# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 02:55:06 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  35  15  .  2022-03-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   1.257  -0.2195   0.2766   0.3702
 L3A  C1    C  CH2   0  -0.424  -2.8998  -0.6246   0.4677
 L3A  N1    N  NH2   0  -0.792  -0.9799  -2.2212   0.4674
 L3A  C2    C  CH1   0  -0.339  -1.4990  -0.9632  -0.0575
 L3A  C4    C  CH2   0  -0.725   1.3000  -0.2723  -0.4658
 L3A  C5    C  CH1   0  -0.377   2.5707   0.3377   0.1207
 L3A  C6    C  C     0   0.570   3.7902  -0.3245  -0.4834
 L3A  C7    C  CH3   0  -0.668   2.6689   1.8546  -0.0876
 L3A  C8    C  CH1   0  -0.246  -3.6515   0.5591  -0.1466
 L3A  O31   O  O     0  -0.725  -0.0817   0.4744   1.8441
 L3A  O32   O  OH1   0  -0.755  -0.6366   1.6833  -0.3256
 L3A  O61   O  OH1   0  -0.594   4.8813  -0.0942   0.2382
 L3A  O62   O  O     0  -0.438   3.8001  -0.9670  -1.5033
 L3A  C81   C  CH3   0  -0.660  -3.7243   0.4713  -1.6674
 L3A  C82   C  CH3   0  -0.649  -5.0546   0.6228   0.4513
 L3A  H1    H  HCH2  0   0.230  -3.5049  -1.5257   0.3125
 L3A  H1A   H  HCH2  0   0.230  -2.8370  -0.4875   1.5526
 L3A  HN1   H  HNH2  0   0.350  -1.1258  -2.2613   1.4691
 L3A  HN1A  H  HNH2  0   0.362  -1.5018  -2.9934   0.0723
 L3A  H2    H  HCH1  0   0.272  -1.5154  -1.0488  -1.1485
 L3A  H4    H  HCH2  0   0.297   1.3156  -1.3585  -0.3584
 L3A  H4A   H  HCH2  0   0.283   1.2151  -0.0641  -1.5354
 L3A  H5    H  HCH1  0   0.284   2.5935   0.1416   1.1966
 L3A  H7    H  HCH3  0   0.251   1.8637   2.3662   0.4359
 L3A  H7A   H  HCH3  0   0.251   3.6073   2.2498   0.2980
 L3A  H7B   H  HCH3  0   0.235   2.6005   2.1106  -1.1459
 L3A  H8    H  HCH1  0   0.228  -3.1402   1.4867   0.1215
 L3A  H81   H  HCH3  0   0.217  -2.7430   0.5515  -2.1375
 L3A  H81A  H  HCH3  0   0.217  -4.1654  -0.4772  -1.9844
 L3A  H81B  H  HCH3  0   0.231  -4.3399   1.2747  -2.0748
 L3A  H82   H  HCH3  0   0.225  -5.0220   0.7028   1.5396
 L3A  H82A  H  HCH3  0   0.226  -5.6047   1.4864   0.0737
 L3A  H82B  H  HCH3  0   0.213  -5.6299  -0.2722   0.2020
 L3A  H19   H  HOH1  0   0.483  -0.5663   1.7069  -1.2879
 L3A  H20   H  HOH1  0   0.480   5.6528  -0.4974  -0.1874

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  1.832  0.020  1.832
 L3A  P    C4    single  1.819  0.020  1.819
 L3A  P    O31   double  1.493  0.020  1.493
 L3A  P    O32   single  1.624  0.020  1.624
 L3A  C1   C2    single  1.534  0.020  1.534
 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  1.459  0.020  1.459
 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  1.513  0.020  1.513
 L3A  C5   C7    single  1.534  0.020  1.534
 L3A  C5   H5    single  0.970  0.020  1.090
 L3A  C6   O61   single  1.328  0.020  1.328
 L3A  C6   O62   double  1.205  0.020  1.205
 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  1.525  0.020  1.525
 L3A  C8   C82   single  1.527  0.020  1.527
 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
 L3A  O32  H19   single  0.850  0.020  0.980
 L3A  O61  H20   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
 L3A  O32   P    O31   109.38  3.000
 L3A  O32   P    C4    106.20  3.000
 L3A  O31   P    C4    114.61  3.000
 L3A  O32   P    C2    107.87  3.000
 L3A  O31   P    C2    112.60  3.000
 L3A  C4    P    C2    105.77  3.000
 L3A  H1A   C1   H1    105.94  3.000
 L3A  H1A   C1   C8    109.20  3.000
 L3A  H1    C1   C8    107.92  3.000
 L3A  H1A   C1   C2    108.32  3.000
 L3A  H1    C1   C2    105.91  3.000
 L3A  C8    C1   C2    118.80  3.000
 L3A  HN1A  N1   HN1   106.35  3.000
 L3A  HN1A  N1   C2    109.51  3.000
 L3A  HN1   N1   C2    109.80  3.000
 L3A  H2    C2   N1    107.26  3.000
 L3A  H2    C2   C1    110.17  3.000
 L3A  N1    C2   C1    113.09  3.000
 L3A  H2    C2   P     107.22  3.000
 L3A  N1    C2   P     104.54  3.000
 L3A  C1    C2   P     114.11  3.000
 L3A  H4A   C4   H4    106.67  3.000
 L3A  H4A   C4   C5    111.37  3.000
 L3A  H4    C4   C5    110.36  3.000
 L3A  H4A   C4   P     109.11  3.000
 L3A  H4    C4   P     105.49  3.000
 L3A  C5    C4   P     113.46  3.000
 L3A  H5    C5   C7    108.03  3.000
 L3A  H5    C5   C6    107.30  3.000
 L3A  C7    C5   C6    109.08  3.000
 L3A  H5    C5   C4    108.88  3.000
 L3A  C7    C5   C4    113.34  3.000
 L3A  C6    C5   C4    110.03  3.000
 L3A  O62   C6   O61   123.04  3.000
 L3A  O62   C6   C5    125.28  3.000
 L3A  O61   C6   C5    111.67  3.000
 L3A  H7B   C7   H7A   108.20  3.000
 L3A  H7B   C7   H7    108.06  3.000
 L3A  H7A   C7   H7    107.26  3.000
 L3A  H7B   C7   C5    111.08  3.000
 L3A  H7A   C7   C5    111.47  3.000
 L3A  H7    C7   C5    110.62  3.000
 L3A  H8    C8   C82   107.37  3.000
 L3A  H8    C8   C81   108.42  3.000
 L3A  C82   C8   C81   110.43  3.000
 L3A  H8    C8   C1    109.16  3.000
 L3A  C82   C8   C1    109.05  3.000
 L3A  C81   C8   C1    112.28  3.000
 L3A  H19   O32  P     115.45  3.000
 L3A  H20   O61  C6    110.08  3.000
 L3A  H81B  C81  H81A  107.64  3.000
 L3A  H81B  C81  H81   107.00  3.000
 L3A  H81A  C81  H81   107.57  3.000
 L3A  H81B  C81  C8    110.91  3.000
 L3A  H81A  C81  C8    111.01  3.000
 L3A  H81   C81  C8    112.48  3.000
 L3A  H82B  C82  H82A  107.68  3.000
 L3A  H82B  C82  H82   107.65  3.000
 L3A  H82A  C82  H82   107.58  3.000
 L3A  H82B  C82  C8    111.12  3.000
 L3A  H82A  C82  C8    111.15  3.000
 L3A  H82   C82  C8    111.48  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  CONST_01  H20  O61  C6  C5   180.00   0.0  0
 L3A  Var_01    C5   C4   P   C2  -160.67  30.0  3
 L3A  Var_02    C81  C8   C1  C2    52.55  30.0  3
 L3A  Var_03    H81  C81  C8  C1   -65.33  30.0  3
 L3A  Var_04    H82  C82  C8  C1    57.12  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
 L3A  chir_04  P   C4  O31  O32  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
 L3A  plan-1  C5   0.020
 L3A  plan-1  C6   0.020
 L3A  plan-1  O61  0.020
 L3A  plan-1  O62  0.020
 L3A  plan-1  H20  0.020

