# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  1 10:08:00 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2R)-2-{[(S)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]methyl}pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[P](O)(=O)C[C@H](CCC(O)=O)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
 LDE  LDE  '(2R)-2-{[(S)-[(1R)-1-amino-3-methylbutyl](hydroxy)phosphoryl]methyl}pentanedioic acid'  peptide  38  19  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LDE
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
 LDE  C1    C  CH2    0  -0.415   4.0765   0.0191   0.4845
 LDE  N1    N  NH2    0  -0.795   2.4255  -0.3328   2.3061
 LDE  C2    C  CH1    0  -0.320   2.6602   0.2950   1.0051
 LDE  P3    P  P      0   1.185   1.3485  -0.3072  -0.1645
 LDE  C4    C  CH2    0  -0.672  -0.2109   0.0785   0.7288
 LDE  C5    C  CH1    0  -0.315  -1.4564  -0.1230  -0.1363
 LDE  C6    C  C      0   0.419  -1.7263  -1.6159  -0.3968
 LDE  C7    C  CH2    0  -0.385  -2.6775   0.5297   0.5182
 LDE  CD    C  C      0   0.407  -5.1684   1.1965   0.2263
 LDE  CG    C  CH1    0  -0.227   4.5188   0.7013  -0.8120
 LDE  O31   O  OP    -1  -0.826   1.5295  -1.8114  -0.2816
 LDE  O32   O  O      0  -0.819   1.3812   0.5320  -1.4321
 LDE  O61   O  OC    -1  -0.632  -1.7699  -2.0056  -1.5821
 LDE  O62   O  O      0  -0.632  -1.9247  -2.3288   0.6115
 LDE  CD1   C  CH3    0  -0.660   4.3339   2.2134  -0.7593
 LDE  CD2   C  CH3    0  -0.650   5.9747   0.3495  -1.1070
 LDE  OE1   O  O      0  -0.612  -5.0210   1.9038   1.2432
 LDE  OE2   O  OC    -1  -0.638  -6.2359   1.0318  -0.4045
 LDE  CG1   C  CH2    0  -0.587  -3.9370   0.4611  -0.3300
 LDE  H1    H  HCH2   0   0.195   4.7826   0.3091   1.2763
 LDE  H1A   H  HCH2   0   0.205   4.1872  -1.0653   0.3683
 LDE  HN1   H  HNH2   0   0.325   2.4442  -1.3390   2.1821
 LDE  HN1A  H  HNH2   0   0.331   3.1995  -0.1209   2.9269
 LDE  H2    H  HCH1   0   0.213   2.5229   1.3749   1.1312
 LDE  H4    H  HCH2   0   0.216  -0.2827  -0.5277   1.6330
 LDE  H4A   H  HCH2   0   0.204  -0.1565   1.1229   1.0582
 LDE  H5    H  HCH1   0   0.180  -1.2871   0.3696  -1.0997
 LDE  H7    H  HCH2   0   0.187  -2.8555   0.0596   1.4899
 LDE  H7A   H  HCH2   0   0.191  -2.4447   1.5775   0.7295
 LDE  HG    H  HCH1   0   0.217   3.9031   0.3208  -1.6300
 LDE  HD1   H  HCH3   0   0.214   4.7281   2.6894  -1.6603
 LDE  HD1A  H  HCH3   0   0.228   3.2804   2.4804  -0.6837
 LDE  HD1B  H  HCH3   0   0.201   4.8582   2.6460   0.0975
 LDE  HD2   H  HCH3   0   0.218   6.1221  -0.7307  -1.1687
 LDE  HD2A  H  HCH3   0   0.218   6.3034   0.7830  -2.0534
 LDE  HD2B  H  HCH3   0   0.205   6.6375   0.7279  -0.3239
 LDE  HG1   H  HCH2   0   0.210  -3.7255   0.8691  -1.3269
 LDE  HG1A  H  HCH2   0   0.216  -4.2192  -0.5811  -0.5114

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
 LDE  CG   C1    single  1.530  0.020  1.530
 LDE  C1   C2    single  1.534  0.020  1.534
 LDE  C1   H1    single  0.970  0.020  1.090
 LDE  C1   H1A   single  0.970  0.020  1.090
 LDE  N1   C2    single  1.464  0.020  1.464
 LDE  N1   HN1   single  0.890  0.020  1.040
 LDE  N1   HN1A  single  0.890  0.020  1.040
 LDE  C2   P3    single  1.858  0.020  1.858
 LDE  C2   H2    single  0.970  0.020  1.090
 LDE  O32  P3    deloc   1.521  0.020  1.521
 LDE  O31  P3    deloc   1.520  0.020  1.520
 LDE  P3   C4    single  1.838  0.020  1.838
 LDE  C4   C5    single  1.530  0.020  1.530
 LDE  C4   H4    single  0.970  0.020  1.090
 LDE  C4   H4A   single  0.970  0.020  1.090
 LDE  C6   C5    single  1.539  0.020  1.539
 LDE  C5   C7    single  1.531  0.020  1.531
 LDE  C5   H5    single  0.970  0.020  1.090
 LDE  O62  C6    deloc   1.251  0.020  1.251
 LDE  O61  C6    deloc   1.249  0.020  1.249
 LDE  C7   CG1   single  1.520  0.020  1.520
 LDE  C7   H7    single  0.970  0.020  1.090
 LDE  C7   H7A   single  0.970  0.020  1.090
 LDE  OE1  CD    deloc   1.248  0.020  1.248
 LDE  CD   OE2   deloc   1.251  0.020  1.251
 LDE  CD   CG1   single  1.538  0.020  1.538
 LDE  CD2  CG    single  1.527  0.020  1.527
 LDE  CG   CD1   single  1.524  0.020  1.524
 LDE  CG   HG    single  0.970  0.020  1.090
 LDE  CD1  HD1   single  0.970  0.020  1.090
 LDE  CD1  HD1A  single  0.970  0.020  1.090
 LDE  CD1  HD1B  single  0.970  0.020  1.090
 LDE  CD2  HD2   single  0.970  0.020  1.090
 LDE  CD2  HD2A  single  0.970  0.020  1.090
 LDE  CD2  HD2B  single  0.970  0.020  1.090
 LDE  CG1  HG1   single  0.970  0.020  1.090
 LDE  CG1  HG1A  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
 LDE  H1A   C1   H1    105.81  3.000
 LDE  H1A   C1   CG    108.78  3.000
 LDE  H1    C1   CG    107.86  3.000
 LDE  H1A   C1   C2    107.89  3.000
 LDE  H1    C1   C2    107.52  3.000
 LDE  CG    C1   C2    118.31  3.000
 LDE  HN1A  N1   HN1   105.55  3.000
 LDE  HN1A  N1   C2    109.39  3.000
 LDE  HN1   N1   C2    108.31  3.000
 LDE  H2    C2   P3    107.66  3.000
 LDE  H2    C2   N1    107.48  3.000
 LDE  P3    C2   N1    107.90  3.000
 LDE  H2    C2   C1    109.39  3.000
 LDE  P3    C2   C1    112.33  3.000
 LDE  N1    C2   C1    111.87  3.000
 LDE  O32   P3   O31   118.65  3.000
 LDE  O31   P3   C4    110.26  3.000
 LDE  O32   P3   C4    107.92  3.000
 LDE  C4    P3   C2    103.00  3.000
 LDE  O31   P3   C2    106.58  3.000
 LDE  O32   P3   C2    109.31  3.000
 LDE  H4A   C4   H4    106.47  3.000
 LDE  H4A   C4   C5    109.62  3.000
 LDE  H4    C4   C5    109.99  3.000
 LDE  H4A   C4   P3    107.69  3.000
 LDE  H4    C4   P3    110.00  3.000
 LDE  C5    C4   P3    112.85  3.000
 LDE  H5    C5   C7    107.91  3.000
 LDE  H5    C5   C6    108.33  3.000
 LDE  C7    C5   C6    110.24  3.000
 LDE  H5    C5   C4    108.20  3.000
 LDE  C7    C5   C4    110.57  3.000
 LDE  C6    C5   C4    111.48  3.000
 LDE  O62   C6   O61   125.58  3.000
 LDE  O61   C6   C5    118.00  3.000
 LDE  O62   C6   C5    116.38  3.000
 LDE  H7A   C7   H7    105.94  3.000
 LDE  H7A   C7   CG1   109.11  3.000
 LDE  H7    C7   CG1   109.96  3.000
 LDE  H7A   C7   C5    108.73  3.000
 LDE  H7    C7   C5    109.03  3.000
 LDE  CG1   C7   C5    113.76  3.000
 LDE  CG1   CD   OE2   115.97  3.000
 LDE  CG1   CD   OE1   118.12  3.000
 LDE  OE2   CD   OE1   125.91  3.000
 LDE  HG    CG   CD2   108.22  3.000
 LDE  HG    CG   CD1   107.64  3.000
 LDE  CD2   CG   CD1   110.55  3.000
 LDE  HG    CG   C1    108.43  3.000
 LDE  CD1   CG   C1    112.21  3.000
 LDE  CD2   CG   C1    109.67  3.000
 LDE  HD1B  CD1  HD1A  108.20  3.000
 LDE  HD1B  CD1  HD1   107.51  3.000
 LDE  HD1A  CD1  HD1   107.42  3.000
 LDE  HD1B  CD1  CG    111.18  3.000
 LDE  HD1A  CD1  CG    111.27  3.000
 LDE  HD1   CD1  CG    111.10  3.000
 LDE  HD2B  CD2  HD2A  107.51  3.000
 LDE  HD2B  CD2  HD2   107.51  3.000
 LDE  HD2A  CD2  HD2   107.65  3.000
 LDE  HD2B  CD2  CG    111.10  3.000
 LDE  HD2A  CD2  CG    111.30  3.000
 LDE  HD2   CD2  CG    111.57  3.000
 LDE  HG1A  CG1  HG1   104.66  3.000
 LDE  HG1A  CG1  CD    107.98  3.000
 LDE  HG1   CG1  CD    107.75  3.000
 LDE  HG1A  CG1  C7    110.43  3.000
 LDE  HG1   CG1  C7    109.28  3.000
 LDE  CD    CG1  C7    116.10  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
 LDE  Var_01  CD2  CG   C1   C2   177.07  30.0  1
 LDE  Var_02  C5   C4   P3   C2   170.74  30.0  3
 LDE  Var_03  CD   CG1  C7   C5  -175.37  30.0  3
 LDE  Var_04  OE1  CD   CG1  C7     7.28  30.0  2
 LDE  Var_05  HD2  CD2  CG   C1    56.92  30.0  3
 LDE  Var_06  HD1  CD1  CG   C1   175.48  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
 LDE  chir_01  C2  C1  N1  P3  positiv
 LDE  chir_03  C5  C7  C6  C4  positiv

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
 LDE  plan-1  C5   0.020
 LDE  plan-1  C6   0.020
 LDE  plan-1  O61  0.020
 LDE  plan-1  O62  0.020
 LDE  plan-2  CD   0.020
 LDE  plan-2  OE1  0.020
 LDE  plan-2  OE2  0.020
 LDE  plan-2  CG1  0.020

