# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 02:11:48 2021
#   Inital geometry file: a 64 line input string
#   Ligand name: (2~{S})-2-methyl-3,4-dihydro-2~{H}-naphthalen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCc2ccccc2C1=O
#
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
 P6N  P6N  (2~{S})-2-methyl-3,4-dihydro-2~{H}-naphthalen-1-one  ligand  24  12  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P6N
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
 P6N  C11   C  C     0   0.385  6.2746  -0.4950  18.6725
 P6N  C10   C  CR6   0  -0.046  5.4661   0.4029  19.5406
 P6N  C01   C  CH3   0  -0.659  8.0067  -2.3242  18.4846
 P6N  C02   C  CH1   0  -0.375  6.9068  -1.7012  19.3294
 P6N  C03   C  CH2   0  -0.443  7.3786  -1.3362  20.7363
 P6N  C04   C  CH2   0  -0.513  6.2112  -0.8724  21.5899
 P6N  C05   C  CR6   0   0.110  5.4318   0.2281  20.9292
 P6N  C06   C  CR16  0  -0.305  4.6536   1.0947  21.6944
 P6N  C07   C  CR16  0  -0.235  3.9227   2.1096  21.1004
 P6N  C08   C  CR16  0  -0.260  3.9607   2.2833  19.7197
 P6N  C09   C  CR16  0  -0.264  4.7324   1.4356  18.9488
 P6N  O12   O  O     0  -0.404  6.3955  -0.2708  17.4854
 P6N  H013  H  HCH3  0   0.235  8.3767  -3.2265  18.9717
 P6N  H1    H  HCH3  0   0.237  7.6544  -2.6028  17.4930
 P6N  H012  H  HCH3  0   0.225  8.8489  -1.6406  18.3656
 P6N  H021  H  HCH1  0   0.272  6.0904  -2.4310  19.4405
 P6N  H031  H  HCH2  0   0.250  7.8555  -2.2035  21.1964
 P6N  H032  H  HCH2  0   0.236  8.1392  -0.5514  20.6760
 P6N  H041  H  HCH2  0   0.255  5.5400  -1.7200  21.7700
 P6N  H042  H  HCH2  0   0.261  6.5544  -0.5417  22.5720
 P6N  H061  H  HCR6  0   0.256  4.6268   0.9721  22.7707
 P6N  H071  H  HCR6  0   0.264  3.3254   2.7717  21.7140
 P6N  H081  H  HCR6  0   0.260  3.3938   3.0780  19.2533
 P6N  H091  H  HCR6  0   0.258  4.7668   1.5671  17.8752

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
 P6N  O12  C11   double    1.214  0.020  1.214
 P6N  C01  C02   single    1.520  0.020  1.520
 P6N  C11  C02   single    1.512  0.020  1.512
 P6N  C11  C10   single    1.488  0.020  1.488
 P6N  C09  C10   aromatic  1.398  0.020  1.398
 P6N  C09  C08   aromatic  1.381  0.020  1.381
 P6N  C02  C03   single    1.528  0.020  1.528
 P6N  C10  C05   aromatic  1.400  0.020  1.400
 P6N  C08  C07   aromatic  1.392  0.020  1.392
 P6N  C03  C04   single    1.519  0.020  1.519
 P6N  C05  C04   single    1.502  0.020  1.502
 P6N  C05  C06   aromatic  1.394  0.020  1.394
 P6N  C07  C06   aromatic  1.385  0.020  1.385
 P6N  C01  H013  single    0.970  0.020  1.090
 P6N  C01  H1    single    0.970  0.020  1.090
 P6N  C01  H012  single    0.970  0.020  1.090
 P6N  C02  H021  single    0.970  0.020  1.090
 P6N  C03  H031  single    0.970  0.020  1.090
 P6N  C03  H032  single    0.970  0.020  1.090
 P6N  C04  H041  single    0.970  0.020  1.090
 P6N  C04  H042  single    0.970  0.020  1.090
 P6N  C06  H061  single    0.930  0.020  1.080
 P6N  C07  H071  single    0.930  0.020  1.080
 P6N  C08  H081  single    0.930  0.020  1.080
 P6N  C09  H091  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
 P6N  O12   C11  C02   122.04  3.000
 P6N  C02   C11  C10   117.08  3.000
 P6N  O12   C11  C10   120.87  3.000
 P6N  C09   C10  C05   119.94  3.000
 P6N  C05   C10  C11   121.11  3.000
 P6N  C09   C10  C11   118.95  3.000
 P6N  H012  C01  H1    108.11  3.000
 P6N  H012  C01  H013  107.78  3.000
 P6N  H1    C01  H013  107.76  3.000
 P6N  H012  C01  C02   111.24  3.000
 P6N  H1    C01  C02   112.14  3.000
 P6N  H013  C01  C02   109.66  3.000
 P6N  H021  C02  C03   107.12  3.000
 P6N  H021  C02  C01   108.72  3.000
 P6N  C03   C02  C01   112.71  3.000
 P6N  H021  C02  C11   105.23  3.000
 P6N  C03   C02  C11   109.79  3.000
 P6N  C01   C02  C11   112.83  3.000
 P6N  H032  C03  H031  106.82  3.000
 P6N  H032  C03  C04   110.25  3.000
 P6N  H031  C03  C04   109.98  3.000
 P6N  H032  C03  C02   109.57  3.000
 P6N  H031  C03  C02   109.46  3.000
 P6N  C04   C03  C02   110.68  3.000
 P6N  H042  C04  H041  106.19  3.000
 P6N  H042  C04  C05   109.70  3.000
 P6N  H041  C04  C05   108.73  3.000
 P6N  H042  C04  C03   110.89  3.000
 P6N  H041  C04  C03   109.08  3.000
 P6N  C05   C04  C03   112.06  3.000
 P6N  C06   C05  C04   120.26  3.000
 P6N  C06   C05  C10   118.73  3.000
 P6N  C04   C05  C10   121.01  3.000
 P6N  H061  C06  C07   119.73  3.000
 P6N  H061  C06  C05   119.26  3.000
 P6N  C07   C06  C05   121.00  3.000
 P6N  H071  C07  C08   120.07  3.000
 P6N  H071  C07  C06   119.77  3.000
 P6N  C08   C07  C06   120.16  3.000
 P6N  H081  C08  C09   120.19  3.000
 P6N  H081  C08  C07   120.32  3.000
 P6N  C09   C08  C07   119.48  3.000
 P6N  H091  C09  C08   119.79  3.000
 P6N  H091  C09  C10   119.53  3.000
 P6N  C08   C09  C10   120.68  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
 P6N  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 P6N  CONST_02  C07   C06  C05  C10     0.00   0.0  0
 P6N  CONST_03  C08   C09  C10  C05     0.00   0.0  0
 P6N  CONST_04  C08   C07  C06  C05     0.00   0.0  0
 P6N  CONST_05  C09   C10  C05  C06     0.00   0.0  0
 P6N  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 P6N  CONST_07  H091  C09  C10  C11     0.00   0.0  0
 P6N  CONST_08  H081  C08  C09  C10   180.00   0.0  0
 P6N  CONST_09  H061  C06  C05  C10   180.00   0.0  0
 P6N  CONST_10  H071  C07  C06  C05   180.00   0.0  0
 P6N  Var_01    C03   C04  C05  C10    22.93  30.0  1
 P6N  Var_02    C09   C10  C11  C02  -172.33  30.0  1
 P6N  Var_03    C05   C04  C03  C02   -52.91  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
 P6N  chir_01  C02  C01  C11  C03  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
 P6N  plan-1  C11   0.020
 P6N  plan-1  C10   0.020
 P6N  plan-1  C02   0.020
 P6N  plan-1  O12   0.020
 P6N  plan-2  C11   0.020
 P6N  plan-2  C10   0.020
 P6N  plan-2  C04   0.020
 P6N  plan-2  C05   0.020
 P6N  plan-2  C06   0.020
 P6N  plan-2  C07   0.020
 P6N  plan-2  C08   0.020
 P6N  plan-2  C09   0.020
 P6N  plan-2  H061  0.020
 P6N  plan-2  H071  0.020
 P6N  plan-2  H081  0.020
 P6N  plan-2  H091  0.020

