# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:30:17 2021
#   Inital geometry file: a 111 line input string
#   Ligand name: methyl (2S)-2-{[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]oxy}-3-phenylpropanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](Cc1ccccc1)O[P](O)(=O)[C@@H](N)CC(C)C
#
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
 ZPH  ZPH  'methyl (2S)-2-{[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]oxy}-3-phenylpropanoate'  peptide  46  22  .  2022-09-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_ZPH
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
 ZPH  C1   C  CH1   0  -0.371  23.3789   9.8244  21.3635
 ZPH  C2   C  CH2   0  -0.435  23.4627   9.4073  19.8951
 ZPH  C3   C  CH1   0  -0.219  23.0628   7.9547  19.6237
 ZPH  C4   C  CH3   0  -0.653  23.1861   7.6665  18.1308
 ZPH  C5   C  CH3   0  -0.667  23.8936   6.9675  20.4349
 ZPH  N    N  NH2   0  -0.784  22.0545   9.5978  21.9001
 ZPH  P1   P  P     0   1.393  23.9662  11.5491  21.5211
 ZPH  O1   O  O     0  -0.709  25.3318  11.8523  21.0200
 ZPH  O2   O  OH1   0  -0.753  22.8097  12.4706  20.8702
 ZPH  C6   C  CH1   0  -0.074  24.0876  13.0105  23.7283
 ZPH  C7   C  CH2   0  -0.548  22.8391  13.8631  23.9845
 ZPH  C8   C  CR6   0   0.133  21.7868  13.1334  24.7702
 ZPH  C9   C  CR16  0  -0.307  21.7610  13.1966  26.1615
 ZPH  C10  C  CR16  0  -0.306  20.8311  12.3546  24.1206
 ZPH  C11  C  CR16  0  -0.240  20.8110  12.4905  26.8882
 ZPH  C12  C  CR16  0  -0.241  19.8792  11.6485  24.8428
 ZPH  C13  C  CR16  0  -0.269  19.8694  11.7106  26.2307
 ZPH  C14  C  C     0   0.576  24.8094  12.6358  25.0128
 ZPH  C15  C  CH3   0  -0.425  25.9236  13.5380  26.8785
 ZPH  O3   O  O2    0  -0.588  23.7393  11.7958  23.0938
 ZPH  O4   O  O2    0  -0.453  25.2226  13.7205  25.6456
 ZPH  O5   O  O     0  -0.425  24.9873  11.5120  25.3951
 ZPH  H1   H  HCH1  0   0.282  24.0907   9.2257  21.9405
 ZPH  H    H  HCH2  0   0.233  22.8238  10.0636  19.2940
 ZPH  H3   H  HCH2  0   0.236  24.4859   9.5662  19.5411
 ZPH  H4   H  HCH1  0   0.222  22.0144   7.8314  19.9094
 ZPH  H5   H  HCH3  0   0.227  22.8740   6.6470  17.8995
 ZPH  H6   H  HCH3  0   0.224  22.5668   8.3436  17.5396
 ZPH  H7   H  HCH3  0   0.213  24.2192   7.7811  17.7928
 ZPH  H8   H  HCH3  0   0.229  23.6318   5.9395  20.1794
 ZPH  H9   H  HCH3  0   0.214  24.9614   7.0939  20.2385
 ZPH  H10  H  HCH3  0   0.230  23.7342   7.0827  21.5075
 ZPH  H11  H  HNH2  0   0.362  21.9993   9.8421  22.8800
 ZPH  H12  H  HOH1  0   0.492  23.0428  12.8376  20.0077
 ZPH  H13  H  HCH1  0   0.292  24.7851  13.5955  23.1161
 ZPH  H14  H  HCH2  0   0.276  23.1444  14.7756  24.4977
 ZPH  H15  H  HCH2  0   0.277  22.4452  14.1701  23.0150
 ZPH  H16  H  HCR6  0   0.250  22.4804  13.8141  26.6871
 ZPH  H17  H  HCR6  0   0.246  20.8226  12.3136  23.0381
 ZPH  H18  H  HCR6  0   0.256  20.8036  12.5557  27.9688
 ZPH  H19  H  HCR6  0   0.256  19.1405  11.0537  24.3209
 ZPH  H20  H  HCR6  0   0.256  19.1259  11.1634  26.7955
 ZPH  H21  H  HCH3  0   0.256  26.1683  14.5345  27.2322
 ZPH  H22  H  HCH3  0   0.241  25.3009  13.0340  27.6168
 ZPH  H23  H  HCH3  0   0.245  26.8406  12.9691  26.7300
 ZPH  H2   H  HNH2  0   0.350  21.3607  10.1469  21.4081

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
 ZPH  C1   C2   single    1.529  0.020  1.529
 ZPH  C1   N    single    1.447  0.020  1.447
 ZPH  C1   P1   single    1.829  0.020  1.829
 ZPH  C1   H1   single    0.970  0.020  1.090
 ZPH  C2   C3   single    1.531  0.020  1.531
 ZPH  C2   H    single    0.970  0.020  1.090
 ZPH  C2   H3   single    0.970  0.020  1.090
 ZPH  C3   C4   single    1.525  0.020  1.525
 ZPH  C3   C5   single    1.524  0.020  1.524
 ZPH  C3   H4   single    0.970  0.020  1.090
 ZPH  C4   H5   single    0.970  0.020  1.090
 ZPH  C4   H6   single    0.970  0.020  1.090
 ZPH  C4   H7   single    0.970  0.020  1.090
 ZPH  C5   H8   single    0.970  0.020  1.090
 ZPH  C5   H9   single    0.970  0.020  1.090
 ZPH  C5   H10  single    0.970  0.020  1.090
 ZPH  N    H11  single    0.890  0.020  1.040
 ZPH  P1   O1   double    1.486  0.020  1.486
 ZPH  P1   O2   single    1.616  0.020  1.616
 ZPH  P1   O3   single    1.608  0.020  1.608
 ZPH  O2   H12  single    0.850  0.020  0.980
 ZPH  C6   C7   single    1.533  0.020  1.533
 ZPH  C6   C14  single    1.520  0.020  1.520
 ZPH  C6   O3   single    1.414  0.020  1.414
 ZPH  C6   H13  single    0.970  0.020  1.090
 ZPH  C7   C8   single    1.502  0.020  1.502
 ZPH  C7   H14  single    0.970  0.020  1.090
 ZPH  C7   H15  single    0.970  0.020  1.090
 ZPH  C8   C9   aromatic  1.393  0.020  1.393
 ZPH  C8   C10  aromatic  1.394  0.020  1.394
 ZPH  C9   C11  aromatic  1.389  0.020  1.389
 ZPH  C9   H16  single    0.930  0.020  1.080
 ZPH  C10  C12  aromatic  1.388  0.020  1.388
 ZPH  C10  H17  single    0.930  0.020  1.080
 ZPH  C11  C13  aromatic  1.388  0.020  1.388
 ZPH  C11  H18  single    0.930  0.020  1.080
 ZPH  C12  C13  aromatic  1.389  0.020  1.389
 ZPH  C12  H19  single    0.930  0.020  1.080
 ZPH  C13  H20  single    0.930  0.020  1.080
 ZPH  C14  O4   single    1.322  0.020  1.322
 ZPH  C14  O5   double    1.200  0.020  1.200
 ZPH  C15  O4   single    1.430  0.020  1.430
 ZPH  C15  H21  single    0.970  0.020  1.090
 ZPH  C15  H22  single    0.970  0.020  1.090
 ZPH  C15  H23  single    0.970  0.020  1.090
 ZPH  N    H2   single    0.890  0.020  1.040

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
 ZPH  H1   C1   P1   105.17  3.000
 ZPH  H1   C1   N    108.31  3.000
 ZPH  P1   C1   N    114.19  3.000
 ZPH  H1   C1   C2   108.75  3.000
 ZPH  P1   C1   C2   108.81  3.000
 ZPH  N    C1   C2   111.32  3.000
 ZPH  H3   C2   H    106.30  3.000
 ZPH  H3   C2   C3   108.95  3.000
 ZPH  H    C2   C3   108.59  3.000
 ZPH  H3   C2   C1   108.80  3.000
 ZPH  H    C2   C1   109.36  3.000
 ZPH  C3   C2   C1   114.51  3.000
 ZPH  H4   C3   C5   108.09  3.000
 ZPH  H4   C3   C4   108.17  3.000
 ZPH  C5   C3   C4   110.76  3.000
 ZPH  H4   C3   C2   108.12  3.000
 ZPH  C5   C3   C2   112.20  3.000
 ZPH  C4   C3   C2   109.37  3.000
 ZPH  H7   C4   H6   107.68  3.000
 ZPH  H7   C4   H5   107.63  3.000
 ZPH  H6   C4   H5   107.61  3.000
 ZPH  H7   C4   C3   111.05  3.000
 ZPH  H6   C4   C3   111.53  3.000
 ZPH  H5   C4   C3   111.15  3.000
 ZPH  H10  C5   H9   107.90  3.000
 ZPH  H10  C5   H8   107.14  3.000
 ZPH  H9   C5   H8   107.54  3.000
 ZPH  H10  C5   C3   112.05  3.000
 ZPH  H9   C5   C3   111.22  3.000
 ZPH  H8   C5   C3   110.78  3.000
 ZPH  H2   N    H11  107.61  3.000
 ZPH  H2   N    C1   111.23  3.000
 ZPH  H11  N    C1   111.80  3.000
 ZPH  O3   P1   O2   101.86  3.000
 ZPH  O3   P1   O1   115.35  3.000
 ZPH  O2   P1   O1   113.93  3.000
 ZPH  O3   P1   C1   100.58  3.000
 ZPH  O2   P1   C1   105.86  3.000
 ZPH  O1   P1   C1   117.30  3.000
 ZPH  H12  O2   P1   113.81  3.000
 ZPH  H13  C6   O3   111.36  3.000
 ZPH  H13  C6   C14  107.53  3.000
 ZPH  O3   C6   C14  106.52  3.000
 ZPH  H13  C6   C7   108.33  3.000
 ZPH  O3   C6   C7   110.61  3.000
 ZPH  C14  C6   C7   112.49  3.000
 ZPH  H15  C7   H14  106.50  3.000
 ZPH  H15  C7   C8   110.40  3.000
 ZPH  H14  C7   C8   110.87  3.000
 ZPH  H15  C7   C6   107.58  3.000
 ZPH  H14  C7   C6   108.42  3.000
 ZPH  C8   C7   C6   112.81  3.000
 ZPH  C10  C8   C9   118.57  3.000
 ZPH  C10  C8   C7   120.53  3.000
 ZPH  C9   C8   C7   120.88  3.000
 ZPH  H16  C9   C11  119.33  3.000
 ZPH  H16  C9   C8   119.86  3.000
 ZPH  C11  C9   C8   120.81  3.000
 ZPH  H17  C10  C12  119.69  3.000
 ZPH  H17  C10  C8   119.50  3.000
 ZPH  C12  C10  C8   120.81  3.000
 ZPH  H18  C11  C13  120.13  3.000
 ZPH  H18  C11  C9   119.75  3.000
 ZPH  C13  C11  C9   120.11  3.000
 ZPH  H19  C12  C13  120.09  3.000
 ZPH  H19  C12  C10  119.78  3.000
 ZPH  C13  C12  C10  120.13  3.000
 ZPH  H20  C13  C12  120.23  3.000
 ZPH  H20  C13  C11  120.19  3.000
 ZPH  C12  C13  C11  119.57  3.000
 ZPH  O5   C14  O4   124.70  3.000
 ZPH  O5   C14  C6   124.77  3.000
 ZPH  O4   C14  C6   110.52  3.000
 ZPH  H23  C15  H22  109.38  3.000
 ZPH  H23  C15  H21  109.52  3.000
 ZPH  H22  C15  H21  109.44  3.000
 ZPH  H23  C15  O4   111.21  3.000
 ZPH  H22  C15  O4   111.30  3.000
 ZPH  H21  C15  O4   105.92  3.000
 ZPH  C6   O3   P1   122.40  3.000
 ZPH  C15  O4   C14  117.47  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
 ZPH  CONST_01  C13  C11  C9   C8      0.00   0.0  0
 ZPH  CONST_02  C13  C12  C10  C8      0.00   0.0  0
 ZPH  CONST_03  C12  C10  C8   C9      0.00   0.0  0
 ZPH  CONST_04  C12  C13  C11  C9      0.00   0.0  0
 ZPH  CONST_05  C11  C9   C8   C10     0.00   0.0  0
 ZPH  CONST_06  C11  C13  C12  C10     0.00   0.0  0
 ZPH  CONST_07  C11  C9   C8   C7    180.00   0.0  0
 ZPH  CONST_08  C12  C10  C8   C7    180.00   0.0  0
 ZPH  CONST_09  H18  C11  C9   C8    180.00   0.0  0
 ZPH  CONST_10  H19  C12  C10  C8    180.00   0.0  0
 ZPH  CONST_11  H17  C10  C8   C9    180.00   0.0  0
 ZPH  CONST_12  H20  C13  C11  C9    180.00   0.0  0
 ZPH  CONST_13  H16  C9   C8   C10   180.00   0.0  0
 ZPH  Var_01    C9   C8   C7   C6     90.59  30.0  2
 ZPH  Var_02    C4   C3   C2   C1    179.89  30.0  3
 ZPH  Var_03    O5   C14  O4   C15    -0.45  30.0  2
 ZPH  Var_04    H5   C4   C3   C2   -178.01  30.0  3
 ZPH  Var_05    H8   C5   C3   C2   -176.56  30.0  3
 ZPH  Var_06    H21  C15  O4   C14  -179.82  30.0  3

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
 ZPH  chir_01  C1  C2  N    P1  positiv
 ZPH  chir_03  C6  C7  C14  O3  negativ
 ZPH  chir_04  P1  O1  O2   O3  both

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
 ZPH  plan-1  C7   0.020
 ZPH  plan-1  C8   0.020
 ZPH  plan-1  C9   0.020
 ZPH  plan-1  C10  0.020
 ZPH  plan-1  C11  0.020
 ZPH  plan-1  C12  0.020
 ZPH  plan-1  C13  0.020
 ZPH  plan-1  H16  0.020
 ZPH  plan-1  H17  0.020
 ZPH  plan-1  H18  0.020
 ZPH  plan-1  H19  0.020
 ZPH  plan-1  H20  0.020
 ZPH  plan-2  C6   0.020
 ZPH  plan-2  C14  0.020
 ZPH  plan-2  O4   0.020
 ZPH  plan-2  O5   0.020

