# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 12:02:56 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: 3-{[6-(7-chloro-1-benzothiophen-2-yl)-1H-indol-1-yl]methyl}-1H-pyrazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]nc(Cn2ccc3ccc(cc23)c4sc5c(Cl)cccc5c4)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
 NL3  NL3  '3-{[6-(7-chloro-1-benzothiophen-2-yl)-1H-indol-1-yl]methyl}-1H-pyrazole-5-carboxylic acid'  ligand  41  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NL3
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
 NL3  C10  C   CH2    0  -0.414  33.2422  49.1234  -24.0548
 NL3  C11  C   CR5    0   0.264  32.0941  48.3816  -24.6582
 NL3  C12  C   CR15   0  -0.522  30.8405  48.1031  -24.0899
 NL3  C13  C   CR5    0   0.237  30.1595  47.4018  -25.0631
 NL3  C16  C   C      0   0.371  28.7799  46.7935  -25.1036
 NL3  C17  C   CR5    0  -0.201  32.3410  52.5528  -28.2266
 NL3  C18  C   CR15   0  -0.283  32.5248  53.5998  -29.0728
 NL3  C19  C   CR16   0  -0.317  32.6277  54.0289  -31.5928
 NL3  C2   C   CR15   0  -0.018  32.7500  51.0248  -22.4946
 NL3  C20  C   CR16   0  -0.266  32.5473  53.4478  -32.8420
 NL3  C21  C   CR16   0  -0.243  32.3145  52.0760  -32.9923
 NL3  C22  C   CR6    0  -0.095  32.1628  51.2838  -31.8728
 NL3  C23  C   CR56   0   0.238  32.4724  53.2314  -30.4535
 NL3  C24  C   CR56   0  -0.134  32.2407  51.8542  -30.6095
 NL3  C3   C   CR15   0  -0.425  32.3840  52.3380  -22.5750
 NL3  C4   C   CR16   0  -0.323  31.9872  53.7993  -24.6985
 NL3  C5   C   CR16   0  -0.334  32.0010  53.7449  -26.0744
 NL3  C6   C   CR6    0   0.122  32.3342  52.5580  -26.7660
 NL3  C7   C   CR16   0  -0.373  32.6539  51.4081  -26.0548
 NL3  C8   C   CR56   0   0.408  32.6328  51.4698  -24.6664
 NL3  C9   C   CR56   0   0.046  32.3040  52.6504  -23.9639
 NL3  N1   N   NR5    0  -0.523  32.9096  50.4982  -23.7464
 NL3  N14  N   NR15   0  -0.466  31.0097  47.3124  -26.1030
 NL3  N15  N   N      0  -0.284  32.1781  47.8948  -25.8875
 NL3  O18  O   OC    -1  -0.577  28.0890  46.9569  -24.0851
 NL3  O19  O   O      0  -0.593  28.4935  46.1939  -26.1566
 NL3  S1   S   S2     0   0.234  32.0786  51.0538  -29.0893
 NL3  CL1  CL  CL     0  -0.119  31.8793  49.5850  -32.0109
 NL3  H1   H   HCH2   0   0.284  33.5602  48.6526  -23.1244
 NL3  H2   H   HCH2   0   0.279  34.0953  49.0966  -24.7360
 NL3  H3   H   HCR5   0   0.253  30.4857  48.3722  -23.1086
 NL3  H4   H   HCR5   0   0.266  32.7189  54.6101  -28.7399
 NL3  H5   H   HCR6   0   0.261  32.8096  55.0909  -31.4898
 NL3  H6   H   HCR5   0   0.286  32.9175  50.4085  -21.6246
 NL3  H7   H   HCR6   0   0.268  32.6658  54.0564  -33.7284
 NL3  H8   H   HCR6   0   0.280  32.2550  51.6381  -33.9793
 NL3  H9   H   HCR5   0   0.248  32.1993  52.9985  -21.7432
 NL3  H10  H   HCR6   0   0.249  31.7217  54.7202  -24.1947
 NL3  H11  H   HCR6   0   0.248  31.7273  54.6269  -26.6384
 NL3  H12  H   HCR6   0   0.262  32.9238  50.4897  -26.5619
 NL3  H13  H   HNR5   0   0.404  30.8166  46.8548  -26.9806

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
 NL3  C20  C21  aromatic  1.400  0.020  1.400
 NL3  C20  C19  aromatic  1.380  0.020  1.380
 NL3  C21  C22  aromatic  1.380  0.020  1.380
 NL3  C19  C23  aromatic  1.399  0.020  1.399
 NL3  C22  CL1  single    1.728  0.020  1.728
 NL3  C22  C24  aromatic  1.388  0.020  1.388
 NL3  C23  C24  aromatic  1.405  0.020  1.405
 NL3  C23  C18  aromatic  1.430  0.020  1.430
 NL3  C24  S1   aromatic  1.726  0.020  1.726
 NL3  O19  C16  deloc     1.245  0.020  1.245
 NL3  C18  C17  aromatic  1.359  0.020  1.359
 NL3  S1   C17  aromatic  1.749  0.020  1.749
 NL3  C17  C6   single    1.461  0.020  1.461
 NL3  C16  O18  deloc     1.242  0.020  1.242
 NL3  C16  C13  single    1.508  0.020  1.508
 NL3  N14  C13  aromatic  1.346  0.020  1.346
 NL3  N14  N15  aromatic  1.323  0.020  1.323
 NL3  C13  C12  aromatic  1.379  0.020  1.379
 NL3  C6   C7   aromatic  1.389  0.020  1.389
 NL3  C6   C5   aromatic  1.413  0.020  1.413
 NL3  N15  C11  aromatic  1.325  0.020  1.325
 NL3  C7   C8   aromatic  1.390  0.020  1.390
 NL3  C5   C4   aromatic  1.377  0.020  1.377
 NL3  C12  C11  aromatic  1.404  0.020  1.404
 NL3  C11  C10  single    1.494  0.020  1.494
 NL3  C8   C9   aromatic  1.413  0.020  1.413
 NL3  C8   N1   aromatic  1.366  0.020  1.366
 NL3  C4   C9   aromatic  1.400  0.020  1.400
 NL3  C10  N1   single    1.448  0.020  1.448
 NL3  C9   C3   aromatic  1.426  0.020  1.426
 NL3  N1   C2   aromatic  1.367  0.020  1.367
 NL3  C3   C2   aromatic  1.366  0.020  1.366
 NL3  C10  H1   single    0.970  0.020  1.090
 NL3  C10  H2   single    0.970  0.020  1.090
 NL3  C12  H3   single    0.930  0.020  1.080
 NL3  C18  H4   single    0.930  0.020  1.080
 NL3  C19  H5   single    0.930  0.020  1.080
 NL3  C2   H6   single    0.930  0.020  1.080
 NL3  C20  H7   single    0.930  0.020  1.080
 NL3  C21  H8   single    0.930  0.020  1.080
 NL3  C3   H9   single    0.930  0.020  1.080
 NL3  C4   H10  single    0.930  0.020  1.080
 NL3  C5   H11  single    0.930  0.020  1.080
 NL3  C7   H12  single    0.930  0.020  1.080
 NL3  N14  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
 NL3  H2   C10  H1   107.09  3.000
 NL3  H2   C10  N1   109.61  3.000
 NL3  H1   C10  N1   107.18  3.000
 NL3  H2   C10  C11  109.64  3.000
 NL3  H1   C10  C11  110.76  3.000
 NL3  N1   C10  C11  112.40  3.000
 NL3  N15  C11  C12  111.05  3.000
 NL3  C12  C11  C10  128.39  3.000
 NL3  N15  C11  C10  120.56  3.000
 NL3  H3   C12  C13  127.36  3.000
 NL3  H3   C12  C11  127.80  3.000
 NL3  C13  C12  C11  104.84  3.000
 NL3  N14  C13  C16  122.01  3.000
 NL3  N14  C13  C12  105.48  3.000
 NL3  C16  C13  C12  132.50  3.000
 NL3  O19  C16  O18  128.99  3.000
 NL3  O18  C16  C13  115.71  3.000
 NL3  O19  C16  C13  115.30  3.000
 NL3  S1   C17  C6   119.70  3.000
 NL3  C6   C17  C18  128.36  3.000
 NL3  S1   C17  C18  111.93  3.000
 NL3  H4   C18  C23  123.00  3.000
 NL3  H4   C18  C17  123.54  3.000
 NL3  C23  C18  C17  113.44  3.000
 NL3  H5   C19  C23  120.03  3.000
 NL3  H5   C19  C20  120.60  3.000
 NL3  C23  C19  C20  119.37  3.000
 NL3  H6   C2   N1   119.99  3.000
 NL3  H6   C2   C3   129.66  3.000
 NL3  N1   C2   C3   110.35  3.000
 NL3  H7   C20  C21  118.80  3.000
 NL3  H7   C20  C19  119.90  3.000
 NL3  C21  C20  C19  121.30  3.000
 NL3  H8   C21  C22  120.13  3.000
 NL3  H8   C21  C20  120.27  3.000
 NL3  C22  C21  C20  119.60  3.000
 NL3  CL1  C22  C24  119.07  3.000
 NL3  C24  C22  C21  119.75  3.000
 NL3  CL1  C22  C21  121.18  3.000
 NL3  C24  C23  C19  119.11  3.000
 NL3  C24  C23  C18  111.45  3.000
 NL3  C19  C23  C18  129.43  3.000
 NL3  S1   C24  C23  111.85  3.000
 NL3  S1   C24  C22  127.29  3.000
 NL3  C23  C24  C22  120.86  3.000
 NL3  H9   C3   C9   127.42  3.000
 NL3  H9   C3   C2   126.13  3.000
 NL3  C9   C3   C2   106.44  3.000
 NL3  H10  C4   C9   120.62  3.000
 NL3  H10  C4   C5   120.06  3.000
 NL3  C9   C4   C5   119.31  3.000
 NL3  H11  C5   C6   119.27  3.000
 NL3  H11  C5   C4   119.08  3.000
 NL3  C6   C5   C4   121.63  3.000
 NL3  C7   C6   C5   119.92  3.000
 NL3  C5   C6   C17  119.56  3.000
 NL3  C7   C6   C17  120.52  3.000
 NL3  H12  C7   C8   120.60  3.000
 NL3  H12  C7   C6   121.29  3.000
 NL3  C8   C7   C6   118.11  3.000
 NL3  N1   C8   C9   107.86  3.000
 NL3  N1   C8   C7   129.64  3.000
 NL3  C9   C8   C7   122.50  3.000
 NL3  C8   C9   C4   118.53  3.000
 NL3  C4   C9   C3   134.72  3.000
 NL3  C8   C9   C3   106.75  3.000
 NL3  C8   N1   C2   108.59  3.000
 NL3  C2   N1   C10  125.99  3.000
 NL3  C8   N1   C10  125.34  3.000
 NL3  H13  N14  N15  120.70  3.000
 NL3  H13  N14  C13  125.56  3.000
 NL3  N15  N14  C13  113.74  3.000
 NL3  N14  N15  C11  104.89  3.000
 NL3  C24  S1   C17   91.31  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
 NL3  CONST_01  C13  N14  N15  C11     0.00   0.0  0
 NL3  CONST_02  N14  C13  C12  C11     0.00   0.0  0
 NL3  CONST_03  N15  N14  C13  C12     0.00   0.0  0
 NL3  CONST_04  N14  N15  C11  C12     0.00   0.0  0
 NL3  CONST_05  N15  C11  C12  C13     0.00   0.0  0
 NL3  CONST_06  C19  C23  C18  C17   180.00   0.0  0
 NL3  CONST_07  C24  C23  C18  C17     0.00   0.0  0
 NL3  CONST_08  C22  C24  S1   C17   180.00   0.0  0
 NL3  CONST_09  C23  C24  S1   C17     0.00   0.0  0
 NL3  CONST_10  C8   C7   C6   C17   180.00   0.0  0
 NL3  CONST_11  C4   C5   C6   C17   180.00   0.0  0
 NL3  CONST_12  C20  C19  C23  C18   180.00   0.0  0
 NL3  CONST_13  C22  C24  C23  C18   180.00   0.0  0
 NL3  CONST_14  S1   C24  C23  C18     0.00   0.0  0
 NL3  CONST_15  C24  S1   C17  C18     0.00   0.0  0
 NL3  CONST_18  C22  C21  C20  C19     0.00   0.0  0
 NL3  CONST_19  C22  C24  C23  C19     0.00   0.0  0
 NL3  CONST_20  S1   C24  C23  C19   180.00   0.0  0
 NL3  CONST_21  C7   C8   N1   C2    180.00   0.0  0
 NL3  CONST_22  C9   C8   N1   C2      0.00   0.0  0
 NL3  CONST_23  C8   C9   C3   C2      0.00   0.0  0
 NL3  CONST_24  C4   C9   C3   C2    180.00   0.0  0
 NL3  CONST_25  C24  C22  C21  C20     0.00   0.0  0
 NL3  CONST_26  C24  C23  C19  C20     0.00   0.0  0
 NL3  CONST_27  C23  C19  C20  C21     0.00   0.0  0
 NL3  CONST_28  C23  C24  C22  C21     0.00   0.0  0
 NL3  CONST_29  S1   C24  C22  C21   180.00   0.0  0
 NL3  CONST_30  S1   C17  C18  C23     0.00   0.0  0
 NL3  CONST_31  C6   C17  C18  C23   180.00   0.0  0
 NL3  CONST_32  C6   C17  S1   C24   180.00   0.0  0
 NL3  CONST_33  C7   C8   C9   C3    180.00   0.0  0
 NL3  CONST_34  N1   C8   C9   C3      0.00   0.0  0
 NL3  CONST_35  C5   C4   C9   C3    180.00   0.0  0
 NL3  CONST_36  C8   N1   C2   C3      0.00   0.0  0
 NL3  CONST_37  C7   C6   C5   C4      0.00   0.0  0
 NL3  CONST_38  C7   C8   C9   C4      0.00   0.0  0
 NL3  CONST_39  N1   C8   C9   C4    180.00   0.0  0
 NL3  CONST_41  C8   C7   C6   C5      0.00   0.0  0
 NL3  CONST_42  C8   C9   C4   C5      0.00   0.0  0
 NL3  CONST_43  C9   C8   C7   C6      0.00   0.0  0
 NL3  CONST_44  N1   C8   C7   C6    180.00   0.0  0
 NL3  CONST_45  C9   C4   C5   C6      0.00   0.0  0
 NL3  CONST_47  N1   C2   C3   C9      0.00   0.0  0
 NL3  CONST_48  N14  N15  C11  C10   180.00   0.0  0
 NL3  CONST_49  C13  C12  C11  C10   180.00   0.0  0
 NL3  CONST_50  C7   C8   N1   C10     0.00   0.0  0
 NL3  CONST_51  C9   C8   N1   C10   180.00   0.0  0
 NL3  CONST_52  C3   C2   N1   C10   180.00   0.0  0
 NL3  CONST_53  C16  C13  C12  C11   180.00   0.0  0
 NL3  CONST_54  N15  N14  C13  C16   180.00   0.0  0
 NL3  CONST_55  CL1  C22  C21  C20   180.00   0.0  0
 NL3  CONST_56  CL1  C22  C24  C23   180.00   0.0  0
 NL3  CONST_57  CL1  C22  C24  S1      0.00   0.0  0
 NL3  CONST_58  H13  N14  N15  C11   180.00   0.0  0
 NL3  CONST_59  H12  C7   C6   C17     0.00   0.0  0
 NL3  CONST_60  H11  C5   C6   C17     0.00   0.0  0
 NL3  CONST_61  H5   C19  C23  C18     0.00   0.0  0
 NL3  CONST_62  H8   C21  C20  C19   180.00   0.0  0
 NL3  CONST_63  H4   C18  C23  C19     0.00   0.0  0
 NL3  CONST_64  H7   C20  C21  C22   180.00   0.0  0
 NL3  CONST_65  H10  C4   C9   C3      0.00   0.0  0
 NL3  CONST_66  H9   C3   C9   C4      0.00   0.0  0
 NL3  CONST_67  H6   C2   N1   C8    180.00   0.0  0
 NL3  CONST_68  H3   C12  C13  N14   180.00   0.0  0
 NL3  Var_01    C8   N1   C10  C11   -66.99  30.0  2
 NL3  Var_02    N1   C10  C11  C12   -62.06  30.0  2
 NL3  Var_03    O19  C16  C13  C12  -178.52  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
 NL3  plan-1  C10  0.020
 NL3  plan-1  C11  0.020
 NL3  plan-1  C12  0.020
 NL3  plan-1  C13  0.020
 NL3  plan-1  C16  0.020
 NL3  plan-1  N14  0.020
 NL3  plan-1  N15  0.020
 NL3  plan-1  H3   0.020
 NL3  plan-1  H13  0.020
 NL3  plan-2  C17  0.020
 NL3  plan-2  C18  0.020
 NL3  plan-2  C19  0.020
 NL3  plan-2  C20  0.020
 NL3  plan-2  C21  0.020
 NL3  plan-2  C22  0.020
 NL3  plan-2  C23  0.020
 NL3  plan-2  C24  0.020
 NL3  plan-2  C6   0.020
 NL3  plan-2  S1   0.020
 NL3  plan-2  CL1  0.020
 NL3  plan-2  H4   0.020
 NL3  plan-2  H5   0.020
 NL3  plan-2  H7   0.020
 NL3  plan-2  H8   0.020
 NL3  plan-3  C10  0.020
 NL3  plan-3  C17  0.020
 NL3  plan-3  C2   0.020
 NL3  plan-3  C3   0.020
 NL3  plan-3  C4   0.020
 NL3  plan-3  C5   0.020
 NL3  plan-3  C6   0.020
 NL3  plan-3  C7   0.020
 NL3  plan-3  C8   0.020
 NL3  plan-3  C9   0.020
 NL3  plan-3  N1   0.020
 NL3  plan-3  H6   0.020
 NL3  plan-3  H9   0.020
 NL3  plan-3  H10  0.020
 NL3  plan-3  H11  0.020
 NL3  plan-3  H12  0.020
 NL3  plan-4  C13  0.020
 NL3  plan-4  C16  0.020
 NL3  plan-4  O18  0.020
 NL3  plan-4  O19  0.020

