# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:11:07 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: N,N'-bis(3-ammoniopropyl)butane-1,4-diaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]CCC[NH2+]CCCC[NH2+]CCC[NH3+]
#
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
 SPK  SPK  N,N'-bis(3-ammoniopropyl)butane-1,4-diaminium  ligand  44  14  .  2021-08-18  2021-08-18  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SPK
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
 SPK  N1    N  NT3   1  -0.777  -8.0502   0.2716  -0.0057
 SPK  C2    C  CH2   0  -0.304  -6.8137  -0.5468   0.0090
 SPK  C3    C  CH2   0  -0.494  -5.5829   0.3395   0.0107
 SPK  C4    C  CH2   0  -0.287  -4.3406  -0.5314   0.0264
 SPK  N5    N  NT2   1  -0.669  -3.1099   0.3010   0.0092
 SPK  C6    C  CH2   0  -0.284  -1.8524  -0.4963  -0.0031
 SPK  C7    C  CH2   0  -0.473  -0.6352   0.4070  -0.0070
 SPK  C8    C  CH2   0  -0.473   0.6412  -0.4266  -0.0107
 SPK  C9    C  CH2   0  -0.284   1.8584   0.4767  -0.0128
 SPK  N10   N  NT2   1  -0.669   3.1159  -0.3207  -0.0210
 SPK  C11   C  CH2   0  -0.287   4.3468   0.5116  -0.0396
 SPK  C12   C  CH2   0  -0.494   5.5889  -0.3592  -0.0155
 SPK  C13   C  CH2   0  -0.304   6.8197   0.5270  -0.0148
 SPK  N14   N  NT3   1  -0.777   8.0561  -0.2914   0.0093
 SPK  H1A   H  HNT3  0   0.473  -8.1003   0.8765  -0.8255
 SPK  H1B   H  HNT3  0   0.473  -8.1258   0.8676   0.8184
 SPK  H1C   H  HNT3  0   0.483  -8.8827  -0.3171  -0.0223
 SPK  H2A   H  HCH2  0   0.306  -6.8603  -1.1734   0.8967
 SPK  H2B   H  HCH2  0   0.306  -6.8473  -1.1856  -0.8707
 SPK  H3A   H  HCH2  0   0.283  -5.5821   0.9741  -0.8788
 SPK  H3B   H  HCH2  0   0.284  -5.5941   0.9913   0.8874
 SPK  H4A   H  HCH2  0   0.306  -4.2947  -1.1480   0.9226
 SPK  H4B   H  HCH2  0   0.305  -4.2965  -1.1803  -0.8464
 SPK  H5A   H  HNT2  0   0.469  -3.1265   0.9157  -0.8072
 SPK  H5B   H  HNT2  0   0.469  -3.1084   0.9220   0.8210
 SPK  H6A   H  HCH2  0   0.299  -1.8748  -1.1342   0.8789
 SPK  H6B   H  HCH2  0   0.300  -1.8867  -1.1264  -0.8906
 SPK  H7A   H  HCH2  0   0.266  -0.6572   1.0536  -0.8880
 SPK  H7B   H  HCH2  0   0.265  -0.6516   1.0547   0.8735
 SPK  H8A   H  HCH2  0   0.265   0.6622  -1.0747   0.8693
 SPK  H8B   H  HCH2  0   0.266   0.6580  -1.0729  -0.8921
 SPK  H9A   H  HCH2  0   0.299   1.8826   1.1136  -0.8954
 SPK  H9B   H  HCH2  0   0.300   1.8908   1.1075   0.8742
 SPK  H101  H  HNT2  0   0.469   3.1316  -0.9327   0.7975
 SPK  H102  H  HNT2  0   0.469   3.1153  -0.9444  -0.8307
 SPK  H111  H  HCH2  0   0.306   4.3034   1.1233  -0.9393
 SPK  H112  H  HCH2  0   0.305   4.3000   1.1652   0.8296
 SPK  H121  H  HCH2  0   0.283   5.5855  -0.9890   0.8774
 SPK  H122  H  HCH2  0   0.284   5.6028  -1.0157  -0.8887
 SPK  H131  H  HCH2  0   0.306   6.8695   1.1484  -0.9061
 SPK  H132  H  HCH2  0   0.306   6.8503   1.1709   0.8612
 SPK  H141  H  HNT3  0   0.473   8.1027  -0.8922   0.8323
 SPK  H142  H  HNT3  0   0.473   8.1350  -0.8915  -0.8115
 SPK  H143  H  HNT3  0   0.483   8.8885   0.2975   0.0264

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
 SPK  N1   C2    single  1.483  0.020  1.483
 SPK  N1   H1A   single  0.890  0.020  1.040
 SPK  N1   H1B   single  0.890  0.020  1.040
 SPK  N1   H1C   single  0.890  0.020  1.040
 SPK  C2   C3    single  1.517  0.020  1.517
 SPK  C2   H2A   single  0.970  0.020  1.090
 SPK  C2   H2B   single  0.970  0.020  1.090
 SPK  C3   C4    single  1.517  0.020  1.517
 SPK  C3   H3A   single  0.970  0.020  1.090
 SPK  C3   H3B   single  0.970  0.020  1.090
 SPK  C4   N5    single  1.486  0.020  1.486
 SPK  C4   H4A   single  0.970  0.020  1.090
 SPK  C4   H4B   single  0.970  0.020  1.090
 SPK  N5   C6    single  1.489  0.020  1.489
 SPK  N5   H5A   single  0.890  0.020  1.040
 SPK  N5   H5B   single  0.890  0.020  1.040
 SPK  C6   C7    single  1.516  0.020  1.516
 SPK  C6   H6A   single  0.970  0.020  1.090
 SPK  C6   H6B   single  0.970  0.020  1.090
 SPK  C7   C8    single  1.525  0.020  1.525
 SPK  C7   H7A   single  0.970  0.020  1.090
 SPK  C7   H7B   single  0.970  0.020  1.090
 SPK  C8   C9    single  1.516  0.020  1.516
 SPK  C8   H8A   single  0.970  0.020  1.090
 SPK  C8   H8B   single  0.970  0.020  1.090
 SPK  C9   N10   single  1.489  0.020  1.489
 SPK  C9   H9A   single  0.970  0.020  1.090
 SPK  C9   H9B   single  0.970  0.020  1.090
 SPK  N10  C11   single  1.486  0.020  1.486
 SPK  N10  H101  single  0.890  0.020  1.040
 SPK  N10  H102  single  0.890  0.020  1.040
 SPK  C11  C12   single  1.517  0.020  1.517
 SPK  C11  H111  single  0.970  0.020  1.090
 SPK  C11  H112  single  0.970  0.020  1.090
 SPK  C12  C13   single  1.517  0.020  1.517
 SPK  C12  H121  single  0.970  0.020  1.090
 SPK  C12  H122  single  0.970  0.020  1.090
 SPK  C13  N14   single  1.483  0.020  1.483
 SPK  C13  H131  single  0.970  0.020  1.090
 SPK  C13  H132  single  0.970  0.020  1.090
 SPK  N14  H141  single  0.890  0.020  1.040
 SPK  N14  H142  single  0.890  0.020  1.040
 SPK  N14  H143  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
 SPK  H1C   N1   H1B   106.86  3.000
 SPK  H1C   N1   H1A   106.81  3.000
 SPK  H1B   N1   H1A   107.41  3.000
 SPK  H1C   N1   C2    111.24  3.000
 SPK  H1B   N1   C2    112.11  3.000
 SPK  H1A   N1   C2    112.10  3.000
 SPK  H2B   C2   H2A   108.69  3.000
 SPK  H2B   C2   C3    111.67  3.000
 SPK  H2A   C2   C3    111.75  3.000
 SPK  H2B   C2   N1    106.88  3.000
 SPK  H2A   C2   N1    106.87  3.000
 SPK  C3    C2   N1    110.74  3.000
 SPK  H3B   C3   H3A   107.86  3.000
 SPK  H3B   C3   C4    110.03  3.000
 SPK  H3A   C3   C4    109.95  3.000
 SPK  H3B   C3   C2    109.95  3.000
 SPK  H3A   C3   C2    109.82  3.000
 SPK  C4    C3   C2    109.21  3.000
 SPK  H4B   C4   H4A   108.70  3.000
 SPK  H4B   C4   N5    106.92  3.000
 SPK  H4A   C4   N5    106.97  3.000
 SPK  H4B   C4   C3    111.53  3.000
 SPK  H4A   C4   C3    111.60  3.000
 SPK  N5    C4   C3    110.89  3.000
 SPK  H5B   N5   H5A   105.61  3.000
 SPK  H5B   N5   C6    109.31  3.000
 SPK  H5A   N5   C6    109.22  3.000
 SPK  H5B   N5   C4    109.41  3.000
 SPK  H5A   N5   C4    109.44  3.000
 SPK  C6    N5   C4    113.55  3.000
 SPK  H6B   C6   H6A   108.70  3.000
 SPK  H6B   C6   C7    111.60  3.000
 SPK  H6A   C6   C7    111.58  3.000
 SPK  H6B   C6   N5    106.86  3.000
 SPK  H6A   C6   N5    106.84  3.000
 SPK  C7    C6   N5    111.04  3.000
 SPK  H7B   C7   H7A   107.36  3.000
 SPK  H7B   C7   C8    109.78  3.000
 SPK  H7A   C7   C8    109.77  3.000
 SPK  H7B   C7   C6    109.82  3.000
 SPK  H7A   C7   C6    109.78  3.000
 SPK  C8    C7   C6    110.27  3.000
 SPK  H8B   C8   H8A   107.36  3.000
 SPK  H8B   C8   C9    109.81  3.000
 SPK  H8A   C8   C9    109.82  3.000
 SPK  H8B   C8   C7    109.76  3.000
 SPK  H8A   C8   C7    109.77  3.000
 SPK  C9    C8   C7    110.27  3.000
 SPK  H9B   C9   H9A   108.71  3.000
 SPK  H9B   C9   N10   106.83  3.000
 SPK  H9A   C9   N10   106.86  3.000
 SPK  H9B   C9   C8    111.59  3.000
 SPK  H9A   C9   C8    111.57  3.000
 SPK  N10   C9   C8    111.04  3.000
 SPK  H102  N10  H101  105.61  3.000
 SPK  H102  N10  C11   109.41  3.000
 SPK  H101  N10  C11   109.43  3.000
 SPK  H102  N10  C9    109.31  3.000
 SPK  H101  N10  C9    109.22  3.000
 SPK  C11   N10  C9    113.56  3.000
 SPK  H112  C11  H111  108.71  3.000
 SPK  H112  C11  C12   111.55  3.000
 SPK  H111  C11  C12   111.61  3.000
 SPK  H112  C11  N10   106.90  3.000
 SPK  H111  C11  N10   106.98  3.000
 SPK  C12   C11  N10   110.88  3.000
 SPK  H122  C12  H121  107.87  3.000
 SPK  H122  C12  C13   109.95  3.000
 SPK  H121  C12  C13   109.81  3.000
 SPK  H122  C12  C11   110.04  3.000
 SPK  H121  C12  C11   109.95  3.000
 SPK  C13   C12  C11   109.20  3.000
 SPK  H132  C13  H131  108.70  3.000
 SPK  H132  C13  N14   106.87  3.000
 SPK  H131  C13  N14   106.88  3.000
 SPK  H132  C13  C12   111.67  3.000
 SPK  H131  C13  C12   111.75  3.000
 SPK  N14   C13  C12   110.74  3.000
 SPK  H143  N14  H142  106.87  3.000
 SPK  H143  N14  H141  106.81  3.000
 SPK  H142  N14  H141  107.41  3.000
 SPK  H143  N14  C13   111.23  3.000
 SPK  H142  N14  C13   112.10  3.000
 SPK  H141  N14  C13   112.10  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
 SPK  Var_01  C4    C3   C2   N1    179.97  30.0  3
 SPK  Var_02  N5    C4   C3   C2    179.20  30.0  3
 SPK  Var_03  C6    N5   C4   C3   -178.88  30.0  3
 SPK  Var_04  C7    C6   N5   C4   -179.45  30.0  3
 SPK  Var_05  C8    C7   C6   N5    179.65  30.0  3
 SPK  Var_06  C9    C8   C7   C6   -179.93  30.0  3
 SPK  Var_07  N10   C9   C8   C7   -179.81  30.0  3
 SPK  Var_08  C11   N10  C9   C8    179.32  30.0  3
 SPK  Var_09  C12   C11  N10  C9    178.72  30.0  3
 SPK  Var_10  C13   C12  C11  N10  -179.17  30.0  3
 SPK  Var_11  N14   C13  C12  C11   179.97  30.0  3
 SPK  Var_12  H1A   N1   C2   C3     59.56  30.0  3
 SPK  Var_13  H141  N14  C13  C12   -59.49  30.0  3

