# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 03:24:00 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (3~{S},4~{R})-2,2-dimethyl-3-oxidanyl-4-(2-oxidanylidenepyrrolidin-1-yl)-3,4-dihydrochromene-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)Oc2ccc(cc2[C@H]([C@@H]1O)N3CCCC3=O)C#N
#
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
 ETJ  ETJ  "(3S,4R)-2,2-dimethyl-3-oxidanyl-4-(2-oxidanylidenepyrrolidin-1-yl)-3,4-dihydrochromene-6-carbonitrile"
  ligand  39  21  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ETJ
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
 ETJ  C1   C  CH1   0   0.042  137.0260  132.6981  112.5136
 ETJ  C3   C  CR6   0   0.001  137.2338  132.5680  114.9909
 ETJ  C4   C  CH2   0  -0.277  134.3626  133.2865  113.9865
 ETJ  C5   C  CH2   0  -0.474  132.9793  132.8269  114.4434
 ETJ  C7   C  C     0   0.540  134.3143  130.9405  113.8239
 ETJ  C8   C  CH2   0  -0.587  132.8775  131.4086  113.8932
 ETJ  C9   C  CH3   0  -0.663  139.0503  133.5521  111.2953
 ETJ  C10  C  CH3   0  -0.674  139.2116  131.3746  112.5212
 ETJ  C11  C  CR16  0  -0.288  136.7168  132.4088  116.2655
 ETJ  C12  C  CR16  0  -0.352  139.0796  133.8226  115.9444
 ETJ  C13  C  CR6   0  -0.002  137.3645  132.9477  117.3738
 ETJ  N    N  NT    0  -0.486  135.1056  132.0395  113.9033
 ETJ  C    C  CH1   0  -0.149  136.5386  131.9902  113.7809
 ETJ  O    O  O2    0  -0.475  138.9957  133.4999  113.6443
 ETJ  C14  C  CR16  0  -0.237  138.5535  133.6632  117.2058
 ETJ  C15  C  CSP   0   0.043  136.8093  132.7758  118.6737
 ETJ  C2   C  CT    0   0.166  138.5605  132.7525  112.4907
 ETJ  C6   C  CR6   0   0.401  138.4280  133.2789  114.8332
 ETJ  N1   N  NS    0  -0.258  136.3615  132.6392  119.7275
 ETJ  O1   O  OH1   0  -0.660  136.5869  132.0331  111.3623
 ETJ  H1   H  HCH1  0   0.246  136.6732  133.7401  112.5275
 ETJ  H2   H  HCH2  0   0.248  134.3186  133.7821  113.0115
 ETJ  H3   H  HCH2  0   0.251  132.9369  132.8101  115.5335
 ETJ  H4   H  HCH2  0   0.274  132.2720  130.7349  114.4978
 ETJ  H5   H  HCH2  0   0.273  132.4680  131.3965  112.8786
 ETJ  H6   H  HCH3  0   0.239  138.5850  134.5381  111.2603
 ETJ  H7   H  HCH3  0   0.243  140.1321  133.6818  111.3419
 ETJ  H8   H  HCH3  0   0.243  138.8170  133.0315  110.3690
 ETJ  H9   H  HCH3  0   0.244  138.9857  130.8190  113.4321
 ETJ  H10  H  HCH3  0   0.248  138.8786  130.7766  111.6741
 ETJ  H11  H  HCH3  0   0.250  140.2954  131.4731  112.4535
 ETJ  H12  H  HCR6  0   0.280  135.7904  131.8641  116.3991
 ETJ  H13  H  HCR6  0   0.278  140.0002  134.3733  115.8019
 ETJ  H14  H  HCH1  0   0.293  136.7984  130.9303  113.6982
 ETJ  H15  H  HCR6  0   0.280  139.0616  134.0870  118.0614
 ETJ  H16  H  HOH1  0   0.462  135.6759  132.2853  111.1833
 ETJ  H17  H  HCH2  0   0.257  134.8320  133.9753  114.6900
 ETJ  H18  H  HCH2  0   0.257  132.1909  133.4868  114.0878
 ETJ  O2   O  O     0  -0.479  134.7036  129.7931  113.7038

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
 ETJ  O1   C1   single    1.400  0.020  1.400
 ETJ  C10  C2   single    1.524  0.020  1.524
 ETJ  C9   C2   single    1.519  0.020  1.519
 ETJ  C2   C1   single    1.536  0.020  1.536
 ETJ  C2   O    single    1.442  0.020  1.442
 ETJ  C1   C    single    1.531  0.020  1.531
 ETJ  C4   C5   single    1.528  0.020  1.528
 ETJ  C4   N    single    1.454  0.020  1.454
 ETJ  O    C6   single    1.336  0.020  1.336
 ETJ  C    N    single    1.439  0.020  1.439
 ETJ  C    C3   single    1.510  0.020  1.510
 ETJ  C5   C8   single    1.525  0.020  1.525
 ETJ  N    C7   single    1.357  0.020  1.357
 ETJ  C8   C7   single    1.513  0.020  1.513
 ETJ  C7   O2   double    1.218  0.020  1.218
 ETJ  C6   C3   aromatic  1.399  0.020  1.399
 ETJ  C6   C12  aromatic  1.398  0.020  1.398
 ETJ  C3   C11  aromatic  1.385  0.020  1.385
 ETJ  C12  C14  aromatic  1.376  0.020  1.376
 ETJ  C11  C13  aromatic  1.392  0.020  1.392
 ETJ  C14  C13  aromatic  1.398  0.020  1.398
 ETJ  C13  C15  single    1.424  0.020  1.424
 ETJ  C15  N1   triple    1.153  0.020  1.153
 ETJ  C1   H1   single    0.970  0.020  1.090
 ETJ  C4   H2   single    0.970  0.020  1.090
 ETJ  C5   H3   single    0.970  0.020  1.090
 ETJ  C8   H4   single    0.970  0.020  1.090
 ETJ  C8   H5   single    0.970  0.020  1.090
 ETJ  C9   H6   single    0.970  0.020  1.090
 ETJ  C9   H7   single    0.970  0.020  1.090
 ETJ  C9   H8   single    0.970  0.020  1.090
 ETJ  C10  H9   single    0.970  0.020  1.090
 ETJ  C10  H10  single    0.970  0.020  1.090
 ETJ  C10  H11  single    0.970  0.020  1.090
 ETJ  C11  H12  single    0.930  0.020  1.080
 ETJ  C12  H13  single    0.930  0.020  1.080
 ETJ  C    H14  single    0.970  0.020  1.090
 ETJ  C14  H15  single    0.930  0.020  1.080
 ETJ  O1   H16  single    0.850  0.020  0.980
 ETJ  C4   H17  single    0.970  0.020  1.090
 ETJ  C5   H18  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
 ETJ  H1   C1   O1   111.07  3.000
 ETJ  H1   C1   C2   106.68  3.000
 ETJ  O1   C1   C2   108.54  3.000
 ETJ  H1   C1   C    108.99  3.000
 ETJ  C2   C1   C    110.29  3.000
 ETJ  O1   C1   C    111.17  3.000
 ETJ  C6   C3   C    119.81  3.000
 ETJ  C6   C3   C11  118.75  3.000
 ETJ  C    C3   C11  121.44  3.000
 ETJ  H17  C4   H2   107.81  3.000
 ETJ  H17  C4   N    111.01  3.000
 ETJ  H2   C4   N    110.97  3.000
 ETJ  H17  C4   C5   112.75  3.000
 ETJ  H2   C4   C5   111.48  3.000
 ETJ  N    C4   C5   102.82  3.000
 ETJ  H18  C5   H3   107.92  3.000
 ETJ  H18  C5   C8   113.44  3.000
 ETJ  H3   C5   C8   110.10  3.000
 ETJ  H18  C5   C4   112.08  3.000
 ETJ  H3   C5   C4   109.80  3.000
 ETJ  C8   C5   C4   103.44  3.000
 ETJ  N    C7   C8   107.50  3.000
 ETJ  C8   C7   O2   126.86  3.000
 ETJ  N    C7   O2   125.64  3.000
 ETJ  H5   C8   H4   107.45  3.000
 ETJ  H5   C8   C7   108.03  3.000
 ETJ  H4   C8   C7   111.23  3.000
 ETJ  H5   C8   C5   111.71  3.000
 ETJ  H4   C8   C5   114.35  3.000
 ETJ  C7   C8   C5   103.94  3.000
 ETJ  H8   C9   H7   107.83  3.000
 ETJ  H8   C9   H6   108.29  3.000
 ETJ  H7   C9   H6   108.48  3.000
 ETJ  H8   C9   C2   110.43  3.000
 ETJ  H7   C9   C2   110.41  3.000
 ETJ  H6   C9   C2   111.31  3.000
 ETJ  H11  C10  H10  107.77  3.000
 ETJ  H11  C10  H9   107.69  3.000
 ETJ  H10  C10  H9   107.85  3.000
 ETJ  H11  C10  C2   109.97  3.000
 ETJ  H10  C10  C2   110.50  3.000
 ETJ  H9   C10  C2   112.87  3.000
 ETJ  H12  C11  C13  119.63  3.000
 ETJ  H12  C11  C3   119.40  3.000
 ETJ  C13  C11  C3   120.97  3.000
 ETJ  H13  C12  C6   119.32  3.000
 ETJ  H13  C12  C14  120.33  3.000
 ETJ  C6   C12  C14  120.35  3.000
 ETJ  C15  C13  C14  120.21  3.000
 ETJ  C15  C13  C11  119.91  3.000
 ETJ  C14  C13  C11  119.88  3.000
 ETJ  C    N    C7   123.24  3.000
 ETJ  C7   N    C4   113.58  3.000
 ETJ  C    N    C4   122.90  3.000
 ETJ  H14  C    N    106.02  3.000
 ETJ  H14  C    C3   108.77  3.000
 ETJ  N    C    C3   112.16  3.000
 ETJ  H14  C    C1   108.03  3.000
 ETJ  C3   C    C1   109.85  3.000
 ETJ  N    C    C1   111.81  3.000
 ETJ  C6   O    C2   119.87  3.000
 ETJ  H15  C14  C13  120.34  3.000
 ETJ  H15  C14  C12  120.01  3.000
 ETJ  C13  C14  C12  119.65  3.000
 ETJ  N1   C15  C13  180.00  3.000
 ETJ  O    C2   C10  108.89  3.000
 ETJ  O    C2   C9   105.04  3.000
 ETJ  C10  C2   C9   110.72  3.000
 ETJ  O    C2   C1   107.94  3.000
 ETJ  C9   C2   C1   110.64  3.000
 ETJ  C10  C2   C1   113.23  3.000
 ETJ  O    C6   C12  116.42  3.000
 ETJ  C12  C6   C3   120.39  3.000
 ETJ  O    C6   C3   123.18  3.000
 ETJ  H16  O1   C1   108.99  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
 ETJ  CONST_01  C14  C12  C6   C3      0.00   0.0  0
 ETJ  CONST_02  C14  C13  C11  C3      0.00   0.0  0
 ETJ  CONST_03  C12  C6   C3   C11     0.00   0.0  0
 ETJ  CONST_04  C12  C14  C13  C11     0.00   0.0  0
 ETJ  CONST_05  C6   C3   C11  C13     0.00   0.0  0
 ETJ  CONST_06  C6   C12  C14  C13     0.00   0.0  0
 ETJ  CONST_07  C8   C7   N    C4      0.00   0.0  0
 ETJ  CONST_08  C    N    C7   C8    180.00   0.0  0
 ETJ  CONST_09  C15  C13  C11  C3    180.00   0.0  0
 ETJ  CONST_10  C15  C13  C14  C12   180.00   0.0  0
 ETJ  CONST_11  C4   N    C7   O2    180.00   0.0  0
 ETJ  CONST_12  C    N    C7   O2      0.00   0.0  0
 ETJ  CONST_13  H13  C12  C6   C3    180.00   0.0  0
 ETJ  CONST_14  H15  C14  C13  C11   180.00   0.0  0
 ETJ  CONST_15  H13  C12  C14  C13   180.00   0.0  0
 ETJ  CONST_16  H12  C11  C3   C       0.00   0.0  0
 ETJ  CONST_17  H13  C12  C6   O       0.00   0.0  0
 ETJ  CONST_18  H12  C11  C13  C14   180.00   0.0  0
 ETJ  CONST_19  H12  C11  C3   C6    180.00   0.0  0
 ETJ  CONST_20  H15  C14  C12  C6    180.00   0.0  0
 ETJ  Var_01    C6   O    C2   C1     43.63  30.0  1
 ETJ  Var_02    C2   O    C6   C3    -14.23  30.0  1
 ETJ  Var_03    C7   C8   C5   C4     27.58  30.0  1
 ETJ  Var_04    C    N    C4   C5   -166.58  30.0  1
 ETJ  Var_05    C7   N    C4   C5     19.35  30.0  1
 ETJ  Var_06    N    C7   C8   C5    -16.80  30.0  1
 ETJ  Var_07    N    C4   C5   C8    -28.19  30.0  1
 ETJ  Var_08    C2   O    C6   C12   166.94  30.0  1
 ETJ  Var_09    C5   C8   C7   O2    163.95  30.0  1
 ETJ  Var_10    C6   O    C2   C9    161.70  30.0  1
 ETJ  Var_11    C6   O    C2   C10   -79.67  30.0  1
 ETJ  Var_12    H4   C8   C5   C4    149.04  30.0  1
 ETJ  Var_13    H5   C8   C5   C4    -88.66  30.0  1
 ETJ  Var_14    H2   C4   N    C7    -99.96  30.0  1
 ETJ  Var_15    H17  C4   N    C7    140.16  30.0  1
 ETJ  Var_16    H3   C5   C8   C7    -89.70  30.0  1
 ETJ  Var_17    H18  C5   C8   C7    149.24  30.0  1
 ETJ  Var_18    H2   C4   C5   C8     90.75  30.0  1
 ETJ  Var_19    H17  C4   C5   C8   -147.81  30.0  1
 ETJ  Var_20    H3   C5   C4   N      89.29  30.0  1
 ETJ  Var_21    H18  C5   C4   N    -150.77  30.0  1
 ETJ  Var_22    H4   C8   C7   N    -140.31  30.0  1
 ETJ  Var_23    H5   C8   C7   N     102.00  30.0  1
 ETJ  Var_24    H2   C4   N    C      74.12  30.0  1
 ETJ  Var_25    H17  C4   N    C     -45.76  30.0  1
 ETJ  Var_26    H9   C10  C2   C1    -62.51  30.0  3
 ETJ  Var_27    H10  C10  C2   C1     58.36  30.0  3
 ETJ  Var_28    H11  C10  C2   C1    177.21  30.0  3
 ETJ  Var_29    H6   C9   C2   C1     53.24  30.0  3
 ETJ  Var_30    H7   C9   C2   C1    173.78  30.0  3
 ETJ  Var_31    H8   C9   C2   C1    -67.07  30.0  3
 ETJ  Var_32    H4   C8   C7   O2     40.44  30.0  1
 ETJ  Var_33    H5   C8   C7   O2    -77.25  30.0  1
 ETJ  Var_34    H9   C10  C2   O      57.57  30.0  3
 ETJ  Var_35    H10  C10  C2   O     178.43  30.0  3
 ETJ  Var_36    H11  C10  C2   O     -62.71  30.0  3
 ETJ  Var_37    H6   C9   C2   O     -63.00  30.0  3
 ETJ  Var_38    H7   C9   C2   O      57.54  30.0  3
 ETJ  Var_39    H8   C9   C2   O     176.69  30.0  3
 ETJ  Var_40    H9   C10  C2   C9    172.57  30.0  3
 ETJ  Var_41    H10  C10  C2   C9    -66.57  30.0  3
 ETJ  Var_42    H11  C10  C2   C9     52.29  30.0  3
 ETJ  Var_43    H6   C9   C2   C10   179.62  30.0  3
 ETJ  Var_44    H7   C9   C2   C10   -59.84  30.0  3
 ETJ  Var_45    H8   C9   C2   C10    59.31  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
 ETJ  chir_01  C1  O1  C2  C   positiv
 ETJ  chir_02  C   N   C1  C3  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
 ETJ  plan-1  C4   0.020
 ETJ  plan-1  C7   0.020
 ETJ  plan-1  C8   0.020
 ETJ  plan-1  N    0.020
 ETJ  plan-1  C    0.020
 ETJ  plan-1  O2   0.020
 ETJ  plan-2  C3   0.020
 ETJ  plan-2  C11  0.020
 ETJ  plan-2  C12  0.020
 ETJ  plan-2  C13  0.020
 ETJ  plan-2  C    0.020
 ETJ  plan-2  O    0.020
 ETJ  plan-2  C14  0.020
 ETJ  plan-2  C15  0.020
 ETJ  plan-2  C6   0.020
 ETJ  plan-2  N1   0.020
 ETJ  plan-2  H12  0.020
 ETJ  plan-2  H13  0.020
 ETJ  plan-2  H15  0.020

