# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 16:00:41 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(1S)-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
 M2Y  M2Y  '[(1S)-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_M2Y
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
 M2Y  C4    C   CR6    0   0.547  -0.7432  -1.4730  -0.1790
 M2Y  C5    C   CR56   0   0.032   0.6782  -1.5510  -0.1021
 M2Y  C6    C   CR56   0  -0.031   1.2054  -2.8332  -0.0148
 M2Y  N1    N   N      0  -0.452   0.5014  -3.9646  -0.0015
 M2Y  N3    N   N      0  -0.474  -1.4492  -2.6102  -0.1832
 M2Y  CAN   C   CR16   0  -0.270   4.2357   1.0319   0.3053
 M2Y  CAO   C   CR6    0  -0.082   5.4253   1.7344   0.2674
 M2Y  CLAZ  CL  CL     0  -0.124   5.3986   3.4120   0.7129
 M2Y  CAP   C   CR6    0   0.153   6.6356   1.1471  -0.1009
 M2Y  CAS   C   CH3    0  -0.721   7.9197   1.9145  -0.1344
 M2Y  CAQ   C   CR16   0  -0.298   6.5888  -0.2034  -0.4356
 M2Y  CAR   C   CR16   0  -0.299   5.4084  -0.9267  -0.4150
 M2Y  CAM   C   CR6    0   0.129   4.2083  -0.3189  -0.0462
 M2Y  CAJ   C   CR5    0  -0.209   2.9444  -1.0497  -0.0367
 M2Y  SAK   S   S2     0   0.206   2.9333  -2.7929   0.0673
 M2Y  CAI   C   CR15   0  -0.273   1.6836  -0.5434  -0.1152
 M2Y  C2    C   CR16   0   0.036  -0.8018  -3.7615  -0.0953
 M2Y  NAA   N   NH1    0  -0.641  -1.3652  -0.3062  -0.3004
 M2Y  CAB   C   CH1    0  -0.347  -2.7948  -0.1010  -0.1208
 M2Y  PBA   P   P      0   1.189  -3.0983   0.3987   1.6757
 M2Y  OBC   O   OP    -1  -0.882  -4.5980   0.2141   1.9072
 M2Y  OBD   O   O      0  -0.884  -2.2230  -0.5709   2.4761
 M2Y  OBB   O   OP    -1  -0.897  -2.6089   1.8545   1.7283
 M2Y  CAL   C   CH2    0  -0.510  -3.2461   0.9319  -1.1602
 M2Y  CAT   C   CR6    0   0.138  -4.7326   1.1331  -1.2386
 M2Y  CAU   C   CR16   0  -0.258  -5.3751   2.0729  -0.4353
 M2Y  CAV   C   CR16   0  -0.258  -6.7420   2.2808  -0.5393
 M2Y  CAW   C   CR16   0  -0.278  -7.4995   1.5324  -1.4343
 M2Y  CAX   C   CR16   0  -0.247  -6.8746   0.5808  -2.2281
 M2Y  CAY   C   CR16   0  -0.328  -5.5009   0.3894  -2.1306
 M2Y  H1    H   HCR6   0   0.278   3.3303   1.5327   0.6213
 M2Y  H2    H   HCH3   0   0.254   8.1714   2.3135   0.8494
 M2Y  H3    H   HCH3   0   0.253   8.7410   1.2785  -0.4589
 M2Y  H4    H   HCH3   0   0.253   7.8601   2.7627  -0.8180
 M2Y  H5    H   HCR6   0   0.264   7.5052  -0.7000  -0.7292
 M2Y  H6    H   HCR6   0   0.259   5.4322  -1.9693  -0.7072
 M2Y  H7    H   HCR5   0   0.270   1.4885   0.5162  -0.2093
 M2Y  H8    H   HCR6   0   0.248  -1.4224  -4.6522  -0.1003
 M2Y  H9    H   HNH1   0   0.384  -0.8054   0.5198  -0.1507
 M2Y  H10   H   HCH1   0   0.226  -3.2792  -1.0558  -0.3286
 M2Y  H13   H   HCH2   0   0.226  -2.7657   1.8862  -0.9285
 M2Y  H14   H   HCH2   0   0.224  -2.8815   0.6243  -2.1453
 M2Y  H15   H   HCR6   0   0.228  -4.7848   2.6380   0.2739
 M2Y  H16   H   HCR6   0   0.242  -7.2236   3.0255   0.0827
 M2Y  H17   H   HCR6   0   0.245  -8.5669   1.6950  -1.5149
 M2Y  H18   H   HCR6   0   0.244  -7.4534  -0.0053  -2.9310
 M2Y  H19   H   HCR6   0   0.236  -5.0183  -0.3454  -2.7664

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
 M2Y  OBD  PBA   deloc     1.532  0.020  1.532
 M2Y  OBC  PBA   deloc     1.529  0.020  1.529
 M2Y  PBA  OBB   deloc     1.537  0.020  1.537
 M2Y  PBA  CAB   single    1.889  0.020  1.889
 M2Y  CAB  NAA   single    1.455  0.020  1.455
 M2Y  CAB  CAL   single    1.533  0.020  1.533
 M2Y  NAA  C4    single    1.328  0.020  1.328
 M2Y  CAL  CAT   single    1.502  0.020  1.502
 M2Y  C4   N3    aromatic  1.339  0.020  1.339
 M2Y  C4   C5    aromatic  1.426  0.020  1.426
 M2Y  N3   C2    aromatic  1.324  0.020  1.324
 M2Y  CAI  C5    aromatic  1.423  0.020  1.423
 M2Y  CAI  CAJ   aromatic  1.361  0.020  1.361
 M2Y  C5   C6    aromatic  1.389  0.020  1.389
 M2Y  C2   N1    aromatic  1.322  0.020  1.322
 M2Y  CAJ  CAM   single    1.460  0.020  1.460
 M2Y  CAJ  SAK   aromatic  1.746  0.020  1.746
 M2Y  CAR  CAM   aromatic  1.395  0.020  1.395
 M2Y  CAR  CAQ   aromatic  1.385  0.020  1.385
 M2Y  CAM  CAN   aromatic  1.396  0.020  1.396
 M2Y  C6   N1    aromatic  1.333  0.020  1.333
 M2Y  C6   SAK   aromatic  1.730  0.020  1.730
 M2Y  CAQ  CAP   aromatic  1.392  0.020  1.392
 M2Y  CAT  CAU   aromatic  1.393  0.020  1.393
 M2Y  CAT  CAY   aromatic  1.392  0.020  1.392
 M2Y  CAN  CAO   aromatic  1.382  0.020  1.382
 M2Y  CAP  CAO   aromatic  1.395  0.020  1.395
 M2Y  CAP  CAS   single    1.496  0.020  1.496
 M2Y  CAO  CLAZ  single    1.736  0.020  1.736
 M2Y  CAU  CAV   aromatic  1.387  0.020  1.387
 M2Y  CAY  CAX   aromatic  1.390  0.020  1.390
 M2Y  CAV  CAW   aromatic  1.391  0.020  1.391
 M2Y  CAX  CAW   aromatic  1.388  0.020  1.388
 M2Y  CAN  H1    single    0.930  0.020  1.080
 M2Y  CAS  H2    single    0.970  0.020  1.090
 M2Y  CAS  H3    single    0.970  0.020  1.090
 M2Y  CAS  H4    single    0.970  0.020  1.090
 M2Y  CAQ  H5    single    0.930  0.020  1.080
 M2Y  CAR  H6    single    0.930  0.020  1.080
 M2Y  CAI  H7    single    0.930  0.020  1.080
 M2Y  C2   H8    single    0.930  0.020  1.080
 M2Y  NAA  H9    single    0.890  0.020  1.040
 M2Y  CAB  H10   single    0.970  0.020  1.090
 M2Y  CAL  H13   single    0.970  0.020  1.090
 M2Y  CAL  H14   single    0.970  0.020  1.090
 M2Y  CAU  H15   single    0.930  0.020  1.080
 M2Y  CAV  H16   single    0.930  0.020  1.080
 M2Y  CAW  H17   single    0.930  0.020  1.080
 M2Y  CAX  H18   single    0.930  0.020  1.080
 M2Y  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
 M2Y  NAA   C4   N3    119.95  3.000
 M2Y  N3    C4   C5    118.65  3.000
 M2Y  NAA   C4   C5    121.34  3.000
 M2Y  CAI   C5   C6    112.70  3.000
 M2Y  C6    C5   C4    115.61  3.000
 M2Y  CAI   C5   C4    131.68  3.000
 M2Y  SAK   C6   N1    123.15  3.000
 M2Y  SAK   C6   C5    111.13  3.000
 M2Y  N1    C6   C5    125.72  3.000
 M2Y  C2    N1   C6    112.93  3.000
 M2Y  C2    N3   C4    118.74  3.000
 M2Y  H1    CAN  CAM   120.34  3.000
 M2Y  H1    CAN  CAO   119.54  3.000
 M2Y  CAM   CAN  CAO   120.11  3.000
 M2Y  CAP   CAO  CLAZ  119.21  3.000
 M2Y  CLAZ  CAO  CAN   118.09  3.000
 M2Y  CAP   CAO  CAN   122.69  3.000
 M2Y  CAQ   CAP  CAS   121.39  3.000
 M2Y  CAS   CAP  CAO   122.32  3.000
 M2Y  CAQ   CAP  CAO   116.28  3.000
 M2Y  H4    CAS  H3    107.98  3.000
 M2Y  H4    CAS  H2    107.05  3.000
 M2Y  H3    CAS  H2    107.96  3.000
 M2Y  H4    CAS  CAP   111.46  3.000
 M2Y  H3    CAS  CAP   110.77  3.000
 M2Y  H2    CAS  CAP   111.43  3.000
 M2Y  H5    CAQ  CAR   119.08  3.000
 M2Y  H5    CAQ  CAP   118.79  3.000
 M2Y  CAR   CAQ  CAP   122.13  3.000
 M2Y  H6    CAR  CAM   120.65  3.000
 M2Y  H6    CAR  CAQ   118.69  3.000
 M2Y  CAM   CAR  CAQ   120.65  3.000
 M2Y  CAJ   CAM  CAR   121.90  3.000
 M2Y  CAR   CAM  CAN   118.12  3.000
 M2Y  CAJ   CAM  CAN   119.97  3.000
 M2Y  CAI   CAJ  SAK   111.65  3.000
 M2Y  SAK   CAJ  CAM   120.37  3.000
 M2Y  CAI   CAJ  CAM   127.98  3.000
 M2Y  CAJ   SAK  C6     91.53  3.000
 M2Y  H7    CAI  CAJ   122.46  3.000
 M2Y  H7    CAI  C5    124.54  3.000
 M2Y  CAJ   CAI  C5    112.98  3.000
 M2Y  H8    C2   N3    115.71  3.000
 M2Y  H8    C2   N1    115.95  3.000
 M2Y  N3    C2   N1    128.34  3.000
 M2Y  H9    NAA  CAB   114.29  3.000
 M2Y  H9    NAA  C4    116.48  3.000
 M2Y  CAB   NAA  C4    124.94  3.000
 M2Y  H10   CAB  CAL   109.26  3.000
 M2Y  H10   CAB  PBA   109.96  3.000
 M2Y  CAL   CAB  PBA   114.78  3.000
 M2Y  H10   CAB  NAA   106.81  3.000
 M2Y  CAL   CAB  NAA   107.49  3.000
 M2Y  PBA   CAB  NAA   108.21  3.000
 M2Y  OBB   PBA  OBD   113.56  3.000
 M2Y  OBB   PBA  OBC   114.94  3.000
 M2Y  OBD   PBA  OBC   113.89  3.000
 M2Y  OBB   PBA  CAB   103.41  3.000
 M2Y  OBC   PBA  CAB   105.65  3.000
 M2Y  OBD   PBA  CAB   103.75  3.000
 M2Y  H14   CAL  H13   106.84  3.000
 M2Y  H14   CAL  CAT   108.69  3.000
 M2Y  H13   CAL  CAT   109.21  3.000
 M2Y  H14   CAL  CAB   108.83  3.000
 M2Y  H13   CAL  CAB   108.36  3.000
 M2Y  CAT   CAL  CAB   114.64  3.000
 M2Y  CAY   CAT  CAU   118.36  3.000
 M2Y  CAY   CAT  CAL   120.53  3.000
 M2Y  CAU   CAT  CAL   121.10  3.000
 M2Y  H15   CAU  CAV   120.57  3.000
 M2Y  H15   CAU  CAT   118.60  3.000
 M2Y  CAV   CAU  CAT   120.83  3.000
 M2Y  H16   CAV  CAW   119.82  3.000
 M2Y  H16   CAV  CAU   119.89  3.000
 M2Y  CAW   CAV  CAU   120.29  3.000
 M2Y  H17   CAW  CAX   120.29  3.000
 M2Y  H17   CAW  CAV   120.26  3.000
 M2Y  CAX   CAW  CAV   119.46  3.000
 M2Y  H18   CAX  CAY   119.94  3.000
 M2Y  H18   CAX  CAW   120.12  3.000
 M2Y  CAY   CAX  CAW   119.94  3.000
 M2Y  H19   CAY  CAX   119.45  3.000
 M2Y  H19   CAY  CAT   119.44  3.000
 M2Y  CAX   CAY  CAT   121.10  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
 M2Y  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 M2Y  CONST_02  CAJ  CAI  C5   C4    180.00   0.0  0
 M2Y  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 M2Y  CONST_04  SAK  C6   C5   C4    180.00   0.0  0
 M2Y  CONST_05  C2   N3   C4   C5      0.00   0.0  0
 M2Y  CONST_06  CAM  CAJ  CAI  C5    180.00   0.0  0
 M2Y  CONST_07  SAK  CAJ  CAI  C5      0.00   0.0  0
 M2Y  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 M2Y  CONST_09  CAJ  SAK  C6   C5      0.00   0.0  0
 M2Y  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 M2Y  CONST_11  CAJ  CAI  C5   C6      0.00   0.0  0
 M2Y  CONST_12  N3   C2   N1   C6      0.00   0.0  0
 M2Y  CONST_13  CAI  CAJ  SAK  C6      0.00   0.0  0
 M2Y  CONST_14  CAM  CAJ  SAK  C6    180.00   0.0  0
 M2Y  CONST_15  CAI  C5   C6   N1    180.00   0.0  0
 M2Y  CONST_16  CAJ  SAK  C6   N1    180.00   0.0  0
 M2Y  CONST_17  CAI  C5   C4   N3    180.00   0.0  0
 M2Y  CONST_20  CAQ  CAR  CAM  CAN     0.00   0.0  0
 M2Y  CONST_21  CAQ  CAP  CAO  CAN     0.00   0.0  0
 M2Y  CONST_22  CAJ  CAM  CAN  CAO   180.00   0.0  0
 M2Y  CONST_23  CAR  CAM  CAN  CAO     0.00   0.0  0
 M2Y  CONST_24  CAR  CAQ  CAP  CAO     0.00   0.0  0
 M2Y  CONST_25  CAM  CAR  CAQ  CAP     0.00   0.0  0
 M2Y  CONST_26  CAM  CAN  CAO  CAP     0.00   0.0  0
 M2Y  CONST_27  CAJ  CAM  CAR  CAQ   180.00   0.0  0
 M2Y  CONST_30  CAI  C5   C6   SAK     0.00   0.0  0
 M2Y  CONST_31  C2   N1   C6   SAK   180.00   0.0  0
 M2Y  CONST_32  CAW  CAV  CAU  CAT     0.00   0.0  0
 M2Y  CONST_33  CAW  CAX  CAY  CAT     0.00   0.0  0
 M2Y  CONST_34  CAX  CAY  CAT  CAU     0.00   0.0  0
 M2Y  CONST_35  CAX  CAW  CAV  CAU     0.00   0.0  0
 M2Y  CONST_36  CAY  CAT  CAU  CAV     0.00   0.0  0
 M2Y  CONST_37  CAY  CAX  CAW  CAV     0.00   0.0  0
 M2Y  CONST_38  NAA  C4   C5   C6    180.00   0.0  0
 M2Y  CONST_39  CAS  CAP  CAO  CAN   180.00   0.0  0
 M2Y  CONST_40  CAM  CAN  CAO  CLAZ  180.00   0.0  0
 M2Y  CONST_41  CAQ  CAP  CAO  CLAZ  180.00   0.0  0
 M2Y  CONST_42  CAR  CAQ  CAP  CAS   180.00   0.0  0
 M2Y  CONST_43  NAA  C4   C5   CAI     0.00   0.0  0
 M2Y  CONST_44  NAA  C4   N3   C2    180.00   0.0  0
 M2Y  CONST_45  CAV  CAU  CAT  CAL   180.00   0.0  0
 M2Y  CONST_46  CAX  CAY  CAT  CAL   180.00   0.0  0
 M2Y  CONST_47  H8   C2   N3   C4    180.00   0.0  0
 M2Y  CONST_48  H7   CAI  C5   C4      0.00   0.0  0
 M2Y  CONST_49  H6   CAR  CAM  CAN   180.00   0.0  0
 M2Y  CONST_50  H5   CAQ  CAP  CAO   180.00   0.0  0
 M2Y  CONST_51  H1   CAN  CAO  CAP   180.00   0.0  0
 M2Y  CONST_52  H16  CAV  CAU  CAT   180.00   0.0  0
 M2Y  CONST_53  H18  CAX  CAY  CAT   180.00   0.0  0
 M2Y  CONST_54  H19  CAY  CAT  CAU   180.00   0.0  0
 M2Y  CONST_55  H17  CAW  CAV  CAU   180.00   0.0  0
 M2Y  CONST_56  H15  CAU  CAV  CAW   180.00   0.0  0
 M2Y  CONST_57  CAB  NAA  C4   C5    180.00   0.0  0
 M2Y  CONST_59  H9   NAA  C4   C5      0.00   0.0  0
 M2Y  Var_01    CAU  CAT  CAL  CAB    88.81  30.0  2
 M2Y  Var_02    H2   CAS  CAP  CAO    60.51  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
 M2Y  chir_01  CAB  PBA  NAA  CAL  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
 M2Y  plan-1  CAN   0.020
 M2Y  plan-1  CAO   0.020
 M2Y  plan-1  CLAZ  0.020
 M2Y  plan-1  CAP   0.020
 M2Y  plan-1  CAS   0.020
 M2Y  plan-1  CAQ   0.020
 M2Y  plan-1  CAR   0.020
 M2Y  plan-1  CAM   0.020
 M2Y  plan-1  CAJ   0.020
 M2Y  plan-1  H1    0.020
 M2Y  plan-1  H5    0.020
 M2Y  plan-1  H6    0.020
 M2Y  plan-2  CAL   0.020
 M2Y  plan-2  CAT   0.020
 M2Y  plan-2  CAU   0.020
 M2Y  plan-2  CAV   0.020
 M2Y  plan-2  CAW   0.020
 M2Y  plan-2  CAX   0.020
 M2Y  plan-2  CAY   0.020
 M2Y  plan-2  H15   0.020
 M2Y  plan-2  H16   0.020
 M2Y  plan-2  H17   0.020
 M2Y  plan-2  H18   0.020
 M2Y  plan-2  H19   0.020
 M2Y  plan-3  C4    0.020
 M2Y  plan-3  C5    0.020
 M2Y  plan-3  C6    0.020
 M2Y  plan-3  N1    0.020
 M2Y  plan-3  N3    0.020
 M2Y  plan-3  CAM   0.020
 M2Y  plan-3  CAJ   0.020
 M2Y  plan-3  SAK   0.020
 M2Y  plan-3  CAI   0.020
 M2Y  plan-3  C2    0.020
 M2Y  plan-3  NAA   0.020
 M2Y  plan-3  H7    0.020
 M2Y  plan-3  H8    0.020
 M2Y  plan-4  C4    0.020
 M2Y  plan-4  NAA   0.020
 M2Y  plan-4  CAB   0.020
 M2Y  plan-4  H9    0.020

