# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:19:54 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: ({[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2sc3ncnc(NC([P](O)(O)=O)[P](O)(O)=O)c3c2
#
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
 1MV  1MV  '({[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}methanediyl)bis(phosphonic acid)'  ligand  41  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1MV
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
 1MV  OAU  O  O     0  -0.686   2.9944  -0.7570   2.6321
 1MV  PAS  P  P     0   1.383   3.4233  -1.1537   1.2754
 1MV  OAV  O  OH1   0  -0.731   4.9860  -1.3363   1.0101
 1MV  OAW  O  OH1   0  -0.742   2.6861  -2.5111   0.8483
 1MV  CAR  C  CH1   0  -0.674   2.9914   0.0731  -0.0136
 1MV  PAT  P  P     0   1.395   3.7270  -0.1591  -1.6731
 1MV  OAX  O  O     0  -0.679   5.1800   0.0679  -1.7897
 1MV  OAZ  O  OH1   0  -0.754   3.1902  -1.6426  -1.9767
 1MV  OAY  O  OH1   0  -0.731   2.9233   0.8459  -2.6221
 1MV  NAJ  N  NH1   0  -0.698   1.5547   0.1461  -0.0980
 1MV  C4   C  CR6   0   0.546   0.8376   1.1780   0.4079
 1MV  N3   N  N     0  -0.467   1.4782   2.2453   0.8566
 1MV  C2   C  CR16  0   0.054   0.7629   3.2592   1.3386
 1MV  N1   N  N     0  -0.428  -0.5482   3.3372   1.4332
 1MV  C6   C  CR56  0  -0.019  -1.1843   2.2607   0.9778
 1MV  SAE  S  S2    0   0.231  -2.9039   2.0935   0.9799
 1MV  C5   C  CR56  0   0.053  -0.5739   1.1303   0.4400
 1MV  CAC  C  CR15  0  -0.268  -1.5083   0.1331   0.0385
 1MV  CAD  C  CR5   0  -0.201  -2.7970   0.5020   0.2669
 1MV  CAK  C  CR6   0   0.123  -4.0118  -0.2576  -0.0173
 1MV  CAL  C  CR16  0  -0.304  -5.1893  -0.0501   0.7010
 1MV  CAM  C  CR16  0  -0.282  -6.3282  -0.7913   0.4264
 1MV  CAN  C  CR6   0   0.088  -6.3339  -1.7648  -0.5681
 1MV  CAQ  C  CH3   0  -0.722  -7.5710  -2.5520  -0.8825
 1MV  CAO  C  CR16  0  -0.274  -5.1539  -1.9704  -1.2837
 1MV  CAP  C  CR16  0  -0.304  -4.0152  -1.2308  -1.0206
 1MV  H1   H  HOH1  0   0.505   5.4613  -1.8311   1.6937
 1MV  H2   H  HOH1  0   0.491   2.9376  -2.8781  -0.0112
 1MV  H3   H  HCH1  0   0.368   3.3589   1.0403   0.3438
 1MV  H4   H  HOH1  0   0.508   3.4966  -2.0371  -2.8065
 1MV  H5   H  HOH1  0   0.495   1.9634   0.7361  -2.6497
 1MV  H6   H  HNH1  0   0.418   1.0556  -0.6964  -0.3388
 1MV  H7   H  HCR6  0   0.265   1.3290   4.1124   1.6939
 1MV  H8   H  HCR5  0   0.276  -1.2415  -0.8268  -0.3819
 1MV  H10  H  HCR6  0   0.255  -5.2235   0.6802   1.5007
 1MV  H11  H  HCR6  0   0.255  -7.2248  -0.6111   1.0071
 1MV  H12  H  HCH3  0   0.252  -8.0617  -2.1648  -1.7780
 1MV  H13  H  HCH3  0   0.247  -7.3397  -3.6002  -1.0722
 1MV  H14  H  HCH3  0   0.246  -8.2926  -2.5062  -0.0684
 1MV  H15  H  HCR6  0   0.255  -5.1272  -2.7171  -2.0683
 1MV  H16  H  HCR6  0   0.256  -3.1246  -1.4029  -1.6120

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
 1MV  OAU  PAS  double    1.477  0.020  1.477
 1MV  PAS  OAV  single    1.596  0.020  1.596
 1MV  PAS  OAW  single    1.603  0.020  1.603
 1MV  PAS  CAR  single    1.831  0.020  1.831
 1MV  CAR  PAT  single    1.830  0.020  1.830
 1MV  CAR  NAJ  single    1.441  0.020  1.441
 1MV  PAT  OAX  double    1.475  0.020  1.475
 1MV  PAT  OAZ  single    1.607  0.020  1.607
 1MV  PAT  OAY  single    1.599  0.020  1.599
 1MV  NAJ  C4   single    1.355  0.020  1.355
 1MV  C4   N3   aromatic  1.323  0.020  1.323
 1MV  C4   C5   aromatic  1.413  0.020  1.413
 1MV  N3   C2   aromatic  1.331  0.020  1.331
 1MV  C2   N1   aromatic  1.317  0.020  1.317
 1MV  N1   C6   aromatic  1.331  0.020  1.331
 1MV  C6   SAE  aromatic  1.728  0.020  1.728
 1MV  C6   C5   aromatic  1.393  0.020  1.393
 1MV  SAE  CAD  aromatic  1.747  0.020  1.747
 1MV  C5   CAC  aromatic  1.424  0.020  1.424
 1MV  CAC  CAD  aromatic  1.360  0.020  1.360
 1MV  CAD  CAK  single    1.461  0.020  1.461
 1MV  CAK  CAL  aromatic  1.395  0.020  1.395
 1MV  CAK  CAP  aromatic  1.398  0.020  1.398
 1MV  CAL  CAM  aromatic  1.386  0.020  1.386
 1MV  CAM  CAN  aromatic  1.392  0.020  1.392
 1MV  CAN  CAQ  single    1.500  0.020  1.500
 1MV  CAN  CAO  aromatic  1.395  0.020  1.395
 1MV  CAO  CAP  aromatic  1.383  0.020  1.383
 1MV  OAV  H1   single    0.850  0.020  0.980
 1MV  OAW  H2   single    0.850  0.020  0.980
 1MV  CAR  H3   single    0.970  0.020  1.090
 1MV  OAZ  H4   single    0.850  0.020  0.980
 1MV  OAY  H5   single    0.850  0.020  0.980
 1MV  NAJ  H6   single    0.860  0.020  1.020
 1MV  C2   H7   single    0.930  0.020  1.080
 1MV  CAC  H8   single    0.930  0.020  1.080
 1MV  CAL  H10  single    0.930  0.020  1.080
 1MV  CAM  H11  single    0.930  0.020  1.080
 1MV  CAQ  H12  single    0.970  0.020  1.090
 1MV  CAQ  H13  single    0.970  0.020  1.090
 1MV  CAQ  H14  single    0.970  0.020  1.090
 1MV  CAO  H15  single    0.930  0.020  1.080
 1MV  CAP  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
 1MV  CAR  PAS  OAW  105.74  3.000
 1MV  CAR  PAS  OAV  100.99  3.000
 1MV  OAW  PAS  OAV  108.02  3.000
 1MV  CAR  PAS  OAU  113.46  3.000
 1MV  OAW  PAS  OAU  109.79  3.000
 1MV  OAV  PAS  OAU  117.89  3.000
 1MV  H1   OAV  PAS  114.95  3.000
 1MV  H2   OAW  PAS  115.99  3.000
 1MV  H3   CAR  NAJ  108.00  3.000
 1MV  H3   CAR  PAT  105.86  3.000
 1MV  NAJ  CAR  PAT  110.74  3.000
 1MV  H3   CAR  PAS  106.44  3.000
 1MV  NAJ  CAR  PAS  108.08  3.000
 1MV  PAT  CAR  PAS  117.29  3.000
 1MV  OAY  PAT  OAZ  107.47  3.000
 1MV  OAY  PAT  OAX  110.57  3.000
 1MV  OAZ  PAT  OAX  117.14  3.000
 1MV  OAY  PAT  CAR  104.86  3.000
 1MV  OAZ  PAT  CAR   98.87  3.000
 1MV  OAX  PAT  CAR  116.62  3.000
 1MV  H4   OAZ  PAT  115.62  3.000
 1MV  H5   OAY  PAT  116.41  3.000
 1MV  H6   NAJ  C4   117.62  3.000
 1MV  H6   NAJ  CAR  117.72  3.000
 1MV  C4   NAJ  CAR  122.99  3.000
 1MV  C5   C4   N3   120.21  3.000
 1MV  C5   C4   NAJ  120.78  3.000
 1MV  N3   C4   NAJ  119.00  3.000
 1MV  C2   N3   C4   118.49  3.000
 1MV  H7   C2   N1   116.73  3.000
 1MV  H7   C2   N3   115.96  3.000
 1MV  N1   C2   N3   127.31  3.000
 1MV  C6   N1   C2   113.79  3.000
 1MV  C5   C6   SAE  110.99  3.000
 1MV  C5   C6   N1   125.39  3.000
 1MV  SAE  C6   N1   123.62  3.000
 1MV  CAD  SAE  C6    91.54  3.000
 1MV  CAC  C5   C6   112.93  3.000
 1MV  CAC  C5   C4   132.28  3.000
 1MV  C6   C5   C4   114.79  3.000
 1MV  H8   CAC  CAD  122.68  3.000
 1MV  H8   CAC  C5   124.69  3.000
 1MV  CAD  CAC  C5   112.61  3.000
 1MV  CAK  CAD  CAC  127.91  3.000
 1MV  CAK  CAD  SAE  120.15  3.000
 1MV  CAC  CAD  SAE  111.94  3.000
 1MV  CAP  CAK  CAL  118.11  3.000
 1MV  CAP  CAK  CAD  120.25  3.000
 1MV  CAL  CAK  CAD  121.64  3.000
 1MV  H10  CAL  CAM  118.73  3.000
 1MV  H10  CAL  CAK  120.46  3.000
 1MV  CAM  CAL  CAK  120.80  3.000
 1MV  H11  CAM  CAN  119.74  3.000
 1MV  H11  CAM  CAL  119.00  3.000
 1MV  CAN  CAM  CAL  121.26  3.000
 1MV  CAO  CAN  CAQ  120.85  3.000
 1MV  CAO  CAN  CAM  117.78  3.000
 1MV  CAQ  CAN  CAM  121.36  3.000
 1MV  H14  CAQ  H13  108.13  3.000
 1MV  H14  CAQ  H12  107.49  3.000
 1MV  H13  CAQ  H12  107.07  3.000
 1MV  H14  CAQ  CAN  111.58  3.000
 1MV  H13  CAQ  CAN  111.48  3.000
 1MV  H12  CAQ  CAN  110.89  3.000
 1MV  H15  CAO  CAP  119.08  3.000
 1MV  H15  CAO  CAN  119.59  3.000
 1MV  CAP  CAO  CAN  121.32  3.000
 1MV  H16  CAP  CAO  119.22  3.000
 1MV  H16  CAP  CAK  120.05  3.000
 1MV  CAO  CAP  CAK  120.72  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
 1MV  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 1MV  CONST_02  N1   C6   C5   C4     0.00   0.0  0
 1MV  CONST_03  SAE  C6   C5   C4   180.00   0.0  0
 1MV  CONST_04  CAD  CAC  C5   C4   180.00   0.0  0
 1MV  CONST_05  C6   C5   C4   N3     0.00   0.0  0
 1MV  CONST_06  CAC  C5   C4   N3   180.00   0.0  0
 1MV  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 1MV  CONST_08  C5   C4   N3   C2     0.00   0.0  0
 1MV  CONST_09  SAE  C6   N1   C2   180.00   0.0  0
 1MV  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 1MV  CONST_11  CAD  SAE  C6   N1   180.00   0.0  0
 1MV  CONST_12  CAC  C5   C6   N1   180.00   0.0  0
 1MV  CONST_13  CAC  CAD  SAE  C6     0.00   0.0  0
 1MV  CONST_14  CAK  CAD  SAE  C6   180.00   0.0  0
 1MV  CONST_15  CAD  CAC  C5   C6     0.00   0.0  0
 1MV  CONST_16  CAC  C5   C6   SAE    0.00   0.0  0
 1MV  CONST_17  C5   CAC  CAD  SAE    0.00   0.0  0
 1MV  CONST_20  CAD  SAE  C6   C5     0.00   0.0  0
 1MV  CONST_21  CAK  CAD  CAC  C5   180.00   0.0  0
 1MV  CONST_24  CAM  CAL  CAK  CAD  180.00   0.0  0
 1MV  CONST_25  CAO  CAP  CAK  CAD  180.00   0.0  0
 1MV  CONST_26  CAN  CAM  CAL  CAK    0.00   0.0  0
 1MV  CONST_27  CAN  CAO  CAP  CAK    0.00   0.0  0
 1MV  CONST_28  CAO  CAP  CAK  CAL    0.00   0.0  0
 1MV  CONST_29  CAO  CAN  CAM  CAL    0.00   0.0  0
 1MV  CONST_30  CAP  CAK  CAL  CAM    0.00   0.0  0
 1MV  CONST_31  CAP  CAO  CAN  CAM    0.00   0.0  0
 1MV  CONST_32  C2   N3   C4   NAJ  180.00   0.0  0
 1MV  CONST_33  C6   C5   C4   NAJ  180.00   0.0  0
 1MV  CONST_34  CAC  C5   C4   NAJ    0.00   0.0  0
 1MV  CONST_35  CAQ  CAN  CAM  CAL  180.00   0.0  0
 1MV  CONST_36  CAP  CAO  CAN  CAQ  180.00   0.0  0
 1MV  CONST_37  H7   C2   N3   C4   180.00   0.0  0
 1MV  CONST_38  H8   CAC  C5   C4     0.00   0.0  0
 1MV  CONST_39  H10  CAL  CAK  CAD    0.00   0.0  0
 1MV  CONST_40  H16  CAP  CAK  CAD    0.00   0.0  0
 1MV  CONST_41  H11  CAM  CAL  CAK  180.00   0.0  0
 1MV  CONST_42  H15  CAO  CAP  CAK  180.00   0.0  0
 1MV  CONST_43  N3   C4   NAJ  CAR    0.00   0.0  0
 1MV  CONST_44  C5   C4   NAJ  CAR  180.00   0.0  0
 1MV  CONST_45  H6   NAJ  C4   N3   180.00   0.0  0
 1MV  Var_01    H12  CAQ  CAN  CAM  101.15  30.0  2
 1MV  Var_02    C4   NAJ  CAR  PAS  104.78  30.0  3
 1MV  Var_03    PAT  CAR  PAS  OAU  169.33  30.0  3
 1MV  Var_04    OAX  PAT  CAR  PAS  -69.44  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
 1MV  plan-1  CAD  0.020
 1MV  plan-1  CAK  0.020
 1MV  plan-1  CAL  0.020
 1MV  plan-1  CAM  0.020
 1MV  plan-1  CAN  0.020
 1MV  plan-1  CAQ  0.020
 1MV  plan-1  CAO  0.020
 1MV  plan-1  CAP  0.020
 1MV  plan-1  H10  0.020
 1MV  plan-1  H11  0.020
 1MV  plan-1  H15  0.020
 1MV  plan-1  H16  0.020
 1MV  plan-2  NAJ  0.020
 1MV  plan-2  C4   0.020
 1MV  plan-2  N3   0.020
 1MV  plan-2  C2   0.020
 1MV  plan-2  N1   0.020
 1MV  plan-2  C6   0.020
 1MV  plan-2  SAE  0.020
 1MV  plan-2  C5   0.020
 1MV  plan-2  CAC  0.020
 1MV  plan-2  CAD  0.020
 1MV  plan-2  CAK  0.020
 1MV  plan-2  H7   0.020
 1MV  plan-2  H8   0.020
 1MV  plan-3  CAR  0.020
 1MV  plan-3  NAJ  0.020
 1MV  plan-3  C4   0.020
 1MV  plan-3  H6   0.020

