# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:44:07 2021
#   Inital geometry file: a 76 line input string
#   Ligand name: (3-methoxyphenyl)(pyrrolidin-1-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)C(=O)N2CCCC2
#
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
 R9G  R9G  (3-methoxyphenyl)(pyrrolidin-1-yl)methanone  ligand  30  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R9G
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
 R9G  C4   C  CR16  0  -0.289  17.1309   0.3991  49.6249
 R9G  C5   C  CR6   0  -0.033  16.8696   1.2351  50.7097
 R9G  C6   C  CR16  0  -0.374  15.8622   2.1835  50.6310
 R9G  C7   C  C     0   0.511  17.5884   1.0654  52.0117
 R9G  C8   C  CH2   0  -0.259  19.6954   0.8309  53.2046
 R9G  C9   C  CH2   0  -0.488  21.1423   0.8737  52.7279
 R9G  C10  C  CH2   0  -0.472  21.0844   1.8391  51.5488
 R9G  C11  C  CH2   0  -0.268  19.7808   1.4517  50.8620
 R9G  O1   O  O     0  -0.499  16.9543   0.9362  53.0541
 R9G  N    N  NT    0  -0.467  18.9273   1.0434  51.9794
 R9G  C3   C  CR16  0  -0.233  16.3803   0.5361  48.4702
 R9G  C2   C  CR16  0  -0.382  15.3846   1.5008  48.3691
 R9G  C1   C  CR6   0   0.399  15.1254   2.3340  49.4553
 R9G  O    O  O2    0  -0.471  14.1853   3.2966  49.4664
 R9G  C    C  CH3   0  -0.437  13.3993   3.4872  48.3067
 R9G  H1   H  HCR6  0   0.262  17.8961  -0.3629  49.6859
 R9G  H2   H  HCR6  0   0.264  15.6426   2.8235  51.4773
 R9G  H4   H  HCH2  0   0.248  19.4285  -0.1168  53.6732
 R9G  H5   H  HCH2  0   0.240  21.4599  -0.1153  52.3905
 R9G  H6   H  HCH2  0   0.253  21.8223   1.1927  53.5168
 R9G  H7   H  HCH2  0   0.253  21.9382   1.7589  50.8774
 R9G  H8   H  HCH2  0   0.240  21.0314   2.8699  51.9060
 R9G  H9   H  HCH2  0   0.259  19.3337   2.2728  50.3027
 R9G  H10  H  HCH2  0   0.241  19.9446   0.6234  50.1681
 R9G  H11  H  HCR6  0   0.263  16.5662  -0.1171  47.6276
 R9G  H12  H  HCR6  0   0.283  14.8245   1.5811  47.4474
 R9G  H13  H  HCH3  0   0.260  12.7068   4.2944  48.5320
 R9G  H14  H  HCH3  0   0.229  14.0065   3.7753  47.4443
 R9G  H15  H  HCH3  0   0.229  12.8253   2.5927  48.0510
 R9G  H3   H  HCH2  0   0.238  19.4938   1.6281  53.9258

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
 R9G  C2   C3   aromatic  1.390  0.020  1.390
 R9G  C2   C1   aromatic  1.393  0.020  1.393
 R9G  O    C1   single    1.346  0.020  1.346
 R9G  O    C    single    1.414  0.020  1.414
 R9G  C3   C4   aromatic  1.384  0.020  1.384
 R9G  C1   C6   aromatic  1.396  0.020  1.396
 R9G  C4   C5   aromatic  1.394  0.020  1.394
 R9G  C6   C5   aromatic  1.386  0.020  1.386
 R9G  C5   C7   single    1.497  0.020  1.497
 R9G  C11  C10  single    1.523  0.020  1.523
 R9G  C11  N    single    1.464  0.020  1.464
 R9G  C10  C9   single    1.525  0.020  1.525
 R9G  C7   N    single    1.339  0.020  1.339
 R9G  C7   O1   double    1.227  0.020  1.227
 R9G  N    C8   single    1.462  0.020  1.462
 R9G  C9   C8   single    1.524  0.020  1.524
 R9G  C4   H1   single    0.930  0.020  1.080
 R9G  C6   H2   single    0.930  0.020  1.080
 R9G  C8   H3   single    0.970  0.020  1.090
 R9G  C8   H4   single    0.970  0.020  1.090
 R9G  C9   H5   single    0.970  0.020  1.090
 R9G  C9   H6   single    0.970  0.020  1.090
 R9G  C10  H7   single    0.970  0.020  1.090
 R9G  C10  H8   single    0.970  0.020  1.090
 R9G  C11  H9   single    0.970  0.020  1.090
 R9G  C11  H10  single    0.970  0.020  1.090
 R9G  C3   H11  single    0.930  0.020  1.080
 R9G  C2   H12  single    0.930  0.020  1.080
 R9G  C    H13  single    0.970  0.020  1.090
 R9G  C    H14  single    0.970  0.020  1.090
 R9G  C    H15  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
 R9G  H1   C4   C3   120.03  3.000
 R9G  H1   C4   C5   120.74  3.000
 R9G  C3   C4   C5   119.22  3.000
 R9G  C7   C5   C6   118.43  3.000
 R9G  C7   C5   C4   121.25  3.000
 R9G  C6   C5   C4   120.16  3.000
 R9G  H2   C6   C1   119.16  3.000
 R9G  H2   C6   C5   120.48  3.000
 R9G  C1   C6   C5   120.35  3.000
 R9G  N    C7   O1   122.37  3.000
 R9G  O1   C7   C5   120.18  3.000
 R9G  N    C7   C5   117.44  3.000
 R9G  H4   C8   H3   107.76  3.000
 R9G  H4   C8   N    110.98  3.000
 R9G  H3   C8   N    110.48  3.000
 R9G  H4   C8   C9   113.03  3.000
 R9G  H3   C8   C9   111.14  3.000
 R9G  N    C8   C9   103.45  3.000
 R9G  H6   C9   H5   107.90  3.000
 R9G  H6   C9   C10  113.47  3.000
 R9G  H5   C9   C10  110.21  3.000
 R9G  H6   C9   C8   111.99  3.000
 R9G  H5   C9   C8   110.32  3.000
 R9G  C10  C9   C8   102.92  3.000
 R9G  H8   C10  H7   108.01  3.000
 R9G  H8   C10  C11  110.23  3.000
 R9G  H7   C10  C11  111.97  3.000
 R9G  H8   C10  C9   110.27  3.000
 R9G  H7   C10  C9   113.60  3.000
 R9G  C11  C10  C9   102.72  3.000
 R9G  H10  C11  H9   107.87  3.000
 R9G  H10  C11  N    111.13  3.000
 R9G  H9   C11  N    111.27  3.000
 R9G  H10  C11  C10  110.53  3.000
 R9G  H9   C11  C10  113.02  3.000
 R9G  N    C11  C10  103.04  3.000
 R9G  C11  N    C8   111.96  3.000
 R9G  C8   N    C7   120.49  3.000
 R9G  C11  N    C7   126.62  3.000
 R9G  H11  C3   C2   119.04  3.000
 R9G  H11  C3   C4   119.78  3.000
 R9G  C2   C3   C4   121.19  3.000
 R9G  H12  C2   C1   121.58  3.000
 R9G  H12  C2   C3   118.98  3.000
 R9G  C1   C2   C3   119.44  3.000
 R9G  O    C1   C2   124.35  3.000
 R9G  O    C1   C6   116.04  3.000
 R9G  C2   C1   C6   119.61  3.000
 R9G  C    O    C1   118.56  3.000
 R9G  H15  C    H14  108.83  3.000
 R9G  H15  C    H13  108.76  3.000
 R9G  H14  C    H13  108.76  3.000
 R9G  H15  C    O    111.93  3.000
 R9G  H14  C    O    111.95  3.000
 R9G  H13  C    O    106.51  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
 R9G  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 R9G  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 R9G  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 R9G  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 R9G  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 R9G  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 R9G  CONST_07  O    C1   C6   C5   180.00   0.0  0
 R9G  CONST_08  C3   C4   C5   C7   180.00   0.0  0
 R9G  CONST_09  C1   C6   C5   C7   180.00   0.0  0
 R9G  CONST_10  O    C1   C2   C3   180.00   0.0  0
 R9G  CONST_11  C11  N    C7   C5     0.00   0.0  0
 R9G  CONST_12  C8   N    C7   C5   180.00   0.0  0
 R9G  CONST_13  H12  C2   C3   C4   180.00   0.0  0
 R9G  CONST_14  H2   C6   C5   C4   180.00   0.0  0
 R9G  CONST_15  H11  C3   C4   C5   180.00   0.0  0
 R9G  CONST_16  H1   C4   C5   C6   180.00   0.0  0
 R9G  CONST_17  O1   C7   N    C8     0.00   0.0  0
 R9G  CONST_18  O1   C7   N    C11  180.00   0.0  0
 R9G  Var_01    C10  C11  N    C8   -14.45  30.0  1
 R9G  Var_02    C11  C10  C9   C8   -40.06  30.0  1
 R9G  Var_03    N    C11  C10  C9    33.31  30.0  1
 R9G  Var_04    C11  N    C8   C9   -10.47  30.0  1
 R9G  Var_05    N    C8   C9   C10   31.04  30.0  1
 R9G  Var_06    N    C7   C5   C4    53.16  30.0  2
 R9G  Var_07    H13  C    O    C1   179.43  30.0  3

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
 R9G  plan-1  C4   0.020
 R9G  plan-1  C5   0.020
 R9G  plan-1  C6   0.020
 R9G  plan-1  C7   0.020
 R9G  plan-1  C3   0.020
 R9G  plan-1  C2   0.020
 R9G  plan-1  C1   0.020
 R9G  plan-1  O    0.020
 R9G  plan-1  H1   0.020
 R9G  plan-1  H2   0.020
 R9G  plan-1  H11  0.020
 R9G  plan-1  H12  0.020
 R9G  plan-2  C5   0.020
 R9G  plan-2  C7   0.020
 R9G  plan-2  C8   0.020
 R9G  plan-2  C11  0.020
 R9G  plan-2  O1   0.020
 R9G  plan-2  N    0.020

