# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:09:50 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: N-(3-aminopropyl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNCCCN
#
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
 NSD  NSD  N-(3-aminopropyl)propane-1,3-diamine  ligand  26  9  .  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_NSD
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
 NSD  C1    C  CH2   0  -0.274  -3.7310  -0.4114   0.0434
 NSD  N1    N  NH2   0  -0.800  -4.8992   0.4585   0.0116
 NSD  C2    C  CH2   0  -0.452  -2.4480   0.4046   0.0007
 NSD  N2    N  NH1   0  -0.599   0.0063   0.3268   0.0077
 NSD  C3    C  CH2   0  -0.253  -1.2050  -0.4700   0.0410
 NSD  N3    N  NH2   0  -0.800   4.9133   0.4252   0.0024
 NSD  C4    C  CH2   0  -0.253   1.2128  -0.4773   0.0376
 NSD  C5    C  CH2   0  -0.452   2.4614   0.3890  -0.0060
 NSD  C6    C  CH2   0  -0.274   3.7389  -0.4355   0.0328
 NSD  H1    H  HCH2  0   0.189  -3.7041  -1.0738   0.9210
 NSD  H1A   H  HCH2  0   0.213  -3.7686  -1.0658  -0.8319
 NSD  HN1   H  HNH2  0   0.345  -5.7393  -0.1057   0.0068
 NSD  HN1A  H  HNH2  0   0.337  -4.9368   0.9908   0.8727
 NSD  H2    H  HCH2  0   0.216  -2.4448   1.0156  -0.9080
 NSD  H2A   H  HCH2  0   0.217  -2.4238   1.0984   0.8475
 NSD  H7    H  HNH1  0   0.334   0.0069   0.8819  -0.8412
 NSD  H3    H  HCH2  0   0.212  -1.2032  -1.0534   0.9679
 NSD  H3A   H  HCH2  0   0.183  -1.2490  -1.2050  -0.7802
 NSD  HN3   H  HNH2  0   0.337   4.9574   0.9542   0.8651
 NSD  HN3A  H  HNH2  0   0.345   5.7490  -0.1454  -0.0070
 NSD  H5    H  HCH2  0   0.216   2.4588   1.0011  -0.9141
 NSD  H5A   H  HCH2  0   0.216   2.4448   1.0818   0.8418
 NSD  H6    H  HCH2  0   0.213   3.7711  -1.0883  -0.8440
 NSD  H6A   H  HCH2  0   0.188   3.7067  -1.1000   0.9089
 NSD  H4    H  HCH2  0   0.212   1.2101  -1.0605   0.9648
 NSD  H17   H  HCH2  0   0.183   1.2500  -1.2126  -0.7837

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
 NSD  C1  N1    single  1.457  0.020  1.457
 NSD  C2  C1    single  1.521  0.020  1.521
 NSD  N2  C3    single  1.450  0.020  1.450
 NSD  C3  C2    single  1.520  0.020  1.520
 NSD  C4  N2    single  1.450  0.020  1.450
 NSD  C5  C4    single  1.520  0.020  1.520
 NSD  C6  N3    single  1.456  0.020  1.456
 NSD  C6  C5    single  1.521  0.020  1.521
 NSD  C1  H1    single  0.970  0.020  1.090
 NSD  C1  H1A   single  0.970  0.020  1.090
 NSD  N1  HN1   single  0.890  0.020  1.040
 NSD  N1  HN1A  single  0.890  0.020  1.040
 NSD  C2  H2    single  0.970  0.020  1.090
 NSD  C2  H2A   single  0.970  0.020  1.090
 NSD  N2  H7    single  0.890  0.020  1.040
 NSD  C3  H3    single  0.970  0.020  1.090
 NSD  C3  H3A   single  0.970  0.020  1.090
 NSD  N3  HN3   single  0.890  0.020  1.040
 NSD  N3  HN3A  single  0.890  0.020  1.040
 NSD  C5  H5    single  0.970  0.020  1.090
 NSD  C5  H5A   single  0.970  0.020  1.090
 NSD  C6  H6    single  0.970  0.020  1.090
 NSD  C6  H6A   single  0.970  0.020  1.090
 NSD  C4  H4    single  0.970  0.020  1.090
 NSD  C4  H17   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
 NSD  H1A   C1  H1   106.21  3.000
 NSD  H1A   C1  C2   109.12  3.000
 NSD  H1    C1  C2   108.96  3.000
 NSD  H1A   C1  N1   108.19  3.000
 NSD  H1    C1  N1   113.37  3.000
 NSD  C2    C1  N1   110.82  3.000
 NSD  HN1A  N1  HN1  105.43  3.000
 NSD  HN1A  N1  C1   108.96  3.000
 NSD  HN1   N1  C1   109.44  3.000
 NSD  H2A   C2  H2   106.75  3.000
 NSD  H2A   C2  C3   109.02  3.000
 NSD  H2    C2  C3   109.91  3.000
 NSD  H2A   C2  C1   109.69  3.000
 NSD  H2    C2  C1   108.97  3.000
 NSD  C3    C2  C1   112.35  3.000
 NSD  H7    N2  C4   108.68  3.000
 NSD  H7    N2  C3   108.68  3.000
 NSD  C4    N2  C3   112.94  3.000
 NSD  H3A   C3  H3   105.98  3.000
 NSD  H3A   C3  N2   112.48  3.000
 NSD  H3    C3  N2   108.10  3.000
 NSD  H3A   C3  C2   109.33  3.000
 NSD  H3    C3  C2   109.28  3.000
 NSD  N2    C3  C2   111.48  3.000
 NSD  HN3A  N3  HN3  105.45  3.000
 NSD  HN3A  N3  C6   109.45  3.000
 NSD  HN3   N3  C6   109.02  3.000
 NSD  H17   C4  H4   105.98  3.000
 NSD  H17   C4  C5   109.31  3.000
 NSD  H4    C4  C5   109.25  3.000
 NSD  H17   C4  N2   112.48  3.000
 NSD  H4    C4  N2   108.10  3.000
 NSD  C5    C4  N2   111.51  3.000
 NSD  H5A   C5  H5   106.76  3.000
 NSD  H5A   C5  C6   109.63  3.000
 NSD  H5    C5  C6   109.03  3.000
 NSD  H5A   C5  C4   109.01  3.000
 NSD  H5    C5  C4   109.89  3.000
 NSD  C6    C5  C4   112.34  3.000
 NSD  H6A   C6  H6   106.19  3.000
 NSD  H6A   C6  C5   108.86  3.000
 NSD  H6    C6  C5   109.15  3.000
 NSD  H6A   C6  N3   113.40  3.000
 NSD  H6    C6  N3   108.19  3.000
 NSD  C5    C6  N3   110.88  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
 NSD  Var_01  N2   C3  C2  C1  -179.65  30.0  1
 NSD  Var_02  C3   C2  C1  N1   179.65  30.0  1
 NSD  Var_03  C4   N2  C3  C2  -179.69  30.0  1
 NSD  Var_04  C6   C5  C4  N2   179.66  30.0  1
 NSD  Var_05  C5   C4  N2  C3   179.69  30.0  1
 NSD  Var_06  C4   C5  C6  N3  -179.46  30.0  3
 NSD  Var_07  HN1  N1  C1  C2   177.96  30.0  3
 NSD  Var_08  HN3  N3  C6  C5    67.29  30.0  3

