# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:47:15 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: butane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCN
#
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
 PUT  PUT  'butane-1,4-diamine       '  ligand  18  6  .  2020-10-20  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PUT
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
 PUT  N2    N  NH2   0  -0.801  -0.2712  -0.0118   3.0894
 PUT  C4    C  CH2   0  -0.270   0.5155  -0.0464   1.8640
 PUT  C3    C  CH2   0  -0.430  -0.3838  -0.0205   0.6375
 PUT  C2    C  CH2   0  -0.430   0.4005  -0.0420  -0.6676
 PUT  C1    C  CH2   0  -0.270  -0.4988  -0.0285  -1.8944
 PUT  N1    N  NH2   0  -0.801   0.2893  -0.0369  -3.1193
 PUT  HN21  H  HNH2  0   0.336  -0.7269   0.8899   3.1634
 PUT  HN22  H  HNH2  0   0.345   0.3463  -0.0682   3.8892
 PUT  H41   H  HCH2  0   0.186   1.2428   0.7751   1.7869
 PUT  H42   H  HCH2  0   0.211   1.0989  -0.9715   1.8577
 PUT  H31   H  HCH2  0   0.212  -1.0667  -0.8754   0.6768
 PUT  H32   H  HCH2  0   0.211  -1.0113   0.8778   0.6702
 PUT  H21   H  HCH2  0   0.211   1.0710   0.8243  -0.7038
 PUT  H22   H  HCH2  0   0.212   1.0408  -0.9294  -0.7037
 PUT  H11   H  HCH2  0   0.211  -1.1268  -0.9237  -1.8849
 PUT  H12   H  HCH2  0   0.186  -1.1851   0.8280  -1.8210
 PUT  HN11  H  HNH2  0   0.345  -0.3292  -0.0707  -3.9196
 PUT  HN12  H  HNH2  0   0.336   0.7853   0.8428  -3.1986

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
 PUT  N2  C4    single  1.457  0.020  1.457
 PUT  N2  HN21  single  0.890  0.020  1.040
 PUT  N2  HN22  single  0.890  0.020  1.040
 PUT  C4  C3    single  1.521  0.020  1.521
 PUT  C4  H41   single  0.970  0.020  1.090
 PUT  C4  H42   single  0.970  0.020  1.090
 PUT  C3  C2    single  1.523  0.020  1.523
 PUT  C3  H31   single  0.970  0.020  1.090
 PUT  C3  H32   single  0.970  0.020  1.090
 PUT  C2  C1    single  1.521  0.020  1.521
 PUT  C2  H21   single  0.970  0.020  1.090
 PUT  C2  H22   single  0.970  0.020  1.090
 PUT  C1  N1    single  1.457  0.020  1.457
 PUT  C1  H11   single  0.970  0.020  1.090
 PUT  C1  H12   single  0.970  0.020  1.090
 PUT  N1  HN11  single  0.890  0.020  1.040
 PUT  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
 PUT  HN22  N2  HN21  105.45  3.000
 PUT  HN22  N2  C4    109.52  3.000
 PUT  HN21  N2  C4    109.01  3.000
 PUT  H42   C4  H41   106.18  3.000
 PUT  H42   C4  C3    108.98  3.000
 PUT  H41   C4  C3    108.76  3.000
 PUT  H42   C4  N2    108.24  3.000
 PUT  H41   C4  N2    113.47  3.000
 PUT  C3    C4  N2    111.02  3.000
 PUT  H32   C3  H31   106.36  3.000
 PUT  H32   C3  C2    109.39  3.000
 PUT  H31   C3  C2    109.94  3.000
 PUT  H32   C3  C4    109.17  3.000
 PUT  H31   C3  C4    109.05  3.000
 PUT  C2    C3  C4    112.73  3.000
 PUT  H22   C2  H21   106.36  3.000
 PUT  H22   C2  C1    109.04  3.000
 PUT  H21   C2  C1    109.15  3.000
 PUT  H22   C2  C3    109.93  3.000
 PUT  H21   C2  C3    109.41  3.000
 PUT  C1    C2  C3    112.74  3.000
 PUT  H12   C1  H11   106.17  3.000
 PUT  H12   C1  N1    113.46  3.000
 PUT  H11   C1  N1    108.26  3.000
 PUT  H12   C1  C2    108.78  3.000
 PUT  H11   C1  C2    108.98  3.000
 PUT  N1    C1  C2    111.00  3.000
 PUT  HN12  N1  HN11  105.44  3.000
 PUT  HN12  N1  C1    109.01  3.000
 PUT  HN11  N1  C1    109.54  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
 PUT  Var_01  C2    C3  C4  N2  179.45  30.0  3
 PUT  Var_02  C1    C2  C3  C4  179.49  30.0  3
 PUT  Var_03  N1    C1  C2  C3  179.46  30.0  3
 PUT  Var_04  HN21  N2  C4  C3  -67.41  30.0  3
 PUT  Var_05  HN11  N1  C1  C2  177.42  30.0  3

