# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:19:39 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (2S)-2-amino-4-[(S)-hydroxy(methoxy)phosphoryl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P](O)(=O)CC[C@H](N)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
 4M8  4M8  '(2S)-2-amino-4-[(S)-hydroxy(methoxy)phosphoryl]butanoic acid'  L-peptide  22  12  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_4M8
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
 4M8  OAG  O  O      0  -0.814  -21.2616  -27.6389  -10.3304
 4M8  P    P  P      0   1.282  -22.5395  -28.2216  -10.8774
 4M8  OAI  O  O2     0  -0.618  -22.3186  -29.8405  -11.1741
 4M8  CAJ  C  CH3    0  -0.398  -21.5389  -30.6115  -10.2898
 4M8  CG   C  CH2    0  -0.723  -23.8078  -28.2480   -9.5608
 4M8  CB   C  CH2    0  -0.421  -24.2015  -26.8393   -9.1282
 4M8  CA   C  CH1    0  -0.202  -25.3126  -26.7960   -8.0732
 4M8  N    N  NH2    0  -0.787  -26.5203  -27.4183   -8.5990
 4M8  C    C  C      0   0.381  -25.4881  -25.3304   -7.5977
 4M8  O    O  O      0  -0.605  -26.4433  -24.6889   -8.0821
 4M8  OXT  O  OC    -1  -0.617  -24.6326  -24.9036   -6.7943
 4M8  H2   H  HCH3   0   0.216  -21.5471  -31.6437  -10.6429
 4M8  H3   H  HCH3   0   0.202  -20.4998  -30.2753  -10.2475
 4M8  H4   H  HCH3   0   0.198  -21.9316  -30.6092   -9.2671
 4M8  H5   H  HCH2   0   0.227  -24.6900  -28.7832   -9.9174
 4M8  H6   H  HCH2   0   0.219  -23.4366  -28.8034   -8.6927
 4M8  H7   H  HCH2   0   0.213  -23.3237  -26.3220   -8.7345
 4M8  H8   H  HCH2   0   0.203  -24.5265  -26.2653  -10.0038
 4M8  H9   H  HCH1   0   0.197  -24.9772  -27.3925   -7.2169
 4M8  H10  H  HNH2   0   0.330  -27.1816  -27.5379   -7.8407
 4M8  H11  H  HNH2   0   0.320  -26.9620  -26.7423   -9.2129
 4M8  O1   O  OP    -1  -0.802  -23.1442  -27.6767  -12.1429

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
 4M8  OAI  P    single  1.661  0.020  1.661
 4M8  OAI  CAJ  single  1.409  0.020  1.409
 4M8  P    OAG  deloc   1.507  0.020  1.507
 4M8  P    CG   single  1.828  0.020  1.828
 4M8  CG   CB   single  1.525  0.020  1.525
 4M8  CB   CA   single  1.521  0.033  1.521
 4M8  N    CA   single  1.458  0.019  1.458
 4M8  O    C    deloc   1.231  0.020  1.231
 4M8  CA   C    single  1.525  0.021  1.525
 4M8  C    OXT  deloc   1.249  0.020  1.249
 4M8  CAJ  H2   single  0.970  0.020  1.090
 4M8  CAJ  H3   single  0.970  0.020  1.090
 4M8  CAJ  H4   single  0.970  0.020  1.090
 4M8  CG   H5   single  0.970  0.020  1.090
 4M8  CG   H6   single  0.970  0.020  1.090
 4M8  CB   H7   single  0.970  0.020  1.090
 4M8  CB   H8   single  0.970  0.020  1.090
 4M8  CA   H9   single  0.970  0.020  1.090
 4M8  N    H10  single  0.890  0.020  1.040
 4M8  N    H11  single  0.890  0.020  1.040
 4M8  P    O1   deloc   1.505  0.020  1.505

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
 4M8  O1   P    CG   109.39  3.000
 4M8  O1   P    OAI  104.85  3.000
 4M8  CG   P    OAI  101.94  3.000
 4M8  O1   P    OAG  120.40  3.000
 4M8  CG   P    OAG  109.41  3.000
 4M8  OAI  P    OAG  109.21  3.000
 4M8  CAJ  OAI  P    119.68  3.000
 4M8  H4   CAJ  H3   107.70  3.000
 4M8  H4   CAJ  H2   107.54  3.000
 4M8  H3   CAJ  H2   108.10  3.000
 4M8  H4   CAJ  OAI  112.74  3.000
 4M8  H3   CAJ  OAI  112.47  3.000
 4M8  H2   CAJ  OAI  108.09  3.000
 4M8  H6   CG   H5   106.51  3.000
 4M8  H6   CG   CB   109.33  3.000
 4M8  H5   CG   CB   109.69  3.000
 4M8  H6   CG   P    110.05  3.000
 4M8  H5   CG   P    109.41  3.000
 4M8  CB   CG   P    111.71  3.000
 4M8  H8   CB   H7   106.15  3.000
 4M8  H8   CB   CA   108.66  3.000
 4M8  H7   CB   CA   108.73  3.000
 4M8  H8   CB   CG   109.49  3.000
 4M8  H7   CB   CG   109.40  3.000
 4M8  CA   CB   CG   114.10  3.000
 4M8  H9   CA   C    108.02  3.000
 4M8  H9   CA   N    107.65  3.000
 4M8  C    CA   N    111.00  2.800
 4M8  H9   CA   CB   107.49  3.000
 4M8  C    CA   CB   110.50  1.500
 4M8  N    CA   CB   110.40  1.500
 4M8  H11  N    H10  104.33  3.000
 4M8  H11  N    CA   107.14  3.000
 4M8  H10  N    CA   108.75  3.000
 4M8  OXT  C    O    126.74  3.000
 4M8  OXT  C    CA   120.80  1.700
 4M8  O    C    CA   120.80  1.700

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
 4M8  Var_01  CB  CG   P    OAG   65.45  30.0  3
 4M8  Var_02  CA  CB   CG   P    177.17  30.0  3
 4M8  Var_03  CG  P    OAI  CAJ  -77.89  30.0  3
 4M8  Var_04  H2  CAJ  OAI  P    178.14  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
 4M8  chir_02  CA  CB  N  C  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
 4M8  plan-1  CA   0.020
 4M8  plan-1  C    0.020
 4M8  plan-1  O    0.020
 4M8  plan-1  OXT  0.020

