# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:05:19 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 6-aminohexanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCC=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
 DNL  DNL  '6-aminohexanal           '  L-peptide  21  8  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DNL
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
 DNL  CA   C  CH2   0  -0.545  -1.9782   0.5870  -0.0901
 DNL  C    C  C1    0   0.189  -3.2211  -0.2082  -0.3305
 DNL  O    O  O     0  -0.383  -4.1781  -0.2517   0.4032
 DNL  CB   C  CH2   0  -0.435  -0.7279  -0.2919  -0.1681
 DNL  CG   C  CH2   0  -0.416   0.5540   0.5177  -0.0204
 DNL  CD   C  CH2   0  -0.426   1.8074  -0.3453  -0.0781
 DNL  CE   C  CH2   0  -0.272   3.0857   0.4681   0.0548
 DNL  NZ   N  NH2   0  -0.801   4.2592  -0.3932   0.0110
 DNL  HA2  H  HCH2  0   0.261  -1.9269   1.3463  -0.8796
 DNL  HA   H  HCH2  0   0.249  -2.0405   1.1048   0.8688
 DNL  H    H  H     0   0.180  -3.2100  -0.7876  -1.2727
 DNL  HB1  H  HCH2  0   0.227  -0.7143  -0.8262  -1.1235
 DNL  HB2  H  HCH2  0   0.232  -0.7706  -1.0566   0.6131
 DNL  HG1  H  HCH2  0   0.217   0.5298   1.0646   0.9282
 DNL  HG2  H  HCH2  0   0.216   0.5942   1.2764  -0.8095
 DNL  HD1  H  HCH2  0   0.214   1.8329  -0.9021  -1.0203
 DNL  HD2  H  HCH2  0   0.213   1.7686  -1.0926   0.7227
 DNL  HE1  H  HCH2  0   0.187   3.0247   1.0794   0.9675
 DNL  HE2  H  HCH2  0   0.212   3.1476   1.1728  -0.7793
 DNL  HZ1  H  HNH2  0   0.345   5.0969   0.1732   0.0522
 DNL  HZ2  H  HNH2  0   0.337   4.2795  -0.9670   0.8454

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
 DNL  CA  C    single  1.525  0.021  1.525
 DNL  CA  CB   single  1.530  0.020  1.530
 DNL  CA  HA2  single  0.970  0.020  1.090
 DNL  CA  HA   single  0.970  0.020  0.970
 DNL  C   O    double  1.231  0.020  1.231
 DNL  C   H    single  0.930  0.020  1.080
 DNL  CB  CG   single  1.523  0.020  1.523
 DNL  CB  HB1  single  0.970  0.020  1.090
 DNL  CB  HB2  single  0.970  0.020  1.090
 DNL  CG  CD   single  1.523  0.020  1.523
 DNL  CG  HG1  single  0.970  0.020  1.090
 DNL  CG  HG2  single  0.970  0.020  1.090
 DNL  CD  CE   single  1.521  0.020  1.521
 DNL  CD  HD1  single  0.970  0.020  1.090
 DNL  CD  HD2  single  0.970  0.020  1.090
 DNL  CE  NZ   single  1.456  0.020  1.456
 DNL  CE  HE1  single  0.970  0.020  1.090
 DNL  CE  HE2  single  0.970  0.020  1.090
 DNL  NZ  HZ1  single  0.890  0.020  1.040
 DNL  NZ  HZ2  single  0.890  0.020  1.040

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
 DNL  HA   CA  HA2  107.86  3.000
 DNL  HA   CA  CB   109.00  3.000
 DNL  HA2  CA  CB   108.84  3.000
 DNL  HA   CA  C    109.00  3.000
 DNL  HA2  CA  C    106.94  3.000
 DNL  CB   CA  C    110.10  1.900
 DNL  H    C   O    120.46  3.000
 DNL  H    C   CA   114.04  3.000
 DNL  O    C   CA   120.80  1.700
 DNL  HB2  CB  HB1  106.41  3.000
 DNL  HB2  CB  CG   109.58  3.000
 DNL  HB1  CB  CG   109.48  3.000
 DNL  HB2  CB  CA   109.47  3.000
 DNL  HB1  CB  CA   109.57  3.000
 DNL  CG   CB  CA   112.17  3.000
 DNL  HG2  CG  HG1  106.20  3.000
 DNL  HG2  CG  CD   109.57  3.000
 DNL  HG1  CG  CD   109.51  3.000
 DNL  HG2  CG  CB   109.22  3.000
 DNL  HG1  CG  CB   109.32  3.000
 DNL  CD   CG  CB   112.81  3.000
 DNL  HD2  CD  HD1  106.44  3.000
 DNL  HD2  CD  CE   109.30  3.000
 DNL  HD1  CD  CE   109.12  3.000
 DNL  HD2  CD  CG   109.24  3.000
 DNL  HD1  CD  CG   109.88  3.000
 DNL  CE   CD  CG   112.67  3.000
 DNL  HE2  CE  HE1  106.12  3.000
 DNL  HE2  CE  NZ   108.21  3.000
 DNL  HE1  CE  NZ   113.47  3.000
 DNL  HE2  CE  CD   109.00  3.000
 DNL  HE1  CE  CD   108.85  3.000
 DNL  NZ   CE  CD   111.00  3.000
 DNL  HZ2  NZ  HZ1  105.48  3.000
 DNL  HZ2  NZ  CE   109.05  3.000
 DNL  HZ1  NZ  CE   109.56  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
 DNL  Var_01  CD   CG  CB  CA  179.27  30.0  3
 DNL  Var_02  CG   CB  CA  C   176.09  30.0  3
 DNL  Var_03  CB   CA  C   O   126.05  30.0  2
 DNL  Var_04  CE   CD  CG  CB  179.39  30.0  3
 DNL  Var_05  NZ   CE  CD  CG  179.32  30.0  3
 DNL  Var_06  HZ1  NZ  CE  CD  177.06  30.0  3

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
 DNL  plan-1  CA  0.020
 DNL  plan-1  C   0.020
 DNL  plan-1  O   0.020
 DNL  plan-1  H   0.020

