# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:40:04 2021
#   Inital geometry file: a 115 line input string
#   Ligand name: 6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)pyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Oc1cc2cc(F)ccc2nc1N)C3=C(C=CC(=O)N3)n4cccn4
#
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
 VUD  VUD  6-{(1S)-1-[(2-amino-6-fluoroquinolin-3-yl)oxy]ethyl}-5-(1H-pyrazol-1-yl)pyridin-2(1H)-one  ligand  43  27  .  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_VUD
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
 VUD  C4   C  CR6   0   0.143  3.6172  -22.9734  41.8429
 VUD  C7   C  CR6   0   0.534  1.7559  -24.2467  43.5547
 VUD  C6   C  CR16  0  -0.480  1.3258  -23.4567  42.4302
 VUD  C13  C  CR15  0  -0.033  5.9060  -20.8354  40.3831
 VUD  O15  O  O2    0  -0.491  5.7146  -24.0790  44.5880
 VUD  C20  C  CR6   0   0.523  5.4253  -18.2566  46.2465
 VUD  C21  C  CR16  0  -0.421  5.5731  -18.5108  47.6129
 VUD  C18  C  CR66  0   0.111  5.5413  -20.5873  45.7459
 VUD  C16  C  CR6   0   0.257  5.6841  -22.9390  45.3154
 VUD  C19  C  CR16  0  -0.502  5.4046  -19.2549  45.3145
 VUD  C1   C  CH3   0  -0.660  5.9174  -25.3588  42.6108
 VUD  C2   C  CH1   0  -0.056  5.5043  -24.0162  43.1885
 VUD  C3   C  CR6   0   0.391  4.0497  -23.7285  42.8901
 VUD  C5   C  CR16  0  -0.084  2.2240  -22.8457  41.6198
 VUD  N8   N  NR16  0  -0.715  3.1353  -24.3195  43.6891
 VUD  O9   O  O     0  -0.490  1.0278  -24.8239  44.3507
 VUD  N10  N  NR5   0  -0.390  4.5349  -22.3166  40.9955
 VUD  C11  C  CR15  0   0.027  4.8773  -22.6631  39.7354
 VUD  C12  C  CR15  0  -0.498  5.7729  -21.7201  39.2981
 VUD  N14  N  N     0  -0.287  5.1504  -21.1996  41.3998
 VUD  C17  C  CR16  0  -0.330  5.5336  -21.6791  44.8361
 VUD  C22  C  CR16  0  -0.286  5.7041  -19.8095  48.0383
 VUD  C23  C  CR66  0   0.192  5.6939  -20.8776  47.1189
 VUD  N24  N  N     0  -0.490  5.8284  -22.1461  47.5797
 VUD  C25  C  CR6   0   0.368  5.8304  -23.1422  46.7373
 VUD  N26  N  NH2   0  -0.828  6.0171  -24.4008  47.2019
 VUD  H2   H  HCR6  0   0.285  0.2633  -23.3589  42.2575
 VUD  H3   H  HCR5  0   0.270  6.5206  -19.9511  40.4552
 VUD  H4   H  HCR6  0   0.279  5.5843  -17.6912  48.3191
 VUD  H5   H  HCR6  0   0.272  5.2868  -19.0308  44.2611
 VUD  H6   H  HCH3  0   0.267  6.9758  -25.5336  42.7988
 VUD  H7   H  HCH3  0   0.248  5.3422  -26.1774  43.0430
 VUD  H8   H  HCH3  0   0.254  5.7610  -25.3626  41.5331
 VUD  H9   H  HCH1  0   0.278  6.1268  -23.2328  42.7489
 VUD  H10  H  HCR6  0   0.296  1.8825  -22.2465  40.7848
 VUD  H11  H  HCR5  0   0.301  4.4671  -23.5394  39.2599
 VUD  H12  H  HCR5  0   0.271  6.2620  -21.6747  38.3398
 VUD  H13  H  HCR6  0   0.320  5.4154  -21.4679  43.7794
 VUD  H14  H  HCR6  0   0.265  5.8191  -20.0296  49.0918
 VUD  H15  H  HNH2  0   0.393  5.9308  -24.5363  48.1954
 VUD  H16  H  HNH2  0   0.397  5.7630  -25.1892  46.6330
 VUD  H1   H  HNR6  0   0.421  3.4676  -24.8660  44.4757
 VUD  F27  F  F     0  -0.320  5.3011  -16.9776  45.8480

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
 VUD  C12  C11  aromatic  1.372  0.020  1.372
 VUD  C12  C13  aromatic  1.406  0.020  1.406
 VUD  C11  N10  aromatic  1.351  0.020  1.351
 VUD  C13  N14  aromatic  1.318  0.020  1.318
 VUD  N10  N14  aromatic  1.338  0.020  1.338
 VUD  N10  C4   single    1.411  0.020  1.411
 VUD  C5   C4   single    1.417  0.020  1.417
 VUD  C5   C6   double    1.355  0.020  1.355
 VUD  C4   C3   double    1.362  0.020  1.362
 VUD  C1   C2   single    1.519  0.020  1.519
 VUD  C6   C7   single    1.440  0.020  1.440
 VUD  C3   C2   single    1.513  0.020  1.513
 VUD  C3   N8   single    1.350  0.020  1.350
 VUD  C2   O15  single    1.417  0.020  1.417
 VUD  C7   N8   single    1.388  0.020  1.388
 VUD  C7   O9   double    1.224  0.020  1.224
 VUD  O15  C16  single    1.353  0.020  1.353
 VUD  C17  C16  aromatic  1.356  0.020  1.356
 VUD  C17  C18  aromatic  1.421  0.020  1.421
 VUD  C19  C18  aromatic  1.407  0.020  1.407
 VUD  C19  C20  aromatic  1.366  0.020  1.366
 VUD  C16  C25  aromatic  1.444  0.020  1.444
 VUD  F27  C20  single    1.345  0.020  1.345
 VUD  C18  C23  aromatic  1.412  0.020  1.412
 VUD  C20  C21  aromatic  1.398  0.020  1.398
 VUD  C25  N26  single    1.355  0.020  1.355
 VUD  C25  N24  aromatic  1.305  0.020  1.305
 VUD  C23  N24  aromatic  1.356  0.020  1.356
 VUD  C23  C22  aromatic  1.409  0.020  1.409
 VUD  C21  C22  aromatic  1.373  0.020  1.373
 VUD  C6   H2   single    0.930  0.020  1.080
 VUD  C13  H3   single    0.930  0.020  1.080
 VUD  C21  H4   single    0.930  0.020  1.080
 VUD  C19  H5   single    0.930  0.020  1.080
 VUD  C1   H6   single    0.970  0.020  1.090
 VUD  C1   H7   single    0.970  0.020  1.090
 VUD  C1   H8   single    0.970  0.020  1.090
 VUD  C2   H9   single    0.970  0.020  1.090
 VUD  C5   H10  single    0.930  0.020  1.080
 VUD  C11  H11  single    0.930  0.020  1.080
 VUD  C12  H12  single    0.930  0.020  1.080
 VUD  C17  H13  single    0.930  0.020  1.080
 VUD  C22  H14  single    0.930  0.020  1.080
 VUD  N26  H15  single    0.890  0.020  1.040
 VUD  N26  H16  single    0.890  0.020  1.040
 VUD  N8   H1   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
 VUD  N10  C4   C5   120.19  3.000
 VUD  C5   C4   C3   118.92  3.000
 VUD  N10  C4   C3   120.89  3.000
 VUD  O9   C7   N8   120.25  3.000
 VUD  O9   C7   C6   126.09  3.000
 VUD  N8   C7   C6   113.66  3.000
 VUD  H2   C6   C5   121.01  3.000
 VUD  H2   C6   C7   117.90  3.000
 VUD  C5   C6   C7   121.08  3.000
 VUD  H3   C13  N14  120.09  3.000
 VUD  H3   C13  C12  128.38  3.000
 VUD  N14  C13  C12  111.53  3.000
 VUD  C2   O15  C16  119.38  3.000
 VUD  F27  C20  C19  119.43  3.000
 VUD  F27  C20  C21  118.18  3.000
 VUD  C19  C20  C21  122.40  3.000
 VUD  H4   C21  C22  120.89  3.000
 VUD  H4   C21  C20  120.10  3.000
 VUD  C22  C21  C20  119.02  3.000
 VUD  C23  C18  C17  117.73  3.000
 VUD  C23  C18  C19  120.23  3.000
 VUD  C17  C18  C19  122.04  3.000
 VUD  C25  C16  C17  119.34  3.000
 VUD  C25  C16  O15  114.13  3.000
 VUD  C17  C16  O15  126.54  3.000
 VUD  H5   C19  C18  120.30  3.000
 VUD  H5   C19  C20  120.92  3.000
 VUD  C18  C19  C20  118.77  3.000
 VUD  H8   C1   H7   108.30  3.000
 VUD  H8   C1   H6   108.05  3.000
 VUD  H7   C1   H6   108.90  3.000
 VUD  H8   C1   C2   109.91  3.000
 VUD  H7   C1   C2   111.69  3.000
 VUD  H6   C1   C2   109.91  3.000
 VUD  H9   C2   C3   109.39  3.000
 VUD  H9   C2   C1   109.01  3.000
 VUD  C3   C2   C1   110.77  3.000
 VUD  H9   C2   O15  110.16  3.000
 VUD  C3   C2   O15  110.25  3.000
 VUD  C1   C2   O15  107.23  3.000
 VUD  N8   C3   C2   116.82  3.000
 VUD  N8   C3   C4   118.86  3.000
 VUD  C2   C3   C4   124.25  3.000
 VUD  H10  C5   C6   120.10  3.000
 VUD  H10  C5   C4   118.78  3.000
 VUD  C6   C5   C4   121.12  3.000
 VUD  H1   N8   C3   118.23  3.000
 VUD  H1   N8   C7   115.41  3.000
 VUD  C3   N8   C7   126.35  3.000
 VUD  N14  N10  C11  112.29  3.000
 VUD  N14  N10  C4   120.42  3.000
 VUD  C11  N10  C4   127.27  3.000
 VUD  H11  C11  C12  131.80  3.000
 VUD  H11  C11  N10  121.56  3.000
 VUD  C12  C11  N10  106.65  3.000
 VUD  H12  C12  C11  127.52  3.000
 VUD  H12  C12  C13  128.10  3.000
 VUD  C11  C12  C13  104.38  3.000
 VUD  N10  N14  C13  105.15  3.000
 VUD  H13  C17  C16  122.52  3.000
 VUD  H13  C17  C18  118.35  3.000
 VUD  C16  C17  C18  119.13  3.000
 VUD  H14  C22  C23  118.80  3.000
 VUD  H14  C22  C21  120.27  3.000
 VUD  C23  C22  C21  120.94  3.000
 VUD  N24  C23  C22  119.11  3.000
 VUD  C22  C23  C18  118.65  3.000
 VUD  N24  C23  C18  122.24  3.000
 VUD  C25  N24  C23  119.66  3.000
 VUD  N26  C25  N24  119.22  3.000
 VUD  N24  C25  C16  121.89  3.000
 VUD  N26  C25  C16  118.85  3.000
 VUD  H16  N26  H15  115.57  3.000
 VUD  H16  N26  C25  120.00  3.000
 VUD  H15  N26  C25  116.86  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
 VUD  CONST_01  N10  C11  C12  C13    0.00   0.0  0
 VUD  CONST_02  C11  N10  N14  C13    0.00   0.0  0
 VUD  CONST_03  C17  C18  C19  C20  180.00   0.0  0
 VUD  CONST_04  C23  C18  C19  C20    0.00   0.0  0
 VUD  CONST_05  C23  C22  C21  C20    0.00   0.0  0
 VUD  CONST_06  C18  C19  C20  C21    0.00   0.0  0
 VUD  CONST_07  C18  C23  C22  C21    0.00   0.0  0
 VUD  CONST_08  N24  C23  C22  C21  180.00   0.0  0
 VUD  CONST_09  C25  C16  C17  C18    0.00   0.0  0
 VUD  CONST_10  C25  N24  C23  C18    0.00   0.0  0
 VUD  CONST_11  C19  C18  C17  C16  180.00   0.0  0
 VUD  CONST_12  C23  C18  C17  C16    0.00   0.0  0
 VUD  CONST_13  C23  N24  C25  C16    0.00   0.0  0
 VUD  CONST_14  N24  C23  C18  C19  180.00   0.0  0
 VUD  CONST_15  C22  C23  C18  C19    0.00   0.0  0
 VUD  CONST_16  C22  C21  C20  C19    0.00   0.0  0
 VUD  CONST_17  C12  C13  N14  N10    0.00   0.0  0
 VUD  CONST_18  N14  C13  C12  C11    0.00   0.0  0
 VUD  CONST_19  N14  N10  C11  C12    0.00   0.0  0
 VUD  CONST_20  N24  C25  C16  C17    0.00   0.0  0
 VUD  CONST_21  N24  C23  C18  C17    0.00   0.0  0
 VUD  CONST_22  C22  C23  C18  C17  180.00   0.0  0
 VUD  CONST_23  C25  N24  C23  C22  180.00   0.0  0
 VUD  CONST_24  C12  C11  N10  C4   180.00   0.0  0
 VUD  CONST_25  C13  N14  N10  C4   180.00   0.0  0
 VUD  CONST_26  C3   N8   C7   C6     0.00   0.0  0
 VUD  CONST_27  C18  C17  C16  O15  180.00   0.0  0
 VUD  CONST_28  N24  C25  C16  O15  180.00   0.0  0
 VUD  CONST_29  F27  C20  C19  C18  180.00   0.0  0
 VUD  CONST_30  N26  C25  C16  C17  180.00   0.0  0
 VUD  CONST_31  F27  C20  C21  C22  180.00   0.0  0
 VUD  CONST_32  N26  C25  N24  C23  180.00   0.0  0
 VUD  CONST_33  O9   C7   N8   C3   180.00   0.0  0
 VUD  CONST_34  H11  C11  N10  C4     0.00   0.0  0
 VUD  CONST_35  H14  C22  C21  C20  180.00   0.0  0
 VUD  CONST_36  H5   C19  C20  C21  180.00   0.0  0
 VUD  CONST_37  H13  C17  C18  C19    0.00   0.0  0
 VUD  CONST_38  H4   C21  C20  C19  180.00   0.0  0
 VUD  CONST_39  H12  C12  C11  N10  180.00   0.0  0
 VUD  CONST_40  H3   C13  N14  N10  180.00   0.0  0
 VUD  CONST_41  H1   N8   C7   C6   180.00   0.0  0
 VUD  CONST_42  H15  N26  C25  C16  180.00   0.0  0
 VUD  Var_01    C11  N10  C4   C3   105.61  30.0  2
 VUD  Var_02    C17  C16  O15  C2    -3.58  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
 VUD  chir_01  C2  C1  C3  O15  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
 VUD  plan-1  C4   0.020
 VUD  plan-1  C13  0.020
 VUD  plan-1  N10  0.020
 VUD  plan-1  C11  0.020
 VUD  plan-1  C12  0.020
 VUD  plan-1  N14  0.020
 VUD  plan-1  H3   0.020
 VUD  plan-1  H11  0.020
 VUD  plan-1  H12  0.020
 VUD  plan-2  C4   0.020
 VUD  plan-2  C7   0.020
 VUD  plan-2  C6   0.020
 VUD  plan-2  C2   0.020
 VUD  plan-2  C3   0.020
 VUD  plan-2  C5   0.020
 VUD  plan-2  N8   0.020
 VUD  plan-2  O9   0.020
 VUD  plan-2  N10  0.020
 VUD  plan-2  H2   0.020
 VUD  plan-2  H10  0.020
 VUD  plan-2  H1   0.020
 VUD  plan-3  O15  0.020
 VUD  plan-3  C20  0.020
 VUD  plan-3  C21  0.020
 VUD  plan-3  C18  0.020
 VUD  plan-3  C16  0.020
 VUD  plan-3  C19  0.020
 VUD  plan-3  C17  0.020
 VUD  plan-3  C22  0.020
 VUD  plan-3  C23  0.020
 VUD  plan-3  N24  0.020
 VUD  plan-3  C25  0.020
 VUD  plan-3  N26  0.020
 VUD  plan-3  H4   0.020
 VUD  plan-3  H5   0.020
 VUD  plan-3  H13  0.020
 VUD  plan-3  H14  0.020
 VUD  plan-3  F27  0.020
 VUD  plan-4  C25  0.020
 VUD  plan-4  N26  0.020
 VUD  plan-4  H15  0.020
 VUD  plan-4  H16  0.020

