# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 18:53:02 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (5~{S})-1-methyl-5-pyridin-3-yl-pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H](CCC1=O)c2cccnc2
#
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
 U5H  U5H  "(5~{S})-1-methyl-5-pyridin-3-yl-pyrrolidin-2-one"
  ligand  25  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_U5H
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
 U5H  C02  C  CR5   0   0.533   3.9303  -4.6370  5.9410
 U5H  C04  C  CH3   0  -0.527   1.5615  -4.2933  5.4628
 U5H  C05  C  CR15  0  -0.117   2.5494  -6.5177  6.2121
 U5H  C06  C  CR6   0   0.028   1.3753  -6.8708  7.0824
 U5H  C07  C  CR16  0  -0.081   1.0842  -6.1475  8.2365
 U5H  C09  C  CR16  0  -0.073  -0.6944  -7.4706  8.7507
 U5H  C10  C  CR16  0  -0.313  -0.4984  -8.2581  7.6280
 U5H  C11  C  CR16  0  -0.200   0.5528  -7.9456  6.7790
 U5H  C12  C  CH2   0  -0.461   3.9059  -6.8414  6.8600
 U5H  C13  C  CH2   0  -0.587   4.8461  -5.7874  6.2918
 U5H  N03  N  NR5   0  -0.461   2.6596  -5.0909  5.9560
 U5H  N08  N  N     0  -0.398   0.0784  -6.4313  9.0517
 U5H  O01  O  O     0  -0.487   4.2593  -3.4991  5.6519
 U5H  H1   H  HCH3  0   0.253   0.6637  -4.9042  5.4121
 U5H  H2   H  HCH3  0   0.247   1.3558  -3.4501  6.1224
 U5H  H3   H  HCH3  0   0.247   1.7687  -3.9075  4.4639
 U5H  H4   H  HCR5  0   0.265   2.4499  -7.0601  5.2629
 U5H  H5   H  HCR6  0   0.260   1.6952  -5.2914  8.5084
 U5H  H6   H  HCR6  0   0.263  -1.5082  -7.6834  9.4349
 U5H  H7   H  HCR6  0   0.271  -1.1576  -9.0900  7.4212
 U5H  H8   H  HCR6  0   0.269   0.7296  -8.5322  5.8851
 U5H  H9   H  HCH2  0   0.255   3.8308  -6.7311  7.9430
 U5H  H10  H  HCH2  0   0.264   4.2132  -7.8643  6.6517
 U5H  H11  H  HCH2  0   0.274   5.3325  -6.1253  5.3719
 U5H  H12  H  HCH2  0   0.275   5.6322  -5.4785  6.9798

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
 U5H  C04  N03  single    1.444  0.020  1.444
 U5H  O01  C02  double    1.219  0.020  1.219
 U5H  N03  C02  single    1.349  0.020  1.349
 U5H  N03  C05  single    1.454  0.020  1.454
 U5H  C02  C13  single    1.512  0.020  1.512
 U5H  C05  C12  single    1.538  0.020  1.538
 U5H  C05  C06  single    1.504  0.020  1.504
 U5H  C13  C12  single    1.522  0.020  1.522
 U5H  C11  C06  aromatic  1.387  0.020  1.387
 U5H  C11  C10  aromatic  1.387  0.020  1.387
 U5H  C06  C07  aromatic  1.393  0.020  1.393
 U5H  C10  C09  aromatic  1.385  0.020  1.385
 U5H  C07  N08  aromatic  1.325  0.020  1.325
 U5H  C09  N08  aromatic  1.330  0.020  1.330
 U5H  C04  H1   single    0.970  0.020  1.090
 U5H  C04  H2   single    0.970  0.020  1.090
 U5H  C04  H3   single    0.970  0.020  1.090
 U5H  C05  H4   single    0.970  0.020  1.090
 U5H  C07  H5   single    0.930  0.020  1.080
 U5H  C09  H6   single    0.930  0.020  1.080
 U5H  C10  H7   single    0.930  0.020  1.080
 U5H  C11  H8   single    0.930  0.020  1.080
 U5H  C12  H9   single    0.970  0.020  1.090
 U5H  C12  H10  single    0.970  0.020  1.090
 U5H  C13  H11  single    0.970  0.020  1.090
 U5H  C13  H12  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
 U5H  O01  C02  N03  124.80  3.000
 U5H  N03  C02  C13  108.18  3.000
 U5H  O01  C02  C13  126.99  3.000
 U5H  H3   C04  H2   108.45  3.000
 U5H  H3   C04  H1   108.24  3.000
 U5H  H2   C04  H1   107.88  3.000
 U5H  H3   C04  N03  111.33  3.000
 U5H  H2   C04  N03  111.34  3.000
 U5H  H1   C04  N03  109.48  3.000
 U5H  H4   C05  N03  109.85  3.000
 U5H  H4   C05  C12  109.90  3.000
 U5H  N03  C05  C12  102.36  3.000
 U5H  H4   C05  C06  108.28  3.000
 U5H  C12  C05  C06  113.30  3.000
 U5H  N03  C05  C06  113.05  3.000
 U5H  C11  C06  C07  117.37  3.000
 U5H  C07  C06  C05  121.39  3.000
 U5H  C11  C06  C05  121.23  3.000
 U5H  H5   C07  N08  116.21  3.000
 U5H  H5   C07  C06  119.94  3.000
 U5H  N08  C07  C06  123.86  3.000
 U5H  H6   C09  N08  116.53  3.000
 U5H  H6   C09  C10  120.40  3.000
 U5H  N08  C09  C10  123.07  3.000
 U5H  H7   C10  C11  121.22  3.000
 U5H  H7   C10  C09  120.41  3.000
 U5H  C11  C10  C09  118.38  3.000
 U5H  H8   C11  C10  120.44  3.000
 U5H  H8   C11  C06  120.21  3.000
 U5H  C10  C11  C06  119.35  3.000
 U5H  H10  C12  H9   107.72  3.000
 U5H  H10  C12  C13  113.89  3.000
 U5H  H9   C12  C13  110.06  3.000
 U5H  H10  C12  C05  111.49  3.000
 U5H  H9   C12  C05  109.65  3.000
 U5H  C13  C12  C05  103.99  3.000
 U5H  H12  C13  H11  107.33  3.000
 U5H  H12  C13  C12  113.97  3.000
 U5H  H11  C13  C12  111.99  3.000
 U5H  H12  C13  C02  111.59  3.000
 U5H  H11  C13  C02  108.02  3.000
 U5H  C12  C13  C02  103.84  3.000
 U5H  C05  N03  C04  123.00  3.000
 U5H  C05  N03  C02  113.79  3.000
 U5H  C04  N03  C02  121.77  3.000
 U5H  C09  N08  C07  117.97  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
 U5H  CONST_01  C09  C10  C11  C06     0.00   0.0  0
 U5H  CONST_02  C09  N08  C07  C06     0.00   0.0  0
 U5H  CONST_03  C10  C11  C06  C07     0.00   0.0  0
 U5H  CONST_04  C10  C09  N08  C07     0.00   0.0  0
 U5H  CONST_05  N08  C07  C06  C11     0.00   0.0  0
 U5H  CONST_06  N08  C09  C10  C11     0.00   0.0  0
 U5H  CONST_07  C10  C11  C06  C05   180.00   0.0  0
 U5H  CONST_08  N08  C07  C06  C05   180.00   0.0  0
 U5H  CONST_09  C13  C02  N03  C05     0.00   0.0  0
 U5H  CONST_10  C13  C02  N03  C04   180.00   0.0  0
 U5H  CONST_11  O01  C02  N03  C05   180.00   0.0  0
 U5H  CONST_12  H8   C11  C06  C05     0.00   0.0  0
 U5H  CONST_13  H5   C07  C06  C05     0.00   0.0  0
 U5H  CONST_14  H7   C10  C11  C06   180.00   0.0  0
 U5H  CONST_15  H8   C11  C06  C07   180.00   0.0  0
 U5H  CONST_16  H6   C09  N08  C07   180.00   0.0  0
 U5H  CONST_17  H8   C11  C10  C09   180.00   0.0  0
 U5H  CONST_18  H5   C07  N08  C09   180.00   0.0  0
 U5H  CONST_19  H5   C07  C06  C11   180.00   0.0  0
 U5H  CONST_20  H6   C09  C10  C11   180.00   0.0  0
 U5H  CONST_21  H7   C10  C09  N08   180.00   0.0  0
 U5H  CONST_22  O01  C02  N03  C04     0.00   0.0  0
 U5H  Var_01    C05  C12  C13  C02    25.52  30.0  1
 U5H  Var_02    N03  C02  C13  C12   -14.47  30.0  1
 U5H  Var_03    O01  C02  C13  C12   167.55  30.0  1
 U5H  Var_04    H9   C12  C13  C02   -91.86  30.0  1
 U5H  Var_05    H10  C12  C13  C02   147.07  30.0  1
 U5H  Var_06    H11  C13  C12  C05   -90.78  30.0  1
 U5H  Var_07    H12  C13  C12  C05   147.14  30.0  1
 U5H  Var_08    H11  C13  C02  N03   104.59  30.0  1
 U5H  Var_09    H12  C13  C02  N03  -137.67  30.0  1
 U5H  Var_10    H1   C04  N03  C02   170.53  30.0  3
 U5H  Var_11    H2   C04  N03  C02   -70.26  30.0  3
 U5H  Var_12    H3   C04  N03  C02    50.89  30.0  3
 U5H  Var_13    H1   C04  N03  C05     5.07  30.0  3
 U5H  Var_14    H2   C04  N03  C05   124.28  30.0  3
 U5H  Var_15    H3   C04  N03  C05  -114.57  30.0  3
 U5H  Var_16    H11  C13  C02  O01   -73.39  30.0  1
 U5H  Var_17    H12  C13  C02  O01    44.36  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
 U5H  chir_01  C05  N03  C12  C06  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
 U5H  plan-1  C05  0.020
 U5H  plan-1  C06  0.020
 U5H  plan-1  C07  0.020
 U5H  plan-1  C09  0.020
 U5H  plan-1  C10  0.020
 U5H  plan-1  C11  0.020
 U5H  plan-1  N08  0.020
 U5H  plan-1  H5   0.020
 U5H  plan-1  H6   0.020
 U5H  plan-1  H7   0.020
 U5H  plan-1  H8   0.020
 U5H  plan-2  C02  0.020
 U5H  plan-2  C04  0.020
 U5H  plan-2  C05  0.020
 U5H  plan-2  C13  0.020
 U5H  plan-2  N03  0.020
 U5H  plan-2  O01  0.020

