# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 01:55:05 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (2S)-N-(5-methylpyridin-2-yl)oxolane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(NC(=O)[C@@H]2CCCO2)nc1
#
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
 LQV  LQV  "(2S)-N-(5-methylpyridin-2-yl)oxolane-2-carboxamide"
  ligand  29  15  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LQV
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
 LQV  N1   N  NH1   0  -0.708  48.0408  28.8220  115.8557
 LQV  C4   C  CR16  0  -0.362  49.3462  27.2518  114.4652
 LQV  C5   C  CR6   0   0.477  48.2290  28.0540  114.7076
 LQV  C6   C  C     0   0.502  48.8326  28.9470  116.9535
 LQV  C7   C  CR15  0  -0.058  48.3294  30.0015  117.9319
 LQV  C8   C  CH2   0  -0.507  48.7933  31.4063  117.4840
 LQV  C10  C  CH2   0  -0.169  49.7796  30.8063  119.5379
 LQV  C2   C  CR6   0   0.008  48.3536  26.6517  112.3461
 LQV  C3   C  CR16  0  -0.175  49.3903  26.5562  113.2716
 LQV  O1   O  O     0  -0.445  49.8608  28.3285  117.1368
 LQV  C9   C  CH2   0  -0.481  49.2724  32.0273  118.7924
 LQV  O2   O  O     0  -0.485  48.8594  29.7757  119.2114
 LQV  N2   N  N     0  -0.444  47.2325  28.1582  113.8405
 LQV  C11  C  CR16  0  -0.106  47.2982  27.4787  112.7032
 LQV  H1   H  HNH1  0   0.409  47.1820  29.3552  115.8373
 LQV  H2   H  HCR6  0   0.286  50.1504  27.1705  115.1769
 LQV  H3   H  HCR5  0   0.264  47.2353  29.9568  117.9918
 LQV  H4   H  HCH2  0   0.265  47.9902  31.9639  117.0056
 LQV  H5   H  HCH2  0   0.255  49.6195  31.3422  116.7726
 LQV  H6   H  HCH2  0   0.208  50.7941  30.5444  119.2139
 LQV  H7   H  HCH2  0   0.233  49.7906  30.9278  120.6217
 LQV  H8   H  HCH3  0   0.248  49.2108  26.2367  110.4196
 LQV  H9   H  HCH3  0   0.248  48.4878  24.8390  111.1976
 LQV  H10  H  HCH3  0   0.246  47.4587  26.0745  110.4788
 LQV  H11  H  HCR6  0   0.264  50.2474  25.9277  113.0599
 LQV  H12  H  HCH2  0   0.252  50.0440  32.7817  118.6426
 LQV  H13  H  HCH2  0   0.243  48.4441  32.4897  119.3322
 LQV  H14  H  HCR6  0   0.256  46.4550  27.5991  112.0297
 LQV  C1   C  CH3   0  -0.724  48.3763  25.9130  111.0434

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
 LQV  C1   C2   single    1.498  0.020  1.498
 LQV  C2   C11  aromatic  1.388  0.020  1.388
 LQV  C2   C3   aromatic  1.393  0.020  1.393
 LQV  C11  N2   aromatic  1.327  0.020  1.327
 LQV  C3   C4   aromatic  1.382  0.020  1.382
 LQV  N2   C5   aromatic  1.325  0.020  1.325
 LQV  C4   C5   aromatic  1.397  0.020  1.397
 LQV  C5   N1   single    1.394  0.020  1.394
 LQV  N1   C6   single    1.359  0.020  1.359
 LQV  C6   O1   double    1.214  0.020  1.214
 LQV  C6   C7   single    1.524  0.020  1.524
 LQV  C8   C9   single    1.525  0.020  1.525
 LQV  C8   C7   single    1.546  0.020  1.546
 LQV  C9   C10  single    1.518  0.020  1.518
 LQV  C7   O2   single    1.403  0.020  1.403
 LQV  C10  O2   single    1.420  0.020  1.420
 LQV  N1   H1   single    0.860  0.020  1.020
 LQV  C4   H2   single    0.930  0.020  1.080
 LQV  C7   H3   single    0.970  0.020  1.090
 LQV  C8   H4   single    0.970  0.020  1.090
 LQV  C8   H5   single    0.970  0.020  1.090
 LQV  C10  H6   single    0.970  0.020  1.090
 LQV  C10  H7   single    0.970  0.020  1.090
 LQV  C1   H8   single    0.970  0.020  1.090
 LQV  C1   H9   single    0.970  0.020  1.090
 LQV  C1   H10  single    0.970  0.020  1.090
 LQV  C3   H11  single    0.930  0.020  1.080
 LQV  C9   H12  single    0.970  0.020  1.090
 LQV  C9   H13  single    0.970  0.020  1.090
 LQV  C11  H14  single    0.930  0.020  1.080

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
 LQV  H1   N1   C6   117.45  3.000
 LQV  H1   N1   C5   112.97  3.000
 LQV  C6   N1   C5   129.58  3.000
 LQV  H2   C4   C3   120.59  3.000
 LQV  H2   C4   C5   121.74  3.000
 LQV  C3   C4   C5   117.68  3.000
 LQV  N2   C5   C4   122.22  3.000
 LQV  C4   C5   N1   124.57  3.000
 LQV  N2   C5   N1   113.21  3.000
 LQV  O1   C6   C7   122.37  3.000
 LQV  C7   C6   N1   112.94  3.000
 LQV  O1   C6   N1   124.65  3.000
 LQV  H3   C7   O2   108.70  3.000
 LQV  H3   C7   C8   110.63  3.000
 LQV  O2   C7   C8   107.28  3.000
 LQV  H3   C7   C6   109.65  3.000
 LQV  O2   C7   C6   110.45  3.000
 LQV  C8   C7   C6   110.10  3.000
 LQV  H5   C8   H4   107.57  3.000
 LQV  H5   C8   C9   110.19  3.000
 LQV  H4   C8   C9   113.59  3.000
 LQV  H5   C8   C7   111.25  3.000
 LQV  H4   C8   C7   111.81  3.000
 LQV  C9   C8   C7   102.46  3.000
 LQV  H7   C10  H6   108.11  3.000
 LQV  H7   C10  O2   108.42  3.000
 LQV  H6   C10  O2   111.00  3.000
 LQV  H7   C10  C9   113.69  3.000
 LQV  H6   C10  C9   110.86  3.000
 LQV  O2   C10  C9   104.74  3.000
 LQV  C11  C2   C3   115.84  3.000
 LQV  C3   C2   C1   122.19  3.000
 LQV  C11  C2   C1   121.96  3.000
 LQV  H11  C3   C2   119.90  3.000
 LQV  H11  C3   C4   119.06  3.000
 LQV  C2   C3   C4   121.03  3.000
 LQV  H13  C9   H12  108.19  3.000
 LQV  H13  C9   C10  110.58  3.000
 LQV  H12  C9   C10  112.83  3.000
 LQV  H13  C9   C8   111.00  3.000
 LQV  H12  C9   C8   112.73  3.000
 LQV  C10  C9   C8   101.46  3.000
 LQV  C10  O2   C7   109.74  3.000
 LQV  C11  N2   C5   118.92  3.000
 LQV  H14  C11  N2   115.88  3.000
 LQV  H14  C11  C2   119.81  3.000
 LQV  N2   C11  C2   124.31  3.000
 LQV  H10  C1   H9   107.77  3.000
 LQV  H10  C1   H8   107.70  3.000
 LQV  H9   C1   H8   107.15  3.000
 LQV  H10  C1   C2   111.40  3.000
 LQV  H9   C1   C2   111.36  3.000
 LQV  H8   C1   C2   111.26  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
 LQV  CONST_01  C11  C2   C3   C4      0.00   0.0  0
 LQV  CONST_02  C11  N2   C5   C4      0.00   0.0  0
 LQV  CONST_03  C2   C11  N2   C5      0.00   0.0  0
 LQV  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 LQV  CONST_05  N2   C11  C2   C3      0.00   0.0  0
 LQV  CONST_06  N2   C5   C4   C3      0.00   0.0  0
 LQV  CONST_07  C11  N2   C5   N1    180.00   0.0  0
 LQV  CONST_08  C3   C4   C5   N1    180.00   0.0  0
 LQV  CONST_09  C1   C2   C3   C4    180.00   0.0  0
 LQV  CONST_10  N2   C11  C2   C1    180.00   0.0  0
 LQV  CONST_11  H14  C11  N2   C5    180.00   0.0  0
 LQV  CONST_12  H11  C3   C4   C5    180.00   0.0  0
 LQV  CONST_13  H2   C4   C3   C2    180.00   0.0  0
 LQV  CONST_14  H14  C11  C2   C3    180.00   0.0  0
 LQV  CONST_15  H2   C4   C5   N2    180.00   0.0  0
 LQV  CONST_16  H11  C3   C2   C11   180.00   0.0  0
 LQV  CONST_17  C7   C6   N1   C5    180.00   0.0  0
 LQV  CONST_18  C6   N1   C5   C4      0.00   0.0  0
 LQV  CONST_19  N2   C5   N1   C6    180.00   0.0  0
 LQV  CONST_20  H1   N1   C5   C4    180.00   0.0  0
 LQV  CONST_21  H1   N1   C5   N2      0.00   0.0  0
 LQV  CONST_22  O1   C6   N1   C5      0.00   0.0  0
 LQV  CONST_23  H1   N1   C6   C7      0.00   0.0  0
 LQV  CONST_24  H1   N1   C6   O1    180.00   0.0  0
 LQV  Var_01    C10  C9   C8   C7     31.50  30.0  1
 LQV  Var_02    C9   C10  O2   C7     29.86  30.0  1
 LQV  Var_03    O2   C10  C9   C8    -38.00  30.0  1
 LQV  Var_04    H12  C9   C8   C7    152.43  30.0  1
 LQV  Var_05    H13  C9   C8   C7    -86.01  30.0  1
 LQV  Var_06    H6   C10  O2   C7    -89.83  30.0  1
 LQV  Var_07    H7   C10  O2   C7    151.56  30.0  1
 LQV  Var_08    H6   C10  C9   C8     81.79  30.0  1
 LQV  Var_09    H7   C10  C9   C8   -156.18  30.0  1
 LQV  Var_10    H4   C8   C9   C10   152.27  30.0  1
 LQV  Var_11    H5   C8   C9   C10   -86.97  30.0  1
 LQV  Var_12    H12  C9   C10  O2   -158.86  30.0  1
 LQV  Var_13    H13  C9   C10  O2     79.82  30.0  1
 LQV  Var_14    H8   C1   C2   C3    -62.66  30.0  2
 LQV  Var_15    H9   C1   C2   C3     56.80  30.0  2
 LQV  Var_16    H10  C1   C2   C3    177.15  30.0  2
 LQV  Var_17    H8   C1   C2   C11   117.10  30.0  2
 LQV  Var_18    H9   C1   C2   C11  -123.44  30.0  2
 LQV  Var_19    H10  C1   C2   C11    -3.09  30.0  2

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
 LQV  chir_01  C7  C6  C8  O2  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
 LQV  plan-1  N1   0.020
 LQV  plan-1  C4   0.020
 LQV  plan-1  C5   0.020
 LQV  plan-1  C2   0.020
 LQV  plan-1  C3   0.020
 LQV  plan-1  N2   0.020
 LQV  plan-1  C11  0.020
 LQV  plan-1  H2   0.020
 LQV  plan-1  H11  0.020
 LQV  plan-1  H14  0.020
 LQV  plan-1  C1   0.020
 LQV  plan-2  N1   0.020
 LQV  plan-2  C5   0.020
 LQV  plan-2  C6   0.020
 LQV  plan-2  C7   0.020
 LQV  plan-2  O1   0.020
 LQV  plan-2  H1   0.020

