# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 10:05:47 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: N-methylpropane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCN
#
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
 N3D  N3D  N-methylpropane-1,3-diamine  ligand  18  6  .  2021-08-26  2021-08-26  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_N3D
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
 N3D  N1    N  NH2   0  -0.800   3.0883  -0.2576   0.0241
 N3D  C2    C  CH2   0  -0.274   1.8517   0.5113   0.0001
 N3D  C3    C  CH2   0  -0.450   0.6405  -0.4089   0.0098
 N3D  C4    C  CH2   0  -0.256  -0.6699   0.3617  -0.0011
 N3D  N5    N  NH1   0  -0.592  -1.8135  -0.5296   0.0085
 N3D  C6    C  CH3   0  -0.517  -3.0735   0.1838  -0.0076
 N3D  HN1   H  HNH2  0   0.345   3.8783   0.3730  -0.0255
 N3D  HN1A  H  HNH2  0   0.337   3.1703  -0.7234   0.9199
 N3D  H2    H  HCH2  0   0.188   1.7633   1.2238   0.8333
 N3D  H2A   H  HCH2  0   0.213   1.8392   1.1094  -0.9152
 N3D  H3    H  HCH2  0   0.216   0.6898  -1.0722  -0.8602
 N3D  H3A   H  HCH2  0   0.216   0.6713  -1.0496   0.8971
 N3D  H4    H  HCH2  0   0.212  -0.7258   0.9948   0.8912
 N3D  H4A   H  HCH2  0   0.183  -0.6818   1.0509  -0.8626
 N3D  HN5   H  HNH1  0   0.339  -1.7659  -1.1290  -0.8064
 N3D  H6    H  HCH3  0   0.230  -3.9016  -0.5227  -0.0677
 N3D  H6A   H  HCH3  0   0.219  -3.1904   0.7493   0.9194
 N3D  H6B   H  HCH3  0   0.190  -3.1783   0.8964  -0.8387

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
 N3D  N1  C2    single  1.456  0.020  1.456
 N3D  C2  C3    single  1.521  0.020  1.521
 N3D  C3  C4    single  1.520  0.020  1.520
 N3D  C4  N5    single  1.450  0.020  1.450
 N3D  N5  C6    single  1.448  0.020  1.448
 N3D  N1  HN1   single  0.890  0.020  1.040
 N3D  N1  HN1A  single  0.890  0.020  1.040
 N3D  C2  H2    single  0.970  0.020  1.090
 N3D  C2  H2A   single  0.970  0.020  1.090
 N3D  C3  H3    single  0.970  0.020  1.090
 N3D  C3  H3A   single  0.970  0.020  1.090
 N3D  C4  H4    single  0.970  0.020  1.090
 N3D  C4  H4A   single  0.970  0.020  1.090
 N3D  N5  HN5   single  0.890  0.020  1.040
 N3D  C6  H6    single  0.970  0.020  1.090
 N3D  C6  H6A   single  0.970  0.020  1.090
 N3D  C6  H6B   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
 N3D  HN1A  N1  HN1  105.46  3.000
 N3D  HN1A  N1  C2   109.03  3.000
 N3D  HN1   N1  C2   109.46  3.000
 N3D  H2A   C2  H2   106.19  3.000
 N3D  H2A   C2  C3   109.09  3.000
 N3D  H2    C2  C3   108.85  3.000
 N3D  H2A   C2  N1   108.20  3.000
 N3D  H2    C2  N1   113.44  3.000
 N3D  C3    C2  N1   110.89  3.000
 N3D  H3A   C3  H3   106.75  3.000
 N3D  H3A   C3  C4   109.07  3.000
 N3D  H3    C3  C4   109.89  3.000
 N3D  H3A   C3  C2   109.68  3.000
 N3D  H3    C3  C2   108.99  3.000
 N3D  C4    C3  C2   112.31  3.000
 N3D  H4A   C4  H4   105.93  3.000
 N3D  H4A   C4  N5   112.37  3.000
 N3D  H4    C4  N5   108.04  3.000
 N3D  H4A   C4  C3   109.37  3.000
 N3D  H4    C4  C3   109.34  3.000
 N3D  N5    C4  C3   111.61  3.000
 N3D  HN5   N5  C6   108.88  3.000
 N3D  HN5   N5  C4   108.75  3.000
 N3D  C6    N5  C4   112.54  3.000
 N3D  H6B   C6  H6A  107.20  3.000
 N3D  H6B   C6  H6   107.81  3.000
 N3D  H6A   C6  H6   107.52  3.000
 N3D  H6B   C6  N5   114.24  3.000
 N3D  H6A   C6  N5   109.80  3.000
 N3D  H6    C6  N5   110.02  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
 N3D  Var_01  C4   C3  C2  N1   179.44  30.0  3
 N3D  Var_02  N5   C4  C3  C2  -179.99  30.0  3
 N3D  Var_03  C6   N5  C4  C3  -179.75  30.0  3
 N3D  Var_04  HN1  N1  C2  C3   177.43  30.0  3
 N3D  Var_05  H6   C6  N5  C4   176.20  30.0  3

