# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 13:11:24 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (4aR,5R,10bR)-12-methyl-2,3,4,4a,5,6-hexahydro-1H-5,10b-prop[1]eno-1,7-phenanthrolin-8(7H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C[C@H]2CC3=C(C=CC(=O)N3)[C@]4(C1)NCCC[C@H]24
#
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
 HUB  HUB  (4aR,5R,10bR)-12-methyl-2,3,4,4a,5,6-hexahydro-1H-5,10b-prop[1]eno-1,7-phenanthrolin-8(7H)-one  ligand  39  19  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HUB
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
 HUB  C1    C  CR6   0   0.513   0.3476  -0.0658   3.3415
 HUB  O1    O  OC    0  -0.522   0.5620  -0.3459   4.5207
 HUB  N1    N  NR16  0  -0.715   0.5308  -1.0090   2.3519
 HUB  C2    C  CR16  0  -0.472  -0.0915   1.2048   2.8387
 HUB  C3    C  CR16  0  -0.140  -0.3040   1.3925   1.5091
 HUB  C4    C  CR6   0   0.011  -0.1124   0.3681   0.5480
 HUB  C5    C  CR6   0   0.377   0.3253  -0.8365   1.0191
 HUB  C6    C  CH2   0  -0.531   0.5958  -2.0199   0.1466
 HUB  C7    C  CH1   0  -0.299   0.6600  -1.5957  -1.3223
 HUB  C8    C  C1    0  -0.246   1.9601  -0.8859  -1.5771
 HUB  C9    C  CH2   0  -0.420  -3.0195  -0.3552  -1.6444
 HUB  C10   C  CH2   0  -0.429  -1.8843  -1.3430  -1.4067
 HUB  C11   C  CH1   0  -0.226  -0.5249  -0.6990  -1.6771
 HUB  C12   C  CT    0   0.027  -0.3465   0.6336  -0.9390
 HUB  N2    N  NH1   0  -0.612  -1.5012   1.4750  -1.2059
 HUB  C13   C  CH2   0  -0.465   0.8843   1.3378  -1.5223
 HUB  C14   C  C     0   0.097   2.0785   0.4388  -1.6567
 HUB  C15   C  CH3   0  -0.717   3.3905   1.1175  -1.9013
 HUB  C90   C  CH2   0  -0.295  -2.7811   0.9049  -0.8305
 HUB  H1    H  HNR6  0   0.412   0.8572  -1.9151   2.6634
 HUB  H2    H  HCR6  0   0.265  -0.2474   2.0051   3.5491
 HUB  H3    H  HCR6  0   0.254  -0.6343   2.3712   1.1802
 HUB  H6C1  H  HCH2  0   0.279  -0.1806  -2.7744   0.3088
 HUB  H6C2  H  HCH2  0   0.277   1.5383  -2.4886   0.4443
 HUB  H7    H  HCH1  0   0.252   0.6238  -2.4999  -1.9375
 HUB  H8    H  H     0   0.233   2.8463  -1.5083  -1.6652
 HUB  H9C1  H  HCH2  0   0.227  -3.9775  -0.8025  -1.3697
 HUB  H9C2  H  HCH2  0   0.213  -3.0778  -0.0921  -2.7046
 HUB  H101  H  HCH2  0   0.218  -1.9517  -1.6983  -0.3744
 HUB  H102  H  HCH2  0   0.234  -1.9965  -2.2239  -2.0446
 HUB  H11   H  HCH1  0   0.237  -0.4722  -0.4773  -2.7500
 HUB  HA    H  HNH1  0   0.349  -1.3825   2.3952  -0.8029
 HUB  H131  H  HCH2  0   0.236   1.1480   2.2086  -0.9099
 HUB  H132  H  HCH2  0   0.248   0.6202   1.7406  -2.5078
 HUB  H151  H  HCH3  0   0.238   4.2045   0.4019  -2.0157
 HUB  H152  H  HCH3  0   0.234   3.3516   1.7335  -2.8036
 HUB  H153  H  HCH3  0   0.234   3.6416   1.7901  -1.0771
 HUB  H901  H  HCH2  0   0.191  -2.8543   0.6612   0.2415
 HUB  H902  H  HCH2  0   0.234  -3.5558   1.6463  -1.0358

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
 HUB  C1   O1    double    1.231  0.020  1.231
 HUB  C1   N1    aromatic  1.379  0.020  1.379
 HUB  C1   C2    aromatic  1.435  0.020  1.435
 HUB  N1   C5    aromatic  1.360  0.020  1.360
 HUB  N1   H1    single    0.860  0.020  1.020
 HUB  C2   C3    aromatic  1.359  0.020  1.359
 HUB  C2   H2    single    0.930  0.020  1.080
 HUB  C3   C4    aromatic  1.418  0.020  1.418
 HUB  C3   H3    single    0.930  0.020  1.080
 HUB  C4   C5    aromatic  1.365  0.020  1.365
 HUB  C4   C12   single    1.529  0.020  1.529
 HUB  C5   C6    single    1.495  0.020  1.495
 HUB  C6   C7    single    1.530  0.020  1.530
 HUB  C6   H6C1  single    0.970  0.020  1.090
 HUB  C6   H6C2  single    0.970  0.020  1.090
 HUB  C7   C8    single    1.503  0.020  1.503
 HUB  C7   C11   single    1.528  0.020  1.528
 HUB  C7   H7    single    0.970  0.020  1.090
 HUB  C8   C14   double    1.332  0.020  1.332
 HUB  C8   H8    single    0.930  0.020  1.080
 HUB  C9   C10   single    1.523  0.020  1.523
 HUB  C9   C90   single    1.519  0.020  1.519
 HUB  C9   H9C1  single    0.970  0.020  1.090
 HUB  C9   H9C2  single    0.970  0.020  1.090
 HUB  C10  C11   single    1.528  0.020  1.528
 HUB  C10  H101  single    0.970  0.020  1.090
 HUB  C10  H102  single    0.970  0.020  1.090
 HUB  C11  C12   single    1.534  0.020  1.534
 HUB  C11  H11   single    0.970  0.020  1.090
 HUB  C12  N2    single    1.453  0.020  1.453
 HUB  C12  C13   single    1.533  0.020  1.533
 HUB  N2   C90   single    1.451  0.020  1.451
 HUB  N2   HA    single    0.890  0.020  1.040
 HUB  C13  C14   single    1.501  0.020  1.501
 HUB  C13  H131  single    0.970  0.020  1.090
 HUB  C13  H132  single    0.970  0.020  1.090
 HUB  C14  C15   single    1.497  0.020  1.497
 HUB  C15  H151  single    0.970  0.020  1.090
 HUB  C15  H152  single    0.970  0.020  1.090
 HUB  C15  H153  single    0.970  0.020  1.090
 HUB  C90  H901  single    0.970  0.020  1.090
 HUB  C90  H902  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
 HUB  C2    C1   N1    113.24  3.000
 HUB  C2    C1   O1    126.18  3.000
 HUB  N1    C1   O1    120.57  3.000
 HUB  H1    N1   C5    117.65  3.000
 HUB  H1    N1   C1    115.73  3.000
 HUB  C5    N1   C1    126.62  3.000
 HUB  H2    C2   C3    121.18  3.000
 HUB  H2    C2   C1    117.98  3.000
 HUB  C3    C2   C1    120.84  3.000
 HUB  H3    C3   C4    119.20  3.000
 HUB  H3    C3   C2    117.97  3.000
 HUB  C4    C3   C2    122.83  3.000
 HUB  C12   C4   C5    122.54  3.000
 HUB  C12   C4   C3    120.89  3.000
 HUB  C5    C4   C3    116.54  3.000
 HUB  C6    C5   C4    123.71  3.000
 HUB  C6    C5   N1    116.38  3.000
 HUB  C4    C5   N1    119.91  3.000
 HUB  H6C2  C6   H6C1  105.99  3.000
 HUB  H6C2  C6   C7    110.11  3.000
 HUB  H6C1  C6   C7    111.28  3.000
 HUB  H6C2  C6   C5    109.65  3.000
 HUB  H6C1  C6   C5    109.32  3.000
 HUB  C7    C6   C5    110.39  3.000
 HUB  H7    C7   C11   109.19  3.000
 HUB  H7    C7   C8    108.88  3.000
 HUB  C11   C7   C8    110.76  3.000
 HUB  H7    C7   C6    108.01  3.000
 HUB  C11   C7   C6    110.68  3.000
 HUB  C8    C7   C6    109.26  3.000
 HUB  H8    C8   C14   119.49  3.000
 HUB  H8    C8   C7    116.67  3.000
 HUB  C14   C8   C7    123.81  3.000
 HUB  H9C2  C9   H9C1  107.19  3.000
 HUB  H9C2  C9   C90   109.15  3.000
 HUB  H9C1  C9   C90   110.04  3.000
 HUB  H9C2  C9   C10   110.29  3.000
 HUB  H9C1  C9   C10   110.41  3.000
 HUB  C90   C9   C10   109.72  3.000
 HUB  H102  C10  H101  106.41  3.000
 HUB  H102  C10  C11   109.12  3.000
 HUB  H101  C10  C11   111.02  3.000
 HUB  H102  C10  C9    110.79  3.000
 HUB  H101  C10  C9    108.18  3.000
 HUB  C11   C10  C9    111.22  3.000
 HUB  H11   C11  C12   106.83  3.000
 HUB  H11   C11  C10   107.52  3.000
 HUB  C12   C11  C10   112.61  3.000
 HUB  H11   C11  C7    107.97  3.000
 HUB  C12   C11  C7    107.93  3.000
 HUB  C10   C11  C7    113.67  3.000
 HUB  C13   C12  N2    107.57  3.000
 HUB  C13   C12  C11   108.02  3.000
 HUB  N2    C12  C11   108.79  3.000
 HUB  C13   C12  C4    109.08  3.000
 HUB  N2    C12  C4    113.63  3.000
 HUB  C11   C12  C4    109.58  3.000
 HUB  HA    N2   C90   110.97  3.000
 HUB  HA    N2   C12   111.12  3.000
 HUB  C90   N2   C12   115.21  3.000
 HUB  H132  C13  H131  105.55  3.000
 HUB  H132  C13  C14   109.34  3.000
 HUB  H131  C13  C14   109.53  3.000
 HUB  H132  C13  C12   108.49  3.000
 HUB  H131  C13  C12   110.20  3.000
 HUB  C14   C13  C12   113.43  3.000
 HUB  C15   C14  C13   116.12  3.000
 HUB  C15   C14  C8    122.57  3.000
 HUB  C13   C14  C8    121.30  3.000
 HUB  H153  C15  H152  106.49  3.000
 HUB  H153  C15  H151  108.16  3.000
 HUB  H152  C15  H151  108.05  3.000
 HUB  H153  C15  C14   110.92  3.000
 HUB  H152  C15  C14   111.04  3.000
 HUB  H151  C15  C14   111.96  3.000
 HUB  H902  C90  H901  106.62  3.000
 HUB  H902  C90  N2    108.09  3.000
 HUB  H901  C90  N2    113.41  3.000
 HUB  H902  C90  C9    110.56  3.000
 HUB  H901  C90  C9    109.11  3.000
 HUB  N2    C90  C9    109.02  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
 HUB  CONST_01  C4    C5   N1   C1      0.00   0.0  0
 HUB  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 HUB  CONST_03  C3    C2   C1   N1      0.00   0.0  0
 HUB  CONST_04  C3    C4   C5   N1      0.00   0.0  0
 HUB  CONST_05  C5    N1   C1   C2      0.00   0.0  0
 HUB  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 HUB  CONST_07  C5    N1   C1   O1    180.00   0.0  0
 HUB  CONST_08  C3    C2   C1   O1    180.00   0.0  0
 HUB  CONST_09  H3    C3   C2   C1    180.00   0.0  0
 HUB  CONST_10  H2    C2   C1   N1    180.00   0.0  0
 HUB  CONST_11  H1    N1   C1   C2    180.00   0.0  0
 HUB  Var_01    C7    C6   C5   N1   -166.07  30.0  1
 HUB  Var_02    C13   C14  C8   C7     -1.33  30.0  2
 HUB  Var_03    C12   C13  C14  C8     14.99  30.0  3
 HUB  Var_04    C12   N2   C90  C9    -62.42  30.0  1
 HUB  Var_05    N2    C90  C9   C10    57.95  30.0  1
 HUB  Var_06    C90   C9   C10  C11   -53.94  30.0  1
 HUB  Var_07    H151  C15  C14  C8      0.82  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
 HUB  chir_01  C7   C6  C8   C11  positiv
 HUB  chir_02  C11  C7  C10  C12  negativ
 HUB  chir_03  C12  C4  C11  N2   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
 HUB  plan-1  C1   0.020
 HUB  plan-1  O1   0.020
 HUB  plan-1  N1   0.020
 HUB  plan-1  C2   0.020
 HUB  plan-1  C3   0.020
 HUB  plan-1  C4   0.020
 HUB  plan-1  C5   0.020
 HUB  plan-1  C6   0.020
 HUB  plan-1  C12  0.020
 HUB  plan-1  H1   0.020
 HUB  plan-1  H2   0.020
 HUB  plan-1  H3   0.020

