# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:59:14 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  38  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  OH1   0  -0.591  -5.8185  -0.6997   0.3516
 AE1  C3    C  C     0   0.559  -4.8063   0.1530   0.2587
 AE1  O2    O  O     0  -0.441  -4.9487   1.3500   0.2338
 AE1  C2    C  CH2   0  -0.596  -3.4798  -0.5596   0.2220
 AE1  C1    C  CH1   0  -0.351  -2.3402   0.3505  -0.2249
 AE1  N     N  NH2   0  -0.807  -2.3989   0.8193  -1.5974
 AE1  P     P  P     0   1.282  -0.7238  -0.4818  -0.0157
 AE1  O1P   O  OH1   0  -0.764  -0.6591  -1.5654  -1.2208
 AE1  O2P   O  O     0  -0.716  -0.5464  -1.1733   1.2940
 AE1  C8    C  CH2   0  -0.725   0.5291   0.7934  -0.3703
 AE1  C6    C  CH1   0  -0.373   1.9209   0.4290   0.1722
 AE1  C7    C  C     0   0.553   2.7993   1.6491  -0.0060
 AE1  O4    O  O     0  -0.443   3.2053   2.0373  -1.0737
 AE1  O3    O  OH1   0  -0.583   3.0565   2.2690   1.1382
 AE1  C5    C  CH2   0  -0.407   2.5396  -0.7783  -0.5352
 AE1  C16   C  CH1   0  -0.248   3.9265  -1.1864  -0.0342
 AE1  C17   C  CH3   0  -0.659   3.9224  -1.5313   1.4524
 AE1  C18   C  CH3   0  -0.648   4.4368  -2.3651  -0.8579
 AE1  HO1   H  HOH1  0   0.482  -6.6570  -0.2166   0.4068
 AE1  H21   H  HCH2  0   0.284  -3.5546  -1.4348  -0.4291
 AE1  H22   H  HCH2  0   0.302  -3.2901  -0.9483   1.2280
 AE1  H1    H  HCH1  0   0.292  -2.3024   1.2228   0.4332
 AE1  HN1   H  HNH2  0   0.356  -2.7507   0.0948  -2.2111
 AE1  HN2   H  HNH2  0   0.370  -3.0321   1.6029  -1.6794
 AE1  H1P   H  HOH1  0   0.484  -0.5778  -1.1897  -2.1067
 AE1  H81   H  HCH2  0   0.298   0.1694   1.7072   0.1123
 AE1  H82   H  HCH2  0   0.295   0.5619   1.0005  -1.4412
 AE1  H6    H  HCH1  0   0.278   1.8203   0.2195   1.2383
 AE1  HO3   H  HOH1  0   0.480   3.5975   3.0570   0.9743
 AE1  H51   H  HCH2  0   0.233   2.5862  -0.5768  -1.6093
 AE1  H52   H  HCH2  0   0.240   1.8724  -1.6354  -0.4132
 AE1  H16   H  HCH1  0   0.222   4.6206  -0.3521  -0.1897
 AE1  H171  H  HCH3  0   0.231   4.9069  -1.8742   1.7738
 AE1  H172  H  HCH3  0   0.227   3.6600  -0.6758   2.0759
 AE1  H173  H  HCH3  0   0.217   3.2051  -2.3276   1.6663
 AE1  H183  H  HCH3  0   0.228   5.4383  -2.6631  -0.5437
 AE1  H181  H  HCH3  0   0.215   3.7811  -3.2321  -0.7458
 AE1  H182  H  HCH3  0   0.226   4.4806  -2.1190  -1.9203

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    single  1.327  0.020  1.327
 AE1  O1   HO1   single  0.850  0.020  0.980
 AE1  C3   O2    double  1.206  0.020  1.206
 AE1  C3   C2    single  1.506  0.020  1.506
 AE1  C2   C1    single  1.525  0.020  1.525
 AE1  C2   H21   single  0.970  0.020  1.090
 AE1  C2   H22   single  0.970  0.020  1.090
 AE1  C1   N     single  1.452  0.020  1.452
 AE1  C1   P     single  1.830  0.020  1.830
 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   single  1.622  0.020  1.622
 AE1  P    O2P   double  1.492  0.020  1.492
 AE1  P    C8    single  1.823  0.020  1.823
 AE1  O1P  H1P   single  0.850  0.020  0.980
 AE1  C8   C6    single  1.538  0.020  1.538
 AE1  C8   H81   single  0.970  0.020  1.090
 AE1  C8   H82   single  0.970  0.020  1.090
 AE1  C6   C7    single  1.514  0.020  1.514
 AE1  C6   C5    single  1.530  0.020  1.530
 AE1  C6   H6    single  0.970  0.020  1.090
 AE1  C7   O4    double  1.206  0.020  1.206
 AE1  C7   O3    single  1.327  0.020  1.327
 AE1  O3   HO3   single  0.850  0.020  0.980
 AE1  C5   C16   single  1.530  0.020  1.530
 AE1  C5   H51   single  0.970  0.020  1.090
 AE1  C5   H52   single  0.970  0.020  1.090
 AE1  C16  C17   single  1.526  0.020  1.526
 AE1  C16  C18   single  1.526  0.020  1.526
 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  HO1   O1   C3    110.10  3.000
 AE1  C2    C3   O2    124.97  3.000
 AE1  C2    C3   O1    111.69  3.000
 AE1  O2    C3   O1    123.33  3.000
 AE1  H22   C2   H21   105.95  3.000
 AE1  H22   C2   C1    110.58  3.000
 AE1  H21   C2   C1    110.75  3.000
 AE1  H22   C2   C3    107.34  3.000
 AE1  H21   C2   C3    109.45  3.000
 AE1  C1    C2   C3    112.51  3.000
 AE1  H1    C1   P     105.28  3.000
 AE1  H1    C1   N     108.23  3.000
 AE1  P     C1   N     106.90  3.000
 AE1  H1    C1   C2    109.00  3.000
 AE1  P     C1   C2    110.80  3.000
 AE1  N     C1   C2    116.07  3.000
 AE1  HN2   N    HN1   106.74  3.000
 AE1  HN2   N    C1    110.64  3.000
 AE1  HN1   N    C1    110.86  3.000
 AE1  C8    P    O2P   114.42  3.000
 AE1  C8    P    O1P   107.18  3.000
 AE1  O2P   P    O1P   109.75  3.000
 AE1  C8    P    C1    105.47  3.000
 AE1  O2P   P    C1    114.60  3.000
 AE1  O1P   P    C1    104.72  3.000
 AE1  H1P   O1P  P     115.15  3.000
 AE1  H82   C8   H81   106.51  3.000
 AE1  H82   C8   C6    111.35  3.000
 AE1  H81   C8   C6    109.87  3.000
 AE1  H82   C8   P     110.14  3.000
 AE1  H81   C8   P     105.81  3.000
 AE1  C6    C8   P     112.82  3.000
 AE1  H6    C6   C5    109.72  3.000
 AE1  H6    C6   C7    108.86  3.000
 AE1  C5    C6   C7    110.29  3.000
 AE1  H6    C6   C8    107.87  3.000
 AE1  C5    C6   C8    112.95  3.000
 AE1  C7    C6   C8    107.02  3.000
 AE1  O3    C7   O4    123.21  3.000
 AE1  O3    C7   C6    112.80  3.000
 AE1  O4    C7   C6    123.97  3.000
 AE1  HO3   O3   C7    110.00  3.000
 AE1  H52   C5   H51   106.26  3.000
 AE1  H52   C5   C16   107.92  3.000
 AE1  H51   C5   C16   109.40  3.000
 AE1  H52   C5   C6    108.68  3.000
 AE1  H51   C5   C6    109.02  3.000
 AE1  C16   C5   C6    115.19  3.000
 AE1  H16   C16  C18   107.43  3.000
 AE1  H16   C16  C17   108.17  3.000
 AE1  C18   C16  C17   110.62  3.000
 AE1  H16   C16  C5    108.93  3.000
 AE1  C18   C16  C5    109.42  3.000
 AE1  C17   C16  C5    112.14  3.000
 AE1  H173  C17  H172  107.56  3.000
 AE1  H173  C17  H171  107.79  3.000
 AE1  H172  C17  H171  107.17  3.000
 AE1  H173  C17  C16   110.92  3.000
 AE1  H172  C17  C16   112.35  3.000
 AE1  H171  C17  C16   110.83  3.000
 AE1  H182  C18  H181  107.63  3.000
 AE1  H182  C18  H183  107.76  3.000
 AE1  H181  C18  H183  107.73  3.000
 AE1  H182  C18  C16   111.39  3.000
 AE1  H181  C18  C16   110.90  3.000
 AE1  H183  C18  C16   111.25  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  CONST_01  HO1   O1   C3   O2    0.00   0.0  0
 AE1  CONST_02  HO3   O3   C7   C6  180.00   0.0  0
 AE1  Var_01    C1    C2   C3   O1  165.88  30.0  3
 AE1  Var_02    C6    C8   P    C1  161.85  30.0  3
 AE1  Var_03    C17   C16  C5   C6   58.85  30.0  3
 AE1  Var_04    H171  C17  C16  C5  176.72  30.0  3
 AE1  Var_05    H183  C18  C16  C5  178.38  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
 AE1  chir_04  P   O1P  O2P  C8  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
 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-1  HO1  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
 AE1  plan-2  HO3  0.020

