# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 01:09:18 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 3-oxo-N-[(3S)-2-oxopyrrolidin-3-yl]dodecanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)CC(=O)N[C@H]1CCNC1=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
 OHM  OHM  3-oxo-N-[(3S)-2-oxopyrrolidin-3-yl]dodecanamide  ligand  49  21  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OHM
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
 OHM  C21   C  CH3   0  -0.663   4.6491  3.4926  -9.1000
 OHM  C20   C  CH2   0  -0.419   4.5644  4.4471  -7.9169
 OHM  C19   C  CH2   0  -0.406   3.8399  3.8419  -6.7203
 OHM  C18   C  CH2   0  -0.411   3.7490  4.7867  -5.5288
 OHM  C17   C  CH2   0  -0.412   3.0322  4.1770  -4.3301
 OHM  C16   C  CH2   0  -0.413   2.9499  5.1217  -3.1377
 OHM  C15   C  CH2   0  -0.415   2.2356  4.5148  -1.9365
 OHM  C14   C  CH2   0  -0.417   2.1724  5.4660  -0.7476
 OHM  C13   C  CH2   0  -0.559   1.4510  4.8501   0.4398
 OHM  C11   C  C     0   0.415   1.3778  5.7249   1.6603
 OHM  O12   O  O     0  -0.394   1.8188  6.8493   1.6955
 OHM  C10   C  CH2   0  -0.698   0.7192  5.0971   2.8737
 OHM  C8    C  C     0   0.549   0.4813  6.1221   3.9581
 OHM  O9    O  O     0  -0.490  -0.4537  6.9061   3.9085
 OHM  N7    N  NH1   0  -0.637   1.3764  6.1194   4.9570
 OHM  C1    C  CH1   0  -0.194   1.3500  7.0953   6.0099
 OHM  C5    C  CH2   0  -0.472   0.2523  6.9449   7.0613
 OHM  C4    C  CH2   0  -0.264   0.8800  7.5857   8.3004
 OHM  N3    N  NH1   0  -0.625   2.2929  7.3324   8.0961
 OHM  C2    C  C     0   0.535   2.6303  7.0313   6.8381
 OHM  O6    O  O     0  -0.483   3.7398  6.7616   6.4111
 OHM  H211  H  HCH3  0   0.216   3.6550  3.2113  -9.4525
 OHM  H212  H  HCH3  0   0.215   5.1722  2.5742  -8.8256
 OHM  H213  H  HCH3  0   0.226   5.1835  3.9374  -9.9402
 OHM  H201  H  HCH2  0   0.210   4.0544  5.3670  -8.2198
 OHM  H202  H  HCH2  0   0.210   5.5725  4.7464  -7.6141
 OHM  H191  H  HCH2  0   0.205   4.3512  2.9215  -6.4163
 OHM  H192  H  HCH2  0   0.206   2.8310  3.5405  -7.0235
 OHM  H181  H  HCH2  0   0.206   3.2332  5.7051  -5.8310
 OHM  H182  H  HCH2  0   0.206   4.7581  5.0907  -5.2296
 OHM  H171  H  HCH2  0   0.207   3.5462  3.2570  -4.0303
 OHM  H172  H  HCH2  0   0.207   2.0212  3.8769  -4.6268
 OHM  H161  H  HCH2  0   0.208   3.9614  5.4215  -2.8425
 OHM  H162  H  HCH2  0   0.208   2.4362  6.0419  -3.4373
 OHM  H151  H  HCH2  0   0.212   1.2207  4.2234  -2.2276
 OHM  H152  H  HCH2  0   0.212   2.7441  3.5910  -1.6397
 OHM  H141  H  HCH2  0   0.223   3.1876  5.7481  -0.4558
 OHM  H142  H  HCH2  0   0.224   1.6690  6.3891  -1.0476
 OHM  H131  H  HCH2  0   0.272   0.4243  4.5765   0.1703
 OHM  H132  H  HCH2  0   0.269   1.9227  3.9052   0.7338
 OHM  H101  H  HCH2  0   0.304  -0.2326  4.6513   2.5763
 OHM  H102  H  HCH2  0   0.304   1.3507  4.2680   3.2084
 OHM  HN7   H  HNH1  0   0.404   2.1565  5.4818   4.9214
 OHM  H1    H  HCH1  0   0.293   1.3047  8.1040   5.5781
 OHM  H51   H  HCH2  0   0.254   0.0656  5.8845   7.2422
 OHM  H52   H  HCH2  0   0.265  -0.6836  7.4163   6.7724
 OHM  H41   H  HCH2  0   0.244   0.6755  8.6583   8.3508
 OHM  H42   H  HCH2  0   0.260   0.5337  7.1323   9.2277
 OHM  HN3   H  HNH1  0   0.405   2.9829  7.4692   8.8185

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
 OHM  C21  C20   single  1.523  0.020  1.523
 OHM  C21  H211  single  0.970  0.020  1.090
 OHM  C21  H212  single  0.970  0.020  1.090
 OHM  C21  H213  single  0.970  0.020  1.090
 OHM  C20  C19   single  1.524  0.020  1.524
 OHM  C20  H201  single  0.970  0.020  1.090
 OHM  C20  H202  single  0.970  0.020  1.090
 OHM  C19  C18   single  1.523  0.020  1.523
 OHM  C19  H191  single  0.970  0.020  1.090
 OHM  C19  H192  single  0.970  0.020  1.090
 OHM  C18  C17   single  1.524  0.020  1.524
 OHM  C18  H181  single  0.970  0.020  1.090
 OHM  C18  H182  single  0.970  0.020  1.090
 OHM  C17  C16   single  1.523  0.020  1.523
 OHM  C17  H171  single  0.970  0.020  1.090
 OHM  C17  H172  single  0.970  0.020  1.090
 OHM  C16  C15   single  1.524  0.020  1.524
 OHM  C16  H161  single  0.970  0.020  1.090
 OHM  C16  H162  single  0.970  0.020  1.090
 OHM  C15  C14   single  1.524  0.020  1.524
 OHM  C15  H151  single  0.970  0.020  1.090
 OHM  C15  H152  single  0.970  0.020  1.090
 OHM  C14  C13   single  1.520  0.020  1.520
 OHM  C14  H141  single  0.970  0.020  1.090
 OHM  C14  H142  single  0.970  0.020  1.090
 OHM  C13  C11   single  1.503  0.020  1.503
 OHM  C13  H131  single  0.970  0.020  1.090
 OHM  C13  H132  single  0.970  0.020  1.090
 OHM  C11  C10   single  1.517  0.020  1.517
 OHM  C11  O12   double  1.208  0.020  1.208
 OHM  C10  C8    single  1.511  0.020  1.511
 OHM  C10  H101  single  0.970  0.020  1.090
 OHM  C10  H102  single  0.970  0.020  1.090
 OHM  C8   O9    double  1.221  0.020  1.221
 OHM  C8   N7    single  1.341  0.020  1.341
 OHM  N7   C1    single  1.436  0.020  1.436
 OHM  N7   HN7   single  0.860  0.020  1.020
 OHM  C1   C2    single  1.526  0.020  1.526
 OHM  C1   C5    single  1.527  0.020  1.527
 OHM  C1   H1    single  0.970  0.020  1.090
 OHM  C5   C4    single  1.530  0.020  1.530
 OHM  C5   H51   single  0.970  0.020  1.090
 OHM  C5   H52   single  0.970  0.020  1.090
 OHM  C4   N3    single  1.450  0.020  1.450
 OHM  C4   H41   single  0.970  0.020  1.090
 OHM  C4   H42   single  0.970  0.020  1.090
 OHM  N3   C2    single  1.337  0.020  1.337
 OHM  N3   HN3   single  0.860  0.020  1.020
 OHM  C2   O6    double  1.219  0.020  1.219

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
 OHM  H213  C21  H212  107.57  3.000
 OHM  H213  C21  H211  107.61  3.000
 OHM  H212  C21  H211  107.50  3.000
 OHM  H213  C21  C20   111.73  3.000
 OHM  H212  C21  C20   111.02  3.000
 OHM  H211  C21  C20   111.21  3.000
 OHM  H202  C20  H201  106.02  3.000
 OHM  H202  C20  C19   109.23  3.000
 OHM  H201  C20  C19   109.24  3.000
 OHM  H202  C20  C21   109.58  3.000
 OHM  H201  C20  C21   109.74  3.000
 OHM  C19   C20  C21   112.80  3.000
 OHM  H192  C19  H191  105.99  3.000
 OHM  H192  C19  C18   109.39  3.000
 OHM  H191  C19  C18   109.37  3.000
 OHM  H192  C19  C20   109.25  3.000
 OHM  H191  C19  C20   109.24  3.000
 OHM  C18   C19  C20   113.33  3.000
 OHM  H182  C18  H181  106.04  3.000
 OHM  H182  C18  C17   109.23  3.000
 OHM  H181  C18  C17   109.32  3.000
 OHM  H182  C18  C19   109.31  3.000
 OHM  H181  C18  C19   109.41  3.000
 OHM  C17   C18  C19   113.27  3.000
 OHM  H172  C17  H171  106.08  3.000
 OHM  H172  C17  C16   109.39  3.000
 OHM  H171  C17  C16   109.38  3.000
 OHM  H172  C17  C18   109.31  3.000
 OHM  H171  C17  C18   109.30  3.000
 OHM  C16   C17  C18   113.14  3.000
 OHM  H162  C16  H161  106.07  3.000
 OHM  H162  C16  C15   109.28  3.000
 OHM  H161  C16  C15   109.23  3.000
 OHM  H162  C16  C17   109.40  3.000
 OHM  H161  C16  C17   109.31  3.000
 OHM  C15   C16  C17   113.29  3.000
 OHM  H152  C15  H151  106.13  3.000
 OHM  H152  C15  C14   109.53  3.000
 OHM  H151  C15  C14   109.57  3.000
 OHM  H152  C15  C16   109.38  3.000
 OHM  H151  C15  C16   109.32  3.000
 OHM  C14   C15  C16   112.70  3.000
 OHM  H142  C14  H141  106.43  3.000
 OHM  H142  C14  C13   109.75  3.000
 OHM  H141  C14  C13   109.69  3.000
 OHM  H142  C14  C15   109.39  3.000
 OHM  H141  C14  C15   109.32  3.000
 OHM  C13   C14  C15   112.10  3.000
 OHM  H132  C13  H131  104.71  3.000
 OHM  H132  C13  C11   107.74  3.000
 OHM  H131  C13  C11   107.41  3.000
 OHM  H132  C13  C14   110.77  3.000
 OHM  H131  C13  C14   110.71  3.000
 OHM  C11   C13  C14   114.93  3.000
 OHM  C10   C11  O12   121.36  3.000
 OHM  O12   C11  C13   123.19  3.000
 OHM  C10   C11  C13   115.45  3.000
 OHM  H102  C10  H101  106.07  3.000
 OHM  H102  C10  C8    112.66  3.000
 OHM  H101  C10  C8    109.58  3.000
 OHM  H102  C10  C11   107.92  3.000
 OHM  H101  C10  C11   109.24  3.000
 OHM  C8    C10  C11   111.21  3.000
 OHM  N7    C8   O9    122.86  3.000
 OHM  N7    C8   C10   115.34  3.000
 OHM  O9    C8   C10   121.80  3.000
 OHM  HN7   N7   C1    118.04  3.000
 OHM  HN7   N7   C8    119.43  3.000
 OHM  C1    N7   C8    122.17  3.000
 OHM  H1    C1   C2    106.65  3.000
 OHM  H1    C1   C5    109.36  3.000
 OHM  C2    C1   C5    103.02  3.000
 OHM  H1    C1   N7    109.68  3.000
 OHM  C5    C1   N7    116.81  3.000
 OHM  C2    C1   N7    110.73  3.000
 OHM  H52   C5   H51   108.54  3.000
 OHM  H52   C5   C4    112.76  3.000
 OHM  H51   C5   C4    110.05  3.000
 OHM  H52   C5   C1    113.15  3.000
 OHM  H51   C5   C1    109.43  3.000
 OHM  C4    C5   C1    102.80  3.000
 OHM  H42   C4   H41   108.05  3.000
 OHM  H42   C4   N3    110.92  3.000
 OHM  H41   C4   N3    111.12  3.000
 OHM  H42   C4   C5    112.64  3.000
 OHM  H41   C4   C5    111.82  3.000
 OHM  N3    C4   C5    102.27  3.000
 OHM  HN3   N3   C2    122.14  3.000
 OHM  HN3   N3   C4    122.83  3.000
 OHM  C2    N3   C4    114.70  3.000
 OHM  O6    C2   N3    127.53  3.000
 OHM  O6    C2   C1    125.64  3.000
 OHM  N3    C2   C1    106.83  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
 OHM  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 OHM  CONST_02  O6    C2   N3   C4    180.00   0.0  0
 OHM  CONST_03  HN3   N3   C2   C1    180.00   0.0  0
 OHM  CONST_04  C1    N7   C8   C10   180.00   0.0  0
 OHM  CONST_05  C1    N7   C8   O9      0.00   0.0  0
 OHM  CONST_06  HN7   N7   C8   C10     0.00   0.0  0
 OHM  Var_01    N3    C4   C5   C1    -29.77  30.0  1
 OHM  Var_02    C2    N3   C4   C5     18.50  30.0  1
 OHM  Var_03    C18   C19  C20  C21   179.96  30.0  3
 OHM  Var_04    C17   C18  C19  C20  -179.63  30.0  3
 OHM  Var_05    C16   C17  C18  C19   179.68  30.0  3
 OHM  Var_06    C15   C16  C17  C18  -179.92  30.0  3
 OHM  Var_07    C14   C15  C16  C17   179.46  30.0  3
 OHM  Var_08    C13   C14  C15  C16   179.69  30.0  3
 OHM  Var_09    C11   C13  C14  C15   178.74  30.0  3
 OHM  Var_10    C10   C11  C13  C14  -177.18  30.0  3
 OHM  Var_11    C8    C10  C11  C13  -170.21  30.0  3
 OHM  Var_12    O9    C8   C10  C11    78.62  30.0  3
 OHM  Var_13    H211  C21  C20  C19    60.60  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
 OHM  chir_01  C1  N7  C2  C5  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
 OHM  plan-1  C10  0.020
 OHM  plan-1  C8   0.020
 OHM  plan-1  O9   0.020
 OHM  plan-1  N7   0.020
 OHM  plan-1  C1   0.020
 OHM  plan-1  HN7  0.020
 OHM  plan-2  C13  0.020
 OHM  plan-2  C11  0.020
 OHM  plan-2  O12  0.020
 OHM  plan-2  C10  0.020
 OHM  plan-3  C1   0.020
 OHM  plan-3  C4   0.020
 OHM  plan-3  N3   0.020
 OHM  plan-3  C2   0.020
 OHM  plan-3  O6   0.020
 OHM  plan-3  HN3  0.020

