# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:15:58 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (3S,3'S)-N~1~,N~1~'-butane-1,4-diyldibutane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CCNCCCCNCC[C@H](C)N
#
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
 SPZ  SPZ  (3S,3'S)-N~1~,N~1~'-butane-1,4-diyldibutane-1,3-diamine  ligand  46  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SPZ
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
 SPZ  N1B   N  NH2   0  -0.786  -7.0068  -1.1281   0.8959
 SPZ  C1C   C  CH1   0  -0.099  -6.8808  -0.1650  -0.1941
 SPZ  C1A   C  CH3   0  -0.662  -8.0337   0.8355  -0.2579
 SPZ  C1D   C  CH2   0  -0.438  -5.5439   0.5626  -0.0900
 SPZ  C1E   C  CH2   0  -0.241  -4.3343  -0.3590  -0.1124
 SPZ  N1F   N  NH1   0  -0.602  -3.1009   0.4043  -0.0837
 SPZ  C1G   C  CH2   0  -0.245  -1.9133  -0.4270  -0.1133
 SPZ  C1H   C  CH2   0  -0.444  -0.6464   0.4143  -0.0991
 SPZ  C1I   C  CH2   0  -0.445   0.6197  -0.4314  -0.1338
 SPZ  C1J   C  CH2   0  -0.247   1.8836   0.4139  -0.1090
 SPZ  N1K   N  NH1   0  -0.600   3.0763  -0.4091  -0.1689
 SPZ  C1L   C  CH2   0  -0.254   4.3026   0.3652  -0.1161
 SPZ  C1M   C  CH2   0  -0.437   5.5260  -0.5374  -0.1690
 SPZ  C1N   C  CH1   0  -0.103   6.8606   0.2167  -0.1730
 SPZ  C1P   C  CH3   0  -0.651   8.0157  -0.7503  -0.3943
 SPZ  N1O   N  NH2   0  -0.790   7.1262   1.0013   1.0291
 SPZ  HN1B  H  HNH2  0   0.331  -7.0320  -0.6248   1.7768
 SPZ  HN1A  H  HNH2  0   0.342  -7.9055  -1.5915   0.8282
 SPZ  H1C   H  HCH1  0   0.213  -6.8790  -0.7411  -1.1270
 SPZ  H1A   H  HCH3  0   0.213  -8.0626   1.4471   0.6475
 SPZ  H1AA  H  HCH3  0   0.217  -7.9377   1.5074  -1.1127
 SPZ  H1AB  H  HCH3  0   0.225  -8.9928   0.3210  -0.3438
 SPZ  H1D   H  HCH2  0   0.218  -5.4710   1.2715  -0.9219
 SPZ  H1DA  H  HCH2  0   0.211  -5.5266   1.1642   0.8268
 SPZ  H1E   H  HCH2  0   0.215  -4.3564  -1.0130   0.7625
 SPZ  H1EA  H  HCH2  0   0.177  -4.3998  -1.0232  -0.9913
 SPZ  HN1F  H  HNH1  0   0.332  -3.0818   1.0221  -0.8878
 SPZ  H1G   H  HCH2  0   0.211  -1.9260  -1.0746   0.7700
 SPZ  H1GA  H  HCH2  0   0.182  -1.8917  -1.1021  -0.9855
 SPZ  H1H   H  HCH2  0   0.214  -0.6523   1.0916  -0.9607
 SPZ  H1HA  H  HCH2  0   0.216  -0.6480   1.0480   0.7932
 SPZ  H1I   H  HCH2  0   0.214   0.6239  -1.1151   0.7228
 SPZ  H1IA  H  HCH2  0   0.217   0.6254  -1.0582  -1.0309
 SPZ  H1J   H  HCH2  0   0.211   1.8864   1.0832  -0.9761
 SPZ  H1JA  H  HCH2  0   0.182   1.8658   1.0674   0.7795
 SPZ  HN1K  H  HNH1  0   0.333   3.0664  -1.0505   0.6168
 SPZ  H1L   H  HCH2  0   0.212   4.3186   1.0406  -0.9787
 SPZ  H1LA  H  HCH2  0   0.178   4.3445   1.0093   0.7775
 SPZ  H1M   H  HCH2  0   0.209   5.5129  -1.2263   0.6853
 SPZ  H1MA  H  HCH2  0   0.215   5.4591  -1.1576  -1.0686
 SPZ  H1N   H  HCH1  0   0.214   6.8446   0.9225  -1.0119
 SPZ  H1P   H  HCH3  0   0.222   7.8941  -1.3053  -1.3250
 SPZ  H1PA  H  HCH3  0   0.227   8.9671  -0.2196  -0.4375
 SPZ  H1PB  H  HCH3  0   0.214   8.0742  -1.4789   0.4188
 SPZ  HN1O  H  HNH2  0   0.344   6.4097   1.7045   1.1580
 SPZ  HN1C  H  HNH2  0   0.332   7.0699   0.3980   1.8428

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
 SPZ  N1B  C1C   single  1.460  0.020  1.460
 SPZ  C1C  C1A   single  1.528  0.020  1.528
 SPZ  C1C  C1D   single  1.526  0.020  1.526
 SPZ  C1D  C1E   single  1.521  0.020  1.521
 SPZ  C1E  N1F   single  1.451  0.020  1.451
 SPZ  N1F  C1G   single  1.450  0.020  1.450
 SPZ  C1G  C1H   single  1.521  0.020  1.521
 SPZ  C1H  C1I   single  1.523  0.020  1.523
 SPZ  C1I  C1J   single  1.521  0.020  1.521
 SPZ  C1J  N1K   single  1.450  0.020  1.450
 SPZ  N1K  C1L   single  1.451  0.020  1.451
 SPZ  C1L  C1M   single  1.521  0.020  1.521
 SPZ  C1M  C1N   single  1.533  0.020  1.533
 SPZ  C1N  C1P   single  1.523  0.020  1.523
 SPZ  C1N  N1O   single  1.460  0.020  1.460
 SPZ  N1B  HN1B  single  0.890  0.020  1.040
 SPZ  N1B  HN1A  single  0.890  0.020  1.040
 SPZ  C1C  H1C   single  0.970  0.020  1.090
 SPZ  C1A  H1A   single  0.970  0.020  1.090
 SPZ  C1A  H1AA  single  0.970  0.020  1.090
 SPZ  C1A  H1AB  single  0.970  0.020  1.090
 SPZ  C1D  H1D   single  0.970  0.020  1.090
 SPZ  C1D  H1DA  single  0.970  0.020  1.090
 SPZ  C1E  H1E   single  0.970  0.020  1.090
 SPZ  C1E  H1EA  single  0.970  0.020  1.090
 SPZ  N1F  HN1F  single  0.890  0.020  1.040
 SPZ  C1G  H1G   single  0.970  0.020  1.090
 SPZ  C1G  H1GA  single  0.970  0.020  1.090
 SPZ  C1H  H1H   single  0.970  0.020  1.090
 SPZ  C1H  H1HA  single  0.970  0.020  1.090
 SPZ  C1I  H1I   single  0.970  0.020  1.090
 SPZ  C1I  H1IA  single  0.970  0.020  1.090
 SPZ  C1J  H1J   single  0.970  0.020  1.090
 SPZ  C1J  H1JA  single  0.970  0.020  1.090
 SPZ  N1K  HN1K  single  0.890  0.020  1.040
 SPZ  C1L  H1L   single  0.970  0.020  1.090
 SPZ  C1L  H1LA  single  0.970  0.020  1.090
 SPZ  C1M  H1M   single  0.970  0.020  1.090
 SPZ  C1M  H1MA  single  0.970  0.020  1.090
 SPZ  C1N  H1N   single  0.970  0.020  1.090
 SPZ  C1P  H1P   single  0.970  0.020  1.090
 SPZ  C1P  H1PA  single  0.970  0.020  1.090
 SPZ  C1P  H1PB  single  0.970  0.020  1.090
 SPZ  N1O  HN1O  single  0.890  0.020  1.040
 SPZ  N1O  HN1C  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
 SPZ  HN1A  N1B  HN1B  105.23  3.000
 SPZ  HN1A  N1B  C1C   109.17  3.000
 SPZ  HN1B  N1B  C1C   108.85  3.000
 SPZ  H1C   C1C  C1D   107.89  3.000
 SPZ  H1C   C1C  C1A   108.05  3.000
 SPZ  C1D   C1C  C1A   110.60  3.000
 SPZ  H1C   C1C  N1B   106.78  3.000
 SPZ  C1D   C1C  N1B   109.83  3.000
 SPZ  C1A   C1C  N1B   113.45  3.000
 SPZ  H1AB  C1A  H1AA  107.80  3.000
 SPZ  H1AB  C1A  H1A   107.80  3.000
 SPZ  H1AA  C1A  H1A   107.85  3.000
 SPZ  H1AB  C1A  C1C   110.95  3.000
 SPZ  H1AA  C1A  C1C   111.68  3.000
 SPZ  H1A   C1A  C1C   110.59  3.000
 SPZ  H1DA  C1D  H1D   106.19  3.000
 SPZ  H1DA  C1D  C1E   109.40  3.000
 SPZ  H1D   C1D  C1E   109.15  3.000
 SPZ  H1DA  C1D  C1C   109.42  3.000
 SPZ  H1D   C1D  C1C   108.37  3.000
 SPZ  C1E   C1D  C1C   114.01  3.000
 SPZ  H1EA  C1E  H1E   106.04  3.000
 SPZ  H1EA  C1E  N1F   112.51  3.000
 SPZ  H1E   C1E  N1F   108.44  3.000
 SPZ  H1EA  C1E  C1D   109.22  3.000
 SPZ  H1E   C1E  C1D   109.57  3.000
 SPZ  N1F   C1E  C1D   110.91  3.000
 SPZ  HN1F  N1F  C1G   108.52  3.000
 SPZ  HN1F  N1F  C1E   108.71  3.000
 SPZ  C1G   N1F  C1E   113.22  3.000
 SPZ  H1GA  C1G  H1G   106.02  3.000
 SPZ  H1GA  C1G  C1H   109.25  3.000
 SPZ  H1G   C1G  C1H   109.22  3.000
 SPZ  H1GA  C1G  N1F   112.52  3.000
 SPZ  H1G   C1G  N1F   108.24  3.000
 SPZ  C1H   C1G  N1F   111.40  3.000
 SPZ  H1HA  C1H  H1H   106.45  3.000
 SPZ  H1HA  C1H  C1I   109.96  3.000
 SPZ  H1H   C1H  C1I   109.25  3.000
 SPZ  H1HA  C1H  C1G   109.07  3.000
 SPZ  H1H   C1H  C1G   109.27  3.000
 SPZ  C1I   C1H  C1G   112.65  3.000
 SPZ  H1IA  C1I  H1I   106.46  3.000
 SPZ  H1IA  C1I  C1J   109.11  3.000
 SPZ  H1I   C1I  C1J   109.32  3.000
 SPZ  H1IA  C1I  C1H   109.94  3.000
 SPZ  H1I   C1I  C1H   109.37  3.000
 SPZ  C1J   C1I  C1H   112.45  3.000
 SPZ  H1JA  C1J  H1J   106.00  3.000
 SPZ  H1JA  C1J  N1K   112.51  3.000
 SPZ  H1J   C1J  N1K   108.18  3.000
 SPZ  H1JA  C1J  C1I   109.21  3.000
 SPZ  H1J   C1J  C1I   109.20  3.000
 SPZ  N1K   C1J  C1I   111.55  3.000
 SPZ  HN1K  N1K  C1L   108.51  3.000
 SPZ  HN1K  N1K  C1J   108.59  3.000
 SPZ  C1L   N1K  C1J   112.99  3.000
 SPZ  H1LA  C1L  H1L   106.11  3.000
 SPZ  H1LA  C1L  C1M   110.14  3.000
 SPZ  H1L   C1L  C1M   109.07  3.000
 SPZ  H1LA  C1L  N1K   111.93  3.000
 SPZ  H1L   C1L  N1K   108.21  3.000
 SPZ  C1M   C1L  N1K   111.21  3.000
 SPZ  H1MA  C1M  H1M   106.46  3.000
 SPZ  H1MA  C1M  C1N   109.25  3.000
 SPZ  H1M   C1M  C1N   108.74  3.000
 SPZ  H1MA  C1M  C1L   108.39  3.000
 SPZ  H1M   C1M  C1L   109.62  3.000
 SPZ  C1N   C1M  C1L   114.10  3.000
 SPZ  H1N   C1N  N1O   106.66  3.000
 SPZ  H1N   C1N  C1P   107.98  3.000
 SPZ  N1O   C1N  C1P   108.84  3.000
 SPZ  H1N   C1N  C1M   107.82  3.000
 SPZ  N1O   C1N  C1M   114.88  3.000
 SPZ  C1P   C1N  C1M   110.39  3.000
 SPZ  H1PB  C1P  H1PA  107.89  3.000
 SPZ  H1PB  C1P  H1P   107.55  3.000
 SPZ  H1PA  C1P  H1P   108.13  3.000
 SPZ  H1PB  C1P  C1N   110.84  3.000
 SPZ  H1PA  C1P  C1N   111.02  3.000
 SPZ  H1P   C1P  C1N   111.26  3.000
 SPZ  HN1C  N1O  HN1O  105.77  3.000
 SPZ  HN1C  N1O  C1N   109.32  3.000
 SPZ  HN1O  N1O  C1N   110.45  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
 SPZ  Var_01  N1F  C1E  C1D  C1C   176.88  30.0  3
 SPZ  Var_02  C1G  N1F  C1E  C1D  -179.58  30.0  3
 SPZ  Var_03  C1H  C1G  N1F  C1E   179.30  30.0  3
 SPZ  Var_04  C1I  C1H  C1G  N1F  -179.83  30.0  3
 SPZ  Var_05  C1J  C1I  C1H  C1G  -179.58  30.0  3
 SPZ  Var_06  N1K  C1J  C1I  C1H  -178.88  30.0  3
 SPZ  Var_07  C1L  N1K  C1J  C1I  -178.67  30.0  3
 SPZ  Var_08  C1M  C1L  N1K  C1J   179.49  30.0  3
 SPZ  Var_09  C1N  C1M  C1L  N1K   177.71  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 SPZ  chir_01  C1C  N1B  C1A  C1D  negativ
 SPZ  chir_02  C1N  C1M  C1P  N1O  positiv

