# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 20:43:43 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  42  26  .  2021-08-07  2021-08-07  
;
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  C      0   0.218   0.0762   0.4664   1.5154
 C8Q  O01   O  OC    -1  -0.603  -4.5429  -2.4863  -1.1858
 C8Q  C02   C  C      0   0.441  -3.4885  -2.0472  -0.6940
 C8Q  O03   O  O      0  -0.572  -2.3205  -2.3517  -0.9672
 C8Q  C04   C  CR15   0  -0.243  -3.7075  -0.9700   0.4085
 C8Q  C05   C  CH2    0  -0.570  -4.4238   0.2615  -0.1233
 C8Q  S06   S  S2     0   0.083  -3.1012   1.2833  -0.8520
 C8Q  C07   C  CR5    0   0.154  -1.9510   0.6067   0.2726
 C8Q  C08   C  C      0   0.197  -0.7083   1.1084   0.5240
 C8Q  O09   O  O2     0  -0.480  -0.2834   2.2387  -0.1043
 C8Q  C10   C  CH3    0  -0.411   0.1834   2.0521  -1.4355
 C8Q  C12   C  CH2    0  -0.629   1.4094   1.0363   1.9341
 C8Q  C13   C  CR6    0   0.130   2.4256   1.2350   0.8375
 C8Q  C14   C  CR16   0  -0.324   2.8296   2.5054   0.5150
 C8Q  C15   C  CR16   0  -0.245   3.7689   2.7485  -0.5049
 C8Q  C16   C  CR16   0  -0.333   4.3039   1.7062  -1.2071
 C8Q  C17   C  CR66   0   0.109   3.9337   0.3766  -0.8998
 C8Q  C18   C  CR16   0  -0.311   4.4916  -0.7156  -1.6055
 C8Q  C19   C  CR16   0  -0.262   4.1450  -2.0021  -1.2982
 C8Q  C20   C  CR16   0  -0.252   3.2240  -2.2520  -0.2616
 C8Q  C21   C  CR16   0  -0.326   2.6638  -1.2153   0.4350
 C8Q  C22   C  CR66   0   0.095   2.9925   0.1304   0.1379
 C8Q  C23   C  C1     0  -0.572  -0.4295  -0.6315   2.1551
 C8Q  C24   C  C      0   0.562  -1.7150  -1.1918   1.8589
 C8Q  O25   O  O      0  -0.530  -2.1924  -2.1990   2.3803
 C8Q  N26   N  NR5    0  -0.524  -2.4393  -0.4764   0.9231
 C8Q  H041  H  HCR5   0   0.294  -4.2839  -1.4039   1.2259
 C8Q  H052  H  HCH2   0   0.301  -5.1550   0.0110  -0.8868
 C8Q  H051  H  HCH2   0   0.301  -4.9123   0.8294   0.6679
 C8Q  H103  H  HCH3   0   0.225  -0.6283   1.7753  -2.1143
 C8Q  H102  H  HCH3   0   0.240   0.6038   3.0006  -1.7622
 C8Q  H101  H  HCH3   0   0.228   0.9602   1.2873  -1.4911
 C8Q  H122  H  HCH2   0   0.289   1.2245   2.0050   2.4055
 C8Q  H121  H  HCH2   0   0.274   1.8212   0.3971   2.7189
 C8Q  H141  H  HCR6   0   0.251   2.4038   3.3469   1.0472
 C8Q  H151  H  HCR6   0   0.256   4.0559   3.7668  -0.7324
 C8Q  H161  H  HCR6   0   0.253   5.0203   1.8820  -2.0008
 C8Q  H181  H  HCR6   0   0.254   5.2039  -0.5159  -2.3971
 C8Q  H191  H  HCR6   0   0.257   4.5770  -2.8291  -1.8466
 C8Q  H201  H  HCR6   0   0.257   2.9576  -3.2716  -0.0154
 C8Q  H211  H  HCR6   0   0.254   1.9586  -1.4339   1.2245
 C8Q  H231  H  H      0   0.261   0.1533  -1.1307   2.9189

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    1.231  0.020  1.231
 C8Q  C23  C24   single    1.433  0.020  1.433
 C8Q  C23  C11   double    1.368  0.020  1.368
 C8Q  C13  C12   single    1.508  0.020  1.508
 C8Q  C13  C14   aromatic  1.372  0.020  1.372
 C8Q  C24  N26   single    1.383  0.020  1.383
 C8Q  C15  C14   aromatic  1.408  0.020  1.408
 C8Q  C12  C11   single    1.509  0.020  1.509
 C8Q  C11  C08   single    1.418  0.020  1.418
 C8Q  N26  C04   single    1.455  0.020  1.455
 C8Q  N26  C07   single    1.355  0.020  1.355
 C8Q  C04  C02   single    1.557  0.020  1.557
 C8Q  C04  C05   single    1.521  0.020  1.521
 C8Q  C08  C07   double    1.364  0.020  1.364
 C8Q  C08  O09   single    1.361  0.020  1.361
 C8Q  C07  S06   single    1.745  0.020  1.745
 C8Q  C02  O03   deloc     1.238  0.020  1.238
 C8Q  C02  O01   deloc     1.244  0.020  1.244
 C8Q  C05  S06   single    1.823  0.020  1.823
 C8Q  O09  C10   single    1.423  0.020  1.423
 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   120.01  3.000
 C8Q  C12   C11  C08   120.78  3.000
 C8Q  C23   C11  C08   119.07  3.000
 C8Q  C04   C02  O03   117.34  3.000
 C8Q  O03   C02  O01   128.76  3.000
 C8Q  C04   C02  O01   113.90  3.000
 C8Q  H041  C04  N26   109.31  3.000
 C8Q  H041  C04  C05   109.60  3.000
 C8Q  N26   C04  C05   105.04  3.000
 C8Q  H041  C04  C02   109.27  3.000
 C8Q  C05   C04  C02   112.27  3.000
 C8Q  N26   C04  C02   111.26  3.000
 C8Q  H051  C05  H052  109.19  3.000
 C8Q  H051  C05  S06   108.87  3.000
 C8Q  H052  C05  S06   109.67  3.000
 C8Q  H051  C05  C04   112.29  3.000
 C8Q  H052  C05  C04   112.09  3.000
 C8Q  S06   C05  C04   104.59  3.000
 C8Q  C07   S06  C05    90.19  3.000
 C8Q  N26   C07  C08   122.29  3.000
 C8Q  C08   C07  S06   125.23  3.000
 C8Q  N26   C07  S06   112.45  3.000
 C8Q  O09   C08  C07   120.33  3.000
 C8Q  O09   C08  C11   121.74  3.000
 C8Q  C07   C08  C11   117.81  3.000
 C8Q  C10   O09  C08   115.17  3.000
 C8Q  H101  C10  H102  108.70  3.000
 C8Q  H101  C10  H103  108.62  3.000
 C8Q  H102  C10  H103  108.73  3.000
 C8Q  H101  C10  O09   111.90  3.000
 C8Q  H102  C10  O09   107.06  3.000
 C8Q  H103  C10  O09   111.74  3.000
 C8Q  H121  C12  H122  105.81  3.000
 C8Q  H121  C12  C13   110.20  3.000
 C8Q  H122  C12  C13   108.11  3.000
 C8Q  H121  C12  C11   108.14  3.000
 C8Q  H122  C12  C11   107.75  3.000
 C8Q  C13   C12  C11   116.31  3.000
 C8Q  C22   C13  C14   119.03  3.000
 C8Q  C14   C13  C12   119.44  3.000
 C8Q  C22   C13  C12   121.52  3.000
 C8Q  H141  C14  C15   118.96  3.000
 C8Q  H141  C14  C13   119.23  3.000
 C8Q  C15   C14  C13   121.80  3.000
 C8Q  H151  C15  C16   120.40  3.000
 C8Q  H151  C15  C14   119.46  3.000
 C8Q  C16   C15  C14   120.14  3.000
 C8Q  H161  C16  C17   119.01  3.000
 C8Q  H161  C16  C15   120.78  3.000
 C8Q  C17   C16  C15   120.22  3.000
 C8Q  C22   C17  C18   119.42  3.000
 C8Q  C22   C17  C16   119.64  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   119.81  3.000
 C8Q  H201  C20  C19   119.69  3.000
 C8Q  C21   C20  C19   120.50  3.000
 C8Q  H211  C21  C22   119.77  3.000
 C8Q  H211  C21  C20   119.05  3.000
 C8Q  C22   C21  C20   121.18  3.000
 C8Q  C21   C22  C17   118.09  3.000
 C8Q  C17   C22  C13   119.16  3.000
 C8Q  C21   C22  C13   122.75  3.000
 C8Q  H231  C23  C24   116.63  3.000
 C8Q  H231  C23  C11   120.07  3.000
 C8Q  C24   C23  C11   123.29  3.000
 C8Q  N26   C24  O25   120.47  3.000
 C8Q  N26   C24  C23   114.04  3.000
 C8Q  O25   C24  C23   125.48  3.000
 C8Q  C24   N26  C07   123.36  3.000
 C8Q  C07   N26  C04   114.56  3.000
 C8Q  C24   N26  C04   121.36  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
 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  Var_01    N26   C07  S06  C05    12.35  30.0  1
 C8Q  Var_02    C22   C13  C12  C11   -66.13  30.0  2
 C8Q  Var_03    C13   C12  C11  C08   -56.76  30.0  3
 C8Q  Var_04    H052  C05  S06  C07  -148.86  30.0  1
 C8Q  Var_05    H103  C10  O09  C08    68.15  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

