# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 00:01:59 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-{2-oxo-2-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylamino]ethyl}-2-sulfanylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Sc1ccccc1C(=O)NCC(=O)NC23CC4CC(CC(C4)C2)C3
#
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
 2W7  2W7  N-{2-oxo-2-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylamino]ethyl}-2-sulfanylbenzamide  ligand  48  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2W7
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
 2W7  S2    S  S2    0  -0.191  -5.5613  -1.2707   1.6494
 2W7  C5    C  CR6   0  -0.164  -5.2360   0.0650   0.5377
 2W7  C6    C  CR16  0  -0.239  -6.2166   1.0554   0.4949
 2W7  C10   C  CR6   0  -0.000  -4.0614   0.2348  -0.2081
 2W7  C7    C  CR16  0  -0.241  -6.0547   2.1864  -0.2882
 2W7  C8    C  CR16  0  -0.255  -4.9072   2.3459  -1.0507
 2W7  C9    C  CR16  0  -0.268  -3.9230   1.3728  -1.0030
 2W7  C11   C  C     0   0.504  -2.9658  -0.7841  -0.2236
 2W7  O2    O  O     0  -0.490  -3.1849  -1.9848  -0.3433
 2W7  N3    N  NH1   0  -0.634  -1.7314  -0.2828  -0.1172
 2W7  C12   C  CH2   0  -0.376  -0.5540  -1.1033  -0.1659
 2W7  C13   C  C     0   0.529   0.6791  -0.2182  -0.0169
 2W7  O3    O  O     0  -0.494   0.5704   0.9757   0.2273
 2W7  N4    N  NH1   0  -0.685   1.8333  -0.8736  -0.1676
 2W7  C14   C  CT    0   0.172   3.1823  -0.3236  -0.0349
 2W7  C18   C  CH2   0  -0.421   3.4458   0.7861  -1.0624
 2W7  C17   C  CH1   0  -0.255   4.8899   1.2783  -0.9362
 2W7  C19   C  CH2   0  -0.418   5.1232   1.8207   0.4756
 2W7  C23   C  CH1   0  -0.255   4.8821   0.7060   1.4960
 2W7  C24   C  CH2   0  -0.420   3.4379   0.2106   1.3811
 2W7  C25   C  CH2   0  -0.418   5.8427  -0.4531   1.2268
 2W7  C20   C  CH1   0  -0.250   5.6024  -0.9929  -0.1841
 2W7  C26   C  CH2   0  -0.464   4.1568  -1.4783  -0.3045
 2W7  C16   C  CH2   0  -0.418   5.8513   0.1197  -1.2043
 2W7  H1    H  HSH1  0   0.258  -4.7869  -2.1990   1.0814
 2W7  H6    H  HCR6  0   0.272  -7.1235   0.9336   1.0741
 2W7  H7    H  HCR6  0   0.269  -6.8353   2.9350  -0.3092
 2W7  H8    H  HCR6  0   0.266  -4.7790   3.2165  -1.6793
 2W7  H9    H  HCR6  0   0.270  -3.0324   1.4916  -1.6076
 2W7  H3    H  HNH1  0   0.409  -1.5888   0.7003   0.0646
 2W7  H122  H  HCH2  0   0.283  -0.5555  -1.8452   0.6391
 2W7  H121  H  HCH2  0   0.280  -0.4999  -1.6579  -1.1068
 2W7  H4    H  HNH1  0   0.405   1.7716  -1.8616  -0.3637
 2W7  HZ12  H  HCH2  0   0.226   3.2636   0.3969  -2.0696
 2W7  HZ11  H  HCH2  0   0.240   2.7538   1.6163  -0.9094
 2W7  HY1   H  HCH1  0   0.228   5.0572   2.0729  -1.6692
 2W7  HX22  H  HCH2  0   0.225   6.1463   2.1991   0.5673
 2W7  HX21  H  HCH2  0   0.224   4.4539   2.6642   0.6735
 2W7  HY3   H  HCH1  0   0.228   5.0460   1.0898   2.5071
 2W7  HZ21  H  HCH2  0   0.239   2.7437   1.0215   1.6108
 2W7  HZ22  H  HCH2  0   0.226   3.2521  -0.5875   2.1080
 2W7  HX31  H  HCH2  0   0.225   6.8796  -0.1182   1.3310
 2W7  HX32  H  HCH2  0   0.224   5.6913  -1.2454   1.9666
 2W7  HY2   H  HCH1  0   0.231   6.2757  -1.8320  -0.3796
 2W7  HZ32  H  HCH2  0   0.239   3.9714  -2.2892   0.4087
 2W7  HZ31  H  HCH2  0   0.239   3.9770  -1.8809  -1.3077
 2W7  HX12  H  HCH2  0   0.224   5.7090  -0.2610  -2.2209
 2W7  HX11  H  HCH2  0   0.225   6.8876   0.4661  -1.1363

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
 2W7  C19  C23   single    1.530  0.020  1.530
 2W7  C19  C17   single    1.530  0.020  1.530
 2W7  C23  C25   single    1.529  0.020  1.529
 2W7  C23  C24   single    1.531  0.020  1.531
 2W7  C25  C20   single    1.530  0.020  1.530
 2W7  C24  C14   single    1.535  0.020  1.535
 2W7  C17  C16   single    1.529  0.020  1.529
 2W7  C17  C18   single    1.531  0.020  1.531
 2W7  C16  C20   single    1.530  0.020  1.530
 2W7  C20  C26   single    1.530  0.020  1.530
 2W7  O3   C13   double    1.223  0.020  1.223
 2W7  C18  C14   single    1.535  0.020  1.535
 2W7  C14  C26   single    1.535  0.020  1.535
 2W7  C14  N4    single    1.463  0.020  1.463
 2W7  C13  N4    single    1.336  0.020  1.336
 2W7  C13  C12   single    1.525  0.020  1.525
 2W7  C12  N3    single    1.436  0.020  1.436
 2W7  N3   C11   single    1.337  0.020  1.337
 2W7  C9   C8    aromatic  1.385  0.020  1.385
 2W7  C9   C10   aromatic  1.395  0.020  1.395
 2W7  C8   C7    aromatic  1.387  0.020  1.387
 2W7  C11  C10   single    1.496  0.020  1.496
 2W7  C11  O2    double    1.226  0.020  1.226
 2W7  C10  C5    aromatic  1.402  0.020  1.402
 2W7  C7   C6    aromatic  1.385  0.020  1.385
 2W7  C5   C6    aromatic  1.394  0.020  1.394
 2W7  C5   S2    single    1.768  0.020  1.768
 2W7  S2   H1    single    1.200  0.020  1.300
 2W7  C6   H6    single    0.930  0.020  1.080
 2W7  C7   H7    single    0.930  0.020  1.080
 2W7  C8   H8    single    0.930  0.020  1.080
 2W7  C9   H9    single    0.930  0.020  1.080
 2W7  N3   H3    single    0.860  0.020  1.020
 2W7  C12  H122  single    0.970  0.020  1.090
 2W7  C12  H121  single    0.970  0.020  1.090
 2W7  N4   H4    single    0.860  0.020  1.020
 2W7  C18  HZ12  single    0.970  0.020  1.090
 2W7  C18  HZ11  single    0.970  0.020  1.090
 2W7  C17  HY1   single    0.970  0.020  1.090
 2W7  C19  HX22  single    0.970  0.020  1.090
 2W7  C19  HX21  single    0.970  0.020  1.090
 2W7  C23  HY3   single    0.970  0.020  1.090
 2W7  C24  HZ21  single    0.970  0.020  1.090
 2W7  C24  HZ22  single    0.970  0.020  1.090
 2W7  C25  HX31  single    0.970  0.020  1.090
 2W7  C25  HX32  single    0.970  0.020  1.090
 2W7  C20  HY2   single    0.970  0.020  1.090
 2W7  C26  HZ32  single    0.970  0.020  1.090
 2W7  C26  HZ31  single    0.970  0.020  1.090
 2W7  C16  HX12  single    0.970  0.020  1.090
 2W7  C16  HX11  single    0.970  0.020  1.090

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
 2W7  H1    S2   C5     98.69  3.000
 2W7  C10   C5   C6    119.14  3.000
 2W7  C6    C5   S2    115.25  3.000
 2W7  C10   C5   S2    125.47  3.000
 2W7  H6    C6   C7    119.48  3.000
 2W7  H6    C6   C5    119.52  3.000
 2W7  C7    C6   C5    121.00  3.000
 2W7  C11   C10  C9    118.49  3.000
 2W7  C11   C10  C5    122.45  3.000
 2W7  C9    C10  C5    119.02  3.000
 2W7  H7    C7   C8    120.45  3.000
 2W7  H7    C7   C6    119.45  3.000
 2W7  C8    C7   C6    120.10  3.000
 2W7  H8    C8   C9    120.10  3.000
 2W7  H8    C8   C7    120.69  3.000
 2W7  C9    C8   C7    119.22  3.000
 2W7  H9    C9   C8    119.22  3.000
 2W7  H9    C9   C10   119.29  3.000
 2W7  C8    C9   C10   121.49  3.000
 2W7  N3    C11  O2    122.68  3.000
 2W7  O2    C11  C10   122.47  3.000
 2W7  N3    C11  C10   114.84  3.000
 2W7  H3    N3   C12   116.52  3.000
 2W7  H3    N3   C11   120.65  3.000
 2W7  C12   N3   C11   122.71  3.000
 2W7  H121  C12  H122  106.80  3.000
 2W7  H121  C12  C13   109.78  3.000
 2W7  H122  C12  C13   108.82  3.000
 2W7  H121  C12  N3    111.07  3.000
 2W7  H122  C12  N3    111.18  3.000
 2W7  C13   C12  N3    109.15  3.000
 2W7  N4    C13  O3    125.31  3.000
 2W7  N4    C13  C12   113.75  3.000
 2W7  O3    C13  C12   120.93  3.000
 2W7  H4    N4   C14   116.24  3.000
 2W7  H4    N4   C13   116.71  3.000
 2W7  C14   N4   C13   127.02  3.000
 2W7  C26   C14  C24   108.55  3.000
 2W7  C26   C14  C18   108.50  3.000
 2W7  C24   C14  C18   109.71  3.000
 2W7  C26   C14  N4    106.66  3.000
 2W7  C18   C14  N4    111.68  3.000
 2W7  C24   C14  N4    111.60  3.000
 2W7  HZ11  C18  HZ12  107.08  3.000
 2W7  HZ11  C18  C17   109.99  3.000
 2W7  HZ12  C18  C17   110.31  3.000
 2W7  HZ11  C18  C14   110.31  3.000
 2W7  HZ12  C18  C14   109.27  3.000
 2W7  C17   C18  C14   109.83  3.000
 2W7  HY1   C17  C16   109.68  3.000
 2W7  HY1   C17  C19   109.72  3.000
 2W7  C16   C17  C19   109.54  3.000
 2W7  HY1   C17  C18   108.82  3.000
 2W7  C16   C17  C18   109.57  3.000
 2W7  C19   C17  C18   109.50  3.000
 2W7  HX21  C19  HX22  106.85  3.000
 2W7  HX21  C19  C23   110.14  3.000
 2W7  HX22  C19  C23   110.07  3.000
 2W7  HX21  C19  C17   110.28  3.000
 2W7  HX22  C19  C17   110.02  3.000
 2W7  C23   C19  C17   109.45  3.000
 2W7  HY3   C23  C25   109.54  3.000
 2W7  HY3   C23  C24   108.92  3.000
 2W7  C25   C23  C24   109.51  3.000
 2W7  HY3   C23  C19   109.71  3.000
 2W7  C24   C23  C19   109.53  3.000
 2W7  C25   C23  C19   109.62  3.000
 2W7  HZ22  C24  HZ21  107.07  3.000
 2W7  HZ22  C24  C23   110.24  3.000
 2W7  HZ21  C24  C23   110.10  3.000
 2W7  HZ22  C24  C14   109.29  3.000
 2W7  HZ21  C24  C14   110.28  3.000
 2W7  C23   C24  C14   109.81  3.000
 2W7  HX32  C25  HX31  106.75  3.000
 2W7  HX32  C25  C20   110.26  3.000
 2W7  HX31  C25  C20   110.16  3.000
 2W7  HX32  C25  C23   110.05  3.000
 2W7  HX31  C25  C23   110.26  3.000
 2W7  C20   C25  C23   109.34  3.000
 2W7  HY2   C20  C16   109.80  3.000
 2W7  HY2   C20  C26   108.93  3.000
 2W7  C16   C20  C26   109.40  3.000
 2W7  HY2   C20  C25   109.81  3.000
 2W7  C26   C20  C25   109.45  3.000
 2W7  C16   C20  C25   109.44  3.000
 2W7  HZ31  C26  HZ32  107.22  3.000
 2W7  HZ31  C26  C20   110.10  3.000
 2W7  HZ32  C26  C20   110.09  3.000
 2W7  HZ31  C26  C14   109.45  3.000
 2W7  HZ32  C26  C14   109.58  3.000
 2W7  C20   C26  C14   110.33  3.000
 2W7  HX11  C16  HX12  106.90  3.000
 2W7  HX11  C16  C20   110.05  3.000
 2W7  HX12  C16  C20   110.19  3.000
 2W7  HX11  C16  C17   110.15  3.000
 2W7  HX12  C16  C17   110.15  3.000
 2W7  C20   C16  C17   109.38  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
 2W7  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 2W7  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 2W7  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 2W7  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 2W7  CONST_05  C7   C8   C9   C10     0.00   0.0  0
 2W7  CONST_06  C7   C6   C5   C10     0.00   0.0  0
 2W7  CONST_07  C9   C10  C5   S2    180.00   0.0  0
 2W7  CONST_08  C7   C6   C5   S2    180.00   0.0  0
 2W7  CONST_09  C11  C10  C5   C6    180.00   0.0  0
 2W7  CONST_10  C11  C10  C9   C8    180.00   0.0  0
 2W7  CONST_11  H9   C9   C10  C5    180.00   0.0  0
 2W7  CONST_12  H7   C7   C6   C5    180.00   0.0  0
 2W7  CONST_13  H8   C8   C7   C6    180.00   0.0  0
 2W7  CONST_14  H6   C6   C5   C10   180.00   0.0  0
 2W7  CONST_15  C12  N3   C11  C10   180.00   0.0  0
 2W7  CONST_16  C14  N4   C13  C12   180.00   0.0  0
 2W7  CONST_17  C14  N4   C13  O3      0.00   0.0  0
 2W7  CONST_18  H3   N3   C11  C10     0.00   0.0  0
 2W7  CONST_19  C12  N3   C11  O2      0.00   0.0  0
 2W7  CONST_20  H4   N4   C13  C12     0.00   0.0  0
 2W7  Var_01    N3   C11  C10  C5   -136.09  30.0  2
 2W7  Var_02    C13  C12  N3   C11   179.94  30.0  1
 2W7  Var_03    O3   C13  C12  N3      6.06  30.0  1

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
 2W7  chir_01  C14  C18  C26  N4   positiv
 2W7  chir_02  C17  C18  C16  C19  positiv
 2W7  chir_03  C23  C19  C25  C24  positiv
 2W7  chir_04  C20  C25  C16  C26  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 2W7  plan-1  S2   0.020
 2W7  plan-1  C5   0.020
 2W7  plan-1  C6   0.020
 2W7  plan-1  C10  0.020
 2W7  plan-1  C7   0.020
 2W7  plan-1  C8   0.020
 2W7  plan-1  C9   0.020
 2W7  plan-1  C11  0.020
 2W7  plan-1  H6   0.020
 2W7  plan-1  H7   0.020
 2W7  plan-1  H8   0.020
 2W7  plan-1  H9   0.020
 2W7  plan-2  C10  0.020
 2W7  plan-2  C11  0.020
 2W7  plan-2  O2   0.020
 2W7  plan-2  N3   0.020
 2W7  plan-2  C12  0.020
 2W7  plan-2  H3   0.020
 2W7  plan-3  C12  0.020
 2W7  plan-3  C13  0.020
 2W7  plan-3  O3   0.020
 2W7  plan-3  N4   0.020
 2W7  plan-3  C14  0.020
 2W7  plan-3  H4   0.020

