# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 11:18:52 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  41  19  .  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_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  -0.440   4.0842  -0.0992   0.3299
 LDE  N1    N  NH2   0  -0.823   2.4402  -0.6883   2.1187
 LDE  C2    C  CH1   0  -0.331   2.6850   0.1049   0.9136
 LDE  P3    P  P     0   1.264   1.3148  -0.3544  -0.2166
 LDE  C4    C  CH2   0  -0.715  -0.1994   0.2294   0.6056
 LDE  C5    C  CH1   0  -0.361  -1.4720  -0.1424  -0.1599
 LDE  C6    C  C     0   0.544  -1.7178  -1.6352  -0.0879
 LDE  C7    C  CH2   0  -0.415  -2.6775   0.5999   0.4318
 LDE  CD    C  C     0   0.556  -5.1115   1.1908   0.1340
 LDE  CG    C  CH1   0  -0.244   4.4928   0.7955  -0.8436
 LDE  O31   O  OH1   0  -0.763   1.2725  -1.9753  -0.1430
 LDE  O32   O  O     0  -0.715   1.3915   0.0818  -1.6432
 LDE  O61   O  OH1   0  -0.585  -1.8770  -2.1893  -1.2807
 LDE  O62   O  O     0  -0.442  -1.7979  -2.2500   0.9469
 LDE  CD1   C  CH3   0  -0.663   4.3751   2.2790  -0.5094
 LDE  CD2   C  CH3   0  -0.652   5.9189   0.4530  -1.2626
 LDE  OE1   O  O     0  -0.442  -5.0610   1.9902   1.0350
 LDE  OE2   O  OH1   0  -0.596  -6.2188   0.9485  -0.5597
 LDE  CG1   C  CH2   0  -0.593  -3.9587   0.3541  -0.3494
 LDE  H1    H  HCH2  0   0.236   4.7917   0.0641   1.1519
 LDE  H1A   H  HCH2  0   0.233   4.1977  -1.1503   0.0403
 LDE  HN1   H  HNH2  0   0.366   3.1277  -1.4259   2.2043
 LDE  HN1A  H  HNH2  0   0.372   2.5191  -0.1164   2.9475
 LDE  H2    H  HCH1  0   0.278   2.5418   1.1610   1.1568
 LDE  H4    H  HCH2  0   0.287  -0.2404  -0.1261   1.6363
 LDE  H4A   H  HCH2  0   0.289  -0.1214   1.3193   0.6506
 LDE  H5    H  HCH1  0   0.278  -1.3608   0.1548  -1.2051
 LDE  H7    H  HCH2  0   0.247  -2.8060   0.3122   1.4775
 LDE  H7A   H  HCH2  0   0.257  -2.4441   1.6660   0.4242
 LDE  HG    H  HCH1  0   0.234   3.8326   0.5863  -1.6875
 LDE  HO31  H  HOH1  0   0.477   1.2894  -2.2933   0.7715
 LDE  HO61  H  HOH1  0   0.479  -2.0520  -3.1383  -1.1854
 LDE  HD1   H  HCH3  0   0.230   4.7476   2.8904  -1.3333
 LDE  HD1A  H  HCH3  0   0.224   3.3431   2.5836  -0.3282
 LDE  HD1B  H  HCH3  0   0.215   4.9587   2.5338   0.3792
 LDE  HD2   H  HCH3  0   0.225   6.0102  -0.5970  -1.5467
 LDE  HD2A  H  HCH3  0   0.227   6.2346   1.0563  -2.1153
 LDE  HD2B  H  HCH3  0   0.213   6.6241   0.6382  -0.4486
 LDE  HOE2  H  HOH1  0   0.480  -6.9422   1.5045  -0.2337
 LDE  HG1   H  HCH2  0   0.287  -3.8064   0.5683  -1.4121
 LDE  HG1A  H  HCH2  0   0.284  -4.2683  -0.6946  -0.3017

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  1.531  0.020  1.531
 LDE  C1   C2    single  1.530  0.020  1.530
 LDE  C1   H1    single  0.970  0.020  1.090
 LDE  C1   H1A   single  0.970  0.020  1.090
 LDE  N1   C2    single  1.463  0.020  1.463
 LDE  N1   HN1   single  0.890  0.020  1.040
 LDE  N1   HN1A  single  0.890  0.020  1.040
 LDE  C2   P3    single  1.835  0.020  1.835
 LDE  C2   H2    single  0.970  0.020  1.090
 LDE  O32  P3    double  1.494  0.020  1.494
 LDE  O31  P3    single  1.623  0.020  1.623
 LDE  P3   C4    single  1.819  0.020  1.819
 LDE  C4   C5    single  1.531  0.020  1.531
 LDE  C4   H4    single  0.970  0.020  1.090
 LDE  C4   H4A   single  0.970  0.020  1.090
 LDE  C6   C5    single  1.515  0.020  1.515
 LDE  C5   C7    single  1.534  0.020  1.534
 LDE  C5   H5    single  0.970  0.020  1.090
 LDE  O62  C6    double  1.206  0.020  1.206
 LDE  O61  C6    single  1.325  0.020  1.325
 LDE  C7   CG1   single  1.521  0.020  1.521
 LDE  C7   H7    single  0.970  0.020  1.090
 LDE  C7   H7A   single  0.970  0.020  1.090
 LDE  OE1  CD    double  1.206  0.020  1.206
 LDE  CD   OE2   single  1.329  0.020  1.329
 LDE  CD   CG1   single  1.504  0.020  1.504
 LDE  CD2  CG    single  1.525  0.020  1.525
 LDE  CG   CD1   single  1.525  0.020  1.525
 LDE  CG   HG    single  0.970  0.020  1.090
 LDE  O31  HO31  single  0.850  0.020  0.980
 LDE  O61  HO61  single  0.850  0.020  0.980
 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  OE2  HOE2  single  0.850  0.020  0.980
 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    105.90  3.000
 LDE  H1A   C1   CG    109.28  3.000
 LDE  H1    C1   CG    108.38  3.000
 LDE  H1A   C1   C2    108.87  3.000
 LDE  H1    C1   C2    106.51  3.000
 LDE  CG    C1   C2    117.29  3.000
 LDE  HN1A  N1   HN1   106.87  3.000
 LDE  HN1A  N1   C2    110.84  3.000
 LDE  HN1   N1   C2    110.56  3.000
 LDE  H2    C2   P3    106.33  3.000
 LDE  H2    C2   N1    108.58  3.000
 LDE  P3    C2   N1    104.28  3.000
 LDE  H2    C2   C1    109.48  3.000
 LDE  P3    C2   C1    114.50  3.000
 LDE  N1    C2   C1    113.26  3.000
 LDE  O32   P3   O31   109.65  3.000
 LDE  O31   P3   C4    106.16  3.000
 LDE  O32   P3   C4    112.37  3.000
 LDE  C4    P3   C2    105.24  3.000
 LDE  O31   P3   C2    103.98  3.000
 LDE  O32   P3   C2    118.48  3.000
 LDE  H4A   C4   H4    106.77  3.000
 LDE  H4A   C4   C5    108.77  3.000
 LDE  H4    C4   C5    111.22  3.000
 LDE  H4A   C4   P3    106.21  3.000
 LDE  H4    C4   P3    110.71  3.000
 LDE  C5    C4   P3    112.83  3.000
 LDE  H5    C5   C7    108.50  3.000
 LDE  H5    C5   C6    109.28  3.000
 LDE  C7    C5   C6    109.33  3.000
 LDE  H5    C5   C4    109.13  3.000
 LDE  C7    C5   C4    110.05  3.000
 LDE  C6    C5   C4    110.52  3.000
 LDE  O62   C6   O61   123.45  3.000
 LDE  O61   C6   C5    112.89  3.000
 LDE  O62   C6   C5    123.63  3.000
 LDE  H7A   C7   H7    106.81  3.000
 LDE  H7A   C7   CG1   109.54  3.000
 LDE  H7    C7   CG1   110.50  3.000
 LDE  H7A   C7   C5    107.57  3.000
 LDE  H7    C7   C5    109.52  3.000
 LDE  CG1   C7   C5    112.68  3.000
 LDE  CG1   CD   OE2   111.68  3.000
 LDE  CG1   CD   OE1   125.23  3.000
 LDE  OE2   CD   OE1   123.09  3.000
 LDE  HG    CG   CD2   108.06  3.000
 LDE  HG    CG   CD1   108.00  3.000
 LDE  CD2   CG   CD1   110.54  3.000
 LDE  HG    CG   C1    108.61  3.000
 LDE  CD1   CG   C1    112.32  3.000
 LDE  CD2   CG   C1    109.20  3.000
 LDE  HO31  O31  P3    111.74  3.000
 LDE  HO61  O61  C6    110.03  3.000
 LDE  HD1B  CD1  HD1A  107.75  3.000
 LDE  HD1B  CD1  HD1   107.51  3.000
 LDE  HD1A  CD1  HD1   106.96  3.000
 LDE  HD1B  CD1  CG    111.32  3.000
 LDE  HD1A  CD1  CG    112.39  3.000
 LDE  HD1   CD1  CG    110.67  3.000
 LDE  HD2B  CD2  HD2A  107.56  3.000
 LDE  HD2B  CD2  HD2   107.63  3.000
 LDE  HD2A  CD2  HD2   107.71  3.000
 LDE  HD2B  CD2  CG    111.14  3.000
 LDE  HD2A  CD2  CG    111.16  3.000
 LDE  HD2   CD2  CG    111.45  3.000
 LDE  HOE2  OE2  CD    109.99  3.000
 LDE  HG1A  CG1  HG1   105.62  3.000
 LDE  HG1A  CG1  CD    107.59  3.000
 LDE  HG1   CG1  CD    108.04  3.000
 LDE  HG1A  CG1  C7    111.76  3.000
 LDE  HG1   CG1  C7    110.48  3.000
 LDE  CD    CG1  C7    113.00  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  CONST_01  HO61  O61  C6   C5    180.00   0.0  0
 LDE  CONST_02  HOE2  OE2  CD   OE1     0.00   0.0  0
 LDE  Var_01    CD2   CG   C1   C2    179.12  30.0  1
 LDE  Var_02    C5    C4   P3   C2   -176.60  30.0  3
 LDE  Var_03    CD    CG1  C7   C5   -173.87  30.0  3
 LDE  Var_04    OE1   CD   CG1  C7      0.58  30.0  2
 LDE  Var_05    HD2   CD2  CG   C1     58.40  30.0  3
 LDE  Var_06    HD1   CD1  CG   C1    175.46  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
 LDE  chir_04  P3  O32  O31  C4  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
 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-1  HO61  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
 LDE  plan-2  HOE2  0.020

