# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:19:55 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (2R,3R)-8-cyclopropyl-7-(naphthalen-1-ylmethyl)-5-oxo-2-phenyl-2,3-dihydro-5H-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1[C@H](SC2=C(C3CC3)C(=CC(=O)N12)Cc4cccc5ccccc45)c6ccccc6
#
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
 EC2  EC2  '(2R,3R)-8-cyclopropyl-7-(naphthalen-1-ylmethyl)-5-oxo-2-phenyl-2,3-dihydro-5H-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid'  ligand  56  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EC2
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
 EC2  O23   O  OH1   0  -0.583   4.7670  -2.2032   1.7209
 EC2  C21   C  C     0   0.581   3.5014  -1.9452   1.9940
 EC2  O22   O  O     0  -0.411   2.9953  -2.0287   3.0788
 EC2  C28   C  CH1   0  -0.219   2.7578  -1.5191   0.7331
 EC2  C29   C  CH1   0  -0.556   3.2206  -0.1539   0.2088
 EC2  C6    C  CR6   0   0.236   2.9550   0.0175  -1.2658
 EC2  C5    C  CR16  0  -0.301   4.0169  -0.1646  -2.1474
 EC2  C4    C  CR16  0  -0.238   3.8243  -0.0740  -3.5193
 EC2  C3    C  CR16  0  -0.263   2.5626   0.2016  -4.0264
 EC2  C2    C  CR16  0  -0.235   1.4988   0.3876  -3.1532
 EC2  C1    C  CR16  0  -0.305   1.6915   0.2982  -1.7824
 EC2  S30   S  S2    0   0.125   2.3017   1.0092   1.2667
 EC2  N27   N  NR6   0  -0.529   1.3531  -1.3686   1.0265
 EC2  C26   C  CR6   0   0.578   0.5419  -2.4891   1.0770
 EC2  O26   O  O     0  -0.512   1.0141  -3.6030   0.8697
 EC2  C22   C  CR6   0   0.161   0.9512  -0.1094   1.3792
 EC2  C23   C  CR6   0  -0.000  -0.3417   0.1787   1.7025
 EC2  C18   C  CH1   0  -0.360  -0.8621   1.5121   2.1078
 EC2  C20   C  CH2   0  -0.446  -0.9753   2.6622   1.1476
 EC2  C19   C  CH2   0  -0.496  -0.0919   2.7811   2.3458
 EC2  C24   C  CR6   0   0.265  -1.2639  -0.9168   1.5989
 EC2  C25   C  CR16  0  -0.559  -0.8283  -2.1814   1.3347
 EC2  C17   C  CH2   0  -0.638  -2.7529  -0.7096   1.7588
 EC2  C16   C  CR6   0   0.135  -3.3832   0.4019   0.9495
 EC2  C7    C  CR16  0  -0.336  -4.1867   1.3083   1.5936
 EC2  C8    C  CR16  0  -0.244  -4.7995   2.3776   0.9136
 EC2  C9    C  CR16  0  -0.336  -4.5936   2.5427  -0.4262
 EC2  C10   C  CR66  0   0.112  -3.7924   1.6229  -1.1408
 EC2  C15   C  CR66  0   0.112  -3.1953   0.5259  -0.4584
 EC2  C11   C  CR16  0  -0.312  -3.5884   1.7739  -2.5329
 EC2  C12   C  CR16  0  -0.262  -2.8395   0.8725  -3.2373
 EC2  C13   C  CR16  0  -0.254  -2.2734  -0.2332  -2.5737
 EC2  C14   C  CR16  0  -0.334  -2.4464  -0.4003  -1.2258
 EC2  H28   H  HCH1  0   0.350   2.9006  -2.2829  -0.0338
 EC2  H29   H  HCH1  0   0.348   4.2816  -0.0026   0.4066
 EC2  H5    H  HCR6  0   0.260   5.0057  -0.3800  -1.7604
 EC2  H1    H  HCR6  0   0.255   0.8426   0.4557  -1.1282
 EC2  H4    H  HCR6  0   0.262   4.6618  -0.2148  -4.1897
 EC2  H3    H  HCR6  0   0.262   2.4087   0.2752  -5.0950
 EC2  H2    H  HCR6  0   0.258   0.5122   0.6101  -3.5386
 EC2  H25   H  HCR6  0   0.275  -1.5332  -2.9999   1.2684
 EC2  H18   H  HCH1  0   0.275  -1.7049   1.4214   2.7820
 EC2  H201  H  HCH2  0   0.246  -0.4939   2.5378   0.1848
 EC2  H202  H  HCH2  0   0.258  -1.9083   3.2096   1.1131
 EC2  H191  H  HCH2  0   0.263  -0.4412   3.3821   3.1759
 EC2  H192  H  HCH2  0   0.256   0.9762   2.8428   2.1988
 EC2  H171  H  HCH2  0   0.285  -3.2449  -1.6546   1.5148
 EC2  H172  H  HCH2  0   0.290  -2.9703  -0.5259   2.8148
 EC2  H7    H  HCR6  0   0.253  -4.3375   1.2163   2.6629
 EC2  H8    H  HCR6  0   0.256  -5.4199   3.0725   1.4644
 EC2  H9    H  HCR6  0   0.253  -5.0439   3.3725  -0.9573
 EC2  H11   H  HCR6  0   0.253  -4.0436   2.6186  -3.0361
 EC2  H14   H  HCR6  0   0.260  -2.0104  -1.2680  -0.7544
 EC2  H12   H  HCR6  0   0.257  -2.6901   0.9982  -4.3017
 EC2  H13   H  HCR6  0   0.258  -1.7010  -0.9616  -3.1336
 EC2  H23   H  HOH1  0   0.493   5.2464  -2.4554   2.5252

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
 EC2  O23  C21   single    1.320  0.020  1.320
 EC2  C21  O22   double    1.200  0.020  1.200
 EC2  C21  C28   single    1.525  0.020  1.525
 EC2  C28  C29   single    1.534  0.020  1.534
 EC2  C28  N27   single    1.443  0.020  1.443
 EC2  C29  C6    single    1.508  0.020  1.508
 EC2  C29  S30   single    1.821  0.020  1.821
 EC2  C6   C5    aromatic  1.392  0.020  1.392
 EC2  C6   C1    aromatic  1.394  0.020  1.394
 EC2  C5   C4    aromatic  1.388  0.020  1.388
 EC2  C4   C3    aromatic  1.388  0.020  1.388
 EC2  C3   C2    aromatic  1.389  0.020  1.389
 EC2  C2   C1    aromatic  1.387  0.020  1.387
 EC2  S30  C22   single    1.757  0.020  1.757
 EC2  N27  C26   single    1.384  0.020  1.384
 EC2  N27  C22   single    1.368  0.020  1.368
 EC2  C26  O26   double    1.228  0.020  1.228
 EC2  C26  C25   single    1.428  0.020  1.428
 EC2  C22  C23   double    1.363  0.020  1.363
 EC2  C23  C18   single    1.488  0.020  1.488
 EC2  C23  C24   single    1.436  0.020  1.436
 EC2  C18  C20   single    1.503  0.020  1.503
 EC2  C18  C19   single    1.503  0.020  1.503
 EC2  C20  C19   single    1.493  0.020  1.493
 EC2  C24  C25   double    1.363  0.020  1.363
 EC2  C24  C17   single    1.512  0.020  1.512
 EC2  C17  C16   single    1.512  0.020  1.512
 EC2  C16  C7    aromatic  1.372  0.020  1.372
 EC2  C16  C15   aromatic  1.426  0.020  1.426
 EC2  C7   C8    aromatic  1.408  0.020  1.408
 EC2  C8   C9    aromatic  1.365  0.020  1.365
 EC2  C9   C10   aromatic  1.414  0.020  1.414
 EC2  C10  C15   aromatic  1.423  0.020  1.423
 EC2  C10  C11   aromatic  1.415  0.020  1.415
 EC2  C15  C14   aromatic  1.417  0.020  1.417
 EC2  C11  C12   aromatic  1.367  0.020  1.367
 EC2  C12  C13   aromatic  1.408  0.020  1.408
 EC2  C13  C14   aromatic  1.369  0.020  1.369
 EC2  C28  H28   single    0.970  0.020  1.090
 EC2  C29  H29   single    0.970  0.020  1.090
 EC2  C5   H5    single    0.930  0.020  1.080
 EC2  C1   H1    single    0.930  0.020  1.080
 EC2  C4   H4    single    0.930  0.020  1.080
 EC2  C3   H3    single    0.930  0.020  1.080
 EC2  C2   H2    single    0.930  0.020  1.080
 EC2  C25  H25   single    0.930  0.020  1.080
 EC2  C18  H18   single    0.970  0.020  1.090
 EC2  C20  H201  single    0.970  0.020  1.090
 EC2  C20  H202  single    0.970  0.020  1.090
 EC2  C19  H191  single    0.970  0.020  1.090
 EC2  C19  H192  single    0.970  0.020  1.090
 EC2  C17  H171  single    0.970  0.020  1.090
 EC2  C17  H172  single    0.970  0.020  1.090
 EC2  C7   H7    single    0.930  0.020  1.080
 EC2  C8   H8    single    0.930  0.020  1.080
 EC2  C9   H9    single    0.930  0.020  1.080
 EC2  C11  H11   single    0.930  0.020  1.080
 EC2  C14  H14   single    0.930  0.020  1.080
 EC2  C12  H12   single    0.930  0.020  1.080
 EC2  C13  H13   single    0.930  0.020  1.080
 EC2  O23  H23   single    0.850  0.020  0.980

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
 EC2  H23   O23  C21   110.68  3.000
 EC2  C28   C21  O22   124.16  3.000
 EC2  C28   C21  O23   110.55  3.000
 EC2  O22   C21  O23   125.29  3.000
 EC2  H28   C28  N27   110.07  3.000
 EC2  H28   C28  C29   110.07  3.000
 EC2  N27   C28  C29   105.69  3.000
 EC2  H28   C28  C21   108.76  3.000
 EC2  N27   C28  C21   109.62  3.000
 EC2  C29   C28  C21   112.60  3.000
 EC2  H29   C29  S30   107.29  3.000
 EC2  H29   C29  C6    109.46  3.000
 EC2  S30   C29  C6    113.99  3.000
 EC2  H29   C29  C28   110.81  3.000
 EC2  S30   C29  C28   102.57  3.000
 EC2  C6    C29  C28   112.47  3.000
 EC2  C1    C6   C5    118.89  3.000
 EC2  C1    C6   C29   123.03  3.000
 EC2  C5    C6   C29   118.04  3.000
 EC2  H5    C5   C4    119.51  3.000
 EC2  H5    C5   C6    119.73  3.000
 EC2  C4    C5   C6    120.76  3.000
 EC2  H4    C4   C3    120.22  3.000
 EC2  H4    C4   C5    119.76  3.000
 EC2  C3    C4   C5    120.02  3.000
 EC2  H3    C3   C2    120.19  3.000
 EC2  H3    C3   C4    120.25  3.000
 EC2  C2    C3   C4    119.56  3.000
 EC2  H2    C2   C1    119.46  3.000
 EC2  H2    C2   C3    120.12  3.000
 EC2  C1    C2   C3    120.42  3.000
 EC2  H1    C1   C2    118.59  3.000
 EC2  H1    C1   C6    121.06  3.000
 EC2  C2    C1   C6    120.35  3.000
 EC2  C22   S30  C29    91.06  3.000
 EC2  C22   N27  C26   124.30  3.000
 EC2  C22   N27  C28   115.75  3.000
 EC2  C26   N27  C28   119.57  3.000
 EC2  C25   C26  O26   126.53  3.000
 EC2  C25   C26  N27   113.23  3.000
 EC2  O26   C26  N27   120.20  3.000
 EC2  C23   C22  N27   122.29  3.000
 EC2  C23   C22  S30   127.55  3.000
 EC2  N27   C22  S30   110.10  3.000
 EC2  C24   C23  C18   118.61  3.000
 EC2  C24   C23  C22   115.51  3.000
 EC2  C18   C23  C22   125.86  3.000
 EC2  H18   C18  C19   111.76  3.000
 EC2  H18   C18  C20   113.79  3.000
 EC2  C19   C18  C20    59.58  3.000
 EC2  H18   C18  C23   111.52  3.000
 EC2  C19   C18  C23   128.35  3.000
 EC2  C20   C18  C23   122.57  3.000
 EC2  H202  C20  H201  114.38  3.000
 EC2  H202  C20  C19   119.68  3.000
 EC2  H201  C20  C19   117.34  3.000
 EC2  H202  C20  C18   118.19  3.000
 EC2  H201  C20  C18   116.52  3.000
 EC2  C19   C20  C18    60.24  3.000
 EC2  H192  C19  H191  113.06  3.000
 EC2  H192  C19  C20   118.71  3.000
 EC2  H191  C19  C20   117.94  3.000
 EC2  H192  C19  C18   122.24  3.000
 EC2  H191  C19  C18   115.13  3.000
 EC2  C20   C19  C18    60.18  3.000
 EC2  C17   C24  C25   117.54  3.000
 EC2  C17   C24  C23   121.36  3.000
 EC2  C25   C24  C23   121.10  3.000
 EC2  H25   C25  C24   120.35  3.000
 EC2  H25   C25  C26   116.81  3.000
 EC2  C24   C25  C26   122.79  3.000
 EC2  H172  C17  H171  105.74  3.000
 EC2  H172  C17  C16   108.08  3.000
 EC2  H171  C17  C16   109.17  3.000
 EC2  H172  C17  C24   108.72  3.000
 EC2  H171  C17  C24   107.53  3.000
 EC2  C16   C17  C24   117.03  3.000
 EC2  C15   C16  C7    118.90  3.000
 EC2  C15   C16  C17   122.50  3.000
 EC2  C7    C16  C17   118.58  3.000
 EC2  H7    C7   C8    118.72  3.000
 EC2  H7    C7   C16   119.25  3.000
 EC2  C8    C7   C16   122.01  3.000
 EC2  H8    C8   C9    120.54  3.000
 EC2  H8    C8   C7    119.44  3.000
 EC2  C9    C8   C7    120.01  3.000
 EC2  H9    C9   C10   119.08  3.000
 EC2  H9    C9   C8    120.73  3.000
 EC2  C10   C9   C8    120.18  3.000
 EC2  C11   C10  C15   119.57  3.000
 EC2  C11   C10  C9    120.64  3.000
 EC2  C15   C10  C9    119.79  3.000
 EC2  C14   C15  C10   117.77  3.000
 EC2  C14   C15  C16   123.20  3.000
 EC2  C10   C15  C16   119.03  3.000
 EC2  H11   C11  C12   120.32  3.000
 EC2  H11   C11  C10   118.65  3.000
 EC2  C12   C11  C10   121.03  3.000
 EC2  H12   C12  C13   119.94  3.000
 EC2  H12   C12  C11   120.38  3.000
 EC2  C13   C12  C11   119.67  3.000
 EC2  H13   C13  C14   119.59  3.000
 EC2  H13   C13  C12   119.81  3.000
 EC2  C14   C13  C12   120.59  3.000
 EC2  H14   C14  C13   118.49  3.000
 EC2  H14   C14  C15   120.16  3.000
 EC2  C13   C14  C15   121.34  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
 EC2  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 EC2  CONST_02  C3   C2   C1   C6      0.00   0.0  0
 EC2  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 EC2  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 EC2  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 EC2  CONST_06  C1   C2   C3   C4      0.00   0.0  0
 EC2  CONST_07  C9   C8   C7   C16     0.00   0.0  0
 EC2  CONST_08  C9   C10  C15  C16     0.00   0.0  0
 EC2  CONST_09  C11  C10  C15  C16   180.00   0.0  0
 EC2  CONST_10  C13  C14  C15  C16   180.00   0.0  0
 EC2  CONST_11  C10  C15  C16  C7      0.00   0.0  0
 EC2  CONST_12  C14  C15  C16  C7    180.00   0.0  0
 EC2  CONST_13  C10  C9   C8   C7      0.00   0.0  0
 EC2  CONST_14  C15  C16  C7   C8      0.00   0.0  0
 EC2  CONST_15  C15  C10  C9   C8      0.00   0.0  0
 EC2  CONST_16  C11  C10  C9   C8    180.00   0.0  0
 EC2  CONST_17  C14  C15  C10  C9    180.00   0.0  0
 EC2  CONST_18  C12  C11  C10  C9    180.00   0.0  0
 EC2  CONST_19  C13  C14  C15  C10     0.00   0.0  0
 EC2  CONST_20  C13  C12  C11  C10     0.00   0.0  0
 EC2  CONST_21  C12  C11  C10  C15     0.00   0.0  0
 EC2  CONST_22  C12  C13  C14  C15     0.00   0.0  0
 EC2  CONST_23  C14  C15  C10  C11     0.00   0.0  0
 EC2  CONST_24  C14  C13  C12  C11     0.00   0.0  0
 EC2  CONST_25  C4   C5   C6   C29   180.00   0.0  0
 EC2  CONST_26  C2   C1   C6   C29   180.00   0.0  0
 EC2  CONST_27  C25  C26  N27  C28   180.00   0.0  0
 EC2  CONST_28  C25  C26  N27  C22     0.00   0.0  0
 EC2  CONST_29  C8   C7   C16  C17   180.00   0.0  0
 EC2  CONST_30  C10  C15  C16  C17   180.00   0.0  0
 EC2  CONST_31  C14  C15  C16  C17     0.00   0.0  0
 EC2  CONST_32  O26  C26  N27  C28     0.00   0.0  0
 EC2  CONST_33  C22  N27  C26  O26   180.00   0.0  0
 EC2  CONST_34  H5   C5   C6   C29     0.00   0.0  0
 EC2  CONST_35  H1   C1   C6   C29     0.00   0.0  0
 EC2  CONST_36  H4   C4   C5   C6    180.00   0.0  0
 EC2  CONST_37  H2   C2   C1   C6    180.00   0.0  0
 EC2  CONST_38  H3   C3   C4   C5    180.00   0.0  0
 EC2  CONST_39  H8   C8   C7   C16   180.00   0.0  0
 EC2  CONST_40  H14  C14  C15  C16     0.00   0.0  0
 EC2  CONST_41  H9   C9   C8   C7    180.00   0.0  0
 EC2  CONST_42  H7   C7   C8   C9    180.00   0.0  0
 EC2  CONST_43  H11  C11  C10  C9      0.00   0.0  0
 EC2  CONST_44  H12  C12  C11  C10   180.00   0.0  0
 EC2  CONST_45  H13  C13  C14  C15   180.00   0.0  0
 EC2  CONST_46  H23  O23  C21  C28   180.00   0.0  0
 EC2  Var_01    N27  C22  S30  C29    18.15  30.0  1
 EC2  Var_02    C20  C18  C23  C22    69.99  30.0  3
 EC2  Var_03    C19  C20  C18  C23  -118.60  30.0  1
 EC2  Var_04    C16  C17  C24  C23    49.79  30.0  3
 EC2  Var_05    C7   C16  C17  C24  -129.70  30.0  2

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
 EC2  chir_01  C28  C21  C29  N27  positiv
 EC2  chir_02  C29  S30  C28  C6   negativ
 EC2  chir_03  C18  C23  C20  C19  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
 EC2  plan-1  C29  0.020
 EC2  plan-1  C6   0.020
 EC2  plan-1  C5   0.020
 EC2  plan-1  C4   0.020
 EC2  plan-1  C3   0.020
 EC2  plan-1  C2   0.020
 EC2  plan-1  C1   0.020
 EC2  plan-1  H5   0.020
 EC2  plan-1  H1   0.020
 EC2  plan-1  H4   0.020
 EC2  plan-1  H3   0.020
 EC2  plan-1  H2   0.020
 EC2  plan-2  C17  0.020
 EC2  plan-2  C16  0.020
 EC2  plan-2  C7   0.020
 EC2  plan-2  C8   0.020
 EC2  plan-2  C9   0.020
 EC2  plan-2  C10  0.020
 EC2  plan-2  C15  0.020
 EC2  plan-2  C11  0.020
 EC2  plan-2  C12  0.020
 EC2  plan-2  C13  0.020
 EC2  plan-2  C14  0.020
 EC2  plan-2  H7   0.020
 EC2  plan-2  H8   0.020
 EC2  plan-2  H9   0.020
 EC2  plan-2  H11  0.020
 EC2  plan-2  H14  0.020
 EC2  plan-2  H12  0.020
 EC2  plan-2  H13  0.020
 EC2  plan-3  O23  0.020
 EC2  plan-3  C21  0.020
 EC2  plan-3  O22  0.020
 EC2  plan-3  C28  0.020
 EC2  plan-3  H23  0.020
 EC2  plan-4  C28  0.020
 EC2  plan-4  S30  0.020
 EC2  plan-4  N27  0.020
 EC2  plan-4  C26  0.020
 EC2  plan-4  O26  0.020
 EC2  plan-4  C22  0.020
 EC2  plan-4  C23  0.020
 EC2  plan-4  C18  0.020
 EC2  plan-4  C24  0.020
 EC2  plan-4  C25  0.020
 EC2  plan-4  C17  0.020
 EC2  plan-4  H25  0.020

