# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:53:55 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: pentan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCN
#
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
 AML  AML  'pentan-1-amine           '  ligand  19  6  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AML
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
 AML  C1    C  CH3   0  -0.662  -0.2343   0.0368   3.1963
 AML  C2    C  CH2   0  -0.417   0.5397  -0.0250   1.8866
 AML  C3    C  CH2   0  -0.412  -0.3698   0.0092   0.6640
 AML  C4    C  CH2   0  -0.424   0.3909  -0.0360  -0.6546
 AML  C5    C  CH2   0  -0.271  -0.5277  -0.0067  -1.8669
 AML  N1    N  NH2   0  -0.801   0.2384  -0.0410  -3.1054
 AML  HC11  H  HCH3  0   0.226   0.4303   0.0049   4.0604
 AML  HC12  H  HCH3  0   0.216  -0.8195   0.9562   3.2632
 AML  HC13  H  HCH3  0   0.215  -0.9293  -0.8010   3.2833
 AML  HC21  H  HCH2  0   0.210   1.2433   0.8117   1.8362
 AML  HC22  H  HCH2  0   0.211   1.1475  -0.9348   1.8601
 AML  HC31  H  HCH2  0   0.207  -1.0696  -0.8329   0.7120
 AML  HC32  H  HCH2  0   0.207  -0.9855   0.9152   0.6995
 AML  HC41  H  HCH2  0   0.209   1.0810   0.8145  -0.7035
 AML  HC42  H  HCH2  0   0.210   1.0099  -0.9382  -0.6966
 AML  HC51  H  HCH2  0   0.210  -1.1769  -0.8864  -1.8412
 AML  HC52  H  HCH2  0   0.185  -1.1919   0.8665  -1.7871
 AML  HN11  H  HNH2  0   0.344  -0.3944  -0.0632  -3.8949
 AML  HN12  H  HNH2  0   0.336   0.7549   0.8257  -3.1978

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
 AML  C1  C2    single  1.523  0.020  1.523
 AML  C1  HC11  single  0.970  0.020  1.090
 AML  C1  HC12  single  0.970  0.020  1.090
 AML  C1  HC13  single  0.970  0.020  1.090
 AML  C2  C3    single  1.524  0.020  1.524
 AML  C2  HC21  single  0.970  0.020  1.090
 AML  C2  HC22  single  0.970  0.020  1.090
 AML  C3  C4    single  1.523  0.020  1.523
 AML  C3  HC31  single  0.970  0.020  1.090
 AML  C3  HC32  single  0.970  0.020  1.090
 AML  C4  C5    single  1.521  0.020  1.521
 AML  C4  HC41  single  0.970  0.020  1.090
 AML  C4  HC42  single  0.970  0.020  1.090
 AML  C5  N1    single  1.457  0.020  1.457
 AML  C5  HC51  single  0.970  0.020  1.090
 AML  C5  HC52  single  0.970  0.020  1.090
 AML  N1  HN11  single  0.890  0.020  1.040
 AML  N1  HN12  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
 AML  HC13  C1  HC12  107.46  3.000
 AML  HC13  C1  HC11  107.60  3.000
 AML  HC12  C1  HC11  107.62  3.000
 AML  HC13  C1  C2    111.15  3.000
 AML  HC12  C1  C2    111.06  3.000
 AML  HC11  C1  C2    111.75  3.000
 AML  HC22  C2  HC21  106.10  3.000
 AML  HC22  C2  C3    109.31  3.000
 AML  HC21  C2  C3    109.24  3.000
 AML  HC22  C2  C1    109.69  3.000
 AML  HC21  C2  C1    109.59  3.000
 AML  C3    C2  C1    112.69  3.000
 AML  HC32  C3  HC31  105.97  3.000
 AML  HC32  C3  C4    109.46  3.000
 AML  HC31  C3  C4    109.52  3.000
 AML  HC32  C3  C2    109.13  3.000
 AML  HC31  C3  C2    109.19  3.000
 AML  C4    C3  C2    113.31  3.000
 AML  HC42  C4  HC41  106.36  3.000
 AML  HC42  C4  C5    109.06  3.000
 AML  HC41  C4  C5    109.24  3.000
 AML  HC42  C4  C3    109.88  3.000
 AML  HC41  C4  C3    109.27  3.000
 AML  C5    C4  C3    112.82  3.000
 AML  HC52  C5  HC51  106.16  3.000
 AML  HC52  C5  N1    113.45  3.000
 AML  HC51  C5  N1    108.25  3.000
 AML  HC52  C5  C4    108.79  3.000
 AML  HC51  C5  C4    108.92  3.000
 AML  N1    C5  C4    111.07  3.000
 AML  HN12  N1  HN11  105.45  3.000
 AML  HN12  N1  C5    109.00  3.000
 AML  HN11  N1  C5    109.57  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
 AML  Var_01  C4    C3  C2  C1  179.34  30.0  3
 AML  Var_02  C5    C4  C3  C2  179.78  30.0  3
 AML  Var_03  N1    C5  C4  C3  179.56  30.0  3
 AML  Var_04  HC11  C1  C2  C3  179.63  30.0  3
 AML  Var_05  HN11  N1  C5  C4  177.44  30.0  3

