# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:48:05 2020
#   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  47  30  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.541   1.5942   0.0668   0.7357
 M2V  C5    C   CR56   0   0.047   0.1834  -0.1331   0.7790
 M2V  C6    C   CR56   0  -0.032  -0.3045  -0.7100   1.9440
 M2V  N1    N   N      0  -0.456   0.4265  -1.0753   2.9965
 M2V  N3    N   N      0  -0.456   2.3245  -0.2701   1.8045
 M2V  CAN   C   CR16   0  -0.264  -4.5547   0.0216   0.2642
 M2V  CAO   C   CR6    0  -0.087  -5.7482   0.1667  -0.4216
 M2V  CLAZ  CL  CL     0  -0.124  -7.2135   0.2726   0.5027
 M2V  CAP   C   CR6    0   0.155  -5.8118   0.2411  -1.8110
 M2V  CAS   C   CH3    0  -0.722  -7.1045   0.4013  -2.5474
 M2V  CAQ   C   CR16   0  -0.295  -4.5977   0.1551  -2.4901
 M2V  CAR   C   CR16   0  -0.299  -3.3928  -0.0003  -1.8289
 M2V  CAM   C   CR6    0   0.122  -3.3511  -0.0652  -0.4353
 M2V  CAJ   C   CR5    0  -0.210  -2.0781  -0.2098   0.2650
 M2V  SAK   S   S2     0   0.201  -2.0221  -0.9143   1.8626
 M2V  CAI   C   CR15   0  -0.269  -0.8393   0.1462  -0.1708
 M2V  C2    C   CR16   0   0.042   1.7151  -0.8166   2.8429
 M2V  NAA   N   NH1    0  -0.640   2.1804   0.5881  -0.3337
 M2V  CAB   C   CH1    0  -0.360   3.6002   0.7529  -0.5671
 M2V  PBA   P   P      0   1.184   3.7981   2.3460  -1.5508
 M2V  OBC   O   OP    -1  -0.889   5.2330   2.3157  -2.0803
 M2V  OBD   O   O      0  -0.897   2.7168   2.1875  -2.6344
 M2V  OBB   O   OP    -1  -0.893   3.5159   3.4712  -0.5538
 M2V  CAL   C   CH2    0  -0.503   4.1638  -0.4628  -1.3204
 M2V  CAT   C   CR6    0   0.150   3.8925  -1.7557  -0.6108
 M2V  CAU   C   CR16   0  -0.299   4.7748  -2.2396   0.3530
 M2V  CAV   C   CR16   0  -0.240   4.4824  -3.3820   1.0828
 M2V  CAW   C   CR16   0  -0.276   3.2921  -4.0645   0.8630
 M2V  CAX   C   CR16   0  -0.234   2.4089  -3.6011  -0.1023
 M2V  CAY   C   CR16   0  -0.309   2.7123  -2.4614  -0.8352
 M2V  H1    H   HCR6   0   0.273  -4.5692  -0.0048   1.3468
 M2V  H2    H   HCH3   0   0.253  -7.6228   1.3143  -2.2506
 M2V  H3    H   HCH3   0   0.253  -6.9318   0.4475  -3.6210
 M2V  H4    H   HCH3   0   0.254  -7.7830  -0.4307  -2.3527
 M2V  H5    H   HCR6   0   0.264  -4.6022   0.2003  -3.5720
 M2V  H6    H   HCR6   0   0.262  -2.4820  -0.0888  -2.4063
 M2V  H7    H   HCR5   0   0.269  -0.6704   0.6145  -1.1313
 M2V  H8    H   HCR6   0   0.243   2.3554  -1.0845   3.6777
 M2V  H9    H   HNH1   0   0.377   1.6116   0.8700  -1.1210
 M2V  H10   H   HCH1   0   0.223   4.1017   0.8321   0.3985
 M2V  H13   H   HCH2   0   0.219   3.7289  -0.4816  -2.3234
 M2V  H14   H   HCH2   0   0.230   5.2371  -0.3091  -1.4425
 M2V  H15   H   HCR6   0   0.233   5.7011  -1.7074   0.5408
 M2V  H16   H   HCR6   0   0.242   5.1835  -3.7421   1.8258
 M2V  H17   H   HCR6   0   0.243   3.0592  -4.9544   1.4342
 M2V  H18   H   HCR6   0   0.242   1.4805  -4.1275  -0.2865
 M2V  H19   H   HCR6   0   0.236   2.0133  -2.1070  -1.5841

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  1.390  0.020  1.390
 M2V  CAV   CAU  aromatic  1.387  0.020  1.387
 M2V  CAW   CAX  aromatic  1.388  0.020  1.388
 M2V  CAU   CAT  aromatic  1.393  0.020  1.393
 M2V  CAX   CAY  aromatic  1.389  0.020  1.389
 M2V  CAT   CAY  aromatic  1.393  0.020  1.393
 M2V  CAT   CAL  single    1.500  0.020  1.500
 M2V  CAL   CAB  single    1.537  0.020  1.537
 M2V  CAS   CAP  single    1.496  0.020  1.496
 M2V  CLAZ  CAO  single    1.736  0.020  1.736
 M2V  CAP   CAO  aromatic  1.393  0.020  1.393
 M2V  CAP   CAQ  aromatic  1.394  0.020  1.394
 M2V  CAO   CAN  aromatic  1.384  0.020  1.384
 M2V  NAA   CAB  single    1.448  0.020  1.448
 M2V  NAA   C4   single    1.326  0.020  1.326
 M2V  CAQ   CAR  aromatic  1.383  0.020  1.383
 M2V  CAN   CAM  aromatic  1.395  0.020  1.395
 M2V  OBD   PBA  deloc     1.539  0.020  1.539
 M2V  CAB   PBA  single    1.883  0.020  1.883
 M2V  CAR   CAM  aromatic  1.396  0.020  1.396
 M2V  CAM   CAJ  single    1.460  0.020  1.460
 M2V  CAI   CAJ  aromatic  1.361  0.020  1.361
 M2V  CAI   C5   aromatic  1.423  0.020  1.423
 M2V  CAJ   SAK  aromatic  1.747  0.020  1.747
 M2V  C4    C5   aromatic  1.426  0.020  1.426
 M2V  C4    N3   aromatic  1.338  0.020  1.338
 M2V  C5    C6   aromatic  1.389  0.020  1.389
 M2V  N3    C2   aromatic  1.322  0.020  1.322
 M2V  PBA   OBC  deloc     1.530  0.020  1.530
 M2V  PBA   OBB  deloc     1.530  0.020  1.530
 M2V  C6    SAK  aromatic  1.732  0.020  1.732
 M2V  C6    N1   aromatic  1.332  0.020  1.332
 M2V  C2    N1   aromatic  1.323  0.020  1.323
 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    0.860  0.020  1.020
 M2V  CAB   H10  single    0.970  0.020  1.090
 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    120.13  3.000
 M2V  N3    C4   C5    118.73  3.000
 M2V  NAA   C4   C5    121.14  3.000
 M2V  CAI   C5   C6    112.89  3.000
 M2V  C6    C5   C4    115.56  3.000
 M2V  CAI   C5   C4    131.55  3.000
 M2V  SAK   C6   N1    123.30  3.000
 M2V  N1    C6   C5    125.72  3.000
 M2V  SAK   C6   C5    110.98  3.000
 M2V  C2    N1   C6    112.89  3.000
 M2V  C2    N3   C4    118.69  3.000
 M2V  H1    CAN  CAM   120.75  3.000
 M2V  H1    CAN  CAO   119.10  3.000
 M2V  CAM   CAN  CAO   120.14  3.000
 M2V  CAP   CAO  CLAZ  119.30  3.000
 M2V  CAP   CAO  CAN   122.64  3.000
 M2V  CLAZ  CAO  CAN   118.06  3.000
 M2V  CAQ   CAP  CAS   121.29  3.000
 M2V  CAQ   CAP  CAO   116.29  3.000
 M2V  CAS   CAP  CAO   122.42  3.000
 M2V  H4    CAS  H3    107.88  3.000
 M2V  H4    CAS  H2    107.11  3.000
 M2V  H3    CAS  H2    107.95  3.000
 M2V  H4    CAS  CAP   111.58  3.000
 M2V  H3    CAS  CAP   110.66  3.000
 M2V  H2    CAS  CAP   111.48  3.000
 M2V  H5    CAQ  CAR   119.08  3.000
 M2V  H5    CAQ  CAP   118.72  3.000
 M2V  CAR   CAQ  CAP   122.20  3.000
 M2V  H6    CAR  CAM   120.26  3.000
 M2V  H6    CAR  CAQ   119.17  3.000
 M2V  CAM   CAR  CAQ   120.57  3.000
 M2V  CAJ   CAM  CAR   120.63  3.000
 M2V  CAJ   CAM  CAN   121.20  3.000
 M2V  CAR   CAM  CAN   118.16  3.000
 M2V  CAI   CAJ  SAK   111.67  3.000
 M2V  SAK   CAJ  CAM   120.43  3.000
 M2V  CAI   CAJ  CAM   127.90  3.000
 M2V  CAJ   SAK  C6     91.56  3.000
 M2V  H7    CAI  CAJ   122.66  3.000
 M2V  H7    CAI  C5    124.42  3.000
 M2V  CAJ   CAI  C5    112.90  3.000
 M2V  H8    C2   N3    115.72  3.000
 M2V  H8    C2   N1    115.91  3.000
 M2V  N3    C2   N1    128.37  3.000
 M2V  H9    NAA  CAB   113.22  3.000
 M2V  H9    NAA  C4    119.25  3.000
 M2V  CAB   NAA  C4    127.44  3.000
 M2V  H10   CAB  CAL   108.82  3.000
 M2V  H10   CAB  PBA   110.65  3.000
 M2V  CAL   CAB  PBA   112.00  3.000
 M2V  H10   CAB  NAA   108.44  3.000
 M2V  PBA   CAB  NAA   106.47  3.000
 M2V  CAL   CAB  NAA   110.39  3.000
 M2V  OBB   PBA  OBD   113.89  3.000
 M2V  OBB   PBA  OBC   114.41  3.000
 M2V  OBD   PBA  OBC   114.41  3.000
 M2V  OBB   PBA  CAB   105.22  3.000
 M2V  OBC   PBA  CAB   105.23  3.000
 M2V  OBD   PBA  CAB   101.94  3.000
 M2V  H14   CAL  H13   106.92  3.000
 M2V  H14   CAL  CAT   110.63  3.000
 M2V  H13   CAL  CAT   110.32  3.000
 M2V  H14   CAL  CAB   107.71  3.000
 M2V  H13   CAL  CAB   108.50  3.000
 M2V  CAT   CAL  CAB   112.56  3.000
 M2V  CAY   CAT  CAU   118.16  3.000
 M2V  CAY   CAT  CAL   120.91  3.000
 M2V  CAU   CAT  CAL   120.81  3.000
 M2V  H15   CAU  CAV   119.54  3.000
 M2V  H15   CAU  CAT   119.35  3.000
 M2V  CAV   CAU  CAT   121.11  3.000
 M2V  H16   CAV  CAW   119.98  3.000
 M2V  H16   CAV  CAU   119.90  3.000
 M2V  CAW   CAV  CAU   120.13  3.000
 M2V  H17   CAW  CAX   120.30  3.000
 M2V  H17   CAW  CAV   120.29  3.000
 M2V  CAX   CAW  CAV   119.41  3.000
 M2V  H18   CAX  CAY   119.77  3.000
 M2V  H18   CAX  CAW   120.10  3.000
 M2V  CAY   CAX  CAW   120.14  3.000
 M2V  H19   CAY  CAX   119.48  3.000
 M2V  H19   CAY  CAT   119.46  3.000
 M2V  CAX   CAY  CAT   121.05  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_57  CAB  NAA  C4   C5    180.00   0.0  0
 M2V  CONST_58  CAB  NAA  C4   N3      0.00   0.0  0
 M2V  CONST_59  H9   NAA  C4   C5      0.00   0.0  0
 M2V  Var_01    CAU  CAT  CAL  CAB   -87.93  30.0  2
 M2V  Var_02    H2   CAS  CAP  CAO    59.28  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

