# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:51:30 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (2S)-2-{[(S)-[(1R)-1-amino-2-carboxyethyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](C[P@@](O)(=O)[C@@H](N)CC(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
 AE1  AE1  '(2S)-2-{[(S)-[(1R)-1-amino-2-carboxyethyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid'  ligand  35  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AE1
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
 AE1  O1    O  OC    -1  -0.629  -5.8819  -0.5743   0.3048
 AE1  C3    C  C      0   0.411  -4.9084   0.1980   0.1781
 AE1  O2    O  O      0  -0.610  -4.9714   1.4393   0.0539
 AE1  C2    C  CH2    0  -0.592  -3.5163  -0.4610   0.2067
 AE1  C1    C  CH1    0  -0.314  -2.3396   0.4314  -0.1786
 AE1  N     N  NH2    0  -0.809  -2.3999   0.9543  -1.5406
 AE1  P     P  P      0   1.190  -0.7521  -0.4968   0.0332
 AE1  O1P   O  OP    -1  -0.835  -0.7013  -1.5588  -1.0557
 AE1  O2P   O  O      0  -0.833  -0.6511  -0.9450   1.4827
 AE1  C8    C  CH2    0  -0.688   0.5294   0.7948  -0.2667
 AE1  C6    C  CH1    0  -0.337   1.9332   0.4127   0.2249
 AE1  C7    C  C      0   0.411   2.8408   1.6541   0.1517
 AE1  O4    O  O      0  -0.625   3.2144   2.0164  -0.9853
 AE1  O3    O  OC    -1  -0.625   3.1160   2.2314   1.2262
 AE1  C5    C  CH2    0  -0.378   2.5123  -0.7632  -0.5597
 AE1  C16   C  CH1    0  -0.233   3.9274  -1.1859  -0.1634
 AE1  C17   C  CH3    0  -0.658   4.0495  -1.4905   1.3262
 AE1  C18   C  CH3    0  -0.648   4.3609  -2.3932  -0.9908
 AE1  H21   H  HCH2   0   0.208  -3.5304  -1.3396  -0.4487
 AE1  H22   H  HCH2   0   0.221  -3.3596  -0.8582   1.2164
 AE1  H1    H  HCH1   0   0.202  -2.3129   1.2867   0.5058
 AE1  HN1   H  HNH2   0   0.319  -2.3583   0.1723  -2.1840
 AE1  HN2   H  HNH2   0   0.332  -3.3082   1.3843  -1.6714
 AE1  H81   H  HCH2   0   0.219   0.2009   1.6984   0.2605
 AE1  H82   H  HCH2   0   0.217   0.5560   1.0509  -1.3284
 AE1  H6    H  HCH1   0   0.195   1.8357   0.1204   1.2735
 AE1  H51   H  HCH2   0   0.190   2.5088  -0.5120  -1.6254
 AE1  H52   H  HCH2   0   0.206   1.8479  -1.6262  -0.4550
 AE1  H16   H  HCH1   0   0.204   4.6090  -0.3603  -0.3968
 AE1  H171  H  HCH3   0   0.216   5.0533  -1.8433   1.5723
 AE1  H172  H  HCH3   0   0.226   3.8524  -0.6096   1.9374
 AE1  H173  H  HCH3   0   0.206   3.3431  -2.2692   1.6263
 AE1  H183  H  HCH3   0   0.217   5.3926  -2.6793  -0.7756
 AE1  H181  H  HCH3   0   0.207   3.7270  -3.2578  -0.7765
 AE1  H182  H  HCH3   0   0.217   4.2886  -2.1909  -2.0616

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
 AE1  O1   C3    deloc   1.249  0.020  1.249
 AE1  C3   O2    deloc   1.249  0.020  1.249
 AE1  C3   C2    single  1.540  0.020  1.540
 AE1  C2   C1    single  1.526  0.020  1.526
 AE1  C2   H21   single  0.970  0.020  1.090
 AE1  C2   H22   single  0.970  0.020  1.090
 AE1  C1   N     single  1.460  0.020  1.460
 AE1  C1   P     single  1.851  0.020  1.851
 AE1  C1   H1    single  0.970  0.020  1.090
 AE1  N    HN1   single  0.890  0.020  1.040
 AE1  N    HN2   single  0.890  0.020  1.040
 AE1  P    O1P   deloc   1.522  0.020  1.522
 AE1  P    O2P   deloc   1.521  0.020  1.521
 AE1  P    C8    single  1.844  0.020  1.844
 AE1  C8   C6    single  1.536  0.020  1.536
 AE1  C8   H81   single  0.970  0.020  1.090
 AE1  C8   H82   single  0.970  0.020  1.090
 AE1  C6   C7    single  1.539  0.020  1.539
 AE1  C6   C5    single  1.528  0.020  1.528
 AE1  C6   H6    single  0.970  0.020  1.090
 AE1  C7   O4    deloc   1.250  0.020  1.250
 AE1  C7   O3    deloc   1.251  0.020  1.251
 AE1  C5   C16   single  1.529  0.020  1.529
 AE1  C5   H51   single  0.970  0.020  1.090
 AE1  C5   H52   single  0.970  0.020  1.090
 AE1  C16  C17   single  1.525  0.020  1.525
 AE1  C16  C18   single  1.527  0.020  1.527
 AE1  C16  H16   single  0.970  0.020  1.090
 AE1  C17  H171  single  0.970  0.020  1.090
 AE1  C17  H172  single  0.970  0.020  1.090
 AE1  C17  H173  single  0.970  0.020  1.090
 AE1  C18  H183  single  0.970  0.020  1.090
 AE1  C18  H181  single  0.970  0.020  1.090
 AE1  C18  H182  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
 AE1  C2    C3   O2    118.20  3.000
 AE1  C2    C3   O1    115.97  3.000
 AE1  O2    C3   O1    125.82  3.000
 AE1  H22   C2   H21   105.20  3.000
 AE1  H22   C2   C1    109.51  3.000
 AE1  H21   C2   C1    109.13  3.000
 AE1  H22   C2   C3    107.53  3.000
 AE1  H21   C2   C3    108.67  3.000
 AE1  C1    C2   C3    116.22  3.000
 AE1  H1    C1   P     107.40  3.000
 AE1  H1    C1   N     107.70  3.000
 AE1  P     C1   N     108.77  3.000
 AE1  H1    C1   C2    108.52  3.000
 AE1  P     C1   C2    109.82  3.000
 AE1  N     C1   C2    114.39  3.000
 AE1  HN2   N    HN1   106.39  3.000
 AE1  HN2   N    C1    108.03  3.000
 AE1  HN1   N    C1    108.31  3.000
 AE1  C8    P    O2P   108.38  3.000
 AE1  C8    P    O1P   110.44  3.000
 AE1  O2P   P    O1P   118.31  3.000
 AE1  C8    P    C1    103.07  3.000
 AE1  O2P   P    C1    108.28  3.000
 AE1  O1P   P    C1    107.26  3.000
 AE1  H82   C8   H81   106.34  3.000
 AE1  H82   C8   C6    110.32  3.000
 AE1  H81   C8   C6    108.97  3.000
 AE1  H82   C8   P     109.83  3.000
 AE1  H81   C8   P     106.90  3.000
 AE1  C6    C8   P     114.14  3.000
 AE1  H6    C6   C5    108.71  3.000
 AE1  H6    C6   C7    108.29  3.000
 AE1  C5    C6   C7    111.89  3.000
 AE1  H6    C6   C8    106.98  3.000
 AE1  C5    C6   C8    111.94  3.000
 AE1  C7    C6   C8    108.85  3.000
 AE1  O3    C7   O4    125.58  3.000
 AE1  O3    C7   C6    117.46  3.000
 AE1  O4    C7   C6    116.94  3.000
 AE1  H52   C5   H51   105.79  3.000
 AE1  H52   C5   C16   108.61  3.000
 AE1  H51   C5   C16   108.58  3.000
 AE1  H52   C5   C6    109.14  3.000
 AE1  H51   C5   C6    108.79  3.000
 AE1  C16   C5   C6    115.50  3.000
 AE1  H16   C16  C18   107.69  3.000
 AE1  H16   C16  C17   107.98  3.000
 AE1  C18   C16  C17   110.40  3.000
 AE1  H16   C16  C5    108.19  3.000
 AE1  C18   C16  C5    109.93  3.000
 AE1  C17   C16  C5    112.48  3.000
 AE1  H173  C17  H172  107.75  3.000
 AE1  H173  C17  H171  107.57  3.000
 AE1  H172  C17  H171  107.51  3.000
 AE1  H173  C17  C16   111.01  3.000
 AE1  H172  C17  C16   111.82  3.000
 AE1  H171  C17  C16   110.99  3.000
 AE1  H182  C18  H181  107.48  3.000
 AE1  H182  C18  H183  107.72  3.000
 AE1  H181  C18  H183  107.58  3.000
 AE1  H182  C18  C16   111.48  3.000
 AE1  H181  C18  C16   110.77  3.000
 AE1  H183  C18  C16   111.63  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
 AE1  Var_01  C1    C2   C3   O1  170.11  30.0  3
 AE1  Var_02  C6    C8   P    C1  163.62  30.0  3
 AE1  Var_03  C17   C16  C5   C6   54.69  30.0  3
 AE1  Var_04  H171  C17  C16  C5  176.81  30.0  3
 AE1  Var_05  H183  C18  C16  C5  176.34  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
 AE1  chir_01  C1  C2  N   P   positiv
 AE1  chir_03  C6  C5  C7  C8  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
 AE1  plan-1  O1  0.020
 AE1  plan-1  C3  0.020
 AE1  plan-1  O2  0.020
 AE1  plan-1  C2  0.020
 AE1  plan-2  C6  0.020
 AE1  plan-2  C7  0.020
 AE1  plan-2  O4  0.020
 AE1  plan-2  O3  0.020

