# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:58:28 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 4-amino-6-{[1-(3-fluorobenzyl)-1H-indazol-5-yl]amino}pyrimidine-5-carbaldehyde O-(2-methoxyethyl)oxime
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCO/N=C/c1c(N)ncnc1Nc2ccc3n(Cc4cccc(F)c4)ncc3c2
#
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
 POX  POX  '4-amino-6-{[1-(3-fluorobenzyl)-1H-indazol-5-yl]amino}pyrimidine-5-carbaldehyde O-(2-methoxyethyl)oxime'  ligand  54  32  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_POX
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
 POX  C1    C  CR6   0   0.125  -5.4913  -1.0870  -0.6028
 POX  C2    C  CR16  0  -0.443  -5.8908  -1.1813   0.7284
 POX  C3    C  CR6   0   0.544  -6.0829  -2.4318   1.2772
 POX  C7    C  CH2   0  -0.402  -5.2694   0.2682  -1.2260
 POX  C8    C  CR15  0  -0.111  -3.3635   2.3080   0.8870
 POX  C9    C  CR6   0   0.346  -0.1284   0.9058  -0.4649
 POX  C10   C  CR16  0  -0.334  -0.7600   0.0534  -1.4012
 POX  C11   C  CR16  0  -0.288  -2.1274  -0.0181  -1.5225
 POX  C12   C  CR56  0   0.460  -2.8808   0.8135  -0.6890
 POX  C13   C  CR56  0  -0.104  -2.2711   1.6636   0.2467
 POX  C14   C  CR16  0  -0.364  -0.8786   1.7062   0.3721
 POX  C15   C  CR16  0   0.066   2.4417   4.1415  -0.2874
 POX  C16   C  CR6   0   0.511   2.1227   1.9077  -0.2677
 POX  C20   C  CH2   0  -0.168   6.9379  -1.3788   0.6747
 POX  C21   C  CH2   0  -0.184   7.1853  -2.8307   0.9866
 POX  C22   C  CH3   0  -0.396   7.0194  -4.9939   0.1276
 POX  C4    C  CR16  0  -0.417  -5.8925  -3.5983   0.5582
 POX  C5    C  CR16  0  -0.224  -5.4941  -3.4925  -0.7653
 POX  C6    C  CR16  0  -0.320  -5.2935  -2.2450  -1.3441
 POX  F1    F  F     0  -0.315  -6.4756  -2.5193   2.5585
 POX  N1    N  NR5   0  -0.390  -4.2193   1.0077  -0.5699
 POX  N2    N  N     0  -0.239  -4.5020   1.8956   0.3894
 POX  N4    N  N     0  -0.471   3.7476   4.0968  -0.1516
 POX  N5    N  N     0  -0.477   1.5977   3.1302  -0.3647
 POX  C17   C  CR6   0  -0.216   3.5025   1.7015  -0.0511
 POX  C18   C  CR6   0   0.490   4.2987   2.8752  -0.0403
 POX  N7    N  N     0  -0.147   5.2793   0.1307   0.2651
 POX  O1    O  O2    0  -0.398   5.5386  -1.1730   0.5705
 POX  O2    O  O2    0  -0.483   6.8053  -3.6254  -0.1061
 POX  H2    H  HCR6  0   0.276  -6.0517  -0.2932   1.3280
 POX  HN6   H  HNH2  0   0.397   6.1297   3.6996   0.1891
 POX  HN6A  H  HNH2  0   0.413   6.1029   1.9566   0.2170
 POX  H7    H  HCH2  0   0.285  -5.0181   0.1605  -2.2821
 POX  H7A   H  HCH2  0   0.298  -6.1723   0.8759  -1.1723
 POX  H8    H  HCR5  0   0.272  -3.3416   3.0470   1.6732
 POX  H10   H  HCR6  0   0.273  -0.1402  -0.5620  -2.0420
 POX  H11   H  HCR6  0   0.271  -2.5832  -0.6835  -2.2439
 POX  H14   H  HCR6  0   0.266  -0.4110   2.3456   1.1069
 POX  H15   H  HCR6  0   0.253   2.0027   5.1324  -0.3573
 POX  H19   H  H     0   0.245   3.3220  -0.4286   0.3972
 POX  H20   H  HCH2  0   0.226   7.3570  -0.7696   1.4820
 POX  H20A  H  HCH2  0   0.224   7.4390  -1.0949  -0.2566
 POX  H21   H  HCH2  0   0.215   8.2557  -2.9449   1.2094
 POX  H21A  H  HCH2  0   0.211   6.6419  -3.1218   1.8974
 POX  H22   H  HCH3  0   0.204   8.0737  -5.2160   0.3314
 POX  H22A  H  HCH3  0   0.205   6.4297  -5.3631   0.9753
 POX  H22B  H  HCH3  0   0.234   6.7179  -5.5404  -0.7653
 POX  H4    H  HCR6  0   0.282  -6.0542  -4.5628   1.0211
 POX  H5    H  HCR6  0   0.271  -5.3365  -4.3901  -1.3480
 POX  H6    H  HCR6  0   0.262  -4.9842  -2.1739  -2.3796
 POX  HN3   H  HNH1  0   0.410   1.6755  -0.0372  -0.6396
 POX  N3    N  NH1   0  -0.785   1.2739   0.8529  -0.3961
 POX  C19   C  C1    0  -0.032   4.0289   0.3780   0.2076
 POX  N6    N  NH2   0  -0.829   5.6243   2.8356   0.0914

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
 POX  C1   C2    aromatic  1.393  0.020  1.393
 POX  C1   C7    single    1.508  0.020  1.508
 POX  C1   C6    aromatic  1.389  0.020  1.389
 POX  C2   C3    aromatic  1.379  0.020  1.379
 POX  C3   C4    aromatic  1.383  0.020  1.383
 POX  C3   F1    single    1.343  0.020  1.343
 POX  N6   C18   single    1.333  0.020  1.333
 POX  C7   N1    single    1.442  0.020  1.442
 POX  C8   C13   aromatic  1.421  0.020  1.421
 POX  C8   N2    aromatic  1.309  0.020  1.309
 POX  C9   C10   aromatic  1.415  0.020  1.415
 POX  C9   C14   aromatic  1.380  0.020  1.380
 POX  C9   N3    single    1.405  0.020  1.405
 POX  C10  C11   aromatic  1.375  0.020  1.375
 POX  C11  C12   aromatic  1.398  0.020  1.398
 POX  C12  C13   aromatic  1.404  0.020  1.404
 POX  C12  N1    aromatic  1.358  0.020  1.358
 POX  C13  C14   aromatic  1.399  0.020  1.399
 POX  C15  N4    aromatic  1.314  0.020  1.314
 POX  C15  N5    aromatic  1.319  0.020  1.319
 POX  C16  N3    single    1.360  0.020  1.360
 POX  C16  N5    aromatic  1.334  0.020  1.334
 POX  C16  C17   aromatic  1.412  0.020  1.412
 POX  C19  C17   single    1.448  0.020  1.448
 POX  C19  N7    double    1.276  0.020  1.276
 POX  C20  C21   single    1.505  0.020  1.505
 POX  C20  O1    single    1.418  0.020  1.418
 POX  C21  O2    single    1.404  0.020  1.404
 POX  C22  O2    single    1.405  0.020  1.405
 POX  C4   C5    aromatic  1.386  0.020  1.386
 POX  C5   C6    aromatic  1.390  0.020  1.390
 POX  N1   N2    aromatic  1.337  0.020  1.337
 POX  N4   C18   aromatic  1.345  0.020  1.345
 POX  C17  C18   aromatic  1.418  0.020  1.418
 POX  N7   O1    single    1.364  0.020  1.364
 POX  C2   H2    single    0.930  0.020  1.080
 POX  N6   HN6   single    0.860  0.020  1.020
 POX  N6   HN6A  single    0.860  0.020  1.020
 POX  C7   H7    single    0.970  0.020  1.090
 POX  C7   H7A   single    0.970  0.020  1.090
 POX  C8   H8    single    0.930  0.020  1.080
 POX  C10  H10   single    0.930  0.020  1.080
 POX  C11  H11   single    0.930  0.020  1.080
 POX  C14  H14   single    0.930  0.020  1.080
 POX  C15  H15   single    0.930  0.020  1.080
 POX  C19  H19   single    0.930  0.020  1.080
 POX  C20  H20   single    0.970  0.020  1.090
 POX  C20  H20A  single    0.970  0.020  1.090
 POX  C21  H21   single    0.970  0.020  1.090
 POX  C21  H21A  single    0.970  0.020  1.090
 POX  C22  H22   single    0.970  0.020  1.090
 POX  C22  H22A  single    0.970  0.020  1.090
 POX  C22  H22B  single    0.970  0.020  1.090
 POX  C4   H4    single    0.930  0.020  1.080
 POX  C5   H5    single    0.930  0.020  1.080
 POX  C6   H6    single    0.930  0.020  1.080
 POX  N3   HN3   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
 POX  C6    C1   C7    120.51  3.000
 POX  C6    C1   C2    119.63  3.000
 POX  C7    C1   C2    119.86  3.000
 POX  H2    C2   C3    120.15  3.000
 POX  H2    C2   C1    121.06  3.000
 POX  C3    C2   C1    118.79  3.000
 POX  F1    C3   C4    118.76  3.000
 POX  F1    C3   C2    118.65  3.000
 POX  C4    C3   C2    122.59  3.000
 POX  H7A   C7   H7    107.08  3.000
 POX  H7A   C7   N1    107.15  3.000
 POX  H7    C7   N1    108.86  3.000
 POX  H7A   C7   C1    111.03  3.000
 POX  H7    C7   C1    110.20  3.000
 POX  N1    C7   C1    112.33  3.000
 POX  H8    C8   N2    120.68  3.000
 POX  H8    C8   C13   128.55  3.000
 POX  N2    C8   C13   110.76  3.000
 POX  N3    C9   C14   122.33  3.000
 POX  N3    C9   C10   117.08  3.000
 POX  C14   C9   C10   120.54  3.000
 POX  H10   C10  C11   119.17  3.000
 POX  H10   C10  C9    118.57  3.000
 POX  C11   C10  C9    122.26  3.000
 POX  H11   C11  C12   122.43  3.000
 POX  H11   C11  C10   120.65  3.000
 POX  C12   C11  C10   116.91  3.000
 POX  N1    C12  C13   106.45  3.000
 POX  N1    C12  C11   131.98  3.000
 POX  C13   C12  C11   121.58  3.000
 POX  C14   C13  C12   120.71  3.000
 POX  C14   C13  C8    135.34  3.000
 POX  C12   C13  C8    103.95  3.000
 POX  H14   C14  C13   120.65  3.000
 POX  H14   C14  C9    121.37  3.000
 POX  C13   C14  C9    117.99  3.000
 POX  H15   C15  N5    115.91  3.000
 POX  H15   C15  N4    116.07  3.000
 POX  N5    C15  N4    128.01  3.000
 POX  C17   C16  N5    121.98  3.000
 POX  C17   C16  N3    120.74  3.000
 POX  N5    C16  N3    117.27  3.000
 POX  H20A  C20  H20   107.92  3.000
 POX  H20A  C20  O1    110.57  3.000
 POX  H20   C20  O1    110.56  3.000
 POX  H20A  C20  C21   110.55  3.000
 POX  H20   C20  C21   108.72  3.000
 POX  O1    C20  C21   108.50  3.000
 POX  H21A  C21  H21   106.60  3.000
 POX  H21A  C21  O2    111.16  3.000
 POX  H21   C21  O2    111.26  3.000
 POX  H21A  C21  C20   110.22  3.000
 POX  H21   C21  C20   107.59  3.000
 POX  O2    C21  C20   109.89  3.000
 POX  H22B  C22  H22A  108.41  3.000
 POX  H22B  C22  H22   108.47  3.000
 POX  H22A  C22  H22   107.77  3.000
 POX  H22B  C22  O2    108.07  3.000
 POX  H22A  C22  O2    112.00  3.000
 POX  H22   C22  O2    112.01  3.000
 POX  H4    C4   C5    121.30  3.000
 POX  H4    C4   C3    120.58  3.000
 POX  C5    C4   C3    118.12  3.000
 POX  H5    C5   C6    119.96  3.000
 POX  H5    C5   C4    119.53  3.000
 POX  C6    C5   C4    120.51  3.000
 POX  H6    C6   C5    119.89  3.000
 POX  H6    C6   C1    119.75  3.000
 POX  C5    C6   C1    120.36  3.000
 POX  N2    N1   C12   111.49  3.000
 POX  N2    N1   C7    120.85  3.000
 POX  C12   N1   C7    127.19  3.000
 POX  N1    N2   C8    107.33  3.000
 POX  C18   N4   C15   116.54  3.000
 POX  C16   N5   C15   116.51  3.000
 POX  C18   C17  C19   123.44  3.000
 POX  C18   C17  C16   115.40  3.000
 POX  C19   C17  C16   121.08  3.000
 POX  C17   C18  N4    121.40  3.000
 POX  C17   C18  N6    122.31  3.000
 POX  N4    C18  N6    116.29  3.000
 POX  O1    N7   C19   112.44  3.000
 POX  N7    O1   C20   110.05  3.000
 POX  C22   O2   C21   112.39  3.000
 POX  HN3   N3   C16   117.37  3.000
 POX  HN3   N3   C9    114.82  3.000
 POX  C16   N3   C9    126.75  3.000
 POX  H19   C19  N7    119.00  3.000
 POX  H19   C19  C17   118.17  3.000
 POX  N7    C19  C17   122.79  3.000
 POX  HN6A  N6   HN6   119.88  3.000
 POX  HN6A  N6   C18   120.68  3.000
 POX  HN6   N6   C18   118.93  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
 POX  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 POX  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 POX  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 POX  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 POX  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 POX  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 POX  CONST_07  C11   C12  C13  C8   180.00   0.0  0
 POX  CONST_08  N1    C12  C13  C8     0.00   0.0  0
 POX  CONST_09  C9    C14  C13  C8   180.00   0.0  0
 POX  CONST_10  C12   N1   N2   C8     0.00   0.0  0
 POX  CONST_11  C12   C11  C10  C9     0.00   0.0  0
 POX  CONST_12  C12   C13  C14  C9     0.00   0.0  0
 POX  CONST_13  C13   C14  C9   C10    0.00   0.0  0
 POX  CONST_14  C13   C12  C11  C10    0.00   0.0  0
 POX  CONST_15  N1    C12  C11  C10  180.00   0.0  0
 POX  CONST_16  C14   C9   C10  C11    0.00   0.0  0
 POX  CONST_17  C14   C13  C12  C11    0.00   0.0  0
 POX  CONST_18  N2    N1   C12  C11  180.00   0.0  0
 POX  CONST_19  N2    C8   C13  C12    0.00   0.0  0
 POX  CONST_20  N1    N2   C8   C13    0.00   0.0  0
 POX  CONST_21  N2    N1   C12  C13    0.00   0.0  0
 POX  CONST_22  N2    C8   C13  C14  180.00   0.0  0
 POX  CONST_23  N1    C12  C13  C14  180.00   0.0  0
 POX  CONST_24  C17   C18  N4   C15    0.00   0.0  0
 POX  CONST_25  C17   C16  N5   C15    0.00   0.0  0
 POX  CONST_26  N4    C15  N5   C16    0.00   0.0  0
 POX  CONST_27  N4    C18  C17  C16    0.00   0.0  0
 POX  CONST_28  C18   N4   C15  N5     0.00   0.0  0
 POX  CONST_29  C18   C17  C16  N5     0.00   0.0  0
 POX  CONST_30  F1    C3   C2   C1   180.00   0.0  0
 POX  CONST_31  C7    C1   C2   C3   180.00   0.0  0
 POX  CONST_32  C15   N4   C18  N6   180.00   0.0  0
 POX  CONST_33  C16   C17  C18  N6   180.00   0.0  0
 POX  CONST_34  C5    C6   C1   C7   180.00   0.0  0
 POX  CONST_35  C11   C12  N1   C7     0.00   0.0  0
 POX  CONST_36  C13   C12  N1   C7   180.00   0.0  0
 POX  CONST_37  C8    N2   N1   C7   180.00   0.0  0
 POX  CONST_38  N3    C9   C10  C11  180.00   0.0  0
 POX  CONST_39  N3    C9   C14  C13  180.00   0.0  0
 POX  CONST_40  N3    C16  N5   C15  180.00   0.0  0
 POX  CONST_41  N5    C16  C17  C19  180.00   0.0  0
 POX  CONST_42  N4    C18  C17  C19  180.00   0.0  0
 POX  CONST_43  F1    C3   C4   C5   180.00   0.0  0
 POX  CONST_44  C18   C17  C16  N3   180.00   0.0  0
 POX  CONST_45  H5    C5   C6   C1   180.00   0.0  0
 POX  CONST_46  H6    C6   C1   C2   180.00   0.0  0
 POX  CONST_47  H4    C4   C3   C2   180.00   0.0  0
 POX  CONST_48  H14   C14  C13  C8     0.00   0.0  0
 POX  CONST_49  H11   C11  C10  C9   180.00   0.0  0
 POX  CONST_50  H10   C10  C11  C12  180.00   0.0  0
 POX  CONST_51  H8    C8   C13  C12  180.00   0.0  0
 POX  CONST_52  H15   C15  N5   C16  180.00   0.0  0
 POX  CONST_53  H2    C2   C3   C4   180.00   0.0  0
 POX  CONST_54  HN6   N6   C18  N4     0.00   0.0  0
 POX  CONST_55  HN6A  N6   C18  N4   180.00   0.0  0
 POX  Var_01    C12   N1   C7   C1    76.11  30.0  2
 POX  Var_02    N1    C7   C1   C2    61.70  30.0  2
 POX  Var_03    N5    C16  N3   C9    -8.07  30.0  1
 POX  Var_04    C16   N3   C9   C10  138.69  30.0  2
 POX  Var_05    N7    C19  C17  C16  172.25  30.0  2
 POX  Var_06    O2    C21  C20  O1    66.87  30.0  3
 POX  Var_07    H22   C22  O2   C21  -59.66  30.0  3
 POX  Var_08    H21   C21  O2   C22   60.72  30.0  2
 POX  Var_09    H20   C20  O1   N7    61.89  30.0  1

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
 POX  plan-1  C1    0.020
 POX  plan-1  C2    0.020
 POX  plan-1  C3    0.020
 POX  plan-1  C7    0.020
 POX  plan-1  C4    0.020
 POX  plan-1  C5    0.020
 POX  plan-1  C6    0.020
 POX  plan-1  F1    0.020
 POX  plan-1  H2    0.020
 POX  plan-1  H4    0.020
 POX  plan-1  H5    0.020
 POX  plan-1  H6    0.020
 POX  plan-2  C15   0.020
 POX  plan-2  C16   0.020
 POX  plan-2  N4    0.020
 POX  plan-2  N5    0.020
 POX  plan-2  C17   0.020
 POX  plan-2  C18   0.020
 POX  plan-2  H15   0.020
 POX  plan-2  N3    0.020
 POX  plan-2  C19   0.020
 POX  plan-2  N6    0.020
 POX  plan-3  C7    0.020
 POX  plan-3  C8    0.020
 POX  plan-3  C9    0.020
 POX  plan-3  C10   0.020
 POX  plan-3  C11   0.020
 POX  plan-3  C12   0.020
 POX  plan-3  C13   0.020
 POX  plan-3  C14   0.020
 POX  plan-3  N1    0.020
 POX  plan-3  N2    0.020
 POX  plan-3  H8    0.020
 POX  plan-3  H10   0.020
 POX  plan-3  H11   0.020
 POX  plan-3  H14   0.020
 POX  plan-3  N3    0.020
 POX  plan-4  C18   0.020
 POX  plan-4  HN6   0.020
 POX  plan-4  HN6A  0.020
 POX  plan-4  N6    0.020
 POX  plan-5  C17   0.020
 POX  plan-5  N7    0.020
 POX  plan-5  O1    0.020
 POX  plan-5  H19   0.020
 POX  plan-5  C19   0.020

