# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 12:09:01 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (1S,3R,5R,7S)-N-(trans-4-aminocyclohexyl)-3-methyl-5-phenyltricyclo[3.3.1.1~3,7~]decane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12C[C@@H]3C[C@](C1)(C[C@@](C3)(C2)c4ccccc4)C(=O)N[C@H]5CC[C@H](N)CC5
#
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
 KHG  KHG  (1S,3R,5R,7S)-N-(trans-4-aminocyclohexyl)-3-methyl-5-phenyltricyclo[3.3.1.1~3,7~]decane-1-carboxamide  ligand  61  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KHG
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
 KHG  C12  C  CR16  0  -0.277  -6.0384   2.5753   0.4116
 KHG  C13  C  CR16  0  -0.242  -5.0309   2.8671  -0.4999
 KHG  C14  C  CR16  0  -0.321  -3.9769   1.9854  -0.6819
 KHG  C15  C  CH2   0  -0.370  -1.4022   0.5763   0.1483
 KHG  C21  C  CH2   0  -0.432   5.9295  -0.4075   0.8810
 KHG  C22  C  CH1   0  -0.075   6.4650   0.5157  -0.2082
 KHG  C27  C  CH2   0  -0.377  -0.3189  -1.5886   0.7667
 KHG  C24  C  CH2   0  -0.447   5.4966   1.6808  -0.4260
 KHG  C01  C  CH3   0  -0.645  -1.7253  -3.5840   1.3026
 KHG  C02  C  CT    0  -0.100  -1.6068  -2.3449   0.4263
 KHG  C03  C  CH2   0  -0.391  -1.5705  -2.7319  -1.0544
 KHG  C04  C  CH1   0  -0.248  -1.4629  -1.4801  -1.9220
 KHG  C05  C  CH2   0  -0.410  -0.1762  -0.7272  -1.5830
 KHG  C06  C  CH2   0  -0.395  -2.8015  -1.4170   0.6646
 KHG  C07  C  CT    0  -0.185  -2.7162  -0.1513  -0.1959
 KHG  C08  C  CH2   0  -0.399  -2.6688  -0.5788  -1.6729
 KHG  C09  C  CR6   0   0.224  -3.8903   0.7880   0.0362
 KHG  C10  C  CR16  0  -0.350  -4.9104   0.5132   0.9453
 KHG  C11  C  CR16  0  -0.235  -5.9717   1.3932   1.1316
 KHG  C16  C  CT    0  -0.278  -0.1855  -0.3228  -0.0977
 KHG  C17  C  C     0   0.616   1.0947   0.4259   0.2788
 KHG  C19  C  CH1   0  -0.040   3.5608   0.2767   0.3536
 KHG  C20  C  CH2   0  -0.460   4.5165  -0.8915   0.5782
 KHG  C25  C  CH2   0  -0.434   4.0862   1.1973  -0.7468
 KHG  N18  N  NH1   0  -0.652   2.2395  -0.2390   0.0504
 KHG  N23  N  NH2   0  -0.794   7.8263   0.9193   0.1172
 KHG  O26  O  O     0  -0.496   1.0818   1.5440   0.7788
 KHG  H1   H  HCR6  0   0.252  -6.8624   3.2621   0.5560
 KHG  H2   H  HCR6  0   0.251  -5.0650   3.7853  -1.0725
 KHG  H3   H  HCR6  0   0.242  -3.2100   2.2414  -1.4029
 KHG  H4   H  HCH2  0   0.233  -1.3117   1.4804  -0.4595
 KHG  H5   H  HCH2  0   0.233  -1.4328   0.9010   1.1920
 KHG  H6   H  HCH2  0   0.235   6.5992  -1.2617   1.0019
 KHG  H7   H  HCH2  0   0.212   5.9303   0.1316   1.8366
 KHG  H8   H  HCH1  0   0.211   6.5131  -0.0596  -1.1416
 KHG  H9   H  HCH2  0   0.234  -0.3192  -1.3149   1.8277
 KHG  H10  H  HCH2  0   0.227   0.5386  -2.2532   0.6182
 KHG  H11  H  HCH2  0   0.209   5.4801   2.2974   0.4810
 KHG  H12  H  HCH2  0   0.230   5.8647   2.3218  -1.2319
 KHG  H13  H  HCH3  0   0.222  -1.7592  -3.3168   2.3616
 KHG  H14  H  HCH3  0   0.223  -2.6321  -4.1476   1.0719
 KHG  H15  H  HCH3  0   0.224  -0.8731  -4.2514   1.1565
 KHG  H16  H  HCH2  0   0.223  -0.7251  -3.4030  -1.2429
 KHG  H17  H  HCH2  0   0.224  -2.4763  -3.2904  -1.3137
 KHG  H18  H  HCH1  0   0.232  -1.4386  -1.7649  -2.9778
 KHG  H19  H  HCH2  0   0.231   0.6805  -1.3643  -1.8222
 KHG  H20  H  HCH2  0   0.238  -0.0888   0.1671  -2.2082
 KHG  H21  H  HCH2  0   0.228  -3.7273  -1.9600   0.4450
 KHG  H22  H  HCH2  0   0.226  -2.8378  -1.1490   1.7266
 KHG  H23  H  HCH2  0   0.231  -2.6096   0.3021  -2.3183
 KHG  H24  H  HCH2  0   0.231  -3.5944  -1.0990  -1.9392
 KHG  H25  H  HCR6  0   0.249  -4.8953  -0.3973   1.5287
 KHG  H26  H  HCR6  0   0.251  -6.7481   1.1481   1.8454
 KHG  H27  H  HCH1  0   0.232   3.4916   0.8510   1.2829
 KHG  H28  H  HCH2  0   0.221   4.5309  -1.5199  -0.3201
 KHG  H29  H  HCH2  0   0.243   4.1493  -1.5161   1.3958
 KHG  H30  H  HCH2  0   0.238   3.4102   2.0452  -0.8721
 KHG  H31  H  HCH2  0   0.213   4.0893   0.6479  -1.6948
 KHG  H32  H  HNH1  0   0.391   2.1947  -1.1399  -0.3988
 KHG  H33  H  HNH2  0   0.341   8.1717   1.5435  -0.6024
 KHG  H34  H  HNH2  0   0.332   7.8132   1.4733   0.9672

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
 KHG  C12  C11  aromatic  1.386  0.020  1.386
 KHG  C12  C13  aromatic  1.390  0.020  1.390
 KHG  C11  C10  aromatic  1.391  0.020  1.391
 KHG  C13  C14  aromatic  1.386  0.020  1.386
 KHG  C10  C09  aromatic  1.394  0.020  1.394
 KHG  C14  C09  aromatic  1.399  0.020  1.399
 KHG  C09  C07  single    1.521  0.020  1.521
 KHG  C15  C07  single    1.541  0.020  1.541
 KHG  C15  C16  single    1.533  0.020  1.533
 KHG  C07  C08  single    1.538  0.020  1.538
 KHG  C07  C06  single    1.533  0.020  1.533
 KHG  C08  C04  single    1.526  0.020  1.526
 KHG  O26  C17  double    1.225  0.020  1.225
 KHG  C24  C25  single    1.525  0.020  1.525
 KHG  C24  C22  single    1.531  0.020  1.531
 KHG  C25  C19  single    1.528  0.020  1.528
 KHG  C17  C16  single    1.530  0.020  1.530
 KHG  C17  N18  single    1.343  0.020  1.343
 KHG  C06  C02  single    1.531  0.020  1.531
 KHG  C16  C05  single    1.539  0.020  1.539
 KHG  C16  C27  single    1.539  0.020  1.539
 KHG  C05  C04  single    1.529  0.020  1.529
 KHG  C04  C03  single    1.527  0.020  1.527
 KHG  N18  C19  single    1.450  0.020  1.450
 KHG  C22  N23  single    1.457  0.020  1.457
 KHG  C22  C21  single    1.525  0.020  1.525
 KHG  C19  C20  single    1.526  0.020  1.526
 KHG  C27  C02  single    1.532  0.020  1.532
 KHG  C02  C03  single    1.531  0.020  1.531
 KHG  C02  C01  single    1.522  0.020  1.522
 KHG  C21  C20  single    1.524  0.020  1.524
 KHG  C12  H1   single    0.930  0.020  1.080
 KHG  C13  H2   single    0.930  0.020  1.080
 KHG  C14  H3   single    0.930  0.020  1.080
 KHG  C15  H4   single    0.970  0.020  1.090
 KHG  C15  H5   single    0.970  0.020  1.090
 KHG  C21  H6   single    0.970  0.020  1.090
 KHG  C21  H7   single    0.970  0.020  1.090
 KHG  C22  H8   single    0.970  0.020  1.090
 KHG  C27  H9   single    0.970  0.020  1.090
 KHG  C27  H10  single    0.970  0.020  1.090
 KHG  C24  H11  single    0.970  0.020  1.090
 KHG  C24  H12  single    0.970  0.020  1.090
 KHG  C01  H13  single    0.970  0.020  1.090
 KHG  C01  H14  single    0.970  0.020  1.090
 KHG  C01  H15  single    0.970  0.020  1.090
 KHG  C03  H16  single    0.970  0.020  1.090
 KHG  C03  H17  single    0.970  0.020  1.090
 KHG  C04  H18  single    0.970  0.020  1.090
 KHG  C05  H19  single    0.970  0.020  1.090
 KHG  C05  H20  single    0.970  0.020  1.090
 KHG  C06  H21  single    0.970  0.020  1.090
 KHG  C06  H22  single    0.970  0.020  1.090
 KHG  C08  H23  single    0.970  0.020  1.090
 KHG  C08  H24  single    0.970  0.020  1.090
 KHG  C10  H25  single    0.930  0.020  1.080
 KHG  C11  H26  single    0.930  0.020  1.080
 KHG  C19  H27  single    0.970  0.020  1.090
 KHG  C20  H28  single    0.970  0.020  1.090
 KHG  C20  H29  single    0.970  0.020  1.090
 KHG  C25  H30  single    0.970  0.020  1.090
 KHG  C25  H31  single    0.970  0.020  1.090
 KHG  N18  H32  single    0.860  0.020  1.020
 KHG  N23  H33  single    0.890  0.020  1.040
 KHG  N23  H34  single    0.890  0.020  1.040

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
 KHG  H1   C12  C11  120.57  3.000
 KHG  H1   C12  C13  120.41  3.000
 KHG  C11  C12  C13  119.02  3.000
 KHG  H2   C13  C14  119.60  3.000
 KHG  H2   C13  C12  120.15  3.000
 KHG  C14  C13  C12  120.26  3.000
 KHG  H3   C14  C09  120.00  3.000
 KHG  H3   C14  C13  118.38  3.000
 KHG  C09  C14  C13  121.61  3.000
 KHG  H5   C15  H4   106.71  3.000
 KHG  H5   C15  C16  110.46  3.000
 KHG  H4   C15  C16  109.28  3.000
 KHG  H5   C15  C07  109.24  3.000
 KHG  H4   C15  C07  109.69  3.000
 KHG  C16  C15  C07  111.35  3.000
 KHG  H7   C21  H6   106.70  3.000
 KHG  H7   C21  C20  109.25  3.000
 KHG  H6   C21  C20  110.00  3.000
 KHG  H7   C21  C22  108.93  3.000
 KHG  H6   C21  C22  109.71  3.000
 KHG  C20  C21  C22  112.09  3.000
 KHG  H8   C22  N23  107.11  3.000
 KHG  H8   C22  C24  107.80  3.000
 KHG  N23  C22  C24  114.34  3.000
 KHG  H8   C22  C21  107.79  3.000
 KHG  N23  C22  C21  109.65  3.000
 KHG  C24  C22  C21  109.90  3.000
 KHG  H10  C27  H9   106.44  3.000
 KHG  H10  C27  C16  110.81  3.000
 KHG  H9   C27  C16  109.79  3.000
 KHG  H10  C27  C02  109.18  3.000
 KHG  H9   C27  C02  109.77  3.000
 KHG  C16  C27  C02  110.75  3.000
 KHG  H12  C24  H11  106.56  3.000
 KHG  H12  C24  C25  110.00  3.000
 KHG  H11  C24  C25  109.77  3.000
 KHG  H12  C24  C22  109.76  3.000
 KHG  H11  C24  C22  108.65  3.000
 KHG  C25  C24  C22  111.94  3.000
 KHG  H15  C01  H14  107.71  3.000
 KHG  H15  C01  H13  107.66  3.000
 KHG  H14  C01  H13  107.77  3.000
 KHG  H15  C01  C02  111.08  3.000
 KHG  H14  C01  C02  111.28  3.000
 KHG  H13  C01  C02  111.18  3.000
 KHG  C06  C02  C03  108.80  3.000
 KHG  C03  C02  C01  110.66  3.000
 KHG  C06  C02  C01  110.05  3.000
 KHG  C01  C02  C27  109.84  3.000
 KHG  C03  C02  C27  108.65  3.000
 KHG  C06  C02  C27  108.79  3.000
 KHG  H17  C03  H16  106.56  3.000
 KHG  H17  C03  C04  109.99  3.000
 KHG  H16  C03  C04  110.49  3.000
 KHG  H17  C03  C02  109.77  3.000
 KHG  H16  C03  C02  109.85  3.000
 KHG  C04  C03  C02  110.12  3.000
 KHG  H18  C04  C08  109.20  3.000
 KHG  H18  C04  C05  108.88  3.000
 KHG  C08  C04  C05  109.76  3.000
 KHG  H18  C04  C03  109.67  3.000
 KHG  C05  C04  C03  109.70  3.000
 KHG  C08  C04  C03  109.62  3.000
 KHG  H20  C05  H19  106.76  3.000
 KHG  H20  C05  C16  109.69  3.000
 KHG  H19  C05  C16  111.63  3.000
 KHG  H20  C05  C04  110.05  3.000
 KHG  H19  C05  C04  108.89  3.000
 KHG  C16  C05  C04  109.77  3.000
 KHG  H22  C06  H21  106.71  3.000
 KHG  H22  C06  C07  110.11  3.000
 KHG  H21  C06  C07  110.10  3.000
 KHG  H22  C06  C02  108.96  3.000
 KHG  H21  C06  C02  109.13  3.000
 KHG  C07  C06  C02  111.69  3.000
 KHG  C09  C07  C08  109.98  3.000
 KHG  C08  C07  C06  108.13  3.000
 KHG  C09  C07  C06  112.41  3.000
 KHG  C06  C07  C15  108.18  3.000
 KHG  C08  C07  C15  108.63  3.000
 KHG  C09  C07  C15  109.41  3.000
 KHG  H24  C08  H23  106.56  3.000
 KHG  H24  C08  C07  109.85  3.000
 KHG  H23  C08  C07  110.15  3.000
 KHG  H24  C08  C04  110.36  3.000
 KHG  H23  C08  C04  109.67  3.000
 KHG  C07  C08  C04  110.19  3.000
 KHG  C10  C09  C07  122.86  3.000
 KHG  C07  C09  C14  119.87  3.000
 KHG  C10  C09  C14  117.27  3.000
 KHG  H25  C10  C11  118.10  3.000
 KHG  H25  C10  C09  120.51  3.000
 KHG  C11  C10  C09  121.39  3.000
 KHG  H26  C11  C10  119.48  3.000
 KHG  H26  C11  C12  120.07  3.000
 KHG  C10  C11  C12  120.45  3.000
 KHG  C17  C16  C05  111.16  3.000
 KHG  C05  C16  C27  109.06  3.000
 KHG  C17  C16  C27  109.68  3.000
 KHG  C27  C16  C15  108.88  3.000
 KHG  C05  C16  C15  108.29  3.000
 KHG  C17  C16  C15  109.73  3.000
 KHG  O26  C17  N18  122.01  3.000
 KHG  N18  C17  C16  115.40  3.000
 KHG  O26  C17  C16  122.57  3.000
 KHG  H27  C19  N18  107.84  3.000
 KHG  H27  C19  C25  108.48  3.000
 KHG  N18  C19  C25  112.14  3.000
 KHG  H27  C19  C20  108.44  3.000
 KHG  N18  C19  C20  109.22  3.000
 KHG  C25  C19  C20  110.60  3.000
 KHG  H29  C20  H28  106.85  3.000
 KHG  H29  C20  C19  109.71  3.000
 KHG  H28  C20  C19  109.05  3.000
 KHG  H29  C20  C21  110.16  3.000
 KHG  H28  C20  C21  109.43  3.000
 KHG  C19  C20  C21  111.52  3.000
 KHG  H31  C25  H30  106.97  3.000
 KHG  H31  C25  C19  108.78  3.000
 KHG  H30  C25  C19  109.74  3.000
 KHG  H31  C25  C24  109.78  3.000
 KHG  H30  C25  C24  110.52  3.000
 KHG  C19  C25  C24  110.95  3.000
 KHG  H32  N18  C19  116.84  3.000
 KHG  H32  N18  C17  118.71  3.000
 KHG  C19  N18  C17  124.39  3.000
 KHG  H34  N23  H33  105.24  3.000
 KHG  H34  N23  C22  109.05  3.000
 KHG  H33  N23  C22  109.31  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
 KHG  CONST_01  C09  C10  C11  C12    0.00   0.0  0
 KHG  CONST_02  C09  C14  C13  C12    0.00   0.0  0
 KHG  CONST_03  C10  C11  C12  C13    0.00   0.0  0
 KHG  CONST_04  C10  C09  C14  C13    0.00   0.0  0
 KHG  CONST_05  C11  C12  C13  C14    0.00   0.0  0
 KHG  CONST_06  C11  C10  C09  C14    0.00   0.0  0
 KHG  CONST_07  C07  C09  C14  C13  180.00   0.0  0
 KHG  CONST_08  C11  C10  C09  C07  180.00   0.0  0
 KHG  CONST_09  H25  C10  C11  C12  180.00   0.0  0
 KHG  CONST_10  H3   C14  C13  C12  180.00   0.0  0
 KHG  CONST_11  H26  C11  C12  C13  180.00   0.0  0
 KHG  CONST_12  H1   C12  C13  C14  180.00   0.0  0
 KHG  CONST_13  H2   C13  C14  C09  180.00   0.0  0
 KHG  CONST_14  C19  N18  C17  C16  180.00   0.0  0
 KHG  CONST_15  O26  C17  N18  C19    0.00   0.0  0
 KHG  CONST_16  H32  N18  C17  C16    0.00   0.0  0
 KHG  Var_01    C19  C25  C24  C22   56.57  30.0  1
 KHG  Var_02    C19  C20  C21  C22  -55.64  30.0  1

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
 KHG  chir_01  C22  C24  N23  C21  negativ
 KHG  chir_02  C02  C27  C06  C01  positiv
 KHG  chir_03  C04  C03  C05  C08  positiv
 KHG  chir_04  C07  C15  C09  C06  positiv
 KHG  chir_05  C16  C15  C05  C27  positiv
 KHG  chir_06  C19  N18  C25  C20  positiv

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
 KHG  plan-1  C12  0.020
 KHG  plan-1  C13  0.020
 KHG  plan-1  C14  0.020
 KHG  plan-1  C07  0.020
 KHG  plan-1  C09  0.020
 KHG  plan-1  C10  0.020
 KHG  plan-1  C11  0.020
 KHG  plan-1  H1   0.020
 KHG  plan-1  H2   0.020
 KHG  plan-1  H3   0.020
 KHG  plan-1  H25  0.020
 KHG  plan-1  H26  0.020
 KHG  plan-2  C16  0.020
 KHG  plan-2  C17  0.020
 KHG  plan-2  C19  0.020
 KHG  plan-2  N18  0.020
 KHG  plan-2  O26  0.020
 KHG  plan-2  H32  0.020

