# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 23:40:07 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 5-pyrimidin-2-yl-D-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CCCc1ncccn1)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
 ZUK  ZUK  5-pyrimidin-2-yl-D-norvaline  D-peptide  26  14  .  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_ZUK
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
 ZUK  C    C  C      0   0.394  2.8632  4.9259   6.5617
 ZUK  N    N  NH2    0  -0.835  3.3482  2.8345   7.7507
 ZUK  O    O  O      0  -0.605  1.7420  4.4476   6.2902
 ZUK  CA   C  CH1    0  -0.183  3.6336  4.2633   7.7318
 ZUK  CB   C  CH2    0  -0.452  3.2864  5.0295   9.0281
 ZUK  CD   C  CH2    0  -0.525  4.7588  3.6821  10.7098
 ZUK  CE   C  CR6    0   0.376  3.6138  3.0128  11.4074
 ZUK  CG   C  CH2    0  -0.438  4.3714  5.0352  10.1046
 ZUK  CT   C  CR16   0  -0.348  1.5372  1.8563  12.6375
 ZUK  CH1  C  CR16   0  -0.030  2.1444  2.9975  13.1352
 ZUK  CH2  C  CR16   0  -0.018  2.0681  1.3488  11.4667
 ZUK  OXT  O  OC    -1  -0.610  3.4059  5.9099   6.0223
 ZUK  NZ1  N  N      0  -0.402  3.1727  3.5747  12.5309
 ZUK  NZ2  N  N      0  -0.421  3.0989  1.9190  10.8543
 ZUK  HN   H  HNH2   0   0.347  3.4858  2.4360   8.6710
 ZUK  HA   H  HCH1   0   0.188  4.7050  4.4097   7.5459
 ZUK  HT   H  HCR6   0   0.282  0.6983  1.3922  13.1348
 ZUK  HB   H  HCH2   0   0.213  2.3421  4.6472   9.4313
 ZUK  HD   H  HCH2   0   0.248  5.1631  3.0140   9.9487
 ZUK  HG   H  HCH2   0   0.228  4.0566  5.6940  10.9185
 ZUK  HBA  H  HCH2   0   0.224  3.1020  6.0799   8.7834
 ZUK  HDA  H  HCH2   0   0.262  5.5565  3.8494  11.4377
 ZUK  HGA  H  HCH2   0   0.230  5.2766  5.4832   9.6853
 ZUK  HH1  H  HCR6   0   0.276  1.7918  3.4610  14.0502
 ZUK  HH2  H  HCR6   0   0.277  1.6560  0.4592  11.0034
 ZUK  HNA  H  HNH2   0   0.320  2.3604  2.7345   7.5473

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
 ZUK  C    CA   single    1.525  0.021  1.525
 ZUK  N    HN   single    0.890  0.020  1.040
 ZUK  N    CA   single    1.458  0.019  1.458
 ZUK  N    HNA  single    0.890  0.020  1.040
 ZUK  O    C    deloc     1.231  0.020  1.231
 ZUK  CA   HA   single    0.970  0.020  0.970
 ZUK  CA   CB   single    1.521  0.033  1.521
 ZUK  CB   HBA  single    0.970  0.020  1.090
 ZUK  CB   CG   single    1.528  0.020  1.528
 ZUK  CD   HDA  single    0.970  0.020  1.090
 ZUK  CD   CE   single    1.498  0.020  1.498
 ZUK  CE   NZ1  aromatic  1.331  0.020  1.331
 ZUK  CG   CD   single    1.532  0.020  1.532
 ZUK  CG   HGA  single    0.970  0.020  1.090
 ZUK  CT   CH1  aromatic  1.385  0.020  1.385
 ZUK  CT   HT   single    0.930  0.020  1.080
 ZUK  CH1  HH1  single    0.930  0.020  1.080
 ZUK  CH2  CT   aromatic  1.382  0.020  1.382
 ZUK  OXT  C    deloc     1.246  0.020  1.246
 ZUK  NZ1  CH1  aromatic  1.325  0.020  1.325
 ZUK  NZ2  CE   aromatic  1.329  0.020  1.329
 ZUK  NZ2  CH2  aromatic  1.328  0.020  1.328
 ZUK  HB   CB   single    0.970  0.020  1.090
 ZUK  HD   CD   single    0.970  0.020  1.090
 ZUK  HG   CG   single    0.970  0.020  1.090
 ZUK  HH2  CH2  single    0.930  0.020  1.080

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
 ZUK  OXT  C    CA   120.80  1.700
 ZUK  OXT  C    O    126.81  3.000
 ZUK  CA   C    O    120.80  1.700
 ZUK  HNA  N    HN   106.03  3.000
 ZUK  HNA  N    CA   106.57  3.000
 ZUK  HN   N    CA   111.79  3.000
 ZUK  HA   CA   CB   109.00  3.000
 ZUK  CB   CA   N    110.40  1.500
 ZUK  HA   CA   N    110.00  3.000
 ZUK  CB   CA   C    110.50  1.500
 ZUK  HA   CA   C    110.00  3.000
 ZUK  N    CA   C    111.00  2.800
 ZUK  HBA  CB   HB   105.78  3.000
 ZUK  HB   CB   CG   110.73  3.000
 ZUK  HBA  CB   CG   105.88  3.000
 ZUK  HB   CB   CA   109.22  3.000
 ZUK  CG   CB   CA   115.67  3.000
 ZUK  HBA  CB   CA   109.04  3.000
 ZUK  HDA  CD   HD   106.74  3.000
 ZUK  HD   CD   CG   111.05  3.000
 ZUK  HDA  CD   CG   108.21  3.000
 ZUK  HD   CD   CE   109.55  3.000
 ZUK  CG   CD   CE   112.66  3.000
 ZUK  HDA  CD   CE   108.43  3.000
 ZUK  NZ2  CE   NZ1  124.75  3.000
 ZUK  NZ2  CE   CD   118.02  3.000
 ZUK  NZ1  CE   CD   117.23  3.000
 ZUK  HGA  CG   HG   106.08  3.000
 ZUK  HG   CG   CD   108.12  3.000
 ZUK  HGA  CG   CD   107.70  3.000
 ZUK  HG   CG   CB   108.79  3.000
 ZUK  HGA  CG   CB   108.60  3.000
 ZUK  CD   CG   CB   117.03  3.000
 ZUK  HT   CT   CH2  122.04  3.000
 ZUK  CH2  CT   CH1  116.01  3.000
 ZUK  HT   CT   CH1  121.95  3.000
 ZUK  HH1  CH1  NZ1  116.80  3.000
 ZUK  NZ1  CH1  CT   122.36  3.000
 ZUK  HH1  CH1  CT   120.84  3.000
 ZUK  HH2  CH2  NZ2  116.77  3.000
 ZUK  HH2  CH2  CT   121.14  3.000
 ZUK  NZ2  CH2  CT   122.09  3.000
 ZUK  CH1  NZ1  CE   117.27  3.000
 ZUK  CH2  NZ2  CE   117.53  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
 ZUK  CONST_01  CT   CH1  NZ1  CE     0.00   0.0  0
 ZUK  CONST_02  CT   CH2  NZ2  CE     0.00   0.0  0
 ZUK  CONST_03  NZ2  CH2  CT   CH1    0.00   0.0  0
 ZUK  CONST_04  NZ2  CE   NZ1  CH1    0.00   0.0  0
 ZUK  CONST_05  NZ1  CH1  CT   CH2    0.00   0.0  0
 ZUK  CONST_06  NZ1  CE   NZ2  CH2    0.00   0.0  0
 ZUK  CONST_07  CH1  NZ1  CE   CD   180.00   0.0  0
 ZUK  CONST_08  CH2  NZ2  CE   CD   180.00   0.0  0
 ZUK  CONST_09  HH1  CH1  NZ1  CE   180.00   0.0  0
 ZUK  CONST_10  HH2  CH2  NZ2  CE   180.00   0.0  0
 ZUK  CONST_11  HT   CT   CH1  NZ1  180.00   0.0  0
 ZUK  Var_01    NZ1  CE   CD   CG   -68.60  30.0  2
 ZUK  Var_02    CE   CD   CG   CB   -61.58  30.0  3
 ZUK  Var_03    CD   CG   CB   CA   -63.34  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
 ZUK  chir_01  CA  C  N  CB  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
 ZUK  plan-1  CD   0.020
 ZUK  plan-1  CE   0.020
 ZUK  plan-1  CT   0.020
 ZUK  plan-1  CH1  0.020
 ZUK  plan-1  CH2  0.020
 ZUK  plan-1  NZ1  0.020
 ZUK  plan-1  NZ2  0.020
 ZUK  plan-1  HT   0.020
 ZUK  plan-1  HH1  0.020
 ZUK  plan-1  HH2  0.020
 ZUK  plan-2  C    0.020
 ZUK  plan-2  O    0.020
 ZUK  plan-2  CA   0.020
 ZUK  plan-2  OXT  0.020

