# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 06:43:17 2021
#   Inital geometry file: a 106 line input string
#   Ligand name: (2R)-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}oxane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1cnnc1c2cccc(NC(=O)[C@H]3CCCCO3)n2
#
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
 V3S  V3S  (2R)-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}oxane-2-carboxamide  ligand  44  23  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V3S
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
 V3S  C5   C  CR15  0   0.071   3.5634   9.2468  20.9569
 V3S  C8   C  CR5   0   0.429   3.1926   7.4161  21.9989
 V3S  C10  C  CR16  0  -0.317   3.3377   5.1126  22.8759
 V3S  C13  C  CR6   0   0.498   1.5350   5.8264  24.7963
 V3S  C15  C  C     0   0.506   0.0428   5.7349  26.7771
 V3S  C17  C  CH1   0  -0.034  -0.8564   6.6417  27.6027
 V3S  C20  C  CH2   0  -0.456  -1.3549   9.1191  28.9609
 V3S  C21  C  CH2   0  -0.180  -1.9196   8.7503  27.6018
 V3S  C2   C  CH1   0  -0.119   2.4850   9.5802  23.1957
 V3S  C3   C  CH3   0  -0.644   1.0126   9.8449  22.9237
 V3S  N4   N  NR5   0  -0.463   3.0581   8.7659  22.1128
 V3S  N6   N  N     0  -0.324   3.9837   8.2771  20.1941
 V3S  N7   N  N     0  -0.330   3.7513   7.1255  20.8506
 V3S  C9   C  CR6   0   0.201   2.8001   6.3919  22.9707
 V3S  C11  C  CR16  0  -0.147   2.9207   4.1739  23.8046
 V3S  C12  C  CR16  0  -0.365   2.0074   4.5137  24.7882
 V3S  O16  O  O     0  -0.463   0.2186   4.5770  27.1068
 V3S  C18  C  CH2   0  -0.458  -0.2298   6.8861  28.9763
 V3S  C19  C  CH2   0  -0.455  -1.0916   7.8572  29.7751
 V3S  O22  O  O2    0  -0.507  -1.0733   7.8459  26.9103
 V3S  N23  N  N     0  -0.484   1.9206   6.7274  23.9039
 V3S  H1   H  HCR5  0   0.304   3.6130  10.2958  20.7142
 V3S  H2   H  HCR6  0   0.273   4.0561   4.8675  22.1077
 V3S  H3   H  HCH1  0   0.249  -1.8080   6.1047  27.7381
 V3S  H4   H  HCH2  0   0.228  -0.4260   9.6831  28.8344
 V3S  H5   H  HCH2  0   0.241  -2.0612   9.7751  29.4742
 V3S  H6   H  HCH2  0   0.244  -2.0220   9.6254  26.9600
 V3S  H7   H  HCH2  0   0.207  -2.9169   8.3045  27.7211
 V3S  H8   H  HCH3  0   0.256   2.9067  11.3820  24.2606
 V3S  H9   H  HCH3  0   0.251   4.3386  10.6661  23.5259
 V3S  H10  H  HCH3  0   0.234   3.1647  11.5453  22.5316
 V3S  H11  H  HCH1  0   0.278   2.5750   8.9852  24.1002
 V3S  H12  H  HCH3  0   0.239   0.5746  10.3852  23.7628
 V3S  H13  H  HCH3  0   0.229   0.8813  10.4519  22.0265
 V3S  H14  H  HCH3  0   0.244   0.4623   8.9136  22.7991
 V3S  H15  H  HCR6  0   0.280   3.3125   3.1662  23.7688
 V3S  H16  H  HCR6  0   0.293   1.6808   3.7891  25.5147
 V3S  H17  H  HNH1  0   0.411   0.3815   7.3062  25.5593
 V3S  H18  H  HCH2  0   0.253  -0.1243   5.9362  29.5017
 V3S  H19  H  HCH2  0   0.237   0.7747   7.3012  28.8449
 V3S  H20  H  HCH2  0   0.246  -0.6026   8.1011  30.7195
 V3S  H21  H  HCH2  0   0.226  -2.0436   7.3787  30.0268
 V3S  N14  N  NH1   0  -0.712   0.6255   6.3369  25.7139
 V3S  C1   C  CH3   0  -0.674   3.2775  10.8651  23.3763

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
 V3S  N6   N7   aromatic  1.346  0.020  1.346
 V3S  N6   C5   aromatic  1.303  0.020  1.303
 V3S  N7   C8   aromatic  1.310  0.020  1.310
 V3S  C5   N4   aromatic  1.350  0.020  1.350
 V3S  C8   N4   aromatic  1.361  0.020  1.361
 V3S  C8   C9   single    1.465  0.020  1.465
 V3S  N4   C2   single    1.471  0.020  1.471
 V3S  C10  C9   aromatic  1.391  0.020  1.391
 V3S  C10  C11  aromatic  1.385  0.020  1.385
 V3S  C9   N23  aromatic  1.326  0.020  1.326
 V3S  C3   C2   single    1.520  0.020  1.520
 V3S  C2   C1   single    1.520  0.020  1.520
 V3S  N23  C13  aromatic  1.325  0.020  1.325
 V3S  C11  C12  aromatic  1.385  0.020  1.385
 V3S  C13  C12  aromatic  1.395  0.020  1.395
 V3S  C13  N14  single    1.389  0.020  1.389
 V3S  N14  C15  single    1.354  0.020  1.354
 V3S  C15  O16  double    1.217  0.020  1.217
 V3S  C15  C17  single    1.521  0.020  1.521
 V3S  O22  C21  single    1.418  0.020  1.418
 V3S  O22  C17  single    1.406  0.020  1.406
 V3S  C21  C20  single    1.517  0.020  1.517
 V3S  C17  C18  single    1.529  0.020  1.529
 V3S  C20  C19  single    1.525  0.020  1.525
 V3S  C18  C19  single    1.524  0.020  1.524
 V3S  C5   H1   single    0.930  0.020  1.080
 V3S  C10  H2   single    0.930  0.020  1.080
 V3S  C17  H3   single    0.970  0.020  1.090
 V3S  C20  H4   single    0.970  0.020  1.090
 V3S  C20  H5   single    0.970  0.020  1.090
 V3S  C21  H6   single    0.970  0.020  1.090
 V3S  C21  H7   single    0.970  0.020  1.090
 V3S  C1   H8   single    0.970  0.020  1.090
 V3S  C1   H9   single    0.970  0.020  1.090
 V3S  C1   H10  single    0.970  0.020  1.090
 V3S  C2   H11  single    0.970  0.020  1.090
 V3S  C3   H12  single    0.970  0.020  1.090
 V3S  C3   H13  single    0.970  0.020  1.090
 V3S  C3   H14  single    0.970  0.020  1.090
 V3S  C11  H15  single    0.930  0.020  1.080
 V3S  C12  H16  single    0.930  0.020  1.080
 V3S  N14  H17  single    0.860  0.020  1.020
 V3S  C18  H18  single    0.970  0.020  1.090
 V3S  C18  H19  single    0.970  0.020  1.090
 V3S  C19  H20  single    0.970  0.020  1.090
 V3S  C19  H21  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
 V3S  H1   C5   N6   125.28  3.000
 V3S  H1   C5   N4   123.83  3.000
 V3S  N6   C5   N4   110.90  3.000
 V3S  C9   C8   N7   122.73  3.000
 V3S  C9   C8   N4   127.67  3.000
 V3S  N7   C8   N4   109.60  3.000
 V3S  H2   C10  C11  121.57  3.000
 V3S  H2   C10  C9   120.95  3.000
 V3S  C11  C10  C9   117.48  3.000
 V3S  N23  C13  N14  112.67  3.000
 V3S  N14  C13  C12  124.84  3.000
 V3S  N23  C13  C12  122.50  3.000
 V3S  O16  C15  N14  125.02  3.000
 V3S  O16  C15  C17  120.38  3.000
 V3S  N14  C15  C17  114.57  3.000
 V3S  H3   C17  O22  110.18  3.000
 V3S  H3   C17  C18  108.76  3.000
 V3S  O22  C17  C18  111.63  3.000
 V3S  H3   C17  C15  106.68  3.000
 V3S  C18  C17  C15  109.91  3.000
 V3S  O22  C17  C15  109.55  3.000
 V3S  H5   C20  H4   107.08  3.000
 V3S  H5   C20  C19  110.97  3.000
 V3S  H4   C20  C19  109.99  3.000
 V3S  H5   C20  C21  109.05  3.000
 V3S  H4   C20  C21  109.74  3.000
 V3S  C19  C20  C21  109.96  3.000
 V3S  H7   C21  H6   107.71  3.000
 V3S  H7   C21  O22  109.62  3.000
 V3S  H6   C21  O22  106.31  3.000
 V3S  H7   C21  C20  109.82  3.000
 V3S  H6   C21  C20  111.54  3.000
 V3S  O22  C21  C20  111.69  3.000
 V3S  H11  C2   N4   106.10  3.000
 V3S  H11  C2   C3   108.93  3.000
 V3S  N4   C2   C3   109.99  3.000
 V3S  H11  C2   C1   108.72  3.000
 V3S  C3   C2   C1   112.27  3.000
 V3S  N4   C2   C1   110.62  3.000
 V3S  H14  C3   H13  108.72  3.000
 V3S  H14  C3   H12  108.00  3.000
 V3S  H13  C3   H12  107.99  3.000
 V3S  H14  C3   C2   111.16  3.000
 V3S  H13  C3   C2   111.13  3.000
 V3S  H12  C3   C2   109.74  3.000
 V3S  C2   N4   C8   130.46  3.000
 V3S  C2   N4   C5   125.37  3.000
 V3S  C8   N4   C5   104.16  3.000
 V3S  N7   N6   C5   107.19  3.000
 V3S  N6   N7   C8   108.15  3.000
 V3S  N23  C9   C10  122.49  3.000
 V3S  N23  C9   C8   117.89  3.000
 V3S  C10  C9   C8   119.61  3.000
 V3S  H15  C11  C12  119.41  3.000
 V3S  H15  C11  C10  120.01  3.000
 V3S  C12  C11  C10  120.58  3.000
 V3S  H16  C12  C11  120.94  3.000
 V3S  H16  C12  C13  121.78  3.000
 V3S  C11  C12  C13  117.28  3.000
 V3S  H19  C18  H18  107.41  3.000
 V3S  H19  C18  C19  109.88  3.000
 V3S  H18  C18  C19  110.92  3.000
 V3S  H19  C18  C17  109.19  3.000
 V3S  H18  C18  C17  109.46  3.000
 V3S  C19  C18  C17  109.92  3.000
 V3S  H21  C19  H20  106.77  3.000
 V3S  H21  C19  C18  109.49  3.000
 V3S  H20  C19  C18  110.03  3.000
 V3S  H21  C19  C20  109.53  3.000
 V3S  H20  C19  C20  110.77  3.000
 V3S  C18  C19  C20  110.18  3.000
 V3S  C21  O22  C17  113.46  3.000
 V3S  C9   N23  C13  119.67  3.000
 V3S  H17  N14  C15  116.26  3.000
 V3S  H17  N14  C13  114.15  3.000
 V3S  C15  N14  C13  129.59  3.000
 V3S  H10  C1   H9   108.72  3.000
 V3S  H10  C1   H8   107.31  3.000
 V3S  H9   C1   H8   107.85  3.000
 V3S  H10  C1   C2   112.42  3.000
 V3S  H9   C1   C2   111.68  3.000
 V3S  H8   C1   C2   108.67  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
 V3S  CONST_01  C8   N7   N6   C5      0.00   0.0  0
 V3S  CONST_02  N7   C8   N4   C5      0.00   0.0  0
 V3S  CONST_03  C9   C8   N4   C5    180.00   0.0  0
 V3S  CONST_04  N6   C5   N4   C8      0.00   0.0  0
 V3S  CONST_05  C11  C10  C9   C8    180.00   0.0  0
 V3S  CONST_06  C13  N23  C9   C8    180.00   0.0  0
 V3S  CONST_09  C13  N23  C9   C10     0.00   0.0  0
 V3S  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 V3S  CONST_11  N7   N6   C5   N4      0.00   0.0  0
 V3S  CONST_12  N6   N7   C8   N4      0.00   0.0  0
 V3S  CONST_14  C9   C8   N7   N6    180.00   0.0  0
 V3S  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 V3S  CONST_17  C12  C13  N23  C9      0.00   0.0  0
 V3S  CONST_18  N23  C9   C10  C11     0.00   0.0  0
 V3S  CONST_19  N23  C13  C12  C11     0.00   0.0  0
 V3S  CONST_20  N6   C5   N4   C2    180.00   0.0  0
 V3S  CONST_21  N7   C8   N4   C2    180.00   0.0  0
 V3S  CONST_22  C9   C8   N4   C2      0.00   0.0  0
 V3S  CONST_23  N14  C13  N23  C9    180.00   0.0  0
 V3S  CONST_24  N14  C13  C12  C11   180.00   0.0  0
 V3S  CONST_25  H1   C5   N4   C8    180.00   0.0  0
 V3S  CONST_26  H2   C10  C9   C8      0.00   0.0  0
 V3S  CONST_27  H16  C12  C11  C10   180.00   0.0  0
 V3S  CONST_28  H15  C11  C12  C13   180.00   0.0  0
 V3S  CONST_29  C17  C15  N14  C13   180.00   0.0  0
 V3S  CONST_30  N23  C13  N14  C15   180.00   0.0  0
 V3S  CONST_31  C12  C13  N14  C15     0.00   0.0  0
 V3S  CONST_32  H17  N14  C13  C12   180.00   0.0  0
 V3S  CONST_33  O16  C15  N14  C13     0.00   0.0  0
 V3S  Var_01    C20  C21  O22  C17    59.13  30.0  1
 V3S  Var_02    C20  C19  C18  C17   -52.63  30.0  1
 V3S  Var_03    C18  C19  C20  C21    52.94  30.0  1
 V3S  Var_04    O22  C21  C20  C19   -55.35  30.0  1
 V3S  Var_05    C3   C2   N4   C5     86.21  30.0  2
 V3S  Var_06    H12  C3   C2   N4    175.86  30.0  3
 V3S  Var_07    H8   C1   C2   N4   -173.00  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
 V3S  chir_01  C17  C15  O22  C18  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
 V3S  plan-1  C5   0.020
 V3S  plan-1  C8   0.020
 V3S  plan-1  C2   0.020
 V3S  plan-1  N4   0.020
 V3S  plan-1  N6   0.020
 V3S  plan-1  N7   0.020
 V3S  plan-1  C9   0.020
 V3S  plan-1  H1   0.020
 V3S  plan-2  C8   0.020
 V3S  plan-2  C10  0.020
 V3S  plan-2  C13  0.020
 V3S  plan-2  C9   0.020
 V3S  plan-2  C11  0.020
 V3S  plan-2  C12  0.020
 V3S  plan-2  N23  0.020
 V3S  plan-2  H2   0.020
 V3S  plan-2  H15  0.020
 V3S  plan-2  H16  0.020
 V3S  plan-2  N14  0.020
 V3S  plan-3  C13  0.020
 V3S  plan-3  C15  0.020
 V3S  plan-3  C17  0.020
 V3S  plan-3  O16  0.020
 V3S  plan-3  H17  0.020
 V3S  plan-3  N14  0.020

