# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:57:47 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-[[4-chloranyl-2-nitro-5-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)amino]phenyl]amino]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCNc1cc(Nc2ccc3NC(=O)Nc3c2)c(Cl)cc1[N+]([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
 80L  80L  '3-[[4-chloranyl-2-nitro-5-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)amino]phenyl]amino]propanoic acid'  ligand  40  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_80L
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
 80L  C4   C   CR16   0  -0.518  -1.0492   0.1364  -0.1291
 80L  C5   C   CR16   0  -0.265  -3.7292   0.7296   0.1724
 80L  C6   C   CR56   0   0.326   3.5933   2.1860  -0.3764
 80L  C7   C   CR56   0   0.343   2.9201   1.5801   0.6918
 80L  C8   C   CR6    0   0.287   0.8506   2.3573  -0.1655
 80L  C10  C   CR6    0   0.518  -1.4357   1.4658  -0.0288
 80L  C13  C   CR5    0   0.611   5.1348   1.1721   0.9378
 80L  C15  C   CH2    0  -0.636   0.0664  -4.0391  -0.4423
 80L  C1   C   CR16   0  -0.309   2.9052   2.8888  -1.3437
 80L  C2   C   CR16   0  -0.317   1.5195   2.9561  -1.2310
 80L  C3   C   CR16   0  -0.352   1.5510   1.6675   0.8273
 80L  C9   C   CR6    0   0.450  -1.9504  -0.9414  -0.0688
 80L  C11  C   CR6    0   0.150  -3.3338  -0.6138   0.0887
 80L  C12  C   CR6    0  -0.173  -2.8232   1.7418   0.1184
 80L  C14  C   C      0   0.425   1.5185  -4.5167  -0.6304
 80L  C16  C   CH2    0  -0.253  -0.0868  -2.5344  -0.3372
 80L  N17  N   NR15   0  -0.737   4.9321   1.9192  -0.1963
 80L  N18  N   NR15   0  -0.741   3.8821   0.9780   1.4692
 80L  N19  N   NH1    0  -0.785  -0.5499   2.4890  -0.0742
 80L  N20  N   NH1    0  -0.683  -1.4846  -2.1919  -0.1677
 80L  N21  N   N      1   0.338  -4.3536  -1.5872   0.1593
 80L  O22  O   O      0  -0.422  -5.5107  -1.2313   0.2946
 80L  O23  O   O      0  -0.494   6.1944   0.7681   1.3785
 80L  O24  O   O      0  -0.603   2.4109  -3.6476  -0.6506
 80L  O25  O   O     -1  -0.446  -4.0571  -2.7746   0.0823
 80L  O26  O   OC    -1  -0.624   1.6720  -5.7489  -0.7439
 80L  CL1  CL  CL     0  -0.118  -3.3622   3.3866   0.2322
 80L  H1   H   HCR6   0   0.300  -0.0018  -0.0760  -0.2772
 80L  H2   H   HCR6   0   0.306  -4.7770   0.9651   0.2875
 80L  H3   H   HCH2   0   0.238  -0.5357  -4.4144  -1.2769
 80L  H4   H   HCH2   0   0.239  -0.3403  -4.5166   0.4559
 80L  H5   H   HCR6   0   0.276   3.4165   3.3607  -2.1715
 80L  H6   H   HCR6   0   0.269   0.9488   3.4801  -1.9867
 80L  H7   H   HCR6   0   0.289   1.0379   1.2217   1.6693
 80L  H8   H   HCH2   0   0.229   0.4977  -2.1559   0.5068
 80L  H9   H   HCH2   0   0.231   0.3092  -2.0538  -1.2367
 80L  H10  H   HNR5   0   0.421   5.6803   2.2068  -0.8066
 80L  H11  H   HNR5   0   0.421   3.7180   0.4543   2.3140
 80L  H12  H   HNH1   0   0.400  -0.9222   3.4175  -0.2015
 80L  H13  H   HNH1   0   0.408  -2.1601  -2.9363  -0.1354

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
 80L  O23  C13  double    1.217  0.020  1.217
 80L  C13  N17  single    1.373  0.020  1.373
 80L  C13  N18  single    1.375  0.020  1.375
 80L  N17  C6   single    1.377  0.020  1.377
 80L  N18  C7   single    1.376  0.020  1.376
 80L  C6   C7   aromatic  1.400  0.020  1.400
 80L  C6   C1   aromatic  1.380  0.020  1.380
 80L  C7   C3   aromatic  1.379  0.020  1.379
 80L  C1   C2   aromatic  1.392  0.020  1.392
 80L  C3   C8   aromatic  1.397  0.020  1.397
 80L  C2   C8   aromatic  1.393  0.020  1.393
 80L  C8   N19  single    1.410  0.020  1.410
 80L  N19  C10  single    1.354  0.020  1.354
 80L  O24  C14  deloc     1.246  0.020  1.246
 80L  C10  C4   aromatic  1.388  0.020  1.388
 80L  C10  C12  aromatic  1.422  0.020  1.422
 80L  CL1  C12  single    1.735  0.020  1.735
 80L  C14  O26  deloc     1.247  0.020  1.247
 80L  C14  C15  single    1.540  0.020  1.540
 80L  C4   C9   aromatic  1.406  0.020  1.406
 80L  C12  C5   aromatic  1.360  0.020  1.360
 80L  C15  C16  single    1.516  0.020  1.516
 80L  C9   N20  single    1.338  0.020  1.338
 80L  C9   C11  aromatic  1.430  0.020  1.430
 80L  C16  N20  single    1.449  0.020  1.449
 80L  C5   C11  aromatic  1.403  0.020  1.403
 80L  C11  N21  single    1.412  0.020  1.412
 80L  N21  O25  single    1.226  0.020  1.226
 80L  N21  O22  double    1.218  0.020  1.218
 80L  C4   H1   single    0.930  0.020  1.080
 80L  C5   H2   single    0.930  0.020  1.080
 80L  C15  H3   single    0.970  0.020  1.090
 80L  C15  H4   single    0.970  0.020  1.090
 80L  C1   H5   single    0.930  0.020  1.080
 80L  C2   H6   single    0.930  0.020  1.080
 80L  C3   H7   single    0.930  0.020  1.080
 80L  C16  H8   single    0.970  0.020  1.090
 80L  C16  H9   single    0.970  0.020  1.090
 80L  N17  H10  single    0.860  0.020  1.020
 80L  N18  H11  single    0.860  0.020  1.020
 80L  N19  H12  single    0.860  0.020  1.020
 80L  N20  H13  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
 80L  H1   C4   C9   118.50  3.000
 80L  H1   C4   C10  117.96  3.000
 80L  C9   C4   C10  123.54  3.000
 80L  H2   C5   C12  119.23  3.000
 80L  H2   C5   C11  119.25  3.000
 80L  C12  C5   C11  121.52  3.000
 80L  N17  C6   C1   132.49  3.000
 80L  C1   C6   C7   121.02  3.000
 80L  N17  C6   C7   106.49  3.000
 80L  N18  C7   C3   131.81  3.000
 80L  C3   C7   C6   121.67  3.000
 80L  N18  C7   C6   106.51  3.000
 80L  N19  C8   C3   119.88  3.000
 80L  N19  C8   C2   119.10  3.000
 80L  C3   C8   C2   121.00  3.000
 80L  N19  C10  C12  119.67  3.000
 80L  C12  C10  C4   117.71  3.000
 80L  N19  C10  C4   122.62  3.000
 80L  O23  C13  N18  127.36  3.000
 80L  N18  C13  N17  105.16  3.000
 80L  O23  C13  N17  127.48  3.000
 80L  H4   C15  H3   105.74  3.000
 80L  H4   C15  C16  109.77  3.000
 80L  H3   C15  C16  109.71  3.000
 80L  H4   C15  C14  108.37  3.000
 80L  H3   C15  C14  108.60  3.000
 80L  C16  C15  C14  114.30  3.000
 80L  H5   C1   C2   120.77  3.000
 80L  H5   C1   C6   121.54  3.000
 80L  C2   C1   C6   117.68  3.000
 80L  H6   C2   C1   119.46  3.000
 80L  H6   C2   C8   119.27  3.000
 80L  C1   C2   C8   121.27  3.000
 80L  H7   C3   C8   121.24  3.000
 80L  H7   C3   C7   121.42  3.000
 80L  C8   C3   C7   117.34  3.000
 80L  N20  C9   C11  123.98  3.000
 80L  C11  C9   C4   116.68  3.000
 80L  N20  C9   C4   119.34  3.000
 80L  N21  C11  C9   123.12  3.000
 80L  N21  C11  C5   116.98  3.000
 80L  C9   C11  C5   119.90  3.000
 80L  CL1  C12  C10  119.60  3.000
 80L  CL1  C12  C5   119.76  3.000
 80L  C10  C12  C5   120.65  3.000
 80L  O26  C14  O24  126.84  3.000
 80L  O26  C14  C15  115.70  3.000
 80L  O24  C14  C15  117.46  3.000
 80L  H9   C16  H8   106.79  3.000
 80L  H9   C16  N20  109.97  3.000
 80L  H8   C16  N20  110.08  3.000
 80L  H9   C16  C15  110.02  3.000
 80L  H8   C16  C15  110.05  3.000
 80L  N20  C16  C15  109.89  3.000
 80L  H10  N17  C13  123.09  3.000
 80L  H10  N17  C6   125.99  3.000
 80L  C13  N17  C6   110.92  3.000
 80L  H11  N18  C13  123.09  3.000
 80L  H11  N18  C7   125.99  3.000
 80L  C13  N18  C7   110.92  3.000
 80L  H12  N19  C10  117.28  3.000
 80L  H12  N19  C8   116.40  3.000
 80L  C10  N19  C8   125.56  3.000
 80L  H13  N20  C16  118.47  3.000
 80L  H13  N20  C9   117.10  3.000
 80L  C16  N20  C9   124.43  3.000
 80L  O25  N21  O22  121.30  3.000
 80L  O22  N21  C11  119.36  3.000
 80L  O25  N21  C11  119.33  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
 80L  CONST_01  C5   C12  C10  C4      0.00   0.0  0
 80L  CONST_02  C5   C11  C9   C4      0.00   0.0  0
 80L  CONST_03  C8   C3   C7   C6      0.00   0.0  0
 80L  CONST_04  C8   C2   C1   C6      0.00   0.0  0
 80L  CONST_05  C2   C1   C6   C7      0.00   0.0  0
 80L  CONST_06  C2   C8   C3   C7      0.00   0.0  0
 80L  CONST_07  C11  C9   C4   C10     0.00   0.0  0
 80L  CONST_08  C11  C5   C12  C10     0.00   0.0  0
 80L  CONST_09  C3   C7   C6   C1      0.00   0.0  0
 80L  CONST_10  C3   C8   C2   C1      0.00   0.0  0
 80L  CONST_11  C12  C10  C4   C9      0.00   0.0  0
 80L  CONST_12  C12  C5   C11  C9      0.00   0.0  0
 80L  CONST_13  N18  C13  N17  C6      0.00   0.0  0
 80L  CONST_14  C13  N18  C7   C6      0.00   0.0  0
 80L  CONST_15  N17  C13  N18  C7      0.00   0.0  0
 80L  CONST_16  C13  N17  C6   C7      0.00   0.0  0
 80L  CONST_17  N18  C7   C6   N17     0.00   0.0  0
 80L  CONST_18  CL1  C12  C10  C4    180.00   0.0  0
 80L  CONST_19  N21  C11  C9   C4    180.00   0.0  0
 80L  CONST_20  N19  C10  C12  C5    180.00   0.0  0
 80L  CONST_21  N20  C9   C11  C5    180.00   0.0  0
 80L  CONST_22  N19  C8   C3   C7    180.00   0.0  0
 80L  CONST_23  N20  C9   C4   C10   180.00   0.0  0
 80L  CONST_24  N19  C8   C2   C1    180.00   0.0  0
 80L  CONST_25  N19  C10  C4   C9    180.00   0.0  0
 80L  CONST_26  CL1  C12  C5   C11   180.00   0.0  0
 80L  CONST_27  N21  C11  C5   C12   180.00   0.0  0
 80L  CONST_28  O23  C13  N17  C6    180.00   0.0  0
 80L  CONST_29  O23  C13  N18  C7    180.00   0.0  0
 80L  CONST_30  H7   C3   C7   C6    180.00   0.0  0
 80L  CONST_31  H6   C2   C1   C6    180.00   0.0  0
 80L  CONST_32  H5   C1   C6   C7    180.00   0.0  0
 80L  CONST_33  H2   C5   C12  C10   180.00   0.0  0
 80L  CONST_34  H1   C4   C9   C11   180.00   0.0  0
 80L  CONST_35  H11  N18  C7   C6    180.00   0.0  0
 80L  CONST_36  H10  N17  C6   C7    180.00   0.0  0
 80L  CONST_37  C16  N20  C9   C4      0.00   0.0  0
 80L  CONST_38  O25  N21  C11  C5    180.00   0.0  0
 80L  CONST_39  O22  N21  C11  C5      0.00   0.0  0
 80L  CONST_40  O25  N21  C11  C9      0.00   0.0  0
 80L  CONST_41  O22  N21  C11  C9    180.00   0.0  0
 80L  CONST_42  C16  N20  C9   C11   180.00   0.0  0
 80L  CONST_43  H13  N20  C9   C4    180.00   0.0  0
 80L  Var_01    C8   N19  C10  C4     -2.96  30.0  2
 80L  Var_02    C3   C8   N19  C10   -59.45  30.0  2
 80L  Var_03    C9   N20  C16  C15  -178.73  30.0  3
 80L  Var_04    N20  C16  C15  C14   179.80  30.0  3
 80L  Var_05    O24  C14  C15  C16     1.40  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
 80L  plan-1  C4   0.020
 80L  plan-1  C5   0.020
 80L  plan-1  C10  0.020
 80L  plan-1  C9   0.020
 80L  plan-1  C11  0.020
 80L  plan-1  C12  0.020
 80L  plan-1  N19  0.020
 80L  plan-1  N20  0.020
 80L  plan-1  N21  0.020
 80L  plan-1  CL1  0.020
 80L  plan-1  H1   0.020
 80L  plan-1  H2   0.020
 80L  plan-2  C6   0.020
 80L  plan-2  C7   0.020
 80L  plan-2  C8   0.020
 80L  plan-2  C13  0.020
 80L  plan-2  C1   0.020
 80L  plan-2  C2   0.020
 80L  plan-2  C3   0.020
 80L  plan-2  N17  0.020
 80L  plan-2  N18  0.020
 80L  plan-2  N19  0.020
 80L  plan-2  O23  0.020
 80L  plan-2  H5   0.020
 80L  plan-2  H6   0.020
 80L  plan-2  H7   0.020
 80L  plan-2  H10  0.020
 80L  plan-2  H11  0.020
 80L  plan-3  C9   0.020
 80L  plan-3  C16  0.020
 80L  plan-3  N20  0.020
 80L  plan-3  H13  0.020
 80L  plan-4  C11  0.020
 80L  plan-4  N21  0.020
 80L  plan-4  O22  0.020
 80L  plan-4  O25  0.020
 80L  plan-5  C15  0.020
 80L  plan-5  C14  0.020
 80L  plan-5  O24  0.020
 80L  plan-5  O26  0.020

