# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:06:49 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: N-{4-chloro-5-[1-ethyl-7-(methylamino)-2-oxo-1,2-dihydro-1,6-naphthyridin-3-yl]-2-fluorophenyl}-N'-phenylurea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C(=Cc2cnc(NC)cc12)c3cc(NC(=O)Nc4ccccc4)c(F)cc3Cl
#
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
 JWY  JWY  N-{4-chloro-5-[1-ethyl-7-(methylamino)-2-oxo-1,2-dihydro-1,6-naphthyridin-3-yl]-2-fluorophenyl}-N'-phenylurea  ligand  54  33  .  2021-08-12  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JWY
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
 JWY  C1   C   CR16  0  -0.348  -1.0459  -0.7919   0.3466
 JWY  C2   C   CR6   0   0.181   0.1764  -1.4284   0.1572
 JWY  C3   C   CR6   0  -0.111   0.1911  -2.8183   0.0709
 JWY  C4   C   CR16  0  -0.355  -0.9761  -3.5570   0.1579
 JWY  C5   C   CR6   0   0.227  -2.2413  -1.5010   0.4287
 JWY  C6   C   CR6   0   0.485  -2.1670  -2.8853   0.3215
 JWY  C8   C   CR6   0  -0.223   1.4174  -0.6332   0.1048
 JWY  C11  C   CR16  0  -0.158   1.8672   0.0646   1.1700
 JWY  C12  C   CR66  0  -0.088   3.0722   0.8067   1.0966
 JWY  C13  C   CR66  0   0.521   3.8093   0.8214  -0.1057
 JWY  C15  C   CR6   0   0.561   2.1382  -0.5945  -1.1600
 JWY  C16  C   CR16  0  -0.512   5.0147   1.5147  -0.1289
 JWY  C17  C   CR6   0   0.510   5.4351   2.1795   1.0313
 JWY  C19  C   CR16  0  -0.110   3.5921   1.5122   2.1848
 JWY  O20  O   O     0  -0.467   1.7407  -1.1788  -2.1562
 JWY  N14  N   NR6   0  -0.614   3.3070   0.1566  -1.1993
 JWY  C22  C   CH3   0  -0.664   5.1076  -0.8990  -2.5341
 JWY  N18  N   N     0  -0.461   4.7181   2.1802   2.1749
 JWY  N32  N   NH1   0  -0.643   6.5923   2.8606   1.0724
 JWY  C33  C   CH3   0  -0.534   7.5273   2.9465  -0.0164
 JWY  CL9  CL  CL    0  -0.116   1.6894  -3.6627  -0.0903
 JWY  F10  F   F     0  -0.305  -3.3020  -3.5938   0.4017
 JWY  N7   N   NH1   0  -0.784  -3.4804  -0.9039   0.6508
 JWY  C23  C   C     0   0.722  -3.8993   0.2643   0.0626
 JWY  O31  O   O     0  -0.490  -3.2128   0.9061  -0.7094
 JWY  N24  N   NH1   0  -0.784  -5.1623   0.6151   0.4476
 JWY  C25  C   CR6   0   0.368  -5.8773   1.7465   0.0414
 JWY  C26  C   CR16  0  -0.301  -5.7167   2.3518  -1.2057
 JWY  C27  C   CR16  0  -0.250  -6.4948   3.4514  -1.5412
 JWY  C28  C   CR16  0  -0.272  -7.4428   3.9563  -0.6623
 JWY  C29  C   CR16  0  -0.247  -7.6109   3.3432   0.5721
 JWY  C30  C   CR16  0  -0.338  -6.8331   2.2521   0.9243
 JWY  H1   H   HCR6  0   0.281  -1.0552   0.2840   0.4359
 JWY  H2   H   HCR6  0   0.304  -0.9675  -4.6369   0.0975
 JWY  H3   H   HCR6  0   0.272   1.3232   0.0444   2.1080
 JWY  H4   H   HCR6  0   0.288   5.6360   1.5432  -1.0098
 JWY  H5   H   HCR6  0   0.270   3.0331   1.5138   3.1166
 JWY  H6   H   HCH2  0   0.279   3.3190   0.0474  -3.2677
 JWY  H7   H   HCH2  0   0.262   4.4665   1.1717  -2.5980
 JWY  H8   H   HCH3  0   0.233   5.8328  -0.8039  -1.7264
 JWY  H9   H   HCH3  0   0.239   4.6622  -1.8918  -2.4766
 JWY  H10  H   HCH3  0   0.243   5.6463  -0.8270  -3.4786
 JWY  H11  H   HNH1  0   0.394   6.8265   3.2951   1.9490
 JWY  H12  H   HCH3  0   0.238   7.0981   3.4440  -0.8895
 JWY  H13  H   HCH3  0   0.270   8.3851   3.5269   0.3104
 JWY  H14  H   HCH3  0   0.237   7.8851   1.9621  -0.3287
 JWY  H15  H   HNH1  0   0.413  -4.1660  -1.4621   1.1358
 JWY  H16  H   HNH1  0   0.413  -5.5733   0.1026   1.2135
 JWY  H17  H   HCR6  0   0.269  -5.0046   1.9697  -1.9198
 JWY  H18  H   HCR6  0   0.258  -6.3598   3.9096  -2.5125
 JWY  H19  H   HCR6  0   0.255  -8.0448   4.8123  -0.9369
 JWY  H20  H   HCR6  0   0.259  -8.3462   3.7185   1.2718
 JWY  H21  H   HCR6  0   0.268  -6.9654   1.7890   1.8952
 JWY  C21  C   CH2   0  -0.346   4.0392   0.1793  -2.4661

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
 JWY  N32  C33  single    1.438  0.020  1.438
 JWY  N32  C17  single    1.343  0.020  1.343
 JWY  N18  C17  aromatic  1.350  0.020  1.350
 JWY  N18  C19  aromatic  1.309  0.020  1.309
 JWY  C17  C16  aromatic  1.402  0.020  1.402
 JWY  C19  C12  aromatic  1.397  0.020  1.397
 JWY  C16  C13  aromatic  1.391  0.020  1.391
 JWY  C12  C13  aromatic  1.410  0.020  1.410
 JWY  C12  C11  single    1.417  0.020  1.417
 JWY  C13  N14  single    1.375  0.020  1.375
 JWY  C11  C8   double    1.350  0.020  1.350
 JWY  C29  C30  aromatic  1.385  0.020  1.385
 JWY  C29  C28  aromatic  1.388  0.020  1.388
 JWY  N14  C21  single    1.463  0.020  1.463
 JWY  N14  C15  single    1.390  0.020  1.390
 JWY  C30  C25  aromatic  1.396  0.020  1.396
 JWY  C8   C15  single    1.456  0.020  1.456
 JWY  C8   C2   single    1.475  0.020  1.475
 JWY  C21  C22  single    1.519  0.020  1.519
 JWY  C28  C27  aromatic  1.388  0.020  1.388
 JWY  C15  O20  double    1.221  0.020  1.221
 JWY  O31  C23  double    1.216  0.020  1.216
 JWY  C2   C1   aromatic  1.391  0.020  1.391
 JWY  C2   C3   aromatic  1.393  0.020  1.393
 JWY  C1   C5   aromatic  1.392  0.020  1.392
 JWY  CL9  C3   single    1.727  0.020  1.727
 JWY  C25  N24  single    1.399  0.020  1.399
 JWY  C25  C26  aromatic  1.395  0.020  1.395
 JWY  C23  N24  single    1.366  0.020  1.366
 JWY  C23  N7   single    1.373  0.020  1.373
 JWY  C3   C4   aromatic  1.384  0.020  1.384
 JWY  C27  C26  aromatic  1.388  0.020  1.388
 JWY  C5   N7   single    1.393  0.020  1.393
 JWY  C5   C6   aromatic  1.390  0.020  1.390
 JWY  C4   C6   aromatic  1.377  0.020  1.377
 JWY  C6   F10  single    1.340  0.020  1.340
 JWY  C1   H1   single    0.930  0.020  1.080
 JWY  C4   H2   single    0.930  0.020  1.080
 JWY  C11  H3   single    0.930  0.020  1.080
 JWY  C16  H4   single    0.930  0.020  1.080
 JWY  C19  H5   single    0.930  0.020  1.080
 JWY  C21  H6   single    0.970  0.020  1.090
 JWY  C21  H7   single    0.970  0.020  1.090
 JWY  C22  H8   single    0.970  0.020  1.090
 JWY  C22  H9   single    0.970  0.020  1.090
 JWY  C22  H10  single    0.970  0.020  1.090
 JWY  N32  H11  single    0.860  0.020  1.020
 JWY  C33  H12  single    0.970  0.020  1.090
 JWY  C33  H13  single    0.970  0.020  1.090
 JWY  C33  H14  single    0.970  0.020  1.090
 JWY  N7   H15  single    0.860  0.020  1.020
 JWY  N24  H16  single    0.860  0.020  1.020
 JWY  C26  H17  single    0.930  0.020  1.080
 JWY  C27  H18  single    0.930  0.020  1.080
 JWY  C28  H19  single    0.930  0.020  1.080
 JWY  C29  H20  single    0.930  0.020  1.080
 JWY  C30  H21  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
 JWY  H1   C1   C5   119.69  3.000
 JWY  H1   C1   C2   118.35  3.000
 JWY  C5   C1   C2   121.97  3.000
 JWY  C8   C2   C3   121.81  3.000
 JWY  C3   C2   C1   118.31  3.000
 JWY  C8   C2   C1   119.83  3.000
 JWY  CL9  C3   C4   118.45  3.000
 JWY  C4   C3   C2   121.33  3.000
 JWY  CL9  C3   C2   120.18  3.000
 JWY  H2   C4   C6   120.04  3.000
 JWY  H2   C4   C3   121.51  3.000
 JWY  C6   C4   C3   118.45  3.000
 JWY  N7   C5   C6   119.11  3.000
 JWY  C6   C5   C1   117.17  3.000
 JWY  N7   C5   C1   123.69  3.000
 JWY  F10  C6   C5   118.46  3.000
 JWY  F10  C6   C4   118.78  3.000
 JWY  C5   C6   C4   122.75  3.000
 JWY  C15  C8   C11  120.43  3.000
 JWY  C15  C8   C2   117.49  3.000
 JWY  C11  C8   C2   122.06  3.000
 JWY  H3   C11  C12  118.75  3.000
 JWY  H3   C11  C8   120.37  3.000
 JWY  C12  C11  C8   120.86  3.000
 JWY  C19  C12  C13  117.66  3.000
 JWY  C13  C12  C11  119.60  3.000
 JWY  C19  C12  C11  122.72  3.000
 JWY  N14  C13  C16  122.99  3.000
 JWY  N14  C13  C12  118.82  3.000
 JWY  C16  C13  C12  118.19  3.000
 JWY  N14  C15  O20  120.61  3.000
 JWY  O20  C15  C8   122.32  3.000
 JWY  N14  C15  C8   117.07  3.000
 JWY  H4   C16  C17  119.40  3.000
 JWY  H4   C16  C13  121.75  3.000
 JWY  C17  C16  C13  118.85  3.000
 JWY  N32  C17  N18  115.56  3.000
 JWY  N18  C17  C16  122.84  3.000
 JWY  N32  C17  C16  121.61  3.000
 JWY  H5   C19  N18  116.62  3.000
 JWY  H5   C19  C12  118.50  3.000
 JWY  N18  C19  C12  124.88  3.000
 JWY  C21  N14  C15  116.98  3.000
 JWY  C15  N14  C13  123.10  3.000
 JWY  C21  N14  C13  119.88  3.000
 JWY  H10  C22  H9   107.94  3.000
 JWY  H10  C22  H8   107.93  3.000
 JWY  H9   C22  H8   108.21  3.000
 JWY  H10  C22  C21  109.85  3.000
 JWY  H9   C22  C21  110.90  3.000
 JWY  H8   C22  C21  111.89  3.000
 JWY  C19  N18  C17  117.58  3.000
 JWY  H11  N32  C33  118.87  3.000
 JWY  H11  N32  C17  116.49  3.000
 JWY  C33  N32  C17  124.56  3.000
 JWY  H14  C33  H13  107.98  3.000
 JWY  H14  C33  H12  108.08  3.000
 JWY  H13  C33  H12  107.90  3.000
 JWY  H14  C33  N32  112.06  3.000
 JWY  H13  C33  N32  108.52  3.000
 JWY  H12  C33  N32  112.14  3.000
 JWY  H15  N7   C23  118.00  3.000
 JWY  H15  N7   C5   116.36  3.000
 JWY  C23  N7   C5   124.58  3.000
 JWY  N24  C23  O31  124.42  3.000
 JWY  N24  C23  N7   112.31  3.000
 JWY  O31  C23  N7   123.27  3.000
 JWY  H16  N24  C25  115.03  3.000
 JWY  H16  N24  C23  117.39  3.000
 JWY  C25  N24  C23  126.75  3.000
 JWY  C30  C25  C26  119.14  3.000
 JWY  C26  C25  N24  123.48  3.000
 JWY  C30  C25  N24  117.34  3.000
 JWY  H17  C26  C27  119.39  3.000
 JWY  H17  C26  C25  120.93  3.000
 JWY  C27  C26  C25  119.67  3.000
 JWY  H18  C27  C28  119.96  3.000
 JWY  H18  C27  C26  118.83  3.000
 JWY  C28  C27  C26  121.20  3.000
 JWY  H19  C28  C29  120.51  3.000
 JWY  H19  C28  C27  120.48  3.000
 JWY  C29  C28  C27  119.01  3.000
 JWY  H20  C29  C30  119.35  3.000
 JWY  H20  C29  C28  120.26  3.000
 JWY  C30  C29  C28  120.38  3.000
 JWY  H21  C30  C29  119.71  3.000
 JWY  H21  C30  C25  119.70  3.000
 JWY  C29  C30  C25  120.58  3.000
 JWY  H7   C21  H6   106.36  3.000
 JWY  H7   C21  C22  111.44  3.000
 JWY  H6   C21  C22  110.31  3.000
 JWY  H7   C21  N14  108.39  3.000
 JWY  H6   C21  N14  107.78  3.000
 JWY  C22  C21  N14  112.30  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
 JWY  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 JWY  CONST_02  C4   C6   C5   C1     0.00   0.0  0
 JWY  CONST_03  C6   C5   C1   C2     0.00   0.0  0
 JWY  CONST_04  C6   C4   C3   C2     0.00   0.0  0
 JWY  CONST_05  C5   C1   C2   C3     0.00   0.0  0
 JWY  CONST_06  C5   C6   C4   C3     0.00   0.0  0
 JWY  CONST_07  C17  N18  C19  C12    0.00   0.0  0
 JWY  CONST_08  C17  C16  C13  C12    0.00   0.0  0
 JWY  CONST_09  N18  C17  C16  C13    0.00   0.0  0
 JWY  CONST_10  N18  C19  C12  C13    0.00   0.0  0
 JWY  CONST_11  C19  N18  C17  C16    0.00   0.0  0
 JWY  CONST_12  C19  C12  C13  C16    0.00   0.0  0
 JWY  CONST_13  C28  C29  C30  C25    0.00   0.0  0
 JWY  CONST_14  C28  C27  C26  C25    0.00   0.0  0
 JWY  CONST_15  C29  C30  C25  C26    0.00   0.0  0
 JWY  CONST_16  C29  C28  C27  C26    0.00   0.0  0
 JWY  CONST_17  C30  C29  C28  C27    0.00   0.0  0
 JWY  CONST_18  C30  C25  C26  C27    0.00   0.0  0
 JWY  CONST_19  C8   C2   C3   C4   180.00   0.0  0
 JWY  CONST_20  C8   C2   C1   C5   180.00   0.0  0
 JWY  CONST_21  C13  N14  C15  C8     0.00   0.0  0
 JWY  CONST_22  CL9  C3   C2   C1   180.00   0.0  0
 JWY  CONST_23  F10  C6   C5   C1   180.00   0.0  0
 JWY  CONST_24  N7   C5   C1   C2   180.00   0.0  0
 JWY  CONST_25  F10  C6   C4   C3   180.00   0.0  0
 JWY  CONST_26  N7   C5   C6   C4   180.00   0.0  0
 JWY  CONST_27  CL9  C3   C4   C6   180.00   0.0  0
 JWY  CONST_28  CL9  C3   C2   C8     0.00   0.0  0
 JWY  CONST_29  N32  C17  C16  C13  180.00   0.0  0
 JWY  CONST_30  N32  C17  N18  C19  180.00   0.0  0
 JWY  CONST_31  C29  C30  C25  N24  180.00   0.0  0
 JWY  CONST_32  C27  C26  C25  N24  180.00   0.0  0
 JWY  CONST_33  C21  N14  C15  C8   180.00   0.0  0
 JWY  CONST_34  O20  C15  N14  C13  180.00   0.0  0
 JWY  CONST_35  H2   C4   C3   C2   180.00   0.0  0
 JWY  CONST_36  H1   C1   C2   C3   180.00   0.0  0
 JWY  CONST_37  H5   C19  C12  C11    0.00   0.0  0
 JWY  CONST_38  H4   C16  C13  C12  180.00   0.0  0
 JWY  CONST_39  H20  C29  C30  C25  180.00   0.0  0
 JWY  CONST_40  H18  C27  C26  C25  180.00   0.0  0
 JWY  CONST_41  H21  C30  C25  C26  180.00   0.0  0
 JWY  CONST_42  H19  C28  C27  C26  180.00   0.0  0
 JWY  CONST_43  H17  C26  C27  C28  180.00   0.0  0
 JWY  CONST_46  C33  N32  C17  C16    0.00   0.0  0
 JWY  CONST_47  C33  N32  C17  N18  180.00   0.0  0
 JWY  CONST_50  O20  C15  N14  C21    0.00   0.0  0
 JWY  CONST_52  H11  N32  C17  C16  180.00   0.0  0
 JWY  CONST_54  O31  C23  N7   C5     0.00   0.0  0
 JWY  CONST_55  C25  N24  C23  O31    0.00   0.0  0
 JWY  CONST_56  N24  C23  N7   C5   180.00   0.0  0
 JWY  CONST_57  C25  N24  C23  N7   180.00   0.0  0
 JWY  Var_01    C11  C8   C2   C1    64.61  30.0  2
 JWY  Var_02    C22  C21  N14  C13   85.19  30.0  3
 JWY  Var_03    H12  C33  N32  C17   63.05  30.0  3
 JWY  Var_04    H8   C22  C21  N14  -58.48  30.0  3

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
 JWY  plan-1  C1   0.020
 JWY  plan-1  C2   0.020
 JWY  plan-1  C3   0.020
 JWY  plan-1  C4   0.020
 JWY  plan-1  C5   0.020
 JWY  plan-1  C6   0.020
 JWY  plan-1  C8   0.020
 JWY  plan-1  CL9  0.020
 JWY  plan-1  F10  0.020
 JWY  plan-1  N7   0.020
 JWY  plan-1  H1   0.020
 JWY  plan-1  H2   0.020
 JWY  plan-2  N24  0.020
 JWY  plan-2  C25  0.020
 JWY  plan-2  C26  0.020
 JWY  plan-2  C27  0.020
 JWY  plan-2  C28  0.020
 JWY  plan-2  C29  0.020
 JWY  plan-2  C30  0.020
 JWY  plan-2  H17  0.020
 JWY  plan-2  H18  0.020
 JWY  plan-2  H19  0.020
 JWY  plan-2  H20  0.020
 JWY  plan-2  H21  0.020
 JWY  plan-3  C2   0.020
 JWY  plan-3  C8   0.020
 JWY  plan-3  C11  0.020
 JWY  plan-3  C12  0.020
 JWY  plan-3  C13  0.020
 JWY  plan-3  C15  0.020
 JWY  plan-3  C16  0.020
 JWY  plan-3  C17  0.020
 JWY  plan-3  C19  0.020
 JWY  plan-3  O20  0.020
 JWY  plan-3  N14  0.020
 JWY  plan-3  N18  0.020
 JWY  plan-3  N32  0.020
 JWY  plan-3  H3   0.020
 JWY  plan-3  H4   0.020
 JWY  plan-3  H5   0.020
 JWY  plan-3  C21  0.020
 JWY  plan-4  C5   0.020
 JWY  plan-4  N7   0.020
 JWY  plan-4  C23  0.020
 JWY  plan-4  O31  0.020
 JWY  plan-4  N24  0.020
 JWY  plan-4  C25  0.020
 JWY  plan-4  H15  0.020
 JWY  plan-4  H16  0.020
 JWY  plan-5  C17  0.020
 JWY  plan-5  N32  0.020
 JWY  plan-5  C33  0.020
 JWY  plan-5  H11  0.020

