# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:29:06 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: N-formyl-D-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@@H](NC=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
 DNG  DNG  'N-formyl-D-norleucine    '  D-peptide  23  11  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DNG
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
 DNG  C    C  C      0   0.415  35.1148  8.7492  4.4641
 DNG  N    N  NH1    0  -0.559  36.4482  8.0132  6.4410
 DNG  O    O  O      0  -0.605  34.8590  8.5881  3.2547
 DNG  C1   C  C1     0   0.239  35.8330  7.5471  7.5281
 DNG  O1   O  O      0  -0.502  34.9580  6.6947  7.5532
 DNG  CA   C  CH1    0  -0.224  36.0854  7.6955  5.0781
 DNG  CB   C  CH2    0  -0.431  37.3448  7.4975  4.2351
 DNG  CD   C  CH2    0  -0.425  39.4310  6.0787  3.8240
 DNG  CE   C  CH3    0  -0.664  40.4519  7.2092  3.8044
 DNG  CG   C  CH2    0  -0.411  38.2248  6.3509  4.7193
 DNG  OXT  O  OC    -1  -0.591  34.6710  9.6280  5.2216
 DNG  H    H  HNH1   0   0.388  37.0817  8.7856  6.5775
 DNG  HC1  H  H      0   0.183  36.2220  8.0123  8.4482
 DNG  HA   H  HCH1   0   0.239  35.5457  6.7438  5.1058
 DNG  HB   H  HCH2   0   0.224  37.0362  7.3052  3.2065
 DNG  HBA  H  HCH2   0   0.216  37.9149  8.4331  4.2159
 DNG  HD   H  HCH2   0   0.218  39.9224  5.1637  4.1658
 DNG  HDA  H  HCH2   0   0.208  39.0884  5.8747  2.8047
 DNG  HE   H  HCH3   0   0.214  40.8042  7.4342  4.8132
 DNG  HEA  H  HCH3   0   0.220  40.0374  8.1288  3.3895
 DNG  HEB  H  HCH3   0   0.225  41.3227  6.9445  3.2033
 DNG  HG   H  HCH2   0   0.214  37.6145  5.4438  4.7809
 DNG  HGA  H  HCH2   0   0.208  38.5763  6.5496  5.7363

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
 DNG  O    C    deloc   1.231  0.020  1.231
 DNG  C    CA   single  1.525  0.021  1.525
 DNG  C    OXT  deloc   1.242  0.020  1.242
 DNG  CA   N    single  1.458  0.019  1.458
 DNG  N    H    single  0.860  0.020  0.860
 DNG  N    C1   single  1.333  0.020  1.333
 DNG  O1   C1   double  1.222  0.020  1.222
 DNG  C1   HC1  single  0.930  0.020  1.080
 DNG  CB   CA   single  1.521  0.033  1.521
 DNG  HA   CA   single  0.970  0.020  0.970
 DNG  HB   CB   single  0.970  0.020  1.090
 DNG  HBA  CB   single  0.970  0.020  1.090
 DNG  CB   CG   single  1.524  0.020  1.524
 DNG  HDA  CD   single  0.970  0.020  1.090
 DNG  CE   CD   single  1.523  0.020  1.523
 DNG  CD   HD   single  0.970  0.020  1.090
 DNG  CD   CG   single  1.527  0.020  1.527
 DNG  HEB  CE   single  0.970  0.020  1.090
 DNG  HEA  CE   single  0.970  0.020  1.090
 DNG  CE   HE   single  0.970  0.020  1.090
 DNG  CG   HGA  single  0.970  0.020  1.090
 DNG  CG   HG   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
 DNG  OXT  C   CA   120.80  1.700
 DNG  OXT  C   O    127.57  3.000
 DNG  CA   C   O    120.80  1.700
 DNG  H    N   CA   114.00  3.000
 DNG  H    N   C1   116.57  3.000
 DNG  CA   N   C1   125.18  3.000
 DNG  HC1  C1  O1   122.02  3.000
 DNG  HC1  C1  N    111.74  3.000
 DNG  O1   C1  N    126.24  3.000
 DNG  HA   CA  CB   109.00  3.000
 DNG  HA   CA  N    110.00  3.000
 DNG  CB   CA  N    110.40  1.500
 DNG  HA   CA  C    110.00  3.000
 DNG  CB   CA  C    110.50  1.500
 DNG  N    CA  C    111.00  2.800
 DNG  HBA  CB  HB   106.33  3.000
 DNG  HBA  CB  CG   110.33  3.000
 DNG  HB   CB  CG   109.28  3.000
 DNG  CG   CB  CA   113.45  3.000
 DNG  HBA  CB  CA   109.14  3.000
 DNG  HB   CB  CA   108.05  3.000
 DNG  HDA  CD  HD   106.01  3.000
 DNG  HD   CD  CG   108.72  3.000
 DNG  HDA  CD  CG   109.40  3.000
 DNG  CG   CD  CE   113.87  3.000
 DNG  HD   CD  CE   108.89  3.000
 DNG  HDA  CD  CE   109.64  3.000
 DNG  HEB  CE  HEA  107.36  3.000
 DNG  HEA  CE  HE   107.47  3.000
 DNG  HEB  CE  HE   107.55  3.000
 DNG  HE   CE  CD   110.93  3.000
 DNG  HEA  CE  CD   112.08  3.000
 DNG  HEB  CE  CD   111.23  3.000
 DNG  HGA  CG  HG   106.09  3.000
 DNG  HG   CG  CD   109.00  3.000
 DNG  HGA  CG  CD   108.89  3.000
 DNG  HG   CG  CB   108.61  3.000
 DNG  HGA  CG  CB   110.13  3.000
 DNG  CD   CG  CB   113.83  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
 DNG  CONST_01  CA   N   C1  O1    0.00   0.0  0
 DNG  CONST_02  H    N   C1  O1  180.00   0.0  0
 DNG  Var_01    CD   CG  CB  CA  175.71  30.0  3
 DNG  Var_02    CE   CD  CG  CB   66.10  30.0  1
 DNG  Var_03    HEB  CE  CD  CG  176.42  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
 DNG  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
 DNG  plan-1  N    0.020
 DNG  plan-1  C1   0.020
 DNG  plan-1  O1   0.020
 DNG  plan-1  CA   0.020
 DNG  plan-1  H    0.020
 DNG  plan-1  HC1  0.020
 DNG  plan-2  C    0.020
 DNG  plan-2  O    0.020
 DNG  plan-2  CA   0.020
 DNG  plan-2  OXT  0.020

