# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:40:01 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (1R,2R,4S,5S,7s)-7-{[(2S)-3-hydroxy-2-phenylpropanoyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1(C)[C@@H]2CC(C[C@H]1[C@@H]3O[C@H]23)OC(=O)[C@H](CO)c4ccccc4
#
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
 3C0  3C0  (1R,2R,4S,5S,7s)-7-{[(2S)-3-hydroxy-2-phenylpropanoyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane  ligand  47  23  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3C0
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
 3C0  C10  C  CH2   0  -0.123   1.9281   1.7221  -1.0353
 3C0  C13  C  CH1   0  -0.007  -1.2111  -1.0634  -0.6845
 3C0  C15  C  CR15  0  -0.153  -3.2777   0.4451  -0.8346
 3C0  C17  C  CR15  0   0.010  -2.2594   0.7968   1.2955
 3C0  C22  C  CR15  0  -0.149  -2.8633  -0.5908   1.2248
 3C0  N19  N  N     1  -0.407  -3.9636  -0.4534   0.1832
 3C0  C14  C  CH2   0  -0.512  -2.2407  -0.3744  -1.5973
 3C0  C16  C  CR15  0   0.010  -2.5101   1.4361   0.0178
 3C0  O18  O  O2    0  -0.459  -3.1440   1.8951   1.1972
 3C0  C23  C  CH2   0  -0.532  -1.7708  -1.5105   0.6814
 3C0  O12  O  O2    0  -0.445  -0.1511  -0.1129  -0.5062
 3C0  C02  C  C     0   0.632   1.0600  -0.5380  -0.1794
 3C0  O01  O  O     0  -0.436   1.3441  -1.6994  -0.0351
 3C0  C03  C  CH1   0  -0.532   2.0255   0.6167   0.0267
 3C0  O11  O  OH1   0  -0.652   0.7951   2.5198  -0.8061
 3C0  C04  C  CR6   0   0.168   3.4379   0.1023   0.1333
 3C0  C05  C  CR16  0  -0.317   4.1253   0.1686   1.3396
 3C0  C06  C  CR16  0  -0.239   5.4369  -0.2806   1.4361
 3C0  C07  C  CR16  0  -0.268   6.0777  -0.7999   0.3207
 3C0  C08  C  CR16  0  -0.244   5.3990  -0.8686  -0.8904
 3C0  C09  C  CR16  0  -0.292   4.0888  -0.4232  -0.9816
 3C0  H1   H  HCH2  0   0.218   2.8465   2.3171  -0.9632
 3C0  H2   H  HCH2  0   0.208   1.9222   1.2744  -2.0369
 3C0  H3   H  HCH1  0   0.298  -0.8213  -1.9396  -1.2042
 3C0  H4   H  HCR5  0   0.328  -4.0333   0.8712  -1.4946
 3C0  H5   H  HCR5  0   0.298  -1.3617   0.9338   1.8879
 3C0  H6   H  HCH3  0   0.290  -5.9693   0.1485  -0.0532
 3C0  H7   H  HCH3  0   0.290  -5.5633  -0.4880   1.5532
 3C0  H8   H  HCH3  0   0.317  -5.0707   1.1507   1.0972
 3C0  H9   H  HCH3  0   0.297  -3.6033  -2.3448  -0.7999
 3C0  H10  H  HCH3  0   0.307  -4.8724  -2.3341   0.4222
 3C0  H11  H  HCH3  0   0.307  -5.1443  -1.5671  -1.1561
 3C0  H12  H  HCR5  0   0.328  -3.2982  -0.9719   2.1485
 3C0  H13  H  HCH2  0   0.315  -1.7168   0.2959  -2.2806
 3C0  H14  H  HCH2  0   0.299  -2.7297  -1.1076  -2.2372
 3C0  H15  H  HCR5  0   0.304  -1.8142   2.1065  -0.4731
 3C0  H16  H  HCH2  0   0.300  -2.1337  -2.5353   0.6152
 3C0  H17  H  HCH2  0   0.317  -0.9730  -1.5504   1.4244
 3C0  H18  H  HCH1  0   0.308   1.7514   1.0697   0.9882
 3C0  H19  H  HOH1  0   0.457   0.6852   3.1039  -1.5618
 3C0  H20  H  HCR6  0   0.255   3.6338   0.5748   2.2156
 3C0  H21  H  HCR6  0   0.257   5.9558  -0.2242   2.3843
 3C0  H22  H  HCR6  0   0.256   7.0993  -1.1497   0.3935
 3C0  H23  H  HCR6  0   0.257   5.8907  -1.2723  -1.7659
 3C0  H24  H  HCR6  0   0.251   3.5737  -0.4884  -1.9333
 3C0  C20  C  CH3   0  -0.555  -5.2249   0.1462   0.7379
 3C0  C21  C  CH3   0  -0.559  -4.4110  -1.7638  -0.3792

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
 3C0  C07  C06  aromatic  1.387  0.020  1.387
 3C0  C07  C08  aromatic  1.390  0.020  1.390
 3C0  C06  C05  aromatic  1.390  0.020  1.390
 3C0  O18  C16  single    1.415  0.020  1.415
 3C0  O18  C17  single    1.414  0.020  1.414
 3C0  C08  C09  aromatic  1.387  0.020  1.387
 3C0  C05  C04  aromatic  1.390  0.020  1.390
 3C0  C16  C17  single    1.451  0.020  1.451
 3C0  C16  C15  single    1.516  0.020  1.516
 3C0  C17  C22  single    1.515  0.020  1.515
 3C0  C20  N19  single    1.503  0.020  1.503
 3C0  C09  C04  aromatic  1.394  0.020  1.394
 3C0  C04  C03  single    1.507  0.020  1.507
 3C0  C15  N19  single    1.521  0.020  1.521
 3C0  C15  C14  single    1.526  0.020  1.526
 3C0  N19  C22  single    1.521  0.020  1.521
 3C0  N19  C21  single    1.495  0.020  1.495
 3C0  C22  C23  single    1.528  0.020  1.528
 3C0  C03  C10  single    1.536  0.020  1.536
 3C0  C03  C02  single    1.519  0.020  1.519
 3C0  O12  C13  single    1.435  0.020  1.435
 3C0  O12  C02  single    1.324  0.020  1.324
 3C0  C14  C13  single    1.539  0.020  1.539
 3C0  C23  C13  single    1.542  0.020  1.542
 3C0  C10  O11  single    1.404  0.020  1.404
 3C0  C02  O01  double    1.204  0.020  1.204
 3C0  C10  H1   single    0.970  0.020  1.090
 3C0  C10  H2   single    0.970  0.020  1.090
 3C0  C13  H3   single    0.970  0.020  1.090
 3C0  C15  H4   single    0.970  0.020  1.090
 3C0  C17  H5   single    0.970  0.020  1.090
 3C0  C20  H6   single    0.970  0.020  1.090
 3C0  C20  H7   single    0.970  0.020  1.090
 3C0  C20  H8   single    0.970  0.020  1.090
 3C0  C21  H9   single    0.970  0.020  1.090
 3C0  C21  H10  single    0.970  0.020  1.090
 3C0  C21  H11  single    0.970  0.020  1.090
 3C0  C22  H12  single    0.970  0.020  1.090
 3C0  C14  H13  single    0.970  0.020  1.090
 3C0  C14  H14  single    0.970  0.020  1.090
 3C0  C16  H15  single    0.970  0.020  1.090
 3C0  C23  H16  single    0.970  0.020  1.090
 3C0  C23  H17  single    0.970  0.020  1.090
 3C0  C03  H18  single    0.970  0.020  1.090
 3C0  O11  H19  single    0.850  0.020  0.980
 3C0  C05  H20  single    0.930  0.020  1.080
 3C0  C06  H21  single    0.930  0.020  1.080
 3C0  C07  H22  single    0.930  0.020  1.080
 3C0  C08  H23  single    0.930  0.020  1.080
 3C0  C09  H24  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
 3C0  H2   C10  H1   106.61  3.000
 3C0  H2   C10  O11  112.11  3.000
 3C0  H1   C10  O11  110.90  3.000
 3C0  H2   C10  C03  109.74  3.000
 3C0  H1   C10  C03  106.97  3.000
 3C0  O11  C10  C03  110.31  3.000
 3C0  H3   C13  O12  109.11  3.000
 3C0  H3   C13  C23  108.59  3.000
 3C0  O12  C13  C23  110.49  3.000
 3C0  H3   C13  C14  108.43  3.000
 3C0  C23  C13  C14  114.35  3.000
 3C0  O12  C13  C14  105.75  3.000
 3C0  H4   C15  C16  115.84  3.000
 3C0  H4   C15  C14  112.23  3.000
 3C0  C16  C15  C14  106.74  3.000
 3C0  H4   C15  N19  108.87  3.000
 3C0  C14  C15  N19  108.89  3.000
 3C0  C16  C15  N19  103.78  3.000
 3C0  H5   C17  O18  117.25  3.000
 3C0  H5   C17  C16  124.65  3.000
 3C0  O18  C17  C16   59.22  3.000
 3C0  H5   C17  C22  118.12  3.000
 3C0  C16  C17  C22  107.08  3.000
 3C0  O18  C17  C22  117.32  3.000
 3C0  H12  C22  C23  112.10  3.000
 3C0  H12  C22  N19  108.86  3.000
 3C0  C23  C22  N19  109.15  3.000
 3C0  H12  C22  C17  116.09  3.000
 3C0  C23  C22  C17  106.43  3.000
 3C0  N19  C22  C17  103.74  3.000
 3C0  C22  N19  C21  113.26  3.000
 3C0  C21  N19  C20  103.74  3.000
 3C0  C22  N19  C20  112.98  3.000
 3C0  C21  N19  C15  113.65  3.000
 3C0  C22  N19  C15  100.68  3.000
 3C0  C20  N19  C15  112.95  3.000
 3C0  H14  C14  H13  105.14  3.000
 3C0  H14  C14  C15  110.49  3.000
 3C0  H13  C14  C15  108.02  3.000
 3C0  H14  C14  C13  110.33  3.000
 3C0  H13  C14  C13  108.98  3.000
 3C0  C15  C14  C13  113.49  3.000
 3C0  H15  C16  O18  117.67  3.000
 3C0  H15  C16  C17  124.10  3.000
 3C0  O18  C16  C17   59.09  3.000
 3C0  H15  C16  C15  118.35  3.000
 3C0  C17  C16  C15  107.14  3.000
 3C0  O18  C16  C15  116.99  3.000
 3C0  C16  O18  C17   61.69  3.000
 3C0  H17  C23  H16  104.52  3.000
 3C0  H17  C23  C22  107.62  3.000
 3C0  H16  C23  C22  110.47  3.000
 3C0  H17  C23  C13  110.39  3.000
 3C0  H16  C23  C13  109.87  3.000
 3C0  C22  C23  C13  113.57  3.000
 3C0  C02  O12  C13  119.57  3.000
 3C0  C03  C02  O01  124.53  3.000
 3C0  O01  C02  O12  123.69  3.000
 3C0  C03  C02  O12  111.76  3.000
 3C0  H18  C03  C04  108.24  3.000
 3C0  H18  C03  C02  105.89  3.000
 3C0  C04  C03  C02  110.23  3.000
 3C0  H18  C03  C10  107.02  3.000
 3C0  C02  C03  C10  114.39  3.000
 3C0  C04  C03  C10  110.74  3.000
 3C0  H19  O11  C10  108.00  3.000
 3C0  C09  C04  C05  118.76  3.000
 3C0  C09  C04  C03  120.65  3.000
 3C0  C05  C04  C03  120.58  3.000
 3C0  H20  C05  C06  119.55  3.000
 3C0  H20  C05  C04  119.68  3.000
 3C0  C06  C05  C04  120.77  3.000
 3C0  H21  C06  C07  120.16  3.000
 3C0  H21  C06  C05  119.76  3.000
 3C0  C07  C06  C05  120.07  3.000
 3C0  H22  C07  C08  120.24  3.000
 3C0  H22  C07  C06  120.19  3.000
 3C0  C08  C07  C06  119.57  3.000
 3C0  H23  C08  C09  119.72  3.000
 3C0  H23  C08  C07  120.10  3.000
 3C0  C09  C08  C07  120.18  3.000
 3C0  H24  C09  C08  119.16  3.000
 3C0  H24  C09  C04  120.20  3.000
 3C0  C08  C09  C04  120.64  3.000
 3C0  H8   C20  H7   109.76  3.000
 3C0  H8   C20  H6   109.80  3.000
 3C0  H7   C20  H6   109.52  3.000
 3C0  H8   C20  N19  112.01  3.000
 3C0  H7   C20  N19  107.79  3.000
 3C0  H6   C20  N19  107.89  3.000
 3C0  H11  C21  H10  109.62  3.000
 3C0  H11  C21  H9   108.88  3.000
 3C0  H10  C21  H9   108.82  3.000
 3C0  H11  C21  N19  108.20  3.000
 3C0  H10  C21  N19  108.04  3.000
 3C0  H9   C21  N19  113.23  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
 3C0  CONST_01  C07  C06  C05  C04     0.00   0.0  0
 3C0  CONST_02  C07  C08  C09  C04     0.00   0.0  0
 3C0  CONST_03  C08  C07  C06  C05     0.00   0.0  0
 3C0  CONST_04  C08  C09  C04  C05     0.00   0.0  0
 3C0  CONST_05  C09  C08  C07  C06     0.00   0.0  0
 3C0  CONST_06  C09  C04  C05  C06     0.00   0.0  0
 3C0  CONST_07  C06  C05  C04  C03   180.00   0.0  0
 3C0  CONST_08  C08  C09  C04  C03   180.00   0.0  0
 3C0  CONST_09  H21  C06  C05  C04   180.00   0.0  0
 3C0  CONST_10  H23  C08  C09  C04   180.00   0.0  0
 3C0  CONST_11  H22  C07  C06  C05   180.00   0.0  0
 3C0  CONST_12  H24  C09  C04  C05   180.00   0.0  0
 3C0  CONST_13  H20  C05  C06  C07   180.00   0.0  0
 3C0  Var_01    H15  C16  O18  C17  -115.08  30.0  1
 3C0  Var_02    H6   C20  N19  C15    70.03  30.0  3
 3C0  Var_03    H9   C21  N19  C15    58.63  30.0  3
 3C0  Var_04    C03  C02  O12  C13  -177.36  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
 3C0  chir_01  C13  O12  C14  C23  positiv
 3C0  chir_02  C15  N19  C14  C16  positiv
 3C0  chir_04  C22  C17  N19  C23  negativ
 3C0  chir_06  C03  C04  C10  C02  negativ
 3C0  chir_07  C17  O18  C16  C22  both
 3C0  chir_08  C16  O18  C15  C17  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
 3C0  plan-1  C03  0.020
 3C0  plan-1  C04  0.020
 3C0  plan-1  C05  0.020
 3C0  plan-1  C06  0.020
 3C0  plan-1  C07  0.020
 3C0  plan-1  C08  0.020
 3C0  plan-1  C09  0.020
 3C0  plan-1  H20  0.020
 3C0  plan-1  H21  0.020
 3C0  plan-1  H22  0.020
 3C0  plan-1  H23  0.020
 3C0  plan-1  H24  0.020
 3C0  plan-2  O12  0.020
 3C0  plan-2  C02  0.020
 3C0  plan-2  O01  0.020
 3C0  plan-2  C03  0.020

