# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:48:48 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 6-(2,4-dichlorophenyl)-8-ethyl-2-{[3-fluoro-4-(piperazin-1-yl)phenyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C(=Cc2cnc(Nc3ccc(N4CCNCC4)c(F)c3)nc12)c5ccc(Cl)cc5Cl
#
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
 981  981  6-(2,4-dichlorophenyl)-8-ethyl-2-{[3-fluoro-4-(piperazin-1-yl)phenyl]amino}pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  58  35  .  2021-08-06  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_981
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
 981  CAB   C   CR6   0  -0.061  -7.9056  -0.9765   0.4646
 981  CAC   C   CR16  0  -0.146  -7.1725  -1.3969  -0.6306
 981  CAD   C   CR6   0  -0.124  -5.8513  -0.9872  -0.7431
 981  CAG   C   CH2   0  -0.299   7.9633  -1.1846   1.4021
 981  CAH   C   CH2   0  -0.300   9.2219  -2.0092   1.2097
 981  CAJ   C   CR16  0  -0.189  -7.3450  -0.1608   1.4355
 981  CAK   C   CR16  0  -0.302  -6.0259   0.2314   1.2951
 981  CAL   C   CR6   0   0.190  -5.2470  -0.1743   0.2127
 981  CAM   C   CR6   0  -0.206  -3.8368   0.2479   0.1151
 981  CAN   C   CR16  0  -0.157  -2.8140  -0.6251   0.2259
 981  CAO   C   CR66  0  -0.110  -1.4731  -0.1722   0.1410
 981  CAP   C   CR16  0  -0.007  -0.3487  -0.9822   0.2615
 981  CAR   C   CR16  0  -0.495   3.7954  -0.5768   0.1608
 981  CAS   C   CR6   0   0.555   5.1074  -0.9965   0.1951
 981  CAT   C   CR6   0   0.140   6.2080  -0.1476   0.0932
 981  CAV   C   CH2   0  -0.302   8.5353   0.1248  -0.5329
 981  CAW   C   CH2   0  -0.296   9.7854  -0.7169  -0.7171
 981  CAX   C   CR6   0   0.567  -3.5831   1.6707  -0.0990
 981  CAZ   C   CR66  0   0.570  -1.2123   1.1943  -0.0753
 981  CBB   C   CR6   0   0.624   1.0150   0.7893  -0.0112
 981  CBD   C   CR6   0   0.369   3.5239   0.7809  -0.0141
 981  CBE   C   CR16  0  -0.360   4.6004   1.6608  -0.1361
 981  CBF   C   CR16  0  -0.313   5.9053   1.2041  -0.0727
 981  CBI   C   CH3   0  -0.666  -1.7665   4.2523   0.8409
 981  NAI   N   NH1   0  -0.600  10.2417  -1.1984   0.5725
 981  NAQ   N   N     0  -0.477   0.8834  -0.5274   0.1879
 981  NAU   N   NT    0  -0.502   7.5073  -0.6702   0.1143
 981  NAY   N   NR6   0  -0.589  -2.2540   2.0653  -0.2194
 981  NBA   N   N     0  -0.506   0.0184   1.6632  -0.1458
 981  NBC   N   NH1   0  -0.764   2.2497   1.3375  -0.0873
 981  OBG   O   O     0  -0.456  -4.4811   2.4919  -0.1787
 981  CLAA  CL  CL    0  -0.113  -9.5520  -1.4819   0.6183
 981  CLAE  CL  CL    0  -0.111  -4.9649  -1.5040  -2.1361
 981  H1    H   HCR6  0   0.303  -7.6182  -2.0274  -1.3870
 981  H2    H   HCH2  0   0.250   7.1932  -1.8080   1.8537
 981  H3    H   HCH2  0   0.236   9.5820  -2.3428   2.1848
 981  H4    H   HCR6  0   0.287  -7.9245   0.1643   2.2881
 981  H5    H   HCR6  0   0.273  -5.5810   0.8585   2.0562
 981  H6    H   HCR6  0   0.283  -3.0001  -1.6794   0.3938
 981  H7    H   HCR6  0   0.285  -0.4701  -2.0484   0.4243
 981  H8    H   HCR6  0   0.304   3.0038  -1.3040   0.2443
 981  H9    H   HCH2  0   0.206   8.7970   1.0248   0.0449
 981  H10   H   HCH2  0   0.248   8.1741   0.4526  -1.5092
 981  H11   H   HCH2  0   0.195   9.5602  -1.5305  -1.4244
 981  H12   H   HCH2  0   0.236  10.5640  -0.1001  -1.1699
 981  H13   H   HCR6  0   0.273   4.4203   2.7204  -0.2726
 981  H14   H   HCR6  0   0.276   6.7057   1.9268  -0.1583
 981  H15   H   HCH2  0   0.267  -2.8079   3.8959  -1.0152
 981  H16   H   HCH2  0   0.266  -1.0904   3.5480  -1.0819
 981  H17   H   HCH3  0   0.240  -1.5796   5.3023   0.6164
 981  H18   H   HCH3  0   0.235  -2.6456   4.1968   1.4819
 981  H19   H   HCH3  0   0.235  -0.9093   3.8696   1.3938
 981  H20   H   HNH1  0   0.355  11.0869  -1.7414   0.4559
 981  H21   H   HNH1  0   0.416   2.2295   2.3375  -0.2242
 981  H22   H   HCH2  0   0.210   8.1666  -0.3608   2.1032
 981  H23   H   HCH2  0   0.195   8.9626  -2.9088   0.6296
 981  CBH   C   CH2   0  -0.321  -1.9742   3.4853  -0.4529
 981  FAF   F   F     0  -0.316   5.3270  -2.3163   0.3268

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
 981  CLAE  CAD  single    1.730  0.020  1.730
 981  CAC   CAD  aromatic  1.388  0.020  1.388
 981  CAC   CAB  aromatic  1.383  0.020  1.383
 981  CLAA  CAB  single    1.729  0.020  1.729
 981  CAD   CAL  aromatic  1.393  0.020  1.393
 981  CAB   CAJ  aromatic  1.386  0.020  1.386
 981  CAL   CAM  single    1.475  0.020  1.475
 981  CAL   CAK  aromatic  1.394  0.020  1.394
 981  CAN   CAM  double    1.349  0.020  1.349
 981  CAN   CAO  single    1.418  0.020  1.418
 981  CAP   NAQ  aromatic  1.315  0.020  1.315
 981  CAP   CAO  aromatic  1.391  0.020  1.391
 981  CAJ   CAK  aromatic  1.383  0.020  1.383
 981  CAM   CAX  single    1.461  0.020  1.461
 981  NAQ   CBB  aromatic  1.338  0.020  1.338
 981  CAO   CAZ  aromatic  1.408  0.020  1.408
 981  CBB   NBA  aromatic  1.332  0.020  1.332
 981  CBB   NBC  single    1.353  0.020  1.353
 981  CAZ   NBA  aromatic  1.319  0.020  1.319
 981  CAZ   NAY  single    1.366  0.020  1.366
 981  CAX   OBG  double    1.219  0.020  1.219
 981  CAX   NAY  single    1.392  0.020  1.392
 981  NBC   CBD  single    1.392  0.020  1.392
 981  NAY   CBH  single    1.466  0.020  1.466
 981  CBE   CBD  aromatic  1.396  0.020  1.396
 981  CBE   CBF  aromatic  1.384  0.020  1.384
 981  CBD   CAR  aromatic  1.396  0.020  1.396
 981  CBI   CBH  single    1.518  0.020  1.518
 981  CBF   CAT  aromatic  1.395  0.020  1.395
 981  CAR   CAS  aromatic  1.378  0.020  1.378
 981  CAT   CAS  aromatic  1.394  0.020  1.394
 981  CAT   NAU  single    1.401  0.020  1.401
 981  CAS   FAF  single    1.344  0.020  1.344
 981  CAV   NAU  single    1.452  0.020  1.452
 981  CAV   CAW  single    1.518  0.020  1.518
 981  NAU   CAG  single    1.460  0.020  1.460
 981  CAG   CAH  single    1.517  0.020  1.517
 981  CAW   NAI  single    1.450  0.020  1.450
 981  CAH   NAI  single    1.450  0.020  1.450
 981  CAC   H1   single    0.930  0.020  1.080
 981  CAG   H2   single    0.970  0.020  1.090
 981  CAH   H3   single    0.970  0.020  1.090
 981  CAJ   H4   single    0.930  0.020  1.080
 981  CAK   H5   single    0.930  0.020  1.080
 981  CAN   H6   single    0.930  0.020  1.080
 981  CAP   H7   single    0.930  0.020  1.080
 981  CAR   H8   single    0.930  0.020  1.080
 981  CAV   H9   single    0.970  0.020  1.090
 981  CAV   H10  single    0.970  0.020  1.090
 981  CAW   H11  single    0.970  0.020  1.090
 981  CAW   H12  single    0.970  0.020  1.090
 981  CBE   H13  single    0.930  0.020  1.080
 981  CBF   H14  single    0.930  0.020  1.080
 981  CBH   H15  single    0.970  0.020  1.090
 981  CBH   H16  single    0.970  0.020  1.090
 981  CBI   H17  single    0.970  0.020  1.090
 981  CBI   H18  single    0.970  0.020  1.090
 981  CBI   H19  single    0.970  0.020  1.090
 981  NAI   H20  single    0.890  0.020  1.040
 981  NBC   H21  single    0.860  0.020  1.020
 981  CAG   H22  single    0.970  0.020  1.090
 981  CAH   H23  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
 981  CLAA  CAB  CAJ  119.66  3.000
 981  CAJ   CAB  CAC  121.26  3.000
 981  CLAA  CAB  CAC  119.09  3.000
 981  H1    CAC  CAD  120.53  3.000
 981  H1    CAC  CAB  120.85  3.000
 981  CAD   CAC  CAB  118.62  3.000
 981  CLAE  CAD  CAL  120.31  3.000
 981  CAL   CAD  CAC  121.99  3.000
 981  CLAE  CAD  CAC  117.70  3.000
 981  H22   CAG  H2   107.15  3.000
 981  H22   CAG  NAU  110.84  3.000
 981  H2    CAG  NAU  110.28  3.000
 981  H22   CAG  CAH  109.53  3.000
 981  H2    CAG  CAH  109.16  3.000
 981  NAU   CAG  CAH  109.81  3.000
 981  H23   CAH  H3   107.37  3.000
 981  H23   CAH  NAI  113.00  3.000
 981  H3    CAH  NAI  109.35  3.000
 981  H23   CAH  CAG  108.39  3.000
 981  H3    CAH  CAG  109.06  3.000
 981  NAI   CAH  CAG  109.59  3.000
 981  H4    CAJ  CAK  120.39  3.000
 981  H4    CAJ  CAB  120.83  3.000
 981  CAK   CAJ  CAB  118.78  3.000
 981  H5    CAK  CAL  119.03  3.000
 981  H5    CAK  CAJ  119.02  3.000
 981  CAL   CAK  CAJ  121.95  3.000
 981  CAM   CAL  CAK  120.15  3.000
 981  CAK   CAL  CAD  117.41  3.000
 981  CAM   CAL  CAD  122.44  3.000
 981  CAX   CAM  CAN  120.70  3.000
 981  CAX   CAM  CAL  117.03  3.000
 981  CAN   CAM  CAL  122.28  3.000
 981  H6    CAN  CAO  118.85  3.000
 981  H6    CAN  CAM  120.80  3.000
 981  CAO   CAN  CAM  120.35  3.000
 981  CAZ   CAO  CAP  115.39  3.000
 981  CAZ   CAO  CAN  119.63  3.000
 981  CAP   CAO  CAN  124.98  3.000
 981  H7    CAP  NAQ  116.92  3.000
 981  H7    CAP  CAO  119.64  3.000
 981  NAQ   CAP  CAO  123.44  3.000
 981  H8    CAR  CBD  121.54  3.000
 981  H8    CAR  CAS  119.45  3.000
 981  CBD   CAR  CAS  118.99  3.000
 981  FAF   CAS  CAT  118.43  3.000
 981  FAF   CAS  CAR  117.20  3.000
 981  CAT   CAS  CAR  124.37  3.000
 981  NAU   CAT  CBF  124.37  3.000
 981  NAU   CAT  CAS  120.28  3.000
 981  CBF   CAT  CAS  115.31  3.000
 981  H10   CAV  H9   107.61  3.000
 981  H10   CAV  NAU  109.20  3.000
 981  H9    CAV  NAU  112.46  3.000
 981  H10   CAV  CAW  109.30  3.000
 981  H9    CAV  CAW  108.73  3.000
 981  NAU   CAV  CAW  109.49  3.000
 981  H12   CAW  H11  107.27  3.000
 981  H12   CAW  NAI  109.39  3.000
 981  H11   CAW  NAI  112.97  3.000
 981  H12   CAW  CAV  108.92  3.000
 981  H11   CAW  CAV  108.61  3.000
 981  NAI   CAW  CAV  109.59  3.000
 981  OBG   CAX  NAY  120.44  3.000
 981  NAY   CAX  CAM  117.04  3.000
 981  OBG   CAX  CAM  122.52  3.000
 981  NBA   CAZ  NAY  118.65  3.000
 981  NAY   CAZ  CAO  119.60  3.000
 981  NBA   CAZ  CAO  121.75  3.000
 981  NBC   CBB  NBA  114.28  3.000
 981  NBC   CBB  NAQ  119.79  3.000
 981  NBA   CBB  NAQ  125.93  3.000
 981  NBC   CBD  CBE  116.70  3.000
 981  CBE   CBD  CAR  118.31  3.000
 981  NBC   CBD  CAR  124.99  3.000
 981  H13   CBE  CBF  119.03  3.000
 981  H13   CBE  CBD  119.96  3.000
 981  CBF   CBE  CBD  121.02  3.000
 981  H14   CBF  CBE  118.27  3.000
 981  H14   CBF  CAT  119.75  3.000
 981  CBE   CBF  CAT  121.99  3.000
 981  H19   CBI  H18  108.57  3.000
 981  H19   CBI  H17  107.94  3.000
 981  H18   CBI  H17  107.98  3.000
 981  H19   CBI  CBH  111.26  3.000
 981  H18   CBI  CBH  111.42  3.000
 981  H17   CBI  CBH  109.55  3.000
 981  H20   NAI  CAW  109.80  3.000
 981  H20   NAI  CAH  109.76  3.000
 981  CAW   NAI  CAH  110.80  3.000
 981  CBB   NAQ  CAP  116.14  3.000
 981  CAV   NAU  CAT  116.48  3.000
 981  CAV   NAU  CAG  111.41  3.000
 981  CAT   NAU  CAG  115.76  3.000
 981  CBH   NAY  CAZ  119.28  3.000
 981  CBH   NAY  CAX  118.08  3.000
 981  CAZ   NAY  CAX  122.59  3.000
 981  CBB   NBA  CAZ  117.35  3.000
 981  H21   NBC  CBD  114.92  3.000
 981  H21   NBC  CBB  113.00  3.000
 981  CBD   NBC  CBB  132.08  3.000
 981  H16   CBH  H15  107.62  3.000
 981  H16   CBH  NAY  107.66  3.000
 981  H15   CBH  NAY  107.59  3.000
 981  H16   CBH  CBI  110.66  3.000
 981  H15   CBH  CBI  110.80  3.000
 981  NAY   CBH  CBI  112.31  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
 981  CONST_01  CAL   CAD  CAC  CAB     0.00   0.0  0
 981  CONST_02  CAL   CAK  CAJ  CAB     0.00   0.0  0
 981  CONST_03  CAK   CAL  CAD  CAC     0.00   0.0  0
 981  CONST_04  CAK   CAJ  CAB  CAC     0.00   0.0  0
 981  CONST_05  CAJ   CAB  CAC  CAD     0.00   0.0  0
 981  CONST_06  CAJ   CAK  CAL  CAD     0.00   0.0  0
 981  CONST_07  CBB   NAQ  CAP  CAO     0.00   0.0  0
 981  CONST_08  CBB   NBA  CAZ  CAO     0.00   0.0  0
 981  CONST_09  NBA   CBB  NAQ  CAP     0.00   0.0  0
 981  CONST_10  NBA   CAZ  CAO  CAP     0.00   0.0  0
 981  CONST_11  CBF   CBE  CBD  CAR     0.00   0.0  0
 981  CONST_12  CBF   CAT  CAS  CAR     0.00   0.0  0
 981  CONST_13  CBE   CBD  CAR  CAS     0.00   0.0  0
 981  CONST_14  CBE   CBF  CAT  CAS     0.00   0.0  0
 981  CONST_15  CBD   CBE  CBF  CAT     0.00   0.0  0
 981  CONST_16  CBD   CAR  CAS  CAT     0.00   0.0  0
 981  CONST_17  NAQ   CAP  CAO  CAZ     0.00   0.0  0
 981  CONST_18  NAQ   CBB  NBA  CAZ     0.00   0.0  0
 981  CONST_19  CAM   CAL  CAD  CAC   180.00   0.0  0
 981  CONST_20  CAM   CAL  CAK  CAJ   180.00   0.0  0
 981  CONST_21  NAU   CAT  CAS  CAR   180.00   0.0  0
 981  CONST_22  NAU   CAT  CBF  CBE   180.00   0.0  0
 981  CONST_23  CAZ   NAY  CAX  CAM     0.00   0.0  0
 981  CONST_24  CLAE  CAD  CAC  CAB   180.00   0.0  0
 981  CONST_25  CLAA  CAB  CAC  CAD   180.00   0.0  0
 981  CONST_26  CLAE  CAD  CAL  CAK   180.00   0.0  0
 981  CONST_27  CLAA  CAB  CAJ  CAK   180.00   0.0  0
 981  CONST_28  CLAE  CAD  CAL  CAM     0.00   0.0  0
 981  CONST_29  NBC   CBB  NAQ  CAP   180.00   0.0  0
 981  CONST_30  NBC   CBD  CAR  CAS   180.00   0.0  0
 981  CONST_31  NBC   CBB  NBA  CAZ   180.00   0.0  0
 981  CONST_32  FAF   CAS  CAR  CBD   180.00   0.0  0
 981  CONST_33  NBC   CBD  CBE  CBF   180.00   0.0  0
 981  CONST_34  FAF   CAS  CAT  CBF   180.00   0.0  0
 981  CONST_35  NAU   CAT  CAS  FAF     0.00   0.0  0
 981  CONST_36  CBH   NAY  CAX  CAM   180.00   0.0  0
 981  CONST_37  OBG   CAX  NAY  CAZ   180.00   0.0  0
 981  CONST_38  H5    CAK  CAJ  CAB   180.00   0.0  0
 981  CONST_39  H4    CAJ  CAB  CAC   180.00   0.0  0
 981  CONST_40  H1    CAC  CAB  CAJ   180.00   0.0  0
 981  CONST_41  H7    CAP  CAO  CAN     0.00   0.0  0
 981  CONST_42  H13   CBE  CBD  CAR   180.00   0.0  0
 981  CONST_43  H14   CBF  CAT  CAS   180.00   0.0  0
 981  CONST_44  H8    CAR  CAS  CAT   180.00   0.0  0
 981  CONST_45  OBG   CAX  NAY  CBH     0.00   0.0  0
 981  Var_01    CAN   CAM  CAL  CAD   -67.00  30.0  2
 981  Var_02    CBF   CAT  NAU  CAG   111.20  30.0  2
 981  Var_03    CAW   CAV  NAU  CAG    57.83  30.0  1
 981  Var_04    CAW   NAI  CAH  CAG   -59.44  30.0  1
 981  Var_05    CAT   NAU  CAG  CAH   166.33  30.0  1
 981  Var_06    CAV   CAW  NAI  CAH    59.92  30.0  1
 981  Var_07    NAU   CAV  CAW  NAI   -58.26  30.0  1
 981  Var_08    NAU   CAG  CAH  NAI    57.32  30.0  1
 981  Var_09    CBB   NBC  CBD  CAR     0.41  30.0  1
 981  Var_10    NAQ   CBB  NBC  CBD     1.02  30.0  2
 981  Var_11    CBI   CBH  NAY  CAX    91.51  30.0  3
 981  Var_12    H17   CBI  CBH  NAY  -179.02  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
 981  plan-1  CAB   0.020
 981  plan-1  CAC   0.020
 981  plan-1  CAD   0.020
 981  plan-1  CAJ   0.020
 981  plan-1  CAK   0.020
 981  plan-1  CAL   0.020
 981  plan-1  CAM   0.020
 981  plan-1  CLAA  0.020
 981  plan-1  CLAE  0.020
 981  plan-1  H1    0.020
 981  plan-1  H4    0.020
 981  plan-1  H5    0.020
 981  plan-2  CAR   0.020
 981  plan-2  CAS   0.020
 981  plan-2  CAT   0.020
 981  plan-2  CBD   0.020
 981  plan-2  CBE   0.020
 981  plan-2  CBF   0.020
 981  plan-2  NAU   0.020
 981  plan-2  NBC   0.020
 981  plan-2  H8    0.020
 981  plan-2  H13   0.020
 981  plan-2  H14   0.020
 981  plan-2  FAF   0.020
 981  plan-3  CAL   0.020
 981  plan-3  CAM   0.020
 981  plan-3  CAN   0.020
 981  plan-3  CAO   0.020
 981  plan-3  CAP   0.020
 981  plan-3  CAX   0.020
 981  plan-3  CAZ   0.020
 981  plan-3  CBB   0.020
 981  plan-3  NAQ   0.020
 981  plan-3  NAY   0.020
 981  plan-3  NBA   0.020
 981  plan-3  NBC   0.020
 981  plan-3  OBG   0.020
 981  plan-3  H6    0.020
 981  plan-3  H7    0.020
 981  plan-3  CBH   0.020

