# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:47:35 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [[(2~{S})-2-[[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoyl]amino]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2sc3ncnc(N[C@@H](Cc4ccccc4)C(=O)N[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
 7AM  7AM  '[[(2~{S})-2-[[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino]-3-phenyl-propanoyl]amino]phosphonic acid'  ligand  53  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7AM
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
 7AM  CAP  C  CR16  0  -0.303  -5.5822  -1.5659   0.2912
 7AM  CAQ  C  CR16  0  -0.282  -6.8172  -1.2996   0.8616
 7AM  CAR  C  CR6   0   0.087  -7.0954  -0.0637   1.4392
 7AM  CAU  C  CH3   0  -0.722  -8.4198   0.2140   2.0852
 7AM  CAS  C  CR16  0  -0.274  -6.0924   0.9055   1.4156
 7AM  CAT  C  CR16  0  -0.304  -4.8595   0.6501   0.8418
 7AM  CAK  C  CR6   0   0.120  -4.5796  -0.5959   0.2745
 7AM  CAD  C  CR5   0  -0.203  -3.2679  -0.8600  -0.3119
 7AM  SAE  S  S2    0   0.225  -3.1000  -2.0329  -1.5958
 7AM  CAC  C  CR15  0  -0.265  -2.0780  -0.2835   0.0063
 7AM  C5   C  CR56  0   0.058  -0.9995  -0.7797  -0.7805
 7AM  C6   C  CR56  0  -0.027  -1.3986  -1.7450  -1.7003
 7AM  N1   N  N     0  -0.435  -0.5987  -2.3705  -2.5621
 7AM  C2   C  CR16  0   0.049   0.6612  -1.9920  -2.4854
 7AM  N3   N  N     0  -0.476   1.1868  -1.0920  -1.6600
 7AM  C4   C  CR6   0   0.542   0.3834  -0.4794  -0.7959
 7AM  N    N  NH1   0  -0.668   0.9285   0.4210   0.0348
 7AM  CA   C  CH1   0  -0.183   2.3269   0.7375  -0.0027
 7AM  C    C  C     0   0.590   3.1647  -0.4970   0.3129
 7AM  O    O  O     0  -0.455   2.8148  -1.3366   1.1160
 7AM  NAN  N  NH1   0  -0.828   4.3675  -0.5495  -0.3234
 7AM  PBC  P  P     0   1.433   5.4905  -1.7966  -0.1114
 7AM  OBD  O  O     0  -0.691   6.5488  -1.7622  -1.1354
 7AM  OBF  O  OH1   0  -0.733   5.9216  -1.5487   1.4043
 7AM  OBE  O  OH1   0  -0.738   4.6811  -3.1676  -0.1512
 7AM  CB   C  CH2   0  -0.558   2.6453   1.8323   1.0262
 7AM  CG   C  CR6   0   0.131   1.8603   3.0876   0.7600
 7AM  CD1  C  CR16  0  -0.330   0.7962   3.4482   1.5810
 7AM  CE1  C  CR16  0  -0.238   0.0472   4.5886   1.3141
 7AM  CZ   C  CR16  0  -0.266   0.3579   5.3832   0.2205
 7AM  CE2  C  CR16  0  -0.238   1.4227   5.0340  -0.6025
 7AM  CD2  C  CR16  0  -0.296   2.1668   3.8949  -0.3343
 7AM  H1   H  HCR6  0   0.254  -5.4024  -2.5486  -0.1291
 7AM  H2   H  HCR6  0   0.255  -7.5745  -2.0741   0.8598
 7AM  H3   H  HCH3  0   0.252  -8.3602   0.0787   3.1672
 7AM  H4   H  HCH3  0   0.246  -8.7450   1.2391   1.9075
 7AM  H5   H  HCH3  0   0.246  -9.1951  -0.4565   1.7166
 7AM  H6   H  HCR6  0   0.254  -6.2828   1.8837   1.8413
 7AM  H7   H  HCR6  0   0.255  -4.1165   1.4369   0.8160
 7AM  H8   H  HCR5  0   0.266  -1.9789   0.4543   0.7905
 7AM  H9   H  HCR6  0   0.261   1.3537  -2.4684  -3.1705
 7AM  H10  H  HNH1  0   0.409   0.3484   0.8631   0.7286
 7AM  H11  H  HCH1  0   0.294   2.5938   1.1015  -1.0007
 7AM  H12  H  HNH1  0   0.436   4.5669   0.1306  -1.0452
 7AM  H13  H  HOH1  0   0.502   6.5023  -2.2299   1.7722
 7AM  H14  H  HOH1  0   0.492   3.9342  -3.2131   0.4654
 7AM  H15  H  HCH2  0   0.282   2.4303   1.4582   2.0302
 7AM  H16  H  HCH2  0   0.289   3.7162   2.0395   0.9848
 7AM  H17  H  HCR6  0   0.259   0.5536   2.8400   2.4455
 7AM  H18  H  HCR6  0   0.259  -0.7763   4.8550   1.9639
 7AM  H19  H  HCR6  0   0.258  -0.2218   6.2727   0.0107
 7AM  H20  H  HCR6  0   0.258   1.6760   5.6528  -1.4537
 7AM  H21  H  HCR6  0   0.252   2.9968   3.6349  -0.9817

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
 7AM  OBD  PBC  double    1.473  0.020  1.473
 7AM  OBE  PBC  single    1.593  0.020  1.593
 7AM  PBC  NAN  single    1.692  0.020  1.692
 7AM  PBC  OBF  single    1.595  0.020  1.595
 7AM  CD2  CE2  aromatic  1.387  0.020  1.387
 7AM  CD2  CG   aromatic  1.394  0.020  1.394
 7AM  NAN  C    single    1.362  0.020  1.362
 7AM  CE2  CZ   aromatic  1.390  0.020  1.390
 7AM  CB   CG   single    1.504  0.020  1.504
 7AM  CB   CA   single    1.536  0.020  1.536
 7AM  CG   CD1  aromatic  1.392  0.020  1.392
 7AM  C    O    double    1.213  0.020  1.213
 7AM  C    CA   single    1.525  0.020  1.525
 7AM  CZ   CE1  aromatic  1.387  0.020  1.387
 7AM  CA   N    single    1.434  0.020  1.434
 7AM  CD1  CE1  aromatic  1.390  0.020  1.390
 7AM  N    C4   single    1.341  0.020  1.341
 7AM  N3   C4   aromatic  1.329  0.020  1.329
 7AM  N3   C2   aromatic  1.329  0.020  1.329
 7AM  C4   C5   aromatic  1.415  0.020  1.415
 7AM  C2   N1   aromatic  1.318  0.020  1.318
 7AM  C5   CAC  aromatic  1.424  0.020  1.424
 7AM  C5   C6   aromatic  1.392  0.020  1.392
 7AM  CAC  CAD  aromatic  1.360  0.020  1.360
 7AM  CAP  CAQ  aromatic  1.386  0.020  1.386
 7AM  CAP  CAK  aromatic  1.395  0.020  1.395
 7AM  C6   N1   aromatic  1.332  0.020  1.332
 7AM  C6   SAE  aromatic  1.729  0.020  1.729
 7AM  CAQ  CAR  aromatic  1.392  0.020  1.392
 7AM  CAD  CAK  single    1.461  0.020  1.461
 7AM  CAD  SAE  aromatic  1.747  0.020  1.747
 7AM  CAK  CAT  aromatic  1.397  0.020  1.397
 7AM  CAR  CAU  single    1.500  0.020  1.500
 7AM  CAR  CAS  aromatic  1.395  0.020  1.395
 7AM  CAT  CAS  aromatic  1.384  0.020  1.384
 7AM  CAP  H1   single    0.930  0.020  1.080
 7AM  CAQ  H2   single    0.930  0.020  1.080
 7AM  CAU  H3   single    0.970  0.020  1.090
 7AM  CAU  H4   single    0.970  0.020  1.090
 7AM  CAU  H5   single    0.970  0.020  1.090
 7AM  CAS  H6   single    0.930  0.020  1.080
 7AM  CAT  H7   single    0.930  0.020  1.080
 7AM  CAC  H8   single    0.930  0.020  1.080
 7AM  C2   H9   single    0.930  0.020  1.080
 7AM  N    H10  single    0.860  0.020  1.020
 7AM  CA   H11  single    0.970  0.020  1.090
 7AM  NAN  H12  single    0.860  0.020  1.020
 7AM  OBF  H13  single    0.850  0.020  0.980
 7AM  OBE  H14  single    0.850  0.020  0.980
 7AM  CB   H15  single    0.970  0.020  1.090
 7AM  CB   H16  single    0.970  0.020  1.090
 7AM  CD1  H17  single    0.930  0.020  1.080
 7AM  CE1  H18  single    0.930  0.020  1.080
 7AM  CZ   H19  single    0.930  0.020  1.080
 7AM  CE2  H20  single    0.930  0.020  1.080
 7AM  CD2  H21  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
 7AM  H1   CAP  CAK  120.43  3.000
 7AM  H1   CAP  CAQ  118.79  3.000
 7AM  CAK  CAP  CAQ  120.77  3.000
 7AM  H2   CAQ  CAR  119.71  3.000
 7AM  H2   CAQ  CAP  119.00  3.000
 7AM  CAR  CAQ  CAP  121.28  3.000
 7AM  CAS  CAR  CAU  120.91  3.000
 7AM  CAS  CAR  CAQ  117.78  3.000
 7AM  CAU  CAR  CAQ  121.31  3.000
 7AM  H5   CAU  H4   108.15  3.000
 7AM  H5   CAU  H3   107.33  3.000
 7AM  H4   CAU  H3   107.12  3.000
 7AM  H5   CAU  CAR  111.64  3.000
 7AM  H4   CAU  CAR  111.55  3.000
 7AM  H3   CAU  CAR  110.83  3.000
 7AM  H6   CAS  CAT  119.08  3.000
 7AM  H6   CAS  CAR  119.62  3.000
 7AM  CAT  CAS  CAR  121.29  3.000
 7AM  H7   CAT  CAK  120.06  3.000
 7AM  H7   CAT  CAS  119.16  3.000
 7AM  CAK  CAT  CAS  120.76  3.000
 7AM  CAD  CAK  CAT  120.27  3.000
 7AM  CAT  CAK  CAP  118.11  3.000
 7AM  CAD  CAK  CAP  121.63  3.000
 7AM  CAC  CAD  SAE  111.87  3.000
 7AM  SAE  CAD  CAK  120.18  3.000
 7AM  CAC  CAD  CAK  127.96  3.000
 7AM  C6   SAE  CAD   91.56  3.000
 7AM  H8   CAC  C5   124.68  3.000
 7AM  H8   CAC  CAD  122.62  3.000
 7AM  C5   CAC  CAD  112.68  3.000
 7AM  C4   C5   C6   114.85  3.000
 7AM  C6   C5   CAC  112.93  3.000
 7AM  C4   C5   CAC  132.22  3.000
 7AM  N1   C6   C5   125.53  3.000
 7AM  N1   C6   SAE  123.50  3.000
 7AM  C5   C6   SAE  110.96  3.000
 7AM  C2   N1   C6   113.68  3.000
 7AM  H9   C2   N3   115.93  3.000
 7AM  H9   C2   N1   116.59  3.000
 7AM  N3   C2   N1   127.48  3.000
 7AM  C4   N3   C2   118.46  3.000
 7AM  N    C4   N3   117.80  3.000
 7AM  N3   C4   C5   119.98  3.000
 7AM  N    C4   C5   122.21  3.000
 7AM  H10  N    CA   118.88  3.000
 7AM  H10  N    C4   119.19  3.000
 7AM  CA   N    C4   121.89  3.000
 7AM  H11  CA   CB   108.84  3.000
 7AM  H11  CA   C    108.89  3.000
 7AM  CB   CA   C    108.94  3.000
 7AM  H11  CA   N    109.56  3.000
 7AM  C    CA   N    110.58  3.000
 7AM  CB   CA   N    109.99  3.000
 7AM  NAN  C    O    122.50  3.000
 7AM  O    C    CA   122.60  3.000
 7AM  NAN  C    CA   114.82  3.000
 7AM  H12  NAN  PBC  117.01  3.000
 7AM  H12  NAN  C    118.80  3.000
 7AM  PBC  NAN  C    123.80  3.000
 7AM  OBE  PBC  OBF  107.15  3.000
 7AM  OBF  PBC  OBD  117.57  3.000
 7AM  OBE  PBC  OBD  111.58  3.000
 7AM  OBF  PBC  NAN  100.60  3.000
 7AM  OBE  PBC  NAN  107.10  3.000
 7AM  OBD  PBC  NAN  111.88  3.000
 7AM  H13  OBF  PBC  114.46  3.000
 7AM  H14  OBE  PBC  114.59  3.000
 7AM  H16  CB   H15  107.03  3.000
 7AM  H16  CB   CG   110.29  3.000
 7AM  H15  CB   CG   110.22  3.000
 7AM  H16  CB   CA   108.26  3.000
 7AM  H15  CB   CA   109.31  3.000
 7AM  CG   CB   CA   111.60  3.000
 7AM  CD2  CG   CD1  118.76  3.000
 7AM  CD1  CG   CB   120.72  3.000
 7AM  CD2  CG   CB   120.50  3.000
 7AM  H17  CD1  CE1  119.51  3.000
 7AM  H17  CD1  CG   119.74  3.000
 7AM  CE1  CD1  CG   120.75  3.000
 7AM  H18  CE1  CZ   120.18  3.000
 7AM  H18  CE1  CD1  119.77  3.000
 7AM  CZ   CE1  CD1  120.05  3.000
 7AM  H19  CZ   CE2  120.12  3.000
 7AM  H19  CZ   CE1  120.25  3.000
 7AM  CE2  CZ   CE1  119.62  3.000
 7AM  H20  CE2  CD2  119.75  3.000
 7AM  H20  CE2  CZ   120.07  3.000
 7AM  CD2  CE2  CZ   120.18  3.000
 7AM  H21  CD2  CE2  119.49  3.000
 7AM  H21  CD2  CG   119.88  3.000
 7AM  CE2  CD2  CG   120.64  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
 7AM  CONST_01  CAS  CAR  CAQ  CAP    0.00   0.0  0
 7AM  CONST_04  CAS  CAT  CAK  CAP    0.00   0.0  0
 7AM  CONST_05  CAD  CAK  CAP  CAQ  180.00   0.0  0
 7AM  CONST_06  CAT  CAK  CAP  CAQ    0.00   0.0  0
 7AM  CONST_07  CAT  CAS  CAR  CAQ    0.00   0.0  0
 7AM  CONST_08  CAK  CAP  CAQ  CAR    0.00   0.0  0
 7AM  CONST_09  CAK  CAT  CAS  CAR    0.00   0.0  0
 7AM  CONST_10  CAD  CAK  CAT  CAS  180.00   0.0  0
 7AM  CONST_13  C5   CAC  CAD  CAK  180.00   0.0  0
 7AM  CONST_14  C6   SAE  CAD  CAK  180.00   0.0  0
 7AM  CONST_15  C4   C5   CAC  CAD  180.00   0.0  0
 7AM  CONST_16  C6   C5   CAC  CAD    0.00   0.0  0
 7AM  CONST_17  C5   C6   SAE  CAD    0.00   0.0  0
 7AM  CONST_18  N1   C6   SAE  CAD  180.00   0.0  0
 7AM  CONST_19  C4   C5   C6   SAE  180.00   0.0  0
 7AM  CONST_20  CAC  C5   C6   SAE    0.00   0.0  0
 7AM  CONST_21  C2   N1   C6   SAE  180.00   0.0  0
 7AM  CONST_22  C5   CAC  CAD  SAE    0.00   0.0  0
 7AM  CONST_23  N3   C4   C5   CAC  180.00   0.0  0
 7AM  CONST_24  N1   C6   C5   CAC  180.00   0.0  0
 7AM  CONST_25  C6   SAE  CAD  CAC    0.00   0.0  0
 7AM  CONST_26  C2   N3   C4   C5     0.00   0.0  0
 7AM  CONST_27  C2   N1   C6   C5     0.00   0.0  0
 7AM  CONST_28  N3   C4   C5   C6     0.00   0.0  0
 7AM  CONST_29  N3   C2   N1   C6     0.00   0.0  0
 7AM  CONST_30  C4   N3   C2   N1     0.00   0.0  0
 7AM  CONST_31  C4   C5   C6   N1     0.00   0.0  0
 7AM  CONST_32  CZ   CE2  CD2  CG     0.00   0.0  0
 7AM  CONST_33  CZ   CE1  CD1  CG     0.00   0.0  0
 7AM  CONST_34  CE2  CD2  CG   CD1    0.00   0.0  0
 7AM  CONST_35  CE2  CZ   CE1  CD1    0.00   0.0  0
 7AM  CONST_36  CD2  CE2  CZ   CE1    0.00   0.0  0
 7AM  CONST_37  CD2  CG   CD1  CE1    0.00   0.0  0
 7AM  CONST_38  CAU  CAR  CAQ  CAP  180.00   0.0  0
 7AM  CONST_39  CAT  CAS  CAR  CAU  180.00   0.0  0
 7AM  CONST_40  N    C4   C5   CAC    0.00   0.0  0
 7AM  CONST_41  N    C4   C5   C6   180.00   0.0  0
 7AM  CONST_42  N    C4   N3   C2   180.00   0.0  0
 7AM  CONST_43  CE2  CD2  CG   CB   180.00   0.0  0
 7AM  CONST_44  CE1  CD1  CG   CB   180.00   0.0  0
 7AM  CONST_45  H7   CAT  CAK  CAP  180.00   0.0  0
 7AM  CONST_46  H6   CAS  CAR  CAQ  180.00   0.0  0
 7AM  CONST_47  H1   CAP  CAQ  CAR  180.00   0.0  0
 7AM  CONST_48  H2   CAQ  CAR  CAS  180.00   0.0  0
 7AM  CONST_49  H8   CAC  CAD  CAK    0.00   0.0  0
 7AM  CONST_50  H9   C2   N1   C6   180.00   0.0  0
 7AM  CONST_51  H20  CE2  CD2  CG   180.00   0.0  0
 7AM  CONST_52  H18  CE1  CD1  CG   180.00   0.0  0
 7AM  CONST_53  H21  CD2  CG   CD1  180.00   0.0  0
 7AM  CONST_54  H19  CZ   CE1  CD1  180.00   0.0  0
 7AM  CONST_55  H17  CD1  CE1  CZ   180.00   0.0  0
 7AM  CONST_56  CA   N    C4   C5   180.00   0.0  0
 7AM  CONST_57  CA   N    C4   N3     0.00   0.0  0
 7AM  CONST_58  H10  N    C4   C5     0.00   0.0  0
 7AM  CONST_59  PBC  NAN  C    CA   180.00   0.0  0
 7AM  CONST_60  PBC  NAN  C    O      0.00   0.0  0
 7AM  CONST_61  H12  NAN  C    CA     0.00   0.0  0
 7AM  Var_01    CD2  CG   CB   CA   -71.49  30.0  2
 7AM  Var_02    H3   CAU  CAR  CAQ   97.58  30.0  2
 7AM  Var_03    OBD  PBC  NAN  C    166.95  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
 7AM  chir_01  CA  CB  C  N  negativ

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
 7AM  plan-1  CAP  0.020
 7AM  plan-1  CAQ  0.020
 7AM  plan-1  CAR  0.020
 7AM  plan-1  CAU  0.020
 7AM  plan-1  CAS  0.020
 7AM  plan-1  CAT  0.020
 7AM  plan-1  CAK  0.020
 7AM  plan-1  CAD  0.020
 7AM  plan-1  H1   0.020
 7AM  plan-1  H2   0.020
 7AM  plan-1  H6   0.020
 7AM  plan-1  H7   0.020
 7AM  plan-2  CB   0.020
 7AM  plan-2  CG   0.020
 7AM  plan-2  CD1  0.020
 7AM  plan-2  CE1  0.020
 7AM  plan-2  CZ   0.020
 7AM  plan-2  CE2  0.020
 7AM  plan-2  CD2  0.020
 7AM  plan-2  H17  0.020
 7AM  plan-2  H18  0.020
 7AM  plan-2  H19  0.020
 7AM  plan-2  H20  0.020
 7AM  plan-2  H21  0.020
 7AM  plan-3  CAK  0.020
 7AM  plan-3  CAD  0.020
 7AM  plan-3  SAE  0.020
 7AM  plan-3  CAC  0.020
 7AM  plan-3  C5   0.020
 7AM  plan-3  C6   0.020
 7AM  plan-3  N1   0.020
 7AM  plan-3  C2   0.020
 7AM  plan-3  N3   0.020
 7AM  plan-3  C4   0.020
 7AM  plan-3  N    0.020
 7AM  plan-3  H8   0.020
 7AM  plan-3  H9   0.020
 7AM  plan-4  CA   0.020
 7AM  plan-4  C    0.020
 7AM  plan-4  O    0.020
 7AM  plan-4  NAN  0.020
 7AM  plan-4  PBC  0.020
 7AM  plan-4  H12  0.020
 7AM  plan-5  C4   0.020
 7AM  plan-5  N    0.020
 7AM  plan-5  CA   0.020
 7AM  plan-5  H10  0.020

