# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:53:28 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: N-(3-aminopropyl)butane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCNCCCN
#
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
 SPD  SPD  N-(3-aminopropyl)butane-1,4-diamine  ligand  29  10  .  2020-11-11  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SPD
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
 SPD  N1    N  NH2   0  -0.801  -0.2888   0.0538   5.5778
 SPD  C2    C  CH2   0  -0.271   0.5111  -0.0106   4.3624
 SPD  C3    C  CH2   0  -0.428  -0.3738   0.0178   3.1255
 SPD  C4    C  CH2   0  -0.446   0.4256  -0.0395   1.8306
 SPD  C5    C  CH2   0  -0.246  -0.4620  -0.0220   0.5959
 SPD  N6    N  NH1   0  -0.600   0.3208  -0.0661  -0.6243
 SPD  C7    C  CH2   0  -0.253  -0.4972  -0.0271  -1.8217
 SPD  C8    C  CH2   0  -0.453   0.3556  -0.0283  -3.0805
 SPD  C9    C  CH2   0  -0.273  -0.4850  -0.0076  -4.3480
 SPD  N10   N  NH2   0  -0.800   0.3615   0.0037  -5.5330
 SPD  HN11  H  HNH2  0   0.336  -0.7311   0.9634   5.6345
 SPD  HN12  H  HNH2  0   0.345   0.3184  -0.0015   6.3855
 SPD  H21   H  HCH2  0   0.187   1.2548   0.7961   4.2842
 SPD  H22   H  HCH2  0   0.211   1.0768  -0.9466   4.3737
 SPD  H31   H  HCH2  0   0.214  -1.0753  -0.8214   3.1688
 SPD  H32   H  HCH2  0   0.212  -0.9811   0.9302   3.1382
 SPD  H41   H  HCH2  0   0.213   1.1155   0.8111   1.7910
 SPD  H42   H  HCH2  0   0.216   1.0452  -0.9418   1.8147
 SPD  H51   H  HCH2  0   0.212  -1.1203  -0.8971   0.6128
 SPD  H52   H  HCH2  0   0.182  -1.1257   0.8582   0.6388
 SPD  HN6   H  HNH1  0   0.333   0.9466   0.7321  -0.6350
 SPD  H71   H  HCH2  0   0.212  -1.1443  -0.9110  -1.8225
 SPD  H72   H  HCH2  0   0.183  -1.1731   0.8443  -1.8397
 SPD  H81   H  HCH2  0   0.214   1.0151   0.8476  -3.0713
 SPD  H82   H  HCH2  0   0.219   1.0024  -0.9100  -3.0855
 SPD  H91   H  HCH2  0   0.213  -1.1045  -0.9084  -4.3790
 SPD  H92   H  HCH2  0   0.189  -1.1817   0.8420  -4.3010
 SPD  H101  H  HNH2  0   0.345  -0.2198  -0.0222  -6.3611
 SPD  H102  H  HNH2  0   0.337   0.8545   0.8876  -5.5777

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
 SPD  N1   C2    single  1.456  0.020  1.456
 SPD  N1   HN11  single  0.890  0.020  1.040
 SPD  N1   HN12  single  0.890  0.020  1.040
 SPD  C2   C3    single  1.521  0.020  1.521
 SPD  C2   H21   single  0.970  0.020  1.090
 SPD  C2   H22   single  0.970  0.020  1.090
 SPD  C3   C4    single  1.523  0.020  1.523
 SPD  C3   H31   single  0.970  0.020  1.090
 SPD  C3   H32   single  0.970  0.020  1.090
 SPD  C4   C5    single  1.521  0.020  1.521
 SPD  C4   H41   single  0.970  0.020  1.090
 SPD  C4   H42   single  0.970  0.020  1.090
 SPD  C5   N6    single  1.450  0.020  1.450
 SPD  C5   H51   single  0.970  0.020  1.090
 SPD  C5   H52   single  0.970  0.020  1.090
 SPD  N6   C7    single  1.451  0.020  1.451
 SPD  N6   HN6   single  0.890  0.020  1.040
 SPD  C7   C8    single  1.520  0.020  1.520
 SPD  C7   H71   single  0.970  0.020  1.090
 SPD  C7   H72   single  0.970  0.020  1.090
 SPD  C8   C9    single  1.521  0.020  1.521
 SPD  C8   H81   single  0.970  0.020  1.090
 SPD  C8   H82   single  0.970  0.020  1.090
 SPD  C9   N10   single  1.456  0.020  1.456
 SPD  C9   H91   single  0.970  0.020  1.090
 SPD  C9   H92   single  0.970  0.020  1.090
 SPD  N10  H101  single  0.890  0.020  1.040
 SPD  N10  H102  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
 SPD  HN12  N1   HN11  105.45  3.000
 SPD  HN12  N1   C2    109.51  3.000
 SPD  HN11  N1   C2    109.04  3.000
 SPD  H22   C2   H21   106.17  3.000
 SPD  H22   C2   C3    108.98  3.000
 SPD  H21   C2   C3    108.77  3.000
 SPD  H22   C2   N1    108.26  3.000
 SPD  H21   C2   N1    113.48  3.000
 SPD  C3    C2   N1    110.99  3.000
 SPD  H32   C3   H31   106.42  3.000
 SPD  H32   C3   C4    109.39  3.000
 SPD  H31   C3   C4    109.95  3.000
 SPD  H32   C3   C2    109.17  3.000
 SPD  H31   C3   C2    109.05  3.000
 SPD  C4    C3   C2    112.67  3.000
 SPD  H42   C4   H41   106.44  3.000
 SPD  H42   C4   C5    109.15  3.000
 SPD  H41   C4   C5    109.22  3.000
 SPD  H42   C4   C3    109.91  3.000
 SPD  H41   C4   C3    109.38  3.000
 SPD  C5    C4   C3    112.56  3.000
 SPD  H52   C5   H51   105.98  3.000
 SPD  H52   C5   N6    112.44  3.000
 SPD  H51   C5   N6    108.25  3.000
 SPD  H52   C5   C4    109.19  3.000
 SPD  H51   C5   C4    109.21  3.000
 SPD  N6    C5   C4    111.57  3.000
 SPD  HN6   N6   C7    108.54  3.000
 SPD  HN6   N6   C5    108.54  3.000
 SPD  C7    N6   C5    112.91  3.000
 SPD  H72   C7   H71   105.99  3.000
 SPD  H72   C7   C8    109.32  3.000
 SPD  H71   C7   C8    109.27  3.000
 SPD  H72   C7   N6    112.35  3.000
 SPD  H71   C7   N6    108.18  3.000
 SPD  C8    C7   N6    111.54  3.000
 SPD  H82   C8   H81   106.77  3.000
 SPD  H82   C8   C9    109.52  3.000
 SPD  H81   C8   C9    109.18  3.000
 SPD  H82   C8   C7    109.64  3.000
 SPD  H81   C8   C7    109.25  3.000
 SPD  C9    C8   C7    112.33  3.000
 SPD  H92   C9   H91   106.19  3.000
 SPD  H92   C9   N10   113.39  3.000
 SPD  H91   C9   N10   108.21  3.000
 SPD  H92   C9   C8    108.97  3.000
 SPD  H91   C9   C8    108.99  3.000
 SPD  N10   C9   C8    110.91  3.000
 SPD  H102  N10  H101  105.41  3.000
 SPD  H102  N10  C9    109.00  3.000
 SPD  H101  N10  C9    109.37  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
 SPD  Var_01  C4    C3   C2  N1   179.66  30.0  3
 SPD  Var_02  C5    C4   C3  C2   179.55  30.0  3
 SPD  Var_03  N6    C5   C4  C3   179.53  30.0  3
 SPD  Var_04  C7    N6   C5  C4  -178.99  30.0  3
 SPD  Var_05  C8    C7   N6  C5   178.11  30.0  3
 SPD  Var_06  C9    C8   C7  N6   179.19  30.0  3
 SPD  Var_07  N10   C9   C8  C7   179.45  30.0  3
 SPD  Var_08  HN11  N1   C2  C3   -67.20  30.0  3
 SPD  Var_09  H101  N10  C9  C8   177.62  30.0  3

