# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:59:47 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: N~6~-[(3R,5R)-5-amino-3-methyl-D-prolyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](N)N[C@H]1C(=O)NCCCC[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
 XPL  XPL  N~6~-[(3R,5R)-5-amino-3-methyl-D-prolyl]-L-lysine  L-peptide  42  19  .  2016-04-26  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_XPL
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
 XPL  C     C  C      0   0.403  20.7275  91.2279  89.0616
 XPL  N     N  NH2    0  -0.814  18.4526  92.1213  88.9867
 XPL  O     O  O      0  -0.600  21.3061  92.1943  88.5256
 XPL  CA    C  CH1    0  -0.152  19.2645  90.9584  88.6201
 XPL  CB    C  CH2    0  -0.437  19.1189  90.7345  87.1148
 XPL  CD    C  CH2    0  -0.493  21.0168  88.9949  86.6995
 XPL  CE    C  CH2    0  -0.237  21.9024  89.8893  85.8471
 XPL  CG    C  CH2    0  -0.441  19.5364  89.3531  86.6124
 XPL  NZ    N  NH1    0  -0.645  23.2774  89.4297  85.9077
 XPL  OXT   O  OC    -1  -0.612  21.1982  90.4704  89.9361
 XPL  C2    C  C      0   0.537  24.2839  90.0404  85.2649
 XPL  N2    N  NH1    0  -0.594  25.7733  88.0326  85.1388
 XPL  O2    O  O      0  -0.491  24.1096  91.0306  84.5668
 XPL  N3    N  NH2    0  -0.794  28.0621  87.5073  84.7896
 XPL  CA2   C  CH1    0  -0.200  25.6690  89.4490  85.4743
 XPL  CD2   C  CH2    0  -0.468  27.3609  88.5765  86.8831
 XPL  CE2   C  CH1    0   0.053  27.0003  87.5546  85.7796
 XPL  CG2   C  CH1    0  -0.247  26.1963  89.5679  86.9136
 XPL  HN    H  HNH2   0   0.331  17.4773  91.9060  88.8153
 XPL  HNA   H  HNH2   0   0.333  18.5181  92.2839  89.9847
 XPL  HA    H  HCH1   0   0.166  18.9236  90.0435  89.1297
 XPL  HB    H  HCH2   0   0.213  18.0608  90.8564  86.8564
 XPL  HBA   H  HCH2   0   0.213  19.6457  91.5284  86.5791
 XPL  HD    H  HCH2   0   0.234  21.1376  87.9598  86.3643
 XPL  HDA   H  HCH2   0   0.233  21.3553  89.0240  87.7374
 XPL  HE    H  HCH2   0   0.223  21.5540  89.8754  84.8100
 XPL  HEA   H  HCH2   0   0.234  21.8432  90.9226  86.1940
 XPL  HG    H  HCH2   0   0.223  18.9710  88.5973  87.1657
 XPL  HGA   H  HCH2   0   0.219  19.2193  89.2542  85.5694
 XPL  HNZ   H  HNH1   0   0.399  23.4768  88.6633  86.5311
 XPL  HN2   H  HNH1   0   0.344  24.9859  87.5184  85.5128
 XPL  HN3   H  HNH2   0   0.340  28.9376  87.2744  85.2438
 XPL  HN3A  H  HNH2   0   0.340  27.8791  86.7563  84.1348
 XPL  HA2   H  HCH1   0   0.242  26.3413  90.0093  84.8158
 XPL  HD2   H  HCH2   0   0.243  27.5236  88.1027  87.8515
 XPL  HD2A  H  HCH2   0   0.229  28.2845  89.0955  86.6112
 XPL  HE2   H  HCH1   0   0.214  26.7859  86.5714  86.2162
 XPL  HG2   H  HCH1   0   0.233  25.4272  89.1860  87.5949
 XPL  CB2   C  CH3    0  -0.659  26.5700  90.9778  87.3328
 XPL  HB2   H  HCH3   0   0.233  26.9849  90.9924  88.3410
 XPL  HB2A  H  HCH3   0   0.220  27.3199  91.3981  86.6593
 XPL  HB2B  H  HCH3   0   0.230  25.7036  91.6413  87.3257

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
 XPL  CA   C     single  1.525  0.033  1.525
 XPL  C    O     deloc   1.231  0.019  1.231
 XPL  C    OXT   deloc   1.249  0.020  1.249
 XPL  CA   N     single  1.458  0.020  1.458
 XPL  N    HN    single  0.890  0.020  1.040
 XPL  N    HNA   single  0.890  0.020  1.040
 XPL  CB   CA    single  1.521  0.020  1.521
 XPL  CA   HA    single  0.970  0.021  0.970
 XPL  CG   CB    single  1.528  0.020  1.528
 XPL  CB   HB    single  0.970  0.020  1.090
 XPL  CB   HBA   single  0.970  0.020  1.090
 XPL  CE   CD    single  1.520  0.020  1.520
 XPL  CG   CD    single  1.526  0.020  1.526
 XPL  CD   HD    single  0.970  0.020  1.090
 XPL  CD   HDA   single  0.970  0.020  1.090
 XPL  CE   NZ    single  1.451  0.020  1.451
 XPL  CE   HE    single  0.970  0.020  1.090
 XPL  CE   HEA   single  0.970  0.020  1.090
 XPL  CG   HG    single  0.970  0.020  1.090
 XPL  CG   HGA   single  0.970  0.020  1.090
 XPL  C2   NZ    single  1.341  0.020  1.341
 XPL  NZ   HNZ   single  0.860  0.020  1.020
 XPL  O2   C2    double  1.224  0.020  1.224
 XPL  C2   CA2   single  1.521  0.020  1.521
 XPL  N2   CA2   single  1.459  0.020  1.459
 XPL  N2   CE2   single  1.464  0.020  1.464
 XPL  N2   HN2   single  0.890  0.020  1.040
 XPL  N3   CE2   single  1.452  0.020  1.452
 XPL  N3   HN3   single  0.890  0.020  1.040
 XPL  N3   HN3A  single  0.890  0.020  1.040
 XPL  CA2  CG2   single  1.537  0.020  1.537
 XPL  CA2  HA2   single  0.970  0.020  1.090
 XPL  CG2  CB2   single  1.518  0.020  1.518
 XPL  CB2  HB2   single  0.970  0.020  1.090
 XPL  CB2  HB2A  single  0.970  0.020  1.090
 XPL  CB2  HB2B  single  0.970  0.020  1.090
 XPL  CE2  CD2   single  1.547  0.020  1.547
 XPL  CD2  CG2   single  1.530  0.020  1.530
 XPL  CD2  HD2   single  0.970  0.020  1.090
 XPL  CD2  HD2A  single  0.970  0.020  1.090
 XPL  CE2  HE2   single  0.970  0.020  1.090
 XPL  CG2  HG2   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
 XPL  OXT   C    CA    114.69  3.000
 XPL  OXT   C    O     126.58  3.000
 XPL  CA    C    O     120.80  1.700
 XPL  HNA   N    HN    105.24  3.000
 XPL  HNA   N    CA    109.76  3.000
 XPL  HN    N    CA    108.81  3.000
 XPL  HA    CA   CB    109.00  3.000
 XPL  HA    CA   N     110.00  3.000
 XPL  CB    CA   N     110.40  1.500
 XPL  HA    CA   C     110.00  3.000
 XPL  CB    CA   C     110.50  1.500
 XPL  N     CA   C     111.00  2.800
 XPL  HBA   CB   HB    105.60  3.000
 XPL  HBA   CB   CG    111.34  3.000
 XPL  HB    CB   CG    106.67  3.000
 XPL  HBA   CB   CA    109.29  3.000
 XPL  HB    CB   CA    107.93  3.000
 XPL  CG    CB   CA    115.47  3.000
 XPL  HDA   CD   HD    106.37  3.000
 XPL  HDA   CD   CG    110.41  3.000
 XPL  HD    CD   CG    108.16  3.000
 XPL  HDA   CD   CE    109.68  3.000
 XPL  HD    CD   CE    108.68  3.000
 XPL  CG    CD   CE    113.28  3.000
 XPL  HEA   CE   HE    107.22  3.000
 XPL  HEA   CE   NZ    109.75  3.000
 XPL  HE    CE   NZ    109.71  3.000
 XPL  HEA   CE   CD    110.32  3.000
 XPL  HE    CE   CD    109.79  3.000
 XPL  NZ    CE   CD    110.01  3.000
 XPL  HGA   CG   HG    105.65  3.000
 XPL  HGA   CG   CD    108.32  3.000
 XPL  HG    CG   CD    108.09  3.000
 XPL  HGA   CG   CB    108.41  3.000
 XPL  HG    CG   CB    108.48  3.000
 XPL  CD    CG   CB    117.30  3.000
 XPL  HNZ   NZ   C2    119.61  3.000
 XPL  HNZ   NZ   CE    117.01  3.000
 XPL  C2    NZ   CE    123.15  3.000
 XPL  CA2   C2   O2    121.53  3.000
 XPL  CA2   C2   NZ    116.14  3.000
 XPL  O2    C2   NZ    122.33  3.000
 XPL  HN2   N2   CE2   108.93  3.000
 XPL  HN2   N2   CA2   110.65  3.000
 XPL  CE2   N2   CA2   106.03  3.000
 XPL  HN3A  N3   HN3   105.99  3.000
 XPL  HN3A  N3   CE2   109.43  3.000
 XPL  HN3   N3   CE2   109.48  3.000
 XPL  HA2   CA2  CG2   108.23  3.000
 XPL  HA2   CA2  N2    108.33  3.000
 XPL  CG2   CA2  N2    105.41  3.000
 XPL  HA2   CA2  C2    106.11  3.000
 XPL  CG2   CA2  C2    114.28  3.000
 XPL  N2    CA2  C2    114.26  3.000
 XPL  HD2A  CD2  HD2   107.52  3.000
 XPL  HD2A  CD2  CG2   109.89  3.000
 XPL  HD2   CD2  CG2   112.18  3.000
 XPL  HD2A  CD2  CE2   109.45  3.000
 XPL  HD2   CD2  CE2   112.43  3.000
 XPL  CG2   CD2  CE2   105.36  3.000
 XPL  HE2   CE2  CD2   110.72  3.000
 XPL  HE2   CE2  N3    112.64  3.000
 XPL  CD2   CE2  N3    109.72  3.000
 XPL  HE2   CE2  N2    107.63  3.000
 XPL  CD2   CE2  N2    106.97  3.000
 XPL  N3    CE2  N2    108.96  3.000
 XPL  HG2   CG2  CD2   108.71  3.000
 XPL  HG2   CG2  CB2   108.95  3.000
 XPL  CD2   CG2  CB2   114.84  3.000
 XPL  HG2   CG2  CA2   108.32  3.000
 XPL  CD2   CG2  CA2   101.09  3.000
 XPL  CB2   CG2  CA2   114.51  3.000
 XPL  HB2B  CB2  HB2A  107.89  3.000
 XPL  HB2B  CB2  HB2   107.46  3.000
 XPL  HB2A  CB2  HB2   107.69  3.000
 XPL  HB2B  CB2  CG2   111.57  3.000
 XPL  HB2A  CB2  CG2   110.87  3.000
 XPL  HB2   CB2  CG2   111.19  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
 XPL  CONST_01  CA2  C2  NZ  CE    180.00   0.0  0
 XPL  CONST_02  HNZ  NZ  C2  CA2     0.00   0.0  0
 XPL  CONST_03  O2   C2  NZ  CE      0.00   0.0  0
 XPL  Var_01    CD   CG  CB  CA    -67.15  30.0  1
 XPL  Var_02    CE   CD  CG  CB    -63.08  30.0  3
 XPL  Var_03    C2   NZ  CE  CD   -179.11  30.0  3
 XPL  Var_04    NZ   CE  CD  CG   -175.99  30.0  1

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
 XPL  chir_01  CA   C    N    CB   negativ
 XPL  chir_02  CA2  C2   N2   CG2  positiv
 XPL  chir_03  CE2  N2   N3   CD2  negativ
 XPL  chir_04  CG2  CD2  CB2  CA2  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
 XPL  plan-1  CE   0.020
 XPL  plan-1  NZ   0.020
 XPL  plan-1  C2   0.020
 XPL  plan-1  O2   0.020
 XPL  plan-1  CA2  0.020
 XPL  plan-1  HNZ  0.020
 XPL  plan-2  C    0.020
 XPL  plan-2  O    0.020
 XPL  plan-2  CA   0.020
 XPL  plan-2  OXT  0.020

