# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:24:54 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (4R)-4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC2CCCC2)[C@@H]3CNC(=O)C3
#
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
 ROL  ROL  (4R)-4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one  ligand  41  20  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ROL
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
 ROL  C5    C  CR6   0   0.192   0.2816  -0.1455  -1.3137
 ROL  C6    C  CR16  0  -0.459  -0.2128  -0.2433  -0.0106
 ROL  C7    C  CR6   0   0.341   0.6236  -0.1546   1.0918
 ROL  C8    C  CR6   0   0.278   2.0049   0.0427   0.8932
 ROL  C9    C  CR16  0  -0.368   2.4964   0.1392  -0.3987
 ROL  C10   C  CR16  0  -0.338   1.6408   0.0447  -1.4938
 ROL  C3    C  CH1   0  -0.398  -0.6667  -0.2533  -2.4757
 ROL  C2    C  CH2   0  -0.567  -0.6693   0.9246  -3.4550
 ROL  C1    C  C     0   0.510  -1.1145   0.3113  -4.7675
 ROL  O1    O  O     0  -0.495  -1.5021   0.9094  -5.7581
 ROL  N1    N  NH1   0  -0.622  -0.9817  -1.0212  -4.6478
 ROL  C4    C  CH2   0  -0.226  -0.4034  -1.4569  -3.3962
 ROL  O3    O  O2    0  -0.483   0.2364  -0.2536   2.3768
 ROL  C11   C  CH1   0   0.027  -1.1356  -0.4699   2.6862
 ROL  C15   C  CH2   0  -0.472  -1.2494  -0.8708   4.1720
 ROL  C14   C  CH2   0  -0.446  -2.1179   0.2012   4.8388
 ROL  C13   C  CH2   0  -0.448  -2.9827   0.7237   3.6949
 ROL  C12   C  CH2   0  -0.482  -2.0010   0.7917   2.5284
 ROL  O2    O  O2    0  -0.465   2.7504   0.1206   2.0133
 ROL  C16   C  CH3   0  -0.436   4.1465   0.2791   1.8723
 ROL  H61   H  HCR6  0   0.272  -1.2763  -0.3934   0.1215
 ROL  H91   H  HCR6  0   0.280   3.5531   0.2888  -0.5754
 ROL  H101  H  HCR6  0   0.247   2.0618   0.1245  -2.4889
 ROL  H31   H  HCH1  0   0.277  -1.6819  -0.3600  -2.0841
 ROL  H21   H  HCH2  0   0.280  -1.3206   1.7429  -3.1498
 ROL  H22   H  HCH2  0   0.274   0.3325   1.3422  -3.5976
 ROL  H1    H  HNH1  0   0.398  -1.1159  -1.6443  -5.4291
 ROL  H41   H  HCH2  0   0.238   0.6673  -1.6570  -3.5016
 ROL  H42   H  HCH2  0   0.257  -0.8807  -2.3654  -3.0299
 ROL  H111  H  HCH1  0   0.236  -1.5183  -1.2817   2.0579
 ROL  H151  H  HCH2  0   0.240  -1.7310  -1.8466   4.2468
 ROL  H152  H  HCH2  0   0.247  -0.2659  -0.9698   4.6332
 ROL  H141  H  HCH2  0   0.235  -2.6984  -0.1910   5.6745
 ROL  H142  H  HCH2  0   0.224  -1.4961   1.0110   5.2289
 ROL  H131  H  HCH2  0   0.224  -3.7852   0.0141   3.4743
 ROL  H132  H  HCH2  0   0.237  -3.4487   1.6868   3.9068
 ROL  H121  H  HCH2  0   0.238  -1.3639   1.6747   2.6350
 ROL  H122  H  HCH2  0   0.243  -2.4936   0.8605   1.5580
 ROL  H161  H  HCH3  0   0.258   4.5599   0.2915   2.8779
 ROL  H162  H  HCH3  0   0.226   4.5977  -0.5471   1.3159
 ROL  H163  H  HCH3  0   0.226   4.4053   1.2183   1.3751

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
 ROL  C5   C6    aromatic  1.397  0.020  1.397
 ROL  C5   C10   aromatic  1.384  0.020  1.384
 ROL  C5   C3    single    1.504  0.020  1.504
 ROL  C6   C7    aromatic  1.387  0.020  1.387
 ROL  C6   H61   single    0.930  0.020  1.080
 ROL  C7   C8    aromatic  1.409  0.020  1.409
 ROL  C7   O3    single    1.346  0.020  1.346
 ROL  C8   C9    aromatic  1.386  0.020  1.386
 ROL  C8   O2    single    1.348  0.020  1.348
 ROL  C9   C10   aromatic  1.393  0.020  1.393
 ROL  C9   H91   single    0.930  0.020  1.080
 ROL  C10  H101  single    0.930  0.020  1.080
 ROL  C3   C2    single    1.532  0.020  1.532
 ROL  C3   C4    single    1.538  0.020  1.538
 ROL  C3   H31   single    0.970  0.020  1.090
 ROL  C2   C1    single    1.516  0.020  1.516
 ROL  C2   H21   single    0.970  0.020  1.090
 ROL  C2   H22   single    0.970  0.020  1.090
 ROL  C1   O1    double    1.220  0.020  1.220
 ROL  C1   N1    single    1.344  0.020  1.344
 ROL  N1   C4    single    1.446  0.020  1.446
 ROL  N1   H1    single    0.860  0.020  1.020
 ROL  C4   H41   single    0.970  0.020  1.090
 ROL  C4   H42   single    0.970  0.020  1.090
 ROL  O3   C11   single    1.423  0.020  1.423
 ROL  C11  C15   single    1.543  0.020  1.543
 ROL  C11  C12   single    1.538  0.020  1.538
 ROL  C11  H111  single    0.970  0.020  1.090
 ROL  C15  C14   single    1.532  0.020  1.532
 ROL  C15  H151  single    0.970  0.020  1.090
 ROL  C15  H152  single    0.970  0.020  1.090
 ROL  C14  C13   single    1.526  0.020  1.526
 ROL  C14  H141  single    0.970  0.020  1.090
 ROL  C14  H142  single    0.970  0.020  1.090
 ROL  C13  C12   single    1.526  0.020  1.526
 ROL  C13  H131  single    0.970  0.020  1.090
 ROL  C13  H132  single    0.970  0.020  1.090
 ROL  C12  H121  single    0.970  0.020  1.090
 ROL  C12  H122  single    0.970  0.020  1.090
 ROL  O2   C16   single    1.412  0.020  1.412
 ROL  C16  H161  single    0.970  0.020  1.090
 ROL  C16  H162  single    0.970  0.020  1.090
 ROL  C16  H163  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
 ROL  C3    C5   C10   121.91  3.000
 ROL  C3    C5   C6    119.51  3.000
 ROL  C10   C5   C6    118.58  3.000
 ROL  H61   C6   C7    120.31  3.000
 ROL  H61   C6   C5    118.12  3.000
 ROL  C7    C6   C5    121.58  3.000
 ROL  O3    C7   C8    115.27  3.000
 ROL  O3    C7   C6    125.51  3.000
 ROL  C8    C7   C6    119.21  3.000
 ROL  O2    C8   C9    125.08  3.000
 ROL  O2    C8   C7    115.66  3.000
 ROL  C9    C8   C7    119.26  3.000
 ROL  H91   C9   C10   118.75  3.000
 ROL  H91   C9   C8    120.56  3.000
 ROL  C10   C9   C8    120.69  3.000
 ROL  H101  C10  C9    118.58  3.000
 ROL  H101  C10  C5    120.74  3.000
 ROL  C9    C10  C5    120.68  3.000
 ROL  H31   C3   C4    107.28  3.000
 ROL  H31   C3   C2    107.60  3.000
 ROL  C4    C3   C2    102.68  3.000
 ROL  H31   C3   C5    108.41  3.000
 ROL  C4    C3   C5    114.24  3.000
 ROL  C2    C3   C5    116.10  3.000
 ROL  H22   C2   H21   107.29  3.000
 ROL  H22   C2   C1    108.08  3.000
 ROL  H21   C2   C1    111.77  3.000
 ROL  H22   C2   C3    112.02  3.000
 ROL  H21   C2   C3    113.55  3.000
 ROL  C1    C2   C3    104.06  3.000
 ROL  N1    C1   O1    126.11  3.000
 ROL  N1    C1   C2    107.15  3.000
 ROL  O1    C1   C2    126.73  3.000
 ROL  H1    N1   C4    122.53  3.000
 ROL  H1    N1   C1    122.02  3.000
 ROL  C4    N1   C1    114.54  3.000
 ROL  H42   C4   H41   107.97  3.000
 ROL  H42   C4   N1    111.53  3.000
 ROL  H41   C4   N1    111.28  3.000
 ROL  H42   C4   C3    112.11  3.000
 ROL  H41   C4   C3    111.61  3.000
 ROL  N1    C4   C3    102.34  3.000
 ROL  C11   O3   C7    119.75  3.000
 ROL  H111  C11  C12   110.63  3.000
 ROL  H111  C11  C15   109.51  3.000
 ROL  C12   C11  C15   105.69  3.000
 ROL  H111  C11  O3    108.95  3.000
 ROL  C12   C11  O3    113.30  3.000
 ROL  C15   C11  O3    108.66  3.000
 ROL  H152  C15  H151  106.74  3.000
 ROL  H152  C15  C14   112.99  3.000
 ROL  H151  C15  C14   110.23  3.000
 ROL  H152  C15  C11   111.35  3.000
 ROL  H151  C15  C11   109.33  3.000
 ROL  C14   C15  C11   106.20  3.000
 ROL  H142  C14  H141  107.20  3.000
 ROL  H142  C14  C13   109.65  3.000
 ROL  H141  C14  C13   113.32  3.000
 ROL  H142  C14  C15   110.56  3.000
 ROL  H141  C14  C15   112.55  3.000
 ROL  C13   C14  C15   103.57  3.000
 ROL  H132  C13  H131  107.37  3.000
 ROL  H132  C13  C12   112.58  3.000
 ROL  H131  C13  C12   110.28  3.000
 ROL  H132  C13  C14   113.50  3.000
 ROL  H131  C13  C14   110.18  3.000
 ROL  C12   C13  C14   102.92  3.000
 ROL  H122  C12  H121  107.38  3.000
 ROL  H122  C12  C13   113.11  3.000
 ROL  H121  C12  C13   109.64  3.000
 ROL  H122  C12  C11   113.41  3.000
 ROL  H121  C12  C11   108.93  3.000
 ROL  C13   C12  C11   104.30  3.000
 ROL  C16   O2   C8    118.05  3.000
 ROL  H163  C16  H162  108.65  3.000
 ROL  H163  C16  H161  108.71  3.000
 ROL  H162  C16  H161  108.80  3.000
 ROL  H163  C16  O2    112.07  3.000
 ROL  H162  C16  O2    111.96  3.000
 ROL  H161  C16  O2    106.54  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
 ROL  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 ROL  CONST_02  C8    C9   C10  C5      0.00   0.0  0
 ROL  CONST_03  C9    C10  C5   C6      0.00   0.0  0
 ROL  CONST_04  C9    C8   C7   C6      0.00   0.0  0
 ROL  CONST_05  C10   C5   C6   C7      0.00   0.0  0
 ROL  CONST_06  C10   C9   C8   C7      0.00   0.0  0
 ROL  CONST_07  C3    C5   C6   C7    180.00   0.0  0
 ROL  CONST_08  C3    C5   C10  C9    180.00   0.0  0
 ROL  CONST_09  C4    N1   C1   C2      0.00   0.0  0
 ROL  CONST_10  O3    C7   C6   C5    180.00   0.0  0
 ROL  CONST_11  O2    C8   C7   C6    180.00   0.0  0
 ROL  CONST_12  O3    C7   C8   C9    180.00   0.0  0
 ROL  CONST_13  O2    C8   C9   C10   180.00   0.0  0
 ROL  CONST_14  C4    N1   C1   O1    180.00   0.0  0
 ROL  CONST_15  H91   C9   C10  C5    180.00   0.0  0
 ROL  CONST_16  H101  C10  C5   C6    180.00   0.0  0
 ROL  CONST_17  H61   C6   C7   C8    180.00   0.0  0
 ROL  CONST_18  H1    N1   C1   C2    180.00   0.0  0
 ROL  Var_01    N1    C1   C2   C3    -16.02  30.0  1
 ROL  Var_02    C1    N1   C4   C3     21.29  30.0  1
 ROL  Var_03    C13   C14  C15  C11    26.66  30.0  1
 ROL  Var_04    C14   C13  C12  C11    39.21  30.0  1
 ROL  Var_05    C12   C13  C14  C15   -40.69  30.0  1
 ROL  Var_06    H161  C16  O2   C8   -178.43  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
 ROL  chir_01  C3   C5  C2   C4   negativ
 ROL  chir_02  C11  O3  C12  C15  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
 ROL  plan-1  C2    0.020
 ROL  plan-1  C1    0.020
 ROL  plan-1  O1    0.020
 ROL  plan-1  N1    0.020
 ROL  plan-1  C4    0.020
 ROL  plan-1  H1    0.020
 ROL  plan-2  C5    0.020
 ROL  plan-2  C6    0.020
 ROL  plan-2  C7    0.020
 ROL  plan-2  C8    0.020
 ROL  plan-2  C9    0.020
 ROL  plan-2  C10   0.020
 ROL  plan-2  C3    0.020
 ROL  plan-2  O3    0.020
 ROL  plan-2  O2    0.020
 ROL  plan-2  H61   0.020
 ROL  plan-2  H91   0.020
 ROL  plan-2  H101  0.020

