# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:15:54 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: N-[(1S)-2-hydroxy-1-phenylethyl]-3-methoxy-4-(1H-pyrazol-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1c2c[nH]nc2)C(=O)N[C@H](CO)c3ccccc3
#
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
 VFS  VFS  N-[(1S)-2-hydroxy-1-phenylethyl]-3-methoxy-4-(1H-pyrazol-4-yl)benzamide  ligand  44  25  .  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_VFS
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
 VFS  C1   C  CR6   0   0.369  -17.2180  61.3608  -19.0455
 VFS  C2   C  CR6   0  -0.024  -18.4260  61.7752  -18.4550
 VFS  C3   C  CR5   0  -0.108  -19.2790  62.7946  -19.0640
 VFS  C4   C  CR15  0  -0.098  -18.9457  63.9486  -19.8105
 VFS  C5   C  CR15  0   0.008  -20.6584  62.8554  -18.9755
 VFS  C6   C  CR16  0  -0.306  -18.8127  61.1629  -17.2651
 VFS  C8   C  CR6   0  -0.023  -16.8514  59.7873  -17.2453
 VFS  C10  C  CH1   0  -0.162  -13.8150  57.7960  -16.2150
 VFS  C11  C  CH2   0  -0.160  -12.3790  58.2046  -16.5208
 VFS  C12  C  CR6   0   0.140  -14.0514  56.4008  -16.7455
 VFS  C13  C  CR16  0  -0.311  -13.9834  55.3107  -15.8860
 VFS  C14  C  CR16  0  -0.243  -14.1380  54.0171  -16.3667
 VFS  C15  C  CR16  0  -0.268  -14.3685  53.8009  -17.7186
 VFS  C9   C  C     0   0.542  -16.0442  58.7212  -16.5805
 VFS  N2   N  NH1   0  -0.665  -14.7166  58.7647  -16.8005
 VFS  C17  C  CR16  0  -0.297  -14.2776  56.1768  -18.1005
 VFS  C16  C  CR16  0  -0.242  -14.4379  54.8856  -18.5841
 VFS  C18  C  CR16  0  -0.436  -16.4409  60.3808  -18.4384
 VFS  O    O  O2    0  -0.465  -16.8926  61.9479  -20.2089
 VFS  C    C  CH3   0  -0.442  -15.6967  61.5685  -20.8607
 VFS  C7   C  CR16  0  -0.288  -18.0534  60.1710  -16.6677
 VFS  N1   N  NR15  0  -0.426  -21.0369  63.9616  -19.6262
 VFS  N    N  N     0  -0.267  -20.0176  64.6429  -20.1364
 VFS  H1   H  HCR5  0   0.255  -17.9688  64.3000  -20.1001
 VFS  H2   H  HCR5  0   0.292  -21.3738  62.1901  -18.5200
 VFS  H3   H  HCR6  0   0.256  -19.7297  61.4839  -16.7868
 VFS  H4   H  HCH1  0   0.265  -13.9440  57.7803  -15.1260
 VFS  H5   H  HCH2  0   0.212  -12.2195  58.1689  -17.6063
 VFS  H6   H  HCH2  0   0.223  -11.7136  57.4588  -16.0706
 VFS  H7   H  HCR6  0   0.250  -13.8140  55.4737  -14.8279
 VFS  H8   H  HCR6  0   0.255  -14.0856  53.1798  -15.6830
 VFS  H9   H  HCR6  0   0.255  -14.4965  52.7944  -18.0956
 VFS  H10  H  HNH1  0   0.404  -14.3139  59.6112  -17.1705
 VFS  H11  H  HCR6  0   0.248  -14.3369  57.0143  -18.7855
 VFS  H12  H  HCR6  0   0.254  -14.6158  54.7261  -19.6399
 VFS  H13  H  HOH1  0   0.462  -11.3082  59.8097  -16.3335
 VFS  H14  H  HCR6  0   0.280  -15.5283  60.0486  -18.9153
 VFS  H15  H  HCH3  0   0.264  -15.6380  62.1665  -21.7664
 VFS  H16  H  HCH3  0   0.231  -14.8151  61.7720  -20.2473
 VFS  H17  H  HCH3  0   0.231  -15.7012  60.5108  -21.1369
 VFS  H18  H  HCR6  0   0.255  -18.3851  59.7175  -15.7439
 VFS  H19  H  HNR5  0   0.423  -21.9789  64.2939  -19.7567
 VFS  O1   O  OH1   0  -0.667  -12.1551  59.4948  -16.0046
 VFS  O2   O  O     0  -0.476  -16.5682  57.8637  -15.8849

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
 VFS  N    C4   aromatic  1.318  0.020  1.318
 VFS  N    N1   aromatic  1.328  0.020  1.328
 VFS  C    O    single    1.414  0.020  1.414
 VFS  C4   C3   aromatic  1.414  0.020  1.414
 VFS  O    C1   single    1.343  0.020  1.343
 VFS  N1   C5   aromatic  1.338  0.020  1.338
 VFS  C3   C5   aromatic  1.384  0.020  1.384
 VFS  C3   C2   single    1.462  0.020  1.462
 VFS  C1   C2   aromatic  1.407  0.020  1.407
 VFS  C1   C18  aromatic  1.390  0.020  1.390
 VFS  C2   C6   aromatic  1.393  0.020  1.393
 VFS  C16  C17  aromatic  1.388  0.020  1.388
 VFS  C16  C15  aromatic  1.389  0.020  1.389
 VFS  C18  C8   aromatic  1.394  0.020  1.394
 VFS  C17  C12  aromatic  1.392  0.020  1.392
 VFS  C15  C14  aromatic  1.388  0.020  1.388
 VFS  C6   C7   aromatic  1.385  0.020  1.385
 VFS  C8   C7   aromatic  1.388  0.020  1.388
 VFS  C8   C9   single    1.493  0.020  1.493
 VFS  N2   C9   single    1.346  0.020  1.346
 VFS  N2   C10  single    1.447  0.020  1.447
 VFS  O1   C11  single    1.407  0.020  1.407
 VFS  C11  C10  single    1.524  0.020  1.524
 VFS  C12  C10  single    1.511  0.020  1.511
 VFS  C12  C13  aromatic  1.390  0.020  1.390
 VFS  C9   O2   double    1.222  0.020  1.222
 VFS  C14  C13  aromatic  1.389  0.020  1.389
 VFS  C4   H1   single    0.930  0.020  1.080
 VFS  C5   H2   single    0.930  0.020  1.080
 VFS  C6   H3   single    0.930  0.020  1.080
 VFS  C10  H4   single    0.970  0.020  1.090
 VFS  C11  H5   single    0.970  0.020  1.090
 VFS  C11  H6   single    0.970  0.020  1.090
 VFS  C13  H7   single    0.930  0.020  1.080
 VFS  C14  H8   single    0.930  0.020  1.080
 VFS  C15  H9   single    0.930  0.020  1.080
 VFS  N2   H10  single    0.860  0.020  1.020
 VFS  C17  H11  single    0.930  0.020  1.080
 VFS  C16  H12  single    0.930  0.020  1.080
 VFS  O1   H13  single    0.850  0.020  0.980
 VFS  C18  H14  single    0.930  0.020  1.080
 VFS  C    H15  single    0.970  0.020  1.090
 VFS  C    H16  single    0.970  0.020  1.090
 VFS  C    H17  single    0.970  0.020  1.090
 VFS  C7   H18  single    0.930  0.020  1.080
 VFS  N1   H19  single    0.860  0.020  1.020

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
 VFS  O    C1   C18  123.43  3.000
 VFS  C18  C1   C2   120.28  3.000
 VFS  O    C1   C2   116.28  3.000
 VFS  C6   C2   C3   120.02  3.000
 VFS  C6   C2   C1   117.86  3.000
 VFS  C3   C2   C1   122.10  3.000
 VFS  C5   C3   C4   103.46  3.000
 VFS  C5   C3   C2   125.85  3.000
 VFS  C4   C3   C2   130.64  3.000
 VFS  H1   C4   N    119.93  3.000
 VFS  H1   C4   C3   128.43  3.000
 VFS  N    C4   C3   111.64  3.000
 VFS  H2   C5   N1   121.87  3.000
 VFS  H2   C5   C3   131.42  3.000
 VFS  N1   C5   C3   106.70  3.000
 VFS  H3   C6   C7   119.08  3.000
 VFS  H3   C6   C2   118.83  3.000
 VFS  C7   C6   C2   122.09  3.000
 VFS  C7   C8   C18  119.57  3.000
 VFS  C7   C8   C9   118.71  3.000
 VFS  C18  C8   C9   121.71  3.000
 VFS  H4   C10  N2   109.76  3.000
 VFS  H4   C10  C12  108.48  3.000
 VFS  N2   C10  C12  112.24  3.000
 VFS  H4   C10  C11  108.29  3.000
 VFS  C12  C10  C11  108.93  3.000
 VFS  N2   C10  C11  109.05  3.000
 VFS  H6   C11  H5   107.20  3.000
 VFS  H6   C11  O1   112.11  3.000
 VFS  H5   C11  O1   111.68  3.000
 VFS  H6   C11  C10  107.89  3.000
 VFS  H5   C11  C10  109.06  3.000
 VFS  O1   C11  C10  108.79  3.000
 VFS  C17  C12  C13  118.93  3.000
 VFS  C13  C12  C10  119.95  3.000
 VFS  C17  C12  C10  121.05  3.000
 VFS  H7   C13  C14  119.70  3.000
 VFS  H7   C13  C12  119.56  3.000
 VFS  C14  C13  C12  120.74  3.000
 VFS  H8   C14  C15  120.18  3.000
 VFS  H8   C14  C13  119.78  3.000
 VFS  C15  C14  C13  120.05  3.000
 VFS  H9   C15  C16  120.20  3.000
 VFS  H9   C15  C14  120.24  3.000
 VFS  C16  C15  C14  119.55  3.000
 VFS  N2   C9   O2   122.57  3.000
 VFS  O2   C9   C8   121.50  3.000
 VFS  N2   C9   C8   115.93  3.000
 VFS  H10  N2   C9   118.76  3.000
 VFS  H10  N2   C10  117.51  3.000
 VFS  C9   N2   C10  121.78  3.000
 VFS  H11  C17  C16  119.50  3.000
 VFS  H11  C17  C12  120.00  3.000
 VFS  C16  C17  C12  120.50  3.000
 VFS  H12  C16  C17  119.72  3.000
 VFS  H12  C16  C15  120.05  3.000
 VFS  C17  C16  C15  120.23  3.000
 VFS  H14  C18  C8   119.66  3.000
 VFS  H14  C18  C1   119.70  3.000
 VFS  C8   C18  C1   120.60  3.000
 VFS  C    O    C1   119.14  3.000
 VFS  H17  C    H16  108.98  3.000
 VFS  H17  C    H15  108.78  3.000
 VFS  H16  C    H15  108.76  3.000
 VFS  H17  C    O    111.88  3.000
 VFS  H16  C    O    111.94  3.000
 VFS  H15  C    O    106.39  3.000
 VFS  H18  C7   C8   120.36  3.000
 VFS  H18  C7   C6   120.06  3.000
 VFS  C8   C7   C6   119.57  3.000
 VFS  H19  N1   N    119.92  3.000
 VFS  H19  N1   C5   126.89  3.000
 VFS  N    N1   C5   113.20  3.000
 VFS  N1   N    C4   105.01  3.000
 VFS  H13  O1   C11  108.36  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
 VFS  CONST_03  C7   C6   C2   C1      0.00   0.0  0
 VFS  CONST_04  C7   C8   C18  C1      0.00   0.0  0
 VFS  CONST_05  N    C4   C3   C2    180.00   0.0  0
 VFS  CONST_06  N1   C5   C3   C2    180.00   0.0  0
 VFS  CONST_07  C8   C18  C1   C2      0.00   0.0  0
 VFS  CONST_08  C8   C7   C6   C2      0.00   0.0  0
 VFS  CONST_09  N1   N    C4   C3      0.00   0.0  0
 VFS  CONST_10  N    N1   C5   C3      0.00   0.0  0
 VFS  CONST_11  C18  C1   C2   C3    180.00   0.0  0
 VFS  CONST_12  C7   C6   C2   C3    180.00   0.0  0
 VFS  CONST_13  C5   N1   N    C4      0.00   0.0  0
 VFS  CONST_14  N1   C5   C3   C4      0.00   0.0  0
 VFS  CONST_16  N    C4   C3   C5      0.00   0.0  0
 VFS  CONST_18  C18  C1   C2   C6      0.00   0.0  0
 VFS  CONST_19  C18  C8   C7   C6      0.00   0.0  0
 VFS  CONST_20  C15  C16  C17  C12     0.00   0.0  0
 VFS  CONST_21  C15  C14  C13  C12     0.00   0.0  0
 VFS  CONST_22  C16  C17  C12  C13     0.00   0.0  0
 VFS  CONST_23  C16  C15  C14  C13     0.00   0.0  0
 VFS  CONST_24  C17  C16  C15  C14     0.00   0.0  0
 VFS  CONST_25  C17  C12  C13  C14     0.00   0.0  0
 VFS  CONST_26  C9   C8   C18  C1    180.00   0.0  0
 VFS  CONST_27  O    C1   C2   C3      0.00   0.0  0
 VFS  CONST_28  O    C1   C2   C6    180.00   0.0  0
 VFS  CONST_29  C9   C8   C7   C6    180.00   0.0  0
 VFS  CONST_30  O    C1   C18  C8    180.00   0.0  0
 VFS  CONST_31  C16  C17  C12  C10   180.00   0.0  0
 VFS  CONST_32  C14  C13  C12  C10   180.00   0.0  0
 VFS  CONST_33  H3   C6   C2   C1    180.00   0.0  0
 VFS  CONST_34  H1   C4   C3   C2      0.00   0.0  0
 VFS  CONST_35  H2   C5   C3   C2      0.00   0.0  0
 VFS  CONST_36  H14  C18  C1   C2    180.00   0.0  0
 VFS  CONST_37  H18  C7   C6   C2    180.00   0.0  0
 VFS  CONST_38  H19  N1   C5   C3    180.00   0.0  0
 VFS  CONST_39  H12  C16  C17  C12   180.00   0.0  0
 VFS  CONST_40  H8   C14  C13  C12   180.00   0.0  0
 VFS  CONST_41  H11  C17  C12  C13   180.00   0.0  0
 VFS  CONST_42  H9   C15  C14  C13   180.00   0.0  0
 VFS  CONST_43  H7   C13  C14  C15   180.00   0.0  0
 VFS  CONST_44  C10  N2   C9   C8    180.00   0.0  0
 VFS  CONST_46  O2   C9   N2   C10     0.00   0.0  0
 VFS  Var_01    C18  C8   C9   O2   -151.46  30.0  3
 VFS  Var_02    H15  C    O    C1   -179.81  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
 VFS  chir_01  C10  N2  C11  C12  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
 VFS  plan-1  C2   0.020
 VFS  plan-1  C3   0.020
 VFS  plan-1  C4   0.020
 VFS  plan-1  C5   0.020
 VFS  plan-1  N1   0.020
 VFS  plan-1  N    0.020
 VFS  plan-1  H1   0.020
 VFS  plan-1  H2   0.020
 VFS  plan-1  H19  0.020
 VFS  plan-2  C1   0.020
 VFS  plan-2  C2   0.020
 VFS  plan-2  C3   0.020
 VFS  plan-2  C6   0.020
 VFS  plan-2  C8   0.020
 VFS  plan-2  C9   0.020
 VFS  plan-2  C18  0.020
 VFS  plan-2  O    0.020
 VFS  plan-2  C7   0.020
 VFS  plan-2  H3   0.020
 VFS  plan-2  H14  0.020
 VFS  plan-2  H18  0.020
 VFS  plan-3  C10  0.020
 VFS  plan-3  C12  0.020
 VFS  plan-3  C13  0.020
 VFS  plan-3  C14  0.020
 VFS  plan-3  C15  0.020
 VFS  plan-3  C17  0.020
 VFS  plan-3  C16  0.020
 VFS  plan-3  H7   0.020
 VFS  plan-3  H8   0.020
 VFS  plan-3  H9   0.020
 VFS  plan-3  H11  0.020
 VFS  plan-3  H12  0.020
 VFS  plan-4  C8   0.020
 VFS  plan-4  C10  0.020
 VFS  plan-4  C9   0.020
 VFS  plan-4  N2   0.020
 VFS  plan-4  H10  0.020
 VFS  plan-4  O2   0.020

