# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:59:27 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: pentan-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(N)CC
#
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
 D0M  D0M  'pentan-3-amine           '  ligand  19  6  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D0M
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
 D0M  N1   N  NH2   0  -0.789   0.0535   1.4598  -0.1398
 D0M  C1   C  CH1   0  -0.081   0.0210   0.0468   0.2205
 D0M  C2   C  CH2   0  -0.418  -1.2240  -0.7007  -0.2705
 D0M  C3   C  CH3   0  -0.672  -2.5350  -0.1383   0.2608
 D0M  C4   C  CH2   0  -0.410   1.2893  -0.6406  -0.2820
 D0M  C5   C  CH3   0  -0.658   2.5726  -0.0757   0.3079
 D0M  H1   H  HNH2  0   0.330  -0.0736   1.5511  -1.1425
 D0M  H2   H  HCH1  0   0.205   0.0282  -0.0003   1.3173
 D0M  H3   H  HCH2  0   0.206  -1.2348  -0.6866  -1.3665
 D0M  H4   H  HCH2  0   0.211  -1.1393  -1.7530   0.0177
 D0M  H5   H  HCH3  0   0.217  -2.5560  -0.1466   1.3528
 D0M  H6   H  HCH3  0   0.212  -2.7000   0.8896  -0.0663
 D0M  H7   H  HCH3  0   0.230  -3.3849  -0.7256  -0.0881
 D0M  H8   H  HCH2  0   0.215   1.2186  -1.7080  -0.0546
 D0M  H9   H  HCH2  0   0.206   1.3216  -0.5693  -1.3755
 D0M  H10  H  HCH3  0   0.220   2.6757   0.9846   0.0813
 D0M  H11  H  HCH3  0   0.211   2.5866  -0.1839   1.3945
 D0M  H12  H  HCH3  0   0.221   3.4490  -0.5924  -0.0856
 D0M  H13  H  HNH2  0   0.344  -0.7305   1.9437   0.2794

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
 D0M  N1  C1   single  1.459  0.020  1.459
 D0M  N1  H1   single  0.890  0.020  1.040
 D0M  C1  C2   single  1.533  0.020  1.533
 D0M  C1  C4   single  1.528  0.020  1.528
 D0M  C1  H2   single  0.970  0.020  1.090
 D0M  C2  C3   single  1.522  0.020  1.522
 D0M  C2  H3   single  0.970  0.020  1.090
 D0M  C2  H4   single  0.970  0.020  1.090
 D0M  C3  H5   single  0.970  0.020  1.090
 D0M  C3  H6   single  0.970  0.020  1.090
 D0M  C3  H7   single  0.970  0.020  1.090
 D0M  C4  C5   single  1.521  0.020  1.521
 D0M  C4  H8   single  0.970  0.020  1.090
 D0M  C4  H9   single  0.970  0.020  1.090
 D0M  C5  H10  single  0.970  0.020  1.090
 D0M  C5  H11  single  0.970  0.020  1.090
 D0M  C5  H12  single  0.970  0.020  1.090
 D0M  N1  H13  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
 D0M  H13  N1  H1   105.62  3.000
 D0M  H13  N1  C1   110.10  3.000
 D0M  H1   N1  C1   109.18  3.000
 D0M  H2   C1  C4   107.69  3.000
 D0M  H2   C1  C2   107.72  3.000
 D0M  C4   C1  C2   110.45  3.000
 D0M  H2   C1  N1   106.75  3.000
 D0M  C4   C1  N1   109.65  3.000
 D0M  C2   C1  N1   114.29  3.000
 D0M  H4   C2  H3   106.05  3.000
 D0M  H4   C2  C3   109.27  3.000
 D0M  H3   C2  C3   109.61  3.000
 D0M  H4   C2  C1   108.77  3.000
 D0M  H3   C2  C1   108.79  3.000
 D0M  C3   C2  C1   114.04  3.000
 D0M  H7   C3  H6   107.07  3.000
 D0M  H7   C3  H5   107.51  3.000
 D0M  H6   C3  H5   107.70  3.000
 D0M  H7   C3  C2   111.13  3.000
 D0M  H6   C3  C2   111.94  3.000
 D0M  H5   C3  C2   111.27  3.000
 D0M  H9   C4  H8   105.83  3.000
 D0M  H9   C4  C5   109.74  3.000
 D0M  H8   C4  C5   109.66  3.000
 D0M  H9   C4  C1   108.86  3.000
 D0M  H8   C4  C1   108.49  3.000
 D0M  C5   C4  C1   113.94  3.000
 D0M  H12  C5  H11  107.56  3.000
 D0M  H12  C5  H10  108.06  3.000
 D0M  H11  C5  H10  107.59  3.000
 D0M  H12  C5  C4   111.23  3.000
 D0M  H11  C5  C4   111.09  3.000
 D0M  H10  C5  C4   111.14  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
 D0M  Var_01  C3   C2  C1  N1  -59.68  30.0  3
 D0M  Var_02  C5   C4  C1  N1   60.86  30.0  3
 D0M  Var_03  H5   C3  C2  C1  -58.18  30.0  3
 D0M  Var_04  H10  C5  C4  C1  -59.12  30.0  3
 D0M  Var_05  H1   N1  C1  C2  -53.72  30.0  3

