# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 07:31:02 2021
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1R)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-phenylethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1Cl)c2sc3ncnc(N[C@@H](Cc4ccccc4)[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
 M2V  M2V  '[(1R)-1-{[6-(3-chloro-4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}-2-phenylethyl]phosphonic acid'  ligand  49  30  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M2V
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
 M2V  C4    C   CR6   0   0.558   2.3220  40.1795   -6.4177
 M2V  C5    C   CR56  0   0.061   2.9367  38.9080   -6.5083
 M2V  C6    C   CR56  0  -0.022   4.2851  38.8796   -6.1665
 M2V  N1    N   N     0  -0.435   5.0007  39.9250   -5.7597
 M2V  N3    N   N     0  -0.463   3.0285  41.2245   -6.0081
 M2V  CAN   C   CR16  0  -0.264   2.0135  34.6475   -7.2036
 M2V  CAO   C   CR6   0  -0.083   1.8775  33.3225   -7.5735
 M2V  CLAZ  CL  CL    0  -0.122   0.3008  32.6040   -7.4771
 M2V  CAP   C   CR6   0   0.156   2.9540  32.5472   -8.0044
 M2V  CAS   C   CH3   0  -0.722   2.7980  31.1125   -8.3988
 M2V  CAQ   C   CR16  0  -0.298   4.1936  33.1797   -8.0462
 M2V  CAR   C   CR16  0  -0.294   4.3547  34.5074   -7.6884
 M2V  CAM   C   CR6   0   0.122   3.2638  35.2645   -7.2636
 M2V  CAJ   C   CR5   0  -0.207   3.4004  36.6719   -6.8983
 M2V  SAK   S   S2    0   0.226   4.9391  37.2898   -6.3497
 M2V  CAI   C   CR15  0  -0.269   2.4450  37.6390   -6.9268
 M2V  C2    C   CR16  0   0.050   4.3095  41.0465   -5.7047
 M2V  NAA   N   NH1   0  -0.686   1.0194  40.3449   -6.7299
 M2V  CAB   C   CH1   0  -0.376   0.4296  41.6385   -6.9884
 M2V  PBA   P   P     0   1.390  -1.1526  41.6774   -6.0869
 M2V  OBC   O   OH1   0  -0.741  -0.7562  41.5892   -4.5319
 M2V  OBD   O   O     0  -0.710  -2.1293  40.6589   -6.5446
 M2V  OBB   O   OH1   0  -0.742  -1.5715  43.2122   -6.2395
 M2V  CAL   C   CH2   0  -0.538   0.2693  41.8988   -8.4953
 M2V  CAT   C   CR6   0   0.135   1.5923  41.7407   -9.1901
 M2V  CAU   C   CR16  0  -0.313   1.9624  40.5207   -9.7488
 M2V  CAV   C   CR16  0  -0.231   3.2217  40.3470  -10.3068
 M2V  CAW   C   CR16  0  -0.268   4.1266  41.3993  -10.3214
 M2V  CAX   C   CR16  0  -0.238   3.7630  42.6250   -9.7776
 M2V  CAY   C   CR16  0  -0.289   2.5063  42.7910   -9.2146
 M2V  H1    H   HCR6  0   0.279   1.1487  35.1950   -6.8529
 M2V  H2    H   HCH3  0   0.254   2.1035  31.0014   -9.2328
 M2V  H3    H   HCH3  0   0.254   3.7545  30.6887   -8.6985
 M2V  H4    H   HCH3  0   0.254   2.4076  30.5129   -7.5751
 M2V  H5    H   HCR6  0   0.266   5.0573  32.6165   -8.3763
 M2V  H6    H   HCR6  0   0.261   5.3401  34.9508   -7.7619
 M2V  H7    H   HCR5  0   0.277   1.4318  37.4487   -7.2537
 M2V  H8    H   HCR6  0   0.259   4.8455  41.9297   -5.3755
 M2V  H9    H   HNH1  0   0.407   0.5443  39.5511   -7.1320
 M2V  H10   H   HCH1  0   0.321   1.0874  42.3933   -6.5548
 M2V  H11   H   HOH1  0   0.495  -0.7163  40.6876   -4.1877
 M2V  H12   H   HOH1  0   0.499  -2.5006  43.3995   -6.0455
 M2V  H13   H   HCH2  0   0.273  -0.1214  42.9074   -8.6404
 M2V  H14   H   HCH2  0   0.264  -0.4665  41.2068   -8.9125
 M2V  H15   H   HCR6  0   0.247   1.2613  39.6938   -9.7450
 M2V  H16   H   HCR6  0   0.251   3.4961  39.3887  -10.7288
 M2V  H17   H   HCR6  0   0.252   5.1088  41.2668  -10.7569
 M2V  H18   H   HCR6  0   0.252   4.4613  43.4520   -9.7900
 M2V  H19   H   HCR6  0   0.245   2.2318  43.7480   -8.7854

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
 M2V  CAV   CAW  aromatic  1.388  0.020  1.388
 M2V  CAV   CAU  aromatic  1.388  0.020  1.388
 M2V  CAW   CAX  aromatic  1.389  0.020  1.389
 M2V  CAU   CAT  aromatic  1.392  0.020  1.392
 M2V  CAX   CAY  aromatic  1.387  0.020  1.387
 M2V  CAT   CAY  aromatic  1.393  0.020  1.393
 M2V  CAT   CAL  single    1.503  0.020  1.503
 M2V  CAL   CAB  single    1.538  0.020  1.538
 M2V  CAS   CAP  single    1.496  0.020  1.496
 M2V  CLAZ  CAO  single    1.735  0.020  1.735
 M2V  CAP   CAO  aromatic  1.395  0.020  1.395
 M2V  CAP   CAQ  aromatic  1.392  0.020  1.392
 M2V  CAO   CAN  aromatic  1.382  0.020  1.382
 M2V  NAA   CAB  single    1.445  0.020  1.445
 M2V  NAA   C4   single    1.350  0.020  1.350
 M2V  CAQ   CAR  aromatic  1.384  0.020  1.384
 M2V  CAN   CAM  aromatic  1.396  0.020  1.396
 M2V  OBD   PBA  double    1.484  0.020  1.484
 M2V  CAB   PBA  single    1.821  0.020  1.821
 M2V  CAR   CAM  aromatic  1.394  0.020  1.394
 M2V  CAM   CAJ  single    1.460  0.020  1.460
 M2V  CAI   CAJ  aromatic  1.360  0.020  1.360
 M2V  CAI   C5   aromatic  1.424  0.020  1.424
 M2V  CAJ   SAK  aromatic  1.746  0.020  1.746
 M2V  C4    C5   aromatic  1.415  0.020  1.415
 M2V  C4    N3   aromatic  1.326  0.020  1.326
 M2V  C5    C6   aromatic  1.391  0.020  1.391
 M2V  N3    C2   aromatic  1.328  0.020  1.328
 M2V  PBA   OBC  single    1.607  0.020  1.607
 M2V  PBA   OBB  single    1.598  0.020  1.598
 M2V  C6    SAK  aromatic  1.729  0.020  1.729
 M2V  C6    N1   aromatic  1.331  0.020  1.331
 M2V  C2    N1   aromatic  1.318  0.020  1.318
 M2V  CAN   H1   single    0.930  0.020  1.080
 M2V  CAS   H2   single    0.970  0.020  1.090
 M2V  CAS   H3   single    0.970  0.020  1.090
 M2V  CAS   H4   single    0.970  0.020  1.090
 M2V  CAQ   H5   single    0.930  0.020  1.080
 M2V  CAR   H6   single    0.930  0.020  1.080
 M2V  CAI   H7   single    0.930  0.020  1.080
 M2V  C2    H8   single    0.930  0.020  1.080
 M2V  NAA   H9   single    0.890  0.020  1.040
 M2V  CAB   H10  single    0.970  0.020  1.090
 M2V  OBC   H11  single    0.850  0.020  0.980
 M2V  OBB   H12  single    0.850  0.020  0.980
 M2V  CAL   H13  single    0.970  0.020  1.090
 M2V  CAL   H14  single    0.970  0.020  1.090
 M2V  CAU   H15  single    0.930  0.020  1.080
 M2V  CAV   H16  single    0.930  0.020  1.080
 M2V  CAW   H17  single    0.930  0.020  1.080
 M2V  CAX   H18  single    0.930  0.020  1.080
 M2V  CAY   H19  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
 M2V  NAA   C4   N3    119.28  3.000
 M2V  N3    C4   C5    119.76  3.000
 M2V  NAA   C4   C5    120.96  3.000
 M2V  CAI   C5   C6    112.87  3.000
 M2V  C6    C5   C4    115.06  3.000
 M2V  CAI   C5   C4    132.04  3.000
 M2V  SAK   C6   N1    123.47  3.000
 M2V  N1    C6   C5    125.47  3.000
 M2V  SAK   C6   C5    111.06  3.000
 M2V  C2    N1   C6    113.52  3.000
 M2V  C2    N3   C4    118.60  3.000
 M2V  H1    CAN  CAM   120.42  3.000
 M2V  H1    CAN  CAO   119.55  3.000
 M2V  CAM   CAN  CAO   120.03  3.000
 M2V  CAP   CAO  CLAZ  119.23  3.000
 M2V  CAP   CAO  CAN   122.65  3.000
 M2V  CLAZ  CAO  CAN   118.12  3.000
 M2V  CAQ   CAP  CAS   121.37  3.000
 M2V  CAQ   CAP  CAO   116.35  3.000
 M2V  CAS   CAP  CAO   122.28  3.000
 M2V  H4    CAS  H3    107.96  3.000
 M2V  H4    CAS  H2    107.07  3.000
 M2V  H3    CAS  H2    108.02  3.000
 M2V  H4    CAS  CAP   111.42  3.000
 M2V  H3    CAS  CAP   110.76  3.000
 M2V  H2    CAS  CAP   111.44  3.000
 M2V  H5    CAQ  CAR   119.00  3.000
 M2V  H5    CAQ  CAP   118.89  3.000
 M2V  CAR   CAQ  CAP   122.11  3.000
 M2V  H6    CAR  CAM   120.68  3.000
 M2V  H6    CAR  CAQ   118.75  3.000
 M2V  CAM   CAR  CAQ   120.56  3.000
 M2V  CAJ   CAM  CAR   121.76  3.000
 M2V  CAJ   CAM  CAN   119.94  3.000
 M2V  CAR   CAM  CAN   118.29  3.000
 M2V  CAI   CAJ  SAK   111.96  3.000
 M2V  SAK   CAJ  CAM   120.12  3.000
 M2V  CAI   CAJ  CAM   127.91  3.000
 M2V  CAJ   SAK  C6     91.45  3.000
 M2V  H7    CAI  CAJ   122.65  3.000
 M2V  H7    CAI  C5    124.69  3.000
 M2V  CAJ   CAI  C5    112.65  3.000
 M2V  H8    C2   N3    115.90  3.000
 M2V  H8    C2   N1    116.51  3.000
 M2V  N3    C2   N1    127.59  3.000
 M2V  H9    NAA  CAB   116.16  3.000
 M2V  H9    NAA  C4    116.77  3.000
 M2V  CAB   NAA  C4    123.03  3.000
 M2V  H10   CAB  CAL   109.58  3.000
 M2V  H10   CAB  PBA   108.20  3.000
 M2V  CAL   CAB  PBA   113.01  3.000
 M2V  H10   CAB  NAA   107.58  3.000
 M2V  PBA   CAB  NAA   106.57  3.000
 M2V  CAL   CAB  NAA   111.68  3.000
 M2V  OBB   PBA  OBD   117.21  3.000
 M2V  OBB   PBA  OBC   102.10  3.000
 M2V  OBD   PBA  OBC   115.03  3.000
 M2V  OBB   PBA  CAB   101.60  3.000
 M2V  OBC   PBA  CAB   105.28  3.000
 M2V  OBD   PBA  CAB   113.86  3.000
 M2V  H11   OBC  PBA   113.96  3.000
 M2V  H12   OBB  PBA   114.74  3.000
 M2V  H14   CAL  H13   107.06  3.000
 M2V  H14   CAL  CAT   110.46  3.000
 M2V  H13   CAL  CAT   110.55  3.000
 M2V  H14   CAL  CAB   109.70  3.000
 M2V  H13   CAL  CAB   108.91  3.000
 M2V  CAT   CAL  CAB   110.09  3.000
 M2V  CAY   CAT  CAU   118.65  3.000
 M2V  CAY   CAT  CAL   120.44  3.000
 M2V  CAU   CAT  CAL   120.79  3.000
 M2V  H15   CAU  CAV   119.51  3.000
 M2V  H15   CAU  CAT   119.68  3.000
 M2V  CAV   CAU  CAT   120.81  3.000
 M2V  H16   CAV  CAW   120.12  3.000
 M2V  H16   CAV  CAU   119.83  3.000
 M2V  CAW   CAV  CAU   120.05  3.000
 M2V  H17   CAW  CAX   120.19  3.000
 M2V  H17   CAW  CAV   120.20  3.000
 M2V  CAX   CAW  CAV   119.62  3.000
 M2V  H18   CAX  CAY   119.85  3.000
 M2V  H18   CAX  CAW   120.05  3.000
 M2V  CAY   CAX  CAW   120.10  3.000
 M2V  H19   CAY  CAX   119.72  3.000
 M2V  H19   CAY  CAT   119.51  3.000
 M2V  CAX   CAY  CAT   120.77  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
 M2V  CONST_01  CAJ  CAI  C5   C4    180.00   0.0  0
 M2V  CONST_02  SAK  C6   C5   C4    180.00   0.0  0
 M2V  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 M2V  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 M2V  CONST_05  CAM  CAJ  CAI  C5    180.00   0.0  0
 M2V  CONST_06  SAK  CAJ  CAI  C5      0.00   0.0  0
 M2V  CONST_07  C2   N3   C4   C5      0.00   0.0  0
 M2V  CONST_08  CAJ  SAK  C6   C5      0.00   0.0  0
 M2V  CONST_09  C2   N1   C6   C5      0.00   0.0  0
 M2V  CONST_10  CAJ  CAI  C5   C6      0.00   0.0  0
 M2V  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 M2V  CONST_12  CAM  CAJ  SAK  C6    180.00   0.0  0
 M2V  CONST_13  CAI  CAJ  SAK  C6      0.00   0.0  0
 M2V  CONST_14  N3   C2   N1   C6      0.00   0.0  0
 M2V  CONST_15  CAI  C5   C6   N1    180.00   0.0  0
 M2V  CONST_16  CAJ  SAK  C6   N1    180.00   0.0  0
 M2V  CONST_17  CAI  C5   C4   N3    180.00   0.0  0
 M2V  CONST_18  CAQ  CAP  CAO  CAN     0.00   0.0  0
 M2V  CONST_19  CAQ  CAR  CAM  CAN     0.00   0.0  0
 M2V  CONST_22  CAR  CAQ  CAP  CAO     0.00   0.0  0
 M2V  CONST_23  CAR  CAM  CAN  CAO     0.00   0.0  0
 M2V  CONST_24  CAJ  CAM  CAN  CAO   180.00   0.0  0
 M2V  CONST_25  CAM  CAN  CAO  CAP     0.00   0.0  0
 M2V  CONST_26  CAM  CAR  CAQ  CAP     0.00   0.0  0
 M2V  CONST_27  CAJ  CAM  CAR  CAQ   180.00   0.0  0
 M2V  CONST_30  CAI  C5   C6   SAK     0.00   0.0  0
 M2V  CONST_31  C2   N1   C6   SAK   180.00   0.0  0
 M2V  CONST_32  CAW  CAV  CAU  CAT     0.00   0.0  0
 M2V  CONST_33  CAW  CAX  CAY  CAT     0.00   0.0  0
 M2V  CONST_34  CAX  CAW  CAV  CAU     0.00   0.0  0
 M2V  CONST_35  CAX  CAY  CAT  CAU     0.00   0.0  0
 M2V  CONST_36  CAY  CAX  CAW  CAV     0.00   0.0  0
 M2V  CONST_37  CAY  CAT  CAU  CAV     0.00   0.0  0
 M2V  CONST_38  NAA  C4   C5   C6    180.00   0.0  0
 M2V  CONST_39  CAS  CAP  CAO  CAN   180.00   0.0  0
 M2V  CONST_40  CAQ  CAP  CAO  CLAZ  180.00   0.0  0
 M2V  CONST_41  CAM  CAN  CAO  CLAZ  180.00   0.0  0
 M2V  CONST_42  CAR  CAQ  CAP  CAS   180.00   0.0  0
 M2V  CONST_43  NAA  C4   C5   CAI     0.00   0.0  0
 M2V  CONST_44  NAA  C4   N3   C2    180.00   0.0  0
 M2V  CONST_45  CAV  CAU  CAT  CAL   180.00   0.0  0
 M2V  CONST_46  CAX  CAY  CAT  CAL   180.00   0.0  0
 M2V  CONST_47  H7   CAI  C5   C4      0.00   0.0  0
 M2V  CONST_48  H8   C2   N3   C4    180.00   0.0  0
 M2V  CONST_49  H6   CAR  CAM  CAN   180.00   0.0  0
 M2V  CONST_50  H5   CAQ  CAP  CAO   180.00   0.0  0
 M2V  CONST_51  H1   CAN  CAO  CAP   180.00   0.0  0
 M2V  CONST_52  H16  CAV  CAU  CAT   180.00   0.0  0
 M2V  CONST_53  H18  CAX  CAY  CAT   180.00   0.0  0
 M2V  CONST_54  H17  CAW  CAV  CAU   180.00   0.0  0
 M2V  CONST_55  H19  CAY  CAT  CAU   180.00   0.0  0
 M2V  CONST_56  H15  CAU  CAV  CAW   180.00   0.0  0
 M2V  CONST_59  H9   NAA  C4   C5      0.00   0.0  0
 M2V  Var_01    CAU  CAT  CAL  CAB    92.94  30.0  2
 M2V  Var_02    H2   CAS  CAP  CAO    59.98  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 M2V  chir_01  CAB  CAL  NAA  PBA  positiv

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
 M2V  plan-1  CAN   0.020
 M2V  plan-1  CAO   0.020
 M2V  plan-1  CLAZ  0.020
 M2V  plan-1  CAP   0.020
 M2V  plan-1  CAS   0.020
 M2V  plan-1  CAQ   0.020
 M2V  plan-1  CAR   0.020
 M2V  plan-1  CAM   0.020
 M2V  plan-1  CAJ   0.020
 M2V  plan-1  H1    0.020
 M2V  plan-1  H5    0.020
 M2V  plan-1  H6    0.020
 M2V  plan-2  CAL   0.020
 M2V  plan-2  CAT   0.020
 M2V  plan-2  CAU   0.020
 M2V  plan-2  CAV   0.020
 M2V  plan-2  CAW   0.020
 M2V  plan-2  CAX   0.020
 M2V  plan-2  CAY   0.020
 M2V  plan-2  H15   0.020
 M2V  plan-2  H16   0.020
 M2V  plan-2  H17   0.020
 M2V  plan-2  H18   0.020
 M2V  plan-2  H19   0.020
 M2V  plan-3  C4    0.020
 M2V  plan-3  C5    0.020
 M2V  plan-3  C6    0.020
 M2V  plan-3  N1    0.020
 M2V  plan-3  N3    0.020
 M2V  plan-3  CAM   0.020
 M2V  plan-3  CAJ   0.020
 M2V  plan-3  SAK   0.020
 M2V  plan-3  CAI   0.020
 M2V  plan-3  C2    0.020
 M2V  plan-3  NAA   0.020
 M2V  plan-3  H7    0.020
 M2V  plan-3  H8    0.020
 M2V  plan-4  C4    0.020
 M2V  plan-4  NAA   0.020
 M2V  plan-4  CAB   0.020
 M2V  plan-4  H9    0.020

