# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:47:59 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (1R,4R,5R,6S)-4,6-dihydroxy-N-phenyl-2-azabicyclo[3.3.1]nonane-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CC[C@@H]2C[C@H]1[C@@H](O)CN2C(=O)Nc3ccccc3
#
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
 JOG  JOG  (1R,4R,5R,6S)-4,6-dihydroxy-N-phenyl-2-azabicyclo[3.3.1]nonane-2-carboxamide  ligand  40  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JOG
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
 JOG  C10   C  CH2   0  -0.375  -1.0278   1.0730   0.0862
 JOG  C15   C  CR6   0   0.373   2.9733   0.1781  -0.1478
 JOG  C17   C  CR16  0  -0.252   5.1243  -0.6317   0.5708
 JOG  C20   C  CR16  0  -0.344   3.6042   0.8483  -1.1974
 JOG  O01   O  OH1   0  -0.674  -4.4431   0.9455  -1.4574
 JOG  C02   C  CH1   0   0.086  -3.8853  -0.1489  -0.7607
 JOG  C03   C  CH2   0  -0.508  -2.7977  -0.8513  -1.5742
 JOG  C04   C  CH2   0  -0.434  -2.0211  -1.8745  -0.7463
 JOG  C05   C  CH1   0  -0.113  -1.5887  -1.3294   0.6162
 JOG  C06   C  CH2   0  -0.446  -2.8079  -0.8304   1.3738
 JOG  C07   C  CH1   0  -0.319  -3.4213   0.3377   0.6129
 JOG  C08   C  CH1   0   0.056  -2.4100   1.4814   0.6041
 JOG  O09   O  OH1   0  -0.674  -2.3419   1.9428   1.9407
 JOG  N11   N  NT    0  -0.498  -0.5940  -0.2568   0.4991
 JOG  C12   C  C     0   0.733   0.7160  -0.6346   0.4217
 JOG  O13   O  O     0  -0.525   1.1010  -1.7542   0.7319
 JOG  N14   N  NH1   0  -0.799   1.5899   0.3352  -0.0154
 JOG  C16   C  CR16  0  -0.297   3.7497  -0.5593   0.7475
 JOG  C18   C  CR16  0  -0.275   5.7503   0.0312  -0.4763
 JOG  C19   C  CR16  0  -0.248   4.9794   0.7794  -1.3557
 JOG  H101  H  HCH2  0   0.248  -1.0155   1.1776  -1.0038
 JOG  H102  H  HCH2  0   0.267  -0.3259   1.8162   0.4725
 JOG  H171  H  HCR6  0   0.256   5.7124  -1.2094   1.2725
 JOG  H201  H  HCR6  0   0.264   3.0104   1.4245  -1.8979
 JOG  H011  H  HOH1  0   0.449  -4.7571   0.6319  -2.3115
 JOG  H021  H  HCH1  0   0.204  -4.6636  -0.9006  -0.5543
 JOG  H032  H  HCH2  0   0.246  -3.2655  -1.3584  -2.4234
 JOG  H031  H  HCH2  0   0.233  -2.1200  -0.1148  -2.0101
 JOG  H041  H  HCH2  0   0.229  -2.6492  -2.7520  -0.5648
 JOG  H042  H  HCH2  0   0.243  -1.1535  -2.2306  -1.3060
 JOG  H051  H  HCH1  0   0.267  -1.1267  -2.1333   1.1847
 JOG  H061  H  HCH2  0   0.244  -3.5253  -1.6505   1.4649
 JOG  H062  H  HCH2  0   0.252  -2.5377  -0.5356   2.3884
 JOG  H071  H  HCH1  0   0.254  -4.3088   0.6996   1.1426
 JOG  H081  H  HCH1  0   0.235  -2.7578   2.2866  -0.0538
 JOG  H091  H  HOH1  0   0.450  -1.7833   2.7258   1.9632
 JOG  H141  H  HNH1  0   0.421   1.2132   1.1112  -0.5346
 JOG  H161  H  HCR6  0   0.263   3.2946  -1.0656   1.5844
 JOG  H181  H  HCR6  0   0.253   6.8230  -0.0307  -0.6030
 JOG  H191  H  HCR6  0   0.257   5.4461   1.3074  -2.1772

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
 JOG  O09  C08   single    1.416  0.020  1.416
 JOG  C08  C07   single    1.527  0.020  1.527
 JOG  C08  C10   single    1.532  0.020  1.532
 JOG  C07  C02   single    1.529  0.020  1.529
 JOG  C07  C06   single    1.523  0.020  1.523
 JOG  O01  C02   single    1.412  0.020  1.412
 JOG  C02  C03   single    1.529  0.020  1.529
 JOG  C06  C05   single    1.520  0.020  1.520
 JOG  C10  N11   single    1.458  0.020  1.458
 JOG  C03  C04   single    1.528  0.020  1.528
 JOG  N11  C05   single    1.468  0.020  1.468
 JOG  N11  C12   single    1.366  0.020  1.366
 JOG  C05  C04   single    1.530  0.020  1.530
 JOG  C16  C17   aromatic  1.388  0.020  1.388
 JOG  C16  C15   aromatic  1.396  0.020  1.396
 JOG  N14  C12   single    1.377  0.020  1.377
 JOG  N14  C15   single    1.399  0.020  1.399
 JOG  C17  C18   aromatic  1.388  0.020  1.388
 JOG  C12  O13   double    1.224  0.020  1.224
 JOG  C15  C20   aromatic  1.396  0.020  1.396
 JOG  C18  C19   aromatic  1.388  0.020  1.388
 JOG  C20  C19   aromatic  1.386  0.020  1.386
 JOG  C10  H101  single    0.970  0.020  1.090
 JOG  C10  H102  single    0.970  0.020  1.090
 JOG  C17  H171  single    0.930  0.020  1.080
 JOG  C20  H201  single    0.930  0.020  1.080
 JOG  O01  H011  single    0.850  0.020  0.980
 JOG  C02  H021  single    0.970  0.020  1.090
 JOG  C03  H032  single    0.970  0.020  1.090
 JOG  C03  H031  single    0.970  0.020  1.090
 JOG  C04  H041  single    0.970  0.020  1.090
 JOG  C04  H042  single    0.970  0.020  1.090
 JOG  C05  H051  single    0.970  0.020  1.090
 JOG  C06  H061  single    0.970  0.020  1.090
 JOG  C06  H062  single    0.970  0.020  1.090
 JOG  C07  H071  single    0.970  0.020  1.090
 JOG  C08  H081  single    0.970  0.020  1.090
 JOG  O09  H091  single    0.850  0.020  0.980
 JOG  N14  H141  single    0.860  0.020  1.020
 JOG  C16  H161  single    0.930  0.020  1.080
 JOG  C18  H181  single    0.930  0.020  1.080
 JOG  C19  H191  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
 JOG  H102  C10  H101  106.24  3.000
 JOG  H102  C10  N11   109.20  3.000
 JOG  H101  C10  N11   111.44  3.000
 JOG  H102  C10  C08   106.19  3.000
 JOG  H101  C10  C08   108.74  3.000
 JOG  N11   C10  C08   114.57  3.000
 JOG  C16   C15  N14   123.29  3.000
 JOG  N14   C15  C20   117.67  3.000
 JOG  C16   C15  C20   118.98  3.000
 JOG  H171  C17  C18   119.91  3.000
 JOG  H171  C17  C16   118.91  3.000
 JOG  C18   C17  C16   121.17  3.000
 JOG  H201  C20  C19   119.75  3.000
 JOG  H201  C20  C15   119.56  3.000
 JOG  C19   C20  C15   120.69  3.000
 JOG  H011  O01  C02   108.31  3.000
 JOG  H021  C02  C07   105.26  3.000
 JOG  H021  C02  C03   106.79  3.000
 JOG  C07   C02  C03   114.09  3.000
 JOG  H021  C02  O01   110.01  3.000
 JOG  C03   C02  O01   111.99  3.000
 JOG  C07   C02  O01   108.44  3.000
 JOG  H031  C03  H032  105.56  3.000
 JOG  H031  C03  C04   110.65  3.000
 JOG  H032  C03  C04   109.11  3.000
 JOG  H031  C03  C02   110.13  3.000
 JOG  H032  C03  C02   108.76  3.000
 JOG  C04   C03  C02   112.38  3.000
 JOG  H042  C04  H041  106.23  3.000
 JOG  H042  C04  C05   110.37  3.000
 JOG  H041  C04  C05   107.47  3.000
 JOG  H042  C04  C03   110.14  3.000
 JOG  H041  C04  C03   109.58  3.000
 JOG  C05   C04  C03   112.80  3.000
 JOG  H051  C05  N11   107.10  3.000
 JOG  H051  C05  C06   108.84  3.000
 JOG  N11   C05  C06   110.10  3.000
 JOG  H051  C05  C04   108.80  3.000
 JOG  N11   C05  C04   112.39  3.000
 JOG  C06   C05  C04   109.53  3.000
 JOG  H062  C06  H061  106.73  3.000
 JOG  H062  C06  C07   110.94  3.000
 JOG  H061  C06  C07   110.64  3.000
 JOG  H062  C06  C05   110.72  3.000
 JOG  H061  C06  C05   108.76  3.000
 JOG  C07   C06  C05   109.02  3.000
 JOG  H071  C07  C08   106.98  3.000
 JOG  H071  C07  C06   109.76  3.000
 JOG  C08   C07  C06   108.10  3.000
 JOG  H071  C07  C02   107.09  3.000
 JOG  C06   C07  C02   109.08  3.000
 JOG  C08   C07  C02   115.73  3.000
 JOG  H081  C08  O09   110.03  3.000
 JOG  H081  C08  C07   110.09  3.000
 JOG  O09   C08  C07   105.70  3.000
 JOG  H081  C08  C10   106.21  3.000
 JOG  C07   C08  C10   113.58  3.000
 JOG  O09   C08  C10   111.27  3.000
 JOG  H091  O09  C08   108.37  3.000
 JOG  C12   N11  C05   116.91  3.000
 JOG  C12   N11  C10   121.44  3.000
 JOG  C05   N11  C10   119.17  3.000
 JOG  N14   C12  O13   121.67  3.000
 JOG  O13   C12  N11   122.72  3.000
 JOG  N14   C12  N11   115.60  3.000
 JOG  H141  N14  C12   117.98  3.000
 JOG  H141  N14  C15   114.07  3.000
 JOG  C12   N14  C15   125.37  3.000
 JOG  H161  C16  C17   119.48  3.000
 JOG  H161  C16  C15   120.73  3.000
 JOG  C17   C16  C15   119.79  3.000
 JOG  H181  C18  C19   120.48  3.000
 JOG  H181  C18  C17   120.53  3.000
 JOG  C19   C18  C17   118.99  3.000
 JOG  H191  C19  C18   120.28  3.000
 JOG  H191  C19  C20   119.36  3.000
 JOG  C18   C19  C20   120.36  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
 JOG  CONST_01  C18   C17  C16  C15    0.00   0.0  0
 JOG  CONST_02  C18   C19  C20  C15    0.00   0.0  0
 JOG  CONST_03  C20   C15  C16  C17    0.00   0.0  0
 JOG  CONST_04  C20   C19  C18  C17    0.00   0.0  0
 JOG  CONST_05  C19   C18  C17  C16    0.00   0.0  0
 JOG  CONST_06  C19   C20  C15  C16    0.00   0.0  0
 JOG  CONST_07  N14   C15  C16  C17  180.00   0.0  0
 JOG  CONST_08  C19   C20  C15  N14  180.00   0.0  0
 JOG  CONST_09  H171  C17  C16  C15  180.00   0.0  0
 JOG  CONST_10  H191  C19  C20  C15  180.00   0.0  0
 JOG  CONST_11  H161  C16  C15  C20  180.00   0.0  0
 JOG  CONST_12  H181  C18  C19  C20  180.00   0.0  0
 JOG  CONST_13  H201  C20  C15  C16  180.00   0.0  0
 JOG  CONST_14  O13   C12  N11  C10  180.00   0.0  0
 JOG  CONST_16  N11   C12  N14  C15  180.00   0.0  0
 JOG  CONST_19  N14   C12  N11  C10    0.00   0.0  0
 JOG  CONST_22  O13   C12  N14  C15    0.00   0.0  0
 JOG  Var_01    C05   C04  C03  C02  -46.75  30.0  3
 JOG  Var_02    C08   C10  N11  C05   35.50  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
 JOG  chir_01  C02  C07  O01  C03  negativ
 JOG  chir_02  C05  N11  C04  C06  positiv
 JOG  chir_03  C07  C06  C02  C08  positiv
 JOG  chir_04  C08  O09  C07  C10  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
 JOG  plan-1  C15   0.020
 JOG  plan-1  C17   0.020
 JOG  plan-1  C20   0.020
 JOG  plan-1  N14   0.020
 JOG  plan-1  C16   0.020
 JOG  plan-1  C18   0.020
 JOG  plan-1  C19   0.020
 JOG  plan-1  H171  0.020
 JOG  plan-1  H201  0.020
 JOG  plan-1  H161  0.020
 JOG  plan-1  H181  0.020
 JOG  plan-1  H191  0.020
 JOG  plan-2  C10   0.020
 JOG  plan-2  C15   0.020
 JOG  plan-2  C05   0.020
 JOG  plan-2  N11   0.020
 JOG  plan-2  C12   0.020
 JOG  plan-2  O13   0.020
 JOG  plan-2  N14   0.020
 JOG  plan-2  H141  0.020

