# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 16:00:19 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  33  15  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.776   3.8274  -0.6838  -1.6979
 RF9  CA   C  CH1   0  -0.207   3.7730   0.1831  -0.5459
 RF9  C    C  C     0   0.521   4.9812   0.0471   0.3722
 RF9  CB   C  CH2   0  -0.430   2.4923  -0.0637   0.2640
 RF9  CG   C  CH2   0  -0.413   1.2226   0.1951  -0.5351
 RF9  CD   C  CH2   0  -0.440  -0.0353  -0.0468   0.2893
 RF9  CE   C  CH2   0  -0.262  -1.3044   0.3122  -0.4674
 RF9  NZ   N  NH1   0  -0.614  -2.4857  -0.0298   0.3052
 RF9  O1   O  O     0  -0.442   5.7752  -0.8598   0.3319
 RF9  C1   C  CH3   0  -0.652  -4.0234   1.8610   0.0469
 RF9  CX1  C  CH1   0  -0.180  -3.7211   0.4049  -0.3135
 RF9  CX2  C  C     0   0.538  -4.8576  -0.5029   0.1110
 RF9  O3   O  O     0  -0.441  -4.7339  -1.4881   0.7955
 RF9  O2   O  OH1   0  -0.590  -6.0215  -0.1010  -0.3801
 RF9  OXT  O  OH1   0  -0.594   5.0606   1.0441   1.2468
 RF9  H1   H  HNH2  0   0.353   4.6473  -0.4819  -2.2552
 RF9  H2   H  HNH2  0   0.342   3.9146  -1.6491  -1.4043
 RF9  H4   H  HCH1  0   0.265   3.7521   1.2198  -0.8993
 RF9  H5   H  HCH2  0   0.228   2.4960  -1.0959   0.6321
 RF9  H6   H  HCH2  0   0.239   2.4950   0.5791   1.1474
 RF9  H7   H  HCH2  0   0.212   1.2323   1.2288  -0.8974
 RF9  H8   H  HCH2  0   0.224   1.2101  -0.4419  -1.4217
 RF9  H9   H  HCH2  0   0.216  -0.0742  -1.0996   0.5898
 RF9  H10  H  HCH2  0   0.217   0.0016   0.5386   1.2128
 RF9  H11  H  HCH2  0   0.218  -1.3055   1.3886  -0.6604
 RF9  H12  H  HCH2  0   0.195  -1.3005  -0.1746  -1.4559
 RF9  H13  H  HNH1  0   0.347  -2.5043  -1.0332   0.4372
 RF9  H15  H  HCH3  0   0.232  -4.2077   1.9642   1.1165
 RF9  H16  H  HCH3  0   0.241  -3.1708   2.4895  -0.2081
 RF9  H17  H  HCH3  0   0.236  -4.8843   2.2450  -0.4966
 RF9  H18  H  HCH1  0   0.251  -3.6780   0.3262  -1.4141
 RF9  H19  H  HOH1  0   0.484  -6.7243  -0.7107  -0.1092
 RF9  HXT  H  HOH1  0   0.480   5.8223   0.9164   1.8323

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    double  1.206  0.020  1.206
 RF9  CB   CG   single  1.522  0.020  1.522
 RF9  CG   CD   single  1.523  0.020  1.523
 RF9  CD   CE   single  1.521  0.020  1.521
 RF9  CE   NZ   single  1.452  0.020  1.452
 RF9  NZ   CX1  single  1.448  0.020  1.448
 RF9  O3   CX2  double  1.206  0.020  1.206
 RF9  CX1  CX2  single  1.515  0.020  1.515
 RF9  CX1  C1   single  1.530  0.020  1.530
 RF9  CX2  O2   single  1.326  0.020  1.326
 RF9  C    OXT  single  1.329  0.020  1.329
 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
 RF9  O2   H19  single  0.850  0.020  0.980
 RF9  OXT  HXT  single  0.850  0.020  0.980

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   106.27  3.000
 RF9  H2   N    CA   110.15  3.000
 RF9  H1   N    CA   110.51  3.000
 RF9  H4   CA   CB   107.84  3.000
 RF9  H4   CA   C    107.10  3.000
 RF9  CB   CA   C    110.50  1.500
 RF9  H4   CA   N    108.17  3.000
 RF9  C    CA   N    111.00  2.800
 RF9  CB   CA   N    110.40  1.500
 RF9  OXT  C    O1   123.16  3.000
 RF9  OXT  C    CA   120.80  1.700
 RF9  O1   C    CA   124.69  3.000
 RF9  H6   CB   H5   106.41  3.000
 RF9  H6   CB   CG   109.06  3.000
 RF9  H5   CB   CG   109.83  3.000
 RF9  H6   CB   CA   109.26  3.000
 RF9  H5   CB   CA   109.02  3.000
 RF9  CG   CB   CA   113.04  3.000
 RF9  H8   CG   H7   106.39  3.000
 RF9  H8   CG   CD   109.72  3.000
 RF9  H7   CG   CD   109.64  3.000
 RF9  H8   CG   CB   109.67  3.000
 RF9  H7   CG   CB   109.07  3.000
 RF9  CD   CG   CB   112.18  3.000
 RF9  H10  CD   H9   106.49  3.000
 RF9  H10  CD   CE   108.78  3.000
 RF9  H9   CD   CE   109.50  3.000
 RF9  H10  CD   CG   110.13  3.000
 RF9  H9   CD   CG   109.29  3.000
 RF9  CE   CD   CG   112.48  3.000
 RF9  H12  CE   H11  106.05  3.000
 RF9  H12  CE   NZ   112.09  3.000
 RF9  H11  CE   NZ   108.96  3.000
 RF9  H12  CE   CD   109.83  3.000
 RF9  H11  CE   CD   108.73  3.000
 RF9  NZ   CE   CD   111.01  3.000
 RF9  H13  NZ   CX1  109.72  3.000
 RF9  H13  NZ   CE   108.53  3.000
 RF9  CX1  NZ   CE   113.32  3.000
 RF9  H17  C1   H16  107.38  3.000
 RF9  H17  C1   H15  108.84  3.000
 RF9  H16  C1   H15  107.90  3.000
 RF9  H17  C1   CX1  111.99  3.000
 RF9  H16  C1   CX1  109.83  3.000
 RF9  H15  C1   CX1  110.76  3.000
 RF9  H18  CX1  CX2  105.42  3.000
 RF9  H18  CX1  C1   108.08  3.000
 RF9  CX2  CX1  C1   110.85  3.000
 RF9  H18  CX1  NZ   111.78  3.000
 RF9  C1   CX1  NZ   110.70  3.000
 RF9  CX2  CX1  NZ   109.89  3.000
 RF9  O2   CX2  O3   123.23  3.000
 RF9  O2   CX2  CX1  111.91  3.000
 RF9  O3   CX2  CX1  124.85  3.000
 RF9  H19  O2   CX2  110.03  3.000
 RF9  HXT  OXT  C    110.23  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  CONST_01  HXT  OXT  C    CA    180.00   0.0  0
 RF9  CONST_02  H19  O2   CX2  CX1   180.00   0.0  0
 RF9  Var_01    CD   CG   CB   CA   -179.63  30.0  3
 RF9  Var_02    CE   CD   CG   CB    175.58  30.0  3
 RF9  Var_03    NZ   CE   CD   CG    175.44  30.0  3
 RF9  Var_04    CX1  NZ   CE   CD    174.54  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-1  HXT  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
 RF9  plan-2  H19  0.020

