# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 19:55:31 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2E)-3-(3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-5-fluorophenyl)prop-2-enenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Oc2cc(F)cc(\C=C\C#N)c2)c(OCCN3C=CC(=O)NC3=O)c1
#
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
 506  506  (2E)-3-(3-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]-4-fluorophenoxy}-5-fluorophenyl)prop-2-enenitrile  ligand  45  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_506
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
 506  OAC  O  O     0  -0.482  -3.4813  -1.6075   1.1232
 506  CBC  C  CR6   0   0.731  -2.5815  -1.8136   0.3340
 506  NAS  N  NR16  0  -0.730  -1.6500  -2.7997   0.5214
 506  CBB  C  CR6   0   0.572  -0.5944  -3.1467  -0.3104
 506  OAB  O  O     0  -0.461   0.1341  -4.0790  -0.0229
 506  CAK  C  CR16  0  -0.493  -0.4865  -2.3089  -1.4768
 506  CAL  C  CR16  0   0.104  -1.3811  -1.3255  -1.6691
 506  NBD  N  NR6   0  -0.518  -2.4192  -1.0788  -0.8187
 506  CAR  C  CH2   0  -0.361  -3.3629  -0.0040  -1.0979
 506  CAQ  C  CH2   0  -0.169  -3.0638   1.2531  -0.3164
 506  OAT  O  O2    0  -0.486  -1.7522   1.6757  -0.6720
 506  CBA  C  CR6   0   0.345  -1.2678   2.7287   0.0247
 506  CAO  C  CR16  0  -0.495  -1.7195   4.0206  -0.2129
 506  CAV  C  CR6   0   0.541  -1.1567   5.0620   0.4978
 506  FAD  F  F     0  -0.312  -1.5948   6.3069   0.2632
 506  CAI  C  CR16  0  -0.423  -0.1588   4.8678   1.4328
 506  CAJ  C  CR16  0  -0.296   0.2882   3.5749   1.6600
 506  CAZ  C  CR6   0   0.230  -0.2700   2.5095   0.9728
 506  OAU  O  O2    0  -0.500   0.1217   1.2328   1.2747
 506  CAY  C  CR6   0   0.430   0.9941   0.5805   0.4675
 506  CAP  C  CR16  0  -0.404   1.4359  -0.6573   0.9238
 506  CAN  C  CR16  0  -0.502   1.4550   1.0921  -0.7359
 506  CAW  C  CR6   0   0.588   2.3474   0.3226  -1.4631
 506  FAE  F  F     0  -0.311   2.7790   0.8098  -2.6343
 506  CAM  C  CR16  0  -0.504   2.8078  -0.9031  -1.0475
 506  CAX  C  CR6   0   0.165   2.3472  -1.3959   0.1768
 506  CAH  C  C1    0  -0.175   2.7944  -2.6748   0.7169
 506  CAG  C  C1    0  -0.355   3.7503  -3.4506   0.1893
 506  CAF  C  CSP   0   0.087   4.1072  -4.6830   0.7944
 506  NAA  N  NS    0  -0.268   4.4099  -5.6903   1.2687
 506  H1   H  HNR6  0   0.424  -1.7658  -3.3503   1.3632
 506  H2   H  HCR6  0   0.288   0.3132  -2.4684  -2.1823
 506  H3   H  HCR6  0   0.319  -1.3286  -0.6776  -2.5317
 506  H4   H  HCH2  0   0.285  -3.3226   0.1986  -2.1673
 506  H5   H  HCH2  0   0.291  -4.3740  -0.3365  -0.8697
 506  H6   H  HCH2  0   0.249  -3.8081   2.0127  -0.5764
 506  H7   H  HCH2  0   0.243  -3.1282   1.0732   0.7600
 506  H8   H  HCR6  0   0.300  -2.4900   4.2060  -0.9508
 506  H9   H  HCR6  0   0.290   0.2632   5.7034   1.9744
 506  H10  H  HCR6  0   0.289   1.0634   3.3930   2.3927
 506  H11  H  HCR6  0   0.283   1.0756  -1.0358   1.8722
 506  H12  H  HCR6  0   0.303   1.1479   2.0570  -1.1167
 506  H13  H  HCR6  0   0.281   3.5008  -1.4561  -1.6666
 506  H14  H  H     0   0.289   2.3077  -2.9943   1.6305
 506  H15  H  H     0   0.320   4.2905  -3.1957  -0.7137

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
 506  FAD  CAV  single    1.340  0.020  1.340
 506  CAV  CAI  aromatic  1.381  0.020  1.381
 506  CAV  CAO  aromatic  1.381  0.020  1.381
 506  CAI  CAJ  aromatic  1.387  0.020  1.387
 506  CAO  CBA  aromatic  1.389  0.020  1.389
 506  OAC  CBC  double    1.214  0.020  1.214
 506  CAJ  CAZ  aromatic  1.385  0.020  1.385
 506  CBA  CAZ  aromatic  1.394  0.020  1.394
 506  CBA  OAT  single    1.352  0.020  1.352
 506  NAS  CBC  single    1.369  0.020  1.369
 506  NAS  CBB  single    1.388  0.020  1.388
 506  CBC  NBD  single    1.377  0.020  1.377
 506  CAZ  OAU  single    1.369  0.020  1.369
 506  OAT  CAQ  single    1.423  0.020  1.423
 506  OAB  CBB  double    1.218  0.020  1.218
 506  CBB  CAK  single    1.440  0.020  1.440
 506  NBD  CAR  single    1.457  0.020  1.457
 506  NBD  CAL  single    1.364  0.020  1.364
 506  OAU  CAY  single    1.356  0.020  1.356
 506  CAQ  CAR  single    1.510  0.020  1.510
 506  CAK  CAL  double    1.343  0.020  1.343
 506  CAN  CAY  aromatic  1.386  0.020  1.386
 506  CAN  CAW  aromatic  1.385  0.020  1.385
 506  CAY  CAP  aromatic  1.391  0.020  1.391
 506  FAE  CAW  single    1.340  0.020  1.340
 506  CAW  CAM  aromatic  1.374  0.020  1.374
 506  CAP  CAX  aromatic  1.391  0.020  1.391
 506  CAM  CAX  aromatic  1.398  0.020  1.398
 506  CAX  CAH  single    1.459  0.020  1.459
 506  CAH  CAG  double    1.339  0.020  1.339
 506  CAG  CAF  single    1.419  0.020  1.419
 506  CAF  NAA  triple    1.154  0.020  1.154
 506  NAS  H1   single    0.860  0.020  1.020
 506  CAK  H2   single    0.930  0.020  1.080
 506  CAL  H3   single    0.930  0.020  1.080
 506  CAR  H4   single    0.970  0.020  1.090
 506  CAR  H5   single    0.970  0.020  1.090
 506  CAQ  H6   single    0.970  0.020  1.090
 506  CAQ  H7   single    0.970  0.020  1.090
 506  CAO  H8   single    0.930  0.020  1.080
 506  CAI  H9   single    0.930  0.020  1.080
 506  CAJ  H10  single    0.930  0.020  1.080
 506  CAP  H11  single    0.930  0.020  1.080
 506  CAN  H12  single    0.930  0.020  1.080
 506  CAM  H13  single    0.930  0.020  1.080
 506  CAH  H14  single    0.930  0.020  1.080
 506  CAG  H15  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
 506  NBD  CBC  NAS  114.76  3.000
 506  NBD  CBC  OAC  122.75  3.000
 506  NAS  CBC  OAC  122.49  3.000
 506  H1   NAS  CBB  116.70  3.000
 506  H1   NAS  CBC  115.32  3.000
 506  CBB  NAS  CBC  127.97  3.000
 506  CAK  CBB  OAB  126.29  3.000
 506  CAK  CBB  NAS  113.38  3.000
 506  OAB  CBB  NAS  120.32  3.000
 506  H2   CAK  CAL  120.56  3.000
 506  H2   CAK  CBB  119.96  3.000
 506  CAL  CAK  CBB  119.47  3.000
 506  H3   CAL  NBD  115.23  3.000
 506  H3   CAL  CAK  121.41  3.000
 506  NBD  CAL  CAK  123.36  3.000
 506  CAR  NBD  CAL  120.44  3.000
 506  CAL  NBD  CBC  121.00  3.000
 506  CAR  NBD  CBC  118.53  3.000
 506  H5   CAR  H4   107.28  3.000
 506  H5   CAR  CAQ  109.25  3.000
 506  H4   CAR  CAQ  110.24  3.000
 506  H5   CAR  NBD  109.64  3.000
 506  H4   CAR  NBD  107.54  3.000
 506  CAQ  CAR  NBD  112.74  3.000
 506  H7   CAQ  H6   107.93  3.000
 506  H7   CAQ  OAT  110.44  3.000
 506  H6   CAQ  OAT  111.18  3.000
 506  H7   CAQ  CAR  111.15  3.000
 506  H6   CAQ  CAR  108.66  3.000
 506  OAT  CAQ  CAR  107.48  3.000
 506  CBA  OAT  CAQ  115.63  3.000
 506  CAZ  CBA  CAO  119.70  3.000
 506  CAZ  CBA  OAT  118.97  3.000
 506  CAO  CBA  OAT  121.31  3.000
 506  H8   CAO  CAV  120.78  3.000
 506  H8   CAO  CBA  120.47  3.000
 506  CAV  CAO  CBA  118.75  3.000
 506  CAI  CAV  FAD  119.03  3.000
 506  CAI  CAV  CAO  122.47  3.000
 506  FAD  CAV  CAO  118.50  3.000
 506  H9   CAI  CAJ  120.83  3.000
 506  H9   CAI  CAV  120.82  3.000
 506  CAJ  CAI  CAV  118.35  3.000
 506  H10  CAJ  CAZ  119.69  3.000
 506  H10  CAJ  CAI  119.90  3.000
 506  CAZ  CAJ  CAI  120.39  3.000
 506  OAU  CAZ  CAJ  119.51  3.000
 506  OAU  CAZ  CBA  120.09  3.000
 506  CAJ  CAZ  CBA  120.33  3.000
 506  CAY  OAU  CAZ  120.09  3.000
 506  CAN  CAY  CAP  120.49  3.000
 506  CAP  CAY  OAU  115.92  3.000
 506  CAN  CAY  OAU  123.58  3.000
 506  H11  CAP  CAX  120.19  3.000
 506  H11  CAP  CAY  119.51  3.000
 506  CAX  CAP  CAY  120.29  3.000
 506  H12  CAN  CAW  119.59  3.000
 506  H12  CAN  CAY  122.70  3.000
 506  CAW  CAN  CAY  117.71  3.000
 506  CAM  CAW  FAE  118.75  3.000
 506  CAM  CAW  CAN  123.57  3.000
 506  FAE  CAW  CAN  117.68  3.000
 506  H13  CAM  CAX  122.16  3.000
 506  H13  CAM  CAW  119.86  3.000
 506  CAX  CAM  CAW  117.98  3.000
 506  CAH  CAX  CAM  122.17  3.000
 506  CAH  CAX  CAP  117.88  3.000
 506  CAM  CAX  CAP  119.94  3.000
 506  H14  CAH  CAG  118.82  3.000
 506  H14  CAH  CAX  115.67  3.000
 506  CAG  CAH  CAX  125.50  3.000
 506  H15  CAG  CAF  115.77  3.000
 506  H15  CAG  CAH  123.25  3.000
 506  CAF  CAG  CAH  120.97  3.000
 506  NAA  CAF  CAG  180.00  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
 506  CONST_01  CAI  CAV  CAO  CBA     0.00   0.0  0
 506  CONST_02  CAI  CAJ  CAZ  CBA     0.00   0.0  0
 506  CONST_03  CAJ  CAI  CAV  CAO     0.00   0.0  0
 506  CONST_04  CAJ  CAZ  CBA  CAO     0.00   0.0  0
 506  CONST_05  CAZ  CAJ  CAI  CAV     0.00   0.0  0
 506  CONST_06  CAZ  CBA  CAO  CAV     0.00   0.0  0
 506  CONST_07  CAM  CAW  CAN  CAY     0.00   0.0  0
 506  CONST_08  CAM  CAX  CAP  CAY     0.00   0.0  0
 506  CONST_09  CAW  CAN  CAY  CAP     0.00   0.0  0
 506  CONST_10  CAW  CAM  CAX  CAP     0.00   0.0  0
 506  CONST_11  CAX  CAP  CAY  CAN     0.00   0.0  0
 506  CONST_12  CAX  CAM  CAW  CAN     0.00   0.0  0
 506  CONST_13  CAL  NBD  CBC  NAS     0.00   0.0  0
 506  CONST_14  NBD  CBC  NAS  CBB     0.00   0.0  0
 506  CONST_15  CAV  CAO  CBA  OAT   180.00   0.0  0
 506  CONST_16  CAJ  CAZ  CBA  OAT   180.00   0.0  0
 506  CONST_17  FAD  CAV  CAO  CBA   180.00   0.0  0
 506  CONST_18  OAU  CAZ  CBA  CAO   180.00   0.0  0
 506  CONST_19  CAJ  CAI  CAV  FAD   180.00   0.0  0
 506  CONST_20  OAU  CAZ  CAJ  CAI   180.00   0.0  0
 506  CONST_21  CAW  CAN  CAY  OAU   180.00   0.0  0
 506  CONST_22  CAX  CAP  CAY  OAU   180.00   0.0  0
 506  CONST_23  FAE  CAW  CAN  CAY   180.00   0.0  0
 506  CONST_24  CAH  CAX  CAP  CAY   180.00   0.0  0
 506  CONST_25  CAH  CAX  CAM  CAW   180.00   0.0  0
 506  CONST_26  CAX  CAM  CAW  FAE   180.00   0.0  0
 506  CONST_27  CBB  NAS  CBC  OAC   180.00   0.0  0
 506  CONST_28  CAL  NBD  CBC  OAC   180.00   0.0  0
 506  CONST_29  CAR  NBD  CBC  NAS   180.00   0.0  0
 506  CONST_30  H10  CAJ  CAZ  CBA   180.00   0.0  0
 506  CONST_31  H9   CAI  CAV  CAO   180.00   0.0  0
 506  CONST_32  H8   CAO  CAV  CAI   180.00   0.0  0
 506  CONST_33  H12  CAN  CAY  CAP   180.00   0.0  0
 506  CONST_34  H13  CAM  CAX  CAP   180.00   0.0  0
 506  CONST_35  H11  CAP  CAY  CAN   180.00   0.0  0
 506  CONST_36  H1   NAS  CBC  NBD   180.00   0.0  0
 506  CONST_37  CAR  NBD  CBC  OAC     0.00   0.0  0
 506  CONST_38  CAF  CAG  CAH  CAX   180.00   0.0  0
 506  CONST_39  H15  CAG  CAH  CAX     0.00   0.0  0
 506  CONST_40  H14  CAH  CAG  CAF     0.00   0.0  0
 506  Var_01    CAN  CAY  OAU  CAZ    -5.28  30.0  2
 506  Var_02    CAQ  CAR  NBD  CBC    79.31  30.0  3
 506  Var_03    CAO  CBA  OAT  CAQ   -74.52  30.0  1
 506  Var_04    CAG  CAH  CAX  CAP  -173.74  30.0  2
 506  Var_05    OAT  CAQ  CAR  NBD    59.53  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
 506  plan-1  OAC  0.020
 506  plan-1  CBC  0.020
 506  plan-1  NAS  0.020
 506  plan-1  CBB  0.020
 506  plan-1  OAB  0.020
 506  plan-1  CAK  0.020
 506  plan-1  CAL  0.020
 506  plan-1  NBD  0.020
 506  plan-1  CAR  0.020
 506  plan-1  H1   0.020
 506  plan-1  H2   0.020
 506  plan-1  H3   0.020
 506  plan-2  CAX  0.020
 506  plan-2  CAH  0.020
 506  plan-2  CAG  0.020
 506  plan-2  CAF  0.020
 506  plan-2  H14  0.020
 506  plan-2  H15  0.020
 506  plan-3  OAT  0.020
 506  plan-3  CBA  0.020
 506  plan-3  CAO  0.020
 506  plan-3  CAV  0.020
 506  plan-3  FAD  0.020
 506  plan-3  CAI  0.020
 506  plan-3  CAJ  0.020
 506  plan-3  CAZ  0.020
 506  plan-3  OAU  0.020
 506  plan-3  H8   0.020
 506  plan-3  H9   0.020
 506  plan-3  H10  0.020
 506  plan-4  OAU  0.020
 506  plan-4  CAY  0.020
 506  plan-4  CAP  0.020
 506  plan-4  CAN  0.020
 506  plan-4  CAW  0.020
 506  plan-4  FAE  0.020
 506  plan-4  CAM  0.020
 506  plan-4  CAX  0.020
 506  plan-4  CAH  0.020
 506  plan-4  H11  0.020
 506  plan-4  H12  0.020
 506  plan-4  H13  0.020

