# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:57:00 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: pentane-1,5-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCN
#
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
 N2P  N2P  'pentane-1,5-diamine      '  ligand  21  7  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N2P
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
 N2P  C1    C  CH2   0  -0.271   0.4586  -0.0175   2.5443
 N2P  C2    C  CH2   0  -0.424  -0.3774  -0.0036   1.2736
 N2P  C3    C  CH2   0  -0.423   0.4731  -0.0006   0.0099
 N2P  C4    C  CH2   0  -0.424  -0.3552  -0.0006  -1.2685
 N2P  NE2   N  NH2   0  -0.801  -0.3887   0.0033   3.7290
 N2P  C5    C  CH2   0  -0.271   0.5026   0.0174  -2.5246
 N2P  N1    N  NH2   0  -0.801  -0.3244   0.0075  -3.7233
 N2P  H1C1  H  HCH2  0   0.186   1.1758   0.8157   2.5051
 N2P  H1C2  H  HCH2  0   0.210   1.0560  -0.9335   2.5665
 N2P  H2C1  H  HCH2  0   0.211  -1.0425  -0.8738   1.2722
 N2P  H2C2  H  HCH2  0   0.210  -1.0247   0.8811   1.2761
 N2P  H3C1  H  HCH2  0   0.210   1.1307   0.8759   0.0158
 N2P  H3C2  H  HCH2  0   0.210   1.1340  -0.8746   0.0153
 N2P  H4C1  H  HCH2  0   0.210  -0.9994  -0.8875  -1.2830
 N2P  H4C2  H  HCH2  0   0.211  -1.0238   0.8663  -1.2782
 N2P  HE21  H  HNH2  0   0.344   0.1905  -0.0365   4.5581
 N2P  HE22  H  HNH2  0   0.336  -0.8666   0.8952   3.7770
 N2P  H5C1  H  HCH2  0   0.210   1.1042   0.9310  -2.5312
 N2P  H5C2  H  HCH2  0   0.186   1.2163  -0.8184  -2.4778
 N2P  H1N1  H  HNH2  0   0.344   0.2667   0.0535  -4.5434
 N2P  H1N2  H  HNH2  0   0.336  -0.8045  -0.8823  -3.7860

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
 N2P  C1   C2    single  1.521  0.020  1.521
 N2P  C1   NE2   single  1.457  0.020  1.457
 N2P  C1   H1C1  single  0.970  0.020  1.090
 N2P  C1   H1C2  single  0.970  0.020  1.090
 N2P  C2   C3    single  1.523  0.020  1.523
 N2P  C2   H2C1  single  0.970  0.020  1.090
 N2P  C2   H2C2  single  0.970  0.020  1.090
 N2P  C3   C4    single  1.523  0.020  1.523
 N2P  C3   H3C1  single  0.970  0.020  1.090
 N2P  C3   H3C2  single  0.970  0.020  1.090
 N2P  C4   C5    single  1.521  0.020  1.521
 N2P  C4   H4C1  single  0.970  0.020  1.090
 N2P  C4   H4C2  single  0.970  0.020  1.090
 N2P  NE2  HE21  single  0.890  0.020  1.040
 N2P  NE2  HE22  single  0.890  0.020  1.040
 N2P  C5   N1    single  1.456  0.020  1.456
 N2P  C5   H5C1  single  0.970  0.020  1.090
 N2P  C5   H5C2  single  0.970  0.020  1.090
 N2P  N1   H1N1  single  0.890  0.020  1.040
 N2P  N1   H1N2  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
 N2P  H1C2  C1   H1C1  106.20  3.000
 N2P  H1C2  C1   NE2   108.25  3.000
 N2P  H1C1  C1   NE2   113.41  3.000
 N2P  H1C2  C1   C2    108.95  3.000
 N2P  H1C1  C1   C2    108.76  3.000
 N2P  NE2   C1   C2    111.08  3.000
 N2P  H2C2  C2   H2C1  106.42  3.000
 N2P  H2C2  C2   C3    109.26  3.000
 N2P  H2C1  C2   C3    109.85  3.000
 N2P  H2C2  C2   C1    109.27  3.000
 N2P  H2C1  C2   C1    109.12  3.000
 N2P  C3    C2   C1    112.71  3.000
 N2P  H3C2  C3   H3C1  106.03  3.000
 N2P  H3C2  C3   C4    109.40  3.000
 N2P  H3C1  C3   C4    109.32  3.000
 N2P  H3C2  C3   C2    109.33  3.000
 N2P  H3C1  C3   C2    109.40  3.000
 N2P  C4    C3   C2    113.12  3.000
 N2P  H4C2  C4   H4C1  106.36  3.000
 N2P  H4C2  C4   C5    109.13  3.000
 N2P  H4C1  C4   C5    109.27  3.000
 N2P  H4C2  C4   C3    109.85  3.000
 N2P  H4C1  C4   C3    109.31  3.000
 N2P  C5    C4   C3    112.73  3.000
 N2P  HE22  NE2  HE21  105.42  3.000
 N2P  HE22  NE2  C1    109.00  3.000
 N2P  HE21  NE2  C1    109.44  3.000
 N2P  H5C2  C5   H5C1  106.13  3.000
 N2P  H5C2  C5   N1    113.47  3.000
 N2P  H5C1  C5   N1    108.24  3.000
 N2P  H5C2  C5   C4    108.77  3.000
 N2P  H5C1  C5   C4    108.97  3.000
 N2P  N1    C5   C4    111.06  3.000
 N2P  H1N2  N1   H1N1  105.46  3.000
 N2P  H1N2  N1   C5    109.03  3.000
 N2P  H1N1  N1   C5    109.58  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
 N2P  Var_01  C4    C3   C2  C1  179.43  30.0  3
 N2P  Var_02  C5    C4   C3  C2  179.39  30.0  3
 N2P  Var_03  NE2   C1   C2  C3  179.02  30.0  1
 N2P  Var_04  N1    C5   C4  C3  179.61  30.0  3
 N2P  Var_05  HE21  NE2  C1  C2  178.20  30.0  3
 N2P  Var_06  H1N1  N1   C5  C4  177.97  30.0  3

