# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:06:08 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: 5-chloranyl-3-phenyl-1~{H}-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1[nH]c2ccc(Cl)cc2c1c3ccccc3
#
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
 QVK  QVK  5-chloranyl-3-phenyl-1~{H}-indole-2-carboxamide  ligand  30  19  .  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_QVK
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
 QVK  C13  C   CR5   0   0.038  17.1846  31.0796  15.2745
 QVK  C15  C   CR16  0  -0.297  15.1014  32.3998  14.9713
 QVK  C17  C   CR16  0  -0.262  13.3954  32.4581  16.6678
 QVK  N01  N   NH2   0  -0.811  15.7103  28.4011  15.3217
 QVK  C02  C   C     0   0.433  17.0443  28.4536  15.2564
 QVK  O03  O   O     0  -0.485  17.7636  27.4627  15.2944
 QVK  C04  C   CR5   0   0.198  17.6577  29.7953  15.1100
 QVK  N05  N   NR15  0  -0.728  18.9623  29.8388  14.7036
 QVK  C06  C   CR56  0   0.363  19.3633  31.1276  14.5829
 QVK  C07  C   CR16  0  -0.302  20.5934  31.6647  14.2004
 QVK  C08  C   CR16  0  -0.237  20.7160  33.0359  14.1855
 QVK  C09  C   CR6   0  -0.046  19.6313  33.8526  14.5501
 QVK  CL1  CL  CL    0  -0.139  19.8544  35.5765  14.5196
 QVK  C11  C   CR16  0  -0.328  18.4132  33.3389  14.9270
 QVK  C12  C   CR56  0   0.059  18.2703  31.9457  14.9359
 QVK  C14  C   CR6   0  -0.041  15.8701  31.5336  15.7505
 QVK  C16  C   CR16  0  -0.241  13.8739  32.8594  15.4275
 QVK  C18  C   CR16  0  -0.237  14.1530  31.5976  17.4518
 QVK  C19  C   CR16  0  -0.302  15.3830  31.1427  16.9992
 QVK  H1   H   HCR6  0   0.257  15.4612  32.7058  13.9966
 QVK  H2   H   HCR6  0   0.260  12.4378  32.8165  17.0219
 QVK  H3   H   HNH2  0   0.410  15.2510  27.5102  15.4209
 QVK  H4   H   HNH2  0   0.419  15.1271  29.2126  15.2134
 QVK  H5   H   HNR5  0   0.414  19.5182  29.0211  14.5082
 QVK  H6   H   HCR6  0   0.277  21.4277  31.0333  13.9253
 QVK  H7   H   HCR6  0   0.278  21.6535  33.4885  13.8933
 QVK  H8   H   HCR6  0   0.271  17.5937  33.9879  15.2069
 QVK  H9   H   HCR6  0   0.260  13.2898  33.5296  14.8106
 QVK  H10  H   HCR6  0   0.260  13.7909  31.2846  18.4222
 QVK  H11  H   HCR6  0   0.258  15.9767  30.4852  17.6217

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
 QVK  C07  C08  aromatic  1.377  0.020  1.377
 QVK  C07  C06  aromatic  1.396  0.020  1.396
 QVK  C08  C09  aromatic  1.406  0.020  1.406
 QVK  CL1  C09  single    1.739  0.020  1.739
 QVK  C06  N05  aromatic  1.355  0.020  1.355
 QVK  C06  C12  aromatic  1.410  0.020  1.410
 QVK  C09  C11  aromatic  1.375  0.020  1.375
 QVK  N05  C04  aromatic  1.367  0.020  1.367
 QVK  C15  C16  aromatic  1.388  0.020  1.388
 QVK  C15  C14  aromatic  1.396  0.020  1.396
 QVK  C12  C11  aromatic  1.401  0.020  1.401
 QVK  C12  C13  aromatic  1.430  0.020  1.430
 QVK  C04  C02  single    1.483  0.020  1.483
 QVK  C04  C13  aromatic  1.379  0.020  1.379
 QVK  N01  C02  single    1.337  0.020  1.337
 QVK  C02  O03  double    1.225  0.020  1.225
 QVK  C13  C14  single    1.470  0.020  1.470
 QVK  C16  C17  aromatic  1.389  0.020  1.389
 QVK  C14  C19  aromatic  1.396  0.020  1.396
 QVK  C17  C18  aromatic  1.389  0.020  1.389
 QVK  C19  C18  aromatic  1.387  0.020  1.387
 QVK  C15  H1   single    0.930  0.020  1.080
 QVK  C17  H2   single    0.930  0.020  1.080
 QVK  N01  H3   single    0.860  0.020  1.020
 QVK  N01  H4   single    0.860  0.020  1.020
 QVK  N05  H5   single    0.860  0.020  1.020
 QVK  C07  H6   single    0.930  0.020  1.080
 QVK  C08  H7   single    0.930  0.020  1.080
 QVK  C11  H8   single    0.930  0.020  1.080
 QVK  C16  H9   single    0.930  0.020  1.080
 QVK  C18  H10  single    0.930  0.020  1.080
 QVK  C19  H11  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
 QVK  C14  C13  C12  124.66  3.000
 QVK  C14  C13  C04  129.30  3.000
 QVK  C12  C13  C04  105.99  3.000
 QVK  H1   C15  C16  119.74  3.000
 QVK  H1   C15  C14  119.65  3.000
 QVK  C16  C15  C14  120.60  3.000
 QVK  H2   C17  C18  120.21  3.000
 QVK  H2   C17  C16  120.10  3.000
 QVK  C18  C17  C16  119.69  3.000
 QVK  H4   N01  H3   117.40  3.000
 QVK  H4   N01  C02  122.82  3.000
 QVK  H3   N01  C02  119.65  3.000
 QVK  C04  C02  O03  119.48  3.000
 QVK  O03  C02  N01  123.55  3.000
 QVK  C04  C02  N01  116.96  3.000
 QVK  N05  C04  C02  116.94  3.000
 QVK  C02  C04  C13  133.58  3.000
 QVK  N05  C04  C13  109.47  3.000
 QVK  H5   N05  C06  126.24  3.000
 QVK  H5   N05  C04  123.92  3.000
 QVK  C06  N05  C04  109.83  3.000
 QVK  C12  C06  C07  121.90  3.000
 QVK  C12  C06  N05  107.46  3.000
 QVK  C07  C06  N05  130.64  3.000
 QVK  H6   C07  C08  120.66  3.000
 QVK  H6   C07  C06  121.65  3.000
 QVK  C08  C07  C06  117.69  3.000
 QVK  H7   C08  C09  119.74  3.000
 QVK  H7   C08  C07  119.80  3.000
 QVK  C09  C08  C07  120.46  3.000
 QVK  C11  C09  CL1  119.28  3.000
 QVK  C11  C09  C08  122.53  3.000
 QVK  CL1  C09  C08  118.19  3.000
 QVK  H8   C11  C12  121.18  3.000
 QVK  H8   C11  C09  121.19  3.000
 QVK  C12  C11  C09  117.63  3.000
 QVK  C11  C12  C06  119.77  3.000
 QVK  C11  C12  C13  132.97  3.000
 QVK  C06  C12  C13  107.25  3.000
 QVK  C19  C14  C15  118.75  3.000
 QVK  C19  C14  C13  121.00  3.000
 QVK  C15  C14  C13  120.22  3.000
 QVK  H9   C16  C17  120.15  3.000
 QVK  H9   C16  C15  119.67  3.000
 QVK  C17  C16  C15  120.18  3.000
 QVK  H10  C18  C19  119.63  3.000
 QVK  H10  C18  C17  120.19  3.000
 QVK  C19  C18  C17  120.17  3.000
 QVK  H11  C19  C18  119.85  3.000
 QVK  H11  C19  C14  119.54  3.000
 QVK  C18  C19  C14  120.61  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
 QVK  CONST_01  C07  C06  C12  C13  180.00   0.0  0
 QVK  CONST_02  N05  C06  C12  C13    0.00   0.0  0
 QVK  CONST_03  C09  C11  C12  C13  180.00   0.0  0
 QVK  CONST_04  C06  N05  C04  C13    0.00   0.0  0
 QVK  CONST_05  C16  C15  C14  C13  180.00   0.0  0
 QVK  CONST_06  C18  C19  C14  C13  180.00   0.0  0
 QVK  CONST_07  C18  C17  C16  C15    0.00   0.0  0
 QVK  CONST_10  C18  C19  C14  C15    0.00   0.0  0
 QVK  CONST_11  C14  C15  C16  C17    0.00   0.0  0
 QVK  CONST_12  C14  C19  C18  C17    0.00   0.0  0
 QVK  CONST_13  C07  C06  N05  C04  180.00   0.0  0
 QVK  CONST_14  C12  C06  N05  C04    0.00   0.0  0
 QVK  CONST_15  C06  C12  C13  C04    0.00   0.0  0
 QVK  CONST_16  C11  C12  C13  C04  180.00   0.0  0
 QVK  CONST_18  C08  C07  C06  N05  180.00   0.0  0
 QVK  CONST_19  C11  C12  C06  N05  180.00   0.0  0
 QVK  CONST_20  C12  C13  C04  N05    0.00   0.0  0
 QVK  CONST_21  C14  C13  C04  N05  180.00   0.0  0
 QVK  CONST_22  C09  C08  C07  C06    0.00   0.0  0
 QVK  CONST_23  C09  C11  C12  C06    0.00   0.0  0
 QVK  CONST_24  C14  C13  C12  C06  180.00   0.0  0
 QVK  CONST_25  C11  C09  C08  C07    0.00   0.0  0
 QVK  CONST_26  C11  C12  C06  C07    0.00   0.0  0
 QVK  CONST_27  C12  C06  C07  C08    0.00   0.0  0
 QVK  CONST_28  C12  C11  C09  C08    0.00   0.0  0
 QVK  CONST_29  C14  C13  C12  C11    0.00   0.0  0
 QVK  CONST_31  C19  C14  C15  C16    0.00   0.0  0
 QVK  CONST_32  C19  C18  C17  C16    0.00   0.0  0
 QVK  CONST_33  C06  N05  C04  C02  180.00   0.0  0
 QVK  CONST_34  C12  C13  C04  C02  180.00   0.0  0
 QVK  CONST_35  C14  C13  C04  C02    0.00   0.0  0
 QVK  CONST_36  CL1  C09  C08  C07  180.00   0.0  0
 QVK  CONST_37  C12  C11  C09  CL1  180.00   0.0  0
 QVK  CONST_38  H8   C11  C12  C13    0.00   0.0  0
 QVK  CONST_39  H5   N05  C04  C13  180.00   0.0  0
 QVK  CONST_40  H1   C15  C14  C13    0.00   0.0  0
 QVK  CONST_41  H11  C19  C14  C13    0.00   0.0  0
 QVK  CONST_42  H2   C17  C16  C15  180.00   0.0  0
 QVK  CONST_43  H6   C07  C06  N05    0.00   0.0  0
 QVK  CONST_44  H7   C08  C07  C06  180.00   0.0  0
 QVK  CONST_45  H9   C16  C15  C14  180.00   0.0  0
 QVK  CONST_46  H10  C18  C19  C14  180.00   0.0  0
 QVK  CONST_47  H3   N01  C02  C04  180.00   0.0  0
 QVK  CONST_48  H4   N01  C02  C04    0.00   0.0  0
 QVK  Var_01    N01  C02  C04  C13   14.80  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
 QVK  plan-1  C13  0.020
 QVK  plan-1  C15  0.020
 QVK  plan-1  C17  0.020
 QVK  plan-1  C14  0.020
 QVK  plan-1  C16  0.020
 QVK  plan-1  C18  0.020
 QVK  plan-1  C19  0.020
 QVK  plan-1  H1   0.020
 QVK  plan-1  H2   0.020
 QVK  plan-1  H9   0.020
 QVK  plan-1  H10  0.020
 QVK  plan-1  H11  0.020
 QVK  plan-2  C13  0.020
 QVK  plan-2  C02  0.020
 QVK  plan-2  C04  0.020
 QVK  plan-2  N05  0.020
 QVK  plan-2  C06  0.020
 QVK  plan-2  C07  0.020
 QVK  plan-2  C08  0.020
 QVK  plan-2  C09  0.020
 QVK  plan-2  CL1  0.020
 QVK  plan-2  C11  0.020
 QVK  plan-2  C12  0.020
 QVK  plan-2  C14  0.020
 QVK  plan-2  H5   0.020
 QVK  plan-2  H6   0.020
 QVK  plan-2  H7   0.020
 QVK  plan-2  H8   0.020
 QVK  plan-3  N01  0.020
 QVK  plan-3  C02  0.020
 QVK  plan-3  O03  0.020
 QVK  plan-3  C04  0.020
 QVK  plan-3  H3   0.020
 QVK  plan-3  H4   0.020

