# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 01:55:31 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 3-[(2S)-azetidin-2-ylmethoxy]-5-[(1S,2R)-2-(2-methoxyethyl)cyclopropyl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCC[C@H]1C[C@@H]1c2cncc(OC[C@@H]3CCN3)c2
#
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
 0VC  0VC  3-[(2S)-azetidin-2-ylmethoxy]-5-[(1S,2R)-2-(2-methoxyethyl)cyclopropyl]pyridine  ligand  41  19  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0VC
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
 0VC  C18  C  CH3   0  -0.396   7.7377   1.4967  -0.4162
 0VC  O17  O  O2    0  -0.488   6.3901   1.7537  -0.1188
 0VC  C16  C  CH2   0  -0.118   5.5637   0.6408  -0.3569
 0VC  C15  C  CH2   0  -0.479   4.1361   0.9852   0.0223
 0VC  C13  C  CH1   0  -0.225   3.2128  -0.1806  -0.2195
 0VC  C12  C  CH1   0  -0.395   1.9776  -0.3408   0.6285
 0VC  C14  C  CH2   0  -0.466   3.1355  -1.2954   0.7671
 0VC  C6   C  CR6   0   0.160   0.6903  -0.7665   0.0383
 0VC  C5   C  CR16  0  -0.162   0.6019  -1.7250  -0.9766
 0VC  N4   N  N     0  -0.382  -0.5417  -2.1048  -1.5167
 0VC  C3   C  CR16  0  -0.206  -1.6800  -1.5674  -1.0888
 0VC  C2   C  CR6   0   0.341  -1.7085  -0.6078  -0.0796
 0VC  C1   C  CR16  0  -0.333  -0.4974  -0.2087   0.4821
 0VC  O7   O  O2    0  -0.473  -2.8202  -0.0313   0.4025
 0VC  C39  C  CH2   0  -0.171  -4.0836  -0.4256  -0.1131
 0VC  C8   C  C     0  -0.096  -5.1379   0.3631   0.6163
 0VC  C9   C  C     0  -0.501  -6.5819   0.2277   0.1084
 0VC  C10  C  C     0  -0.274  -6.6503   1.7571   0.2416
 0VC  N11  N  N     0  -0.605  -5.1801   1.7971   0.2974
 0VC  H1   H  HCH3  0   0.202   7.8849   1.2371  -1.4716
 0VC  H2   H  HCH3  0   0.232   8.3111   2.3978  -0.2000
 0VC  H3   H  HCH3  0   0.202   8.1427   0.6758   0.1883
 0VC  H4   H  HCH2  0   0.194   5.6109   0.3429  -1.4154
 0VC  H5   H  HCH2  0   0.197   5.9031  -0.2271   0.2280
 0VC  H6   H  HCH2  0   0.232   4.0978   1.2689   1.0784
 0VC  H7   H  HCH2  0   0.239   3.7967   1.8505  -0.5542
 0VC  H8   H  HCH1  0   0.260   3.0956  -0.4621  -1.2626
 0VC  H9   H  HCH1  0   0.261   1.8716   0.3836   1.4296
 0VC  H10  H  HCH2  0   0.258   3.0069  -2.3073   0.4028
 0VC  H11  H  HCH2  0   0.260   3.7300  -1.2248   1.6708
 0VC  H12  H  HCR6  0   0.250   1.4952  -2.2037  -1.3656
 0VC  H13  H  HCR6  0   0.273  -2.5858  -1.9179  -1.5692
 0VC  H14  H  HCR6  0   0.270  -0.4957   0.5387   1.2675
 0VC  H15  H  HCH2  0   0.219  -4.1431  -0.2210  -1.1883
 0VC  H16  H  HCH2  0   0.228  -4.2457  -1.4990   0.0416
 0VC  H17  H  H     0   0.230  -5.0738   0.1558   1.6920
 0VC  H18  H  H     0   0.239  -6.6371  -0.1115  -0.9269
 0VC  H19  H  H     0   0.248  -7.2669  -0.3623   0.7128
 0VC  H20  H  H     0   0.218  -7.0926   2.3115  -0.5890
 0VC  H21  H  H     0   0.214  -7.1435   2.0700   1.1670
 0VC  H22  H  H     0   0.343  -4.7953   2.4034   1.0100

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
 0VC  N11  C8   single    1.470  0.020  1.470
 0VC  N11  C10  single    1.472  0.020  1.472
 0VC  C8   C39  single    1.505  0.020  1.505
 0VC  C8   C9   single    1.537  0.020  1.537
 0VC  C10  C9   single    1.537  0.020  1.537
 0VC  C39  O7   single    1.420  0.020  1.420
 0VC  O7   C2   single    1.342  0.020  1.342
 0VC  C2   C1   aromatic  1.393  0.020  1.393
 0VC  C2   C3   aromatic  1.393  0.020  1.393
 0VC  C14  C13  single    1.491  0.020  1.491
 0VC  C14  C12  single    1.507  0.020  1.507
 0VC  C1   C6   aromatic  1.385  0.020  1.385
 0VC  C3   N4   aromatic  1.330  0.020  1.330
 0VC  C13  C12  single    1.507  0.020  1.507
 0VC  C13  C15  single    1.507  0.020  1.507
 0VC  C6   C12  single    1.479  0.020  1.479
 0VC  C6   C5   aromatic  1.399  0.020  1.399
 0VC  N4   C5   aromatic  1.320  0.020  1.320
 0VC  C15  C16  single    1.517  0.020  1.517
 0VC  C16  O17  single    1.407  0.020  1.407
 0VC  O17  C18  single    1.404  0.020  1.404
 0VC  C18  H1   single    0.970  0.020  1.090
 0VC  C18  H2   single    0.970  0.020  1.090
 0VC  C18  H3   single    0.970  0.020  1.090
 0VC  C16  H4   single    0.970  0.020  1.090
 0VC  C16  H5   single    0.970  0.020  1.090
 0VC  C15  H6   single    0.970  0.020  1.090
 0VC  C15  H7   single    0.970  0.020  1.090
 0VC  C13  H8   single    0.970  0.020  1.090
 0VC  C12  H9   single    0.970  0.020  1.090
 0VC  C14  H10  single    0.970  0.020  1.090
 0VC  C14  H11  single    0.970  0.020  1.090
 0VC  C5   H12  single    0.930  0.020  1.080
 0VC  C3   H13  single    0.930  0.020  1.080
 0VC  C1   H14  single    0.930  0.020  1.080
 0VC  C39  H15  single    0.970  0.020  1.090
 0VC  C39  H16  single    0.970  0.020  1.090
 0VC  C8   H17  single    0.970  0.020  1.090
 0VC  C9   H18  single    0.970  0.020  1.090
 0VC  C9   H19  single    0.970  0.020  1.090
 0VC  C10  H20  single    0.970  0.020  1.090
 0VC  C10  H21  single    0.970  0.020  1.090
 0VC  N11  H22  single    0.890  0.020  1.040

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
 0VC  H3   C18  H2   108.37  3.000
 0VC  H3   C18  H1   107.67  3.000
 0VC  H2   C18  H1   108.42  3.000
 0VC  H3   C18  O17  112.01  3.000
 0VC  H2   C18  O17  108.16  3.000
 0VC  H1   C18  O17  112.09  3.000
 0VC  C16  O17  C18  112.54  3.000
 0VC  H5   C16  H4   106.54  3.000
 0VC  H5   C16  C15  109.67  3.000
 0VC  H4   C16  C15  110.02  3.000
 0VC  H5   C16  O17  110.66  3.000
 0VC  H4   C16  O17  110.59  3.000
 0VC  C15  C16  O17  109.33  3.000
 0VC  H7   C15  H6   107.03  3.000
 0VC  H7   C15  C13  109.72  3.000
 0VC  H6   C15  C13  109.52  3.000
 0VC  H7   C15  C16  109.87  3.000
 0VC  H6   C15  C16  109.46  3.000
 0VC  C13  C15  C16  111.16  3.000
 0VC  H8   C13  C14  115.85  3.000
 0VC  H8   C13  C12  115.10  3.000
 0VC  C14  C13  C12   60.37  3.000
 0VC  H8   C13  C15  114.87  3.000
 0VC  C12  C13  C15  119.62  3.000
 0VC  C14  C13  C15  120.28  3.000
 0VC  H9   C12  C6   113.68  3.000
 0VC  H9   C12  C14  115.46  3.000
 0VC  C6   C12  C14  121.55  3.000
 0VC  H9   C12  C13  115.13  3.000
 0VC  C6   C12  C13  121.31  3.000
 0VC  C14  C12  C13   59.29  3.000
 0VC  H11  C14  H10  113.98  3.000
 0VC  H11  C14  C12  117.18  3.000
 0VC  H10  C14  C12  118.01  3.000
 0VC  H11  C14  C13  118.34  3.000
 0VC  H10  C14  C13  118.83  3.000
 0VC  C12  C14  C13   60.35  3.000
 0VC  C1   C6   C5   117.01  3.000
 0VC  C5   C6   C12  122.81  3.000
 0VC  C1   C6   C12  120.18  3.000
 0VC  H12  C5   N4   116.06  3.000
 0VC  H12  C5   C6   120.67  3.000
 0VC  N4   C5   C6   123.27  3.000
 0VC  C3   N4   C5   119.58  3.000
 0VC  H13  C3   C2   121.80  3.000
 0VC  H13  C3   N4   116.24  3.000
 0VC  C2   C3   N4   121.95  3.000
 0VC  O7   C2   C1   116.88  3.000
 0VC  C1   C2   C3   118.14  3.000
 0VC  O7   C2   C3   124.98  3.000
 0VC  H14  C1   C2   119.40  3.000
 0VC  H14  C1   C6   120.55  3.000
 0VC  C2   C1   C6   120.05  3.000
 0VC  C39  O7   C2   119.15  3.000
 0VC  H16  C39  H15  108.24  3.000
 0VC  H16  C39  C8   109.93  3.000
 0VC  H15  C39  C8   109.85  3.000
 0VC  H16  C39  O7   110.61  3.000
 0VC  H15  C39  O7   110.65  3.000
 0VC  C8   C39  O7   107.55  3.000
 0VC  H17  C8   N11  113.50  3.000
 0VC  H17  C8   C9   111.23  3.000
 0VC  N11  C8   C9    89.27  3.000
 0VC  H17  C8   C39  109.58  3.000
 0VC  C9   C8   C39  116.86  3.000
 0VC  N11  C8   C39  115.23  3.000
 0VC  H19  C9   H18  109.08  3.000
 0VC  H19  C9   C10  117.63  3.000
 0VC  H18  C9   C10  112.92  3.000
 0VC  H19  C9   C8   117.13  3.000
 0VC  H18  C9   C8   112.87  3.000
 0VC  C10  C9   C8    85.73  3.000
 0VC  H21  C10  H20  108.39  3.000
 0VC  H21  C10  N11  114.23  3.000
 0VC  H20  C10  N11  114.80  3.000
 0VC  H21  C10  C9   112.21  3.000
 0VC  H20  C10  C9   117.22  3.000
 0VC  N11  C10  C9    89.19  3.000
 0VC  H22  N11  C10  115.02  3.000
 0VC  H22  N11  C8   114.90  3.000
 0VC  C10  N11  C8    90.59  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
 0VC  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 0VC  CONST_02  C3   N4   C5   C6      0.00   0.0  0
 0VC  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 0VC  CONST_04  C2   C3   N4   C5      0.00   0.0  0
 0VC  CONST_05  C1   C2   C3   N4      0.00   0.0  0
 0VC  CONST_06  C1   C6   C5   N4      0.00   0.0  0
 0VC  CONST_07  C2   C1   C6   C12   180.00   0.0  0
 0VC  CONST_08  N4   C5   C6   C12   180.00   0.0  0
 0VC  CONST_09  O7   C2   C1   C6    180.00   0.0  0
 0VC  CONST_10  O7   C2   C3   N4    180.00   0.0  0
 0VC  CONST_11  H14  C1   C6   C12     0.00   0.0  0
 0VC  CONST_12  H12  C5   C6   C12     0.00   0.0  0
 0VC  CONST_13  H13  C3   N4   C5    180.00   0.0  0
 0VC  Var_01    C6   C12  C14  C13   110.15  30.0  1
 0VC  Var_02    C1   C6   C12  C13  -141.64  30.0  3
 0VC  Var_03    C9   C10  N11  C8    -17.53  30.0  1
 0VC  Var_04    C12  C14  C13  C15   109.05  30.0  1
 0VC  Var_05    C14  C13  C15  C16    80.17  30.0  1
 0VC  Var_06    C8   C39  O7   C2    179.24  30.0  1
 0VC  Var_07    C13  C15  C16  O17   179.89  30.0  1
 0VC  Var_08    C15  C16  O17  C18   178.49  30.0  1
 0VC  Var_09    H1   C18  O17  C16    60.96  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
 0VC  chir_03  C8   N11  C39  C9   positiv
 0VC  chir_04  C13  C14  C12  C15  both
 0VC  chir_05  C12  C14  C13  C6   both

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
 0VC  plan-1  C12  0.020
 0VC  plan-1  C6   0.020
 0VC  plan-1  C5   0.020
 0VC  plan-1  N4   0.020
 0VC  plan-1  C3   0.020
 0VC  plan-1  C2   0.020
 0VC  plan-1  C1   0.020
 0VC  plan-1  O7   0.020
 0VC  plan-1  H12  0.020
 0VC  plan-1  H13  0.020
 0VC  plan-1  H14  0.020

