# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:24:20 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 1-(3-hydroxypropyl)-2-{[(3-nitrophenyl)carbonyl]amino}-1H-benzimidazol-5-yl 2,2-dimethylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C(=O)Oc1ccc2n(CCCO)c(NC(=O)c3cccc(c3)[N+]([O-])=O)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
 T12  T12  '1-(3-hydroxypropyl)-2-{[(3-nitrophenyl)carbonyl]amino}-1H-benzimidazol-5-yl 2,2-dimethylpropanoate'  ligand  56  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T12
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
 T12  O56   O  O     -1  -0.370   1.7388  13.8905   5.3908
 T12  N54   N  N      1   0.331   1.4867  12.8534   4.8270
 T12  O55   O  O      0  -0.372   0.4569  12.2383   4.9673
 T12  C13   C  CR6    0   0.283   2.4893  12.3097   3.9193
 T12  C12   C  CR16   0  -0.259   3.6902  12.9819   3.7572
 T12  C11   C  CR16   0  -0.236   4.6418  12.4412   2.9072
 T12  C10   C  CR16   0  -0.238   4.3915  11.2544   2.2393
 T12  C14   C  CR16   0  -0.320   2.2112  11.1287   3.2498
 T12  C15   C  CR6    0  -0.053   3.1704  10.6012   2.3962
 T12  C51   C  C      0   0.552   2.9631   9.3137   1.6683
 T12  O53   O  O      0  -0.416   3.8888   8.5882   1.3860
 T12  N50   N  NH1    0  -0.782   1.6612   9.0490   1.3366
 T12  C21   C  CR5    0   0.709   1.2177   7.8743   0.7669
 T12  N22   N  N      0  -0.476   1.7340   6.6954   0.9573
 T12  C3    C  CR56   0   0.153   0.9610   5.8549   0.1975
 T12  C4    C  CR16   0  -0.404   1.0607   4.4774   0.0156
 T12  C5    C  CR6    0   0.358   0.1237   3.8834  -0.8049
 T12  O23   O  O2     0  -0.503   0.1573   2.5091  -0.9635
 T12  C24   C  C      0   0.628   0.7357   2.0085  -2.0709
 T12  O26   O  O      0  -0.418   1.2442   2.7103  -2.9015
 T12  C25   C  CT     0  -0.252   0.6589   0.4932  -2.1025
 T12  C35   C  CH3    0  -0.639  -0.8006   0.0482  -1.9428
 T12  C31   C  CH3    0  -0.634   1.2078  -0.0115  -3.4343
 T12  C27   C  CH3    0  -0.641   1.5037  -0.0677  -0.9497
 T12  C6    C  CR16   0  -0.333  -0.8882   4.6060  -1.4428
 T12  C2    C  CR56   0   0.357  -0.0547   6.5784  -0.4446
 T12  C1    C  CR16   0  -0.306  -0.9925   5.9754  -1.2691
 T12  N20   N  NR5    0  -0.572   0.1306   7.8841  -0.0549
 T12  C39   C  CH2    0  -0.355  -0.5840   9.0330  -0.5762
 T12  C40   C  CH2    0  -0.465   0.1232   9.6598  -1.7695
 T12  C43   C  CH2    0  -0.142  -0.6674  10.8345  -2.3140
 T12  O46   O  OH1    0  -0.671   0.0328  11.3754  -3.4113
 T12  H12   H  HCR6   0   0.309   3.8933  13.9051   4.2798
 T12  H11   H  HCR6   0   0.289   5.5858  12.9494   2.7709
 T12  H10   H  HCR6   0   0.287   5.1448  10.8377   1.5849
 T12  H14   H  HCR6   0   0.305   1.2722  10.6215   3.4224
 T12  HN50  H  HNH1   0   0.435   0.9831   9.7860   1.4620
 T12  H4    H  HCR6   0   0.271   1.8353   3.8969   0.5001
 T12  H351  H  HCH3   0   0.241  -1.2118   0.3154  -0.9700
 T12  H352  H  HCH3   0   0.237  -1.4389   0.4812  -2.7149
 T12  H353  H  HCH3   0   0.238  -0.8572  -1.0368  -2.0389
 T12  H311  H  HCH3   0   0.234   0.6405   0.3769  -4.2808
 T12  H312  H  HCH3   0   0.234   1.1423  -1.0998  -3.4628
 T12  H313  H  HCH3   0   0.234   2.2541   0.2604  -3.5730
 T12  H271  H  HCH3   0   0.242   1.1441   0.2642   0.0237
 T12  H272  H  HCH3   0   0.241   1.4570  -1.1575  -0.9696
 T12  H273  H  HCH3   0   0.238   2.5519   0.2205  -1.0454
 T12  H6    H  HCR6   0   0.272  -1.6014   4.0880  -2.0707
 T12  H1    H  HCR6   0   0.278  -1.7763   6.5351  -1.7616
 T12  H391  H  HCH2   0   0.276  -0.7289   9.7612   0.2236
 T12  H392  H  HCH2   0   0.284  -1.5840   8.6952  -0.8493
 T12  H401  H  HCH2   0   0.245   0.2492   8.9061  -2.5512
 T12  H402  H  HCH2   0   0.244   1.1209   9.9937  -1.4721
 T12  H431  H  HCH2   0   0.198  -0.8055  11.5798  -1.5195
 T12  H432  H  HCH2   0   0.198  -1.6698  10.4933  -2.6045
 T12  HO46  H  HOH1   0   0.455  -0.4811  12.1082  -3.7619

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
 T12  O56  N54   single    1.207  0.020  1.207
 T12  N54  O55   double    1.208  0.020  1.208
 T12  N54  C13   single    1.458  0.020  1.458
 T12  C13  C14   aromatic  1.386  0.020  1.386
 T12  C13  C12   aromatic  1.386  0.020  1.386
 T12  C12  C11   aromatic  1.386  0.020  1.386
 T12  C12  H12   single    0.930  0.020  1.080
 T12  C11  C10   aromatic  1.385  0.020  1.385
 T12  C11  H11   single    0.930  0.020  1.080
 T12  C10  C15   aromatic  1.394  0.020  1.394
 T12  C10  H10   single    0.930  0.020  1.080
 T12  C14  C15   aromatic  1.388  0.020  1.388
 T12  C14  H14   single    0.930  0.020  1.080
 T12  C15  C51   single    1.493  0.020  1.493
 T12  C51  N50   single    1.369  0.020  1.369
 T12  C51  O53   double    1.210  0.020  1.210
 T12  N50  C21   single    1.379  0.020  1.379
 T12  N50  HN50  single    0.860  0.020  1.020
 T12  C21  N20   aromatic  1.363  0.020  1.363
 T12  C21  N22   aromatic  1.301  0.020  1.301
 T12  N22  C3    aromatic  1.372  0.020  1.372
 T12  C3   C4    aromatic  1.393  0.020  1.393
 T12  C3   C2    aromatic  1.403  0.020  1.403
 T12  C4   C5    aromatic  1.380  0.020  1.380
 T12  C4   H4    single    0.930  0.020  1.080
 T12  C5   O23   single    1.384  0.020  1.384
 T12  C5   C6    aromatic  1.398  0.020  1.398
 T12  O23  C24   single    1.346  0.020  1.346
 T12  C24  C25   single    1.518  0.020  1.518
 T12  C24  O26   double    1.200  0.020  1.200
 T12  C25  C31   single    1.526  0.020  1.526
 T12  C25  C27   single    1.535  0.020  1.535
 T12  C25  C35   single    1.534  0.020  1.534
 T12  C35  H351  single    0.970  0.020  1.090
 T12  C35  H352  single    0.970  0.020  1.090
 T12  C35  H353  single    0.970  0.020  1.090
 T12  C31  H311  single    0.970  0.020  1.090
 T12  C31  H312  single    0.970  0.020  1.090
 T12  C31  H313  single    0.970  0.020  1.090
 T12  C27  H271  single    0.970  0.020  1.090
 T12  C27  H272  single    0.970  0.020  1.090
 T12  C27  H273  single    0.970  0.020  1.090
 T12  C6   C1    aromatic  1.384  0.020  1.384
 T12  C6   H6    single    0.930  0.020  1.080
 T12  C2   C1    aromatic  1.387  0.020  1.387
 T12  C2   N20   aromatic  1.375  0.020  1.375
 T12  C1   H1    single    0.930  0.020  1.080
 T12  N20  C39   single    1.450  0.020  1.450
 T12  C39  C40   single    1.522  0.020  1.522
 T12  C39  H391  single    0.970  0.020  1.090
 T12  C39  H392  single    0.970  0.020  1.090
 T12  C40  C43   single    1.517  0.020  1.517
 T12  C40  H401  single    0.970  0.020  1.090
 T12  C40  H402  single    0.970  0.020  1.090
 T12  C43  O46   single    1.410  0.020  1.410
 T12  C43  H431  single    0.970  0.020  1.090
 T12  C43  H432  single    0.970  0.020  1.090
 T12  O46  HO46  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
 T12  C13   N54  O55   117.96  3.000
 T12  C13   N54  O56   117.89  3.000
 T12  O55   N54  O56   124.15  3.000
 T12  C14   C13  C12   122.06  3.000
 T12  C12   C13  N54   119.21  3.000
 T12  C14   C13  N54   118.73  3.000
 T12  H12   C12  C11   120.08  3.000
 T12  H12   C12  C13   121.40  3.000
 T12  C11   C12  C13   118.53  3.000
 T12  H11   C11  C10   120.01  3.000
 T12  H11   C11  C12   119.58  3.000
 T12  C10   C11  C12   120.41  3.000
 T12  H10   C10  C15   119.86  3.000
 T12  H10   C10  C11   119.75  3.000
 T12  C15   C10  C11   120.38  3.000
 T12  H14   C14  C15   121.33  3.000
 T12  H14   C14  C13   119.80  3.000
 T12  C15   C14  C13   118.83  3.000
 T12  C51   C15  C14   122.10  3.000
 T12  C51   C15  C10   118.08  3.000
 T12  C14   C15  C10   119.77  3.000
 T12  N50   C51  O53   123.72  3.000
 T12  O53   C51  C15   121.65  3.000
 T12  N50   C51  C15   114.62  3.000
 T12  HN50  N50  C21   117.21  3.000
 T12  HN50  N50  C51   117.88  3.000
 T12  C21   N50  C51   124.79  3.000
 T12  N20   C21  N22   114.29  3.000
 T12  N22   C21  N50   125.73  3.000
 T12  N20   C21  N50   119.97  3.000
 T12  C3    N22  C21   104.51  3.000
 T12  C2    C3   C4    120.14  3.000
 T12  C2    C3   N22   110.22  3.000
 T12  C4    C3   N22   129.64  3.000
 T12  H4    C4   C5    121.42  3.000
 T12  H4    C4   C3    121.53  3.000
 T12  C5    C4   C3    117.05  3.000
 T12  C6    C5   O23   118.60  3.000
 T12  C6    C5   C4    122.72  3.000
 T12  O23   C5   C4    118.63  3.000
 T12  C24   O23  C5    118.30  3.000
 T12  C25   C24  O26   126.21  3.000
 T12  O26   C24  O23   122.27  3.000
 T12  C25   C24  O23   111.52  3.000
 T12  C27   C25  C31   109.67  3.000
 T12  C27   C25  C35   109.83  3.000
 T12  C31   C25  C35   109.70  3.000
 T12  C35   C25  C24   109.61  3.000
 T12  C27   C25  C24   108.74  3.000
 T12  C31   C25  C24   109.28  3.000
 T12  H353  C35  H352  107.57  3.000
 T12  H353  C35  H351  107.64  3.000
 T12  H352  C35  H351  108.28  3.000
 T12  H353  C35  C25   109.19  3.000
 T12  H352  C35  C25   111.57  3.000
 T12  H351  C35  C25   112.39  3.000
 T12  H313  C31  H312  107.65  3.000
 T12  H313  C31  H311  108.16  3.000
 T12  H312  C31  H311  107.69  3.000
 T12  H313  C31  C25   111.95  3.000
 T12  H312  C31  C25   109.34  3.000
 T12  H311  C31  C25   111.87  3.000
 T12  H273  C27  H272  107.66  3.000
 T12  H273  C27  H271  108.35  3.000
 T12  H272  C27  H271  107.85  3.000
 T12  H273  C27  C25   111.48  3.000
 T12  H272  C27  C25   109.13  3.000
 T12  H271  C27  C25   112.21  3.000
 T12  H6    C6   C1    119.78  3.000
 T12  H6    C6   C5    119.64  3.000
 T12  C1    C6   C5    120.58  3.000
 T12  N20   C2   C1    132.26  3.000
 T12  N20   C2   C3    105.22  3.000
 T12  C1    C2   C3    122.52  3.000
 T12  H1    C1   C2    122.39  3.000
 T12  H1    C1   C6    120.62  3.000
 T12  C2    C1   C6    116.99  3.000
 T12  C39   N20  C2    125.73  3.000
 T12  C39   N20  C21   128.00  3.000
 T12  C2    N20  C21   105.75  3.000
 T12  H392  C39  H391  105.58  3.000
 T12  H392  C39  C40   110.94  3.000
 T12  H391  C39  C40   111.19  3.000
 T12  H392  C39  N20   107.25  3.000
 T12  H391  C39  N20   109.30  3.000
 T12  C40   C39  N20   112.28  3.000
 T12  H402  C40  H401  107.45  3.000
 T12  H402  C40  C43   109.68  3.000
 T12  H401  C40  C43   109.71  3.000
 T12  H402  C40  C39   109.67  3.000
 T12  H401  C40  C39   109.28  3.000
 T12  C43   C40  C39   110.98  3.000
 T12  H432  C43  H431  106.71  3.000
 T12  H432  C43  O46   111.52  3.000
 T12  H431  C43  O46   111.42  3.000
 T12  H432  C43  C40   109.28  3.000
 T12  H431  C43  C40   109.35  3.000
 T12  O46   C43  C40   108.52  3.000
 T12  HO46  O46  C43   108.11  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
 T12  CONST_01  C10   C15  C14  C13     0.00   0.0  0
 T12  CONST_02  C10   C11  C12  C13     0.00   0.0  0
 T12  CONST_03  C15   C14  C13  C12     0.00   0.0  0
 T12  CONST_04  C15   C10  C11  C12     0.00   0.0  0
 T12  CONST_05  C14   C13  C12  C11     0.00   0.0  0
 T12  CONST_06  C14   C15  C10  C11     0.00   0.0  0
 T12  CONST_07  C3    C2   N20  C21     0.00   0.0  0
 T12  CONST_08  C1    C2   N20  C21   180.00   0.0  0
 T12  CONST_09  C4    C3   N22  C21   180.00   0.0  0
 T12  CONST_10  C2    C3   N22  C21     0.00   0.0  0
 T12  CONST_11  C2    N20  C21  N22     0.00   0.0  0
 T12  CONST_12  C5    C4   C3   N22   180.00   0.0  0
 T12  CONST_13  C1    C2   C3   N22   180.00   0.0  0
 T12  CONST_14  N20   C2   C3   N22     0.00   0.0  0
 T12  CONST_15  N20   C21  N22  C3      0.00   0.0  0
 T12  CONST_16  C6    C5   C4   C3      0.00   0.0  0
 T12  CONST_17  C6    C1   C2   C3      0.00   0.0  0
 T12  CONST_18  C1    C2   C3   C4      0.00   0.0  0
 T12  CONST_19  N20   C2   C3   C4    180.00   0.0  0
 T12  CONST_20  C1    C6   C5   C4      0.00   0.0  0
 T12  CONST_21  C2    C3   C4   C5      0.00   0.0  0
 T12  CONST_22  C2    C1   C6   C5      0.00   0.0  0
 T12  CONST_23  N20   C2   C1   C6    180.00   0.0  0
 T12  CONST_24  C15   C14  C13  N54   180.00   0.0  0
 T12  CONST_25  C11   C12  C13  N54   180.00   0.0  0
 T12  CONST_26  C51   C15  C14  C13   180.00   0.0  0
 T12  CONST_27  C51   C15  C10  C11   180.00   0.0  0
 T12  CONST_28  C2    N20  C21  N50   180.00   0.0  0
 T12  CONST_29  C3    N22  C21  N50   180.00   0.0  0
 T12  CONST_30  C39   N20  C21  N22   180.00   0.0  0
 T12  CONST_31  O23   C5   C4   C3    180.00   0.0  0
 T12  CONST_32  C39   N20  C2   C3    180.00   0.0  0
 T12  CONST_33  C1    C6   C5   O23   180.00   0.0  0
 T12  CONST_34  C39   N20  C2   C1      0.00   0.0  0
 T12  CONST_35  H11   C11  C12  C13   180.00   0.0  0
 T12  CONST_36  H14   C14  C13  C12   180.00   0.0  0
 T12  CONST_37  H10   C10  C11  C12   180.00   0.0  0
 T12  CONST_38  H12   C12  C11  C10   180.00   0.0  0
 T12  CONST_39  H4    C4   C3   N22     0.00   0.0  0
 T12  CONST_40  H1    C1   C2   C3    180.00   0.0  0
 T12  CONST_41  H6    C6   C5   C4    180.00   0.0  0
 T12  CONST_42  C21   N50  C51  C15   180.00   0.0  0
 T12  CONST_43  C14   C13  N54  O56   180.00   0.0  0
 T12  CONST_44  C12   C13  N54  O56     0.00   0.0  0
 T12  CONST_45  C14   C13  N54  O55     0.00   0.0  0
 T12  CONST_46  C12   C13  N54  O55   180.00   0.0  0
 T12  CONST_50  C21   N50  C51  O53     0.00   0.0  0
 T12  Var_01    N50   C51  C15  C10  -150.81  30.0  2
 T12  Var_02    C40   C39  N20  C21    79.86  30.0  2
 T12  Var_03    C6    C5   O23  C24    82.64  30.0  1
 T12  Var_04    C25   C24  O23  C5   -178.70  30.0  3
 T12  Var_05    C43   C40  C39  N20   178.48  30.0  3
 T12  Var_06    C31   C25  C24  O23   174.68  30.0  3
 T12  Var_07    O46   C43  C40  C39   179.89  30.0  3
 T12  Var_08    H311  C31  C25  C24   -60.14  30.0  3
 T12  Var_09    H271  C27  C25  C24    60.81  30.0  3
 T12  Var_10    H351  C35  C25  C24   -64.70  30.0  3

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
 T12  plan-1  N54   0.020
 T12  plan-1  C13   0.020
 T12  plan-1  C12   0.020
 T12  plan-1  C11   0.020
 T12  plan-1  C10   0.020
 T12  plan-1  C14   0.020
 T12  plan-1  C15   0.020
 T12  plan-1  C51   0.020
 T12  plan-1  H12   0.020
 T12  plan-1  H11   0.020
 T12  plan-1  H10   0.020
 T12  plan-1  H14   0.020
 T12  plan-2  O23   0.020
 T12  plan-2  C24   0.020
 T12  plan-2  O26   0.020
 T12  plan-2  C25   0.020
 T12  plan-3  N50   0.020
 T12  plan-3  C21   0.020
 T12  plan-3  N22   0.020
 T12  plan-3  C3    0.020
 T12  plan-3  C4    0.020
 T12  plan-3  C5    0.020
 T12  plan-3  O23   0.020
 T12  plan-3  C6    0.020
 T12  plan-3  C2    0.020
 T12  plan-3  C1    0.020
 T12  plan-3  N20   0.020
 T12  plan-3  C39   0.020
 T12  plan-3  H4    0.020
 T12  plan-3  H6    0.020
 T12  plan-3  H1    0.020
 T12  plan-4  C15   0.020
 T12  plan-4  C51   0.020
 T12  plan-4  O53   0.020
 T12  plan-4  N50   0.020
 T12  plan-4  C21   0.020
 T12  plan-4  HN50  0.020
 T12  plan-5  O56   0.020
 T12  plan-5  N54   0.020
 T12  plan-5  O55   0.020
 T12  plan-5  C13   0.020

