# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 21:27:29 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (2S)-2-amino-7-methoxy-7-oxoheptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CCCC[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
 1TX  1TX  '(2S)-2-amino-7-methoxy-7-oxoheptanoic acid'  L-peptide  27  13  .  2022-09-22  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_1TX
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
 1TX  C13  C  C      0   0.403   4.0557  -0.2906   0.0847
 1TX  C21  C  CH2    0  -0.425   1.5596  -0.1563  -0.0646
 1TX  C22  C  CH2    0  -0.423   0.2596   0.4893   0.3979
 1TX  C24  C  CH2    0  -0.579  -2.2563   0.3967   0.4133
 1TX  C26  C  CH3    0  -0.425  -5.8642  -0.1188  -0.1068
 1TX  O8   O  O      0  -0.607   4.7479   0.0294  -0.9022
 1TX  C14  C  CH1    0  -0.202   2.8238   0.5855   0.4021
 1TX  N7   N  NH2    0  -0.804   2.9855   1.9171  -0.1610
 1TX  C23  C  CH2    0  -0.414  -0.9781  -0.2557  -0.0882
 1TX  C25  C  C      0   0.599  -3.5134  -0.2926  -0.0426
 1TX  O13  O  O      0  -0.455  -3.5616  -1.3670  -0.5882
 1TX  O14  O  O2     0  -0.457  -4.5932   0.4275   0.2417
 1TX  H5   H  HCH2   0   0.212   1.5937  -1.1833   0.3094
 1TX  H6   H  HCH2   0   0.206   1.5705  -0.2228  -1.1591
 1TX  H7   H  HCH2   0   0.214   0.2519   0.5342   1.4926
 1TX  H8   H  HCH2   0   0.206   0.1999   1.5268   0.0519
 1TX  H9   H  HCH2   0   0.276  -2.2683   0.4127   1.5087
 1TX  H10  H  HCH2   0   0.268  -2.3005   1.4458   0.1075
 1TX  H11  H  HCH3   0   0.237  -6.0553  -1.0549   0.4179
 1TX  H12  H  HCH3   0   0.250  -6.6004   0.6191   0.1988
 1TX  H13  H  HCH3   0   0.237  -5.9483  -0.2862  -1.1805
 1TX  H24  H  HCH1   0   0.196   2.7583   0.6793   1.4934
 1TX  H25  H  HNH2   0   0.326   3.3013   1.8169  -1.1177
 1TX  H34  H  HCH2   0   0.224  -0.9786  -0.2817  -1.1812
 1TX  H35  H  HCH2   0   0.225  -0.9321  -1.2954   0.2456
 1TX  H2   H  HNH2   0   0.331   2.0964   2.3995  -0.1969
 1TX  OXT  O  OC    -1  -0.621   4.2324  -1.2799   0.8244

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
 1TX  C26  O14  single  1.427  0.020  1.427
 1TX  O13  C25  double  1.206  0.020  1.206
 1TX  O14  C25  single  1.329  0.020  1.329
 1TX  C25  C24  single  1.504  0.020  1.504
 1TX  C24  C23  single  1.520  0.020  1.520
 1TX  C23  C22  single  1.524  0.020  1.524
 1TX  C22  C21  single  1.523  0.020  1.523
 1TX  C21  C14  single  1.538  0.020  1.538
 1TX  C14  N7   single  1.455  0.020  1.455
 1TX  C14  C13  single  1.545  0.020  1.545
 1TX  O8   C13  deloc   1.247  0.020  1.247
 1TX  C21  H5   single  0.970  0.020  1.090
 1TX  C21  H6   single  0.970  0.020  1.090
 1TX  C22  H7   single  0.970  0.020  1.090
 1TX  C22  H8   single  0.970  0.020  1.090
 1TX  C24  H9   single  0.970  0.020  1.090
 1TX  C24  H10  single  0.970  0.020  1.090
 1TX  C26  H11  single  0.970  0.020  1.090
 1TX  C26  H12  single  0.970  0.020  1.090
 1TX  C26  H13  single  0.970  0.020  1.090
 1TX  C14  H24  single  0.970  0.020  1.090
 1TX  N7   H25  single  0.890  0.020  1.040
 1TX  C23  H34  single  0.970  0.020  1.090
 1TX  C23  H35  single  0.970  0.020  1.090
 1TX  N7   H2   single  0.890  0.020  1.040
 1TX  C13  OXT  deloc   1.248  0.020  1.248

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
 1TX  OXT  C13  C14  116.16  3.000
 1TX  OXT  C13  O8   126.44  3.000
 1TX  C14  C13  O8   117.36  3.000
 1TX  H6   C21  H5   106.51  3.000
 1TX  H6   C21  C14  108.90  3.000
 1TX  H5   C21  C14  108.88  3.000
 1TX  H6   C21  C22  109.71  3.000
 1TX  H5   C21  C22  108.71  3.000
 1TX  C14  C21  C22  113.88  3.000
 1TX  H8   C22  H7   106.05  3.000
 1TX  H8   C22  C23  108.54  3.000
 1TX  H7   C22  C23  109.45  3.000
 1TX  H8   C22  C21  110.61  3.000
 1TX  H7   C22  C21  109.07  3.000
 1TX  C23  C22  C21  112.89  3.000
 1TX  H10  C24  H9   105.37  3.000
 1TX  H10  C24  C25  108.72  3.000
 1TX  H9   C24  C25  107.49  3.000
 1TX  H10  C24  C23  110.70  3.000
 1TX  H9   C24  C23  110.20  3.000
 1TX  C25  C24  C23  113.95  3.000
 1TX  H13  C26  H12  109.22  3.000
 1TX  H13  C26  H11  109.19  3.000
 1TX  H12  C26  H11  109.22  3.000
 1TX  H13  C26  O14  111.60  3.000
 1TX  H12  C26  O14  105.96  3.000
 1TX  H11  C26  O14  111.55  3.000
 1TX  H24  C14  N7   108.26  3.000
 1TX  H24  C14  C21  107.09  3.000
 1TX  N7   C14  C21  114.54  3.000
 1TX  H24  C14  C13  107.48  3.000
 1TX  N7   C14  C13  110.55  3.000
 1TX  C21  C14  C13  108.64  3.000
 1TX  H2   N7   H25  106.71  3.000
 1TX  H2   N7   C14  110.64  3.000
 1TX  H25  N7   C14  108.05  3.000
 1TX  H35  C23  H34  106.43  3.000
 1TX  H35  C23  C24  110.05  3.000
 1TX  H34  C23  C24  109.85  3.000
 1TX  H35  C23  C22  109.47  3.000
 1TX  H34  C23  C22  109.32  3.000
 1TX  C24  C23  C22  111.58  3.000
 1TX  O14  C25  O13  123.17  3.000
 1TX  O14  C25  C24  111.47  3.000
 1TX  O13  C25  C24  125.36  3.000
 1TX  C25  O14  C26  117.66  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
 1TX  Var_01  C24  C23  C22  C21  178.84  30.0  1
 1TX  Var_02  C25  C24  C23  C22  179.67  30.0  1
 1TX  Var_03  O13  C25  O14  C26    0.81  30.0  3
 1TX  Var_04  C23  C22  C21  C14  179.44  30.0  1
 1TX  Var_05  H11  C26  O14  C25   61.70  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
 1TX  chir_01  C14  C21  N7  C13  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
 1TX  plan-1  C13  0.020
 1TX  plan-1  O8   0.020
 1TX  plan-1  C14  0.020
 1TX  plan-1  OXT  0.020
 1TX  plan-2  C24  0.020
 1TX  plan-2  C25  0.020
 1TX  plan-2  O13  0.020
 1TX  plan-2  O14  0.020

