# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:15:29 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (3R,3'R)-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
 SPJ  SPJ  (3R,3'R)-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_SPJ
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
 SPJ  N1B   N  NH2   0  -0.805  -7.0926  -1.0043  -1.0225
 SPJ  C1C   C  CH1   0  -0.085  -6.8869  -0.1950   0.1756
 SPJ  C1A   C  CH3   0  -0.659  -8.0370   0.7941   0.2979
 SPJ  C1D   C  CH2   0  -0.424  -5.5549   0.5453   0.0953
 SPJ  C1E   C  CH2   0  -0.260  -4.3316  -0.3604   0.0917
 SPJ  N1F   N  NH1   0  -0.600  -3.1077   0.4186   0.1319
 SPJ  C1G   C  CH2   0  -0.247  -1.9129  -0.4031   0.1039
 SPJ  C1H   C  CH2   0  -0.445  -0.6506   0.4450   0.1143
 SPJ  C1I   C  CH2   0  -0.444   0.6166  -0.3997   0.1022
 SPJ  C1J   C  CH2   0  -0.245   1.8828   0.4429   0.1036
 SPJ  N1K   N  NH1   0  -0.603   3.0708  -0.3880   0.0888
 SPJ  C1L   C  CH2   0  -0.241   4.3042   0.3759   0.1035
 SPJ  C1M   C  CH2   0  -0.437   5.5136  -0.5462   0.0938
 SPJ  C1N   C  CH1   0  -0.099   6.8509   0.1826   0.1845
 SPJ  C1P   C  CH3   0  -0.662   8.0038  -0.8169   0.2608
 SPJ  N1O   N  NH2   0  -0.786   6.9751   1.1298  -0.9195
 SPJ  HN1B  H  HNH2  0   0.343  -6.4094  -1.7499  -1.0649
 SPJ  HN1A  H  HNH2  0   0.342  -7.9896  -1.4709  -0.9582
 SPJ  H1C   H  HCH1  0   0.191  -6.8717  -0.8072   1.0924
 SPJ  H1A   H  HCH3  0   0.216  -8.0656   1.4600  -0.5670
 SPJ  H1AA  H  HCH3  0   0.226  -8.9976   0.2784   0.3572
 SPJ  H1AB  H  HCH3  0   0.223  -7.9336   1.4052   1.1950
 SPJ  H1D   H  HCH2  0   0.210  -5.5534   1.1723  -0.8042
 SPJ  H1DA  H  HCH2  0   0.217  -5.4775   1.2214   0.9520
 SPJ  H1E   H  HCH2  0   0.212  -4.3579  -1.0037   0.9783
 SPJ  H1EA  H  HCH2  0   0.183  -4.3574  -1.0360  -0.7787
 SPJ  HN1F  H  HNH1  0   0.334  -3.0932   1.0379  -0.6713
 SPJ  H1G   H  HCH2  0   0.211  -1.9207  -1.0481   0.9892
 SPJ  H1GA  H  HCH2  0   0.183  -1.8872  -1.0807  -0.7661
 SPJ  H1H   H  HCH2  0   0.215  -0.6528   1.1093  -0.7574
 SPJ  H1HA  H  HCH2  0   0.217  -0.6602   1.0915   0.9973
 SPJ  H1I   H  HCH2  0   0.214   0.6199  -1.0597   0.9772
 SPJ  H1IA  H  HCH2  0   0.216   0.6222  -1.0511  -0.7772
 SPJ  H1J   H  HCH2  0   0.211   1.8956   1.0754  -0.7906
 SPJ  H1JA  H  HCH2  0   0.182   1.8600   1.1329   0.9640
 SPJ  HN1K  H  HNH1  0   0.332   3.0524  -0.9924   0.9032
 SPJ  H1L   H  HCH2  0   0.215   4.3247   1.0155  -0.7820
 SPJ  H1LA  H  HCH2  0   0.177   4.3711   1.0542   0.9714
 SPJ  H1M   H  HCH2  0   0.218   5.4419  -1.2420   0.9368
 SPJ  H1MA  H  HCH2  0   0.211   5.4945  -1.1620  -0.8135
 SPJ  H1N   H  HCH1  0   0.213   6.8510   0.7721   1.1090
 SPJ  H1P   H  HCH3  0   0.213   8.0284  -1.4449  -0.6334
 SPJ  H1PA  H  HCH3  0   0.225   8.9634  -0.3013   0.3329
 SPJ  H1PB  H  HCH3  0   0.217   7.9122  -1.4734   1.1280
 SPJ  HN1O  H  HNH2  0   0.342   7.8726   1.5965  -0.8578
 SPJ  HN1C  H  HNH2  0   0.331   7.0021   0.6139  -1.7930

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
 SPJ  N1B  C1C   single  1.460  0.020  1.460
 SPJ  C1C  C1A   single  1.522  0.020  1.522
 SPJ  C1C  C1D   single  1.526  0.020  1.526
 SPJ  C1D  C1E   single  1.522  0.020  1.522
 SPJ  C1E  N1F   single  1.451  0.020  1.451
 SPJ  N1F  C1G   single  1.450  0.020  1.450
 SPJ  C1G  C1H   single  1.521  0.020  1.521
 SPJ  C1H  C1I   single  1.523  0.020  1.523
 SPJ  C1I  C1J   single  1.521  0.020  1.521
 SPJ  C1J  N1K   single  1.450  0.020  1.450
 SPJ  N1K  C1L   single  1.451  0.020  1.451
 SPJ  C1L  C1M   single  1.521  0.020  1.521
 SPJ  C1M  C1N   single  1.526  0.020  1.526
 SPJ  C1N  C1P   single  1.528  0.020  1.528
 SPJ  C1N  N1O   single  1.460  0.020  1.460
 SPJ  N1B  HN1B  single  0.890  0.020  1.040
 SPJ  N1B  HN1A  single  0.890  0.020  1.040
 SPJ  C1C  H1C   single  0.970  0.020  1.090
 SPJ  C1A  H1A   single  0.970  0.020  1.090
 SPJ  C1A  H1AA  single  0.970  0.020  1.090
 SPJ  C1A  H1AB  single  0.970  0.020  1.090
 SPJ  C1D  H1D   single  0.970  0.020  1.090
 SPJ  C1D  H1DA  single  0.970  0.020  1.090
 SPJ  C1E  H1E   single  0.970  0.020  1.090
 SPJ  C1E  H1EA  single  0.970  0.020  1.090
 SPJ  N1F  HN1F  single  0.890  0.020  1.040
 SPJ  C1G  H1G   single  0.970  0.020  1.090
 SPJ  C1G  H1GA  single  0.970  0.020  1.090
 SPJ  C1H  H1H   single  0.970  0.020  1.090
 SPJ  C1H  H1HA  single  0.970  0.020  1.090
 SPJ  C1I  H1I   single  0.970  0.020  1.090
 SPJ  C1I  H1IA  single  0.970  0.020  1.090
 SPJ  C1J  H1J   single  0.970  0.020  1.090
 SPJ  C1J  H1JA  single  0.970  0.020  1.090
 SPJ  N1K  HN1K  single  0.890  0.020  1.040
 SPJ  C1L  H1L   single  0.970  0.020  1.090
 SPJ  C1L  H1LA  single  0.970  0.020  1.090
 SPJ  C1M  H1M   single  0.970  0.020  1.090
 SPJ  C1M  H1MA  single  0.970  0.020  1.090
 SPJ  C1N  H1N   single  0.970  0.020  1.090
 SPJ  C1P  H1P   single  0.970  0.020  1.090
 SPJ  C1P  H1PA  single  0.970  0.020  1.090
 SPJ  C1P  H1PB  single  0.970  0.020  1.090
 SPJ  N1O  HN1O  single  0.890  0.020  1.040
 SPJ  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
 SPJ  HN1A  N1B  HN1B  105.13  3.000
 SPJ  HN1A  N1B  C1C   109.14  3.000
 SPJ  HN1B  N1B  C1C   110.33  3.000
 SPJ  H1C   C1C  C1D   107.53  3.000
 SPJ  H1C   C1C  C1A   107.72  3.000
 SPJ  C1D   C1C  C1A   110.40  3.000
 SPJ  H1C   C1C  N1B   112.12  3.000
 SPJ  C1D   C1C  N1B   110.40  3.000
 SPJ  C1A   C1C  N1B   108.64  3.000
 SPJ  H1AB  C1A  H1AA  107.66  3.000
 SPJ  H1AB  C1A  H1A   108.21  3.000
 SPJ  H1AA  C1A  H1A   107.94  3.000
 SPJ  H1AB  C1A  C1C   111.02  3.000
 SPJ  H1AA  C1A  C1C   111.24  3.000
 SPJ  H1A   C1A  C1C   110.64  3.000
 SPJ  H1DA  C1D  H1D   106.80  3.000
 SPJ  H1DA  C1D  C1E   108.22  3.000
 SPJ  H1D   C1D  C1E   109.71  3.000
 SPJ  H1DA  C1D  C1C   108.68  3.000
 SPJ  H1D   C1D  C1C   108.77  3.000
 SPJ  C1E   C1D  C1C   114.39  3.000
 SPJ  H1EA  C1E  H1E   106.17  3.000
 SPJ  H1EA  C1E  N1F   111.76  3.000
 SPJ  H1E   C1E  N1F   108.23  3.000
 SPJ  H1EA  C1E  C1D   110.36  3.000
 SPJ  H1E   C1E  C1D   109.16  3.000
 SPJ  N1F   C1E  C1D   111.00  3.000
 SPJ  HN1F  N1F  C1G   108.59  3.000
 SPJ  HN1F  N1F  C1E   108.53  3.000
 SPJ  C1G   N1F  C1E   112.96  3.000
 SPJ  H1GA  C1G  H1G   106.01  3.000
 SPJ  H1GA  C1G  C1H   109.19  3.000
 SPJ  H1G   C1G  C1H   109.19  3.000
 SPJ  H1GA  C1G  N1F   112.49  3.000
 SPJ  H1G   C1G  N1F   108.19  3.000
 SPJ  C1H   C1G  N1F   111.58  3.000
 SPJ  H1HA  C1H  H1H   106.48  3.000
 SPJ  H1HA  C1H  C1I   109.96  3.000
 SPJ  H1H   C1H  C1I   109.36  3.000
 SPJ  H1HA  C1H  C1G   109.13  3.000
 SPJ  H1H   C1H  C1G   109.32  3.000
 SPJ  C1I   C1H  C1G   112.41  3.000
 SPJ  H1IA  C1I  H1I   106.44  3.000
 SPJ  H1IA  C1I  C1J   109.04  3.000
 SPJ  H1I   C1I  C1J   109.29  3.000
 SPJ  H1IA  C1I  C1H   109.92  3.000
 SPJ  H1I   C1I  C1H   109.28  3.000
 SPJ  C1J   C1I  C1H   112.67  3.000
 SPJ  H1JA  C1J  H1J   106.01  3.000
 SPJ  H1JA  C1J  N1K   112.54  3.000
 SPJ  H1J   C1J  N1K   108.24  3.000
 SPJ  H1JA  C1J  C1I   109.27  3.000
 SPJ  H1J   C1J  C1I   109.20  3.000
 SPJ  N1K   C1J  C1I   111.39  3.000
 SPJ  HN1K  N1K  C1L   108.73  3.000
 SPJ  HN1K  N1K  C1J   108.57  3.000
 SPJ  C1L   N1K  C1J   113.25  3.000
 SPJ  H1LA  C1L  H1L   106.05  3.000
 SPJ  H1LA  C1L  C1M   109.24  3.000
 SPJ  H1L   C1L  C1M   109.56  3.000
 SPJ  H1LA  C1L  N1K   112.53  3.000
 SPJ  H1L   C1L  N1K   108.42  3.000
 SPJ  C1M   C1L  N1K   110.90  3.000
 SPJ  H1MA  C1M  H1M   106.20  3.000
 SPJ  H1MA  C1M  C1N   109.43  3.000
 SPJ  H1M   C1M  C1N   108.36  3.000
 SPJ  H1MA  C1M  C1L   109.38  3.000
 SPJ  H1M   C1M  C1L   109.16  3.000
 SPJ  C1N   C1M  C1L   114.01  3.000
 SPJ  H1N   C1N  N1O   106.79  3.000
 SPJ  H1N   C1N  C1P   108.03  3.000
 SPJ  N1O   C1N  C1P   113.45  3.000
 SPJ  H1N   C1N  C1M   107.88  3.000
 SPJ  N1O   C1N  C1M   109.85  3.000
 SPJ  C1P   C1N  C1M   110.60  3.000
 SPJ  H1PB  C1P  H1PA  107.78  3.000
 SPJ  H1PB  C1P  H1P   107.84  3.000
 SPJ  H1PA  C1P  H1P   107.80  3.000
 SPJ  H1PB  C1P  C1N   111.71  3.000
 SPJ  H1PA  C1P  C1N   110.96  3.000
 SPJ  H1P   C1P  C1N   110.61  3.000
 SPJ  HN1C  N1O  HN1O  105.25  3.000
 SPJ  HN1C  N1O  C1N   108.86  3.000
 SPJ  HN1O  N1O  C1N   109.15  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
 SPJ  Var_01  N1F  C1E  C1D  C1C  -174.99  30.0  3
 SPJ  Var_02  C1G  N1F  C1E  C1D  -178.88  30.0  3
 SPJ  Var_03  C1H  C1G  N1F  C1E   178.67  30.0  3
 SPJ  Var_04  C1I  C1H  C1G  N1F   179.31  30.0  3
 SPJ  Var_05  C1J  C1I  C1H  C1G   179.63  30.0  3
 SPJ  Var_06  N1K  C1J  C1I  C1H  -179.87  30.0  3
 SPJ  Var_07  C1L  N1K  C1J  C1I  -179.40  30.0  3
 SPJ  Var_08  C1M  C1L  N1K  C1J   179.73  30.0  3
 SPJ  Var_09  C1N  C1M  C1L  N1K  -176.87  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
 SPJ  chir_01  C1C  N1B  C1A  C1D  positiv
 SPJ  chir_02  C1N  C1M  C1P  N1O  negativ

