# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 05:00:42 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: N~1~-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCNC12CC3CC(CC(C3)C1)C2
#
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
 PJG  PJG  N~1~-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethane-1,2-diamine  ligand  36  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PJG
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
 PJG  C1   C  CT    0   0.104  15.7340  12.2059   2.7051
 PJG  C2   C  CH2   0  -0.421  14.3489  12.8138   2.9596
 PJG  C3   C  CH2   0  -0.415  16.3570  11.8512   4.0682
 PJG  C12  C  CH2   0  -0.418  15.3043   9.5870   4.0075
 PJG  C13  C  CH2   0  -0.279  17.9150  12.4768   0.0386
 PJG  C10  C  CH2   0  -0.419  14.0993  11.4960   5.0736
 PJG  C4   C  CH2   0  -0.420  15.5505  10.9143   1.9010
 PJG  C6   C  CH1   0  -0.249  13.4555  11.8392   3.7287
 PJG  C7   C  CH1   0  -0.246  15.4713  10.8644   4.8329
 PJG  C8   C  CH1   0  -0.245  14.6595   9.9300   2.6627
 PJG  N14  N  NH2   0  -0.804  19.2674  12.0878  -0.3342
 PJG  N5   N  NH1   0  -0.623  16.5083  13.1857   1.9483
 PJG  H1   H  HCH2  0   0.218  14.4578  13.7499   3.5210
 PJG  H2   H  HCH2  0   0.221  13.8882  13.0732   2.0008
 PJG  H3   H  HCH2  0   0.221  17.3535  11.4190   3.9285
 PJG  H4   H  HCH2  0   0.213  16.4886  12.7700   4.6516
 PJG  H7   H  HCH2  0   0.221  14.6781   8.8698   4.5486
 PJG  H8   H  HCH2  0   0.220  16.2768   9.1084   3.8515
 PJG  H9   H  HCH2  0   0.185  17.5237  13.3329  -0.5288
 PJG  H10  H  HCH2  0   0.218  17.2473  11.6385  -0.1721
 PJG  H11  H  HCH2  0   0.220  14.1974  12.3968   5.6883
 PJG  H12  H  HCH2  0   0.220  13.4585  10.8032   5.6291
 PJG  H13  H  HCH2  0   0.220  15.1080  11.1520   0.9278
 PJG  H14  H  HCH2  0   0.225  16.5214  10.4481   1.7035
 PJG  H15  H  HCH1  0   0.222  12.4776  12.3011   3.8955
 PJG  H16  H  HCH1  0   0.220  15.9392  10.6238   5.7926
 PJG  H17  H  HCH1  0   0.222  14.5469   9.0184   2.0683
 PJG  H18  H  HCH2  0   0.203  18.2637  11.9724   2.0941
 PJG  H19  H  HCH2  0   0.225  18.5239  13.6542   1.7142
 PJG  H20  H  HNH2  0   0.346  19.2850  11.8119  -1.3071
 PJG  H21  H  HNH2  0   0.336  19.8796  12.8918  -0.2685
 PJG  H23  H  HNH1  0   0.337  16.5549  14.0348   2.4966
 PJG  C11  C  CH2   0  -0.417  13.2866  10.5598   2.9064
 PJG  C9   C  CH2   0  -0.303  17.8510  12.8128   1.5233
 PJG  H5   H  HCH2  0   0.220  12.7986  10.7853   1.9525
 PJG  H6   H  HCH2  0   0.221  12.6380   9.8532   3.4353

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
 PJG  N14  C13  single  1.456  0.020  1.456
 PJG  C13  C9   single  1.524  0.020  1.524
 PJG  C9   N5   single  1.457  0.020  1.457
 PJG  N5   C1   single  1.460  0.020  1.460
 PJG  C4   C1   single  1.532  0.020  1.532
 PJG  C4   C8   single  1.531  0.020  1.531
 PJG  C1   C2   single  1.534  0.020  1.534
 PJG  C1   C3   single  1.540  0.020  1.540
 PJG  C8   C11  single  1.530  0.020  1.530
 PJG  C8   C12  single  1.530  0.020  1.530
 PJG  C2   C6   single  1.530  0.020  1.530
 PJG  C11  C6   single  1.530  0.020  1.530
 PJG  C6   C10  single  1.530  0.020  1.530
 PJG  C3   C7   single  1.531  0.020  1.531
 PJG  C12  C7   single  1.530  0.020  1.530
 PJG  C7   C10  single  1.529  0.020  1.529
 PJG  C2   H1   single  0.970  0.020  1.090
 PJG  C2   H2   single  0.970  0.020  1.090
 PJG  C3   H3   single  0.970  0.020  1.090
 PJG  C3   H4   single  0.970  0.020  1.090
 PJG  C11  H5   single  0.970  0.020  1.090
 PJG  C11  H6   single  0.970  0.020  1.090
 PJG  C12  H7   single  0.970  0.020  1.090
 PJG  C12  H8   single  0.970  0.020  1.090
 PJG  C13  H9   single  0.970  0.020  1.090
 PJG  C13  H10  single  0.970  0.020  1.090
 PJG  C10  H11  single  0.970  0.020  1.090
 PJG  C10  H12  single  0.970  0.020  1.090
 PJG  C4   H13  single  0.970  0.020  1.090
 PJG  C4   H14  single  0.970  0.020  1.090
 PJG  C6   H15  single  0.970  0.020  1.090
 PJG  C7   H16  single  0.970  0.020  1.090
 PJG  C8   H17  single  0.970  0.020  1.090
 PJG  C9   H18  single  0.970  0.020  1.090
 PJG  C9   H19  single  0.970  0.020  1.090
 PJG  N14  H20  single  0.890  0.020  1.040
 PJG  N14  H21  single  0.890  0.020  1.040
 PJG  N5   H23  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
 PJG  N5   C1   C4   110.92  3.000
 PJG  C4   C1   C3   108.59  3.000
 PJG  N5   C1   C3   113.50  3.000
 PJG  C3   C1   C2   108.04  3.000
 PJG  C4   C1   C2   108.23  3.000
 PJG  N5   C1   C2   107.39  3.000
 PJG  H2   C2   H1   106.72  3.000
 PJG  H2   C2   C6   110.22  3.000
 PJG  H1   C2   C6   110.15  3.000
 PJG  H2   C2   C1   109.18  3.000
 PJG  H1   C2   C1   109.48  3.000
 PJG  C6   C2   C1   111.00  3.000
 PJG  H4   C3   H3   106.83  3.000
 PJG  H4   C3   C7   110.12  3.000
 PJG  H3   C3   C7   109.62  3.000
 PJG  H4   C3   C1   109.06  3.000
 PJG  H3   C3   C1   110.24  3.000
 PJG  C7   C3   C1   110.89  3.000
 PJG  H8   C12  H7   106.98  3.000
 PJG  H8   C12  C8   110.30  3.000
 PJG  H7   C12  C8   109.88  3.000
 PJG  H8   C12  C7   110.17  3.000
 PJG  H7   C12  C7   110.04  3.000
 PJG  C8   C12  C7   109.44  3.000
 PJG  H10  C13  H9   106.29  3.000
 PJG  H10  C13  N14  108.27  3.000
 PJG  H9   C13  N14  114.00  3.000
 PJG  H10  C13  C9   109.36  3.000
 PJG  H9   C13  C9   108.44  3.000
 PJG  N14  C13  C9   110.34  3.000
 PJG  H12  C10  H11  106.74  3.000
 PJG  H12  C10  C7   110.09  3.000
 PJG  H11  C10  C7   110.35  3.000
 PJG  H12  C10  C6   109.97  3.000
 PJG  H11  C10  C6   110.28  3.000
 PJG  C7   C10  C6   109.38  3.000
 PJG  H14  C4   H13  106.88  3.000
 PJG  H14  C4   C8   109.40  3.000
 PJG  H13  C4   C8   110.28  3.000
 PJG  H14  C4   C1   110.32  3.000
 PJG  H13  C4   C1   109.37  3.000
 PJG  C8   C4   C1   110.52  3.000
 PJG  H15  C6   C10  109.68  3.000
 PJG  H15  C6   C11  109.64  3.000
 PJG  C10  C6   C11  109.35  3.000
 PJG  H15  C6   C2   109.25  3.000
 PJG  C10  C6   C2   109.82  3.000
 PJG  C11  C6   C2   109.09  3.000
 PJG  H16  C7   C10  109.66  3.000
 PJG  H16  C7   C12  109.64  3.000
 PJG  C10  C7   C12  109.38  3.000
 PJG  H16  C7   C3   109.41  3.000
 PJG  C10  C7   C3   109.36  3.000
 PJG  C12  C7   C3   109.38  3.000
 PJG  H17  C8   C4   108.99  3.000
 PJG  H17  C8   C12  109.51  3.000
 PJG  C4   C8   C12  109.65  3.000
 PJG  H17  C8   C11  109.70  3.000
 PJG  C12  C8   C11  109.29  3.000
 PJG  C4   C8   C11  109.69  3.000
 PJG  H21  N14  H20  105.57  3.000
 PJG  H21  N14  C13  109.44  3.000
 PJG  H20  N14  C13  109.60  3.000
 PJG  H23  N5   C9   109.30  3.000
 PJG  H23  N5   C1   107.86  3.000
 PJG  C9   N5   C1   117.91  3.000
 PJG  H6   C11  H5   106.84  3.000
 PJG  H6   C11  C8   110.04  3.000
 PJG  H5   C11  C8   110.24  3.000
 PJG  H6   C11  C6   110.20  3.000
 PJG  H5   C11  C6   110.19  3.000
 PJG  C8   C11  C6   109.31  3.000
 PJG  H19  C9   H18  105.49  3.000
 PJG  H19  C9   N5   108.60  3.000
 PJG  H18  C9   N5   113.03  3.000
 PJG  H19  C9   C13  108.29  3.000
 PJG  H18  C9   C13  108.81  3.000
 PJG  N5   C9   C13  112.30  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
 PJG  Var_01  C13  C9   N5   C1    104.28  30.0  2
 PJG  Var_02  N5   C9   C13  N14  -178.98  30.0  3
 PJG  Var_03  H20  N14  C13  C9    176.48  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
 PJG  chir_01  C1  C4   C2   C3   negativ
 PJG  chir_02  C6  C2   C11  C10  negativ
 PJG  chir_03  C7  C3   C12  C10  positiv
 PJG  chir_04  C8  C12  C11  C4   negativ

