# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:43:34 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: N~6~-[(1R)-1-carboxyethyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NCCCC[C@H](N)C(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
 RF9  RF9  N~6~-[(1R)-1-carboxyethyl]-L-lysine  L-peptide  31  15  .  2022-07-22  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_RF9
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
 RF9  N    N  NH2    0  -0.787   3.8151  -0.6299  -1.7171
 RF9  CA   C  CH1    0  -0.212   3.7805   0.1909  -0.5147
 RF9  C    C  C      0   0.384   4.9947   0.0237   0.4331
 RF9  CB   C  CH2    0  -0.412   2.4925  -0.0693   0.2722
 RF9  CG   C  CH2    0  -0.405   1.2168   0.1958  -0.5153
 RF9  CD   C  CH2    0  -0.436  -0.0442  -0.0172   0.3124
 RF9  CE   C  CH2    0  -0.252  -1.3179   0.3031  -0.4550
 RF9  NZ   N  NH1    0  -0.614  -2.4974   0.0495   0.3451
 RF9  O1   O  O      0  -0.609   5.7392  -0.9604   0.2505
 RF9  C1   C  CH3    0  -0.642  -4.1130   1.8472  -0.0449
 RF9  CX1  C  CH1    0  -0.198  -3.7467   0.3926  -0.3114
 RF9  CX2  C  C      0   0.411  -4.8804  -0.5764   0.1075
 RF9  O3   O  O      0  -0.608  -4.5397  -1.6617   0.6233
 RF9  O2   O  OC    -1  -0.610  -6.0445  -0.2109  -0.1415
 RF9  OXT  O  OC    -1  -0.625   5.1122   0.8851   1.3304
 RF9  H1   H  HNH2   0   0.332   4.5883  -0.3223  -2.2951
 RF9  H2   H  HNH2   0   0.321   4.0719  -1.5710  -1.4398
 RF9  H4   H  HCH1   0   0.204   3.7571   1.2391  -0.8367
 RF9  H5   H  HCH2   0   0.200   2.4912  -1.1074   0.6289
 RF9  H6   H  HCH2   0   0.212   2.5036   0.5600   1.1655
 RF9  H7   H  HCH2   0   0.198   1.2351   1.2252  -0.8918
 RF9  H8   H  HCH2   0   0.210   1.1947  -0.4493  -1.3967
 RF9  H9   H  HCH2   0   0.205  -0.0807  -1.0570   0.6575
 RF9  H10  H  HCH2   0   0.206  -0.0100   0.6051   1.2124
 RF9  H11  H  HCH2   0   0.202  -1.3005   1.3604  -0.7387
 RF9  H12  H  HCH2   0   0.175  -1.3246  -0.2624  -1.4036
 RF9  H13  H  HNH1   0   0.328  -2.5445  -0.9367   0.5733
 RF9  H15  H  HCH3   0   0.207  -4.3117   2.0092   1.0164
 RF9  H16  H  HCH3   0   0.210  -3.3004   2.5167  -0.3343
 RF9  H17  H  HCH3   0   0.213  -4.9975   2.1442  -0.6054
 RF9  H18  H  HCH1   0   0.191  -3.6535   0.2670  -1.4071

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
 RF9  N    CA   single  1.458  0.019  1.458
 RF9  CA   CB   single  1.521  0.033  1.521
 RF9  CA   C    single  1.525  0.021  1.525
 RF9  O1   C    deloc   1.247  0.020  1.247
 RF9  CB   CG   single  1.523  0.020  1.523
 RF9  CG   CD   single  1.523  0.020  1.523
 RF9  CD   CE   single  1.521  0.020  1.521
 RF9  CE   NZ   single  1.448  0.020  1.448
 RF9  NZ   CX1  single  1.452  0.020  1.452
 RF9  O3   CX2  deloc   1.249  0.020  1.249
 RF9  CX1  CX2  single  1.549  0.020  1.549
 RF9  CX1  C1   single  1.524  0.020  1.524
 RF9  CX2  O2   deloc   1.245  0.020  1.245
 RF9  C    OXT  deloc   1.249  0.020  1.249
 RF9  N    H1   single  0.890  0.020  1.040
 RF9  N    H2   single  0.890  0.020  1.040
 RF9  CA   H4   single  0.970  0.020  1.090
 RF9  CB   H5   single  0.970  0.020  1.090
 RF9  CB   H6   single  0.970  0.020  1.090
 RF9  CG   H7   single  0.970  0.020  1.090
 RF9  CG   H8   single  0.970  0.020  1.090
 RF9  CD   H9   single  0.970  0.020  1.090
 RF9  CD   H10  single  0.970  0.020  1.090
 RF9  CE   H11  single  0.970  0.020  1.090
 RF9  CE   H12  single  0.970  0.020  1.090
 RF9  NZ   H13  single  0.890  0.020  1.040
 RF9  C1   H15  single  0.970  0.020  1.090
 RF9  C1   H16  single  0.970  0.020  1.090
 RF9  C1   H17  single  0.970  0.020  1.090
 RF9  CX1  H18  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
 RF9  H2   N    H1   104.15  3.000
 RF9  H2   N    CA   107.65  3.000
 RF9  H1   N    CA   108.54  3.000
 RF9  H4   CA   CB   107.18  3.000
 RF9  H4   CA   C    107.43  3.000
 RF9  CB   CA   C    110.50  1.500
 RF9  H4   CA   N    107.26  3.000
 RF9  C    CA   N    111.00  2.800
 RF9  CB   CA   N    110.40  1.500
 RF9  OXT  C    O1   126.36  3.000
 RF9  OXT  C    CA   120.80  1.700
 RF9  O1   C    CA   117.61  3.000
 RF9  H6   CB   H5   106.20  3.000
 RF9  H6   CB   CG   109.33  3.000
 RF9  H5   CB   CG   109.37  3.000
 RF9  H6   CB   CA   108.28  3.000
 RF9  H5   CB   CA   109.19  3.000
 RF9  CG   CB   CA   114.16  3.000
 RF9  H8   CG   H7   106.13  3.000
 RF9  H8   CG   CD   109.82  3.000
 RF9  H7   CG   CD   109.38  3.000
 RF9  H8   CG   CB   109.36  3.000
 RF9  H7   CG   CB   109.09  3.000
 RF9  CD   CG   CB   112.84  3.000
 RF9  H10  CD   H9   106.35  3.000
 RF9  H10  CD   CE   108.74  3.000
 RF9  H9   CD   CE   109.31  3.000
 RF9  H10  CD   CG   109.96  3.000
 RF9  H9   CD   CG   109.35  3.000
 RF9  CE   CD   CG   112.93  3.000
 RF9  H12  CE   H11  105.79  3.000
 RF9  H12  CE   NZ   112.34  3.000
 RF9  H11  CE   NZ   108.99  3.000
 RF9  H12  CE   CD   109.30  3.000
 RF9  H11  CE   CD   108.70  3.000
 RF9  NZ   CE   CD   111.50  3.000
 RF9  H13  NZ   CX1  106.96  3.000
 RF9  H13  NZ   CE   109.44  3.000
 RF9  CX1  NZ   CE   114.18  3.000
 RF9  H17  C1   H16  107.52  3.000
 RF9  H17  C1   H15  108.19  3.000
 RF9  H16  C1   H15  107.59  3.000
 RF9  H17  C1   CX1  111.46  3.000
 RF9  H16  C1   CX1  111.11  3.000
 RF9  H15  C1   CX1  110.82  3.000
 RF9  H18  CX1  CX2  104.97  3.000
 RF9  H18  CX1  C1   107.57  3.000
 RF9  CX2  CX1  C1   111.96  3.000
 RF9  H18  CX1  NZ   110.38  3.000
 RF9  C1   CX1  NZ   110.69  3.000
 RF9  CX2  CX1  NZ   111.07  3.000
 RF9  O2   CX2  O3   126.35  3.000
 RF9  O2   CX2  CX1  116.51  3.000
 RF9  O3   CX2  CX1  117.11  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
 RF9  Var_01  CD   CG  CB  CA  -177.64  30.0  3
 RF9  Var_02  CE   CD  CG  CB   177.60  30.0  3
 RF9  Var_03  NZ   CE  CD  CG   178.16  30.0  3
 RF9  Var_04  CX1  NZ  CE  CD   177.40  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
 RF9  chir_01  CA   N   CB   C   negativ
 RF9  chir_02  CX1  NZ  CX2  C1  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
 RF9  plan-1  CA   0.020
 RF9  plan-1  C    0.020
 RF9  plan-1  O1   0.020
 RF9  plan-1  OXT  0.020
 RF9  plan-2  CX1  0.020
 RF9  plan-2  CX2  0.020
 RF9  plan-2  O3   0.020
 RF9  plan-2  O2   0.020

