# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:17:39 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)N1C[C@@H](C)c2c1cc(O)c3ccccc23
#
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
 K9P  K9P  1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one  ligand  45  22  .  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_K9P
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
 K9P  O     O  O     0  -0.482   2.2282  -2.5129  -0.9965
 K9P  C5    C  C     0   0.561   1.6782  -1.4501  -0.7530
 K9P  C4    C  CH2   0  -0.615   2.4732  -0.1964  -0.4724
 K9P  C3    C  CH2   0  -0.402   3.9258  -0.4802  -0.1149
 K9P  C2    C  CH2   0  -0.410   4.6934   0.8041   0.1743
 K9P  C1    C  CH2   0  -0.420   6.1540   0.5553   0.5289
 K9P  C     C  CH3   0  -0.662   6.9160   1.8402   0.8222
 K9P  N     N  NR5   0  -0.604   0.3183  -1.3929  -0.6991
 K9P  C10   C  CR56  0   0.419  -0.5632  -0.3122  -0.5485
 K9P  C11   C  CR16  0  -0.460  -0.3203   1.0596  -0.7473
 K9P  C12   C  CR6   0   0.340  -1.3560   1.9470  -0.5716
 K9P  O1    O  OH1   0  -0.621  -1.1984   3.2709  -0.7417
 K9P  C13   C  CR66  0  -0.042  -2.6627   1.5075  -0.2185
 K9P  C18   C  CR66  0   0.111  -2.8895   0.1129  -0.0573
 K9P  C9    C  CR56  0  -0.074  -1.8159  -0.7785  -0.2310
 K9P  C7    C  CR15  0  -0.319  -1.7909  -2.2729  -0.0695
 K9P  C8    C  CH3   0  -0.656  -1.7955  -2.6889   1.4015
 K9P  C6    C  CH2   0  -0.283  -0.4749  -2.6274  -0.7728
 K9P  C17   C  CR16  0  -0.351  -4.1970  -0.3248   0.2688
 K9P  C16   C  CR16  0  -0.243  -5.2170   0.5716   0.4341
 K9P  C15   C  CR16  0  -0.265  -4.9861   1.9532   0.2803
 K9P  C14   C  CR16  0  -0.274  -3.7361   2.4104  -0.0411
 K9P  H41C  H  HCH2  0   0.275   2.4424   0.4424  -1.3619
 K9P  H42C  H  HCH2  0   0.264   1.9984   0.3739   0.3297
 K9P  H31C  H  HCH2  0   0.223   3.9718  -1.1347   0.7598
 K9P  H32C  H  HCH2  0   0.223   4.4117  -1.0188  -0.9316
 K9P  H21C  H  HCH2  0   0.211   4.6388   1.4662  -0.6969
 K9P  H22C  H  HCH2  0   0.210   4.2094   1.3442   0.9958
 K9P  H11C  H  HCH2  0   0.212   6.2074  -0.1098   1.3964
 K9P  H12C  H  HCH2  0   0.211   6.6403   0.0211  -0.2931
 K9P  HC1   H  HCH3  0   0.226   7.9622   1.6418   1.0576
 K9P  HC2   H  HCH3  0   0.216   6.8920   2.5152  -0.0350
 K9P  HC3   H  HCH3  0   0.216   6.4823   2.3722   1.6712
 K9P  H61C  H  HCH2  0   0.260  -0.6435  -2.8930  -1.8194
 K9P  H62C  H  HCH2  0   0.258   0.0522  -3.4494  -0.2931
 K9P  H11   H  HCR6  0   0.287   0.6431   1.4331  -1.0613
 K9P  H1    H  HOH1  0   0.480  -0.2859   3.4784  -0.9728
 K9P  H14   H  HCR6  0   0.256  -3.5725   3.4728  -0.1599
 K9P  H17   H  HCR6  0   0.249  -4.3883  -1.3839   0.3859
 K9P  H7    H  HCR5  0   0.262  -2.6251  -2.7543  -0.5841
 K9P  H81C  H  HCH3  0   0.235  -2.6944  -2.3392   1.9100
 K9P  H82C  H  HCH3  0   0.236  -1.7590  -3.7749   1.4981
 K9P  H83C  H  HCH3  0   0.227  -0.9332  -2.2734   1.9263
 K9P  H16   H  HCR6  0   0.259  -6.2090   0.2190   0.6850
 K9P  H15   H  HCR6  0   0.257  -5.7999   2.6532   0.4143

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
 K9P  O    C5    double    1.221  0.020  1.221
 K9P  C5   C4    single    1.511  0.020  1.511
 K9P  C5   N     single    1.362  0.020  1.362
 K9P  C4   C3    single    1.523  0.020  1.523
 K9P  C3   C2    single    1.524  0.020  1.524
 K9P  C2   C1    single    1.524  0.020  1.524
 K9P  C1   C     single    1.522  0.020  1.522
 K9P  N    C10   single    1.403  0.020  1.403
 K9P  N    C6    single    1.469  0.020  1.469
 K9P  C10  C11   aromatic  1.407  0.020  1.407
 K9P  C10  C9    aromatic  1.374  0.020  1.374
 K9P  C11  C12   aromatic  1.375  0.020  1.375
 K9P  C12  O1    single    1.344  0.020  1.344
 K9P  C12  C13   aromatic  1.423  0.020  1.423
 K9P  C13  C18   aromatic  1.422  0.020  1.422
 K9P  C13  C14   aromatic  1.414  0.020  1.414
 K9P  C18  C9    aromatic  1.406  0.020  1.406
 K9P  C18  C17   aromatic  1.417  0.020  1.417
 K9P  C9   C7    single    1.503  0.020  1.503
 K9P  C7   C8    single    1.529  0.020  1.529
 K9P  C7   C6    single    1.534  0.020  1.534
 K9P  C17  C16   aromatic  1.368  0.020  1.368
 K9P  C16  C15   aromatic  1.409  0.020  1.409
 K9P  C15  C14   aromatic  1.369  0.020  1.369
 K9P  C4   H41C  single    0.970  0.020  1.090
 K9P  C4   H42C  single    0.970  0.020  1.090
 K9P  C3   H31C  single    0.970  0.020  1.090
 K9P  C3   H32C  single    0.970  0.020  1.090
 K9P  C2   H21C  single    0.970  0.020  1.090
 K9P  C2   H22C  single    0.970  0.020  1.090
 K9P  C1   H11C  single    0.970  0.020  1.090
 K9P  C1   H12C  single    0.970  0.020  1.090
 K9P  C    HC1   single    0.970  0.020  1.090
 K9P  C    HC2   single    0.970  0.020  1.090
 K9P  C    HC3   single    0.970  0.020  1.090
 K9P  C6   H61C  single    0.970  0.020  1.090
 K9P  C6   H62C  single    0.970  0.020  1.090
 K9P  C11  H11   single    0.930  0.020  1.080
 K9P  O1   H1    single    0.850  0.020  0.980
 K9P  C14  H14   single    0.930  0.020  1.080
 K9P  C17  H17   single    0.930  0.020  1.080
 K9P  C7   H7    single    0.970  0.020  1.090
 K9P  C8   H81C  single    0.970  0.020  1.090
 K9P  C8   H82C  single    0.970  0.020  1.090
 K9P  C8   H83C  single    0.970  0.020  1.090
 K9P  C16  H16   single    0.930  0.020  1.080
 K9P  C15  H15   single    0.930  0.020  1.080

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
 K9P  N     C5   C4    118.89  3.000
 K9P  N     C5   O     119.60  3.000
 K9P  C4    C5   O     121.48  3.000
 K9P  H42C  C4   H41C  106.23  3.000
 K9P  H42C  C4   C3    109.84  3.000
 K9P  H41C  C4   C3    109.04  3.000
 K9P  H42C  C4   C5    109.93  3.000
 K9P  H41C  C4   C5    108.56  3.000
 K9P  C3    C4   C5    113.02  3.000
 K9P  H32C  C3   H31C  106.51  3.000
 K9P  H32C  C3   C2    109.47  3.000
 K9P  H31C  C3   C2    109.36  3.000
 K9P  H32C  C3   C4    109.92  3.000
 K9P  H31C  C3   C4    109.85  3.000
 K9P  C2    C3   C4    111.59  3.000
 K9P  H22C  C2   H21C  106.04  3.000
 K9P  H22C  C2   C1    109.23  3.000
 K9P  H21C  C2   C1    109.36  3.000
 K9P  H22C  C2   C3    109.58  3.000
 K9P  H21C  C2   C3    109.47  3.000
 K9P  C1    C2   C3    112.92  3.000
 K9P  H12C  C1   H11C  106.08  3.000
 K9P  H12C  C1   C     109.53  3.000
 K9P  H11C  C1   C     109.62  3.000
 K9P  H12C  C1   C2    109.33  3.000
 K9P  H11C  C1   C2    109.30  3.000
 K9P  C     C1   C2    112.76  3.000
 K9P  HC3   C    HC2   107.49  3.000
 K9P  HC3   C    HC1   107.58  3.000
 K9P  HC2   C    HC1   107.65  3.000
 K9P  HC3   C    C1    111.24  3.000
 K9P  HC2   C    C1    111.08  3.000
 K9P  HC1   C    C1    111.61  3.000
 K9P  C6    N    C10   108.27  3.000
 K9P  C6    N    C5    120.12  3.000
 K9P  C10   N    C5    131.60  3.000
 K9P  C9    C10  C11   121.39  3.000
 K9P  C9    C10  N     109.65  3.000
 K9P  C11   C10  N     128.86  3.000
 K9P  H11   C11  C12   119.07  3.000
 K9P  H11   C11  C10   122.16  3.000
 K9P  C12   C11  C10   118.75  3.000
 K9P  C13   C12  O1    116.31  3.000
 K9P  C13   C12  C11   121.60  3.000
 K9P  O1    C12  C11   122.08  3.000
 K9P  H1    O1   C12   110.69  3.000
 K9P  C14   C13  C18   119.40  3.000
 K9P  C14   C13  C12   122.08  3.000
 K9P  C18   C13  C12   118.51  3.000
 K9P  C17   C18  C9    122.48  3.000
 K9P  C17   C18  C13   118.44  3.000
 K9P  C9    C18  C13   119.07  3.000
 K9P  C7    C9   C18   129.02  3.000
 K9P  C7    C9   C10   110.31  3.000
 K9P  C18   C9   C10   120.63  3.000
 K9P  H7    C7   C6    109.72  3.000
 K9P  H7    C7   C8    109.35  3.000
 K9P  C6    C7   C8    112.39  3.000
 K9P  H7    C7   C9    112.02  3.000
 K9P  C6    C7   C9    101.23  3.000
 K9P  C8    C7   C9    111.95  3.000
 K9P  H83C  C8   H82C  108.05  3.000
 K9P  H83C  C8   H81C  107.76  3.000
 K9P  H82C  C8   H81C  107.80  3.000
 K9P  H83C  C8   C7    110.90  3.000
 K9P  H82C  C8   C7    110.86  3.000
 K9P  H81C  C8   C7    111.34  3.000
 K9P  H62C  C6   H61C  108.26  3.000
 K9P  H62C  C6   C7    112.84  3.000
 K9P  H61C  C6   C7    111.28  3.000
 K9P  H62C  C6   N     110.56  3.000
 K9P  H61C  C6   N     109.60  3.000
 K9P  C7    C6   N     104.24  3.000
 K9P  H17   C17  C16   119.75  3.000
 K9P  H17   C17  C18   119.36  3.000
 K9P  C16   C17  C18   120.89  3.000
 K9P  H16   C16  C15   119.66  3.000
 K9P  H16   C16  C17   119.87  3.000
 K9P  C15   C16  C17   120.47  3.000
 K9P  H15   C15  C14   119.99  3.000
 K9P  H15   C15  C16   119.84  3.000
 K9P  C14   C15  C16   120.17  3.000
 K9P  H14   C14  C15   119.46  3.000
 K9P  H14   C14  C13   119.91  3.000
 K9P  C15   C14  C13   120.62  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
 K9P  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 K9P  CONST_02  C13  C18  C9   C10     0.00   0.0  0
 K9P  CONST_03  C17  C18  C9   C10   180.00   0.0  0
 K9P  CONST_04  C18  C9   C10  C11     0.00   0.0  0
 K9P  CONST_05  C18  C13  C12  C11     0.00   0.0  0
 K9P  CONST_06  C14  C13  C12  C11   180.00   0.0  0
 K9P  CONST_07  C9   C10  C11  C12     0.00   0.0  0
 K9P  CONST_08  C9   C18  C13  C12     0.00   0.0  0
 K9P  CONST_09  C17  C18  C13  C12   180.00   0.0  0
 K9P  CONST_10  C15  C14  C13  C12   180.00   0.0  0
 K9P  CONST_11  C16  C17  C18  C13     0.00   0.0  0
 K9P  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 K9P  CONST_13  C15  C14  C13  C18     0.00   0.0  0
 K9P  CONST_14  C15  C16  C17  C18     0.00   0.0  0
 K9P  CONST_15  C14  C13  C18  C9    180.00   0.0  0
 K9P  CONST_16  C16  C17  C18  C9    180.00   0.0  0
 K9P  CONST_17  C14  C13  C18  C17     0.00   0.0  0
 K9P  CONST_18  C14  C15  C16  C17     0.00   0.0  0
 K9P  CONST_19  O1   C12  C11  C10   180.00   0.0  0
 K9P  CONST_20  C18  C13  C12  O1    180.00   0.0  0
 K9P  CONST_21  C14  C13  C12  O1      0.00   0.0  0
 K9P  CONST_22  H11  C11  C10  N       0.00   0.0  0
 K9P  CONST_23  H14  C14  C13  C12     0.00   0.0  0
 K9P  CONST_24  H17  C17  C18  C13   180.00   0.0  0
 K9P  CONST_25  H15  C15  C14  C13   180.00   0.0  0
 K9P  CONST_26  H16  C16  C17  C18   180.00   0.0  0
 K9P  CONST_27  C10  N    C5   O     180.00   0.0  0
 K9P  CONST_28  C6   N    C5   O       0.00   0.0  0
 K9P  CONST_29  C10  N    C5   C4      0.00   0.0  0
 K9P  CONST_30  C6   N    C5   C4    180.00   0.0  0
 K9P  Var_01    C7   C6   N    C10   -23.56  30.0  1
 K9P  Var_02    C6   N    C10  C11  -163.36  30.0  1
 K9P  Var_03    N    C5   C4   C3    161.02  30.0  1
 K9P  Var_04    C2   C3   C4   C5   -179.46  30.0  3
 K9P  Var_05    C1   C2   C3   C4   -179.70  30.0  3
 K9P  Var_06    C    C1   C2   C3   -179.78  30.0  3
 K9P  Var_07    HC1  C    C1   C2   -179.07  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
 K9P  chir_01  C7  C9  C8  C6  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
 K9P  plan-1  O    0.020
 K9P  plan-1  C5   0.020
 K9P  plan-1  C4   0.020
 K9P  plan-1  N    0.020
 K9P  plan-1  C10  0.020
 K9P  plan-1  C6   0.020
 K9P  plan-2  N    0.020
 K9P  plan-2  C10  0.020
 K9P  plan-2  C11  0.020
 K9P  plan-2  C12  0.020
 K9P  plan-2  O1   0.020
 K9P  plan-2  C13  0.020
 K9P  plan-2  C18  0.020
 K9P  plan-2  C9   0.020
 K9P  plan-2  C7   0.020
 K9P  plan-2  C17  0.020
 K9P  plan-2  C16  0.020
 K9P  plan-2  C15  0.020
 K9P  plan-2  C14  0.020
 K9P  plan-2  H11  0.020
 K9P  plan-2  H14  0.020
 K9P  plan-2  H17  0.020
 K9P  plan-2  H16  0.020
 K9P  plan-2  H15  0.020

