# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:11:23 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
 4RR  4RR  (4R)-4-[3-(cyclopentyloxy)-4-methoxyphenyl]pyrrolidin-2-one  ligand  41  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4RR
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
 4RR  O3    O  O     0  -0.493   6.8707  -3.9105  8.0221
 4RR  C2    C  CR5   0   0.523   6.6526  -2.8220  7.5162
 4RR  C1    C  CH2   0  -0.611   5.5032  -2.4664  6.5943
 4RR  N4    N  NR15  0  -0.626   7.4027  -1.7158  7.6571
 4RR  C5    C  CH2   0  -0.234   6.9646  -0.5904  6.8629
 4RR  C6    C  CR15  0  -0.325   5.4906  -0.9377  6.5958
 4RR  C7    C  CR6   0   0.125   4.9007  -0.2670  5.3839
 4RR  C8    C  CR16  0  -0.449   3.9334  -0.9147  4.6097
 4RR  C9    C  CR6   0   0.360   3.3463  -0.2954  3.5168
 4RR  C16   C  CR6   0   0.274   3.7258   1.0197  3.1798
 4RR  C19   C  CR16  0  -0.371   4.6817   1.6631  3.9467
 4RR  C20   C  CR16  0  -0.331   5.2621   1.0245  5.0410
 4RR  O17   O  O2    0  -0.463   3.1101   1.5491  2.1039
 4RR  C18   C  CH3   0  -0.436   3.4484   2.8674  1.7296
 4RR  O10   O  O2    0  -0.476   2.4343  -0.8555  2.7028
 4RR  C11   C  CH1   0  -0.030   1.8862  -2.1342  3.0150
 4RR  C12   C  CH2   0  -0.453   1.0354  -2.5423  1.8228
 4RR  C13   C  CH2   0  -0.447  -0.2646  -1.7370  1.9740
 4RR  C14   C  CH2   0  -0.442  -0.3626  -1.3833  3.4762
 4RR  C15   C  CH2   0  -0.477   0.8582  -2.0380  4.1379
 4RR  H181  H  HCH3  0   0.225   3.2197   3.5895  2.5185
 4RR  H182  H  HCH3  0   0.258   2.8471   3.1061  0.8555
 4RR  H183  H  HCH3  0   0.225   4.5053   2.9613  1.4651
 4RR  H19   H  HCR6  0   0.279   4.9936   2.6715  3.7105
 4RR  H20   H  HCR6  0   0.249   6.0006   1.5642  5.6206
 4RR  H8    H  HCR6  0   0.277   3.6396  -1.9215  4.8738
 4RR  H11   H  HCH1  0   0.247   2.6889  -2.8521  3.2152
 4RR  H151  H  HCH2  0   0.250   1.2122  -1.4967  5.0167
 4RR  H152  H  HCH2  0   0.239   0.6205  -3.0534  4.4648
 4RR  H141  H  HCH2  0   0.231  -0.3371  -0.3022  3.6162
 4RR  H142  H  HCH2  0   0.232  -1.2922  -1.7362  3.9232
 4RR  H131  H  HCH2  0   0.231  -1.1266  -2.3088  1.6300
 4RR  H132  H  HCH2  0   0.231  -0.2299  -0.8318  1.3670
 4RR  H121  H  HCH2  0   0.238   0.8359  -3.6127  1.9062
 4RR  H122  H  HCH2  0   0.244   1.5413  -2.3830  0.8693
 4RR  H6    H  HCR5  0   0.279   4.9233  -0.6142  7.4761
 4RR  H51   H  HCH2  0   0.236   7.5330  -0.5167  5.9297
 4RR  H52   H  HCH2  0   0.256   7.0831   0.3457  7.4079
 4RR  HN4   H  HNR5  0   0.398   8.2888  -1.7278  8.1386
 4RR  H11A  H  HCH2  0   0.274   5.7320  -2.8668  5.6003
 4RR  H12   H  HCH2  0   0.279   4.5728  -2.9250  6.9270

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
 4RR  O3   C2    double    1.220  0.020  1.220
 4RR  C2   N4    single    1.344  0.020  1.344
 4RR  C2   C1    single    1.516  0.020  1.516
 4RR  C1   C6    single    1.529  0.020  1.529
 4RR  C1   H11A  single    0.970  0.020  1.090
 4RR  C1   H12   single    0.970  0.020  1.090
 4RR  N4   C5    single    1.446  0.020  1.446
 4RR  N4   HN4   single    0.860  0.020  1.020
 4RR  C5   C6    single    1.538  0.020  1.538
 4RR  C5   H51   single    0.970  0.020  1.090
 4RR  C5   H52   single    0.970  0.020  1.090
 4RR  C6   C7    single    1.506  0.020  1.506
 4RR  C6   H6    single    0.970  0.020  1.090
 4RR  C7   C20   aromatic  1.384  0.020  1.384
 4RR  C7   C8    aromatic  1.398  0.020  1.398
 4RR  C8   C9    aromatic  1.387  0.020  1.387
 4RR  C8   H8    single    0.930  0.020  1.080
 4RR  C9   C16   aromatic  1.410  0.020  1.410
 4RR  C9   O10   single    1.345  0.020  1.345
 4RR  C16  O17   single    1.348  0.020  1.348
 4RR  C16  C19   aromatic  1.384  0.020  1.384
 4RR  C19  C20   aromatic  1.394  0.020  1.394
 4RR  C19  H19   single    0.930  0.020  1.080
 4RR  C20  H20   single    0.930  0.020  1.080
 4RR  O17  C18   single    1.412  0.020  1.412
 4RR  C18  H181  single    0.970  0.020  1.090
 4RR  C18  H182  single    0.970  0.020  1.090
 4RR  C18  H183  single    0.970  0.020  1.090
 4RR  O10  C11   single    1.426  0.020  1.426
 4RR  C11  C15   single    1.525  0.020  1.525
 4RR  C11  C12   single    1.520  0.020  1.520
 4RR  C11  H11   single    0.970  0.020  1.090
 4RR  C12  C13   single    1.537  0.020  1.537
 4RR  C12  H121  single    0.970  0.020  1.090
 4RR  C12  H122  single    0.970  0.020  1.090
 4RR  C13  C14   single    1.546  0.020  1.546
 4RR  C13  H131  single    0.970  0.020  1.090
 4RR  C13  H132  single    0.970  0.020  1.090
 4RR  C14  C15   single    1.535  0.020  1.535
 4RR  C14  H141  single    0.970  0.020  1.090
 4RR  C14  H142  single    0.970  0.020  1.090
 4RR  C15  H151  single    0.970  0.020  1.090
 4RR  C15  H152  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
 4RR  N4    C2   C1    107.09  3.000
 4RR  C1    C2   O3    126.66  3.000
 4RR  N4    C2   O3    126.24  3.000
 4RR  H12   C1   H11A  107.55  3.000
 4RR  H12   C1   C6    114.43  3.000
 4RR  H11A  C1   C6    111.59  3.000
 4RR  H12   C1   C2    111.29  3.000
 4RR  H11A  C1   C2    107.92  3.000
 4RR  C6    C1   C2    103.90  3.000
 4RR  HN4   N4   C5    122.54  3.000
 4RR  HN4   N4   C2    122.05  3.000
 4RR  C5    N4   C2    114.46  3.000
 4RR  H52   C5   H51   108.17  3.000
 4RR  H52   C5   C6    112.66  3.000
 4RR  H51   C5   C6    111.39  3.000
 4RR  H52   C5   N4    111.17  3.000
 4RR  H51   C5   N4    111.30  3.000
 4RR  C6    C5   N4    102.13  3.000
 4RR  H6    C6   C7    108.19  3.000
 4RR  H6    C6   C5    106.85  3.000
 4RR  C7    C6   C5    114.50  3.000
 4RR  H6    C6   C1    107.47  3.000
 4RR  C7    C6   C1    116.61  3.000
 4RR  C5    C6   C1    102.60  3.000
 4RR  C20   C7   C8    118.41  3.000
 4RR  C8    C7   C6    120.69  3.000
 4RR  C20   C7   C6    120.85  3.000
 4RR  H8    C8   C9    119.55  3.000
 4RR  H8    C8   C7    118.95  3.000
 4RR  C9    C8   C7    121.50  3.000
 4RR  O10   C9   C16   115.25  3.000
 4RR  O10   C9   C8    125.33  3.000
 4RR  C16   C9   C8    119.41  3.000
 4RR  O17   C16  C19   125.11  3.000
 4RR  C19   C16  C9    119.15  3.000
 4RR  O17   C16  C9    115.74  3.000
 4RR  H19   C19  C20   118.59  3.000
 4RR  H19   C19  C16   120.76  3.000
 4RR  C20   C19  C16   120.64  3.000
 4RR  H20   C20  C19   118.41  3.000
 4RR  H20   C20  C7    120.70  3.000
 4RR  C19   C20  C7    120.88  3.000
 4RR  C18   O17  C16   117.97  3.000
 4RR  H183  C18  H182  108.73  3.000
 4RR  H183  C18  H181  108.66  3.000
 4RR  H182  C18  H181  108.62  3.000
 4RR  H183  C18  O17   112.08  3.000
 4RR  H182  C18  O17   106.60  3.000
 4RR  H181  C18  O17   112.04  3.000
 4RR  C11   O10  C9    120.12  3.000
 4RR  H11   C11  C15   113.62  3.000
 4RR  H11   C11  C12   112.18  3.000
 4RR  C15   C11  C12   102.54  3.000
 4RR  H11   C11  O10   110.25  3.000
 4RR  C12   C11  O10   106.50  3.000
 4RR  C15   C11  O10   111.32  3.000
 4RR  H122  C12  H121  107.13  3.000
 4RR  H122  C12  C13   113.69  3.000
 4RR  H121  C12  C13   110.58  3.000
 4RR  H122  C12  C11   112.75  3.000
 4RR  H121  C12  C11   107.78  3.000
 4RR  C13   C12  C11   104.81  3.000
 4RR  H132  C13  H131  106.55  3.000
 4RR  H132  C13  C14   110.67  3.000
 4RR  H131  C13  C14   112.11  3.000
 4RR  H132  C13  C12   110.69  3.000
 4RR  H131  C13  C12   111.29  3.000
 4RR  C14   C13  C12   105.61  3.000
 4RR  H142  C14  H141  106.75  3.000
 4RR  H142  C14  C15   111.30  3.000
 4RR  H141  C14  C15   110.42  3.000
 4RR  H142  C14  C13   112.23  3.000
 4RR  H141  C14  C13   110.48  3.000
 4RR  C15   C14  C13   105.71  3.000
 4RR  H152  C15  H151  106.89  3.000
 4RR  H152  C15  C14   110.62  3.000
 4RR  H151  C15  C14   113.18  3.000
 4RR  H152  C15  C11   107.95  3.000
 4RR  H151  C15  C11   113.93  3.000
 4RR  C14   C15  C11   104.21  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
 4RR  CONST_01  C16   C19  C20  C7     0.00   0.0  0
 4RR  CONST_02  C16   C9   C8   C7     0.00   0.0  0
 4RR  CONST_03  C19   C20  C7   C8     0.00   0.0  0
 4RR  CONST_04  C19   C16  C9   C8     0.00   0.0  0
 4RR  CONST_05  C20   C7   C8   C9     0.00   0.0  0
 4RR  CONST_06  C20   C19  C16  C9     0.00   0.0  0
 4RR  CONST_07  C19   C20  C7   C6   180.00   0.0  0
 4RR  CONST_08  C9    C8   C7   C6   180.00   0.0  0
 4RR  CONST_09  C5    N4   C2   C1     0.00   0.0  0
 4RR  CONST_10  O10   C9   C8   C7   180.00   0.0  0
 4RR  CONST_11  O17   C16  C9   C8   180.00   0.0  0
 4RR  CONST_12  O10   C9   C16  C19  180.00   0.0  0
 4RR  CONST_13  O17   C16  C19  C20  180.00   0.0  0
 4RR  CONST_14  C5    N4   C2   O3   180.00   0.0  0
 4RR  CONST_15  H20   C20  C7   C6     0.00   0.0  0
 4RR  CONST_16  H8    C8   C7   C6     0.00   0.0  0
 4RR  CONST_17  H19   C19  C20  C7   180.00   0.0  0
 4RR  CONST_18  HN4   N4   C2   C1   180.00   0.0  0
 4RR  Var_01    C6    C5   N4   C2    21.83  30.0  1
 4RR  Var_02    C6    C1   C2   N4   -16.60  30.0  1
 4RR  Var_03    C13   C14  C15  C11   26.00  30.0  1
 4RR  Var_04    C14   C13  C12  C11  -23.11  30.0  1
 4RR  Var_05    C15   C14  C13  C12   -1.85  30.0  1
 4RR  Var_06    H181  C18  O17  C16  -61.01  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
 4RR  chir_01  C6   C1   C5   C7   negativ
 4RR  chir_02  C11  O10  C15  C12  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
 4RR  plan-1  O3   0.020
 4RR  plan-1  C2   0.020
 4RR  plan-1  C1   0.020
 4RR  plan-1  N4   0.020
 4RR  plan-1  C5   0.020
 4RR  plan-1  HN4  0.020
 4RR  plan-2  C6   0.020
 4RR  plan-2  C7   0.020
 4RR  plan-2  C8   0.020
 4RR  plan-2  C9   0.020
 4RR  plan-2  C16  0.020
 4RR  plan-2  C19  0.020
 4RR  plan-2  C20  0.020
 4RR  plan-2  O17  0.020
 4RR  plan-2  O10  0.020
 4RR  plan-2  H19  0.020
 4RR  plan-2  H20  0.020
 4RR  plan-2  H8   0.020

