# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 19:50:12 2020
#   Inital geometry file: a 37 line input string
#   Ligand name: propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCN
#
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
 13D  13D  'propane-1,3-diamine      '  ligand  15  5  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_13D
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
 13D  CA    C  CH2   0  -0.276   1.2700   0.5080  -0.0497
 13D  CB    C  CH2   0  -0.438   0.0060  -0.3373  -0.0220
 13D  CC    C  CH2   0  -0.275  -1.2589   0.5071  -0.0093
 13D  ND    N  NH2   0  -0.800  -2.4470  -0.3348   0.0103
 13D  NAA   N  NH2   0  -0.800   2.4587  -0.3338  -0.0542
 13D  HAC1  H  HCH2  0   0.187   1.2407   1.2190   0.7890
 13D  HAC2  H  HCH2  0   0.212   1.2764   1.1123  -0.9613
 13D  HBC1  H  HCH2  0   0.214  -0.0001  -0.9986  -0.8950
 13D  HBC2  H  HCH2  0   0.214   0.0131  -0.9831   0.8624
 13D  HCC1  H  HCH2  0   0.211  -1.2648   1.1273   0.8918
 13D  HCC2  H  HCH2  0   0.187  -1.2296   1.2041  -0.8599
 13D  HDN1  H  HNH2  0   0.345  -3.2740   0.2477   0.0386
 13D  HDN2  H  HNH2  0   0.337  -2.5050  -0.8446  -0.8632
 13D  HAA1  H  HNH2  0   0.345   3.2841   0.2498  -0.1052
 13D  HAA2  H  HNH2  0   0.337   2.5243  -0.8167   0.8339

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
 13D  CA   CB    single  1.521  0.020  1.521
 13D  CA   NAA   single  1.457  0.020  1.457
 13D  CA   HAC1  single  0.970  0.020  1.090
 13D  CA   HAC2  single  0.970  0.020  1.090
 13D  CB   CC    single  1.521  0.020  1.521
 13D  CB   HBC1  single  0.970  0.020  1.090
 13D  CB   HBC2  single  0.970  0.020  1.090
 13D  CC   ND    single  1.456  0.020  1.456
 13D  CC   HCC1  single  0.970  0.020  1.090
 13D  CC   HCC2  single  0.970  0.020  1.090
 13D  ND   HDN1  single  0.890  0.020  1.040
 13D  ND   HDN2  single  0.890  0.020  1.040
 13D  NAA  HAA1  single  0.890  0.020  1.040
 13D  NAA  HAA2  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
 13D  HAC2  CA   HAC1  106.18  3.000
 13D  HAC2  CA   NAA   108.18  3.000
 13D  HAC1  CA   NAA   113.43  3.000
 13D  HAC2  CA   CB    109.09  3.000
 13D  HAC1  CA   CB    108.86  3.000
 13D  NAA   CA   CB    110.92  3.000
 13D  HBC2  CB   HBC1  106.72  3.000
 13D  HBC2  CB   CC    109.03  3.000
 13D  HBC1  CB   CC    109.71  3.000
 13D  HBC2  CB   CA    109.70  3.000
 13D  HBC1  CB   CA    109.01  3.000
 13D  CC    CB   CA    112.50  3.000
 13D  HCC2  CC   HCC1  106.13  3.000
 13D  HCC2  CC   ND    113.48  3.000
 13D  HCC1  CC   ND    108.20  3.000
 13D  HCC2  CC   CB    108.86  3.000
 13D  HCC1  CC   CB    109.04  3.000
 13D  ND    CC   CB    110.95  3.000
 13D  HDN2  ND   HDN1  105.48  3.000
 13D  HDN2  ND   CC    109.03  3.000
 13D  HDN1  ND   CC    109.53  3.000
 13D  HAA2  NAA  HAA1  105.44  3.000
 13D  HAA2  NAA  CA    109.00  3.000
 13D  HAA1  NAA  CA    109.41  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
 13D  Var_01  ND    CC   CB  CA  179.71  30.0  3
 13D  Var_02  NAA   CA   CB  CC  179.71  30.0  1
 13D  Var_03  HAA1  NAA  CA  CB  178.05  30.0  3
 13D  Var_04  HDN1  ND   CC  CB  178.79  30.0  3

