# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 03:43:09 2022
#   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  45  22  .  2022-09-22  2022-09-22
;
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  -0.376  -2.3614  -0.7368   0.9180
 ZPH  C2   C  CH2    0  -0.397  -2.8702   0.1711  -0.2029
 ZPH  C3   C  CH1    0  -0.237  -4.2433  -0.2039  -0.7644
 ZPH  C4   C  CH3    0  -0.647  -4.6642   0.8104  -1.8229
 ZPH  C5   C  CH3    0  -0.657  -4.2641  -1.6184  -1.3355
 ZPH  N    N  NH2    0  -0.803  -3.2540  -0.8383   2.0720
 ZPH  P1   P  P      0   1.308  -0.7333  -0.2130   1.5940
 ZPH  O1   O  O      0  -0.803  -0.8204   1.1864   2.1570
 ZPH  O2   O  OP    -1  -0.792  -0.1401  -1.3069   2.4382
 ZPH  C6   C  CH1    0  -0.008   1.1613   0.8148   0.1100
 ZPH  C7   C  CH2    0  -0.560   1.9875   0.5490  -1.1531
 ZPH  C8   C  CR6    0   0.145   2.6447  -0.8003  -1.1136
 ZPH  C9   C  CR16   0  -0.289   1.9894  -1.9294  -1.5984
 ZPH  C10  C  CR16   0  -0.314   3.9146  -0.9523  -0.5621
 ZPH  C11  C  CR16   0  -0.246   2.5909  -3.1790  -1.5405
 ZPH  C12  C  CR16   0  -0.241   4.5191  -2.2010  -0.4980
 ZPH  C13  C  CR16   0  -0.273   3.8579  -3.3195  -0.9879
 ZPH  C14  C  C      0   0.566   0.6093   2.2319   0.0296
 ZPH  C15  C  CH3    0  -0.424   0.9661   4.4557   0.6980
 ZPH  O3   O  O2     0  -0.612   0.1280  -0.1212   0.1688
 ZPH  O4   O  O2     0  -0.453   1.3349   3.0795   0.7459
 ZPH  O5   O  O      0  -0.453  -0.3069   2.5617  -0.6777
 ZPH  H1   H  HCH1   0   0.234  -2.2223  -1.7503   0.5266
 ZPH  H    H  HCH2   0   0.208  -2.9077   1.1994   0.1719
 ZPH  H3   H  HCH2   0   0.216  -2.1443   0.1793  -1.0199
 ZPH  H4   H  HCH1   0   0.201  -4.9797  -0.1549   0.0466
 ZPH  H5   H  HCH3   0   0.210  -3.9622   0.8162  -2.6609
 ZPH  H6   H  HCH3   0   0.221  -5.6548   0.5849  -2.2223
 ZPH  H7   H  HCH3   0   0.221  -4.6930   1.8219  -1.4128
 ZPH  H8   H  HCH3   0   0.223  -4.0613  -2.3735  -0.5735
 ZPH  H9   H  HCH3   0   0.224  -5.2379  -1.8521  -1.7700
 ZPH  H10  H  HCH3   0   0.212  -3.5132  -1.7337  -2.1217
 ZPH  H11  H  HNH2   0   0.335  -3.4939   0.0936   2.3905
 ZPH  H13  H  HCH1   0   0.235   1.8289   0.7436   0.9780
 ZPH  H14  H  HCH2   0   0.258   1.3324   0.6299  -2.0238
 ZPH  H15  H  HCH2   0   0.264   2.7468   1.3299  -1.2465
 ZPH  H16  H  HCR6   0   0.241   1.0015  -1.8277  -2.0298
 ZPH  H17  H  HCR6   0   0.244   4.4385  -0.0826  -0.1812
 ZPH  H18  H  HCR6   0   0.251   2.0694  -4.0462  -1.9254
 ZPH  H19  H  HCR6   0   0.251   5.5076  -2.3001  -0.0676
 ZPH  H20  H  HCR6   0   0.252   4.3274  -4.2937  -0.9412
 ZPH  H21  H  HCH3   0   0.248   1.6642   4.9769   1.3464
 ZPH  H22  H  HCH3   0   0.235   1.0443   4.8570  -0.3124
 ZPH  H23  H  HCH3   0   0.236  -0.0485   4.6077   1.0660
 ZPH  H2   H  HNH2   0   0.346  -4.1285  -1.2682   1.7962

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    1.462  0.020  1.462
 ZPH  C1   P1   single    1.839  0.020  1.839
 ZPH  C1   H1   single    0.970  0.020  1.090
 ZPH  C2   C3   single    1.530  0.020  1.530
 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    1.526  0.020  1.526
 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   deloc     1.511  0.020  1.511
 ZPH  P1   O2   deloc     1.504  0.020  1.504
 ZPH  P1   O3   single    1.668  0.020  1.668
 ZPH  C6   C7   single    1.533  0.020  1.533
 ZPH  C6   C14  single    1.523  0.020  1.523
 ZPH  C6   O3   single    1.395  0.020  1.395
 ZPH  C6   H13  single    0.970  0.020  1.090
 ZPH  C7   C8   single    1.501  0.020  1.501
 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  1.393  0.020  1.393
 ZPH  C9   C11  aromatic  1.388  0.020  1.388
 ZPH  C9   H16  single    0.930  0.020  1.080
 ZPH  C10  C12  aromatic  1.389  0.020  1.389
 ZPH  C10  H17  single    0.930  0.020  1.080
 ZPH  C11  C13  aromatic  1.389  0.020  1.389
 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    1.326  0.020  1.326
 ZPH  C14  O5   double    1.204  0.020  1.204
 ZPH  C15  O4   single    1.426  0.020  1.426
 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   106.40  3.000
 ZPH  H1   C1   N    107.17  3.000
 ZPH  P1   C1   N    105.67  3.000
 ZPH  H1   C1   C2   109.25  3.000
 ZPH  P1   C1   C2   113.25  3.000
 ZPH  N    C1   C2   114.61  3.000
 ZPH  H3   C2   H    105.76  3.000
 ZPH  H3   C2   C3   108.87  3.000
 ZPH  H    C2   C3   108.96  3.000
 ZPH  H3   C2   C1   109.35  3.000
 ZPH  H    C2   C1   108.54  3.000
 ZPH  C3   C2   C1   114.96  3.000
 ZPH  H4   C3   C5   108.01  3.000
 ZPH  H4   C3   C4   107.36  3.000
 ZPH  C5   C3   C4   110.67  3.000
 ZPH  H4   C3   C2   108.68  3.000
 ZPH  C5   C3   C2   112.14  3.000
 ZPH  C4   C3   C2   109.83  3.000
 ZPH  H7   C4   H6   107.75  3.000
 ZPH  H7   C4   H5   107.46  3.000
 ZPH  H6   C4   H5   107.66  3.000
 ZPH  H7   C4   C3   111.26  3.000
 ZPH  H6   C4   C3   111.52  3.000
 ZPH  H5   C4   C3   111.00  3.000
 ZPH  H10  C5   H9   107.69  3.000
 ZPH  H10  C5   H8   107.54  3.000
 ZPH  H9   C5   H8   107.18  3.000
 ZPH  H10  C5   C3   110.95  3.000
 ZPH  H9   C5   C3   111.08  3.000
 ZPH  H8   C5   C3   112.18  3.000
 ZPH  H2   N    H11  105.76  3.000
 ZPH  H2   N    C1   109.98  3.000
 ZPH  H11  N    C1   109.18  3.000
 ZPH  O3   P1   O2   108.42  3.000
 ZPH  O3   P1   O1   107.29  3.000
 ZPH  O2   P1   O1   119.16  3.000
 ZPH  O3   P1   C1    99.13  3.000
 ZPH  O2   P1   C1   110.39  3.000
 ZPH  O1   P1   C1   110.47  3.000
 ZPH  H13  C6   O3   111.94  3.000
 ZPH  H13  C6   C14  108.82  3.000
 ZPH  O3   C6   C14  110.98  3.000
 ZPH  H13  C6   C7   108.22  3.000
 ZPH  O3   C6   C7   108.52  3.000
 ZPH  C14  C6   C7   108.26  3.000
 ZPH  H15  C7   H14  107.18  3.000
 ZPH  H15  C7   C8   109.89  3.000
 ZPH  H14  C7   C8   110.48  3.000
 ZPH  H15  C7   C6   108.72  3.000
 ZPH  H14  C7   C6   108.70  3.000
 ZPH  C8   C7   C6   111.73  3.000
 ZPH  C10  C8   C9   118.58  3.000
 ZPH  C10  C8   C7   120.50  3.000
 ZPH  C9   C8   C7   120.90  3.000
 ZPH  H16  C9   C11  119.77  3.000
 ZPH  H16  C9   C8   119.46  3.000
 ZPH  C11  C9   C8   120.76  3.000
 ZPH  H17  C10  C12  119.64  3.000
 ZPH  H17  C10  C8   119.48  3.000
 ZPH  C12  C10  C8   120.88  3.000
 ZPH  H18  C11  C13  119.98  3.000
 ZPH  H18  C11  C9   119.84  3.000
 ZPH  C13  C11  C9   120.18  3.000
 ZPH  H19  C12  C13  120.09  3.000
 ZPH  H19  C12  C10  119.87  3.000
 ZPH  C13  C12  C10  120.04  3.000
 ZPH  H20  C13  C12  120.21  3.000
 ZPH  H20  C13  C11  120.24  3.000
 ZPH  C12  C13  C11  119.55  3.000
 ZPH  O5   C14  O4   123.98  3.000
 ZPH  O5   C14  C6   124.18  3.000
 ZPH  O4   C14  C6   111.59  3.000
 ZPH  H23  C15  H22  109.17  3.000
 ZPH  H23  C15  H21  109.26  3.000
 ZPH  H22  C15  H21  109.31  3.000
 ZPH  H23  C15  O4   111.35  3.000
 ZPH  H22  C15  O4   111.60  3.000
 ZPH  H21  C15  O4   106.08  3.000
 ZPH  C6   O3   P1   117.08  3.000
 ZPH  C15  O4   C14  117.22  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  CONST_14  H20  C13  C12  C10   180.00   0.0  0
 ZPH  CONST_15  H19  C12  C13  C11   180.00   0.0  0
 ZPH  CONST_16  H18  C11  C13  C12   180.00   0.0  0
 ZPH  CONST_17  H16  C9   C11  C13   180.00   0.0  0
 ZPH  CONST_18  H17  C10  C12  C13   180.00   0.0  0
 ZPH  Var_01    C9   C8   C7   C6     88.83  30.0  2
 ZPH  Var_02    C10  C8   C7   C6    -89.73  30.0  2
 ZPH  Var_03    H14  C7   C8   C9    -32.33  30.0  2
 ZPH  Var_04    H15  C7   C8   C9   -150.40  30.0  2
 ZPH  Var_05    H14  C7   C8   C10   149.11  30.0  2
 ZPH  Var_06    H15  C7   C8   C10    31.04  30.0  2
 ZPH  Var_07    C4   C3   C2   C1    177.34  30.0  3
 ZPH  Var_08    C5   C3   C2   C1    -59.16  30.0  3
 ZPH  Var_09    C6   O3   P1   C1    149.68  30.0  3
 ZPH  Var_10    C6   O3   P1   O1     34.78  30.0  3
 ZPH  Var_11    C6   O3   P1   O2    -95.13  30.0  3
 ZPH  Var_12    C15  O4   C14  C6    176.72  30.0  3
 ZPH  Var_13    O5   C14  O4   C15     2.14  30.0  2
 ZPH  Var_14    H4   C3   C2   C1     60.17  30.0  3
 ZPH  Var_15    H5   C4   C3   C2     61.59  30.0  3
 ZPH  Var_16    H6   C4   C3   C2   -178.36  30.0  3
 ZPH  Var_17    H7   C4   C3   C2    -58.03  30.0  3
 ZPH  Var_18    H8   C5   C3   C2     62.54  30.0  3
 ZPH  Var_19    H9   C5   C3   C2   -177.52  30.0  3
 ZPH  Var_20    H10  C5   C3   C2    -57.76  30.0  3
 ZPH  Var_21    H    C2   C3   C4     55.29  30.0  2
 ZPH  Var_22    H3   C2   C3   C4    -59.61  30.0  2
 ZPH  Var_23    H8   C5   C3   C4   -174.44  30.0  3
 ZPH  Var_24    H9   C5   C3   C4    -54.50  30.0  3
 ZPH  Var_25    H10  C5   C3   C4     65.26  30.0  3
 ZPH  Var_26    H    C2   C3   C5    178.78  30.0  2
 ZPH  Var_27    H3   C2   C3   C5     63.89  30.0  2
 ZPH  Var_28    H5   C4   C3   C5    -62.76  30.0  3
 ZPH  Var_29    H6   C4   C3   C5     57.29  30.0  3
 ZPH  Var_30    H7   C4   C3   C5    177.62  30.0  3
 ZPH  Var_31    H21  C15  O4   C14   179.54  30.0  3
 ZPH  Var_32    H22  C15  O4   C14   -61.50  30.0  3
 ZPH  Var_33    H23  C15  O4   C14    60.77  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

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

