# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 14:39:35 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (2S)-2-amino-5-methoxy-5-oxopentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=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
 GME  GME  '(2S)-2-amino-5-methoxy-5-oxopentanoic acid (non-preferred name)'  L-peptide  21  11  .  2012-08-28  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_GME
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
 GME  C    C  C      0   0.413  -2.3241  -1.6021  -4.4606
 GME  N    N  NH2    0  -0.808  -0.2240  -1.2264  -5.7315
 GME  O    O  O      0  -0.596  -2.2783  -0.3790  -4.2259
 GME  CA   C  CH1    0  -0.224  -1.3165  -2.1579  -5.5021
 GME  CB   C  CH2    0  -0.413  -0.7777  -3.5309  -5.1077
 GME  CD   C  C      0   0.543   0.4681  -4.9028  -3.4543
 GME  CG   C  CH2    0  -0.599   0.0691  -3.5015  -3.8272
 GME  CX   C  CH3    0  -0.441  -1.4509  -5.0320  -2.0042
 GME  OE1  O  O      0  -0.445   1.4463  -5.4480  -3.9036
 GME  OE2  O  O2     0  -0.432  -0.3188  -5.6147  -2.6455
 GME  H    H  HNH2   0   0.330   0.1543  -1.3571  -6.6603
 GME  HA   H  HCH1   0   0.213  -1.9137  -2.3202  -6.4165
 GME  H1B  H  HCH2   0   0.228  -0.1662  -3.9316  -5.9216
 GME  H2B  H  HCH2   0   0.227  -1.6209  -4.2132  -4.9928
 GME  H1G  H  HCH2   0   0.266   0.9774  -2.9295  -4.0079
 GME  H2G  H  HCH2   0   0.261  -0.4765  -2.9996  -3.0282
 GME  H1X  H  HCH3   0   0.258  -1.9729  -5.8503  -1.5149
 GME  H2X  H  HCH3   0   0.238  -1.1483  -4.3079  -1.2463
 GME  H3X  H  HCH3   0   0.245  -2.1277  -4.5488  -2.7088
 GME  OXT  O  OC    -1  -0.601  -3.1313  -2.4243  -3.9807
 GME  H2   H  HNH2   0   0.335  -0.5932  -0.2862  -5.6859

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
 GME  C    O    deloc   1.231  0.020  1.231
 GME  C    OXT  deloc   1.248  0.020  1.248
 GME  N    H    single  0.860  0.020  0.860
 GME  N    CA   single  1.458  0.019  1.458
 GME  N    H2   single  0.890  0.020  1.040
 GME  CA   C    single  1.525  0.021  1.525
 GME  CA   CB   single  1.530  0.020  1.530
 GME  CB   H2B  single  0.970  0.020  1.090
 GME  CB   CG   single  1.535  0.020  1.535
 GME  CD   OE2  single  1.334  0.020  1.334
 GME  CG   CD   single  1.504  0.020  1.504
 GME  CG   H1G  single  0.970  0.020  1.090
 GME  CX   OE2  single  1.426  0.020  1.426
 GME  CX   H1X  single  0.970  0.020  1.090
 GME  OE1  CD   double  1.207  0.020  1.207
 GME  HA   CA   single  0.970  0.020  0.970
 GME  H1B  CB   single  0.970  0.020  1.090
 GME  H2G  CG   single  0.970  0.020  1.090
 GME  H2X  CX   single  0.970  0.020  1.090
 GME  H3X  CX   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
 GME  OXT  C    CA   116.23  3.000
 GME  CA   C    O    120.80  1.700
 GME  OXT  C    O    126.72  3.000
 GME  H2   N    H    107.35  3.000
 GME  H2   N    CA   108.32  3.000
 GME  H    N    CA   114.00  3.000
 GME  HA   CA   CB   109.00  3.000
 GME  HA   CA   N    110.00  3.000
 GME  CB   CA   N    110.50  1.700
 GME  HA   CA   C    109.00  3.000
 GME  CB   CA   C    110.10  1.900
 GME  N    CA   C    111.00  2.800
 GME  H2B  CB   H1B  106.34  3.000
 GME  H1B  CB   CG   108.61  3.000
 GME  H2B  CB   CG   110.52  3.000
 GME  H1B  CB   CA   109.53  3.000
 GME  CG   CB   CA   113.13  3.000
 GME  H2B  CB   CA   108.48  3.000
 GME  OE2  CD   OE1  117.57  3.000
 GME  OE1  CD   CG   122.94  3.000
 GME  OE2  CD   CG   119.40  3.000
 GME  H2G  CG   H1G  107.30  3.000
 GME  H2G  CG   CD   112.34  3.000
 GME  H1G  CG   CD   108.03  3.000
 GME  H2G  CG   CB   110.12  3.000
 GME  H1G  CG   CB   109.38  3.000
 GME  CD   CG   CB   109.59  3.000
 GME  H3X  CX   H2X  109.09  3.000
 GME  H3X  CX   H1X  109.06  3.000
 GME  H2X  CX   H1X  108.67  3.000
 GME  H3X  CX   OE2  112.55  3.000
 GME  H2X  CX   OE2  111.32  3.000
 GME  H1X  CX   OE2  106.03  3.000
 GME  CX   OE2  CD   121.54  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
 GME  Var_01  CD   CG  CB   CA  175.64  30.0  3
 GME  Var_02  OE2  CD  CG   CB  -90.38  30.0  3
 GME  Var_03  H1X  CX  OE2  CD  173.15  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
 GME  chir_01  CA  N  C  CB  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
 GME  plan-1  C    0.020
 GME  plan-1  O    0.020
 GME  plan-1  CA   0.020
 GME  plan-1  OXT  0.020
 GME  plan-2  CD   0.020
 GME  plan-2  CG   0.020
 GME  plan-2  OE1  0.020
 GME  plan-2  OE2  0.020

