# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 07:23:36 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: {[(2-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(Nc1nc(nc2sccc12)c3ccccc3)[P](O)(O)=O
#
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
 VT0  VT0  '{[(2-phenylthieno[2,3-d]pyrimidin-4-yl)amino]methylene}bis(phosphonic acid)'  ligand  38  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 OK
;

data_comp_VT0
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
 VT0  OAO  O  O     0  -0.681   2.6713  -2.6589  -1.5227
 VT0  PAL  P  P     0   1.394   2.2984  -1.2320  -1.5752
 VT0  OAP  O  OH1   0  -0.755   3.4239  -0.1860  -2.0445
 VT0  OAN  O  OH1   0  -0.729   1.0335  -1.0203  -2.5307
 VT0  CAK  C  CH1   0  -0.675   1.8342  -0.4651   0.0244
 VT0  PAM  P  P     0   1.387   3.1934  -0.1535   1.2113
 VT0  OAR  O  O     0  -0.685   2.7325   0.1935   2.5708
 VT0  OAS  O  OH1   0  -0.731   4.0484  -1.4868   1.0276
 VT0  OAQ  O  OH1   0  -0.744   4.0347   1.0644   0.5964
 VT0  NAJ  N  NH1   0  -0.698   1.1211   0.7701  -0.1615
 VT0  C4   C  CR6   0   0.556  -0.2215   0.8747  -0.0414
 VT0  N3   N  N     0  -0.496  -0.9256  -0.2184   0.1828
 VT0  C5   C  CR56  0   0.011  -0.8646   2.1280  -0.1546
 VT0  CAC  C  CR15  0  -0.199  -0.3771   3.4512  -0.3769
 VT0  CAD  C  CR15  0  -0.461  -1.3799   4.3588  -0.3999
 VT0  SAE  S  S2    0   0.228  -2.9434   3.6564  -0.1556
 VT0  C6   C  CR56  0  -0.013  -2.2494   2.0775  -0.0138
 VT0  N1   N  N     0  -0.465  -2.9628   0.9785   0.2004
 VT0  C2   C  CR6   0   0.404  -2.2551  -0.1340   0.2881
 VT0  CAT  C  CR6   0  -0.017  -2.9896  -1.3978   0.5062
 VT0  CAU  C  CR16  0  -0.281  -4.3754  -1.3909   0.6736
 VT0  CAV  C  CR16  0  -0.240  -5.0661  -2.5768   0.8658
 VT0  CAW  C  CR16  0  -0.255  -4.3845  -3.7873   0.8925
 VT0  CAX  C  CR16  0  -0.239  -3.0058  -3.8027   0.7260
 VT0  CAY  C  CR16  0  -0.282  -2.3122  -2.6174   0.5353
 VT0  H1   H  HOH1  0   0.508   3.8688  -0.3941  -2.8791
 VT0  H2   H  HOH1  0   0.497   0.8119  -0.1107  -2.7685
 VT0  H3   H  HCH1  0   0.364   1.1623  -1.1793   0.5107
 VT0  H4   H  HOH1  0   0.506   4.7740  -1.5995   1.6592
 VT0  H5   H  HOH1  0   0.494   4.4315   0.9054  -0.2722
 VT0  H6   H  HNH1  0   0.419   1.6466   1.6053  -0.3668
 VT0  H8   H  HCR5  0   0.277   0.6611   3.7188  -0.5124
 VT0  H9   H  HCR5  0   0.309  -1.2937   5.4242  -0.5465
 VT0  H12  H  HCR6  0   0.255  -4.9134  -0.4530   0.6523
 VT0  H13  H  HCR6  0   0.259  -6.1405  -2.5558   0.9932
 VT0  H14  H  HCR6  0   0.261  -4.9255  -4.7126   1.0428
 VT0  H15  H  HCR6  0   0.259  -2.4672  -4.7413   0.7426
 VT0  H16  H  HCR6  0   0.260  -1.2390  -2.6375   0.4045

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
 VT0  OAO  PAL  double    1.476  0.020  1.476
 VT0  PAL  OAP  single    1.607  0.020  1.607
 VT0  PAL  OAN  single    1.599  0.020  1.599
 VT0  PAL  CAK  single    1.834  0.020  1.834
 VT0  CAK  PAM  single    1.831  0.020  1.831
 VT0  CAK  NAJ  single    1.438  0.020  1.438
 VT0  PAM  OAR  double    1.477  0.020  1.477
 VT0  PAM  OAS  single    1.595  0.020  1.595
 VT0  PAM  OAQ  single    1.603  0.020  1.603
 VT0  NAJ  C4   single    1.352  0.020  1.352
 VT0  C4   N3   aromatic  1.319  0.020  1.319
 VT0  C4   C5   aromatic  1.413  0.020  1.413
 VT0  N3   C2   aromatic  1.336  0.020  1.336
 VT0  C5   CAC  aromatic  1.428  0.020  1.428
 VT0  C5   C6   aromatic  1.393  0.020  1.393
 VT0  CAC  CAD  aromatic  1.353  0.020  1.353
 VT0  CAD  SAE  aromatic  1.731  0.020  1.731
 VT0  SAE  C6   aromatic  1.731  0.020  1.731
 VT0  C6   N1   aromatic  1.328  0.020  1.328
 VT0  N1   C2   aromatic  1.321  0.020  1.321
 VT0  C2   CAT  single    1.478  0.020  1.478
 VT0  CAT  CAU  aromatic  1.396  0.020  1.396
 VT0  CAT  CAY  aromatic  1.395  0.020  1.395
 VT0  CAU  CAV  aromatic  1.386  0.020  1.386
 VT0  CAV  CAW  aromatic  1.389  0.020  1.389
 VT0  CAW  CAX  aromatic  1.389  0.020  1.389
 VT0  CAX  CAY  aromatic  1.387  0.020  1.387
 VT0  OAP  H1   single    0.850  0.020  0.980
 VT0  OAN  H2   single    0.850  0.020  0.980
 VT0  CAK  H3   single    0.970  0.020  1.090
 VT0  OAS  H4   single    0.850  0.020  0.980
 VT0  OAQ  H5   single    0.850  0.020  0.980
 VT0  NAJ  H6   single    0.860  0.020  1.020
 VT0  CAC  H8   single    0.930  0.020  1.080
 VT0  CAD  H9   single    0.930  0.020  1.080
 VT0  CAU  H12  single    0.930  0.020  1.080
 VT0  CAV  H13  single    0.930  0.020  1.080
 VT0  CAW  H14  single    0.930  0.020  1.080
 VT0  CAX  H15  single    0.930  0.020  1.080
 VT0  CAY  H16  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
 VT0  CAK  PAL  OAN  105.40  3.000
 VT0  CAK  PAL  OAP   99.20  3.000
 VT0  OAN  PAL  OAP  107.06  3.000
 VT0  CAK  PAL  OAO  115.93  3.000
 VT0  OAN  PAL  OAO  110.43  3.000
 VT0  OAP  PAL  OAO  117.57  3.000
 VT0  H1   OAP  PAL  115.70  3.000
 VT0  H2   OAN  PAL  116.95  3.000
 VT0  H3   CAK  NAJ  108.26  3.000
 VT0  H3   CAK  PAM  106.18  3.000
 VT0  NAJ  CAK  PAM  107.80  3.000
 VT0  H3   CAK  PAL  105.67  3.000
 VT0  NAJ  CAK  PAL  111.84  3.000
 VT0  PAM  CAK  PAL  116.66  3.000
 VT0  OAQ  PAM  OAS  108.04  3.000
 VT0  OAQ  PAM  OAR  109.78  3.000
 VT0  OAS  PAM  OAR  118.03  3.000
 VT0  OAQ  PAM  CAK  105.68  3.000
 VT0  OAS  PAM  CAK  100.43  3.000
 VT0  OAR  PAM  CAK  113.89  3.000
 VT0  H4   OAS  PAM  115.08  3.000
 VT0  H5   OAQ  PAM  115.75  3.000
 VT0  H6   NAJ  C4   118.15  3.000
 VT0  H6   NAJ  CAK  118.65  3.000
 VT0  C4   NAJ  CAK  123.18  3.000
 VT0  C5   C4   N3   120.36  3.000
 VT0  C5   C4   NAJ  120.89  3.000
 VT0  N3   C4   NAJ  118.75  3.000
 VT0  C2   N3   C4   119.47  3.000
 VT0  C6   C5   CAC  112.89  3.000
 VT0  C6   C5   C4   114.34  3.000
 VT0  CAC  C5   C4   132.77  3.000
 VT0  H8   CAC  CAD  122.95  3.000
 VT0  H8   CAC  C5   125.25  3.000
 VT0  CAD  CAC  C5   111.80  3.000
 VT0  H9   CAD  SAE  119.47  3.000
 VT0  H9   CAD  CAC  127.27  3.000
 VT0  SAE  CAD  CAC  113.26  3.000
 VT0  C6   SAE  CAD   91.12  3.000
 VT0  N1   C6   SAE  123.57  3.000
 VT0  N1   C6   C5   125.49  3.000
 VT0  SAE  C6   C5   110.93  3.000
 VT0  C2   N1   C6   114.82  3.000
 VT0  CAT  C2   N1   117.62  3.000
 VT0  CAT  C2   N3   116.88  3.000
 VT0  N1   C2   N3   125.50  3.000
 VT0  CAY  CAT  CAU  118.93  3.000
 VT0  CAY  CAT  C2   120.61  3.000
 VT0  CAU  CAT  C2   120.45  3.000
 VT0  H12  CAU  CAV  119.80  3.000
 VT0  H12  CAU  CAT  119.72  3.000
 VT0  CAV  CAU  CAT  120.48  3.000
 VT0  H13  CAV  CAW  120.11  3.000
 VT0  H13  CAV  CAU  119.64  3.000
 VT0  CAW  CAV  CAU  120.25  3.000
 VT0  H14  CAW  CAX  120.22  3.000
 VT0  H14  CAW  CAV  120.15  3.000
 VT0  CAX  CAW  CAV  119.63  3.000
 VT0  H15  CAX  CAY  119.64  3.000
 VT0  H15  CAX  CAW  120.12  3.000
 VT0  CAY  CAX  CAW  120.24  3.000
 VT0  H16  CAY  CAX  119.81  3.000
 VT0  H16  CAY  CAT  119.71  3.000
 VT0  CAX  CAY  CAT  120.48  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
 VT0  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 VT0  CONST_02  CAT  C2   N3   C4    180.00   0.0  0
 VT0  CONST_03  CAD  CAC  C5   C4    180.00   0.0  0
 VT0  CONST_04  SAE  C6   C5   C4    180.00   0.0  0
 VT0  CONST_05  N1   C6   C5   C4      0.00   0.0  0
 VT0  CONST_06  CAC  C5   C4   N3    180.00   0.0  0
 VT0  CONST_07  C6   C5   C4   N3      0.00   0.0  0
 VT0  CONST_08  C6   N1   C2   N3      0.00   0.0  0
 VT0  CONST_09  CAU  CAT  C2   N3    180.00   0.0  0
 VT0  CONST_10  CAY  CAT  C2   N3      0.00   0.0  0
 VT0  CONST_11  C2   N3   C4   C5      0.00   0.0  0
 VT0  CONST_12  SAE  CAD  CAC  C5      0.00   0.0  0
 VT0  CONST_13  CAD  SAE  C6   C5      0.00   0.0  0
 VT0  CONST_14  C2   N1   C6   C5      0.00   0.0  0
 VT0  CONST_15  SAE  C6   C5   CAC     0.00   0.0  0
 VT0  CONST_16  N1   C6   C5   CAC   180.00   0.0  0
 VT0  CONST_17  C6   SAE  CAD  CAC     0.00   0.0  0
 VT0  CONST_18  C6   C5   CAC  CAD     0.00   0.0  0
 VT0  CONST_19  N1   C6   SAE  CAD   180.00   0.0  0
 VT0  CONST_20  C2   N1   C6   SAE   180.00   0.0  0
 VT0  CONST_21  CAT  C2   N1   C6    180.00   0.0  0
 VT0  CONST_22  CAU  CAT  C2   N1      0.00   0.0  0
 VT0  CONST_23  CAY  CAT  C2   N1    180.00   0.0  0
 VT0  CONST_24  CAV  CAU  CAT  C2    180.00   0.0  0
 VT0  CONST_25  CAX  CAY  CAT  C2    180.00   0.0  0
 VT0  CONST_26  CAW  CAV  CAU  CAT     0.00   0.0  0
 VT0  CONST_27  CAW  CAX  CAY  CAT     0.00   0.0  0
 VT0  CONST_28  CAX  CAY  CAT  CAU     0.00   0.0  0
 VT0  CONST_29  CAX  CAW  CAV  CAU     0.00   0.0  0
 VT0  CONST_30  CAY  CAT  CAU  CAV     0.00   0.0  0
 VT0  CONST_31  CAY  CAX  CAW  CAV     0.00   0.0  0
 VT0  CONST_32  C2   N3   C4   NAJ   180.00   0.0  0
 VT0  CONST_33  CAC  C5   C4   NAJ     0.00   0.0  0
 VT0  CONST_34  C6   C5   C4   NAJ   180.00   0.0  0
 VT0  CONST_35  H8   CAC  C5   C4      0.00   0.0  0
 VT0  CONST_36  H9   CAD  CAC  C5    180.00   0.0  0
 VT0  CONST_37  H12  CAU  CAT  C2      0.00   0.0  0
 VT0  CONST_38  H16  CAY  CAT  C2      0.00   0.0  0
 VT0  CONST_39  H13  CAV  CAU  CAT   180.00   0.0  0
 VT0  CONST_40  H15  CAX  CAY  CAT   180.00   0.0  0
 VT0  CONST_41  H14  CAW  CAV  CAU   180.00   0.0  0
 VT0  CONST_42  N3   C4   NAJ  CAK     0.00   0.0  0
 VT0  CONST_43  C5   C4   NAJ  CAK   180.00   0.0  0
 VT0  CONST_44  H6   NAJ  C4   N3    180.00   0.0  0
 VT0  Var_01    C4   NAJ  CAK  PAL   101.70  30.0  3
 VT0  Var_02    PAM  CAK  PAL  OAO    72.45  30.0  3
 VT0  Var_03    OAR  PAM  CAK  PAL  -167.77  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
 VT0  plan-1  C2   0.020
 VT0  plan-1  CAT  0.020
 VT0  plan-1  CAU  0.020
 VT0  plan-1  CAV  0.020
 VT0  plan-1  CAW  0.020
 VT0  plan-1  CAX  0.020
 VT0  plan-1  CAY  0.020
 VT0  plan-1  H12  0.020
 VT0  plan-1  H13  0.020
 VT0  plan-1  H14  0.020
 VT0  plan-1  H15  0.020
 VT0  plan-1  H16  0.020
 VT0  plan-2  NAJ  0.020
 VT0  plan-2  C4   0.020
 VT0  plan-2  N3   0.020
 VT0  plan-2  C5   0.020
 VT0  plan-2  CAC  0.020
 VT0  plan-2  CAD  0.020
 VT0  plan-2  SAE  0.020
 VT0  plan-2  C6   0.020
 VT0  plan-2  N1   0.020
 VT0  plan-2  C2   0.020
 VT0  plan-2  CAT  0.020
 VT0  plan-2  H8   0.020
 VT0  plan-2  H9   0.020
 VT0  plan-3  CAK  0.020
 VT0  plan-3  NAJ  0.020
 VT0  plan-3  C4   0.020
 VT0  plan-3  H6   0.020

