# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 13:12:37 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: methyl (1R,2R,3S,5S)-3-{[(S)-hydroxy(phenyl)phosphoryl]oxy}-8-methyl-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)O[P@](O)(=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
 TGN  TGN  'methyl (1R,2R,3S,5S)-3-{[(S)-hydroxy(phenyl)phosphoryl]oxy}-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate'  ligand  45  23  .  2021-08-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TGN
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
 TGN  C8    C  CH1   0  -0.402  -1.6481   0.0349  -0.7123
 TGN  C10   C  CH1   0  -0.126  -3.1652  -0.1846  -0.5818
 TGN  N12   N  NT    0  -0.372  -3.5626  -0.0811   0.8112
 TGN  C14   C  CH3   0  -0.531  -4.9904   0.1000   0.9774
 TGN  C18   C  CH2   0  -0.472  -3.5268  -1.6341  -0.9956
 TGN  C21   C  CH2   0  -0.480  -3.4499  -2.4175   0.3308
 TGN  C24   C  CH1   0  -0.141  -3.0635  -1.3334   1.3658
 TGN  C26   C  CH2   0  -0.426  -1.5494  -1.1935   1.5201
 TGN  C29   C  CH1   0   0.033  -0.9005  -0.9879   0.1638
 TGN  O1    O  O2    0  -0.611   0.4592  -0.5670   0.3710
 TGN  P2    P  P     0   1.372   1.6566  -1.0782  -0.5674
 TGN  O17   O  O     0  -0.694   1.8706  -2.5420  -0.6221
 TGN  O3    O  OH1   0  -0.746   1.3293  -0.5450  -2.0485
 TGN  C4    C  CR6   0  -0.238   3.0355  -0.1264   0.0667
 TGN  C5    C  CR16  0  -0.269   2.8736   1.1164   0.6780
 TGN  C13   C  CR16  0  -0.276   4.3166  -0.6478  -0.1089
 TGN  C7    C  CR16  0  -0.232   3.9842   1.8322   1.0989
 TGN  C9    C  CR16  0  -0.251   5.2593   1.3146   0.9117
 TGN  C11   C  CR16  0  -0.234   5.4242   0.0737   0.3111
 TGN  C6    C  C     0   0.618  -1.2182   1.4452  -0.3733
 TGN  O7    O  O     0  -0.416  -1.5620   2.0937   0.5765
 TGN  O5    O  O2    0  -0.478  -0.3583   1.9106  -1.2878
 TGN  C1    C  CH3   0  -0.432   0.1286   3.2445  -1.1159
 TGN  H8    H  HCH1  0   0.287  -1.3823  -0.1510  -1.7556
 TGN  H10   H  HCH1  0   0.263  -3.6846   0.5583  -1.1907
 TGN  H141  H  HCH3  0   0.200  -5.6136  -0.6943   0.5415
 TGN  H142  H  HCH3  0   0.235  -5.2283   0.1576   2.0402
 TGN  H143  H  HCH3  0   0.235  -5.2916   1.0426   0.5193
 TGN  H181  H  HCH2  0   0.247  -2.8619  -2.0267  -1.7669
 TGN  H182  H  HCH2  0   0.254  -4.5346  -1.6614  -1.4102
 TGN  H211  H  HCH2  0   0.245  -2.7298  -3.2369   0.2997
 TGN  H212  H  HCH2  0   0.250  -4.4148  -2.8582   0.5827
 TGN  H24   H  HCH1  0   0.249  -3.5054  -1.5191   2.3463
 TGN  H261  H  HCH2  0   0.250  -1.1280  -2.0861   1.9882
 TGN  H262  H  HCH2  0   0.245  -1.3404  -0.3443   2.1742
 TGN  H29   H  HCH1  0   0.269  -0.9009  -1.9417  -0.3732
 TGN  HO3   H  HOH1  0   0.485   1.0739   0.3863  -2.1156
 TGN  H5    H  HCR6  0   0.266   1.8882   1.5278   0.8494
 TGN  H13   H  HCR6  0   0.273   4.4558  -1.6168  -0.5708
 TGN  H7    H  HCR6  0   0.268   3.8517   2.7935   1.5772
 TGN  H9    H  HCR6  0   0.270   6.1248   1.8766   1.2374
 TGN  H11   H  HCR6  0   0.268   6.4158  -0.3353   0.1713
 TGN  H11A  H  HCH3  0   0.250  -0.6818   3.9689  -1.1860
 TGN  H12   H  HCH3  0   0.237   0.6372   3.3677  -0.1603
 TGN  H13A  H  HCH3  0   0.257   0.8345   3.4106  -1.9239

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
 TGN  C8   C10   single    1.538  0.020  1.538
 TGN  C8   C29   single    1.540  0.020  1.540
 TGN  C8   C6    single    1.513  0.020  1.513
 TGN  C8   H8    single    0.970  0.020  1.090
 TGN  C10  N12   single    1.452  0.020  1.452
 TGN  C10  C18   single    1.550  0.020  1.550
 TGN  C10  H10   single    0.970  0.020  1.090
 TGN  N12  C14   single    1.449  0.020  1.449
 TGN  N12  C24   single    1.458  0.020  1.458
 TGN  C14  H141  single    0.970  0.020  1.090
 TGN  C14  H142  single    0.970  0.020  1.090
 TGN  C14  H143  single    0.970  0.020  1.090
 TGN  C18  C21   single    1.542  0.020  1.542
 TGN  C18  H181  single    0.970  0.020  1.090
 TGN  C18  H182  single    0.970  0.020  1.090
 TGN  C21  C24   single    1.548  0.020  1.548
 TGN  C21  H211  single    0.970  0.020  1.090
 TGN  C21  H212  single    0.970  0.020  1.090
 TGN  C24  C26   single    1.528  0.020  1.528
 TGN  C24  H24   single    0.970  0.020  1.090
 TGN  C26  C29   single    1.517  0.020  1.517
 TGN  C26  H261  single    0.970  0.020  1.090
 TGN  C26  H262  single    0.970  0.020  1.090
 TGN  C29  O1    single    1.438  0.020  1.438
 TGN  C29  H29   single    0.970  0.020  1.090
 TGN  O1   P2    single    1.605  0.020  1.605
 TGN  P2   O17   double    1.480  0.020  1.480
 TGN  P2   O3    single    1.608  0.020  1.608
 TGN  P2   C4    single    1.791  0.020  1.791
 TGN  O3   HO3   single    0.850  0.020  0.980
 TGN  C4   C5    aromatic  1.394  0.020  1.394
 TGN  C4   C13   aromatic  1.394  0.020  1.394
 TGN  C5   C7    aromatic  1.387  0.020  1.387
 TGN  C5   H5    single    0.930  0.020  1.080
 TGN  C13  C11   aromatic  1.387  0.020  1.387
 TGN  C13  H13   single    0.930  0.020  1.080
 TGN  C7   C9    aromatic  1.389  0.020  1.389
 TGN  C7   H7    single    0.930  0.020  1.080
 TGN  C9   C11   aromatic  1.388  0.020  1.388
 TGN  C9   H9    single    0.930  0.020  1.080
 TGN  C11  H11   single    0.930  0.020  1.080
 TGN  C6   O7    double    1.200  0.020  1.200
 TGN  C6   O5    single    1.339  0.020  1.339
 TGN  O5   C1    single    1.430  0.020  1.430
 TGN  C1   H11A  single    0.970  0.020  1.090
 TGN  C1   H12   single    0.970  0.020  1.090
 TGN  C1   H13A  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
 TGN  H8    C8   C6    107.67  3.000
 TGN  H8    C8   C29   108.19  3.000
 TGN  C6    C8   C29   110.71  3.000
 TGN  H8    C8   C10   107.25  3.000
 TGN  C6    C8   C10   113.21  3.000
 TGN  C29   C8   C10   109.61  3.000
 TGN  H10   C10  C18   112.10  3.000
 TGN  H10   C10  N12   110.87  3.000
 TGN  C18   C10  N12   105.00  3.000
 TGN  H10   C10  C8    108.95  3.000
 TGN  C18   C10  C8    109.93  3.000
 TGN  N12   C10  C8    109.94  3.000
 TGN  C24   N12  C14   113.65  3.000
 TGN  C24   N12  C10   102.13  3.000
 TGN  C14   N12  C10   112.87  3.000
 TGN  H143  C14  H142  107.67  3.000
 TGN  H143  C14  H141  107.54  3.000
 TGN  H142  C14  H141  107.51  3.000
 TGN  H143  C14  N12   109.39  3.000
 TGN  H142  C14  N12   109.47  3.000
 TGN  H141  C14  N12   115.00  3.000
 TGN  H182  C18  H181  106.58  3.000
 TGN  H182  C18  C21   111.13  3.000
 TGN  H181  C18  C21   113.24  3.000
 TGN  H182  C18  C10   109.92  3.000
 TGN  H181  C18  C10   112.52  3.000
 TGN  C21   C18  C10   103.51  3.000
 TGN  H212  C21  H211  106.68  3.000
 TGN  H212  C21  C24   110.46  3.000
 TGN  H211  C21  C24   112.35  3.000
 TGN  H212  C21  C18   111.09  3.000
 TGN  H211  C21  C18   112.94  3.000
 TGN  C24   C21  C18   103.40  3.000
 TGN  H24   C24  C26   109.03  3.000
 TGN  H24   C24  C21   112.36  3.000
 TGN  C26   C24  C21   112.26  3.000
 TGN  H24   C24  N12   110.45  3.000
 TGN  C26   C24  N12   107.40  3.000
 TGN  C21   C24  N12   105.18  3.000
 TGN  H262  C26  H261  107.75  3.000
 TGN  H262  C26  C29   110.38  3.000
 TGN  H261  C26  C29   109.19  3.000
 TGN  H262  C26  C24   108.73  3.000
 TGN  H261  C26  C24   110.52  3.000
 TGN  C29   C26  C24   110.23  3.000
 TGN  H29   C29  O1    109.03  3.000
 TGN  H29   C29  C26   108.68  3.000
 TGN  O1    C29  C26   108.36  3.000
 TGN  H29   C29  C8    107.43  3.000
 TGN  O1    C29  C8    110.27  3.000
 TGN  C26   C29  C8    113.01  3.000
 TGN  P2    O1   C29   121.86  3.000
 TGN  C4    P2   O3    107.85  3.000
 TGN  C4    P2   O17   115.29  3.000
 TGN  O3    P2   O17   108.86  3.000
 TGN  C4    P2   O1    101.42  3.000
 TGN  O3    P2   O1    106.33  3.000
 TGN  O17   P2   O1    116.38  3.000
 TGN  HO3   O3   P2    115.89  3.000
 TGN  C13   C4   C5    119.68  3.000
 TGN  C13   C4   P2    117.65  3.000
 TGN  C5    C4   P2    122.64  3.000
 TGN  H5    C5   C7    119.03  3.000
 TGN  H5    C5   C4    120.95  3.000
 TGN  C7    C5   C4    120.01  3.000
 TGN  H13   C13  C11   119.49  3.000
 TGN  H13   C13  C4    120.44  3.000
 TGN  C11   C13  C4    120.07  3.000
 TGN  H7    C7   C9    120.22  3.000
 TGN  H7    C7   C5    119.65  3.000
 TGN  C9    C7   C5    120.13  3.000
 TGN  H9    C9   C11   119.95  3.000
 TGN  H9    C9   C7    120.01  3.000
 TGN  C11   C9   C7    120.03  3.000
 TGN  H11   C11  C9    120.19  3.000
 TGN  H11   C11  C13   119.75  3.000
 TGN  C9    C11  C13   120.07  3.000
 TGN  O5    C6   O7    122.45  3.000
 TGN  O5    C6   C8    110.70  3.000
 TGN  O7    C6   C8    126.84  3.000
 TGN  C1    O5   C6    117.43  3.000
 TGN  H13A  C1   H12   109.38  3.000
 TGN  H13A  C1   H11A  109.52  3.000
 TGN  H12   C1   H11A  109.18  3.000
 TGN  H13A  C1   O5    105.94  3.000
 TGN  H12   C1   O5    111.70  3.000
 TGN  H11A  C1   O5    111.06  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
 TGN  CONST_01  C9    C7   C5   C4     0.00   0.0  0
 TGN  CONST_02  C9    C11  C13  C4     0.00   0.0  0
 TGN  CONST_03  C11   C13  C4   C5     0.00   0.0  0
 TGN  CONST_04  C11   C9   C7   C5     0.00   0.0  0
 TGN  CONST_05  C7    C5   C4   C13    0.00   0.0  0
 TGN  CONST_06  C7    C9   C11  C13    0.00   0.0  0
 TGN  CONST_07  C7    C5   C4   P2   180.00   0.0  0
 TGN  CONST_08  C11   C13  C4   P2   180.00   0.0  0
 TGN  CONST_09  H7    C7   C5   C4   180.00   0.0  0
 TGN  CONST_10  H11   C11  C13  C4   180.00   0.0  0
 TGN  CONST_11  H13   C13  C4   C5   180.00   0.0  0
 TGN  CONST_12  H9    C9   C7   C5   180.00   0.0  0
 TGN  CONST_13  H5    C5   C4   C13  180.00   0.0  0
 TGN  Var_01    C24   C21  C18  C10    0.43  30.0  3
 TGN  Var_02    C4    P2   O1   C29  175.14  30.0  3
 TGN  Var_03    C5    C4   P2   O1   -27.28  30.0  2
 TGN  Var_04    H141  C14  N12  C10   58.13  30.0  3
 TGN  Var_05    H11A  C1   O5   C6   -63.61  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
 TGN  chir_01  C8   C10  C29  C6   positiv
 TGN  chir_02  C10  N12  C18  C8   positiv
 TGN  chir_03  C24  N12  C21  C26  negativ
 TGN  chir_04  C29  O1   C8   C26  positiv
 TGN  chir_05  P2   O17  O3   C4   both

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
 TGN  plan-1  P2   0.020
 TGN  plan-1  C4   0.020
 TGN  plan-1  C5   0.020
 TGN  plan-1  C13  0.020
 TGN  plan-1  C7   0.020
 TGN  plan-1  C9   0.020
 TGN  plan-1  C11  0.020
 TGN  plan-1  H5   0.020
 TGN  plan-1  H13  0.020
 TGN  plan-1  H7   0.020
 TGN  plan-1  H9   0.020
 TGN  plan-1  H11  0.020
 TGN  plan-2  C8   0.020
 TGN  plan-2  C6   0.020
 TGN  plan-2  O7   0.020
 TGN  plan-2  O5   0.020

