# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 12:57:11 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(Nc2ccc3NC(=O)Nc3c2)c(Cl)c1
#
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
 80R  80R  5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one  ligand  30  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_80R
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
 80R  C4   C   CR16   0  -0.252  -2.1500   1.4816  -0.5938
 80R  C5   C   CR16   0  -0.352   1.8429  -0.0167   0.6396
 80R  C6   C   CR16   0  -0.228  -3.5376  -0.3397   0.1709
 80R  C7   C   CR56   0   0.326   3.9453  -0.4246  -0.5021
 80R  C8   C   CR56   0   0.342   3.1649   0.2989   0.4079
 80R  C10  C   CR6    0   0.471  -1.1255  -0.6452  -0.0242
 80R  C13  C   CR5    0   0.611   5.2493   1.1856   0.4131
 80R  C1   C   CR16   0  -0.306   3.4138  -1.4824  -1.2106
 80R  C2   C   CR16   0  -0.320   2.0720  -1.7887  -1.0059
 80R  C3   C   CR16   0  -0.338  -1.0367   0.6843  -0.4768
 80R  C9   C   CR6    0   0.290   1.2966  -1.0689  -0.0988
 80R  C11  C   CR6    0   0.216  -3.4027   0.9737  -0.2660
 80R  C12  C   CR6    0  -0.137  -2.4176  -1.1257   0.2867
 80R  N14  N   NR15   0  -0.737   5.2013   0.1385  -0.4742
 80R  N15  N   NR15   0  -0.741   3.9849   1.2629   0.9467
 80R  N16  N   NH1    0  -0.776  -0.0458  -1.4495   0.1007
 80R  N17  N   N      1   0.323  -4.5693   1.8020  -0.3832
 80R  O18  O   O      0  -0.397  -5.6477   1.3226  -0.1035
 80R  O20  O   O     -1  -0.396  -4.4249   2.9464  -0.7567
 80R  CL1  CL  CL     0  -0.102  -2.5962  -2.7592   0.8347
 80R  H1   H   HCR6   0   0.299  -2.0341   2.4944  -0.9512
 80R  H2   H   HCR6   0   0.291   1.2545   0.5231   1.3700
 80R  H3   H   HCR6   0   0.312  -4.5052  -0.7486   0.4237
 80R  H4   H   HCR6   0   0.277   4.0103  -2.0492  -1.9122
 80R  H5   H   HCR6   0   0.271   1.6205  -2.6006  -1.5611
 80R  H6   H   HCR6   0   0.298  -0.0751   1.0917  -0.7533
 80R  H7   H   HNR5   0   0.421   5.9906  -0.1455  -1.0323
 80R  H8   H   HNR5   0   0.421   3.7190   1.9508   1.6330
 80R  H9   H   HNH1   0   0.404  -0.2158  -2.4351   0.2308
 80R  O19  O   O      0  -0.494   6.2045   1.8933   0.6718

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
 80R  O19  C13  double    1.217  0.020  1.217
 80R  C13  N14  single    1.373  0.020  1.373
 80R  C13  N15  single    1.375  0.020  1.375
 80R  N14  C7   single    1.377  0.020  1.377
 80R  N15  C8   single    1.375  0.020  1.375
 80R  C7   C8   aromatic  1.400  0.020  1.400
 80R  C7   C1   aromatic  1.380  0.020  1.380
 80R  C8   C5   aromatic  1.379  0.020  1.379
 80R  C1   C2   aromatic  1.391  0.020  1.391
 80R  C5   C9   aromatic  1.397  0.020  1.397
 80R  C2   C9   aromatic  1.394  0.020  1.394
 80R  C9   N16  single    1.409  0.020  1.409
 80R  N16  C10  single    1.352  0.020  1.352
 80R  C10  C3   aromatic  1.407  0.020  1.407
 80R  C10  C12  aromatic  1.413  0.020  1.413
 80R  CL1  C12  single    1.732  0.020  1.732
 80R  C3   C4   aromatic  1.374  0.020  1.374
 80R  C12  C6   aromatic  1.373  0.020  1.373
 80R  C4   C11  aromatic  1.391  0.020  1.391
 80R  C6   C11  aromatic  1.391  0.020  1.391
 80R  C11  N17  single    1.436  0.020  1.436
 80R  N17  O20  single    1.212  0.020  1.212
 80R  N17  O18  double    1.213  0.020  1.213
 80R  C4   H1   single    0.930  0.020  1.080
 80R  C5   H2   single    0.930  0.020  1.080
 80R  C6   H3   single    0.930  0.020  1.080
 80R  C1   H4   single    0.930  0.020  1.080
 80R  C2   H5   single    0.930  0.020  1.080
 80R  C3   H6   single    0.930  0.020  1.080
 80R  N14  H7   single    0.860  0.020  1.020
 80R  N15  H8   single    0.860  0.020  1.020
 80R  N16  H9   single    0.860  0.020  1.020

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
 80R  H1   C4   C11  121.13  3.000
 80R  H1   C4   C3   119.03  3.000
 80R  C11  C4   C3   119.84  3.000
 80R  H2   C5   C9   121.33  3.000
 80R  H2   C5   C8   121.37  3.000
 80R  C9   C5   C8   117.30  3.000
 80R  H3   C6   C12  119.60  3.000
 80R  H3   C6   C11  121.19  3.000
 80R  C12  C6   C11  119.21  3.000
 80R  N14  C7   C1   132.49  3.000
 80R  C1   C7   C8   121.01  3.000
 80R  N14  C7   C8   106.49  3.000
 80R  N15  C8   C7   106.53  3.000
 80R  C7   C8   C5   121.69  3.000
 80R  N15  C8   C5   131.78  3.000
 80R  N16  C10  C12  120.50  3.000
 80R  C12  C10  C3   116.72  3.000
 80R  N16  C10  C3   122.77  3.000
 80R  O19  C13  N15  127.37  3.000
 80R  N15  C13  N14  105.16  3.000
 80R  O19  C13  N14  127.47  3.000
 80R  H4   C1   C2   120.80  3.000
 80R  H4   C1   C7   121.50  3.000
 80R  C2   C1   C7   117.69  3.000
 80R  H5   C2   C9   119.29  3.000
 80R  H5   C2   C1   119.47  3.000
 80R  C9   C2   C1   121.24  3.000
 80R  H6   C3   C10  119.66  3.000
 80R  H6   C3   C4   118.72  3.000
 80R  C10  C3   C4   121.62  3.000
 80R  N16  C9   C2   118.85  3.000
 80R  N16  C9   C5   120.08  3.000
 80R  C2   C9   C5   121.03  3.000
 80R  N17  C11  C6   119.45  3.000
 80R  N17  C11  C4   120.13  3.000
 80R  C6   C11  C4   120.42  3.000
 80R  CL1  C12  C10  118.98  3.000
 80R  CL1  C12  C6   118.84  3.000
 80R  C10  C12  C6   122.18  3.000
 80R  H7   N14  C13  123.05  3.000
 80R  H7   N14  C7   126.03  3.000
 80R  C13  N14  C7   110.91  3.000
 80R  H8   N15  C13  123.07  3.000
 80R  H8   N15  C8   126.02  3.000
 80R  C13  N15  C8   110.91  3.000
 80R  H9   N16  C9   116.28  3.000
 80R  H9   N16  C10  117.30  3.000
 80R  C9   N16  C10  125.93  3.000
 80R  O20  N17  O18  123.37  3.000
 80R  O18  N17  C11  118.40  3.000
 80R  O20  N17  C11  118.23  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
 80R  CONST_01  C12  C10  C3   C4     0.00   0.0  0
 80R  CONST_02  C12  C6   C11  C4     0.00   0.0  0
 80R  CONST_03  C1   C7   C8   C5     0.00   0.0  0
 80R  CONST_04  C1   C2   C9   C5     0.00   0.0  0
 80R  CONST_05  C3   C10  C12  C6     0.00   0.0  0
 80R  CONST_06  C3   C4   C11  C6     0.00   0.0  0
 80R  CONST_07  C9   C5   C8   C7     0.00   0.0  0
 80R  CONST_08  C9   C2   C1   C7     0.00   0.0  0
 80R  CONST_09  C2   C1   C7   C8     0.00   0.0  0
 80R  CONST_10  C2   C9   C5   C8     0.00   0.0  0
 80R  CONST_11  C11  C4   C3   C10    0.00   0.0  0
 80R  CONST_12  C11  C6   C12  C10    0.00   0.0  0
 80R  CONST_13  N15  C13  N14  C7     0.00   0.0  0
 80R  CONST_14  C13  N15  C8   C7     0.00   0.0  0
 80R  CONST_15  N14  C13  N15  C8     0.00   0.0  0
 80R  CONST_16  C13  N14  C7   C8     0.00   0.0  0
 80R  CONST_17  N15  C8   C7   N14    0.00   0.0  0
 80R  CONST_18  N16  C10  C3   C4   180.00   0.0  0
 80R  CONST_19  N16  C10  C12  C6   180.00   0.0  0
 80R  CONST_20  N16  C9   C5   C8   180.00   0.0  0
 80R  CONST_21  N16  C9   C2   C1   180.00   0.0  0
 80R  CONST_22  CL1  C12  C10  C3   180.00   0.0  0
 80R  CONST_23  N17  C11  C4   C3   180.00   0.0  0
 80R  CONST_24  CL1  C12  C6   C11  180.00   0.0  0
 80R  CONST_25  N17  C11  C6   C12  180.00   0.0  0
 80R  CONST_26  O19  C13  N14  C7   180.00   0.0  0
 80R  CONST_27  O19  C13  N15  C8   180.00   0.0  0
 80R  CONST_28  H3   C6   C11  C4   180.00   0.0  0
 80R  CONST_29  H5   C2   C9   C5   180.00   0.0  0
 80R  CONST_30  H1   C4   C11  C6   180.00   0.0  0
 80R  CONST_31  H2   C5   C8   C7   180.00   0.0  0
 80R  CONST_32  H4   C1   C7   C8   180.00   0.0  0
 80R  CONST_33  H6   C3   C4   C11  180.00   0.0  0
 80R  CONST_34  H8   N15  C8   C7   180.00   0.0  0
 80R  CONST_35  H7   N14  C7   C8   180.00   0.0  0
 80R  CONST_36  O20  N17  C11  C4     0.00   0.0  0
 80R  CONST_37  O18  N17  C11  C4   180.00   0.0  0
 80R  CONST_38  O20  N17  C11  C6   180.00   0.0  0
 80R  CONST_39  O18  N17  C11  C6     0.00   0.0  0
 80R  Var_01    C10  N16  C9   C5    57.06  30.0  2
 80R  Var_02    C9   N16  C10  C3     4.88  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
 80R  plan-1  C4   0.020
 80R  plan-1  C6   0.020
 80R  plan-1  C10  0.020
 80R  plan-1  C3   0.020
 80R  plan-1  C11  0.020
 80R  plan-1  C12  0.020
 80R  plan-1  N16  0.020
 80R  plan-1  N17  0.020
 80R  plan-1  CL1  0.020
 80R  plan-1  H1   0.020
 80R  plan-1  H3   0.020
 80R  plan-1  H6   0.020
 80R  plan-2  C5   0.020
 80R  plan-2  C7   0.020
 80R  plan-2  C8   0.020
 80R  plan-2  C13  0.020
 80R  plan-2  C1   0.020
 80R  plan-2  C2   0.020
 80R  plan-2  C9   0.020
 80R  plan-2  N14  0.020
 80R  plan-2  N15  0.020
 80R  plan-2  N16  0.020
 80R  plan-2  H2   0.020
 80R  plan-2  H4   0.020
 80R  plan-2  H5   0.020
 80R  plan-2  H7   0.020
 80R  plan-2  H8   0.020
 80R  plan-2  O19  0.020
 80R  plan-3  C11  0.020
 80R  plan-3  N17  0.020
 80R  plan-3  O18  0.020
 80R  plan-3  O20  0.020

