# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:54:03 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: ~{N}1,~{N}4-bis(3-azanylpropyl)cyclohexane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCN[C@@H]1CC[C@H](CC1)NCCCN
#
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
 GXQ  GXQ  ~{N}1,~{N}4-bis(3-azanylpropyl)cyclohexane-1,4-diamine  ligand  44  16  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GXQ
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
 GXQ  C1    C  CH2   0  -0.274  -6.3341  -0.4472   0.3756
 GXQ  N1    N  NH2   0  -0.799  -7.6115   0.0086  -0.1541
 GXQ  C2    C  CH2   0  -0.453  -5.1813   0.3445  -0.2217
 GXQ  N2    N  NH1   0  -0.613  -2.7460   0.6580  -0.2651
 GXQ  C3    C  CH2   0  -0.264  -3.8318  -0.1256   0.2967
 GXQ  N3    N  NH1   0  -0.613   2.7704  -0.6453   0.2876
 GXQ  C4    C  CH1   0  -0.022  -1.4302   0.2922   0.2383
 GXQ  C5    C  CH2   0  -0.455  -0.4282   1.3940  -0.0892
 GXQ  C6    C  CH2   0  -0.440   0.9781   1.0422   0.3815
 GXQ  C7    C  CH1   0  -0.022   1.4564  -0.2774  -0.2186
 GXQ  C8    C  CH2   0  -0.455   0.4542  -1.3798   0.1062
 GXQ  C9    C  CH2   0  -0.440  -0.9527  -1.0277  -0.3621
 GXQ  C11   C  CH2   0  -0.453   5.2051  -0.3386   0.2566
 GXQ  C12   C  CH2   0  -0.273   6.3637   0.4592  -0.3208
 GXQ  N13   N  NH2   0  -0.799   7.6372  -0.0226   0.1955
 GXQ  H12   H  HCH2  0   0.189  -6.2713  -0.3956   1.4725
 GXQ  H11   H  HCH2  0   0.213  -6.2145  -1.5025   0.1150
 GXQ  H1    H  HNH2  0   0.345  -8.3559  -0.5559   0.2349
 GXQ  H14   H  HNH2  0   0.337  -7.7892   0.9510   0.1715
 GXQ  H22   H  HCH2  0   0.219  -5.2069   0.2590  -1.3113
 GXQ  H23   H  HCH2  0   0.214  -5.3102   1.4074   0.0151
 GXQ  H21   H  HNH1  0   0.336  -2.9126   1.6307  -0.0298
 GXQ  H33   H  HCH2  0   0.184  -3.8320  -0.0993   1.3997
 GXQ  H32   H  HCH2  0   0.217  -3.6938  -1.1746   0.0210
 GXQ  H3    H  HNH1  0   0.336   2.9382  -1.6165   0.0470
 GXQ  H41   H  HCH1  0   0.179  -1.4476   0.1733   1.3379
 GXQ  H52   H  HCH2  0   0.215  -0.4293   1.5615  -1.1718
 GXQ  H51   H  HCH2  0   0.230  -0.7478   2.3332   0.3728
 GXQ  H61   H  HCH2  0   0.234   1.6601   1.8563   0.1240
 GXQ  H62   H  HCH2  0   0.210   0.9969   0.9531   1.4734
 GXQ  H71   H  HCH1  0   0.179   1.4761  -0.1575  -1.3180
 GXQ  H82   H  HCH2  0   0.231   0.7740  -2.3176  -0.3582
 GXQ  H81   H  HCH2  0   0.214   0.4563  -1.5508   1.1885
 GXQ  H92   H  HCH2  0   0.234  -1.6344  -1.8412  -0.1022
 GXQ  H91   H  HCH2  0   0.210  -0.9733  -0.9385  -1.4539
 GXQ  H102  H  HCH2  0   0.183   3.8661   0.1253  -1.3657
 GXQ  H101  H  HCH2  0   0.217   3.7219   1.1882   0.0218
 GXQ  H111  H  HCH2  0   0.217   5.2155  -0.2650   1.3492
 GXQ  H112  H  HCH2  0   0.216   5.3413  -1.3969   0.0106
 GXQ  H121  H  HCH2  0   0.213   6.3708   0.3438  -1.4082
 GXQ  H122  H  HCH2  0   0.188   6.1913   1.5284  -0.1283
 GXQ  H4    H  HNH2  0   0.345   8.3907   0.5114  -0.2186
 GXQ  H132  H  HNH2  0   0.337   7.6860   0.1692   1.1890
 GXQ  C10   C  CH2   0  -0.263   3.8596   0.1415  -0.2624

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
 GXQ  N13  C12   single  1.456  0.020  1.456
 GXQ  C12  C11   single  1.521  0.020  1.521
 GXQ  C11  C10   single  1.520  0.020  1.520
 GXQ  C10  N3    single  1.452  0.020  1.452
 GXQ  N3   C7    single  1.455  0.020  1.455
 GXQ  C7   C8    single  1.525  0.020  1.525
 GXQ  C7   C6    single  1.526  0.020  1.526
 GXQ  C8   C9    single  1.524  0.020  1.524
 GXQ  C6   C5    single  1.524  0.020  1.524
 GXQ  C9   C4    single  1.527  0.020  1.527
 GXQ  C5   C4    single  1.525  0.020  1.525
 GXQ  C4   N2    single  1.456  0.020  1.456
 GXQ  N2   C3    single  1.452  0.020  1.452
 GXQ  C3   C2    single  1.520  0.020  1.520
 GXQ  C2   C1    single  1.521  0.020  1.521
 GXQ  C1   N1    single  1.456  0.020  1.456
 GXQ  C1   H12   single  0.970  0.020  1.090
 GXQ  C1   H11   single  0.970  0.020  1.090
 GXQ  N1   H1    single  0.890  0.020  1.040
 GXQ  N1   H14   single  0.890  0.020  1.040
 GXQ  C2   H22   single  0.970  0.020  1.090
 GXQ  C2   H23   single  0.970  0.020  1.090
 GXQ  N2   H21   single  0.890  0.020  1.040
 GXQ  C3   H33   single  0.970  0.020  1.090
 GXQ  C3   H32   single  0.970  0.020  1.090
 GXQ  N3   H3    single  0.890  0.020  1.040
 GXQ  C4   H41   single  0.970  0.020  1.090
 GXQ  C5   H52   single  0.970  0.020  1.090
 GXQ  C5   H51   single  0.970  0.020  1.090
 GXQ  C6   H61   single  0.970  0.020  1.090
 GXQ  C6   H62   single  0.970  0.020  1.090
 GXQ  C7   H71   single  0.970  0.020  1.090
 GXQ  C8   H82   single  0.970  0.020  1.090
 GXQ  C8   H81   single  0.970  0.020  1.090
 GXQ  C9   H92   single  0.970  0.020  1.090
 GXQ  C9   H91   single  0.970  0.020  1.090
 GXQ  C10  H102  single  0.970  0.020  1.090
 GXQ  C10  H101  single  0.970  0.020  1.090
 GXQ  C11  H111  single  0.970  0.020  1.090
 GXQ  C11  H112  single  0.970  0.020  1.090
 GXQ  C12  H121  single  0.970  0.020  1.090
 GXQ  C12  H122  single  0.970  0.020  1.090
 GXQ  N13  H4    single  0.890  0.020  1.040
 GXQ  N13  H132  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
 GXQ  H11   C1   H12   106.06  3.000
 GXQ  H11   C1   C2    109.02  3.000
 GXQ  H12   C1   C2    108.91  3.000
 GXQ  H11   C1   N1    108.13  3.000
 GXQ  H12   C1   N1    113.46  3.000
 GXQ  C2    C1   N1    111.05  3.000
 GXQ  H14   N1   H1    105.45  3.000
 GXQ  H14   N1   C1    109.16  3.000
 GXQ  H1    N1   C1    109.33  3.000
 GXQ  H23   C2   H22   106.75  3.000
 GXQ  H23   C2   C3    109.30  3.000
 GXQ  H22   C2   C3    109.67  3.000
 GXQ  H23   C2   C1    109.31  3.000
 GXQ  H22   C2   C1    109.45  3.000
 GXQ  C3    C2   C1    112.21  3.000
 GXQ  H21   N2   C4    108.01  3.000
 GXQ  H21   N2   C3    107.75  3.000
 GXQ  C4    N2   C3    113.98  3.000
 GXQ  H32   C3   H33   105.96  3.000
 GXQ  H32   C3   N2    109.01  3.000
 GXQ  H33   C3   N2    111.97  3.000
 GXQ  H32   C3   C2    108.83  3.000
 GXQ  H33   C3   C2    109.47  3.000
 GXQ  N2    C3   C2    111.40  3.000
 GXQ  H3    N3   C10   107.75  3.000
 GXQ  H3    N3   C7    107.99  3.000
 GXQ  C10   N3   C7    114.11  3.000
 GXQ  H41   C4   C9    107.64  3.000
 GXQ  H41   C4   C5    107.55  3.000
 GXQ  C9    C4   C5    109.56  3.000
 GXQ  H41   C4   N2    110.89  3.000
 GXQ  C5    C4   N2    109.76  3.000
 GXQ  C9    C4   N2    111.35  3.000
 GXQ  H51   C5   H52   106.60  3.000
 GXQ  H51   C5   C6    109.70  3.000
 GXQ  H52   C5   C6    109.96  3.000
 GXQ  H51   C5   C4    109.73  3.000
 GXQ  H52   C5   C4    108.79  3.000
 GXQ  C6    C5   C4    111.91  3.000
 GXQ  H62   C6   H61   106.54  3.000
 GXQ  H62   C6   C7    108.42  3.000
 GXQ  H61   C6   C7    110.84  3.000
 GXQ  H62   C6   C5    110.02  3.000
 GXQ  H61   C6   C5    109.34  3.000
 GXQ  C7    C6   C5    111.54  3.000
 GXQ  H71   C7   C8    107.57  3.000
 GXQ  H71   C7   C6    107.61  3.000
 GXQ  C8    C7   C6    109.59  3.000
 GXQ  H71   C7   N3    110.91  3.000
 GXQ  C6    C7   N3    111.39  3.000
 GXQ  C8    C7   N3    109.66  3.000
 GXQ  H81   C8   H82   106.56  3.000
 GXQ  H81   C8   C9    109.96  3.000
 GXQ  H82   C8   C9    109.71  3.000
 GXQ  H81   C8   C7    108.78  3.000
 GXQ  H82   C8   C7    109.70  3.000
 GXQ  C9    C8   C7    111.98  3.000
 GXQ  H91   C9   H92   106.61  3.000
 GXQ  H91   C9   C8    110.02  3.000
 GXQ  H92   C9   C8    109.32  3.000
 GXQ  H91   C9   C4    108.40  3.000
 GXQ  H92   C9   C4    110.80  3.000
 GXQ  C8    C9   C4    111.57  3.000
 GXQ  H112  C11  H111  106.73  3.000
 GXQ  H112  C11  C12   109.09  3.000
 GXQ  H111  C11  C12   109.66  3.000
 GXQ  H112  C11  C10   109.79  3.000
 GXQ  H111  C11  C10   109.13  3.000
 GXQ  C12   C11  C10   112.28  3.000
 GXQ  H122  C12  H121  106.11  3.000
 GXQ  H122  C12  N13   113.37  3.000
 GXQ  H121  C12  N13   108.18  3.000
 GXQ  H122  C12  C11   108.91  3.000
 GXQ  H121  C12  C11   109.10  3.000
 GXQ  N13   C12  C11   110.99  3.000
 GXQ  H132  N13  H4    105.40  3.000
 GXQ  H132  N13  C12   109.10  3.000
 GXQ  H4    N13  C12   109.36  3.000
 GXQ  H101  C10  H102  105.95  3.000
 GXQ  H101  C10  C11   108.97  3.000
 GXQ  H102  C10  C11   109.36  3.000
 GXQ  H101  C10  N3    109.02  3.000
 GXQ  H102  C10  N3    112.04  3.000
 GXQ  C11   C10  N3    111.32  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
 GXQ  Var_01  C7   C8   C9   C4    -56.71  30.0  1
 GXQ  Var_02  C7   C6   C5   C4     56.89  30.0  1
 GXQ  Var_03  C4   N2   C3   C2    177.50  30.0  1
 GXQ  Var_04  C11  C10  N3   C7   -177.26  30.0  1
 GXQ  Var_05  N2   C3   C2   C1   -178.92  30.0  1
 GXQ  Var_06  C3   C2   C1   N1   -179.06  30.0  1
 GXQ  Var_07  C12  C11  C10  N3    179.23  30.0  1
 GXQ  Var_08  N13  C12  C11  C10   179.94  30.0  1
 GXQ  Var_09  H1   N1   C1   C2    178.03  30.0  3
 GXQ  Var_10  H4   N13  C12  C11   178.82  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
 GXQ  chir_01  C4  C9  C5  N2  negativ
 GXQ  chir_02  C7  N3  C8  C6  negativ

