# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 03:09:11 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: methyl (1R,2R,3S,5S)-8-methyl-3-[(phenylcarbonyl)oxy]-8-azabicyclo[3.2.1]octane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H]1[C@H](C[C@@H]2CC[C@H]1N2C)OC(=O)c3ccccc3
#
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
 COC  COC  'methyl (1R,2R,3S,5S)-8-methyl-3-[(phenylcarbonyl)oxy]-8-azabicyclo[3.2.1]octane-2-carboxylate'  ligand  43  22  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_COC
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
 COC  C1   C  CH3   0  -0.428   3.3382   0.7505  -0.5049
 COC  O5   O  O2    0  -0.433   1.9680   0.3973  -0.6895
 COC  C6   C  C     0   0.627   1.7079  -0.7735  -1.2367
 COC  O7   O  O     0  -0.469   2.5684  -1.5470  -1.5856
 COC  C8   C  CH1   0  -0.393   0.2380  -1.0812  -1.4246
 COC  C10  C  CR15  0  -0.138  -0.0880  -0.9117  -2.9222
 COC  N12  N  NR5   0  -0.389   0.0654   0.5004  -3.2449
 COC  C14  C  CH3   0  -0.530   0.2021   0.7387  -4.6693
 COC  C18  C  CH2   0  -0.475  -1.5631  -1.2513  -3.2378
 COC  C21  C  CH2   0  -0.476  -2.2865   0.1019  -3.0930
 COC  C24  C  CR15  0  -0.134  -1.1562   1.0731  -2.6795
 COC  C26  C  CH2   0  -0.442  -0.9965   1.1364  -1.1601
 COC  C29  C  CH1   0   0.051  -0.7627  -0.2649  -0.6087
 COC  O1   O  O2    0  -0.475  -0.3149  -0.2380   0.7522
 COC  C2   C  C     0   0.607  -1.2069  -0.1303   1.7245
 COC  O3   O  O     0  -0.446  -2.4003  -0.0789   1.5464
 COC  C4   C  CR6   0  -0.095  -0.5736  -0.0783   3.0669
 COC  C5   C  CR16  0  -0.257  -1.4041  -0.0298   4.1854
 COC  C7   C  CR16  0  -0.242  -0.8592   0.0237   5.4581
 COC  C9   C  CR16  0  -0.243   0.5199   0.0320   5.6245
 COC  C11  C  CR16  0  -0.240   1.3524  -0.0128   4.5136
 COC  C13  C  CR16  0  -0.271   0.8114  -0.0684   3.2384
 COC  H2   H  HCH3  0   0.238   3.8534   0.0344   0.1349
 COC  H3   H  HCH3  0   0.240   3.8630   0.8230  -1.4575
 COC  H4   H  HCH3  0   0.250   3.3317   1.7236  -0.0230
 COC  H9   H  HCH1  0   0.297   0.1164  -2.1386  -1.1686
 COC  H11  H  HCR5  0   0.263   0.6059  -1.5204  -3.5043
 COC  H15  H  HCH3  0   0.236   0.2909   1.8098  -4.8525
 COC  H16  H  HCH3  0   0.236   1.1152   0.2638  -5.0296
 COC  H17  H  HCH3  0   0.203  -0.6302   0.3637  -5.2813
 COC  H19  H  HCH2  0   0.249  -1.9612  -2.0250  -2.5792
 COC  H20  H  HCH2  0   0.254  -1.6446  -1.6361  -4.2545
 COC  H22  H  HCH2  0   0.244  -3.0931   0.0754  -2.3583
 COC  H23  H  HCH2  0   0.249  -2.7336   0.4116  -4.0381
 COC  H25  H  HCR5  0   0.248  -1.3140   2.0827  -3.0630
 COC  H27  H  HCH2  0   0.244  -1.8975   1.5628  -0.7138
 COC  H28  H  HCH2  0   0.249  -0.1628   1.7937  -0.9128
 COC  H30  H  HCH1  0   0.265  -1.7073  -0.8149  -0.6416
 COC  H6   H  HCR6  0   0.263  -2.4786  -0.0349   4.0614
 COC  H8   H  HCR6  0   0.265  -1.5116   0.0600   6.3203
 COC  H10  H  HCR6  0   0.267   0.9451   0.0751   6.6189
 COC  H12  H  HCR6  0   0.266   2.4269  -0.0038   4.6393
 COC  H14  H  HCR6  0   0.265   1.4724  -0.0970   2.3834

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
 COC  C1   O5   single    1.427  0.020  1.427
 COC  C1   H2   single    0.970  0.020  1.090
 COC  C1   H3   single    0.970  0.020  1.090
 COC  C1   H4   single    0.970  0.020  1.090
 COC  O5   C6   single    1.318  0.020  1.318
 COC  C6   O7   double    1.209  0.020  1.209
 COC  C6   C8   single    1.513  0.020  1.513
 COC  C8   C10  single    1.542  0.020  1.542
 COC  C8   C29  single    1.528  0.020  1.528
 COC  C8   H9   single    0.970  0.020  1.090
 COC  C10  N12  single    1.457  0.020  1.457
 COC  C10  C18  single    1.546  0.020  1.546
 COC  C10  H11  single    0.970  0.020  1.090
 COC  N12  C14  single    1.451  0.020  1.451
 COC  N12  C24  single    1.463  0.020  1.463
 COC  C14  H15  single    0.970  0.020  1.090
 COC  C14  H16  single    0.970  0.020  1.090
 COC  C14  H17  single    0.970  0.020  1.090
 COC  C18  C21  single    1.541  0.020  1.541
 COC  C18  H19  single    0.970  0.020  1.090
 COC  C18  H20  single    0.970  0.020  1.090
 COC  C21  C24  single    1.547  0.020  1.547
 COC  C21  H22  single    0.970  0.020  1.090
 COC  C21  H23  single    0.970  0.020  1.090
 COC  C24  C26  single    1.529  0.020  1.529
 COC  C24  H25  single    0.970  0.020  1.090
 COC  C26  C29  single    1.524  0.020  1.524
 COC  C26  H27  single    0.970  0.020  1.090
 COC  C26  H28  single    0.970  0.020  1.090
 COC  C29  O1   single    1.433  0.020  1.433
 COC  C29  H30  single    0.970  0.020  1.090
 COC  O1   C2   single    1.324  0.020  1.324
 COC  C2   O3   double    1.208  0.020  1.208
 COC  C2   C4   single    1.485  0.020  1.485
 COC  C4   C5   aromatic  1.394  0.020  1.394
 COC  C4   C13  aromatic  1.396  0.020  1.396
 COC  C5   C7   aromatic  1.385  0.020  1.385
 COC  C5   H6   single    0.930  0.020  1.080
 COC  C7   C9   aromatic  1.389  0.020  1.389
 COC  C7   H8   single    0.930  0.020  1.080
 COC  C9   C11  aromatic  1.389  0.020  1.389
 COC  C9   H10  single    0.930  0.020  1.080
 COC  C11  C13  aromatic  1.386  0.020  1.386
 COC  C11  H12  single    0.930  0.020  1.080
 COC  C13  H14  single    0.930  0.020  1.080

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
 COC  H4   C1   H3   109.34  3.000
 COC  H4   C1   H2   109.34  3.000
 COC  H3   C1   H2   109.22  3.000
 COC  H4   C1   O5   105.87  3.000
 COC  H3   C1   O5   111.45  3.000
 COC  H2   C1   O5   111.55  3.000
 COC  C6   O5   C1   117.58  3.000
 COC  C8   C6   O7   121.70  3.000
 COC  C8   C6   O5   115.07  3.000
 COC  O7   C6   O5   123.21  3.000
 COC  H9   C8   C29  108.57  3.000
 COC  H9   C8   C10  108.05  3.000
 COC  C29  C8   C10  108.76  3.000
 COC  H9   C8   C6   105.97  3.000
 COC  C29  C8   C6   117.46  3.000
 COC  C10  C8   C6   107.67  3.000
 COC  H11  C10  C18  112.04  3.000
 COC  H11  C10  N12  110.83  3.000
 COC  C18  C10  N12  105.55  3.000
 COC  H11  C10  C8   108.81  3.000
 COC  C18  C10  C8   112.07  3.000
 COC  N12  C10  C8   107.43  3.000
 COC  C24  N12  C14  113.20  3.000
 COC  C24  N12  C10  101.89  3.000
 COC  C14  N12  C10  112.75  3.000
 COC  H17  C14  H16  107.55  3.000
 COC  H17  C14  H15  107.66  3.000
 COC  H16  C14  H15  107.70  3.000
 COC  H17  C14  N12  114.79  3.000
 COC  H16  C14  N12  109.38  3.000
 COC  H15  C14  N12  109.51  3.000
 COC  H20  C18  H19  106.58  3.000
 COC  H20  C18  C21  111.25  3.000
 COC  H19  C18  C21  113.24  3.000
 COC  H20  C18  C10  109.83  3.000
 COC  H19  C18  C10  112.37  3.000
 COC  C21  C18  C10  103.64  3.000
 COC  H23  C21  H22  106.70  3.000
 COC  H23  C21  C24  110.67  3.000
 COC  H22  C21  C24  112.05  3.000
 COC  H23  C21  C18  111.12  3.000
 COC  H22  C21  C18  112.88  3.000
 COC  C24  C21  C18  103.50  3.000
 COC  H25  C24  C26  109.02  3.000
 COC  H25  C24  C21  112.41  3.000
 COC  C26  C24  C21  111.59  3.000
 COC  H25  C24  N12  110.31  3.000
 COC  C26  C24  N12  108.24  3.000
 COC  C21  C24  N12  105.14  3.000
 COC  H28  C26  H27  107.63  3.000
 COC  H28  C26  C29  110.79  3.000
 COC  H27  C26  C29  109.73  3.000
 COC  H28  C26  C24  109.28  3.000
 COC  H27  C26  C24  109.64  3.000
 COC  C29  C26  C24  109.73  3.000
 COC  H30  C29  O1   107.94  3.000
 COC  H30  C29  C26  108.60  3.000
 COC  O1   C29  C26  111.98  3.000
 COC  H30  C29  C8   106.32  3.000
 COC  O1   C29  C8   108.22  3.000
 COC  C26  C29  C8   113.49  3.000
 COC  C2   O1   C29  119.25  3.000
 COC  C4   C2   O3   123.58  3.000
 COC  C4   C2   O1   112.30  3.000
 COC  O3   C2   O1   124.12  3.000
 COC  C13  C4   C5   119.50  3.000
 COC  C13  C4   C2   122.31  3.000
 COC  C5   C4   C2   118.19  3.000
 COC  H6   C5   C7   119.74  3.000
 COC  H6   C5   C4   119.99  3.000
 COC  C7   C5   C4   120.27  3.000
 COC  H8   C7   C9   120.20  3.000
 COC  H8   C7   C5   119.76  3.000
 COC  C9   C7   C5   120.05  3.000
 COC  H10  C9   C11  120.05  3.000
 COC  H10  C9   C7   120.02  3.000
 COC  C11  C9   C7   119.93  3.000
 COC  H12  C11  C13  119.66  3.000
 COC  H12  C11  C9   120.14  3.000
 COC  C13  C11  C9   120.20  3.000
 COC  H14  C13  C11  119.33  3.000
 COC  H14  C13  C4   120.62  3.000
 COC  C11  C13  C4   120.04  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
 COC  CONST_01  C9   C7   C5   C4      0.00   0.0  0
 COC  CONST_02  C9   C11  C13  C4      0.00   0.0  0
 COC  CONST_03  C11  C13  C4   C5      0.00   0.0  0
 COC  CONST_04  C11  C9   C7   C5      0.00   0.0  0
 COC  CONST_05  C13  C4   C5   C7      0.00   0.0  0
 COC  CONST_06  C13  C11  C9   C7      0.00   0.0  0
 COC  CONST_07  C7   C5   C4   C2    180.00   0.0  0
 COC  CONST_08  C11  C13  C4   C2    180.00   0.0  0
 COC  CONST_09  H8   C7   C5   C4    180.00   0.0  0
 COC  CONST_10  H12  C11  C13  C4    180.00   0.0  0
 COC  CONST_11  H14  C13  C4   C5    180.00   0.0  0
 COC  CONST_12  H10  C9   C7   C5    180.00   0.0  0
 COC  CONST_13  H6   C5   C7   C9    180.00   0.0  0
 COC  Var_01    C24  C21  C18  C10    -1.16  30.0  3
 COC  Var_02    C4   C2   O1   C29  -178.37  30.0  3
 COC  Var_03    C5   C4   C2   O1   -176.97  30.0  2
 COC  Var_04    H15  C14  N12  C10   178.76  30.0  3
 COC  Var_05    C8   C6   O5   C1   -179.13  30.0  3
 COC  Var_06    H2   C1   O5   C6    -59.64  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
 COC  chir_01  C8   C6   C10  C29  positiv
 COC  chir_02  C10  N12  C18  C8   positiv
 COC  chir_03  C24  N12  C26  C21  positiv
 COC  chir_04  C29  O1   C26  C8   negativ

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
 COC  plan-1  C2   0.020
 COC  plan-1  C4   0.020
 COC  plan-1  C5   0.020
 COC  plan-1  C7   0.020
 COC  plan-1  C9   0.020
 COC  plan-1  C11  0.020
 COC  plan-1  C13  0.020
 COC  plan-1  H6   0.020
 COC  plan-1  H8   0.020
 COC  plan-1  H10  0.020
 COC  plan-1  H12  0.020
 COC  plan-1  H14  0.020
 COC  plan-2  O5   0.020
 COC  plan-2  C6   0.020
 COC  plan-2  O7   0.020
 COC  plan-2  C8   0.020
 COC  plan-3  O1   0.020
 COC  plan-3  C2   0.020
 COC  plan-3  O3   0.020
 COC  plan-3  C4   0.020

