# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 23:55:16 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: N,N'-bis(3-aminopropyl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCNCCCNCCCN
#
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
 SPE  SPE  N,N'-bis(3-aminopropyl)propane-1,3-diamine  ligand  37  13  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SPE
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
 SPE  N1    N  NH2   0  -0.800  -0.5075  -0.0147   7.3526
 SPE  C2    C  CH2   0  -0.273   0.3758  -0.0651   6.1958
 SPE  C3    C  CH2   0  -0.453  -0.4185   0.0265   4.9021
 SPE  C4    C  CH2   0  -0.253   0.4745  -0.0219   3.6725
 SPE  N5    N  NH1   0  -0.599  -0.2987   0.0709   2.4489
 SPE  C6    C  CH2   0  -0.250   0.5243   0.0012   1.2565
 SPE  C7    C  CH2   0  -0.468  -0.3185   0.0724  -0.0070
 SPE  C8    C  CH2   0  -0.250   0.5312   0.0134  -1.2668
 SPE  N9    N  NH1   0  -0.599  -0.2873   0.0742  -2.4625
 SPE  C10   C  CH2   0  -0.253   0.4931   0.0075  -3.6835
 SPE  C11   C  CH2   0  -0.453  -0.3969   0.0326  -4.9161
 SPE  C12   C  CH2   0  -0.273   0.4039  -0.0148  -6.2085
 SPE  N13   N  NH2   0  -0.800  -0.4791  -0.0010  -7.3667
 SPE  HN11  H  HNH2  0   0.337  -0.9361   0.9020   7.4011
 SPE  HN12  H  HNH2  0   0.345   0.0421  -0.0996   8.1982
 SPE  H21   H  HCH2  0   0.189   1.1444   0.7217   6.1981
 SPE  H22   H  HCH2  0   0.212   0.9142  -1.0168   6.2184
 SPE  H31   H  HCH2  0   0.216  -1.1415  -0.7949   4.8682
 SPE  H32   H  HCH2  0   0.217  -0.9961   0.9568   4.8887
 SPE  H41   H  HCH2  0   0.212   1.1734   0.8209   3.6996
 SPE  H42   H  HCH2  0   0.183   1.0959  -0.9326   3.7090
 SPE  HN5   H  HNH1  0   0.334  -0.9630  -0.6950   2.4278
 SPE  H61   H  HCH2  0   0.213   1.2218   0.8454   1.2731
 SPE  H62   H  HCH2  0   0.184   1.1480  -0.9080   1.2294
 SPE  H71   H  HCH2  0   0.217  -1.0324  -0.7598  -0.0131
 SPE  H72   H  HCH2  0   0.222  -0.9069   0.9939  -0.0044
 SPE  H81   H  HCH2  0   0.213   1.2177   0.8666  -1.2787
 SPE  H82   H  HCH2  0   0.184   1.1666  -0.8877  -1.2380
 SPE  HN9   H  HNH1  0   0.334  -0.9357  -0.7055  -2.4501
 SPE  H101  H  HCH2  0   0.212   1.1662   0.8713  -3.7065
 SPE  H102  H  HCH2  0   0.183   1.1417  -0.8839  -3.7190
 SPE  H111  H  HCH2  0   0.214  -1.0818  -0.8230  -4.8850
 SPE  H112  H  HCH2  0   0.219  -1.0165   0.9336  -4.9032
 SPE  H121  H  HCH2  0   0.213   1.0493   0.8666  -6.2600
 SPE  H122  H  HCH2  0   0.189   1.0752  -0.8856  -6.1815
 SPE  HN31  H  HNH2  0   0.345   0.0756   0.0066  -8.2131
 SPE  HN32  H  HNH2  0   0.337  -1.0003  -0.8692  -7.3943

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
 SPE  N1   C2    single  1.456  0.020  1.456
 SPE  N1   HN11  single  0.890  0.020  1.040
 SPE  N1   HN12  single  0.890  0.020  1.040
 SPE  C2   C3    single  1.521  0.020  1.521
 SPE  C2   H21   single  0.970  0.020  1.090
 SPE  C2   H22   single  0.970  0.020  1.090
 SPE  C3   C4    single  1.520  0.020  1.520
 SPE  C3   H31   single  0.970  0.020  1.090
 SPE  C3   H32   single  0.970  0.020  1.090
 SPE  C4   N5    single  1.450  0.020  1.450
 SPE  C4   H41   single  0.970  0.020  1.090
 SPE  C4   H42   single  0.970  0.020  1.090
 SPE  N5   C6    single  1.450  0.020  1.450
 SPE  N5   HN5   single  0.890  0.020  1.040
 SPE  C6   C7    single  1.520  0.020  1.520
 SPE  C6   H61   single  0.970  0.020  1.090
 SPE  C6   H62   single  0.970  0.020  1.090
 SPE  C7   C8    single  1.521  0.020  1.521
 SPE  C7   H71   single  0.970  0.020  1.090
 SPE  C7   H72   single  0.970  0.020  1.090
 SPE  C8   N9    single  1.450  0.020  1.450
 SPE  C8   H81   single  0.970  0.020  1.090
 SPE  C8   H82   single  0.970  0.020  1.090
 SPE  N9   C10   single  1.451  0.020  1.451
 SPE  N9   HN9   single  0.890  0.020  1.040
 SPE  C10  C11   single  1.520  0.020  1.520
 SPE  C10  H101  single  0.970  0.020  1.090
 SPE  C10  H102  single  0.970  0.020  1.090
 SPE  C11  C12   single  1.521  0.020  1.521
 SPE  C11  H111  single  0.970  0.020  1.090
 SPE  C11  H112  single  0.970  0.020  1.090
 SPE  C12  N13   single  1.457  0.020  1.457
 SPE  C12  H121  single  0.970  0.020  1.090
 SPE  C12  H122  single  0.970  0.020  1.090
 SPE  N13  HN31  single  0.890  0.020  1.040
 SPE  N13  HN32  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
 SPE  HN12  N1   HN11  105.41  3.000
 SPE  HN12  N1   C2    109.35  3.000
 SPE  HN11  N1   C2    109.02  3.000
 SPE  H22   C2   H21   106.16  3.000
 SPE  H22   C2   C3    109.10  3.000
 SPE  H21   C2   C3    108.89  3.000
 SPE  H22   C2   N1    108.19  3.000
 SPE  H21   C2   N1    113.41  3.000
 SPE  C3    C2   N1    110.91  3.000
 SPE  H32   C3   H31   106.78  3.000
 SPE  H32   C3   C4    109.08  3.000
 SPE  H31   C3   C4    109.81  3.000
 SPE  H32   C3   C2    109.69  3.000
 SPE  H31   C3   C2    109.03  3.000
 SPE  C4    C3   C2    112.29  3.000
 SPE  H42   C4   H41   105.96  3.000
 SPE  H42   C4   N5    112.39  3.000
 SPE  H41   C4   N5    108.18  3.000
 SPE  H42   C4   C3    109.29  3.000
 SPE  H41   C4   C3    109.28  3.000
 SPE  N5    C4   C3    111.54  3.000
 SPE  HN5   N5   C6    108.56  3.000
 SPE  HN5   N5   C4    108.57  3.000
 SPE  C6    N5   C4    112.83  3.000
 SPE  H62   C6   H61   106.00  3.000
 SPE  H62   C6   C7    109.37  3.000
 SPE  H61   C6   C7    109.24  3.000
 SPE  H62   C6   N5    112.37  3.000
 SPE  H61   C6   N5    108.17  3.000
 SPE  C7    C6   N5    111.50  3.000
 SPE  H72   C7   H71   106.82  3.000
 SPE  H72   C7   C8    109.59  3.000
 SPE  H71   C7   C8    109.26  3.000
 SPE  H72   C7   C6    109.62  3.000
 SPE  H71   C7   C6    109.27  3.000
 SPE  C8    C7   C6    112.14  3.000
 SPE  H82   C8   H81   106.00  3.000
 SPE  H82   C8   N9    112.39  3.000
 SPE  H81   C8   N9    108.19  3.000
 SPE  H82   C8   C7    109.39  3.000
 SPE  H81   C8   C7    109.21  3.000
 SPE  N9    C8   C7    111.47  3.000
 SPE  HN9   N9   C10   108.59  3.000
 SPE  HN9   N9   C8    108.58  3.000
 SPE  C10   N9   C8    112.86  3.000
 SPE  H102  C10  H101  105.98  3.000
 SPE  H102  C10  C11   109.36  3.000
 SPE  H101  C10  C11   109.24  3.000
 SPE  H102  C10  N9    112.37  3.000
 SPE  H101  C10  N9    108.18  3.000
 SPE  C11   C10  N9    111.52  3.000
 SPE  H112  C11  H111  106.77  3.000
 SPE  H112  C11  C12   109.51  3.000
 SPE  H111  C11  C12   109.19  3.000
 SPE  H112  C11  C10   109.62  3.000
 SPE  H111  C11  C10   109.25  3.000
 SPE  C12   C11  C10   112.34  3.000
 SPE  H122  C12  H121  106.20  3.000
 SPE  H122  C12  N13   113.39  3.000
 SPE  H121  C12  N13   108.22  3.000
 SPE  H122  C12  C11   108.98  3.000
 SPE  H121  C12  C11   109.00  3.000
 SPE  N13   C12  C11   110.87  3.000
 SPE  HN32  N13  HN31  105.41  3.000
 SPE  HN32  N13  C12   108.99  3.000
 SPE  HN31  N13  C12   109.44  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
 SPE  Var_01  C4    C3   C2   N1    179.94  30.0  3
 SPE  Var_02  N5    C4   C3   C2   -179.82  30.0  3
 SPE  Var_03  C6    N5   C4   C3   -178.87  30.0  3
 SPE  Var_04  C7    C6   N5   C4    178.83  30.0  3
 SPE  Var_05  C8    C7   C6   N5    179.47  30.0  3
 SPE  Var_06  N9    C8   C7   C6    179.65  30.0  3
 SPE  Var_07  C10   N9   C8   C7   -179.46  30.0  3
 SPE  Var_08  C11   C10  N9   C8    178.34  30.0  3
 SPE  Var_09  C12   C11  C10  N9    179.12  30.0  3
 SPE  Var_10  N13   C12  C11  C10   179.50  30.0  3
 SPE  Var_11  HN11  N1   C2   C3    -66.58  30.0  3
 SPE  Var_12  HN31  N13  C12  C11   177.62  30.0  3

