# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:04:05 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCC2(CC1)C3CC4CC(C3)CC2C4
#
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
 E01  E01  (1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine  ligand  41  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_E01
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
 E01  C1    C  CH1   0  -0.050  -3.2482  -0.0089  -0.2463
 E01  C2    C  CH2   0  -0.431  -2.4186  -1.2456   0.0622
 E01  C3    C  CH2   0  -0.430  -1.0903  -1.2357  -0.6884
 E01  C4    C  CT    0  -0.043  -0.2186   0.0018  -0.4027
 E01  C5    C  CH2   0  -0.430  -1.0994   1.2294  -0.7039
 E01  C6    C  CH2   0  -0.431  -2.4285   1.2383   0.0452
 E01  C14   C  CH2   0  -0.433   1.8840   1.2442  -1.1044
 E01  C15   C  CH2   0  -0.429   1.1886   1.2533   1.3036
 E01  C12   C  CH1   0  -0.234   2.3807   1.2644   0.3433
 E01  C11   C  CH1   0  -0.235   0.3222   0.0127   1.0503
 E01  C10   C  CH2   0  -0.429   1.1966  -1.2195   1.3179
 E01  C7    C  CH1   0  -0.217   1.0166   0.0008  -1.3363
 E01  C8    C  CH2   0  -0.432   1.8926  -1.2339  -1.0903
 E01  C9    C  CH1   0  -0.234   2.3887  -1.2342   0.3578
 E01  C13   C  CH2   0  -0.424   3.2361   0.0192   0.5902
 E01  N1    N  NH2   0  -0.807  -4.4685  -0.0081   0.5507
 E01  H1    H  HCH1  0   0.178  -3.4605  -0.0173  -1.3295
 E01  H2B   H  HCH2  0   0.210  -2.2506  -1.3000   1.1432
 E01  H2A   H  HCH2  0   0.223  -2.9780  -2.1472  -0.2073
 E01  H3B   H  HCH2  0   0.231  -0.5594  -2.1616  -0.4695
 E01  H3A   H  HCH2  0   0.212  -1.2908  -1.2624  -1.7670
 E01  H5B   H  HCH2  0   0.231  -0.5756   2.1613  -0.4941
 E01  H5A   H  HCH2  0   0.212  -1.2985   1.2423  -1.7830
 E01  H6B   H  HCH2  0   0.223  -2.9951   2.1315  -0.2372
 E01  H6A   H  HCH2  0   0.210  -2.2613   1.3092   1.1255
 E01  H14A  H  HCH2  0   0.228   1.3414   2.1622  -1.3427
 E01  H14B  H  HCH2  0   0.219   2.7426   1.2173  -1.7842
 E01  H15A  H  HCH2  0   0.220   1.5506   1.2301   2.3370
 E01  H15B  H  HCH2  0   0.226   0.6084   2.1746   1.2122
 E01  H12   H  HCH1  0   0.216   2.9833   2.1625   0.5121
 E01  H11   H  HCH1  0   0.221  -0.5120   0.0141   1.7583
 E01  H10B  H  HCH2  0   0.220   1.5589  -1.1825   2.3509
 E01  H10A  H  HCH2  0   0.227   0.6221  -2.1453   1.2367
 E01  H7    H  HCH1  0   0.209   0.6609  -0.0064  -2.3739
 E01  H8A   H  HCH2  0   0.228   1.3568  -2.1584  -1.3187
 E01  H8B   H  HCH2  0   0.219   2.7515  -1.2085  -1.7700
 E01  H9    H  HCH1  0   0.216   2.9970  -2.1264   0.5371
 E01  H13A  H  HCH2  0   0.216   4.0986   0.0181  -0.0860
 E01  H13B  H  HCH2  0   0.217   3.6336   0.0263   1.6107
 E01  H1B   H  HNH2  0   0.337  -5.0320   0.7950   0.2971
 E01  H1A   H  HNH2  0   0.338  -5.0288  -0.8157   0.3042

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
 E01  C15  C11   single  1.534  0.020  1.534
 E01  C15  C12   single  1.531  0.020  1.531
 E01  C11  C10   single  1.534  0.020  1.534
 E01  C11  C4    single  1.550  0.020  1.550
 E01  C10  C9    single  1.531  0.020  1.531
 E01  C6   C5    single  1.526  0.020  1.526
 E01  C6   C1    single  1.521  0.020  1.521
 E01  N1   C1    single  1.457  0.020  1.457
 E01  C12  C13   single  1.531  0.020  1.531
 E01  C12  C14   single  1.531  0.020  1.531
 E01  C4   C5    single  1.541  0.020  1.541
 E01  C4   C3    single  1.540  0.020  1.540
 E01  C4   C7    single  1.548  0.020  1.548
 E01  C13  C9    single  1.531  0.020  1.531
 E01  C3   C2    single  1.526  0.020  1.526
 E01  C9   C8    single  1.531  0.020  1.531
 E01  C1   C2    single  1.521  0.020  1.521
 E01  C14  C7    single  1.534  0.020  1.534
 E01  C7   C8    single  1.534  0.020  1.534
 E01  C1   H1    single  0.970  0.020  1.090
 E01  C2   H2B   single  0.970  0.020  1.090
 E01  C2   H2A   single  0.970  0.020  1.090
 E01  C3   H3B   single  0.970  0.020  1.090
 E01  C3   H3A   single  0.970  0.020  1.090
 E01  C5   H5B   single  0.970  0.020  1.090
 E01  C5   H5A   single  0.970  0.020  1.090
 E01  C6   H6B   single  0.970  0.020  1.090
 E01  C6   H6A   single  0.970  0.020  1.090
 E01  C14  H14A  single  0.970  0.020  1.090
 E01  C14  H14B  single  0.970  0.020  1.090
 E01  C15  H15A  single  0.970  0.020  1.090
 E01  C15  H15B  single  0.970  0.020  1.090
 E01  C12  H12   single  0.970  0.020  1.090
 E01  C11  H11   single  0.970  0.020  1.090
 E01  C10  H10B  single  0.970  0.020  1.090
 E01  C10  H10A  single  0.970  0.020  1.090
 E01  C7   H7    single  0.970  0.020  1.090
 E01  C8   H8A   single  0.970  0.020  1.090
 E01  C8   H8B   single  0.970  0.020  1.090
 E01  C9   H9    single  0.970  0.020  1.090
 E01  C13  H13A  single  0.970  0.020  1.090
 E01  C13  H13B  single  0.970  0.020  1.090
 E01  N1   H1B   single  0.890  0.020  1.040
 E01  N1   H1A   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
 E01  H1    C1   N1    112.06  3.000
 E01  H1    C1   C6    107.34  3.000
 E01  N1    C1   C6    110.25  3.000
 E01  H1    C1   C2    107.32  3.000
 E01  N1    C1   C2    110.26  3.000
 E01  C6    C1   C2    109.51  3.000
 E01  H2A   C2   H2B   106.28  3.000
 E01  H2A   C2   C3    109.21  3.000
 E01  H2B   C2   C3    110.63  3.000
 E01  H2A   C2   C1    109.94  3.000
 E01  H2B   C2   C1    108.92  3.000
 E01  C3    C2   C1    111.71  3.000
 E01  H3A   C3   H3B   105.41  3.000
 E01  H3A   C3   C4    107.77  3.000
 E01  H3B   C3   C4    111.70  3.000
 E01  H3A   C3   C2    108.92  3.000
 E01  H3B   C3   C2    108.66  3.000
 E01  C4    C3   C2    113.99  3.000
 E01  C7    C4   C11   106.67  3.000
 E01  C7    C4   C5    109.80  3.000
 E01  C11   C4   C5    112.15  3.000
 E01  C7    C4   C3    109.82  3.000
 E01  C5    C4   C3    106.28  3.000
 E01  C11   C4   C3    112.14  3.000
 E01  H5A   C5   H5B   105.46  3.000
 E01  H5A   C5   C6    108.95  3.000
 E01  H5B   C5   C6    108.62  3.000
 E01  H5A   C5   C4    107.78  3.000
 E01  H5B   C5   C4    111.65  3.000
 E01  C6    C5   C4    114.00  3.000
 E01  H6A   C6   H6B   106.30  3.000
 E01  H6A   C6   C5    110.58  3.000
 E01  H6B   C6   C5    109.20  3.000
 E01  H6A   C6   C1    108.93  3.000
 E01  H6B   C6   C1    109.92  3.000
 E01  C5    C6   C1    111.76  3.000
 E01  H14B  C14  H14A  105.93  3.000
 E01  H14B  C14  C7    109.24  3.000
 E01  H14A  C14  C7    111.55  3.000
 E01  H14B  C14  C12   109.45  3.000
 E01  H14A  C14  C12   110.88  3.000
 E01  C7    C14  C12   109.71  3.000
 E01  H15B  C15  H15A  105.80  3.000
 E01  H15B  C15  C11   111.60  3.000
 E01  H15A  C15  C11   108.98  3.000
 E01  H15B  C15  C12   110.79  3.000
 E01  H15A  C15  C12   109.55  3.000
 E01  C11   C15  C12   110.00  3.000
 E01  H12   C12  C13   109.56  3.000
 E01  H12   C12  C15   109.75  3.000
 E01  C13   C12  C15   109.15  3.000
 E01  H12   C12  C14   109.60  3.000
 E01  C13   C12  C14   108.85  3.000
 E01  C15   C12  C14   109.91  3.000
 E01  H11   C11  C10   108.83  3.000
 E01  H11   C11  C15   108.83  3.000
 E01  C10   C11  C15   107.38  3.000
 E01  H11   C11  C4    109.90  3.000
 E01  C10   C11  C4    110.89  3.000
 E01  C15   C11  C4    110.94  3.000
 E01  H10A  C10  H10B  105.82  3.000
 E01  H10A  C10  C9    110.78  3.000
 E01  H10B  C10  C9    109.52  3.000
 E01  H10A  C10  C11   111.59  3.000
 E01  H10B  C10  C11   109.01  3.000
 E01  C9    C10  C11   110.01  3.000
 E01  H7    C7   C8    109.37  3.000
 E01  H7    C7   C14   109.37  3.000
 E01  C8    C7   C14   107.78  3.000
 E01  H7    C7   C4    108.17  3.000
 E01  C8    C7   C4    111.07  3.000
 E01  C14   C7   C4    111.07  3.000
 E01  H8B   C8   H8A   105.93  3.000
 E01  H8B   C8   C9    109.44  3.000
 E01  H8A   C8   C9    110.89  3.000
 E01  H8B   C8   C7    109.24  3.000
 E01  H8A   C8   C7    111.56  3.000
 E01  C9    C8   C7    109.69  3.000
 E01  H9    C9   C13   109.57  3.000
 E01  H9    C9   C8    109.59  3.000
 E01  C13   C9   C8    108.84  3.000
 E01  H9    C9   C10   109.75  3.000
 E01  C8    C9   C10   109.93  3.000
 E01  C13   C9   C10   109.15  3.000
 E01  H13B  C13  H13A  106.82  3.000
 E01  H13B  C13  C9    110.34  3.000
 E01  H13A  C13  C9    109.94  3.000
 E01  H13B  C13  C12   110.36  3.000
 E01  H13A  C13  C12   109.95  3.000
 E01  C9    C13  C12   109.40  3.000
 E01  H1A   N1   H1B   105.26  3.000
 E01  H1A   N1   C1    109.24  3.000
 E01  H1B   N1   C1    109.22  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
 E01  Var_01  C4   C5  C6  C1  -57.28  30.0  1
 E01  Var_02  C4   C3  C2  C1   57.40  30.0  1
 E01  Var_03  C11  C4  C3  C2   68.47  30.0  3
 E01  Var_04  C6   C5  C4  C3   54.34  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
 E01  chir_01  C1   C6   N1   C2   positiv
 E01  chir_02  C12  C15  C13  C14  negativ
 E01  chir_03  C11  C4   C10  C15  negativ
 E01  chir_04  C7   C4   C14  C8   negativ
 E01  chir_05  C9   C8   C13  C10  negativ

