# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 15:57:33 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc2[nH]c3CCN(Cc3c2c1)C(=O)[C@@H]4CCCC[C@H]4C(=O)NC5(CC5)C#N
#
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
 0LC  0LC  (1R,2R)-N-(1-cyanocyclopropyl)-2-[(8-fluoro-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indol-2-yl)carbonyl]cyclohexanecarboxamide  ligand  55  30  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0LC
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
 0LC  O24  O  O     0  -0.475   3.4264  -0.4658   1.3106
 0LC  C23  C  C     0   0.602   3.6851  -0.1608   0.1590
 0LC  N25  N  NH1   0  -0.669   4.4296  -0.9657  -0.6340
 0LC  C26  C  CT    0   0.088   4.8863  -2.2242  -0.1711
 0LC  C29  C  CSP   0   0.112   5.9594  -2.1681   0.7927
 0LC  N30  N  NS    0  -0.269   6.8186  -2.1252   1.5580
 0LC  C28  C  CH2   0  -0.475   4.8791  -3.3831  -1.1350
 0LC  C27  C  CH2   0  -0.448   3.8914  -3.3500  -0.0273
 0LC  C18  C  CH1   0  -0.372   3.2509   1.1468  -0.4646
 0LC  C19  C  CH2   0  -0.422   4.2945   2.2363  -0.1834
 0LC  C20  C  CH2   0  -0.436   3.8639   3.5656  -0.7927
 0LC  C22  C  CH2   0  -0.431   2.4853   3.9821  -0.2970
 0LC  C21  C  CH2   0  -0.433   1.4480   2.8939  -0.5476
 0LC  C17  C  CH1   0  -0.404   1.8850   1.5634   0.0801
 0LC  C15  C  C     0   0.615   0.8632   0.4667  -0.1855
 0LC  O16  O  O     0  -0.497   1.0946  -0.3896  -1.0312
 0LC  N10  N  NT    0  -0.482  -0.3021   0.4817   0.5009
 0LC  C12  C  CH2   0  -0.336  -0.6255   1.3607   1.6139
 0LC  C13  C  CH2   0  -0.516  -1.8640   2.2067   1.3241
 0LC  C1   C  CR5   0   0.334  -2.9118   1.3044   0.7857
 0LC  C11  C  CH2   0  -0.340  -1.3014  -0.5439   0.2232
 0LC  C2   C  CR5   0  -0.067  -2.6664   0.0537   0.2980
 0LC  C5   C  CR56  0   0.072  -3.9222  -0.4884  -0.1040
 0LC  C7   C  CR16  0  -0.544  -4.3153  -1.7069  -0.6697
 0LC  C6   C  CR6   0   0.521  -5.6529  -1.8767  -0.9326
 0LC  F14  F  F     0  -0.330  -6.0646  -3.0421  -1.4759
 0LC  C8   C  CR16  0  -0.442  -6.6196  -0.9054  -0.6680
 0LC  C9   C  CR16  0  -0.290  -6.2428   0.3039  -0.1113
 0LC  C4   C  CR56  0   0.325  -4.8948   0.5034   0.1661
 0LC  N3   N  NR15  0  -0.747  -4.2455   1.5813   0.7044
 0LC  H1   H  HNH1  0   0.412   4.6897  -0.6676  -1.5608
 0LC  H4   H  HCH2  0   0.292   4.5460  -3.1562  -2.1395
 0LC  H5   H  HCH2  0   0.289   5.7039  -4.0793  -1.0748
 0LC  H6   H  HCH2  0   0.284   4.0186  -4.0303   0.8035
 0LC  H7   H  HCH2  0   0.287   2.8674  -3.0853  -0.2548
 0LC  H8   H  HCH1  0   0.259   3.1830   1.0163  -1.5492
 0LC  H9   H  HCH2  0   0.229   4.4243   2.3486   0.8978
 0LC  H10  H  HCH2  0   0.245   5.2635   1.9343  -0.5878
 0LC  H11  H  HCH2  0   0.238   4.6009   4.3364  -0.5569
 0LC  H12  H  HCH2  0   0.218   3.8470   3.4728  -1.8835
 0LC  H13  H  HCH2  0   0.219   2.5323   4.1924   0.7765
 0LC  H14  H  HCH2  0   0.238   2.1708   4.9083  -0.7827
 0LC  H15  H  HCH2  0   0.252   0.4822   3.2059  -0.1459
 0LC  H16  H  HCH2  0   0.232   1.3047   2.7562  -1.6242
 0LC  H17  H  HCH1  0   0.264   1.9979   1.7143   1.1573
 0LC  H18  H  HCH2  0   0.267  -0.8117   0.7434   2.4978
 0LC  H19  H  HCH2  0   0.275   0.2137   2.0049   1.8542
 0LC  H20  H  HCH2  0   0.268  -2.1902   2.6956   2.2448
 0LC  H21  H  HCH2  0   0.267  -1.6297   3.0007   0.6086
 0LC  H22  H  HCH2  0   0.265  -1.1148  -0.9569  -0.7665
 0LC  H23  H  HCH2  0   0.248  -1.1929  -1.3714   0.9359
 0LC  H24  H  HCR6  0   0.263  -3.6002  -2.4887  -0.8932
 0LC  H25  H  HCR6  0   0.272  -7.6578  -1.1037  -0.8992
 0LC  H26  H  HCR6  0   0.269  -6.9827   1.0655   0.0977
 0LC  H27  H  HNR5  0   0.408  -4.6818   2.4337   1.0140

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
 0LC  C9   C8   aromatic  1.384  0.020  1.384
 0LC  C9   C4   aromatic  1.391  0.020  1.391
 0LC  C8   C6   aromatic  1.396  0.020  1.396
 0LC  N30  C29  triple    1.151  0.020  1.151
 0LC  C4   N3   aromatic  1.369  0.020  1.369
 0LC  C4   C5   aromatic  1.415  0.020  1.415
 0LC  C6   F14  single    1.350  0.020  1.350
 0LC  C6   C7   aromatic  1.374  0.020  1.374
 0LC  N3   C1   aromatic  1.365  0.020  1.365
 0LC  C27  C28  single    1.485  0.020  1.485
 0LC  C27  C26  single    1.509  0.020  1.509
 0LC  C29  C26  single    1.443  0.020  1.443
 0LC  C5   C7   aromatic  1.400  0.020  1.400
 0LC  C5   C2   aromatic  1.426  0.020  1.426
 0LC  O24  C23  double    1.219  0.020  1.219
 0LC  C28  C26  single    1.507  0.020  1.507
 0LC  C26  N25  single    1.417  0.020  1.417
 0LC  C1   C2   aromatic  1.365  0.020  1.365
 0LC  C1   C13  single    1.484  0.020  1.484
 0LC  C2   C11  single    1.492  0.020  1.492
 0LC  C13  C12  single    1.528  0.020  1.528
 0LC  C23  N25  single    1.353  0.020  1.353
 0LC  C23  C18  single    1.512  0.020  1.512
 0LC  C11  N10  single    1.459  0.020  1.459
 0LC  C12  N10  single    1.455  0.020  1.455
 0LC  C19  C18  single    1.535  0.020  1.535
 0LC  C19  C20  single    1.524  0.020  1.524
 0LC  C18  C17  single    1.528  0.020  1.528
 0LC  N10  C15  single    1.353  0.020  1.353
 0LC  C17  C15  single    1.522  0.020  1.522
 0LC  C17  C21  single    1.535  0.020  1.535
 0LC  C15  O16  double    1.226  0.020  1.226
 0LC  C20  C22  single    1.523  0.020  1.523
 0LC  C21  C22  single    1.524  0.020  1.524
 0LC  N25  H1   single    0.860  0.020  1.020
 0LC  C28  H4   single    0.970  0.020  1.090
 0LC  C28  H5   single    0.970  0.020  1.090
 0LC  C27  H6   single    0.970  0.020  1.090
 0LC  C27  H7   single    0.970  0.020  1.090
 0LC  C18  H8   single    0.970  0.020  1.090
 0LC  C19  H9   single    0.970  0.020  1.090
 0LC  C19  H10  single    0.970  0.020  1.090
 0LC  C20  H11  single    0.970  0.020  1.090
 0LC  C20  H12  single    0.970  0.020  1.090
 0LC  C22  H13  single    0.970  0.020  1.090
 0LC  C22  H14  single    0.970  0.020  1.090
 0LC  C21  H15  single    0.970  0.020  1.090
 0LC  C21  H16  single    0.970  0.020  1.090
 0LC  C17  H17  single    0.970  0.020  1.090
 0LC  C12  H18  single    0.970  0.020  1.090
 0LC  C12  H19  single    0.970  0.020  1.090
 0LC  C13  H20  single    0.970  0.020  1.090
 0LC  C13  H21  single    0.970  0.020  1.090
 0LC  C11  H22  single    0.970  0.020  1.090
 0LC  C11  H23  single    0.970  0.020  1.090
 0LC  C7   H24  single    0.930  0.020  1.080
 0LC  C8   H25  single    0.930  0.020  1.080
 0LC  C9   H26  single    0.930  0.020  1.080
 0LC  N3   H27  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
 0LC  C18  C23  N25  115.50  3.000
 0LC  C18  C23  O24  123.02  3.000
 0LC  N25  C23  O24  121.44  3.000
 0LC  H1   N25  C26  118.69  3.000
 0LC  H1   N25  C23  120.33  3.000
 0LC  C26  N25  C23  120.96  3.000
 0LC  C27  C26  C28   58.96  3.000
 0LC  C28  C26  C29  117.42  3.000
 0LC  C27  C26  C29  117.09  3.000
 0LC  C28  C26  N25  118.20  3.000
 0LC  C29  C26  N25  115.04  3.000
 0LC  C27  C26  N25  118.76  3.000
 0LC  N30  C29  C26  180.00  3.000
 0LC  H5   C28  H4   114.93  3.000
 0LC  H5   C28  C27  118.72  3.000
 0LC  H4   C28  C27  118.89  3.000
 0LC  H5   C28  C26  117.12  3.000
 0LC  H4   C28  C26  115.71  3.000
 0LC  C27  C28  C26   60.59  3.000
 0LC  H7   C27  H6   115.27  3.000
 0LC  H7   C27  C28  118.58  3.000
 0LC  H6   C27  C28  118.75  3.000
 0LC  H7   C27  C26  114.93  3.000
 0LC  H6   C27  C26  117.70  3.000
 0LC  C28  C27  C26   60.45  3.000
 0LC  H8   C18  C17  109.28  3.000
 0LC  H8   C18  C19  107.96  3.000
 0LC  C17  C18  C19  110.42  3.000
 0LC  H8   C18  C23  108.87  3.000
 0LC  C17  C18  C23  110.20  3.000
 0LC  C19  C18  C23  110.06  3.000
 0LC  H10  C19  H9   106.78  3.000
 0LC  H10  C19  C20  110.10  3.000
 0LC  H9   C19  C20  109.81  3.000
 0LC  H10  C19  C18  109.82  3.000
 0LC  H9   C19  C18  109.54  3.000
 0LC  C20  C19  C18  110.72  3.000
 0LC  H12  C20  H11  106.58  3.000
 0LC  H12  C20  C22  109.48  3.000
 0LC  H11  C20  C22  110.34  3.000
 0LC  H12  C20  C19  109.18  3.000
 0LC  H11  C20  C19  109.78  3.000
 0LC  C22  C20  C19  111.35  3.000
 0LC  H14  C22  H13  106.59  3.000
 0LC  H14  C22  C21  109.66  3.000
 0LC  H13  C22  C21  109.12  3.000
 0LC  H14  C22  C20  110.35  3.000
 0LC  H13  C22  C20  109.44  3.000
 0LC  C21  C22  C20  111.55  3.000
 0LC  H16  C21  H15  106.38  3.000
 0LC  H16  C21  C17  109.30  3.000
 0LC  H15  C21  C17  110.44  3.000
 0LC  H16  C21  C22  109.91  3.000
 0LC  H15  C21  C22  109.73  3.000
 0LC  C17  C21  C22  110.98  3.000
 0LC  H17  C17  C15  109.91  3.000
 0LC  H17  C17  C21  108.22  3.000
 0LC  C15  C17  C21  111.23  3.000
 0LC  H17  C17  C18  107.24  3.000
 0LC  C21  C17  C18  110.18  3.000
 0LC  C15  C17  C18  109.96  3.000
 0LC  N10  C15  O16  121.37  3.000
 0LC  O16  C15  C17  119.80  3.000
 0LC  N10  C15  C17  118.80  3.000
 0LC  C11  N10  C12  114.72  3.000
 0LC  C12  N10  C15  125.91  3.000
 0LC  C11  N10  C15  119.07  3.000
 0LC  H19  C12  H18  106.73  3.000
 0LC  H19  C12  C13  109.89  3.000
 0LC  H18  C12  C13  109.13  3.000
 0LC  H19  C12  N10  110.87  3.000
 0LC  H18  C12  N10  108.36  3.000
 0LC  C13  C12  N10  111.70  3.000
 0LC  H21  C13  H20  106.88  3.000
 0LC  H21  C13  C1   110.81  3.000
 0LC  H20  C13  C1   111.53  3.000
 0LC  H21  C13  C12  110.63  3.000
 0LC  H20  C13  C12  109.27  3.000
 0LC  C1   C13  C12  107.73  3.000
 0LC  N3   C1   C2   109.90  3.000
 0LC  C2   C1   C13  124.05  3.000
 0LC  N3   C1   C13  126.05  3.000
 0LC  H23  C11  H22  106.71  3.000
 0LC  H23  C11  C2   111.09  3.000
 0LC  H22  C11  C2   110.76  3.000
 0LC  H23  C11  N10  109.80  3.000
 0LC  H22  C11  N10  108.81  3.000
 0LC  C2   C11  N10  109.61  3.000
 0LC  C5   C2   C11  129.75  3.000
 0LC  C11  C2   C1   123.34  3.000
 0LC  C5   C2   C1   106.91  3.000
 0LC  C4   C5   C7   119.62  3.000
 0LC  C7   C5   C2   133.82  3.000
 0LC  C4   C5   C2   106.56  3.000
 0LC  H24  C7   C6   120.95  3.000
 0LC  H24  C7   C5   121.77  3.000
 0LC  C6   C7   C5   117.29  3.000
 0LC  C8   C6   F14  117.76  3.000
 0LC  F14  C6   C7   118.73  3.000
 0LC  C8   C6   C7   123.51  3.000
 0LC  H25  C8   C9   120.50  3.000
 0LC  H25  C8   C6   119.77  3.000
 0LC  C9   C8   C6   119.73  3.000
 0LC  H26  C9   C4   121.55  3.000
 0LC  H26  C9   C8   120.44  3.000
 0LC  C4   C9   C8   118.01  3.000
 0LC  N3   C4   C9   130.64  3.000
 0LC  N3   C4   C5   107.52  3.000
 0LC  C9   C4   C5   121.84  3.000
 0LC  H27  N3   C4   125.62  3.000
 0LC  H27  N3   C1   125.26  3.000
 0LC  C4   N3   C1   109.11  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
 0LC  CONST_01  C9   C4   N3   C1    180.00   0.0  0
 0LC  CONST_02  C5   C4   N3   C1      0.00   0.0  0
 0LC  CONST_03  C4   C5   C2   C1      0.00   0.0  0
 0LC  CONST_04  C7   C5   C2   C1    180.00   0.0  0
 0LC  CONST_05  C9   C4   C5   C2    180.00   0.0  0
 0LC  CONST_06  N3   C4   C5   C2      0.00   0.0  0
 0LC  CONST_07  C6   C7   C5   C2    180.00   0.0  0
 0LC  CONST_08  C4   N3   C1   C2      0.00   0.0  0
 0LC  CONST_09  C8   C9   C4   C5      0.00   0.0  0
 0LC  CONST_10  C8   C6   C7   C5      0.00   0.0  0
 0LC  CONST_11  N3   C1   C2   C5      0.00   0.0  0
 0LC  CONST_12  C9   C8   C6   C7      0.00   0.0  0
 0LC  CONST_13  C9   C4   C5   C7      0.00   0.0  0
 0LC  CONST_14  N3   C4   C5   C7    180.00   0.0  0
 0LC  CONST_15  C4   C9   C8   C6      0.00   0.0  0
 0LC  CONST_16  C4   C5   C7   C6      0.00   0.0  0
 0LC  CONST_17  N3   C4   C9   C8    180.00   0.0  0
 0LC  CONST_18  F14  C6   C7   C5    180.00   0.0  0
 0LC  CONST_19  C9   C8   C6   F14   180.00   0.0  0
 0LC  CONST_20  C11  N10  C15  C17   180.00   0.0  0
 0LC  CONST_21  C12  N10  C15  C17     0.00   0.0  0
 0LC  CONST_22  H27  N3   C1   C13     0.00   0.0  0
 0LC  CONST_23  H24  C7   C5   C2      0.00   0.0  0
 0LC  CONST_24  H26  C9   C4   C5    180.00   0.0  0
 0LC  CONST_25  H25  C8   C6   C7    180.00   0.0  0
 0LC  CONST_26  C18  C23  N25  C26   180.00   0.0  0
 0LC  CONST_27  C11  N10  C15  O16     0.00   0.0  0
 0LC  CONST_28  C12  N10  C15  O16   180.00   0.0  0
 0LC  CONST_29  C26  N25  C23  O24     0.00   0.0  0
 0LC  CONST_30  H1   N25  C23  C18     0.00   0.0  0
 0LC  Var_01    C22  C20  C19  C18    55.73  30.0  1
 0LC  Var_02    C21  C22  C20  C19   -54.88  30.0  1
 0LC  Var_03    C17  C21  C22  C20    55.40  30.0  1
 0LC  Var_04    C5   C2   C11  N10   168.59  30.0  1
 0LC  Var_05    C1   C13  C12  N10    47.26  30.0  1
 0LC  Var_06    N3   C1   C13  C12   163.09  30.0  1
 0LC  Var_07    C2   C11  N10  C12    43.15  30.0  1
 0LC  Var_08    C11  N10  C12  C13   -64.99  30.0  1
 0LC  Var_09    C28  C27  C26  N25   107.38  30.0  1
 0LC  Var_10    H4   C28  C27  C26  -104.94  30.0  1
 0LC  Var_11    C27  C26  N25  C23    72.79  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
 0LC  chir_02  C18  C23  C19  C17  positiv
 0LC  chir_03  C17  C18  C15  C21  positiv
 0LC  chir_04  C26  C29  C28  N25  both

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
 0LC  plan-1  O24  0.020
 0LC  plan-1  C23  0.020
 0LC  plan-1  N25  0.020
 0LC  plan-1  C26  0.020
 0LC  plan-1  C18  0.020
 0LC  plan-1  H1   0.020
 0LC  plan-2  C13  0.020
 0LC  plan-2  C1   0.020
 0LC  plan-2  C11  0.020
 0LC  plan-2  C2   0.020
 0LC  plan-2  C5   0.020
 0LC  plan-2  C7   0.020
 0LC  plan-2  C6   0.020
 0LC  plan-2  F14  0.020
 0LC  plan-2  C8   0.020
 0LC  plan-2  C9   0.020
 0LC  plan-2  C4   0.020
 0LC  plan-2  N3   0.020
 0LC  plan-2  H24  0.020
 0LC  plan-2  H25  0.020
 0LC  plan-2  H26  0.020
 0LC  plan-2  H27  0.020
 0LC  plan-3  C17  0.020
 0LC  plan-3  C15  0.020
 0LC  plan-3  O16  0.020
 0LC  plan-3  N10  0.020
 0LC  plan-3  C12  0.020
 0LC  plan-3  C11  0.020

