# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 07:36:50 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2,4-bis(oxidanylidene)-5-[2-(4-phenylphenyl)ethyl]-1H-pyrimidine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCc2ccc(cc2)c3ccccc3)C(=O)NC(=O)N1
#
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
 W7A  W7A  '2,4-bis(oxidanylidene)-5-[2-(4-phenylphenyl)ethyl]-1H-pyrimidine-6-carboxylic acid'  ligand  41  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W7A
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
 W7A  OAJ  O  OH1   0  -0.592  -4.2134  -2.9388   0.8535
 W7A  CAI  C  C     0   0.526  -3.2348  -2.1409   0.4665
 W7A  OAK  O  O     0  -0.395  -2.1009  -2.4916   0.2841
 W7A  C4   C  CR6   0   0.279  -3.7242  -0.7381   0.2664
 W7A  N3   N  NR16  0  -0.733  -5.0804  -0.6176   0.0914
 W7A  C2   C  CR6   0   0.670  -5.7244   0.5633  -0.1321
 W7A  O2   O  O     0  -0.473  -6.9235   0.6479  -0.2940
 W7A  N1   N  NR16  0  -0.715  -4.8857   1.6463  -0.1598
 W7A  C6   C  CR6   0   0.586  -3.5178   1.6464   0.0053
 W7A  O6   O  O     0  -0.440  -2.8920   2.6862  -0.0606
 W7A  C5   C  CR6   0  -0.119  -2.9043   0.3365   0.2516
 W7A  CAL  C  CH2   0  -0.499  -1.4181   0.3277   0.4369
 W7A  CAM  C  CH2   0  -0.503  -0.6682   0.2042  -0.8989
 W7A  CAN  C  CR6   0   0.113   0.8177   0.1759  -0.6874
 W7A  CAS  C  CR16  0  -0.290   1.5467   1.3551  -0.5539
 W7A  CAR  C  CR16  0  -0.296   2.9130   1.3297  -0.3219
 W7A  CAO  C  CR16  0  -0.295   1.5014  -1.0318  -0.5766
 W7A  CAP  C  CR16  0  -0.295   2.8686  -1.0619  -0.3491
 W7A  CAQ  C  CR6   0   0.071   3.6003   0.1191  -0.2191
 W7A  CAT  C  CR6   0   0.089   5.0585   0.0863   0.0143
 W7A  CAU  C  CR16  0  -0.312   5.6708   1.0124   0.8611
 W7A  CAY  C  CR16  0  -0.240   7.0402   0.9783   1.0808
 W7A  CAX  C  CR16  0  -0.268   7.8252   0.0168   0.4577
 W7A  CAW  C  CR16  0  -0.240   7.2286  -0.9088  -0.3885
 W7A  CAV  C  CR16  0  -0.312   5.8593  -0.8734  -0.6081
 W7A  H1   H  HOH1  0   0.504  -3.8989  -3.8526   0.9385
 W7A  H2   H  HNR6  0   0.431  -5.3232   2.5432  -0.3334
 W7A  H4   H  HCH2  0   0.262  -1.1268   1.2631   0.9166
 W7A  H5   H  HCH2  0   0.266  -1.1100  -0.4732   1.1043
 W7A  H6   H  HCH2  0   0.256  -0.9896  -0.7051  -1.4073
 W7A  H7   H  HCH2  0   0.252  -0.9365   1.0445  -1.5427
 W7A  H8   H  HCR6  0   0.247   1.0414   2.3100  -0.6453
 W7A  H9   H  HCR6  0   0.251   3.4521   2.2659  -0.2444
 W7A  H10  H  HCR6  0   0.247   0.9552  -1.9636  -0.6676
 W7A  H11  H  HCR6  0   0.251   3.3678  -2.0187  -0.2545
 W7A  H12  H  HCR6  0   0.253   5.0696   1.7559   1.3696
 W7A  H13  H  HCR6  0   0.257   7.4942   1.7010   1.7467
 W7A  H14  H  HCR6  0   0.257   8.8932  -0.0110   0.6307
 W7A  H15  H  HCR6  0   0.257   7.8314  -1.6573  -0.8863
 W7A  H16  H  HCR6  0   0.253   5.4115  -1.5891  -1.2866
 W7A  H17  H  HNR6  0   0.439  -5.6611  -1.4441   0.1072

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
 W7A  CAY  CAU  aromatic  1.387  0.020  1.387
 W7A  CAY  CAX  aromatic  1.389  0.020  1.389
 W7A  CAU  CAT  aromatic  1.396  0.020  1.396
 W7A  CAR  CAS  aromatic  1.386  0.020  1.386
 W7A  CAR  CAQ  aromatic  1.396  0.020  1.396
 W7A  CAS  CAN  aromatic  1.393  0.020  1.393
 W7A  CAX  CAW  aromatic  1.389  0.020  1.389
 W7A  CAT  CAQ  single    1.477  0.020  1.477
 W7A  CAT  CAV  aromatic  1.396  0.020  1.396
 W7A  CAQ  CAP  aromatic  1.395  0.020  1.395
 W7A  CAN  CAM  single    1.501  0.020  1.501
 W7A  CAN  CAO  aromatic  1.392  0.020  1.392
 W7A  CAW  CAV  aromatic  1.387  0.020  1.387
 W7A  CAM  CAL  single    1.537  0.020  1.537
 W7A  CAP  CAO  aromatic  1.386  0.020  1.386
 W7A  CAL  C5   single    1.498  0.020  1.498
 W7A  O6   C6   double    1.215  0.020  1.215
 W7A  C5   C6   single    1.467  0.020  1.467
 W7A  C5   C4   double    1.352  0.020  1.352
 W7A  C6   N1   single    1.378  0.020  1.378
 W7A  C4   CAI  single    1.499  0.020  1.499
 W7A  C4   N3   single    1.373  0.020  1.373
 W7A  OAK  CAI  double    1.201  0.020  1.201
 W7A  CAI  OAJ  single    1.321  0.020  1.321
 W7A  N1   C2   single    1.370  0.020  1.370
 W7A  N3   C2   single    1.364  0.020  1.364
 W7A  C2   O2   double    1.213  0.020  1.213
 W7A  OAJ  H1   single    0.850  0.020  0.980
 W7A  N1   H2   single    0.860  0.020  1.020
 W7A  CAL  H4   single    0.970  0.020  1.090
 W7A  CAL  H5   single    0.970  0.020  1.090
 W7A  CAM  H6   single    0.970  0.020  1.090
 W7A  CAM  H7   single    0.970  0.020  1.090
 W7A  CAS  H8   single    0.930  0.020  1.080
 W7A  CAR  H9   single    0.930  0.020  1.080
 W7A  CAO  H10  single    0.930  0.020  1.080
 W7A  CAP  H11  single    0.930  0.020  1.080
 W7A  CAU  H12  single    0.930  0.020  1.080
 W7A  CAY  H13  single    0.930  0.020  1.080
 W7A  CAX  H14  single    0.930  0.020  1.080
 W7A  CAW  H15  single    0.930  0.020  1.080
 W7A  CAV  H16  single    0.930  0.020  1.080
 W7A  N3   H17  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
 W7A  H1   OAJ  CAI  110.76  3.000
 W7A  C4   CAI  OAK  124.15  3.000
 W7A  OAK  CAI  OAJ  124.60  3.000
 W7A  C4   CAI  OAJ  111.25  3.000
 W7A  C5   C4   N3   121.88  3.000
 W7A  N3   C4   CAI  114.94  3.000
 W7A  C5   C4   CAI  123.18  3.000
 W7A  H17  N3   C2   116.08  3.000
 W7A  H17  N3   C4   119.62  3.000
 W7A  C2   N3   C4   124.30  3.000
 W7A  N1   C2   O2   123.18  3.000
 W7A  O2   C2   N3   123.32  3.000
 W7A  N1   C2   N3   113.50  3.000
 W7A  H2   N1   C6   116.70  3.000
 W7A  H2   N1   C2   116.04  3.000
 W7A  C6   N1   C2   127.25  3.000
 W7A  C5   C6   O6   123.89  3.000
 W7A  C5   C6   N1   115.79  3.000
 W7A  O6   C6   N1   120.31  3.000
 W7A  CAL  C5   C6   116.16  3.000
 W7A  C6   C5   C4   117.26  3.000
 W7A  CAL  C5   C4   126.57  3.000
 W7A  H5   CAL  H4   106.63  3.000
 W7A  H5   CAL  CAM  109.64  3.000
 W7A  H4   CAL  CAM  108.72  3.000
 W7A  H5   CAL  C5   111.19  3.000
 W7A  H4   CAL  C5   108.32  3.000
 W7A  CAM  CAL  C5   112.15  3.000
 W7A  H7   CAM  H6   107.12  3.000
 W7A  H7   CAM  CAN  109.92  3.000
 W7A  H6   CAM  CAN  109.99  3.000
 W7A  H7   CAM  CAL  109.31  3.000
 W7A  H6   CAM  CAL  109.18  3.000
 W7A  CAN  CAM  CAL  111.22  3.000
 W7A  CAO  CAN  CAS  118.02  3.000
 W7A  CAO  CAN  CAM  120.91  3.000
 W7A  CAS  CAN  CAM  121.04  3.000
 W7A  H8   CAS  CAR  119.32  3.000
 W7A  H8   CAS  CAN  119.58  3.000
 W7A  CAR  CAS  CAN  121.10  3.000
 W7A  H9   CAR  CAQ  119.95  3.000
 W7A  H9   CAR  CAS  119.13  3.000
 W7A  CAQ  CAR  CAS  120.91  3.000
 W7A  H10  CAO  CAP  119.48  3.000
 W7A  H10  CAO  CAN  119.45  3.000
 W7A  CAP  CAO  CAN  121.08  3.000
 W7A  H11  CAP  CAQ  119.85  3.000
 W7A  H11  CAP  CAO  119.21  3.000
 W7A  CAQ  CAP  CAO  120.93  3.000
 W7A  CAT  CAQ  CAP  120.90  3.000
 W7A  CAP  CAQ  CAR  117.97  3.000
 W7A  CAT  CAQ  CAR  121.13  3.000
 W7A  CAV  CAT  CAU  118.34  3.000
 W7A  CAV  CAT  CAQ  120.73  3.000
 W7A  CAU  CAT  CAQ  120.93  3.000
 W7A  H12  CAU  CAY  119.37  3.000
 W7A  H12  CAU  CAT  119.78  3.000
 W7A  CAY  CAU  CAT  120.84  3.000
 W7A  H13  CAY  CAX  120.07  3.000
 W7A  H13  CAY  CAU  119.67  3.000
 W7A  CAX  CAY  CAU  120.26  3.000
 W7A  H14  CAX  CAW  120.28  3.000
 W7A  H14  CAX  CAY  120.25  3.000
 W7A  CAW  CAX  CAY  119.47  3.000
 W7A  H15  CAW  CAV  119.64  3.000
 W7A  H15  CAW  CAX  120.12  3.000
 W7A  CAV  CAW  CAX  120.23  3.000
 W7A  H16  CAV  CAW  119.37  3.000
 W7A  H16  CAV  CAT  119.75  3.000
 W7A  CAW  CAV  CAT  120.87  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
 W7A  CONST_01  CAQ  CAR  CAS  CAN     0.00   0.0  0
 W7A  CONST_02  CAQ  CAP  CAO  CAN     0.00   0.0  0
 W7A  CONST_03  CAT  CAQ  CAR  CAS   180.00   0.0  0
 W7A  CONST_04  CAP  CAQ  CAR  CAS     0.00   0.0  0
 W7A  CONST_05  CAP  CAO  CAN  CAS     0.00   0.0  0
 W7A  CONST_06  CAO  CAN  CAS  CAR     0.00   0.0  0
 W7A  CONST_09  CAO  CAP  CAQ  CAR     0.00   0.0  0
 W7A  CONST_10  CAT  CAQ  CAP  CAO   180.00   0.0  0
 W7A  CONST_13  CAY  CAU  CAT  CAQ   180.00   0.0  0
 W7A  CONST_14  CAW  CAV  CAT  CAQ   180.00   0.0  0
 W7A  CONST_15  CAX  CAY  CAU  CAT     0.00   0.0  0
 W7A  CONST_16  CAX  CAW  CAV  CAT     0.00   0.0  0
 W7A  CONST_17  CAW  CAX  CAY  CAU     0.00   0.0  0
 W7A  CONST_18  CAW  CAV  CAT  CAU     0.00   0.0  0
 W7A  CONST_19  CAV  CAT  CAU  CAY     0.00   0.0  0
 W7A  CONST_20  CAV  CAW  CAX  CAY     0.00   0.0  0
 W7A  CONST_21  N1   C2   N3   C4      0.00   0.0  0
 W7A  CONST_22  C6   N1   C2   N3      0.00   0.0  0
 W7A  CONST_23  C5   C6   N1   C2      0.00   0.0  0
 W7A  CONST_24  CAR  CAS  CAN  CAM   180.00   0.0  0
 W7A  CONST_25  CAP  CAO  CAN  CAM   180.00   0.0  0
 W7A  CONST_26  O2   C2   N3   C4    180.00   0.0  0
 W7A  CONST_27  O6   C6   N1   C2    180.00   0.0  0
 W7A  CONST_28  C6   N1   C2   O2    180.00   0.0  0
 W7A  CONST_29  H9   CAR  CAS  CAN   180.00   0.0  0
 W7A  CONST_30  H11  CAP  CAO  CAN   180.00   0.0  0
 W7A  CONST_31  H10  CAO  CAN  CAS   180.00   0.0  0
 W7A  CONST_32  H8   CAS  CAN  CAO   180.00   0.0  0
 W7A  CONST_33  H12  CAU  CAT  CAQ     0.00   0.0  0
 W7A  CONST_34  H16  CAV  CAT  CAQ     0.00   0.0  0
 W7A  CONST_35  H13  CAY  CAU  CAT   180.00   0.0  0
 W7A  CONST_36  H15  CAW  CAV  CAT   180.00   0.0  0
 W7A  CONST_37  H14  CAX  CAY  CAU   180.00   0.0  0
 W7A  CONST_38  H2   N1   C2   N3    180.00   0.0  0
 W7A  CONST_39  H17  N3   C2   N1    180.00   0.0  0
 W7A  CONST_40  H1   OAJ  CAI  C4    180.00   0.0  0
 W7A  Var_01    C5   C4   CAI  OAJ   160.35  30.0  2
 W7A  Var_02    CAM  CAL  C5   C4     91.30  30.0  2
 W7A  Var_03    CAN  CAM  CAL  C5   -179.12  30.0  2
 W7A  Var_04    CAS  CAN  CAM  CAL   -84.06  30.0  2

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
 W7A  plan-1  CAI  0.020
 W7A  plan-1  C4   0.020
 W7A  plan-1  N3   0.020
 W7A  plan-1  C2   0.020
 W7A  plan-1  O2   0.020
 W7A  plan-1  N1   0.020
 W7A  plan-1  C6   0.020
 W7A  plan-1  O6   0.020
 W7A  plan-1  C5   0.020
 W7A  plan-1  CAL  0.020
 W7A  plan-1  H2   0.020
 W7A  plan-1  H17  0.020
 W7A  plan-2  CAM  0.020
 W7A  plan-2  CAN  0.020
 W7A  plan-2  CAS  0.020
 W7A  plan-2  CAR  0.020
 W7A  plan-2  CAO  0.020
 W7A  plan-2  CAP  0.020
 W7A  plan-2  CAQ  0.020
 W7A  plan-2  CAT  0.020
 W7A  plan-2  H8   0.020
 W7A  plan-2  H9   0.020
 W7A  plan-2  H10  0.020
 W7A  plan-2  H11  0.020
 W7A  plan-3  CAQ  0.020
 W7A  plan-3  CAT  0.020
 W7A  plan-3  CAU  0.020
 W7A  plan-3  CAY  0.020
 W7A  plan-3  CAX  0.020
 W7A  plan-3  CAW  0.020
 W7A  plan-3  CAV  0.020
 W7A  plan-3  H12  0.020
 W7A  plan-3  H13  0.020
 W7A  plan-3  H14  0.020
 W7A  plan-3  H15  0.020
 W7A  plan-3  H16  0.020
 W7A  plan-4  OAJ  0.020
 W7A  plan-4  CAI  0.020
 W7A  plan-4  OAK  0.020
 W7A  plan-4  C4   0.020
 W7A  plan-4  H1   0.020

