   3.4120   0.4037
 CZG  N8   N  NR15   0  -0.704    4.7456  -1.9836  -0.3580
 CZG  C9   C  CR5    0   0.317    3.5848  -1.2999  -0.1423
 CZG  S10  S  S2     0   0.097    2.0688  -2.1470  -0.1687
 CZG  C11  C  CH2    0  -0.696    0.9712  -0.7362   0.1055
 CZG  C12  C  C      0   0.566   -0.4408  -1.2838   0.1355
 CZG  O13  O  O      0  -0.461   -0.6557  -2.4818   0.1032
 CZG  N14  N  NH1    0  -0.740   -1.3845  -0.3243   0.2100
 CZG  C16  C  CR16   0  -0.329   -3.5566   0.6318  -0.0642
 CZG  C18  C  CR6    0   0.357   -5.5725  -0.6012   0.3404
 CZG  O19  O  O2     0  -0.514   -6.9243  -0.7532   0.4178
 CZG  C23  C  CR16   0  -0.256   -9.4503   2.3439  -0.6634
 CZG  C25  C  CR16   0  -0.301   -8.0901   0.4531  -1.2803
 CZG  C27  C  CR16   0  -0.291   -3.4227  -1.6594   0.6248
 CZG  N28  N  N      0  -0.456    3.7676  -0.0295   0.0746
 CZG  C29  C  CR56   0   0.168    5.1288   0.1457   0.0004
 CZG  C30  C  CR16   0  -0.366    5.8780   1.2999   0.1551
 CZG  H1   H  HCR6   0   0.296    8.9594  -0.0984  -0.3422
 CZG  H2   H  HCR6   0   0.288    7.6177  -2.1441  -0.6175
 CZG  H3   H  HCR6   0   0.282   -5.5038   1.4702  -0.2739
 CZG  H4   H  HCR6   0   0.273   -7.9389   1.0043   2.0646
 CZG  H5   H  HCR6   0   0.264   -9.4734   2.8379   1.4256
 CZG  H6   H  HCR6   0   0.265   -9.2336   1.6111  -2.6697
 CZG  H7   H  HCR6   0   0.273   -5.2929  -2.6368   0.9519
 CZG  H8   H  HNR5   0   0.433    4.8367  -2.9713  -0.5432
 CZG  H9   H  HCH2   0   0.331    1.2126  -0.2538   1.0541
 CZG  H10  H  HCH2   0   0.325    1.0968   0.0009  -0.6883
 CZG  H11  H  HNH1   0   0.424   -1.0595   0.6311   0.1649
 CZG  H12  H  HCR6   0   0.278   -3.0782   1.5598  -0.3535
 CZG  H13  H  HCR6   0   0.261  -10.1210   3.1458  -0.9422
 CZG  H14  H  HCR6   0   0.274   -7.7012  -0.2230  -2.0317
 CZG  H15  H  HCR6   0   0.281   -2.8633  -2.5402   0.8946
 CZG  H17  H  HCR6   0   0.296    5.4010   2.2449   0.3705

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
 CZG  O1   N2   single    1.210  0.020  1.210
 CZG  N28  C29  aromatic  1.374  0.020  1.374
 CZG  N28  C9   aromatic  1.302  0.020  1.302
 CZG  C30  C29  aromatic  1.385  0.020  1.385
 CZG  C30  C4   aromatic  1.387  0.020  1.387
 CZG  O13  C12  double    1.217  0.020  1.217
 CZG  N2   C4   single    1.449  0.020  1.449
 CZG  N2   O3   double    1.211  0.020  1.211
 CZG  S10  C9   single    1.737  0.020  1.737
 CZG  S10  C11  single    1.808  0.020  1.808
 CZG  C29  C7   aromatic  1.407  0.020  1.407
 CZG  C9   N8   aromatic  1.364  0.020  1.364
 CZG  C4   C5   aromatic  1.401  0.020  1.401
 CZG  C24  C25  aromatic  1.388  0.020  1.388
 CZG  C24  C23  aromatic  1.389  0.020  1.389
 CZG  C12  C11  single    1.515  0.020  1.515
 CZG  C12  N14  single    1.348  0.020  1.348
 CZG  C25  C20  aromatic  1.387  0.020  1.387
 CZG  C16  C17  aromatic  1.386  0.020  1.386
 CZG  C16  C15  aromatic  1.392  0.020  1.392
 CZG  C17  C18  aromatic  1.389  0.020  1.389
 CZG  C7   N8   aromatic  1.362  0.020  1.362
 CZG  C7   C6   aromatic  1.389  0.020  1.389
 CZG  C23  C22  aromatic  1.389  0.020  1.389
 CZG  C5   C6   aromatic  1.380  0.020  1.380
 CZG  C20  O19  single    1.373  0.020  1.373
 CZG  C20  C21  aromatic  1.387  0.020  1.387
 CZG  C15  N14  single    1.404  0.020  1.404
 CZG  C15  C27  aromatic  1.395  0.020  1.395
 CZG  C18  O19  single    1.362  0.020  1.362
 CZG  C18  C26  aromatic  1.390  0.020  1.390
 CZG  C22  C21  aromatic  1.389  0.020  1.389
 CZG  C27  C26  aromatic  1.384  0.020  1.384
 CZG  C5   H1   single    0.930  0.020  1.080
 CZG  C6   H2   single    0.930  0.020  1.080
 CZG  C17  H3   single    0.930  0.020  1.080
 CZG  C21  H4   single    0.930  0.020  1.080
 CZG  C22  H5   single    0.930  0.020  1.080
 CZG  C24  H6   single    0.930  0.020  1.080
 CZG  C26  H7   single    0.930  0.020  1.080
 CZG  N8   H8   single    0.860  0.020  1.020
 CZG  C11  H9   single    0.970  0.020  1.090
 CZG  C11  H10  single    0.970  0.020  1.090
 CZG  N14  H11  single    0.860  0.020  1.020
 CZG  C16  H12  single    0.930  0.020  1.080
 CZG  C23  H13  single    0.930  0.020  1.080
 CZG  C25  H14  single    0.930  0.020  1.080
 CZG  C27  H15  single    0.930  0.020  1.080
 CZG  C30  H17  single    0.930  0.020  1.080

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
 CZG  C30  C4   N2   118.40  3.000
 CZG  N2   C4   C5   118.60  3.000
 CZG  C30  C4   C5   123.00  3.000
 CZG  H1   C5   C6   119.22  3.000
 CZG  H1   C5   C4   120.45  3.000
 CZG  C6   C5   C4   120.33  3.000
 CZG  H2   C6   C7   122.07  3.000
 CZG  H2   C6   C5   120.89  3.000
 CZG  C7   C6   C5   117.04  3.000
 CZG  C29  C7   N8   104.70  3.000
 CZG  N8   C7   C6   132.72  3.000
 CZG  C29  C7   C6   122.58  3.000
 CZG  C27  C15  C16  118.62  3.000
 CZG  C27  C15  N14  123.98  3.000
 CZG  C16  C15  N14  117.39  3.000
 CZG  H3   C17  C18  121.61  3.000
 CZG  H3   C17  C16  118.86  3.000
 CZG  C18  C17  C16  119.53  3.000
 CZG  C25  C20  O19  119.67  3.000
 CZG  O19  C20  C21  119.24  3.000
 CZG  C25  C20  C21  121.07  3.000
 CZG  H4   C21  C22  120.70  3.000
 CZG  H4   C21  C20  120.07  3.000
 CZG  C22  C21  C20  119.23  3.000
 CZG  H5   C22  C23  120.13  3.000
 CZG  H5   C22  C21  119.53  3.000
 CZG  C23  C22  C21  120.34  3.000
 CZG  H6   C24  C25  119.53  3.000
 CZG  H6   C24  C23  120.12  3.000
 CZG  C25  C24  C23  120.35  3.000
 CZG  H7   C26  C27  119.39  3.000
 CZG  H7   C26  C18  119.74  3.000
 CZG  C27  C26  C18  120.87  3.000
 CZG  O3   N2   O1   123.42  3.000
 CZG  O3   N2   C4   118.24  3.000
 CZG  O1   N2   C4   118.34  3.000
 CZG  H8   N8   C9   126.61  3.000
 CZG  H8   N8   C7   126.35  3.000
 CZG  C9   N8   C7   107.04  3.000
 CZG  N28  C9   S10  126.95  3.000
 CZG  S10  C9   N8   119.73  3.000
 CZG  N28  C9   N8   113.32  3.000
 CZG  C11  S10  C9    98.45  3.000
 CZG  H10  C11  H9   107.97  3.000
 CZG  H10  C11  C12  111.47  3.000
 CZG  H9   C11  C12  110.41  3.000
 CZG  H10  C11  S10  110.31  3.000
 CZG  H9   C11  S10  110.03  3.000
 CZG  C12  C11  S10  106.66  3.000
 CZG  N14  C12  O13  125.33  3.000
 CZG  N14  C12  C11  113.35  3.000
 CZG  O13  C12  C11  121.31  3.000
 CZG  H11  N14  C12  116.46  3.000
 CZG  H11  N14  C15  115.13  3.000
 CZG  C12  N14  C15  128.27  3.000
 CZG  H12  C16  C17  118.71  3.000
 CZG  H12  C16  C15  119.85  3.000
 CZG  C17  C16  C15  121.44  3.000
 CZG  O19  C18  C26  116.42  3.000
 CZG  C26  C18  C17  119.46  3.000
 CZG  O19  C18  C17  124.11  3.000
 CZG  C18  O19  C20  119.14  3.000
 CZG  H13  C23  C24  120.13  3.000
 CZG  H13  C23  C22  120.07  3.000
 CZG  C24  C23  C22  119.80  3.000
 CZG  H14  C25  C24  120.64  3.000
 CZG  H14  C25  C20  120.14  3.000
 CZG  C24  C25  C20  119.21  3.000
 CZG  H15  C27  C26  118.62  3.000
 CZG  H15  C27  C15  121.29  3.000
 CZG  C26  C27  C15  120.08  3.000
 CZG  C29  N28  C9   104.74  3.000
 CZG  C30  C29  N28  129.50  3.000
 CZG  C30  C29  C7   120.31  3.000
 CZG  N28  C29  C7   110.19  3.000
 CZG  H17  C30  C29  120.84  3.000
 CZG  H17  C30  C4   122.42  3.000
 CZG  C29  C30  C4   116.74  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
 CZG  CONST_01  N28  C29  C30  C4    180.00   0.0  0
 CZG  CONST_02  C7   C29  C30  C4      0.00   0.0  0
 CZG  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 CZG  CONST_04  C29  C30  C4   C5      0.00   0.0  0
 CZG  CONST_05  C29  C7   C6   C5      0.00   0.0  0
 CZG  CONST_06  N8   C7   C6   C5    180.00   0.0  0
 CZG  CONST_07  N28  C29  C7   C6    180.00   0.0  0
 CZG  CONST_08  C30  C29  C7   C6      0.00   0.0  0
 CZG  CONST_09  C9   N8   C7   C6    180.00   0.0  0
 CZG  CONST_10  C30  C4   C5   C6      0.00   0.0  0
 CZG  CONST_11  C9   N28  C29  C7      0.00   0.0  0
 CZG  CONST_12  N28  C9   N8   C7      0.00   0.0  0
 CZG  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 CZG  CONST_14  C18  C26  C27  C15     0.00   0.0  0
 CZG  CONST_15  C27  C15  C16  C17     0.00   0.0  0
 CZG  CONST_16  C27  C26  C18  C17     0.00   0.0  0
 CZG  CONST_17  C23  C24  C25  C20     0.00   0.0  0
 CZG  CONST_18  C23  C22  C21  C20     0.00   0.0  0
 CZG  CONST_19  C24  C25  C20  C21     0.00   0.0  0
 CZG  CONST_20  C24  C23  C22  C21     0.00   0.0  0
 CZG  CONST_21  C25  C24  C23  C22     0.00   0.0  0
 CZG  CONST_22  C25  C20  C21  C22     0.00   0.0  0
 CZG  CONST_23  C16  C17  C18  C26     0.00   0.0  0
 CZG  CONST_24  C16  C15  C27  C26     0.00   0.0  0
 CZG  CONST_25  C29  N28  C9   N8      0.00   0.0  0
 CZG  CONST_26  N28  C29  C7   N8      0.00   0.0  0
 CZG  CONST_27  C30  C29  C7   N8    180.00   0.0  0
 CZG  CONST_28  C30  C29  N28  C9    180.00   0.0  0
 CZG  CONST_29  C29  C7   N8   C9      0.00   0.0  0
 CZG  CONST_30  N2   C4   C5   C6    180.00   0.0  0
 CZG  CONST_31  S10  C9   N8   C7    180.00   0.0  0
 CZG  CONST_32  N14  C15  C16  C17   180.00   0.0  0
 CZG  CONST_33  O19  C20  C21  C22   180.00   0.0  0
 CZG  CONST_34  O19  C20  C25  C24   180.00   0.0  0
 CZG  CONST_35  N14  C15  C27  C26   180.00   0.0  0
 CZG  CONST_36  C29  C30  C4   N2    180.00   0.0  0
 CZG  CONST_37  C29  N28  C9   S10   180.00   0.0  0
 CZG  CONST_38  O19  C18  C17  C16   180.00   0.0  0
 CZG  CONST_39  C27  C26  C18  O19   180.00   0.0  0
 CZG  CONST_40  H2   C6   C5   C4    180.00   0.0  0
 CZG  CONST_41  H17  C30  C4   C5    180.00   0.0  0
 CZG  CONST_42  H8   N8   C7   C6      0.00   0.0  0
 CZG  CONST_43  H1   C5   C6   C7    180.00   0.0  0
 CZG  CONST_44  H3   C17  C16  C15   180.00   0.0  0
 CZG  CONST_45  H7   C26  C27  C15   180.00   0.0  0
 CZG  CONST_46  H6   C24  C25  C20   180.00   0.0  0
 CZG  CONST_47  H5   C22  C21  C20   180.00   0.0  0
 CZG  CONST_48  H14  C25  C20  C21   180.00   0.0  0
 CZG  CONST_49  H13  C23  C22  C21   180.00   0.0  0
 CZG  CONST_50  H15  C27  C15  C16   180.00   0.0  0
 CZG  CONST_51  H12  C16  C17  C18   180.00   0.0  0
 CZG  CONST_52  H4   C21  C22  C23   180.00   0.0  0
 CZG  CONST_53  O1   N2   C4   C5      0.00   0.0  0
 CZG  CONST_54  O3   N2   C4   C5    180.00   0.0  0
 CZG  CONST_55  C30  C4   N2   O1    180.00   0.0  0
 CZG  CONST_56  C30  C4   N2   O3      0.00   0.0  0
 CZG  CONST_59  H11  N14  C15  C16     0.00   0.0  0
 CZG  CONST_60  O13  C12  N14  C15     0.00   0.0  0
 CZG  CONST_61  C11  C12  N14  C15   180.00   0.0  0
 CZG  Var_01    C26  C18  O19  C20  -176.93  30.0  2
 CZG  Var_02    C25  C20  O19  C18    85.77  30.0  3
 CZG  Var_03    N28  C9   S10  C11     2.41  30.0  2
 CZG  Var_04    C12  C11  S10  C9   -179.24  30.0  3
 CZG  Var_05    O13  C12  C11  S10     6.30  30.0  2

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
 CZG  plan-1  C20  0.020
 CZG  plan-1  C21  0.020
 CZG  plan-1  C22  0.020
 CZG  plan-1  C24  0.020
 CZG  plan-1  O19  0.020
 CZG  plan-1  C23  0.020
 CZG  plan-1  C25  0.020
 CZG  plan-1  H4   0.020
 CZG  plan-1  H5   0.020
 CZG  plan-1  H6   0.020
 CZG  plan-1  H13  0.020
 CZG  plan-1  H14  0.020
 CZG  plan-2  C15  0.020
 CZG  plan-2  C17  0.020
 CZG  plan-2  C26  0.020
 CZG  plan-2  N14  0.020
 CZG  plan-2  C16  0.020
 CZG  plan-2  C18  0.020
 CZG  plan-2  O19  0.020
 CZG  plan-2  C27  0.020
 CZG  plan-2  H3   0.020
 CZG  plan-2  H7   0.020
 CZG  plan-2  H12  0.020
 CZG  plan-2  H15  0.020
 CZG  plan-3  C4   0.020
 CZG  plan-3  C5   0.020
 CZG  plan-3  C6   0.020
 CZG  plan-3  C7   0.020
 CZG  plan-3  N2   0.020
 CZG  plan-3  N8   0.020
 CZG  plan-3  C9   0.020
 CZG  plan-3  S10  0.020
 CZG  plan-3  N28  0.020
 CZG  plan-3  C29  0.020
 CZG  plan-3  C30  0.020
 CZG  plan-3  H1   0.020
 CZG  plan-3  H2   0.020
 CZG  plan-3  H8   0.020
 CZG  plan-3  H17  0.020
 CZG  plan-4  C15  0.020
 CZG  plan-4  C11  0.020
 CZG  plan-4  C12  0.020
 CZG  plan-4  O13  0.020
 CZG  plan-4  N14  0.020
 CZG  plan-4  H11  0.020
 CZG  plan-5  C4   0.020
 CZG  plan-5  O1   0.020
 CZG  plan-5  N2   0.020
 CZG  plan-5  O3   0.020

