# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 08:11:32 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2,4-bis(oxidanylidene)-5-(2-phenanthren-9-ylethyl)-1H-pyrimidine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCc2cc3ccccc3c4ccccc24)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
 W73  W73  '2,4-bis(oxidanylidene)-5-(2-phenanthren-9-ylethyl)-1H-pyrimidine-6-carboxylic acid'  ligand  43  27  .  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_W73
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
 W73  OAJ  O  OH1   0  -0.591  -3.9098   3.1346   0.8618
 W73  CAI  C  C     0   0.523  -2.9157   2.3694   0.4502
 W73  OAK  O  O     0  -0.395  -1.7880   2.7448   0.2819
 W73  C4   C  CR6   0   0.279  -3.3784   0.9657   0.1985
 W73  N3   N  NR16  0  -0.732  -4.7218   0.8339  -0.0473
 W73  C2   C  CR6   0   0.671  -5.3384  -0.3499  -0.3279
 W73  O2   O  O     0  -0.471  -6.5266  -0.4461  -0.5500
 W73  N1   N  NR16  0  -0.715  -4.4843  -1.4216  -0.3386
 W73  C6   C  CR6   0   0.592  -3.1273  -1.4085  -0.1030
 W73  O6   O  O     0  -0.440  -2.4857  -2.4403  -0.1597
 W73  C5   C  CR6   0  -0.116  -2.5452  -0.0985   0.2039
 W73  CAL  C  CH2   0  -0.505  -1.0733  -0.0772   0.4804
 W73  CAM  C  CH2   0  -0.540  -0.2483   0.0409  -0.8120
 W73  CAN  C  CR6   0   0.114   1.2315   0.0619  -0.5499
 W73  CAS  C  CR66  0   0.061   1.9482  -1.1449  -0.2108
 W73  CAU  C  CR16  0  -0.341   1.2931  -2.3919  -0.1534
 W73  CAT  C  CR16  0  -0.259   1.9689  -3.5413   0.1778
 W73  CAW  C  CR16  0  -0.244   3.3364  -3.4865   0.4658
 W73  CAV  C  CR16  0  -0.353   4.0008  -2.2851   0.4082
 W73  CAR  C  CR66  0   0.127   3.3360  -1.0916   0.0690
 W73  CAQ  C  CR66  0   0.092   4.0357   0.1755  -0.0041
 W73  CBA  C  CR16  0  -0.349   5.4156   0.3081   0.2399
 W73  CAZ  C  CR16  0  -0.245   6.0400   1.5307   0.1549
 W73  CAY  C  CR16  0  -0.264   5.3088   2.6782  -0.1800
 W73  CAX  C  CR16  0  -0.315   3.9619   2.5759  -0.4256
 W73  CAP  C  CR66  0   0.109   3.3057   1.3332  -0.3435
 W73  CAO  C  CR16  0  -0.430   1.9058   1.2364  -0.6038
 W73  H1   H  HOH1  0   0.504  -3.6125   4.0508   0.9795
 W73  H2   H  HNR6  0   0.431  -4.9008  -2.3198  -0.5525
 W73  H4   H  HCH2  0   0.269  -0.8120   0.7387   1.1496
 W73  H5   H  HCH2  0   0.267  -0.8145  -0.9992   1.0013
 W73  H6   H  HCH2  0   0.254  -0.5053  -0.7728  -1.4943
 W73  H7   H  HCH2  0   0.271  -0.5302   0.9651  -1.3158
 W73  H8   H  HCR6  0   0.257   0.2349  -2.4593  -0.3673
 W73  H9   H  HCR6  0   0.259   1.4422  -4.4859   0.2158
 W73  H10  H  HCR6  0   0.260   3.8729  -4.3876   0.7322
 W73  H11  H  HCR6  0   0.254   5.0587  -2.2719   0.6306
 W73  H12  H  HCR6  0   0.254   6.0122  -0.5569   0.4936
 W73  H13  H  HCR6  0   0.260   7.1029   1.6045   0.3436
 W73  H14  H  HCR6  0   0.258   5.8048   3.6377  -0.2469
 W73  H15  H  HCR6  0   0.256   3.3864   3.4553  -0.6890
 W73  H16  H  HCR6  0   0.246   1.3750   2.1477  -0.8569
 W73  H17  H  HNR6  0   0.439  -5.3136   1.6528  -0.0436

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
 W73  CAW  CAT  aromatic  1.399  0.020  1.399
 W73  CAW  CAV  aromatic  1.374  0.020  1.374
 W73  CAT  CAU  aromatic  1.374  0.020  1.374
 W73  CAV  CAR  aromatic  1.408  0.020  1.408
 W73  CAU  CAS  aromatic  1.410  0.020  1.410
 W73  CAR  CAS  aromatic  1.417  0.020  1.417
 W73  CAR  CAQ  aromatic  1.449  0.020  1.449
 W73  CAS  CAN  aromatic  1.444  0.020  1.444
 W73  CBA  CAQ  aromatic  1.408  0.020  1.408
 W73  CBA  CAZ  aromatic  1.375  0.020  1.375
 W73  CAQ  CAP  aromatic  1.410  0.020  1.410
 W73  CAN  CAM  single    1.503  0.020  1.503
 W73  CAN  CAO  aromatic  1.355  0.020  1.355
 W73  CAZ  CAY  aromatic  1.401  0.020  1.401
 W73  CAM  CAL  single    1.538  0.020  1.538
 W73  CAP  CAO  aromatic  1.427  0.020  1.427
 W73  CAP  CAX  aromatic  1.408  0.020  1.408
 W73  CAY  CAX  aromatic  1.373  0.020  1.373
 W73  CAL  C5   single    1.498  0.020  1.498
 W73  O6   C6   double    1.216  0.020  1.216
 W73  C5   C6   single    1.466  0.020  1.466
 W73  C5   C4   double    1.352  0.020  1.352
 W73  C6   N1   single    1.377  0.020  1.377
 W73  OAK  CAI  double    1.200  0.020  1.200
 W73  C4   CAI  single    1.499  0.020  1.499
 W73  C4   N3   single    1.372  0.020  1.372
 W73  CAI  OAJ  single    1.320  0.020  1.320
 W73  N1   C2   single    1.370  0.020  1.370
 W73  N3   C2   single    1.364  0.020  1.364
 W73  C2   O2   double    1.213  0.020  1.213
 W73  OAJ  H1   single    0.850  0.020  0.980
 W73  N1   H2   single    0.860  0.020  1.020
 W73  CAL  H4   single    0.970  0.020  1.090
 W73  CAL  H5   single    0.970  0.020  1.090
 W73  CAM  H6   single    0.970  0.020  1.090
 W73  CAM  H7   single    0.970  0.020  1.090
 W73  CAU  H8   single    0.930  0.020  1.080
 W73  CAT  H9   single    0.930  0.020  1.080
 W73  CAW  H10  single    0.930  0.020  1.080
 W73  CAV  H11  single    0.930  0.020  1.080
 W73  CBA  H12  single    0.930  0.020  1.080
 W73  CAZ  H13  single    0.930  0.020  1.080
 W73  CAY  H14  single    0.930  0.020  1.080
 W73  CAX  H15  single    0.930  0.020  1.080
 W73  CAO  H16  single    0.930  0.020  1.080
 W73  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
 W73  H1   OAJ  CAI  110.75  3.000
 W73  C4   CAI  OAK  124.00  3.000
 W73  C4   CAI  OAJ  111.26  3.000
 W73  OAK  CAI  OAJ  124.73  3.000
 W73  C5   C4   N3   121.92  3.000
 W73  N3   C4   CAI  114.97  3.000
 W73  C5   C4   CAI  123.11  3.000
 W73  H17  N3   C2   116.06  3.000
 W73  H17  N3   C4   119.67  3.000
 W73  C2   N3   C4   124.26  3.000
 W73  N1   C2   O2   123.17  3.000
 W73  O2   C2   N3   123.34  3.000
 W73  N1   C2   N3   113.49  3.000
 W73  H2   N1   C6   116.72  3.000
 W73  H2   N1   C2   116.03  3.000
 W73  C6   N1   C2   127.25  3.000
 W73  C5   C6   O6   123.94  3.000
 W73  C5   C6   N1   115.81  3.000
 W73  O6   C6   N1   120.24  3.000
 W73  CAL  C5   C6   116.20  3.000
 W73  C6   C5   C4   117.26  3.000
 W73  CAL  C5   C4   126.54  3.000
 W73  H5   CAL  H4   106.47  3.000
 W73  H5   CAL  CAM  109.83  3.000
 W73  H4   CAL  CAM  109.31  3.000
 W73  H5   CAL  C5   108.03  3.000
 W73  H4   CAL  C5   111.13  3.000
 W73  CAM  CAL  C5   111.91  3.000
 W73  H7   CAM  H6   106.39  3.000
 W73  H7   CAM  CAN  108.88  3.000
 W73  H6   CAM  CAN  110.54  3.000
 W73  H7   CAM  CAL  108.35  3.000
 W73  H6   CAM  CAL  109.96  3.000
 W73  CAN  CAM  CAL  112.50  3.000
 W73  CAO  CAN  CAS  119.12  3.000
 W73  CAO  CAN  CAM  119.67  3.000
 W73  CAS  CAN  CAM  121.20  3.000
 W73  CAR  CAS  CAU  118.71  3.000
 W73  CAR  CAS  CAN  120.08  3.000
 W73  CAU  CAS  CAN  121.21  3.000
 W73  H8   CAU  CAT  118.47  3.000
 W73  H8   CAU  CAS  120.11  3.000
 W73  CAT  CAU  CAS  121.42  3.000
 W73  H9   CAT  CAW  120.19  3.000
 W73  H9   CAT  CAU  119.95  3.000
 W73  CAW  CAT  CAU  119.86  3.000
 W73  H10  CAW  CAV  119.91  3.000
 W73  H10  CAW  CAT  120.19  3.000
 W73  CAV  CAW  CAT  119.89  3.000
 W73  H11  CAV  CAR  120.09  3.000
 W73  H11  CAV  CAW  118.37  3.000
 W73  CAR  CAV  CAW  121.54  3.000
 W73  CAQ  CAR  CAV  121.70  3.000
 W73  CAQ  CAR  CAS  119.73  3.000
 W73  CAV  CAR  CAS  118.57  3.000
 W73  CAP  CAQ  CBA  118.16  3.000
 W73  CAP  CAQ  CAR  118.69  3.000
 W73  CBA  CAQ  CAR  123.16  3.000
 W73  H12  CBA  CAZ  118.38  3.000
 W73  H12  CBA  CAQ  120.42  3.000
 W73  CAZ  CBA  CAQ  121.20  3.000
 W73  H13  CAZ  CAY  119.89  3.000
 W73  H13  CAZ  CBA  119.72  3.000
 W73  CAY  CAZ  CBA  120.39  3.000
 W73  H14  CAY  CAX  120.31  3.000
 W73  H14  CAY  CAZ  120.11  3.000
 W73  CAX  CAY  CAZ  119.58  3.000
 W73  H15  CAX  CAP  118.89  3.000
 W73  H15  CAX  CAY  120.27  3.000
 W73  CAP  CAX  CAY  120.84  3.000
 W73  CAO  CAP  CAX  120.43  3.000
 W73  CAX  CAP  CAQ  119.84  3.000
 W73  CAO  CAP  CAQ  119.74  3.000
 W73  H16  CAO  CAP  117.75  3.000
 W73  H16  CAO  CAN  119.59  3.000
 W73  CAP  CAO  CAN  122.65  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
 W73  CONST_01  CAT  CAU  CAS  CAN   180.00   0.0  0
 W73  CONST_02  CAV  CAR  CAS  CAN   180.00   0.0  0
 W73  CONST_03  CAQ  CAR  CAS  CAN     0.00   0.0  0
 W73  CONST_04  CAQ  CAP  CAO  CAN     0.00   0.0  0
 W73  CONST_05  CAX  CAP  CAO  CAN   180.00   0.0  0
 W73  CONST_06  CAW  CAT  CAU  CAS     0.00   0.0  0
 W73  CONST_07  CAW  CAV  CAR  CAS     0.00   0.0  0
 W73  CONST_08  CBA  CAQ  CAR  CAS   180.00   0.0  0
 W73  CONST_09  CAP  CAQ  CAR  CAS     0.00   0.0  0
 W73  CONST_10  CAP  CAO  CAN  CAS     0.00   0.0  0
 W73  CONST_11  CAV  CAW  CAT  CAU     0.00   0.0  0
 W73  CONST_12  CAV  CAR  CAS  CAU     0.00   0.0  0
 W73  CONST_13  CAQ  CAR  CAS  CAU   180.00   0.0  0
 W73  CONST_14  CAO  CAN  CAS  CAU   180.00   0.0  0
 W73  CONST_15  CAR  CAV  CAW  CAT     0.00   0.0  0
 W73  CONST_16  CAR  CAS  CAU  CAT     0.00   0.0  0
 W73  CONST_17  CAQ  CAR  CAV  CAW   180.00   0.0  0
 W73  CONST_18  CBA  CAQ  CAR  CAV     0.00   0.0  0
 W73  CONST_19  CAP  CAQ  CAR  CAV   180.00   0.0  0
 W73  CONST_20  CAO  CAN  CAS  CAR     0.00   0.0  0
 W73  CONST_21  CAZ  CBA  CAQ  CAR   180.00   0.0  0
 W73  CONST_22  CAO  CAP  CAQ  CAR     0.00   0.0  0
 W73  CONST_23  CAX  CAP  CAQ  CAR   180.00   0.0  0
 W73  CONST_24  CAY  CAZ  CBA  CAQ     0.00   0.0  0
 W73  CONST_25  CAY  CAX  CAP  CAQ     0.00   0.0  0
 W73  CONST_26  CAO  CAP  CAQ  CBA   180.00   0.0  0
 W73  CONST_27  CAX  CAP  CAQ  CBA     0.00   0.0  0
 W73  CONST_28  CAX  CAY  CAZ  CBA     0.00   0.0  0
 W73  CONST_29  CAP  CAQ  CBA  CAZ     0.00   0.0  0
 W73  CONST_30  CAP  CAX  CAY  CAZ     0.00   0.0  0
 W73  CONST_31  CAO  CAP  CAX  CAY   180.00   0.0  0
 W73  CONST_32  N1   C2   N3   C4      0.00   0.0  0
 W73  CONST_33  C6   N1   C2   N3      0.00   0.0  0
 W73  CONST_34  C5   C6   N1   C2      0.00   0.0  0
 W73  CONST_35  CAU  CAS  CAN  CAM     0.00   0.0  0
 W73  CONST_36  CAR  CAS  CAN  CAM   180.00   0.0  0
 W73  CONST_37  CAP  CAO  CAN  CAM   180.00   0.0  0
 W73  CONST_38  O2   C2   N3   C4    180.00   0.0  0
 W73  CONST_39  O6   C6   N1   C2    180.00   0.0  0
 W73  CONST_40  C6   N1   C2   O2    180.00   0.0  0
 W73  CONST_41  H8   CAU  CAS  CAN     0.00   0.0  0
 W73  CONST_42  H9   CAT  CAU  CAS   180.00   0.0  0
 W73  CONST_43  H11  CAV  CAR  CAS   180.00   0.0  0
 W73  CONST_44  H16  CAO  CAN  CAS   180.00   0.0  0
 W73  CONST_45  H10  CAW  CAT  CAU   180.00   0.0  0
 W73  CONST_46  H12  CBA  CAQ  CAR     0.00   0.0  0
 W73  CONST_47  H13  CAZ  CBA  CAQ   180.00   0.0  0
 W73  CONST_48  H15  CAX  CAP  CAQ   180.00   0.0  0
 W73  CONST_49  H14  CAY  CAZ  CBA   180.00   0.0  0
 W73  CONST_50  H2   N1   C2   N3    180.00   0.0  0
 W73  CONST_51  H17  N3   C2   N1    180.00   0.0  0
 W73  CONST_52  H1   OAJ  CAI  C4    180.00   0.0  0
 W73  Var_01    C5   C4   CAI  OAJ  -157.50  30.0  2
 W73  Var_02    CAM  CAL  C5   C4    -93.44  30.0  3
 W73  Var_03    CAN  CAM  CAL  C5   -179.94  30.0  1
 W73  Var_04    CAS  CAN  CAM  CAL    75.83  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
 W73  plan-1  CAI  0.020
 W73  plan-1  C4   0.020
 W73  plan-1  N3   0.020
 W73  plan-1  C2   0.020
 W73  plan-1  O2   0.020
 W73  plan-1  N1   0.020
 W73  plan-1  C6   0.020
 W73  plan-1  O6   0.020
 W73  plan-1  C5   0.020
 W73  plan-1  CAL  0.020
 W73  plan-1  H2   0.020
 W73  plan-1  H17  0.020
 W73  plan-2  CAM  0.020
 W73  plan-2  CAN  0.020
 W73  plan-2  CAS  0.020
 W73  plan-2  CAU  0.020
 W73  plan-2  CAT  0.020
 W73  plan-2  CAW  0.020
 W73  plan-2  CAV  0.020
 W73  plan-2  CAR  0.020
 W73  plan-2  CAQ  0.020
 W73  plan-2  CBA  0.020
 W73  plan-2  CAZ  0.020
 W73  plan-2  CAY  0.020
 W73  plan-2  CAX  0.020
 W73  plan-2  CAP  0.020
 W73  plan-2  CAO  0.020
 W73  plan-2  H8   0.020
 W73  plan-2  H9   0.020
 W73  plan-2  H10  0.020
 W73  plan-2  H11  0.020
 W73  plan-2  H12  0.020
 W73  plan-2  H13  0.020
 W73  plan-2  H14  0.020
 W73  plan-2  H15  0.020
 W73  plan-2  H16  0.020
 W73  plan-3  OAJ  0.020
 W73  plan-3  CAI  0.020
 W73  plan-3  OAK  0.020
 W73  plan-3  C4   0.020
 W73  plan-3  H1   0.020

