# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 22:12:11 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (2R)-3-[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]-2-methylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[P](O)(=O)C[C@H](C)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
 L3A  L3A  '(2R)-3-[(R)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]-2-methylpropanoic acid'  peptide  33  15  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L3A
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
 L3A  P     P  P      0   1.182  -0.2378   0.2388   0.4000
 L3A  C1    C  CH2    0  -0.417  -2.9001  -0.7225   0.4448
 L3A  N1    N  NH2    0  -0.795  -1.0181  -2.3372   0.3235
 L3A  C2    C  CH1    0  -0.320  -1.5003  -1.0256  -0.1090
 L3A  C4    C  CH2    0  -0.672   1.2702  -0.3124  -0.4992
 L3A  C5    C  CH1    0  -0.372   2.5673   0.3071   0.0156
 L3A  C6    C  C      0   0.420   3.8432  -0.4096  -0.4888
 L3A  C7    C  CH3    0  -0.654   2.6555   1.8025  -0.2958
 L3A  C8    C  CH1    0  -0.224  -3.6351   0.5228  -0.0573
 L3A  O31   O  O      0  -0.834  -0.0189   0.0482   1.8950
 L3A  O32   O  OP    -1  -0.811  -0.6649   1.6127  -0.0915
 L3A  O61   O  OC    -1  -0.630   4.9288   0.0643  -0.0873
 L3A  O62   O  O      0  -0.607   3.7164  -1.3970  -1.2405
 L3A  C81   C  CH3    0  -0.664  -3.6554   0.6055  -1.5792
 L3A  C82   C  CH3    0  -0.651  -5.0564   0.5344   0.4995
 L3A  H1    H  HCH2   0   0.196  -3.5309  -1.5947   0.2210
 L3A  H1A   H  HCH2   0   0.206  -2.8320  -0.6774   1.5382
 L3A  HN1   H  HNH2   0   0.326  -0.8802  -2.3116   1.3274
 L3A  HN1A  H  HNH2   0   0.332  -1.7388  -3.0322   0.1600
 L3A  H2    H  HCH1   0   0.215  -1.5410  -1.0345  -1.2039
 L3A  H4    H  HCH2   0   0.228   1.3208  -1.3982  -0.4077
 L3A  H4A   H  HCH2   0   0.203   1.1444  -0.1031  -1.5672
 L3A  H5    H  HCH1   0   0.208   2.5721   0.2021   1.1083
 L3A  H7    H  HCH3   0   0.220   1.7968   2.3427   0.1006
 L3A  H7A   H  HCH3   0   0.210   3.5612   2.2389   0.1229
 L3A  H7B   H  HCH3   0   0.198   2.6720   1.9738  -1.3758
 L3A  H8    H  HCH1   0   0.219  -3.1112   1.4043   0.3164
 L3A  H81   H  HCH3   0   0.227  -2.6517   0.7483  -1.9791
 L3A  H81A  H  HCH3   0   0.203  -4.0717  -0.3040  -2.0219
 L3A  H81B  H  HCH3   0   0.216  -4.2664   1.4447  -1.9186
 L3A  H82   H  HCH3   0   0.217  -5.0616   0.4756   1.5901
 L3A  H82A  H  HCH3   0   0.218  -5.5871   1.4455   0.2154
 L3A  H82B  H  HCH3   0   0.205  -5.6320  -0.3149   0.1212

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
 L3A  P    C2    single  1.858  0.020  1.858
 L3A  P    C4    single  1.840  0.020  1.840
 L3A  P    O31   deloc   1.523  0.020  1.523
 L3A  P    O32   deloc   1.520  0.020  1.520
 L3A  C1   C2    single  1.536  0.020  1.536
 L3A  C1   C8    single  1.531  0.020  1.531
 L3A  C1   H1    single  0.970  0.020  1.090
 L3A  C1   H1A   single  0.970  0.020  1.090
 L3A  N1   C2    single  1.463  0.020  1.463
 L3A  N1   HN1   single  0.890  0.020  1.040
 L3A  N1   HN1A  single  0.890  0.020  1.040
 L3A  C2   H2    single  0.970  0.020  1.090
 L3A  C4   C5    single  1.527  0.020  1.527
 L3A  C4   H4    single  0.970  0.020  1.090
 L3A  C4   H4A   single  0.970  0.020  1.090
 L3A  C5   C6    single  1.548  0.020  1.548
 L3A  C5   C7    single  1.530  0.020  1.530
 L3A  C5   H5    single  0.970  0.020  1.090
 L3A  C6   O61   deloc   1.251  0.020  1.251
 L3A  C6   O62   deloc   1.247  0.020  1.247
 L3A  C7   H7    single  0.970  0.020  1.090
 L3A  C7   H7A   single  0.970  0.020  1.090
 L3A  C7   H7B   single  0.970  0.020  1.090
 L3A  C8   C81   single  1.524  0.020  1.524
 L3A  C8   C82   single  1.526  0.020  1.526
 L3A  C8   H8    single  0.970  0.020  1.090
 L3A  C81  H81   single  0.970  0.020  1.090
 L3A  C81  H81A  single  0.970  0.020  1.090
 L3A  C81  H81B  single  0.970  0.020  1.090
 L3A  C82  H82   single  0.970  0.020  1.090
 L3A  C82  H82A  single  0.970  0.020  1.090
 L3A  C82  H82B  single  0.970  0.020  1.090

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
 L3A  O32   P    O31   118.09  3.000
 L3A  O32   P    C4    110.05  3.000
 L3A  O31   P    C4    108.93  3.000
 L3A  O32   P    C2    109.61  3.000
 L3A  O31   P    C2    106.35  3.000
 L3A  C4    P    C2    102.66  3.000
 L3A  H1A   C1   H1    105.74  3.000
 L3A  H1A   C1   C8    108.87  3.000
 L3A  H1    C1   C8    107.65  3.000
 L3A  H1A   C1   C2    108.13  3.000
 L3A  H1    C1   C2    107.04  3.000
 L3A  C8    C1   C2    118.69  3.000
 L3A  HN1A  N1   HN1   105.88  3.000
 L3A  HN1A  N1   C2    109.42  3.000
 L3A  HN1   N1   C2    108.36  3.000
 L3A  H2    C2   N1    107.48  3.000
 L3A  H2    C2   C1    109.15  3.000
 L3A  N1    C2   C1    111.77  3.000
 L3A  H2    C2   P     107.73  3.000
 L3A  N1    C2   P     107.77  3.000
 L3A  C1    C2   P     112.72  3.000
 L3A  H4A   C4   H4    106.10  3.000
 L3A  H4A   C4   C5    110.41  3.000
 L3A  H4    C4   C5    109.64  3.000
 L3A  H4A   C4   P     108.97  3.000
 L3A  H4    C4   P     107.16  3.000
 L3A  C5    C4   P     114.20  3.000
 L3A  H5    C5   C7    107.21  3.000
 L3A  H5    C5   C6    106.05  3.000
 L3A  C7    C5   C6    109.80  3.000
 L3A  H5    C5   C4    107.49  3.000
 L3A  C7    C5   C4    112.14  3.000
 L3A  C6    C5   C4    113.74  3.000
 L3A  O62   C6   O61   125.57  3.000
 L3A  O62   C6   C5    118.62  3.000
 L3A  O61   C6   C5    115.81  3.000
 L3A  H7B   C7   H7A   107.72  3.000
 L3A  H7B   C7   H7    107.07  3.000
 L3A  H7A   C7   H7    108.49  3.000
 L3A  H7B   C7   C5    110.79  3.000
 L3A  H7A   C7   C5    111.18  3.000
 L3A  H7    C7   C5    111.42  3.000
 L3A  H8    C8   C82   108.41  3.000
 L3A  H8    C8   C81   107.73  3.000
 L3A  C82   C8   C81   110.57  3.000
 L3A  H8    C8   C1    108.32  3.000
 L3A  C82   C8   C1    109.49  3.000
 L3A  C81   C8   C1    112.21  3.000
 L3A  H81B  C81  H81A  107.47  3.000
 L3A  H81B  C81  H81   107.49  3.000
 L3A  H81A  C81  H81   108.12  3.000
 L3A  H81B  C81  C8    111.06  3.000
 L3A  H81A  C81  C8    111.35  3.000
 L3A  H81   C81  C8    111.17  3.000
 L3A  H82B  C82  H82A  107.59  3.000
 L3A  H82B  C82  H82   107.52  3.000
 L3A  H82A  C82  H82   107.60  3.000
 L3A  H82B  C82  C8    110.98  3.000
 L3A  H82A  C82  C8    111.35  3.000
 L3A  H82   C82  C8    111.61  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
 L3A  Var_01  C5   C4   P   C2  -164.11  30.0  3
 L3A  Var_02  C81  C8   C1  C2    50.31  30.0  3
 L3A  Var_03  H81  C81  C8  C1   -65.95  30.0  3
 L3A  Var_04  H82  C82  C8  C1    55.86  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
 L3A  chir_02  C2  P   C1  N1  positiv
 L3A  chir_03  C5  C4  C6  C7  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
 L3A  plan-1  C5   0.020
 L3A  plan-1  C6   0.020
 L3A  plan-1  O61  0.020
 L3A  plan-1  O62  0.020

