# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:43:57 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (5S,8R,8aS)-8-hydroxyhexahydro-3H-5,8-ethano[1,3]oxazolo[3,4-a]pyridin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC12CCC(CC1)N3[C@H]2COC3=O
#
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
 JOD  JOD  (5S,8R,8aS)-8-hydroxyhexahydro-3H-5,8-ethano[1,3]oxazolo[3,4-a]pyridin-3-one  ligand  26  13  .  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_JOD
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
 JOD  C10   C  CH2   0  -0.184   0.8796  -1.8798  -0.1267
 JOD  O01   O  OH1   0  -0.674  -2.0387  -1.8318   0.0355
 JOD  C02   C  CT    0   0.212  -1.3963  -0.5837   0.0142
 JOD  C03   C  CH2   0  -0.476  -2.1466   0.4691  -0.8136
 JOD  C04   C  CH2   0  -0.454  -1.2123   1.6728  -1.0688
 JOD  C05   C  CH1   0  -0.141  -0.0319   1.5997  -0.1046
 JOD  C06   C  CH2   0  -0.452  -0.5638   1.4075   1.3169
 JOD  C07   C  CH2   0  -0.487  -1.1576  -0.0137   1.4175
 JOD  N08   N  NR5   0  -0.481   0.7391   0.4113  -0.4642
 JOD  C09   C  CR15  0  -0.113  -0.0461  -0.7912  -0.6830
 JOD  O11   O  O     0  -0.471   2.1084  -1.2029   0.1633
 JOD  C12   C  CR5   0   0.689   1.9357   0.1259   0.1003
 JOD  O13   O  O     0  -0.490   2.7745   0.9034   0.4889
 JOD  H102  H  HCH2  0   0.251   0.5071  -2.3417   0.7896
 JOD  H101  H  HCH2  0   0.265   1.0736  -2.6643  -0.8547
 JOD  H011  H  HOH1  0   0.450  -2.8922  -1.7316   0.4709
 JOD  H032  H  HCH2  0   0.252  -2.4733   0.0269  -1.7570
 JOD  H031  H  HCH2  0   0.244  -3.0455   0.7796  -0.2735
 JOD  H042  H  HCH2  0   0.252  -0.8446   1.6737  -2.0966
 JOD  H041  H  HCH2  0   0.257  -1.7388   2.6156  -0.9212
 JOD  H051  H  HCH1  0   0.271   0.6039   2.4800  -0.1922
 JOD  H062  H  HCH2  0   0.254   0.2301   1.5498   2.0519
 JOD  H061  H  HCH2  0   0.248  -1.3204   2.1679   1.5214
 JOD  H071  H  HCH2  0   0.255  -2.1040   0.0032   1.9643
 JOD  H072  H  HCH2  0   0.246  -0.4938  -0.6729   1.9836
 JOD  H091  H  HCR5  0   0.275  -0.2198  -0.9535  -1.7528

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
 JOD  O13  C12   double  1.208  0.020  1.208
 JOD  O11  C12   single  1.342  0.020  1.342
 JOD  O11  C10   single  1.433  0.020  1.433
 JOD  C06  C07   single  1.544  0.020  1.544
 JOD  C06  C05   single  1.530  0.020  1.530
 JOD  C12  N08   single  1.354  0.020  1.354
 JOD  C07  C02   single  1.533  0.020  1.533
 JOD  C10  C09   single  1.533  0.020  1.533
 JOD  C05  N08   single  1.461  0.020  1.461
 JOD  C05  C04   single  1.526  0.020  1.526
 JOD  N08  C09   single  1.453  0.020  1.453
 JOD  C09  C02   single  1.534  0.020  1.534
 JOD  C02  O01   single  1.404  0.020  1.404
 JOD  C02  C03   single  1.535  0.020  1.535
 JOD  C04  C03   single  1.545  0.020  1.545
 JOD  C10  H102  single  0.970  0.020  1.090
 JOD  C10  H101  single  0.970  0.020  1.090
 JOD  O01  H011  single  0.850  0.020  0.980
 JOD  C03  H032  single  0.970  0.020  1.090
 JOD  C03  H031  single  0.970  0.020  1.090
 JOD  C04  H042  single  0.970  0.020  1.090
 JOD  C04  H041  single  0.970  0.020  1.090
 JOD  C05  H051  single  0.970  0.020  1.090
 JOD  C06  H062  single  0.970  0.020  1.090
 JOD  C06  H061  single  0.970  0.020  1.090
 JOD  C07  H071  single  0.970  0.020  1.090
 JOD  C07  H072  single  0.970  0.020  1.090
 JOD  C09  H091  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
 JOD  H101  C10  H102  108.51  3.000
 JOD  H101  C10  O11   108.86  3.000
 JOD  H102  C10  O11   108.82  3.000
 JOD  H101  C10  C09   112.14  3.000
 JOD  H102  C10  C09   113.51  3.000
 JOD  O11   C10  C09   104.82  3.000
 JOD  H011  O01  C02   108.65  3.000
 JOD  C09   C02  C07   109.23  3.000
 JOD  C09   C02  C03   106.14  3.000
 JOD  C07   C02  C03   108.34  3.000
 JOD  C03   C02  O01   113.22  3.000
 JOD  C09   C02  O01   106.83  3.000
 JOD  C07   C02  O01   112.82  3.000
 JOD  H031  C03  H032  107.20  3.000
 JOD  H031  C03  C04   110.94  3.000
 JOD  H032  C03  C04   110.72  3.000
 JOD  H031  C03  C02   109.28  3.000
 JOD  H032  C03  C02   109.53  3.000
 JOD  C04   C03  C02   109.14  3.000
 JOD  H041  C04  H042  106.82  3.000
 JOD  H041  C04  C05   109.24  3.000
 JOD  H042  C04  C05   109.54  3.000
 JOD  H041  C04  C03   111.07  3.000
 JOD  H042  C04  C03   111.09  3.000
 JOD  C05   C04  C03   109.03  3.000
 JOD  H051  C05  N08   109.23  3.000
 JOD  H051  C05  C06   112.28  3.000
 JOD  N08   C05  C06   108.05  3.000
 JOD  H051  C05  C04   111.22  3.000
 JOD  N08   C05  C04   106.95  3.000
 JOD  C06   C05  C04   108.91  3.000
 JOD  H061  C06  H062  106.69  3.000
 JOD  H061  C06  C07   111.25  3.000
 JOD  H062  C06  C07   110.85  3.000
 JOD  H061  C06  C05   109.12  3.000
 JOD  H062  C06  C05   110.89  3.000
 JOD  C07   C06  C05   108.06  3.000
 JOD  H072  C07  H071  106.02  3.000
 JOD  H072  C07  C06   110.81  3.000
 JOD  H071  C07  C06   110.57  3.000
 JOD  H072  C07  C02   110.13  3.000
 JOD  H071  C07  C02   109.20  3.000
 JOD  C06   C07  C02   110.03  3.000
 JOD  C12   N08  C09   111.48  3.000
 JOD  C09   N08  C05   115.15  3.000
 JOD  C12   N08  C05   122.36  3.000
 JOD  H091  C09  N08   110.81  3.000
 JOD  H091  C09  C02   108.93  3.000
 JOD  N08   C09  C02   107.18  3.000
 JOD  H091  C09  C10   110.16  3.000
 JOD  C02   C09  C10   117.55  3.000
 JOD  N08   C09  C10   101.93  3.000
 JOD  C12   O11  C10   110.37  3.000
 JOD  O13   C12  O11   122.22  3.000
 JOD  O11   C12  N08   110.01  3.000
 JOD  O13   C12  N08   127.76  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
 JOD  Var_01  N08   C12  O11  C10   -11.78  30.0  1
 JOD  Var_02  C05   C06  C07  C02   -16.67  30.0  3
 JOD  Var_03  C05   C04  C03  C02   -15.98  30.0  1
 JOD  Var_04  O11   C12  N08  C05   148.76  30.0  1
 JOD  Var_05  H102  C10  O11  C12  -109.92  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
 JOD  chir_01  C02  C09  O01  C03  positiv
 JOD  chir_02  C05  N08  C04  C06  negativ
 JOD  chir_03  C09  N08  C10  C02  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
 JOD  plan-1  C05  0.020
 JOD  plan-1  N08  0.020
 JOD  plan-1  C09  0.020
 JOD  plan-1  C12  0.020
 JOD  plan-2  N08  0.020
 JOD  plan-2  O11  0.020
 JOD  plan-2  C12  0.020
 JOD  plan-2  O13  0.020

