# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 12:48:38 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: N~6~-carbamoyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(N)=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
 YHA  YHA  "Homocitrulline"  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_YHA
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
 YHA  N    N  NH2    0  -0.787  -41.9635  -3.1417   -6.5221
 YHA  CA   C  CH1    0  -0.211  -42.2067  -2.0950   -7.5066
 YHA  C    C  C      0   0.381  -41.8757  -0.6539   -7.0352
 YHA  O    O  O      0  -0.617  -41.8348   0.2167   -7.9296
 YHA  CB   C  CH2    0  -0.407  -43.6592  -2.1501   -7.9902
 YHA  CG   C  CH2    0  -0.424  -44.0476  -3.4712   -8.6424
 YHA  CD   C  CH2    0  -0.412  -45.4738  -3.4668   -9.1738
 YHA  CE   C  CH2    0  -0.320  -45.9043  -4.7740   -9.8341
 YHA  NZ   N  NH1    0  -0.626  -45.1442  -5.1169  -11.0163
 YHA  CX   C  C      0   0.614  -44.0860  -5.9573  -11.1315
 YHA  NQ   N  NH2    0  -0.836  -43.7134  -6.6429  -10.0092
 YHA  OQ   O  O      0  -0.539  -43.5261  -6.1386  -12.2094
 YHA  H2   H  HNH2   0   0.331  -40.9698  -3.1769   -6.3280
 YHA  H    H  HNH2   0   0.320  -42.3759  -2.8377   -5.6466
 YHA  HA   H  HCH1   0   0.201  -41.5714  -2.3102   -8.3746
 YHA  HB2  H  HCH2   0   0.212  -43.8180  -1.3389   -8.7053
 YHA  HB3  H  HCH2   0   0.201  -44.3308  -1.9485   -7.1462
 YHA  HG2  H  HCH2   0   0.212  -43.9264  -4.2813   -7.9176
 YHA  HG3  H  HCH2   0   0.207  -43.3471  -3.6767   -9.4584
 YHA  HD2  H  HCH2   0   0.216  -45.5999  -2.6498   -9.8919
 YHA  HD3  H  HCH2   0   0.218  -46.1706  -3.2618   -8.3549
 YHA  HE2  H  HCH2   0   0.257  -46.9538  -4.7005  -10.1257
 YHA  HE3  H  HCH2   0   0.236  -45.8566  -5.5963   -9.1180
 YHA  HZ1  H  HNH1   0   0.387  -45.3745  -4.6202  -11.8617
 YHA  HQ2  H  HNH2   0   0.391  -42.8304  -7.1210  -10.0754
 YHA  HQ1  H  HNH2   0   0.399  -43.9127  -6.2800   -9.0925
 YHA  OXT  O  OC    -1  -0.602  -41.7021  -0.4765   -5.8130

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
 YHA  OQ  CX   double  1.228  0.020  1.228
 YHA  NZ  CX   single  1.356  0.020  1.356
 YHA  NZ  CE   single  1.447  0.020  1.447
 YHA  CX  NQ   single  1.367  0.020  1.367
 YHA  CE  CD   single  1.526  0.020  1.526
 YHA  CD  CG   single  1.522  0.020  1.522
 YHA  CG  CB   single  1.524  0.020  1.524
 YHA  CB  CA   single  1.530  0.020  1.530
 YHA  CA  C    single  1.525  0.021  1.525
 YHA  CA  N    single  1.458  0.019  1.458
 YHA  O   C    deloc   1.231  0.020  1.231
 YHA  N   H2   single  0.890  0.020  1.040
 YHA  N   H    single  0.860  0.020  0.860
 YHA  CA  HA   single  0.970  0.020  0.970
 YHA  CB  HB2  single  0.970  0.020  1.090
 YHA  CB  HB3  single  0.970  0.020  1.090
 YHA  CG  HG2  single  0.970  0.020  1.090
 YHA  CG  HG3  single  0.970  0.020  1.090
 YHA  CD  HD2  single  0.970  0.020  1.090
 YHA  CD  HD3  single  0.970  0.020  1.090
 YHA  CE  HE2  single  0.970  0.020  1.090
 YHA  CE  HE3  single  0.970  0.020  1.090
 YHA  NZ  HZ1  single  0.860  0.020  1.020
 YHA  NQ  HQ2  single  0.890  0.020  1.040
 YHA  NQ  HQ1  single  0.890  0.020  1.040
 YHA  C   OXT  deloc   1.247  0.020  1.247

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
 YHA  H    N   H2   104.11  3.000
 YHA  H    N   CA   114.00  3.000
 YHA  H2   N   CA   108.55  3.000
 YHA  HA   CA  CB   109.00  3.000
 YHA  HA   CA  C    109.00  3.000
 YHA  CB   CA  C    110.10  1.900
 YHA  HA   CA  N    110.00  3.000
 YHA  C    CA  N    111.00  2.800
 YHA  CB   CA  N    110.50  1.700
 YHA  OXT  C   O    126.74  3.000
 YHA  OXT  C   CA   117.36  3.000
 YHA  O    C   CA   120.80  1.700
 YHA  HB3  CB  HB2  106.14  3.000
 YHA  HB3  CB  CG   109.42  3.000
 YHA  HB2  CB  CG   109.05  3.000
 YHA  HB3  CB  CA   109.32  3.000
 YHA  HB2  CB  CA   108.52  3.000
 YHA  CG   CB  CA   114.08  3.000
 YHA  HG3  CG  HG2  106.50  3.000
 YHA  HG3  CG  CD   109.86  3.000
 YHA  HG2  CG  CD   109.72  3.000
 YHA  HG3  CG  CB   108.58  3.000
 YHA  HG2  CG  CB   109.29  3.000
 YHA  CD   CG  CB   112.69  3.000
 YHA  HD3  CD  HD2  106.12  3.000
 YHA  HD3  CD  CE   107.73  3.000
 YHA  HD2  CD  CE   108.83  3.000
 YHA  HD3  CD  CG   109.62  3.000
 YHA  HD2  CD  CG   109.82  3.000
 YHA  CE   CD  CG   114.38  3.000
 YHA  HE3  CE  HE2  105.54  3.000
 YHA  HE3  CE  NZ   109.55  3.000
 YHA  HE2  CE  NZ   107.63  3.000
 YHA  HE3  CE  CD   110.43  3.000
 YHA  HE2  CE  CD   109.20  3.000
 YHA  NZ   CE  CD   114.10  3.000
 YHA  HZ1  NZ  CX   114.38  3.000
 YHA  HZ1  NZ  CE   116.67  3.000
 YHA  CX   NZ  CE   128.77  3.000
 YHA  OQ   CX  NQ   121.49  3.000
 YHA  NQ   CX  NZ   116.98  3.000
 YHA  OQ   CX  NZ   121.45  3.000
 YHA  HQ1  NQ  HQ2  113.91  3.000
 YHA  HQ1  NQ  CX   120.89  3.000
 YHA  HQ2  NQ  CX   115.05  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
 YHA  CONST_01  OQ   CX  NZ  CE   180.00   0.0  0
 YHA  CONST_02  NQ   CX  NZ  CE     0.00   0.0  0
 YHA  CONST_03  HZ1  NZ  CX  OQ     0.00   0.0  0
 YHA  CONST_04  HQ2  NQ  CX  OQ     0.00   0.0  0
 YHA  CONST_06  HQ2  NQ  CX  NZ   180.00   0.0  0
 YHA  CONST_08  HZ1  NZ  CX  NQ   180.00   0.0  0
 YHA  Var_01    CD   CG  CB  CA  -177.09  30.0  1
 YHA  Var_02    CE   CD  CG  CB  -179.92  30.0  1
 YHA  Var_03    NZ   CE  CD  CG   -63.10  30.0  1
 YHA  Var_04    CX   NZ  CE  CD    97.40  30.0  1
 YHA  Var_05    HG2  CG  CB  CA    60.64  30.0  1
 YHA  Var_06    HG3  CG  CB  CA   -55.14  30.0  1
 YHA  Var_07    HD2  CD  CG  CB    57.39  30.0  1
 YHA  Var_08    HD3  CD  CG  CB   -58.83  30.0  1
 YHA  Var_09    HE2  CE  CD  CG   176.44  30.0  1
 YHA  Var_10    HE3  CE  CD  CG    60.81  30.0  1
 YHA  Var_11    HZ1  NZ  CE  CD   -77.39  30.0  1
 YHA  Var_12    HB2  CB  CG  CD   -55.60  30.0  3
 YHA  Var_13    HB3  CB  CG  CD    60.10  30.0  3
 YHA  Var_14    HG2  CG  CD  CE   -57.90  30.0  3
 YHA  Var_15    HG3  CG  CD  CE    58.86  30.0  3
 YHA  Var_16    HD2  CD  CE  NZ    60.12  30.0  3
 YHA  Var_17    HD3  CD  CE  NZ   174.77  30.0  3
 YHA  Var_18    HE2  CE  NZ  CX  -141.25  30.0  3
 YHA  Var_19    HE3  CE  NZ  CX   -26.97  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
 YHA  chir_01  CA  CB  C  N  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
 YHA  plan-1  CE   0.020
 YHA  plan-1  NZ   0.020
 YHA  plan-1  CX   0.020
 YHA  plan-1  NQ   0.020
 YHA  plan-1  OQ   0.020
 YHA  plan-1  HZ1  0.020
 YHA  plan-1  HQ2  0.020
 YHA  plan-1  HQ1  0.020
 YHA  plan-2  CA   0.020
 YHA  plan-2  C    0.020
 YHA  plan-2  O    0.020
 YHA  plan-2  OXT  0.020

