# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:21:30 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: {[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-5-yl]methyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2sc3ncncc3c2C[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
 6O3  6O3  '{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-5-yl]methyl}phosphonic acid'  ligand  32  21  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6O3
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
 6O3  OAS  O  O      0  -0.887   0.2789  -2.3340  -1.4040
 6O3  PAR  P  P      0   1.173  -0.4926  -2.8257  -0.1800
 6O3  OAT  O  OP    -1  -0.882  -2.0053  -2.9576  -0.3969
 6O3  OAU  O  OP    -1  -0.904   0.1370  -4.0364   0.5198
 6O3  CAQ  C  CH2    0  -0.849  -0.2937  -1.4486   1.0971
 6O3  CAC  C  CR5    0   0.294  -0.7113  -0.1221   0.5874
 6O3  C5   C  CR56   0   0.016  -2.0908   0.2404   0.3999
 6O3  C6   C  CR16   0  -0.033  -3.2682  -0.4467   0.6910
 6O3  N1   N  N      0  -0.413  -4.4556   0.0865   0.4513
 6O3  C2   C  CR16   0   0.027  -4.4897   1.3027  -0.0956
 6O3  N3   N  N      0  -0.405  -3.4537   2.0493  -0.4300
 6O3  C4   C  CR56   0   0.006  -2.2729   1.5044  -0.1739
 6O3  SAE  S  S2     0   0.193  -0.7585   2.2623  -0.4987
 6O3  CAD  C  CR5    0  -0.336   0.1068   0.8774   0.1517
 6O3  CAJ  C  C      0   0.092   1.5713   0.9456   0.1636
 6O3  CAK  C  C1     0  -0.292   2.2835   1.3124  -0.9788
 6O3  CAL  C  C1     0  -0.285   3.6680   1.3855  -0.9613
 6O3  CAM  C  C      0   0.088   4.3918   1.0932   0.1926
 6O3  CAP  C  CH3    0  -0.722   5.8889   1.1920   0.2167
 6O3  CAN  C  C1     0  -0.287   3.6777   0.7333   1.3336
 6O3  CAO  C  C1     0  -0.294   2.2934   0.6692   1.3254
 6O3  H3   H  HCH2   0   0.214  -0.8775  -1.7088   1.9859
 6O3  H4   H  HCH2   0   0.226   0.7514  -1.4279   1.4050
 6O3  H5   H  HCR6   0   0.264  -3.2377  -1.4448   1.1072
 6O3  H6   H  HCR6   0   0.259  -5.4711   1.7219  -0.2861
 6O3  H7   H  H      0   0.249   1.7539   1.5302  -1.8986
 6O3  H8   H  H      0   0.248   4.1931   1.6670  -1.8664
 6O3  H9   H  HCH3   0   0.249   6.2095   2.2035   0.4750
 6O3  H10  H  HCH3   0   0.244   6.3212   0.5183   0.9561
 6O3  H11  H  HCH3   0   0.244   6.3229   0.9532  -0.7539
 6O3  H12  H  H      0   0.248   4.2111   0.5027   2.2483
 6O3  H13  H  H      0   0.256   1.7685   0.4086   2.2354

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
 6O3  OAS  PAR  deloc     1.528  0.020  1.528
 6O3  OAT  PAR  deloc     1.534  0.020  1.534
 6O3  OAU  PAR  deloc     1.534  0.020  1.534
 6O3  PAR  CAQ  single    1.889  0.020  1.889
 6O3  CAQ  CAC  single    1.481  0.020  1.481
 6O3  CAN  CAO  aromatic  1.386  0.020  1.386
 6O3  CAN  CAM  aromatic  1.393  0.020  1.393
 6O3  CAO  CAJ  aromatic  1.396  0.020  1.396
 6O3  CAP  CAM  single    1.501  0.020  1.501
 6O3  C6   N1   aromatic  1.324  0.020  1.324
 6O3  C6   C5   aromatic  1.394  0.020  1.394
 6O3  CAM  CAL  aromatic  1.393  0.020  1.393
 6O3  CAC  C5   aromatic  1.439  0.020  1.439
 6O3  CAC  CAD  aromatic  1.363  0.020  1.363
 6O3  N1   C2   aromatic  1.334  0.020  1.334
 6O3  C5   C4   aromatic  1.400  0.020  1.400
 6O3  CAJ  CAD  single    1.466  0.020  1.466
 6O3  CAJ  CAK  aromatic  1.395  0.020  1.395
 6O3  CAD  SAE  aromatic  1.758  0.020  1.758
 6O3  CAL  CAK  aromatic  1.387  0.020  1.387
 6O3  C2   N3   aromatic  1.320  0.020  1.320
 6O3  C4   N3   aromatic  1.325  0.020  1.325
 6O3  C4   SAE  aromatic  1.724  0.020  1.724
 6O3  CAQ  H3   single    0.970  0.020  1.090
 6O3  CAQ  H4   single    0.970  0.020  1.090
 6O3  C6   H5   single    0.930  0.020  1.080
 6O3  C2   H6   single    0.930  0.020  1.080
 6O3  CAK  H7   single    0.930  0.020  1.080
 6O3  CAL  H8   single    0.930  0.020  1.080
 6O3  CAP  H9   single    0.970  0.020  1.090
 6O3  CAP  H10  single    0.970  0.020  1.090
 6O3  CAP  H11  single    0.970  0.020  1.090
 6O3  CAN  H12  single    0.930  0.020  1.080
 6O3  CAO  H13  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
 6O3  CAQ  PAR  OAU  102.94  3.000
 6O3  CAQ  PAR  OAT  105.20  3.000
 6O3  OAU  PAR  OAT  113.67  3.000
 6O3  CAQ  PAR  OAS  104.71  3.000
 6O3  OAU  PAR  OAS  114.35  3.000
 6O3  OAT  PAR  OAS  114.35  3.000
 6O3  H4   CAQ  H3   106.66  3.000
 6O3  H4   CAQ  CAC  110.53  3.000
 6O3  H3   CAQ  CAC  110.00  3.000
 6O3  H4   CAQ  PAR  107.81  3.000
 6O3  H3   CAQ  PAR  108.63  3.000
 6O3  CAC  CAQ  PAR  112.99  3.000
 6O3  CAD  CAC  C5   110.43  3.000
 6O3  CAD  CAC  CAQ  126.69  3.000
 6O3  C5   CAC  CAQ  122.75  3.000
 6O3  C4   C5   C6   114.88  3.000
 6O3  C4   C5   CAC  113.93  3.000
 6O3  C6   C5   CAC  131.19  3.000
 6O3  H5   C6   N1   117.82  3.000
 6O3  H5   C6   C5   120.75  3.000
 6O3  N1   C6   C5   121.42  3.000
 6O3  C2   N1   C6   117.68  3.000
 6O3  H6   C2   N3   116.57  3.000
 6O3  H6   C2   N1   116.60  3.000
 6O3  N3   C2   N1   126.83  3.000
 6O3  C4   N3   C2   114.69  3.000
 6O3  SAE  C4   N3   124.42  3.000
 6O3  SAE  C4   C5   111.09  3.000
 6O3  N3   C4   C5   124.49  3.000
 6O3  CAD  SAE  C4    90.93  3.000
 6O3  CAJ  CAD  SAE  117.26  3.000
 6O3  SAE  CAD  CAC  113.61  3.000
 6O3  CAJ  CAD  CAC  129.12  3.000
 6O3  CAO  CAJ  CAK  118.00  3.000
 6O3  CAK  CAJ  CAD  121.03  3.000
 6O3  CAO  CAJ  CAD  120.96  3.000
 6O3  H7   CAK  CAL  119.22  3.000
 6O3  H7   CAK  CAJ  119.89  3.000
 6O3  CAL  CAK  CAJ  120.88  3.000
 6O3  H8   CAL  CAM  119.64  3.000
 6O3  H8   CAL  CAK  119.14  3.000
 6O3  CAM  CAL  CAK  121.21  3.000
 6O3  CAN  CAM  CAP  121.01  3.000
 6O3  CAP  CAM  CAL  121.19  3.000
 6O3  CAN  CAM  CAL  117.78  3.000
 6O3  H11  CAP  H10  108.12  3.000
 6O3  H11  CAP  H9   107.27  3.000
 6O3  H10  CAP  H9   107.20  3.000
 6O3  H11  CAP  CAM  111.63  3.000
 6O3  H10  CAP  CAM  111.47  3.000
 6O3  H9   CAP  CAM  110.95  3.000
 6O3  H12  CAN  CAO  119.13  3.000
 6O3  H12  CAN  CAM  119.60  3.000
 6O3  CAO  CAN  CAM  121.27  3.000
 6O3  H13  CAO  CAN  119.38  3.000
 6O3  H13  CAO  CAJ  119.78  3.000
 6O3  CAN  CAO  CAJ  120.84  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
 6O3  CONST_01  N1   C6   C5   CAC  180.00   0.0  0
 6O3  CONST_02  N3   C4   C5   CAC  180.00   0.0  0
 6O3  CONST_03  SAE  C4   C5   CAC    0.00   0.0  0
 6O3  CONST_06  C4   SAE  CAD  CAC    0.00   0.0  0
 6O3  CONST_07  C2   N1   C6   C5     0.00   0.0  0
 6O3  CONST_08  CAJ  CAD  CAC  C5   180.00   0.0  0
 6O3  CONST_09  SAE  CAD  CAC  C5     0.00   0.0  0
 6O3  CONST_10  C2   N3   C4   C5     0.00   0.0  0
 6O3  CONST_11  CAD  SAE  C4   C5     0.00   0.0  0
 6O3  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 6O3  CONST_13  CAD  CAC  C5   C6   180.00   0.0  0
 6O3  CONST_14  N3   C4   C5   C6     0.00   0.0  0
 6O3  CONST_15  SAE  C4   C5   C6   180.00   0.0  0
 6O3  CONST_16  C4   C5   C6   N1     0.00   0.0  0
 6O3  CONST_17  C4   N3   C2   N1     0.00   0.0  0
 6O3  CONST_18  SAE  C4   N3   C2   180.00   0.0  0
 6O3  CONST_19  CAD  SAE  C4   N3   180.00   0.0  0
 6O3  CONST_20  CAD  CAC  C5   C4     0.00   0.0  0
 6O3  CONST_21  CAJ  CAD  SAE  C4   180.00   0.0  0
 6O3  CONST_24  CAN  CAO  CAJ  CAD  180.00   0.0  0
 6O3  CONST_25  CAL  CAK  CAJ  CAD  180.00   0.0  0
 6O3  CONST_26  CAM  CAN  CAO  CAJ    0.00   0.0  0
 6O3  CONST_27  CAM  CAL  CAK  CAJ    0.00   0.0  0
 6O3  CONST_28  CAN  CAO  CAJ  CAK    0.00   0.0  0
 6O3  CONST_29  CAN  CAM  CAL  CAK    0.00   0.0  0
 6O3  CONST_30  CAO  CAN  CAM  CAL    0.00   0.0  0
 6O3  CONST_31  CAO  CAJ  CAK  CAL    0.00   0.0  0
 6O3  CONST_32  C6   C5   CAC  CAQ    0.00   0.0  0
 6O3  CONST_33  C4   C5   CAC  CAQ  180.00   0.0  0
 6O3  CONST_34  CAJ  CAD  CAC  CAQ    0.00   0.0  0
 6O3  CONST_35  SAE  CAD  CAC  CAQ  180.00   0.0  0
 6O3  CONST_36  CAP  CAM  CAL  CAK  180.00   0.0  0
 6O3  CONST_37  CAO  CAN  CAM  CAP  180.00   0.0  0
 6O3  CONST_38  H5   C6   C5   CAC    0.00   0.0  0
 6O3  CONST_39  H6   C2   N1   C6   180.00   0.0  0
 6O3  CONST_40  H13  CAO  CAJ  CAD    0.00   0.0  0
 6O3  CONST_41  H7   CAK  CAJ  CAD    0.00   0.0  0
 6O3  CONST_42  H12  CAN  CAO  CAJ  180.00   0.0  0
 6O3  CONST_43  H8   CAL  CAK  CAJ  180.00   0.0  0
 6O3  Var_01    C5   CAC  CAQ  PAR   73.75  30.0  2
 6O3  Var_02    H9   CAP  CAM  CAL   87.77  30.0  2
 6O3  Var_03    CAC  CAQ  PAR  OAS   54.22  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
 6O3  plan-1  CAD  0.020
 6O3  plan-1  CAJ  0.020
 6O3  plan-1  CAK  0.020
 6O3  plan-1  CAL  0.020
 6O3  plan-1  CAM  0.020
 6O3  plan-1  CAP  0.020
 6O3  plan-1  CAN  0.020
 6O3  plan-1  CAO  0.020
 6O3  plan-1  H7   0.020
 6O3  plan-1  H8   0.020
 6O3  plan-1  H12  0.020
 6O3  plan-1  H13  0.020
 6O3  plan-2  CAQ  0.020
 6O3  plan-2  CAC  0.020
 6O3  plan-2  C5   0.020
 6O3  plan-2  C6   0.020
 6O3  plan-2  N1   0.020
 6O3  plan-2  C2   0.020
 6O3  plan-2  N3   0.020
 6O3  plan-2  C4   0.020
 6O3  plan-2  SAE  0.020
 6O3  plan-2  CAD  0.020
 6O3  plan-2  CAJ  0.020
 6O3  plan-2  H5   0.020
 6O3  plan-2  H6   0.020

