# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 07:21:13 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-(naphthalen-1-yl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c2cccc(c2c1)c3cccc4ccccc34
#
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
 5BJ  5BJ  '4-(naphthalen-1-yl)-1H-indole-2-carboxylic acid'  ligand  34  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5BJ
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
 5BJ  C1   C  CR56   0   0.051  -0.9870   0.8122   0.0314
 5BJ  C2   C  CR6    0  -0.005   0.2277   1.5216  -0.0056
 5BJ  C3   C  CR56   0   0.348  -2.1826   1.4650  -0.3557
 5BJ  C11  C  CR16   0  -0.321   2.1460   1.4146   1.5326
 5BJ  C12  C  CR16   0  -0.272  -1.0024   3.4709  -0.7972
 5BJ  C14  C  CR66   0   0.116   3.2775  -0.7772   0.2312
 5BJ  C15  C  CR16   0  -0.334   1.4931  -0.7549  -1.4284
 5BJ  C16  C  CR16   0  -0.244   3.3487   0.8550   2.0061
 5BJ  C19  C  CR16   0  -0.330   3.8993  -0.2244   1.3749
 5BJ  C20  C  CR16   0  -0.313   3.8490  -1.8782  -0.4504
 5BJ  C21  C  CR16   0  -0.255   2.0728  -1.8157  -2.0700
 5BJ  C22  C  CR16   0  -0.260   3.2611  -2.3899  -1.5738
 5BJ  C4   C  CR15   0  -0.469  -1.3512  -0.5118   0.4146
 5BJ  C5   C  CR6    0   0.053   1.4972   0.9015   0.4353
 5BJ  C6   C  CR16   0  -0.332   0.1949   2.8441  -0.4159
 5BJ  N7   N  NR15   0  -0.712  -3.1958   0.5695  -0.2142
 5BJ  C8   C  CR16   0  -0.324  -2.2054   2.7952  -0.7743
 5BJ  C9   C  CR5    0   0.173  -2.7073  -0.6203   0.2515
 5BJ  C10  C  CR66   0   0.089   2.0679  -0.2098  -0.2542
 5BJ  O17  O  OC    -1  -0.603  -4.8333  -1.5804   0.2569
 5BJ  O18  O  O      0  -0.585  -3.0974  -2.8212   0.9340
 5BJ  H1   H  HCR6   0   0.251   1.7154   2.2585   2.0573
 5BJ  H2   H  HCR6   0   0.249  -0.9763   4.5053  -1.1147
 5BJ  H3   H  HCR6   0   0.256   0.5844  -0.3220  -1.8246
 5BJ  H4   H  HCR6   0   0.257   3.8281   1.2825   2.8771
 5BJ  H5   H  HCR6   0   0.255   4.8209  -0.6648   1.7357
 5BJ  H6   H  HCR6   0   0.255   4.7684  -2.3079  -0.0704
 5BJ  H7   H  HCR6   0   0.257   1.6190  -2.2154  -2.9676
 5BJ  H8   H  HCR6   0   0.257   3.7088  -3.2291  -2.0900
 5BJ  H9   H  HCR5   0   0.237  -0.6947  -1.2911   0.7666
 5BJ  H10  H  HCR6   0   0.240   1.1181   3.4094  -0.4537
 5BJ  H11  H  HNR5   0   0.395  -4.1724   0.7357  -0.3951
 5BJ  H12  H  HCR6   0   0.257  -3.1295   3.2793  -1.0640
 5BJ  C13  C  C      0   0.362  -3.6281  -1.7821   0.5042

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
 5BJ  O18  C13  deloc     1.243  0.020  1.243
 5BJ  C13  O17  deloc     1.247  0.020  1.247
 5BJ  C13  C9   single    1.504  0.020  1.504
 5BJ  C9   C4   aromatic  1.370  0.020  1.370
 5BJ  C9   N7   aromatic  1.368  0.020  1.368
 5BJ  C4   C1   aromatic  1.426  0.020  1.426
 5BJ  C16  C19  aromatic  1.366  0.020  1.366
 5BJ  C16  C11  aromatic  1.408  0.020  1.408
 5BJ  C19  C14  aromatic  1.414  0.020  1.414
 5BJ  N7   C3   aromatic  1.360  0.020  1.360
 5BJ  C11  C5   aromatic  1.374  0.020  1.374
 5BJ  C1   C3   aromatic  1.416  0.020  1.416
 5BJ  C1   C2   aromatic  1.407  0.020  1.407
 5BJ  C14  C20  aromatic  1.415  0.020  1.415
 5BJ  C14  C10  aromatic  1.422  0.020  1.422
 5BJ  C5   C10  aromatic  1.427  0.020  1.427
 5BJ  C5   C2   single    1.480  0.020  1.480
 5BJ  C20  C22  aromatic  1.367  0.020  1.367
 5BJ  C3   C8   aromatic  1.395  0.020  1.395
 5BJ  C10  C15  aromatic  1.416  0.020  1.416
 5BJ  C2   C6   aromatic  1.385  0.020  1.385
 5BJ  C22  C21  aromatic  1.410  0.020  1.410
 5BJ  C15  C21  aromatic  1.369  0.020  1.369
 5BJ  C8   C12  aromatic  1.380  0.020  1.380
 5BJ  C6   C12  aromatic  1.404  0.020  1.404
 5BJ  C11  H1   single    0.930  0.020  1.080
 5BJ  C12  H2   single    0.930  0.020  1.080
 5BJ  C15  H3   single    0.930  0.020  1.080
 5BJ  C16  H4   single    0.930  0.020  1.080
 5BJ  C19  H5   single    0.930  0.020  1.080
 5BJ  C20  H6   single    0.930  0.020  1.080
 5BJ  C21  H7   single    0.930  0.020  1.080
 5BJ  C22  H8   single    0.930  0.020  1.080
 5BJ  C4   H9   single    0.930  0.020  1.080
 5BJ  C6   H10  single    0.930  0.020  1.080
 5BJ  N7   H11  single    0.860  0.020  1.020
 5BJ  C8   H12  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
 5BJ  C4   C1   C3   106.61  3.000
 5BJ  C3   C1   C2   119.29  3.000
 5BJ  C4   C1   C2   134.09  3.000
 5BJ  C6   C2   C5   120.57  3.000
 5BJ  C6   C2   C1   117.95  3.000
 5BJ  C5   C2   C1   121.43  3.000
 5BJ  C8   C3   N7   130.33  3.000
 5BJ  C8   C3   C1   122.38  3.000
 5BJ  N7   C3   C1   107.29  3.000
 5BJ  H1   C11  C5   119.34  3.000
 5BJ  H1   C11  C16  119.09  3.000
 5BJ  C5   C11  C16  121.55  3.000
 5BJ  H2   C12  C8   119.60  3.000
 5BJ  H2   C12  C6   119.06  3.000
 5BJ  C8   C12  C6   121.35  3.000
 5BJ  C10  C14  C20  119.32  3.000
 5BJ  C10  C14  C19  119.61  3.000
 5BJ  C20  C14  C19  121.06  3.000
 5BJ  H3   C15  C10  119.37  3.000
 5BJ  H3   C15  C21  119.62  3.000
 5BJ  C10  C15  C21  121.00  3.000
 5BJ  H4   C16  C19  120.36  3.000
 5BJ  H4   C16  C11  119.46  3.000
 5BJ  C19  C16  C11  120.18  3.000
 5BJ  H5   C19  C16  120.68  3.000
 5BJ  H5   C19  C14  118.97  3.000
 5BJ  C16  C19  C14  120.35  3.000
 5BJ  H6   C20  C22  120.30  3.000
 5BJ  H6   C20  C14  118.83  3.000
 5BJ  C22  C20  C14  120.87  3.000
 5BJ  H7   C21  C22  119.66  3.000
 5BJ  H7   C21  C15  119.83  3.000
 5BJ  C22  C21  C15  120.51  3.000
 5BJ  H8   C22  C21  119.78  3.000
 5BJ  H8   C22  C20  120.27  3.000
 5BJ  C21  C22  C20  119.95  3.000
 5BJ  H9   C4   C9   125.76  3.000
 5BJ  H9   C4   C1   127.12  3.000
 5BJ  C9   C4   C1   107.12  3.000
 5BJ  C10  C5   C11  119.20  3.000
 5BJ  C10  C5   C2   121.70  3.000
 5BJ  C11  C5   C2   119.10  3.000
 5BJ  H10  C6   C12  118.97  3.000
 5BJ  H10  C6   C2   119.24  3.000
 5BJ  C12  C6   C2   121.79  3.000
 5BJ  H11  N7   C9   123.44  3.000
 5BJ  H11  N7   C3   126.54  3.000
 5BJ  C9   N7   C3   110.01  3.000
 5BJ  H12  C8   C12  121.37  3.000
 5BJ  H12  C8   C3   121.39  3.000
 5BJ  C12  C8   C3   117.24  3.000
 5BJ  N7   C9   C4   108.97  3.000
 5BJ  N7   C9   C13  120.70  3.000
 5BJ  C4   C9   C13  130.33  3.000
 5BJ  C5   C10  C15  122.55  3.000
 5BJ  C15  C10  C14  118.34  3.000
 5BJ  C5   C10  C14  119.09  3.000
 5BJ  O18  C13  O17  128.05  3.000
 5BJ  O17  C13  C9   115.69  3.000
 5BJ  O18  C13  C9   116.25  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
 5BJ  CONST_01  N7   C9   C4   C1     0.00   0.0  0
 5BJ  CONST_02  C9   N7   C3   C1     0.00   0.0  0
 5BJ  CONST_03  C12  C8   C3   C1     0.00   0.0  0
 5BJ  CONST_06  C12  C6   C2   C1     0.00   0.0  0
 5BJ  CONST_07  C9   C4   C1   C2   180.00   0.0  0
 5BJ  CONST_08  N7   C3   C1   C2   180.00   0.0  0
 5BJ  CONST_09  C8   C3   C1   C2     0.00   0.0  0
 5BJ  CONST_10  C16  C11  C5   C2   180.00   0.0  0
 5BJ  CONST_11  C14  C10  C5   C2   180.00   0.0  0
 5BJ  CONST_12  C15  C10  C5   C2     0.00   0.0  0
 5BJ  CONST_13  C8   C12  C6   C2     0.00   0.0  0
 5BJ  CONST_14  C4   C9   N7   C3     0.00   0.0  0
 5BJ  CONST_15  C9   C4   C1   C3     0.00   0.0  0
 5BJ  CONST_16  C5   C2   C1   C3   180.00   0.0  0
 5BJ  CONST_17  C6   C2   C1   C3     0.00   0.0  0
 5BJ  CONST_18  C6   C12  C8   C3     0.00   0.0  0
 5BJ  CONST_19  C14  C19  C16  C11    0.00   0.0  0
 5BJ  CONST_20  C14  C10  C5   C11    0.00   0.0  0
 5BJ  CONST_21  C15  C10  C5   C11  180.00   0.0  0
 5BJ  CONST_23  N7   C3   C8   C12  180.00   0.0  0
 5BJ  CONST_24  C5   C2   C6   C12  180.00   0.0  0
 5BJ  CONST_25  C21  C22  C20  C14    0.00   0.0  0
 5BJ  CONST_26  C21  C15  C10  C14    0.00   0.0  0
 5BJ  CONST_27  C19  C14  C10  C15  180.00   0.0  0
 5BJ  CONST_28  C20  C14  C10  C15    0.00   0.0  0
 5BJ  CONST_29  C20  C22  C21  C15    0.00   0.0  0
 5BJ  CONST_30  C20  C14  C19  C16  180.00   0.0  0
 5BJ  CONST_31  C10  C14  C19  C16    0.00   0.0  0
 5BJ  CONST_32  C10  C5   C11  C16    0.00   0.0  0
 5BJ  CONST_33  C5   C11  C16  C19    0.00   0.0  0
 5BJ  CONST_34  C22  C20  C14  C19  180.00   0.0  0
 5BJ  CONST_35  C5   C10  C14  C19    0.00   0.0  0
 5BJ  CONST_36  C5   C10  C14  C20  180.00   0.0  0
 5BJ  CONST_37  C5   C10  C15  C21  180.00   0.0  0
 5BJ  CONST_38  C10  C14  C20  C22    0.00   0.0  0
 5BJ  CONST_39  C10  C15  C21  C22    0.00   0.0  0
 5BJ  CONST_40  N7   C3   C1   C4     0.00   0.0  0
 5BJ  CONST_41  C8   C3   C1   C4   180.00   0.0  0
 5BJ  CONST_42  C5   C2   C1   C4     0.00   0.0  0
 5BJ  CONST_43  C6   C2   C1   C4   180.00   0.0  0
 5BJ  CONST_45  C9   N7   C3   C8   180.00   0.0  0
 5BJ  CONST_46  C13  C9   C4   C1   180.00   0.0  0
 5BJ  CONST_47  C13  C9   N7   C3   180.00   0.0  0
 5BJ  CONST_48  H11  N7   C3   C1   180.00   0.0  0
 5BJ  CONST_49  H12  C8   C3   C1   180.00   0.0  0
 5BJ  CONST_50  H10  C6   C2   C1   180.00   0.0  0
 5BJ  CONST_51  H9   C4   C1   C2     0.00   0.0  0
 5BJ  CONST_52  H1   C11  C5   C2     0.00   0.0  0
 5BJ  CONST_53  H2   C12  C6   C2   180.00   0.0  0
 5BJ  CONST_54  H5   C19  C16  C11  180.00   0.0  0
 5BJ  CONST_55  H4   C16  C19  C14  180.00   0.0  0
 5BJ  CONST_56  H8   C22  C20  C14  180.00   0.0  0
 5BJ  CONST_57  H3   C15  C10  C14  180.00   0.0  0
 5BJ  CONST_58  H6   C20  C14  C19    0.00   0.0  0
 5BJ  CONST_59  H7   C21  C22  C20  180.00   0.0  0
 5BJ  Var_01    O18  C13  C9   C4     0.23  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
 5BJ  plan-1  C1   0.020
 5BJ  plan-1  C2   0.020
 5BJ  plan-1  C3   0.020
 5BJ  plan-1  C12  0.020
 5BJ  plan-1  C4   0.020
 5BJ  plan-1  C5   0.020
 5BJ  plan-1  C6   0.020
 5BJ  plan-1  N7   0.020
 5BJ  plan-1  C8   0.020
 5BJ  plan-1  C9   0.020
 5BJ  plan-1  H2   0.020
 5BJ  plan-1  H9   0.020
 5BJ  plan-1  H10  0.020
 5BJ  plan-1  H11  0.020
 5BJ  plan-1  H12  0.020
 5BJ  plan-1  C13  0.020
 5BJ  plan-2  C2   0.020
 5BJ  plan-2  C11  0.020
 5BJ  plan-2  C14  0.020
 5BJ  plan-2  C15  0.020
 5BJ  plan-2  C16  0.020
 5BJ  plan-2  C19  0.020
 5BJ  plan-2  C20  0.020
 5BJ  plan-2  C21  0.020
 5BJ  plan-2  C22  0.020
 5BJ  plan-2  C5   0.020
 5BJ  plan-2  C10  0.020
 5BJ  plan-2  H1   0.020
 5BJ  plan-2  H3   0.020
 5BJ  plan-2  H4   0.020
 5BJ  plan-2  H5   0.020
 5BJ  plan-2  H6   0.020
 5BJ  plan-2  H7   0.020
 5BJ  plan-2  H8   0.020
 5BJ  plan-3  C9   0.020
 5BJ  plan-3  O17  0.020
 5BJ  plan-3  O18  0.020
 5BJ  plan-3  C13  0.020

