# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 17:57:27 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: (4aR,4bS,6aS,7S,9aS,9bS,11aR)-N-tert-butyl-4a,6a-dimethyl-2-oxo-2,4a,4b,5,6,6a,7,8,9,9a,9b,10,11,11a-tetradecahydro-1H-indeno[5,4-f]quinoline-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4NC(=O)C=C[C@]4(C)[C@H]3CC[C@]12C
#
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
 FIT  FIT  (4aR,4bS,6aS,7S,9aS,9bS,11aR)-N-tert-butyl-4a,6a-dimethyl-2-oxo-2,4a,4b,5,6,6a,7,8,9,9a,9b,10,11,11a-tetradecahydro-1H-indeno[5,4-f]quinoline-7-carboxamide  ligand  63  27  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FIT
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
 FIT  N1    N  NH1   0  -0.663   5.3363  -0.1724   0.3318
 FIT  C2    C  C1    0  -0.395   4.7363   2.0472   0.9532
 FIT  N2    N  NH1   0  -0.651  -4.2200   0.4867   0.5359
 FIT  C4    C  CH1   0   0.015   3.9442  -0.5407   0.5065
 FIT  C5    C  CH2   0  -0.469   3.6437  -1.9082  -0.0760
 FIT  C6    C  CH2   0  -0.426   2.2033  -2.2822   0.2506
 FIT  O1    O  O     0  -0.502   6.9838   1.3185   0.7808
 FIT  O2    O  O     0  -0.499  -4.4555  -1.0847  -1.0771
 FIT  C1    C  C1    0  -0.111   3.4686   1.8408   0.5948
 FIT  C3    C  C     0   0.509   5.7916   1.0426   0.6981
 FIT  C7    C  CH1   0  -0.232   1.2061  -1.2255  -0.2212
 FIT  C8    C  CH1   0  -0.190   1.5737   0.1745   0.3158
 FIT  C9    C  CT    0  -0.163   3.0272   0.5558  -0.0579
 FIT  C10   C  CH2   0  -0.451   0.5336   1.2252  -0.0897
 FIT  C11   C  CH2   0  -0.415  -0.8891   0.8325   0.3148
 FIT  C12   C  CT    0  -0.052  -1.2594  -0.5374  -0.2445
 FIT  C13   C  CH1   0  -0.179  -0.2086  -1.5552   0.2244
 FIT  C14   C  CH2   0  -0.450  -0.8160  -2.9036  -0.1525
 FIT  C15   C  CH2   0  -0.431  -2.3345  -2.6973   0.0557
 FIT  C16   C  CH1   0  -0.369  -2.5228  -1.1982   0.3591
 FIT  C17   C  CH3   0  -0.680  -1.3766  -0.4685  -1.7708
 FIT  C18   C  CH3   0  -0.667   3.1973   0.7454  -1.5737
 FIT  C19   C  C     0   0.581  -3.8308  -0.6114  -0.1364
 FIT  C20   C  CT    0   0.101  -5.3731   1.3448   0.2450
 FIT  C21   C  CH3   0  -0.642  -6.6822   0.5633   0.3695
 FIT  C22   C  CH3   0  -0.682  -5.3525   2.4498   1.2998
 FIT  C23   C  CH3   0  -0.641  -5.2417   1.9716  -1.1441
 FIT  HN1   H  HNH1  0   0.389   6.0186  -0.9116   0.2397
 FIT  H2    H  H     0   0.262   5.0578   2.9900   1.3769
 FIT  HN2   H  HNH1  0   0.397  -3.6345   0.7767   1.3032
 FIT  H4    H  HCH1  0   0.238   3.7320  -0.5976   1.5860
 FIT  H5    H  HCH2  0   0.235   3.8076  -1.9109  -1.1574
 FIT  H5A   H  HCH2  0   0.245   4.3284  -2.6477   0.3489
 FIT  H6    H  HCH2  0   0.243   1.9599  -3.2472  -0.1995
 FIT  H6A   H  HCH2  0   0.214   2.1014  -2.4125   1.3345
 FIT  H1    H  H     0   0.269   2.7477   2.6413   0.7184
 FIT  H7    H  HCH1  0   0.219   1.2365  -1.2092  -1.3170
 FIT  H8    H  HCH1  0   0.218   1.5391   0.1005   1.4135
 FIT  H10   H  HCH2  0   0.241   0.7699   2.1847   0.3756
 FIT  H10A  H  HCH2  0   0.227   0.5739   1.4008  -1.1675
 FIT  H11   H  HCH2  0   0.218  -0.9563   0.8050   1.4094
 FIT  H11A  H  HCH2  0   0.225  -1.5906   1.6005  -0.0260
 FIT  H13   H  HCH1  0   0.213  -0.2073  -1.5008   1.3246
 FIT  H14   H  HCH2  0   0.222  -0.5914  -3.1492  -1.1940
 FIT  H14A  H  HCH2  0   0.235  -0.4229  -3.7209   0.4529
 FIT  H15   H  HCH2  0   0.234  -2.8972  -2.9837  -0.8323
 FIT  H15A  H  HCH2  0   0.237  -2.7167  -3.3043   0.8772
 FIT  H16   H  HCH1  0   0.253  -2.4683  -1.0487   1.4439
 FIT  H17   H  HCH3  0   0.235  -0.4323  -0.1993  -2.2428
 FIT  H17A  H  HCH3  0   0.239  -1.6948  -1.4130  -2.2120
 FIT  H17B  H  HCH3  0   0.232  -2.1027   0.2916  -2.0658
 FIT  H18   H  HCH3  0   0.240   2.8322  -0.1083  -2.1447
 FIT  H18A  H  HCH3  0   0.243   2.6517   1.6248  -1.9167
 FIT  H18B  H  HCH3  0   0.242   4.2453   0.8923  -1.8342
 FIT  H21   H  HCH3  0   0.225  -6.7606   0.0997   1.3544
 FIT  H21A  H  HCH3  0   0.224  -7.5312   1.2387   0.2509
 FIT  H21B  H  HCH3  0   0.239  -6.7648  -0.2169  -0.3846
 FIT  H22   H  HCH3  0   0.235  -4.4378   3.0435   1.2379
 FIT  H22A  H  HCH3  0   0.242  -6.1966   3.1228   1.1542
 FIT  H22B  H  HCH3  0   0.237  -5.4249   2.0363   2.3079
 FIT  H23   H  HCH3  0   0.238  -5.2687   1.2194  -1.9304
 FIT  H23A  H  HCH3  0   0.224  -6.0582   2.6745  -1.3188
 FIT  H23B  H  HCH3  0   0.225  -4.3034   2.5235  -1.2272

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
 FIT  N1   C4    single  1.451  0.020  1.451
 FIT  N1   C3    single  1.348  0.020  1.348
 FIT  C2   C1    double  1.333  0.020  1.333
 FIT  C2   C3    single  1.479  0.020  1.479
 FIT  N2   C19   single  1.345  0.020  1.345
 FIT  N2   C20   single  1.467  0.020  1.467
 FIT  C4   C5    single  1.516  0.020  1.516
 FIT  C4   C9    single  1.537  0.020  1.537
 FIT  C5   C6    single  1.524  0.020  1.524
 FIT  C6   C7    single  1.528  0.020  1.528
 FIT  O1   C3    double  1.227  0.020  1.227
 FIT  O2   C19   double  1.224  0.020  1.224
 FIT  C1   C9    single  1.507  0.020  1.507
 FIT  C7   C8    single  1.544  0.020  1.544
 FIT  C7   C13   single  1.519  0.020  1.519
 FIT  C8   C9    single  1.548  0.020  1.548
 FIT  C8   C10   single  1.533  0.020  1.533
 FIT  C9   C18   single  1.537  0.020  1.537
 FIT  C10  C11   single  1.530  0.020  1.530
 FIT  C11  C12   single  1.525  0.020  1.525
 FIT  C12  C13   single  1.536  0.020  1.536
 FIT  C12  C16   single  1.548  0.020  1.548
 FIT  C12  C17   single  1.532  0.020  1.532
 FIT  C13  C14   single  1.526  0.020  1.526
 FIT  C14  C15   single  1.547  0.020  1.547
 FIT  C15  C16   single  1.541  0.020  1.541
 FIT  C16  C19   single  1.517  0.020  1.517
 FIT  C20  C21   single  1.530  0.020  1.530
 FIT  C20  C22   single  1.528  0.020  1.528
 FIT  C20  C23   single  1.530  0.020  1.530
 FIT  N1   HN1   single  0.890  0.020  1.040
 FIT  C2   H2    single  0.930  0.020  1.080
 FIT  N2   HN2   single  0.860  0.020  1.020
 FIT  C4   H4    single  0.970  0.020  1.090
 FIT  C5   H5    single  0.970  0.020  1.090
 FIT  C5   H5A   single  0.970  0.020  1.090
 FIT  C6   H6    single  0.970  0.020  1.090
 FIT  C6   H6A   single  0.970  0.020  1.090
 FIT  C1   H1    single  0.930  0.020  1.080
 FIT  C7   H7    single  0.970  0.020  1.090
 FIT  C8   H8    single  0.970  0.020  1.090
 FIT  C10  H10   single  0.970  0.020  1.090
 FIT  C10  H10A  single  0.970  0.020  1.090
 FIT  C11  H11   single  0.970  0.020  1.090
 FIT  C11  H11A  single  0.970  0.020  1.090
 FIT  C13  H13   single  0.970  0.020  1.090
 FIT  C14  H14   single  0.970  0.020  1.090
 FIT  C14  H14A  single  0.970  0.020  1.090
 FIT  C15  H15   single  0.970  0.020  1.090
 FIT  C15  H15A  single  0.970  0.020  1.090
 FIT  C16  H16   single  0.970  0.020  1.090
 FIT  C17  H17   single  0.970  0.020  1.090
 FIT  C17  H17A  single  0.970  0.020  1.090
 FIT  C17  H17B  single  0.970  0.020  1.090
 FIT  C18  H18   single  0.970  0.020  1.090
 FIT  C18  H18A  single  0.970  0.020  1.090
 FIT  C18  H18B  single  0.970  0.020  1.090
 FIT  C21  H21   single  0.970  0.020  1.090
 FIT  C21  H21A  single  0.970  0.020  1.090
 FIT  C21  H21B  single  0.970  0.020  1.090
 FIT  C22  H22   single  0.970  0.020  1.090
 FIT  C22  H22A  single  0.970  0.020  1.090
 FIT  C22  H22B  single  0.970  0.020  1.090
 FIT  C23  H23   single  0.970  0.020  1.090
 FIT  C23  H23A  single  0.970  0.020  1.090
 FIT  C23  H23B  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
 FIT  HN1   N1   C3    117.13  3.000
 FIT  HN1   N1   C4    118.26  3.000
 FIT  C3    N1   C4    121.34  3.000
 FIT  H2    C2   C3    116.56  3.000
 FIT  H2    C2   C1    121.50  3.000
 FIT  C3    C2   C1    121.78  3.000
 FIT  HN2   N2   C20   116.07  3.000
 FIT  HN2   N2   C19   116.58  3.000
 FIT  C20   N2   C19   127.31  3.000
 FIT  H4    C4   C9    106.36  3.000
 FIT  H4    C4   C5    106.96  3.000
 FIT  C9    C4   C5    112.59  3.000
 FIT  H4    C4   N1    108.42  3.000
 FIT  C9    C4   N1    110.32  3.000
 FIT  C5    C4   N1    111.89  3.000
 FIT  H5A   C5   H5    106.77  3.000
 FIT  H5A   C5   C6    110.03  3.000
 FIT  H5    C5   C6    110.67  3.000
 FIT  H5A   C5   C4    109.66  3.000
 FIT  H5    C5   C4    110.63  3.000
 FIT  C6    C5   C4    109.05  3.000
 FIT  H6A   C6   H6    106.36  3.000
 FIT  H6A   C6   C7    109.08  3.000
 FIT  H6    C6   C7    109.78  3.000
 FIT  H6A   C6   C5    109.20  3.000
 FIT  H6    C6   C5    109.83  3.000
 FIT  C7    C6   C5    112.40  3.000
 FIT  H1    C1   C9    118.95  3.000
 FIT  H1    C1   C2    119.15  3.000
 FIT  C9    C1   C2    121.79  3.000
 FIT  O1    C3   C2    121.94  3.000
 FIT  O1    C3   N1    123.32  3.000
 FIT  C2    C3   N1    114.71  3.000
 FIT  H7    C7   C13   108.79  3.000
 FIT  H7    C7   C8    109.12  3.000
 FIT  C13   C7   C8    108.45  3.000
 FIT  H7    C7   C6    107.51  3.000
 FIT  C13   C7   C6    111.54  3.000
 FIT  C8    C7   C6    111.38  3.000
 FIT  H8    C8   C10   106.77  3.000
 FIT  H8    C8   C9    106.66  3.000
 FIT  C10   C8   C9    113.85  3.000
 FIT  H8    C8   C7    106.16  3.000
 FIT  C10   C8   C7    111.59  3.000
 FIT  C9    C8   C7    111.27  3.000
 FIT  C18   C9   C8    111.85  3.000
 FIT  C18   C9   C1    106.82  3.000
 FIT  C8    C9   C1    112.35  3.000
 FIT  C18   C9   C4    112.59  3.000
 FIT  C8    C9   C4    107.21  3.000
 FIT  C1    C9   C4    105.94  3.000
 FIT  H10A  C10  H10   105.72  3.000
 FIT  H10A  C10  C11   109.65  3.000
 FIT  H10   C10  C11   108.30  3.000
 FIT  H10A  C10  C8    110.24  3.000
 FIT  H10   C10  C8    110.04  3.000
 FIT  C11   C10  C8    112.64  3.000
 FIT  H11A  C11  H11   106.80  3.000
 FIT  H11A  C11  C12   111.13  3.000
 FIT  H11   C11  C12   109.18  3.000
 FIT  H11A  C11  C10   109.48  3.000
 FIT  H11   C11  C10   109.10  3.000
 FIT  C12   C11  C10   111.05  3.000
 FIT  C17   C12  C16   110.19  3.000
 FIT  C17   C12  C13   112.72  3.000
 FIT  C16   C12  C13    99.00  3.000
 FIT  C17   C12  C11   110.09  3.000
 FIT  C16   C12  C11   116.00  3.000
 FIT  C13   C12  C11   108.48  3.000
 FIT  H13   C13  C14   106.90  3.000
 FIT  H13   C13  C12   105.84  3.000
 FIT  C14   C13  C12   103.75  3.000
 FIT  H13   C13  C7    106.33  3.000
 FIT  C14   C13  C7    119.33  3.000
 FIT  C12   C13  C7    113.80  3.000
 FIT  H14A  C14  H14   106.65  3.000
 FIT  H14A  C14  C15   112.28  3.000
 FIT  H14   C14  C15   111.09  3.000
 FIT  H14A  C14  C13   112.44  3.000
 FIT  H14   C14  C13   110.61  3.000
 FIT  C15   C14  C13   103.87  3.000
 FIT  H15A  C15  H15   106.66  3.000
 FIT  H15A  C15  C16   110.51  3.000
 FIT  H15   C15  C16   110.67  3.000
 FIT  H15A  C15  C14   111.79  3.000
 FIT  H15   C15  C14   111.24  3.000
 FIT  C16   C15  C14   106.04  3.000
 FIT  H16   C16  C19   108.26  3.000
 FIT  H16   C16  C15   108.74  3.000
 FIT  C19   C16  C15   114.67  3.000
 FIT  H16   C16  C12   106.67  3.000
 FIT  C19   C16  C12   114.28  3.000
 FIT  C15   C16  C12   103.81  3.000
 FIT  H17B  C17  H17A  107.44  3.000
 FIT  H17B  C17  H17   106.70  3.000
 FIT  H17A  C17  H17   106.97  3.000
 FIT  H17B  C17  C12   110.57  3.000
 FIT  H17A  C17  C12   112.74  3.000
 FIT  H17   C17  C12   112.11  3.000
 FIT  H18B  C18  H18A  107.30  3.000
 FIT  H18B  C18  H18   107.61  3.000
 FIT  H18A  C18  H18   107.42  3.000
 FIT  H18B  C18  C9    111.02  3.000
 FIT  H18A  C18  C9    110.76  3.000
 FIT  H18   C18  C9    112.51  3.000
 FIT  C16   C19  O2    122.78  3.000
 FIT  C16   C19  N2    113.71  3.000
 FIT  O2    C19  N2    123.50  3.000
 FIT  C23   C20  C22   109.24  3.000
 FIT  C23   C20  C21   110.90  3.000
 FIT  C22   C20  C21   108.96  3.000
 FIT  C23   C20  N2    110.63  3.000
 FIT  C22   C20  N2    106.00  3.000
 FIT  C21   C20  N2    110.96  3.000
 FIT  H21B  C21  H21A  108.02  3.000
 FIT  H21B  C21  H21   108.38  3.000
 FIT  H21A  C21  H21   107.76  3.000
 FIT  H21B  C21  C20   112.02  3.000
 FIT  H21A  C21  C20   109.92  3.000
 FIT  H21   C21  C20   110.61  3.000
 FIT  H22B  C22  H22A  107.81  3.000
 FIT  H22B  C22  H22   108.28  3.000
 FIT  H22A  C22  H22   107.79  3.000
 FIT  H22B  C22  C20   111.26  3.000
 FIT  H22A  C22  C20   110.12  3.000
 FIT  H22   C22  C20   111.43  3.000
 FIT  H23B  C23  H23A  107.77  3.000
 FIT  H23B  C23  H23   108.41  3.000
 FIT  H23A  C23  H23   108.11  3.000
 FIT  H23B  C23  C20   110.49  3.000
 FIT  H23A  C23  C20   110.18  3.000
 FIT  H23   C23  C20   111.76  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
 FIT  CONST_01  C4   N1   C3   C2     0.00   0.0  0
 FIT  CONST_02  O1   C3   N1   C4   180.00   0.0  0
 FIT  CONST_03  HN1  N1   C3   C2   180.00   0.0  0
 FIT  CONST_04  C20  N2   C19  C16  180.00   0.0  0
 FIT  CONST_05  HN2  N2   C19  C16    0.00   0.0  0
 FIT  CONST_06  C20  N2   C19  O2     0.00   0.0  0
 FIT  Var_01    C1   C2   C3   N1   -12.55  30.0  1
 FIT  Var_02    C7   C6   C5   C4    55.08  30.0  1
 FIT  Var_03    C9   C1   C2   C3     1.70  30.0  1
 FIT  Var_04    C12  C11  C10  C8   -55.16  30.0  1
 FIT  Var_05    C16  C15  C14  C13    7.22  30.0  1
 FIT  Var_06    C21  C20  N2   C19   62.26  30.0  3
 FIT  Var_07    H21  C21  C20  N2    55.35  30.0  3
 FIT  Var_08    H22  C22  C20  N2    61.29  30.0  3
 FIT  Var_09    H23  C23  C20  N2    64.65  30.0  3

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
 FIT  chir_01  C4   N1   C5   C9   positiv
 FIT  chir_02  C7   C13  C8   C6   negativ
 FIT  chir_03  C8   C10  C9   C7   positiv
 FIT  chir_04  C9   C8   C1   C4   negativ
 FIT  chir_05  C12  C16  C13  C11  positiv
 FIT  chir_06  C13  C14  C12  C7   positiv
 FIT  chir_07  C16  C12  C15  C19  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
 FIT  plan-1  N2   0.020
 FIT  plan-1  O2   0.020
 FIT  plan-1  C16  0.020
 FIT  plan-1  C19  0.020
 FIT  plan-1  C20  0.020
 FIT  plan-1  HN2  0.020
 FIT  plan-2  N1   0.020
 FIT  plan-2  C2   0.020
 FIT  plan-2  C4   0.020
 FIT  plan-2  O1   0.020
 FIT  plan-2  C3   0.020
 FIT  plan-2  HN1  0.020

