# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:40:39 2021
#   Inital geometry file: a 102 line input string
#   Ligand name: (4~{S})-7,8-bis(chloranyl)-9-methyl-1-oxidanylidene-spiro[2,4-dihydropyrido[3,4-b]indole-3,4'-piperidine]-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c2c(Cl)c(Cl)ccc2c3[C@H](C#N)C4(CCNCC4)NC(=O)c13
#
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
 KHC  KHC  (4~{S})-7,8-bis(chloranyl)-9-methyl-1-oxidanylidene-spiro[2,4-dihydropyrido[3,4-b]indole-3,4'-piperidine]-4-carbonitrile  ligand  40  24  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KHC
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
 KHC  CL1  CL  CL    0  -0.077  4.9051  13.8310  24.6785
 KHC  C15  C   CR6   0  -0.078  4.2334  12.6669  23.6030
 KHC  C14  C   CR6   0  -0.040  3.6933  11.5011  24.1136
 KHC  CL   CL  CL    0  -0.092  3.7312  11.2049  25.8117
 KHC  C13  C   CR16  0  -0.234  3.0917  10.5372  23.2919
 KHC  C12  C   CR16  0  -0.371  3.0192  10.7288  21.9363
 KHC  C16  C   CR56  0   0.469  4.1736  12.8681  22.2144
 KHC  N    N   NR5   0  -0.600  4.6018  13.9044  21.4324
 KHC  C    C   CH3   0  -0.548  5.4061  15.0413  21.8546
 KHC  C11  C   CR56  0   0.033  3.5635  11.8937  21.3824
 KHC  C10  C   CR5   0   0.105  3.6494  12.3957  20.0601
 KHC  C1   C   CR5   0   0.166  4.2653  13.6119  20.1347
 KHC  C8   C   CH1   0  -0.400  3.1405  11.8832  18.7477
 KHC  C9   C   CSP   0   0.128  3.0770  10.4275  18.7026
 KHC  N3   N   NS    0  -0.251  3.0052   9.2807  18.6558
 KHC  C3   C   CT    0   0.075  4.0229  12.4320  17.5952
 KHC  N1   N   NH1   0  -0.664  4.1168  13.8753  17.7996
 KHC  C2   C   C     0   0.527  4.3783  14.5021  18.9660
 KHC  O    O   O     0  -0.469  4.6037  15.7016  19.0331
 KHC  C7   C   CH2   0  -0.449  3.3420  12.1820  16.2473
 KHC  C6   C   CH2   0  -0.337  4.2260  12.5887  15.0656
 KHC  N2   N   NH1   0  -0.571  5.5573  12.0139  15.0989
 KHC  C5   C   CH2   0  -0.318  6.2230  12.2568  16.3665
 KHC  C4   C   CH2   0  -0.421  5.4215  11.7958  17.5830
 KHC  H1   H   HCR6  0   0.286  2.6790   9.6452  23.7411
 KHC  H2   H   HCR6  0   0.262  2.5412   9.9819  21.3189
 KHC  H3   H   HCH3  0   0.260  6.2669  14.7033  22.4234
 KHC  H4   H   HCH3  0   0.282  5.7609  15.5643  20.9771
 KHC  H5   H   HCH3  0   0.259  4.8207  15.7331  22.4554
 KHC  H6   H   HCH1  0   0.349  2.1129  12.2382  18.5896
 KHC  H7   H   HNH1  0   0.407  4.1493  14.4656  16.9809
 KHC  H8   H   HCH2  0   0.258  2.3867  12.7123  16.2099
 KHC  H9   H   HCH2  0   0.254  3.1215  11.1145  16.1609
 KHC  H10  H   HCH2  0   0.226  4.3180  13.6797  15.0106
 KHC  H11  H   HCH2  0   0.257  3.7352  12.2905  14.1381
 KHC  H12  H   HNH1  0   0.345  5.4910  11.0143  14.9446
 KHC  H14  H   HCH2  0   0.250  7.1888  11.7495  16.3604
 KHC  H15  H   HCH2  0   0.225  6.4392  13.3271  16.4470
 KHC  H16  H   HCH2  0   0.244  5.3264  10.7069  17.5445
 KHC  H17  H   HCH2  0   0.249  5.9598  12.0352  18.5028

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
 KHC  N2   C6   single    1.451  0.020  1.451
 KHC  N2   C5   single    1.452  0.020  1.452
 KHC  C6   C7   single    1.531  0.020  1.531
 KHC  C5   C4   single    1.528  0.020  1.528
 KHC  C7   C3   single    1.531  0.020  1.531
 KHC  C4   C3   single    1.537  0.020  1.537
 KHC  C3   N1   single    1.461  0.020  1.461
 KHC  C3   C8   single    1.552  0.020  1.552
 KHC  N1   C2   single    1.350  0.020  1.350
 KHC  N3   C9   triple    1.150  0.020  1.150
 KHC  C9   C8   single    1.458  0.020  1.458
 KHC  C8   C10  single    1.498  0.020  1.498
 KHC  C2   O    double    1.222  0.020  1.222
 KHC  C2   C1   single    1.474  0.020  1.474
 KHC  C10  C1   aromatic  1.365  0.020  1.365
 KHC  C10  C11  aromatic  1.417  0.020  1.417
 KHC  C1   N    aromatic  1.372  0.020  1.372
 KHC  C11  C12  aromatic  1.400  0.020  1.400
 KHC  C11  C16  aromatic  1.419  0.020  1.419
 KHC  N    C    single    1.455  0.020  1.455
 KHC  N    C16  aromatic  1.367  0.020  1.367
 KHC  C12  C13  aromatic  1.371  0.020  1.371
 KHC  C16  C15  aromatic  1.404  0.020  1.404
 KHC  C13  C14  aromatic  1.402  0.020  1.402
 KHC  C15  C14  aromatic  1.383  0.020  1.383
 KHC  C15  CL1  single    1.721  0.020  1.721
 KHC  C14  CL   single    1.724  0.020  1.724
 KHC  C13  H1   single    0.930  0.020  1.080
 KHC  C12  H2   single    0.930  0.020  1.080
 KHC  C    H3   single    0.970  0.020  1.090
 KHC  C    H4   single    0.970  0.020  1.090
 KHC  C    H5   single    0.970  0.020  1.090
 KHC  C8   H6   single    0.970  0.020  1.090
 KHC  N1   H7   single    0.860  0.020  1.020
 KHC  C7   H8   single    0.970  0.020  1.090
 KHC  C7   H9   single    0.970  0.020  1.090
 KHC  C6   H10  single    0.970  0.020  1.090
 KHC  C6   H11  single    0.970  0.020  1.090
 KHC  N2   H12  single    0.890  0.020  1.040
 KHC  C5   H14  single    0.970  0.020  1.090
 KHC  C5   H15  single    0.970  0.020  1.090
 KHC  C4   H16  single    0.970  0.020  1.090
 KHC  C4   H17  single    0.970  0.020  1.090

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
 KHC  C16  C15  C14  117.99  3.000
 KHC  C14  C15  CL1  119.47  3.000
 KHC  C16  C15  CL1  122.51  3.000
 KHC  C13  C14  CL   117.94  3.000
 KHC  CL   C14  C15  120.00  3.000
 KHC  C13  C14  C15  122.06  3.000
 KHC  H1   C13  C12  120.41  3.000
 KHC  H1   C13  C14  119.19  3.000
 KHC  C12  C13  C14  120.40  3.000
 KHC  H2   C12  C11  121.41  3.000
 KHC  H2   C12  C13  119.45  3.000
 KHC  C11  C12  C13  119.14  3.000
 KHC  C11  C16  N    108.65  3.000
 KHC  N    C16  C15  131.37  3.000
 KHC  C11  C16  C15  119.98  3.000
 KHC  C1   N    C    125.21  3.000
 KHC  C    N    C16  126.83  3.000
 KHC  C1   N    C16  107.61  3.000
 KHC  H5   C    H4   108.50  3.000
 KHC  H5   C    H3   109.60  3.000
 KHC  H4   C    H3   108.39  3.000
 KHC  H5   C    N    111.10  3.000
 KHC  H4   C    N    108.89  3.000
 KHC  H3   C    N    110.30  3.000
 KHC  C10  C11  C16  106.13  3.000
 KHC  C16  C11  C12  120.43  3.000
 KHC  C10  C11  C12  133.44  3.000
 KHC  C8   C10  C1   120.39  3.000
 KHC  C1   C10  C11  106.97  3.000
 KHC  C8   C10  C11  132.51  3.000
 KHC  C2   C1   C10  121.97  3.000
 KHC  C10  C1   N    110.63  3.000
 KHC  C2   C1   N    127.05  3.000
 KHC  H6   C8   C3   108.10  3.000
 KHC  H6   C8   C9   106.11  3.000
 KHC  C3   C8   C9   110.79  3.000
 KHC  H6   C8   C10  109.47  3.000
 KHC  C9   C8   C10  112.55  3.000
 KHC  C3   C8   C10  109.67  3.000
 KHC  N3   C9   C8   180.00  3.000
 KHC  C4   C3   C7   109.29  3.000
 KHC  C4   C3   N1   110.59  3.000
 KHC  C7   C3   N1   108.25  3.000
 KHC  N1   C3   C8   106.38  3.000
 KHC  C4   C3   C8   112.15  3.000
 KHC  C7   C3   C8   110.08  3.000
 KHC  H7   N1   C2   115.02  3.000
 KHC  H7   N1   C3   117.79  3.000
 KHC  C2   N1   C3   126.32  3.000
 KHC  O    C2   N1   122.61  3.000
 KHC  O    C2   C1   124.29  3.000
 KHC  N1   C2   C1   112.95  3.000
 KHC  H9   C7   H8   107.14  3.000
 KHC  H9   C7   C6   108.35  3.000
 KHC  H8   C7   C6   110.45  3.000
 KHC  H9   C7   C3   108.59  3.000
 KHC  H8   C7   C3   109.85  3.000
 KHC  C6   C7   C3   112.30  3.000
 KHC  H11  C6   H10  105.50  3.000
 KHC  H11  C6   N2   108.91  3.000
 KHC  H10  C6   N2   108.57  3.000
 KHC  H11  C6   C7   108.90  3.000
 KHC  H10  C6   C7   110.59  3.000
 KHC  N2   C6   C7   114.01  3.000
 KHC  H12  N2   C5   109.14  3.000
 KHC  H12  N2   C6   109.10  3.000
 KHC  C5   N2   C6   112.00  3.000
 KHC  H15  C5   H14  106.27  3.000
 KHC  H15  C5   C4   109.87  3.000
 KHC  H14  C5   C4   109.18  3.000
 KHC  H15  C5   N2   108.55  3.000
 KHC  H14  C5   N2   108.85  3.000
 KHC  C4   C5   N2   113.83  3.000
 KHC  H17  C4   H16  106.90  3.000
 KHC  H17  C4   C5   110.23  3.000
 KHC  H16  C4   C5   108.53  3.000
 KHC  H17  C4   C3   110.56  3.000
 KHC  H16  C4   C3   109.48  3.000
 KHC  C5   C4   C3   111.03  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
 KHC  CONST_01  C10  C11  C16  C15   180.00   0.0  0
 KHC  CONST_02  C12  C11  C16  C15     0.00   0.0  0
 KHC  CONST_03  C1   N    C16  C15   180.00   0.0  0
 KHC  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 KHC  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 KHC  CONST_06  C11  C16  C15  C14     0.00   0.0  0
 KHC  CONST_07  N    C16  C15  C14   180.00   0.0  0
 KHC  CONST_08  C10  C11  C12  C13   180.00   0.0  0
 KHC  CONST_09  C16  C11  C12  C13     0.00   0.0  0
 KHC  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 KHC  CONST_11  C1   C10  C11  C12   180.00   0.0  0
 KHC  CONST_12  N    C16  C11  C12   180.00   0.0  0
 KHC  CONST_13  C1   C10  C11  C16     0.00   0.0  0
 KHC  CONST_14  C10  C1   N    C16     0.00   0.0  0
 KHC  CONST_15  C11  C10  C1   N       0.00   0.0  0
 KHC  CONST_16  C10  C11  C16  N       0.00   0.0  0
 KHC  CONST_17  C1   N    C16  C11     0.00   0.0  0
 KHC  CONST_18  C3   N1   C2   C1      0.00   0.0  0
 KHC  CONST_19  C11  C16  C15  CL1   180.00   0.0  0
 KHC  CONST_20  N    C16  C15  CL1     0.00   0.0  0
 KHC  CONST_21  C13  C14  C15  CL1   180.00   0.0  0
 KHC  CONST_22  C    N    C16  C15     0.00   0.0  0
 KHC  CONST_23  C12  C13  C14  CL    180.00   0.0  0
 KHC  CONST_24  C16  C15  C14  CL    180.00   0.0  0
 KHC  CONST_25  C2   C1   N    C       0.00   0.0  0
 KHC  CONST_26  C10  C1   N    C     180.00   0.0  0
 KHC  CONST_27  C11  C16  N    C     180.00   0.0  0
 KHC  CONST_28  O    C2   N1   C3    180.00   0.0  0
 KHC  CONST_29  H1   C13  C14  C15   180.00   0.0  0
 KHC  CONST_30  H2   C12  C13  C14   180.00   0.0  0
 KHC  CONST_31  H7   N1   C2   C1    180.00   0.0  0
 KHC  Var_01    N1   C2   C1   N     172.61  30.0  1
 KHC  Var_02    C6   C7   C3   C8   -174.80  30.0  3
 KHC  Var_03    C5   C4   C3   C8    174.80  30.0  3
 KHC  Var_04    C2   N1   C3   C8     46.26  30.0  1
 KHC  Var_05    N2   C6   C7   C3     52.17  30.0  1
 KHC  Var_06    N2   C5   C4   C3    -55.30  30.0  1
 KHC  Var_07    C5   N2   C6   C7    -52.37  30.0  1
 KHC  Var_08    C4   C5   N2   C6     54.30  30.0  1
 KHC  Var_09    H3   C    N    C16    48.72  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 KHC  chir_01  C8  C3  C9  C10  negativ

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
 KHC  plan-1  C1   0.020
 KHC  plan-1  C3   0.020
 KHC  plan-1  N1   0.020
 KHC  plan-1  C2   0.020
 KHC  plan-1  O    0.020
 KHC  plan-1  H7   0.020
 KHC  plan-2  CL1  0.020
 KHC  plan-2  C15  0.020
 KHC  plan-2  C14  0.020
 KHC  plan-2  CL   0.020
 KHC  plan-2  C13  0.020
 KHC  plan-2  C12  0.020
 KHC  plan-2  C16  0.020
 KHC  plan-2  N    0.020
 KHC  plan-2  C    0.020
 KHC  plan-2  C11  0.020
 KHC  plan-2  C10  0.020
 KHC  plan-2  C1   0.020
 KHC  plan-2  C8   0.020
 KHC  plan-2  C2   0.020
 KHC  plan-2  H1   0.020
 KHC  plan-2  H2   0.020

