# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 04:12:36 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (3~{R})-8-methoxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=C2SC[C@H](N2C(=O)C=C1Cc3cccc4ccccc34)C(O)=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
 C8Q  C8Q  '(3~{R})-8-methoxy-7-(naphthalen-1-ylmethyl)-5-oxidanylidene-2,3-dihydro-[1,3]thiazolo[3,2-a]pyridine-3-carboxylic acid'  ligand  43  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C8Q
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
 C8Q  C11   C  CR6   0   0.218   0.0632   0.4617   1.4961
 C8Q  O01   O  OH1   0  -0.584  -4.6574  -2.5881  -0.9938
 C8Q  C02   C  C     0   0.575  -3.5050  -2.0422  -0.6513
 C8Q  O03   O  O     0  -0.411  -2.4319  -2.3572  -1.0868
 C8Q  C04   C  CH1   0  -0.241  -3.7205  -0.9347   0.3725
 C8Q  C05   C  CH2   0  -0.574  -4.4067   0.2918  -0.2227
 C8Q  S06   S  S2    0   0.116  -3.0616   1.2806  -0.9484
 C8Q  C07   C  CR6   0   0.150  -1.9380   0.6175   0.2085
 C8Q  C08   C  CR6   0   0.213  -0.7022   1.1125   0.4889
 C8Q  O09   O  O2    0  -0.477  -0.2594   2.2410  -0.1236
 C8Q  C10   C  CH3   0  -0.414   0.2313   2.0663  -1.4495
 C8Q  C12   C  CH2   0  -0.629   1.3891   1.0292   1.9389
 C8Q  C13   C  CR6   0   0.128   2.4223   1.2311   0.8587
 C8Q  C14   C  CR16  0  -0.324   2.8363   2.5021   0.5521
 C8Q  C15   C  CR16  0  -0.245   3.7889   2.7488  -0.4544
 C8Q  C16   C  CR16  0  -0.332   4.3250   1.7097  -1.1604
 C8Q  C17   C  CR66  0   0.109   3.9446   0.3795  -0.8686
 C8Q  C18   C  CR16  0  -0.310   4.5029  -0.7093  -1.5791
 C8Q  C19   C  CR16  0  -0.261   4.1475  -1.9967  -1.2859
 C8Q  C20   C  CR16  0  -0.252   3.2179  -2.2510  -0.2580
 C8Q  C21   C  CR16  0  -0.327   2.6567  -1.2176   0.4426
 C8Q  C22   C  CR66  0   0.097   2.9926   0.1291   0.1581
 C8Q  C23   C  CR16  0  -0.562  -0.4501  -0.6400   2.1200
 C8Q  C24   C  CR6   0   0.571  -1.7275  -1.2015   1.7950
 C8Q  O25   O  O     0  -0.513  -2.2163  -2.2201   2.2758
 C8Q  N26   N  NR6   0  -0.543  -2.4363  -0.4725   0.8523
 C8Q  H1    H  HOH1  0   0.492  -4.5246  -3.2792  -1.6609
 C8Q  H041  H  HCH1  0   0.346  -4.3148  -1.3231   1.2011
 C8Q  H052  H  HCH2  0   0.323  -5.1357   0.0486  -0.9914
 C8Q  H051  H  HCH2  0   0.327  -4.8976   0.8688   0.5587
 C8Q  H103  H  HCH3  0   0.227  -0.5717   1.8186  -2.1494
 C8Q  H102  H  HCH3  0   0.245   0.6757   3.0120  -1.7505
 C8Q  H101  H  HCH3  0   0.231   0.9933   1.2869  -1.5020
 C8Q  H122  H  HCH2  0   0.294   1.1939   1.9964   2.4093
 C8Q  H121  H  HCH2  0   0.278   1.7871   0.3885   2.7294
 C8Q  H141  H  HCR6  0   0.252   2.4081   3.3415   1.0860
 C8Q  H151  H  HCR6  0   0.256   4.0842   3.7675  -0.6694
 C8Q  H161  H  HCR6  0   0.254   5.0504   1.8883  -1.9452
 C8Q  H181  H  HCR6  0   0.255   5.2227  -0.5063  -2.3630
 C8Q  H191  H  HCR6  0   0.258   4.5796  -2.8209  -1.8381
 C8Q  H201  H  HCR6  0   0.258   2.9462  -3.2714  -0.0213
 C8Q  H211  H  HCR6  0   0.254   1.9472  -1.4405   1.2270
 C8Q  H231  H  HCR6  0   0.273   0.1185  -1.1451   2.8902

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
 C8Q  C19  C20   aromatic  1.409  0.020  1.409
 C8Q  C19  C18   aromatic  1.367  0.020  1.367
 C8Q  C20  C21   aromatic  1.369  0.020  1.369
 C8Q  C18  C17   aromatic  1.415  0.020  1.415
 C8Q  C21  C22   aromatic  1.417  0.020  1.417
 C8Q  C17  C22   aromatic  1.422  0.020  1.422
 C8Q  C17  C16   aromatic  1.414  0.020  1.414
 C8Q  C22  C13   aromatic  1.425  0.020  1.425
 C8Q  C16  C15   aromatic  1.366  0.020  1.366
 C8Q  O25  C24   double    1.228  0.020  1.228
 C8Q  C23  C24   single    1.433  0.020  1.433
 C8Q  C23  C11   double    1.366  0.020  1.366
 C8Q  C13  C12   single    1.508  0.020  1.508
 C8Q  C13  C14   aromatic  1.371  0.020  1.371
 C8Q  C24  N26   single    1.387  0.020  1.387
 C8Q  C15  C14   aromatic  1.408  0.020  1.408
 C8Q  C12  C11   single    1.509  0.020  1.509
 C8Q  C11  C08   single    1.423  0.020  1.423
 C8Q  N26  C04   single    1.447  0.020  1.447
 C8Q  N26  C07   single    1.360  0.020  1.360
 C8Q  C04  C02   single    1.524  0.020  1.524
 C8Q  C04  C05   single    1.526  0.020  1.526
 C8Q  C08  C07   double    1.361  0.020  1.361
 C8Q  C08  O09   single    1.358  0.020  1.358
 C8Q  C07  S06   single    1.744  0.020  1.744
 C8Q  C02  O03   double    1.200  0.020  1.200
 C8Q  C02  O01   single    1.320  0.020  1.320
 C8Q  C05  S06   single    1.820  0.020  1.820
 C8Q  O09  C10   single    1.425  0.020  1.425
 C8Q  O01  H1    single    0.850  0.020  0.980
 C8Q  C04  H041  single    0.970  0.020  1.090
 C8Q  C05  H052  single    0.970  0.020  1.090
 C8Q  C05  H051  single    0.970  0.020  1.090
 C8Q  C10  H103  single    0.970  0.020  1.090
 C8Q  C10  H102  single    0.970  0.020  1.090
 C8Q  C10  H101  single    0.970  0.020  1.090
 C8Q  C12  H122  single    0.970  0.020  1.090
 C8Q  C12  H121  single    0.970  0.020  1.090
 C8Q  C14  H141  single    0.930  0.020  1.080
 C8Q  C15  H151  single    0.930  0.020  1.080
 C8Q  C16  H161  single    0.930  0.020  1.080
 C8Q  C18  H181  single    0.930  0.020  1.080
 C8Q  C19  H191  single    0.930  0.020  1.080
 C8Q  C20  H201  single    0.930  0.020  1.080
 C8Q  C21  H211  single    0.930  0.020  1.080
 C8Q  C23  H231  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
 C8Q  C23   C11  C12   119.97  3.000
 C8Q  C12   C11  C08   120.57  3.000
 C8Q  C23   C11  C08   119.34  3.000
 C8Q  H1    O01  C02   110.70  3.000
 C8Q  C04   C02  O03   124.13  3.000
 C8Q  O03   C02  O01   125.30  3.000
 C8Q  C04   C02  O01   110.57  3.000
 C8Q  H041  C04  N26   110.20  3.000
 C8Q  H041  C04  C05   109.71  3.000
 C8Q  N26   C04  C05   105.76  3.000
 C8Q  H041  C04  C02   109.18  3.000
 C8Q  C05   C04  C02   112.69  3.000
 C8Q  N26   C04  C02   109.24  3.000
 C8Q  H051  C05  H052  108.90  3.000
 C8Q  H051  C05  S06   109.36  3.000
 C8Q  H052  C05  S06   109.58  3.000
 C8Q  H051  C05  C04   110.42  3.000
 C8Q  H052  C05  C04   113.42  3.000
 C8Q  S06   C05  C04   105.05  3.000
 C8Q  C07   S06  C05    90.29  3.000
 C8Q  N26   C07  C08   121.78  3.000
 C8Q  C08   C07  S06   125.71  3.000
 C8Q  N26   C07  S06   112.50  3.000
 C8Q  O09   C08  C07   120.37  3.000
 C8Q  O09   C08  C11   121.60  3.000
 C8Q  C07   C08  C11   117.92  3.000
 C8Q  C10   O09  C08   115.48  3.000
 C8Q  H101  C10  H102  108.81  3.000
 C8Q  H101  C10  H103  108.68  3.000
 C8Q  H102  C10  H103  108.66  3.000
 C8Q  H101  C10  O09   111.89  3.000
 C8Q  H102  C10  O09   106.96  3.000
 C8Q  H103  C10  O09   111.75  3.000
 C8Q  H121  C12  H122  105.82  3.000
 C8Q  H121  C12  C13   110.31  3.000
 C8Q  H122  C12  C13   108.19  3.000
 C8Q  H121  C12  C11   108.17  3.000
 C8Q  H122  C12  C11   107.59  3.000
 C8Q  C13   C12  C11   116.24  3.000
 C8Q  C22   C13  C14   119.08  3.000
 C8Q  C14   C13  C12   119.40  3.000
 C8Q  C22   C13  C12   121.52  3.000
 C8Q  H141  C14  C15   118.96  3.000
 C8Q  H141  C14  C13   119.26  3.000
 C8Q  C15   C14  C13   121.78  3.000
 C8Q  H151  C15  C16   120.42  3.000
 C8Q  H151  C15  C14   119.46  3.000
 C8Q  C16   C15  C14   120.12  3.000
 C8Q  H161  C16  C17   118.99  3.000
 C8Q  H161  C16  C15   120.78  3.000
 C8Q  C17   C16  C15   120.23  3.000
 C8Q  C22   C17  C18   119.41  3.000
 C8Q  C22   C17  C16   119.65  3.000
 C8Q  C18   C17  C16   120.94  3.000
 C8Q  H181  C18  C19   120.28  3.000
 C8Q  H181  C18  C17   118.77  3.000
 C8Q  C19   C18  C17   120.95  3.000
 C8Q  H191  C19  C20   119.88  3.000
 C8Q  H191  C19  C18   120.26  3.000
 C8Q  C20   C19  C18   119.86  3.000
 C8Q  H201  C20  C21   119.80  3.000
 C8Q  H201  C20  C19   119.70  3.000
 C8Q  C21   C20  C19   120.50  3.000
 C8Q  H211  C21  C22   119.82  3.000
 C8Q  H211  C21  C20   119.00  3.000
 C8Q  C22   C21  C20   121.18  3.000
 C8Q  C21   C22  C17   118.10  3.000
 C8Q  C17   C22  C13   119.12  3.000
 C8Q  C21   C22  C13   122.78  3.000
 C8Q  H231  C23  C24   116.55  3.000
 C8Q  H231  C23  C11   120.25  3.000
 C8Q  C24   C23  C11   123.19  3.000
 C8Q  N26   C24  O25   119.93  3.000
 C8Q  N26   C24  C23   113.82  3.000
 C8Q  O25   C24  C23   126.24  3.000
 C8Q  C24   N26  C07   123.76  3.000
 C8Q  C07   N26  C04   115.10  3.000
 C8Q  C24   N26  C04   120.75  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
 C8Q  CONST_01  C20   C21  C22  C13   180.00   0.0  0
 C8Q  CONST_02  C18   C17  C22  C13   180.00   0.0  0
 C8Q  CONST_03  C16   C17  C22  C13     0.00   0.0  0
 C8Q  CONST_04  C16   C15  C14  C13     0.00   0.0  0
 C8Q  CONST_05  C21   C22  C13  C14   180.00   0.0  0
 C8Q  CONST_06  C17   C22  C13  C14     0.00   0.0  0
 C8Q  CONST_07  C17   C16  C15  C14     0.00   0.0  0
 C8Q  CONST_08  C18   C17  C16  C15   180.00   0.0  0
 C8Q  CONST_09  C22   C17  C16  C15     0.00   0.0  0
 C8Q  CONST_10  C22   C13  C14  C15     0.00   0.0  0
 C8Q  CONST_11  C19   C18  C17  C16   180.00   0.0  0
 C8Q  CONST_12  C21   C22  C17  C16   180.00   0.0  0
 C8Q  CONST_13  C20   C19  C18  C17     0.00   0.0  0
 C8Q  CONST_14  C20   C21  C22  C17     0.00   0.0  0
 C8Q  CONST_15  C21   C20  C19  C18     0.00   0.0  0
 C8Q  CONST_16  C21   C22  C17  C18     0.00   0.0  0
 C8Q  CONST_17  C22   C21  C20  C19     0.00   0.0  0
 C8Q  CONST_18  C22   C17  C18  C19     0.00   0.0  0
 C8Q  CONST_19  C23   C24  N26  C04   180.00   0.0  0
 C8Q  CONST_20  C23   C24  N26  C07     0.00   0.0  0
 C8Q  CONST_21  C21   C22  C13  C12     0.00   0.0  0
 C8Q  CONST_22  C17   C22  C13  C12   180.00   0.0  0
 C8Q  CONST_23  C15   C14  C13  C12   180.00   0.0  0
 C8Q  CONST_24  O25   C24  N26  C04     0.00   0.0  0
 C8Q  CONST_25  O25   C24  N26  C07   180.00   0.0  0
 C8Q  CONST_26  H211  C21  C22  C13     0.00   0.0  0
 C8Q  CONST_27  H151  C15  C14  C13   180.00   0.0  0
 C8Q  CONST_28  H161  C16  C15  C14   180.00   0.0  0
 C8Q  CONST_29  H181  C18  C17  C16     0.00   0.0  0
 C8Q  CONST_30  H141  C14  C15  C16   180.00   0.0  0
 C8Q  CONST_31  H191  C19  C18  C17   180.00   0.0  0
 C8Q  CONST_32  H201  C20  C19  C18   180.00   0.0  0
 C8Q  CONST_33  H1    O01  C02  C04   180.00   0.0  0
 C8Q  Var_01    N26   C07  S06  C05    14.00  30.0  1
 C8Q  Var_02    C22   C13  C12  C11   -65.70  30.0  2
 C8Q  Var_03    C13   C12  C11  C08   -56.65  30.0  1
 C8Q  Var_04    H052  C05  S06  C07  -149.84  30.0  1
 C8Q  Var_05    H103  C10  O09  C08    69.16  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
 C8Q  chir_01  C04  N26  C02  C05  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
 C8Q  plan-1  C12   0.020
 C8Q  plan-1  C13   0.020
 C8Q  plan-1  C14   0.020
 C8Q  plan-1  C15   0.020
 C8Q  plan-1  C16   0.020
 C8Q  plan-1  C17   0.020
 C8Q  plan-1  C18   0.020
 C8Q  plan-1  C19   0.020
 C8Q  plan-1  C20   0.020
 C8Q  plan-1  C21   0.020
 C8Q  plan-1  C22   0.020
 C8Q  plan-1  H141  0.020
 C8Q  plan-1  H151  0.020
 C8Q  plan-1  H161  0.020
 C8Q  plan-1  H181  0.020
 C8Q  plan-1  H191  0.020
 C8Q  plan-1  H201  0.020
 C8Q  plan-1  H211  0.020
 C8Q  plan-2  C11   0.020
 C8Q  plan-2  C04   0.020
 C8Q  plan-2  S06   0.020
 C8Q  plan-2  C07   0.020
 C8Q  plan-2  C08   0.020
 C8Q  plan-2  O09   0.020
 C8Q  plan-2  C12   0.020
 C8Q  plan-2  C23   0.020
 C8Q  plan-2  C24   0.020
 C8Q  plan-2  O25   0.020
 C8Q  plan-2  N26   0.020
 C8Q  plan-2  H231  0.020
 C8Q  plan-3  O01   0.020
 C8Q  plan-3  C02   0.020
 C8Q  plan-3  O03   0.020
 C8Q  plan-3  C04   0.020
 C8Q  plan-3  H1    0.020

