# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:48:40 2021
#   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  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_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   0.557   5.9691  71.3188  26.8656
 M2Y  C5    C   CR56  0   0.063   5.0768  72.2817  27.3963
 M2Y  C6    C   CR56  0  -0.023   3.9300  71.7612  27.9870
 M2Y  N1    N   N     0  -0.437   3.6215  70.4693  28.0699
 M2Y  N3    N   N     0  -0.462   5.6623  70.0295  26.9367
 M2Y  CAN   C   CR16  0  -0.263   2.5120  76.1259  28.5817
 M2Y  CAO   C   CR6   0  -0.087   2.2922  77.4705  28.8246
 M2Y  CLAZ  CL  CL    0  -0.122   0.6603  77.9971  29.0882
 M2Y  CAP   C   CR6   0   0.156   3.3242  78.4055  28.8581
 M2Y  CAS   C   CH3   0  -0.722   3.0780  79.8581  29.1176
 M2Y  CAQ   C   CR16  0  -0.295   4.6109  77.9157  28.6400
 M2Y  CAR   C   CR16  0  -0.298   4.8580  76.5753  28.4057
 M2Y  CAM   C   CR6   0   0.123   3.8076  75.6570  28.3674
 M2Y  CAJ   C   CR5   0  -0.205   4.0688  74.2443  28.1048
 M2Y  SAK   S   S2    0   0.221   2.9404  73.0214  28.6370
 M2Y  CAI   C   CR15  0  -0.269   5.1423  73.7017  27.4708
 M2Y  C2    C   CR16  0   0.050   4.5254  69.6780  27.5256
 M2Y  NAA   N   NH1   0  -0.668   7.1250  71.6909  26.2823
 M2Y  CAB   C   CH1   0  -0.394   8.2118  70.7773  26.0358
 M2Y  PBA   P   P     0   1.401   8.9132  71.0453  24.3752
 M2Y  OBC   O   OH1   0  -0.739   7.6977  70.8831  23.3376
 M2Y  OBD   O   O     0  -0.706  10.1067  70.2146  24.0860
 M2Y  OBB   O   OH1   0  -0.751   9.1177  72.6331  24.4019
 M2Y  CAL   C   CH2   0  -0.532   9.2925  70.8497  27.1319
 M2Y  CAT   C   CR6   0   0.130   8.6745  70.6439  28.4860
 M2Y  CAU   C   CR16  0  -0.284   8.4228  69.3605  28.9636
 M2Y  CAV   C   CR16  0  -0.239   7.7772  69.1689  30.1761
 M2Y  CAW   C   CR16  0  -0.267   7.3660  70.2625  30.9278
 M2Y  CAX   C   CR16  0  -0.232   7.6159  71.5463  30.4637
 M2Y  CAY   C   CR16  0  -0.308   8.2688  71.7323  29.2525
 M2Y  H1    H   HCR6  0   0.276   1.6647  75.4525  28.5446
 M2Y  H2    H   HCH3  0   0.254   2.4136  80.2904  28.3678
 M2Y  H3    H   HCH3  0   0.254   2.6094  80.0160  30.0901
 M2Y  H4    H   HCH3  0   0.254   4.0113  80.4174  29.1008
 M2Y  H5    H   HCR6  0   0.266   5.4426  78.6084  28.6667
 M2Y  H6    H   HCR6  0   0.263   5.8782  76.2426  28.2673
 M2Y  H7    H   HCR5  0   0.275   5.9397  74.3009  27.0532
 M2Y  H8    H   HCR6  0   0.257   4.3198  68.6139  27.5615
 M2Y  H9    H   HNH1  0   0.406   7.3563  72.6717  26.3065
 M2Y  H10   H   HCH1  0   0.323   7.7947  69.7678  26.0243
 M2Y  H11   H   HOH1  0   0.496   7.6264  69.9968  22.9592
 M2Y  H12   H   HOH1  0   0.500   9.5166  73.0140  23.6072
 M2Y  H13   H   HCH2  0   0.271  10.0436  70.0843  26.9304
 M2Y  H14   H   HCH2  0   0.264   9.7991  71.8175  27.0939
 M2Y  H15   H   HCR6  0   0.243   8.7310  68.5008  28.3796
 M2Y  H16   H   HCR6  0   0.251   7.5905  68.1642  30.5333
 M2Y  H17   H   HCR6  0   0.251   6.8566  70.1131  31.8712
 M2Y  H18   H   HCR6  0   0.249   7.3049  72.4055  31.0442
 M2Y  H19   H   HCR6  0   0.246   8.4628  72.7383  28.8987

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   double    1.483  0.020  1.483
 M2Y  OBC  PBA   single    1.606  0.020  1.606
 M2Y  PBA  OBB   single    1.601  0.020  1.601
 M2Y  PBA  CAB   single    1.823  0.020  1.823
 M2Y  CAB  NAA   single    1.441  0.020  1.441
 M2Y  CAB  CAL   single    1.541  0.020  1.541
 M2Y  NAA  C4    single    1.347  0.020  1.347
 M2Y  CAL  CAT   single    1.503  0.020  1.503
 M2Y  C4   N3    aromatic  1.327  0.020  1.327
 M2Y  C4   C5    aromatic  1.416  0.020  1.416
 M2Y  N3   C2    aromatic  1.328  0.020  1.328
 M2Y  CAI  C5    aromatic  1.423  0.020  1.423
 M2Y  CAI  CAJ   aromatic  1.360  0.020  1.360
 M2Y  C5   C6    aromatic  1.391  0.020  1.391
 M2Y  C2   N1    aromatic  1.319  0.020  1.319
 M2Y  CAJ  CAM   single    1.460  0.020  1.460
 M2Y  CAJ  SAK   aromatic  1.747  0.020  1.747
 M2Y  CAR  CAM   aromatic  1.396  0.020  1.396
 M2Y  CAR  CAQ   aromatic  1.383  0.020  1.383
 M2Y  CAM  CAN   aromatic  1.394  0.020  1.394
 M2Y  C6   N1    aromatic  1.331  0.020  1.331
 M2Y  C6   SAK   aromatic  1.729  0.020  1.729
 M2Y  CAQ  CAP   aromatic  1.394  0.020  1.394
 M2Y  CAT  CAU   aromatic  1.392  0.020  1.392
 M2Y  CAT  CAY   aromatic  1.392  0.020  1.392
 M2Y  CAN  CAO   aromatic  1.384  0.020  1.384
 M2Y  CAP  CAO   aromatic  1.393  0.020  1.393
 M2Y  CAP  CAS   single    1.496  0.020  1.496
 M2Y  CAO  CLAZ  single    1.735  0.020  1.735
 M2Y  CAU  CAV   aromatic  1.387  0.020  1.387
 M2Y  CAY  CAX   aromatic  1.389  0.020  1.389
 M2Y  CAV  CAW   aromatic  1.389  0.020  1.389
 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  OBC  H11   single    0.850  0.020  0.980
 M2Y  OBB  H12   single    0.850  0.020  0.980
 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    119.34  3.000
 M2Y  N3    C4   C5    119.66  3.000
 M2Y  NAA   C4   C5    121.01  3.000
 M2Y  CAI   C5   C6    112.89  3.000
 M2Y  C6    C5   C4    115.10  3.000
 M2Y  CAI   C5   C4    131.99  3.000
 M2Y  SAK   C6   N1    123.47  3.000
 M2Y  SAK   C6   C5    111.02  3.000
 M2Y  N1    C6   C5    125.51  3.000
 M2Y  C2    N1   C6    113.45  3.000
 M2Y  C2    N3   C4    118.62  3.000
 M2Y  H1    CAN  CAM   120.84  3.000
 M2Y  H1    CAN  CAO   119.08  3.000
 M2Y  CAM   CAN  CAO   120.08  3.000
 M2Y  CAP   CAO  CLAZ  119.31  3.000
 M2Y  CLAZ  CAO  CAN   118.09  3.000
 M2Y  CAP   CAO  CAN   122.60  3.000
 M2Y  CAQ   CAP  CAS   121.35  3.000
 M2Y  CAS   CAP  CAO   122.27  3.000
 M2Y  CAQ   CAP  CAO   116.38  3.000
 M2Y  H4    CAS  H3    107.92  3.000
 M2Y  H4    CAS  H2    107.94  3.000
 M2Y  H3    CAS  H2    107.08  3.000
 M2Y  H4    CAS  CAP   110.81  3.000
 M2Y  H3    CAS  CAP   111.46  3.000
 M2Y  H2    CAS  CAP   111.46  3.000
 M2Y  H5    CAQ  CAR   119.15  3.000
 M2Y  H5    CAQ  CAP   118.71  3.000
 M2Y  CAR   CAQ  CAP   122.14  3.000
 M2Y  H6    CAR  CAM   120.25  3.000
 M2Y  H6    CAR  CAQ   119.22  3.000
 M2Y  CAM   CAR  CAQ   120.53  3.000
 M2Y  CAJ   CAM  CAR   120.45  3.000
 M2Y  CAR   CAM  CAN   118.28  3.000
 M2Y  CAJ   CAM  CAN   121.27  3.000
 M2Y  CAI   CAJ  SAK   111.88  3.000
 M2Y  SAK   CAJ  CAM   120.45  3.000
 M2Y  CAI   CAJ  CAM   127.67  3.000
 M2Y  CAJ   SAK  C6     91.49  3.000
 M2Y  H7    CAI  CAJ   122.76  3.000
 M2Y  H7    CAI  C5    124.51  3.000
 M2Y  CAJ   CAI  C5    112.72  3.000
 M2Y  H8    C2   N3    115.90  3.000
 M2Y  H8    C2   N1    116.44  3.000
 M2Y  N3    C2   N1    127.66  3.000
 M2Y  H9    NAA  CAB   116.61  3.000
 M2Y  H9    NAA  C4    117.08  3.000
 M2Y  CAB   NAA  C4    123.10  3.000
 M2Y  H10   CAB  CAL   108.59  3.000
 M2Y  H10   CAB  PBA   105.86  3.000
 M2Y  CAL   CAB  PBA   111.79  3.000
 M2Y  H10   CAB  NAA   107.44  3.000
 M2Y  CAL   CAB  NAA   112.18  3.000
 M2Y  PBA   CAB  NAA   110.66  3.000
 M2Y  OBB   PBA  OBD   117.14  3.000
 M2Y  OBB   PBA  OBC   101.97  3.000
 M2Y  OBD   PBA  OBC   115.25  3.000
 M2Y  OBB   PBA  CAB   100.36  3.000
 M2Y  OBC   PBA  CAB   106.41  3.000
 M2Y  OBD   PBA  CAB   113.90  3.000
 M2Y  H11   OBC  PBA   113.66  3.000
 M2Y  H12   OBB  PBA   115.43  3.000
 M2Y  H14   CAL  H13   107.19  3.000
 M2Y  H14   CAL  CAT   110.07  3.000
 M2Y  H13   CAL  CAT   110.70  3.000
 M2Y  H14   CAL  CAB   109.99  3.000
 M2Y  H13   CAL  CAB   108.57  3.000
 M2Y  CAT   CAL  CAB   110.25  3.000
 M2Y  CAY   CAT  CAU   118.64  3.000
 M2Y  CAY   CAT  CAL   120.61  3.000
 M2Y  CAU   CAT  CAL   120.64  3.000
 M2Y  H15   CAU  CAV   119.58  3.000
 M2Y  H15   CAU  CAT   119.66  3.000
 M2Y  CAV   CAU  CAT   120.75  3.000
 M2Y  H16   CAV  CAW   120.06  3.000
 M2Y  H16   CAV  CAU   119.80  3.000
 M2Y  CAW   CAV  CAU   120.13  3.000
 M2Y  H17   CAW  CAX   120.26  3.000
 M2Y  H17   CAW  CAV   120.15  3.000
 M2Y  CAX   CAW  CAV   119.60  3.000
 M2Y  H18   CAX  CAY   119.77  3.000
 M2Y  H18   CAX  CAW   120.21  3.000
 M2Y  CAY   CAX  CAW   120.02  3.000
 M2Y  H19   CAY  CAX   119.55  3.000
 M2Y  H19   CAY  CAT   119.60  3.000
 M2Y  CAX   CAY  CAT   120.85  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_59  H9   NAA  C4   C5      0.00   0.0  0
 M2Y  Var_01    CAU  CAT  CAL  CAB    82.70  30.0  2
 M2Y  Var_02    H2   CAS  CAP  CAO   -59.70  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

