# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:11:30 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(cc(C[P](O)(O)=O)c1O)c2ccc(Cl)cc2Cl)C(O)=O
#
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
 QGP  QGP  '(2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid (non-preferred name)'  ligand  42  26  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QGP
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
 QGP  C4   C   CR6   0   0.258   -8.4353  18.6801  -51.8155
 QGP  C5   C   CR6   0   0.037   -7.8406  19.8883  -51.4371
 QGP  C6   C   CR16  0  -0.353   -6.4914  19.8966  -51.1013
 QGP  C7   C   CR6   0   0.080   -5.7360  18.7326  -51.0926
 QGP  C8   C   CR16  0  -0.353   -6.3624  17.5373  -51.4352
 QGP  C9   C   CR6   0   0.102   -7.6983  17.4901  -51.7975
 QGP  C10  C   CR6   0  -0.135   -3.7008  18.0262  -49.7626
 QGP  C11  C   CR6   0  -0.064   -1.5592  18.9680  -50.2298
 QGP  C12  C   CR6   0   0.169   -4.2967  18.7885  -50.7679
 QGP  C13  C   CR16  0  -0.323   -3.4660  19.6527  -51.4828
 QGP  C14  C   CR16  0  -0.185   -2.1094  19.7549  -51.2280
 QGP  C15  C   CR16  0  -0.145   -2.3437  18.1023  -49.4869
 QGP  C16  C   CH2   0  -0.541   -8.3282  16.1818  -52.1759
 QGP  CA   C   CH1   0  -0.187   -9.2762  15.6320  -51.0905
 QGP  N    N   NH2   0  -0.774   -8.6178  15.6020  -49.8103
 QGP  C    C   C     0   0.517   -9.8326  14.3135  -51.6155
 QGP  O    O   O     0  -0.453  -10.6765  14.2483  -52.4767
 QGP  O3   O   OH1   0  -0.765   -9.7166  20.9868  -53.7582
 QGP  O4   O   O     0  -0.701   -7.4369  22.2373  -53.6776
 QGP  O5   O   OH1   0  -0.739   -9.5886  23.2877  -52.6354
 QGP  C1   C   CH2   0  -0.857   -8.6209  21.1723  -51.3627
 QGP  O6   O   OH1   0  -0.640   -9.7355  18.5951  -52.1717
 QGP  CL6  CL  CL    0  -0.115    0.1347  19.0656  -49.8945
 QGP  H1   H   HCR6  0   0.258   -6.0342  20.8351  -50.8102
 QGP  H2   H   HCR6  0   0.248   -5.7892  16.6187  -51.4531
 QGP  H4   H   HCR6  0   0.271   -3.8984  20.2534  -52.2727
 QGP  H5   H   HOH1  0   0.481   -9.6513  12.4397  -51.4449
 QGP  H6   H   HCR6  0   0.286   -1.4932  20.4313  -51.8036
 QGP  H7   H   HCR6  0   0.302   -1.9104  17.5028  -48.6984
 QGP  H8   H   HCH2  0   0.268   -8.8789  16.2724  -53.1136
 QGP  H9   H   HCH2  0   0.262   -7.5331  15.4506  -52.3475
 QGP  H10  H   HCH1  0   0.279  -10.1360  16.3025  -51.0191
 QGP  H11  H   HNH2  0   0.355   -9.2198  15.2024  -49.1029
 QGP  H12  H   HNH2  0   0.344   -7.7760  15.0408  -49.8352
 QGP  H14  H   HOH1  0   0.502   -9.5327  20.8954  -54.7036
 QGP  H15  H   HOH1  0   0.497   -9.4877  24.0067  -53.2745
 QGP  H16  H   HCH2  0   0.325   -8.1238  21.8657  -50.6819
 QGP  H17  H   HCH2  0   0.320   -9.6313  21.0242  -50.9715
 QGP  H3   H   HOH1  0   0.479  -10.0219  19.3975  -52.6327
 QGP  CL0  CL  CL    0  -0.112   -4.6567  16.9751  -48.7721
 QGP  O2   O   OH1   0  -0.585   -9.2797  13.2463  -51.0567
 QGP  P    P   P     0   1.387   -8.7135  21.9862  -52.9689

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
 QGP  O4   P    double    1.482  0.020  1.482
 QGP  O3   P    single    1.621  0.020  1.621
 QGP  O    C    double    1.207  0.020  1.207
 QGP  O5   P    single    1.603  0.020  1.603
 QGP  P    C1   single    1.803  0.020  1.803
 QGP  C16  C9   single    1.501  0.020  1.501
 QGP  C16  CA   single    1.542  0.020  1.542
 QGP  O6   C4   single    1.351  0.020  1.351
 QGP  C    CA   single    1.524  0.020  1.524
 QGP  C    O2   single    1.325  0.020  1.325
 QGP  C9   C4   aromatic  1.400  0.020  1.400
 QGP  C9   C8   aromatic  1.385  0.020  1.385
 QGP  C4   C5   aromatic  1.399  0.020  1.399
 QGP  C8   C7   aromatic  1.392  0.020  1.392
 QGP  C13  C14  aromatic  1.384  0.020  1.384
 QGP  C13  C12  aromatic  1.396  0.020  1.396
 QGP  C5   C1   single    1.504  0.020  1.504
 QGP  C5   C6   aromatic  1.390  0.020  1.390
 QGP  CA   N    single    1.440  0.020  1.440
 QGP  C14  C11  aromatic  1.385  0.020  1.385
 QGP  C7   C6   aromatic  1.388  0.020  1.388
 QGP  C7   C12  single    1.477  0.020  1.477
 QGP  C12  C10  aromatic  1.395  0.020  1.395
 QGP  C11  CL6  single    1.730  0.020  1.730
 QGP  C11  C15  aromatic  1.384  0.020  1.384
 QGP  C10  C15  aromatic  1.387  0.020  1.387
 QGP  C10  CL0  single    1.732  0.020  1.732
 QGP  C6   H1   single    0.930  0.020  1.080
 QGP  C8   H2   single    0.930  0.020  1.080
 QGP  C13  H4   single    0.930  0.020  1.080
 QGP  O2   H5   single    0.850  0.020  0.980
 QGP  C14  H6   single    0.930  0.020  1.080
 QGP  C15  H7   single    0.930  0.020  1.080
 QGP  C16  H8   single    0.970  0.020  1.090
 QGP  C16  H9   single    0.970  0.020  1.090
 QGP  CA   H10  single    0.970  0.020  1.090
 QGP  N    H11  single    0.890  0.020  1.040
 QGP  N    H12  single    0.890  0.020  1.040
 QGP  O3   H14  single    0.850  0.020  0.980
 QGP  O5   H15  single    0.850  0.020  0.980
 QGP  C1   H16  single    0.970  0.020  1.090
 QGP  C1   H17  single    0.970  0.020  1.090
 QGP  O6   H3   single    0.850  0.020  0.980

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
 QGP  O6   C4   C9   117.17  3.000
 QGP  C9   C4   C5   120.46  3.000
 QGP  O6   C4   C5   122.34  3.000
 QGP  C1   C5   C6   119.09  3.000
 QGP  C6   C5   C4   118.89  3.000
 QGP  C1   C5   C4   122.01  3.000
 QGP  H1   C6   C7   119.68  3.000
 QGP  H1   C6   C5   118.65  3.000
 QGP  C7   C6   C5   121.65  3.000
 QGP  C12  C7   C8   121.68  3.000
 QGP  C12  C7   C6   120.01  3.000
 QGP  C8   C7   C6   118.27  3.000
 QGP  H2   C8   C9   118.51  3.000
 QGP  H2   C8   C7   119.61  3.000
 QGP  C9   C8   C7   121.85  3.000
 QGP  C16  C9   C8   120.05  3.000
 QGP  C8   C9   C4   118.83  3.000
 QGP  C16  C9   C4   121.12  3.000
 QGP  CL0  C10  C15  117.36  3.000
 QGP  CL0  C10  C12  120.52  3.000
 QGP  C15  C10  C12  122.08  3.000
 QGP  CL6  C11  C15  119.09  3.000
 QGP  C15  C11  C14  121.12  3.000
 QGP  CL6  C11  C14  119.79  3.000
 QGP  C13  C12  C10  116.95  3.000
 QGP  C10  C12  C7   123.65  3.000
 QGP  C13  C12  C7   119.41  3.000
 QGP  H4   C13  C14  119.00  3.000
 QGP  H4   C13  C12  118.66  3.000
 QGP  C14  C13  C12  122.33  3.000
 QGP  H6   C14  C13  120.46  3.000
 QGP  H6   C14  C11  120.85  3.000
 QGP  C13  C14  C11  118.69  3.000
 QGP  H7   C15  C11  120.73  3.000
 QGP  H7   C15  C10  120.44  3.000
 QGP  C11  C15  C10  118.82  3.000
 QGP  H9   C16  H8   106.72  3.000
 QGP  H9   C16  CA   108.59  3.000
 QGP  H8   C16  CA   108.91  3.000
 QGP  H9   C16  C9   108.50  3.000
 QGP  H8   C16  C9   110.87  3.000
 QGP  CA   C16  C9   113.04  3.000
 QGP  H10  CA   C    105.43  3.000
 QGP  H10  CA   N    108.33  3.000
 QGP  C    CA   N    117.07  3.000
 QGP  H10  CA   C16  108.11  3.000
 QGP  N    CA   C16  110.61  3.000
 QGP  C    CA   C16  106.88  3.000
 QGP  H12  N    H11  107.05  3.000
 QGP  H12  N    CA   111.71  3.000
 QGP  H11  N    CA   110.98  3.000
 QGP  O    C    CA   123.19  3.000
 QGP  CA   C    O2   113.51  3.000
 QGP  O    C    O2   123.28  3.000
 QGP  H14  O3   P    114.61  3.000
 QGP  H15  O5   P    114.15  3.000
 QGP  H17  C1   H16  106.48  3.000
 QGP  H17  C1   P    109.41  3.000
 QGP  H16  C1   P    106.99  3.000
 QGP  H17  C1   C5   112.41  3.000
 QGP  H16  C1   C5   109.68  3.000
 QGP  P    C1   C5   111.58  3.000
 QGP  H3   O6   C4   110.97  3.000
 QGP  H5   O2   C    109.95  3.000
 QGP  C1   P    O5   102.07  3.000
 QGP  C1   P    O4   117.28  3.000
 QGP  O5   P    O4   115.60  3.000
 QGP  C1   P    O3   100.79  3.000
 QGP  O5   P    O3   105.31  3.000
 QGP  O4   P    O3   113.88  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
 QGP  CONST_01  C7   C8   C9   C4     0.00   0.0  0
 QGP  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 QGP  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 QGP  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 QGP  CONST_05  C12  C7   C6   C5   180.00   0.0  0
 QGP  CONST_06  C9   C4   C5   C6     0.00   0.0  0
 QGP  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 QGP  CONST_10  C14  C13  C12  C7   180.00   0.0  0
 QGP  CONST_11  C15  C10  C12  C7   180.00   0.0  0
 QGP  CONST_14  C12  C7   C8   C9   180.00   0.0  0
 QGP  CONST_15  C14  C13  C12  C10    0.00   0.0  0
 QGP  CONST_16  C14  C11  C15  C10    0.00   0.0  0
 QGP  CONST_17  C12  C13  C14  C11    0.00   0.0  0
 QGP  CONST_18  C12  C10  C15  C11    0.00   0.0  0
 QGP  CONST_19  C15  C11  C14  C13    0.00   0.0  0
 QGP  CONST_20  C15  C10  C12  C13    0.00   0.0  0
 QGP  CONST_21  C16  C9   C4   C5   180.00   0.0  0
 QGP  CONST_22  O6   C4   C5   C6   180.00   0.0  0
 QGP  CONST_23  C16  C9   C8   C7   180.00   0.0  0
 QGP  CONST_24  C1   C5   C6   C7   180.00   0.0  0
 QGP  CONST_25  CL0  C10  C12  C7     0.00   0.0  0
 QGP  CONST_26  O6   C4   C9   C8   180.00   0.0  0
 QGP  CONST_27  C1   C5   C4   C9   180.00   0.0  0
 QGP  CONST_28  CL6  C11  C15  C10  180.00   0.0  0
 QGP  CONST_29  CL0  C10  C15  C11  180.00   0.0  0
 QGP  CONST_30  CL6  C11  C14  C13  180.00   0.0  0
 QGP  CONST_31  CL0  C10  C12  C13  180.00   0.0  0
 QGP  CONST_32  H2   C8   C9   C4   180.00   0.0  0
 QGP  CONST_33  H1   C6   C5   C4   180.00   0.0  0
 QGP  CONST_34  H4   C13  C12  C7     0.00   0.0  0
 QGP  CONST_35  H6   C14  C13  C12  180.00   0.0  0
 QGP  CONST_36  H7   C15  C10  C12  180.00   0.0  0
 QGP  CONST_37  H5   O2   C    CA   180.00   0.0  0
 QGP  Var_01    CA   C16  C9   C4   -74.26  30.0  2
 QGP  Var_02    P    C1   C5   C4   -85.06  30.0  2
 QGP  Var_03    O4   P    C1   C5   -53.25  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
 QGP  chir_01  CA  C16  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
 QGP  plan-1  C4   0.020
 QGP  plan-1  C5   0.020
 QGP  plan-1  C6   0.020
 QGP  plan-1  C7   0.020
 QGP  plan-1  C8   0.020
 QGP  plan-1  C9   0.020
 QGP  plan-1  C12  0.020
 QGP  plan-1  C16  0.020
 QGP  plan-1  C1   0.020
 QGP  plan-1  O6   0.020
 QGP  plan-1  H1   0.020
 QGP  plan-1  H2   0.020
 QGP  plan-2  C7   0.020
 QGP  plan-2  C10  0.020
 QGP  plan-2  C11  0.020
 QGP  plan-2  C12  0.020
 QGP  plan-2  C13  0.020
 QGP  plan-2  C14  0.020
 QGP  plan-2  C15  0.020
 QGP  plan-2  CL6  0.020
 QGP  plan-2  H4   0.020
 QGP  plan-2  H6   0.020
 QGP  plan-2  H7   0.020
 QGP  plan-2  CL0  0.020
 QGP  plan-3  CA   0.020
 QGP  plan-3  C    0.020
 QGP  plan-3  O    0.020
 QGP  plan-3  H5   0.020
 QGP  plan-3  O2   0.020

