# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 08:03:17 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 6-hydroxy-3-{(4R)-1-[4-(naphthalen-1-ylamino)-4-oxobutyl]-1,2,3-triazolidin-4-yl}-1-benzofuran-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc2c(occ2[C@@H]3CN(CCCC(=O)Nc4cccc5ccccc45)NN3)cc1O
#
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
 561  561  '6-hydroxy-3-{(4R)-1-[4-(naphthalen-1-ylamino)-4-oxobutyl]-1,2,3-triazolidin-4-yl}-1-benzofuran-5-carboxylic acid'  ligand  57  34  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_561
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
 561  C1    C  CR56   0   0.039    5.0025  -0.5107   0.4357
 561  C2    C  CR56   0   0.385    5.6350  -0.6668   1.6714
 561  C3    C  CR16   0  -0.416    5.4950   0.4428  -0.4469
 561  C4    C  CR6    0  -0.282    6.5915   1.2121  -0.0872
 561  C5    C  CR16   0  -0.462    6.7280   0.0728   2.0778
 561  C6    C  CR5    0   0.004    3.9231  -1.4690   0.4279
 561  C7    C  CR6    0   0.363    7.2112   1.0252   1.1807
 561  C8    C  CR15   0  -0.064    4.0005  -2.1074   1.6121
 561  O1    O  OH1    0  -0.661    8.2642   1.7613   1.5231
 561  O2    O  O      0  -0.446    5.0246  -1.6335   2.3852
 561  C21   C  C      0   0.494    7.1302   2.2492  -1.0396
 561  O4    O  O      0  -0.631    8.1396   2.9051  -0.6284
 561  O5    O  OC    -1  -0.550    6.5826   2.4050  -2.1337
 561  C9    C  CH1    0  -0.201    2.9591  -1.7069  -0.6785
 561  N3    N  NH1    0  -0.475    1.8780  -2.6181  -0.3164
 561  N1    N  NH1    0  -0.356    0.8508  -2.3259  -1.2315
 561  N2    N  NT     0  -0.332    0.8674  -0.9244  -1.4961
 561  C10   C  CH2    0  -0.298    2.2199  -0.4443  -1.1740
 561  C31   C  CH2    0  -0.431   -1.5613  -0.6279  -1.1684
 561  C32   C  CH2    0  -0.597   -2.6135   0.1223  -0.3623
 561  C33   C  CH2    0  -0.262   -0.1614  -0.2545  -0.7129
 561  C34   C  C      0   0.550   -4.0250  -0.1654  -0.8216
 561  O11   O  O      0  -0.471   -4.3146  -0.3350  -1.9917
 561  N11   N  NH1    0  -0.754   -4.9446  -0.1805   0.1788
 561  C41   C  C1     0  -0.310   -9.4748   1.4262   1.0314
 561  C42   C  CR6    0   0.305   -6.3336  -0.3184  -0.0004
 561  C43   C  CR16   0  -0.265   -8.2432  -1.5174  -0.8609
 561  C44   C  CR16   0  -0.294   -6.8515  -1.3744  -0.7051
 561  C45   C  CR6    0   0.076   -7.1999   0.6526   0.5783
 561  C46   C  CR6    0   0.096   -8.6035   0.4806   0.4407
 561  C47   C  CR16   0  -0.321   -9.1029  -0.6187  -0.2942
 561  C48   C  C1     0  -0.304   -6.7205   1.7855   1.2787
 561  C49   C  C1     0  -0.251   -7.5899   2.6848   1.8346
 561  C50   C  C1     0  -0.256   -8.9826   2.5016   1.7177
 561  H3    H  HCR6   0   0.246    5.0446   0.5973  -1.4192
 561  H5    H  HCR6   0   0.266    7.1950  -0.0714   3.0437
 561  H8    H  HCR5   0   0.288    3.4178  -2.9043   2.0467
 561  HO1   H  HOH1   0   0.460    8.4105   2.3683   0.7045
 561  H9    H  HCH1   0   0.269    3.4971  -2.1533  -1.5231
 561  HN3   H  HNH1   0   0.355    1.5273  -2.3846   0.6081
 561  HN1   H  HNH1   0   0.370    1.1003  -2.7898  -2.0976
 561  H101  H  HCH2   0   0.235    2.1892   0.3187  -0.3908
 561  H102  H  HCH2   0   0.243    2.7080  -0.0085  -2.0472
 561  H311  H  HCH2   0   0.236   -1.7072  -1.7040  -1.0572
 561  H312  H  HCH2   0   0.229   -1.6668  -0.3961  -2.2297
 561  H321  H  HCH2   0   0.256   -2.5041  -0.0970   0.7031
 561  H322  H  HCH2   0   0.275   -2.4613   1.2029  -0.4654
 561  H331  H  HCH2   0   0.197   -0.0514  -0.4478   0.3665
 561  H332  H  HCH2   0   0.234   -0.0202   0.8210  -0.8471
 561  HN11  H  HNH1   0   0.410   -4.6133  -0.0035   1.1147
 561  H43   H  HCR6   0   0.262   -8.6262  -2.3605  -1.4204
 561  H44   H  HCR6   0   0.267   -6.1925  -2.1184  -1.1302
 561  H47   H  HCR6   0   0.257  -10.1741  -0.7388  -0.4005
 561  H48   H  H      0   0.244   -5.6562   1.9578   1.3684
 561  H49   H  H      0   0.262   -7.2057   3.5479   2.3622
 561  H50   H  H      0   0.260   -9.6579   3.2189   2.1654
 561  H41   H  H      0   0.258  -10.5438   1.2844   0.9272

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
 561  C1   C6    aromatic  1.443  0.020  1.443
 561  C1   C3    aromatic  1.389  0.020  1.389
 561  C1   C2    aromatic  1.397  0.020  1.397
 561  C2   O2    aromatic  1.348  0.020  1.348
 561  C2   C5    aromatic  1.381  0.020  1.381
 561  C3   C4    aromatic  1.387  0.020  1.387
 561  C3   H3    single    0.930  0.020  1.080
 561  C4   C21   single    1.508  0.020  1.508
 561  C4   C7    aromatic  1.424  0.020  1.424
 561  C5   C7    aromatic  1.395  0.020  1.395
 561  C5   H5    single    0.930  0.020  1.080
 561  C6   C9    single    1.487  0.020  1.487
 561  C6   C8    aromatic  1.348  0.020  1.348
 561  C7   O1    single    1.330  0.020  1.330
 561  C8   O2    aromatic  1.368  0.020  1.368
 561  C8   H8    single    0.930  0.020  1.080
 561  O1   HO1   single    0.850  0.020  0.980
 561  C21  O4    deloc     1.272  0.020  1.272
 561  C21  O5    deloc     1.233  0.020  1.233
 561  C9   N3    single    1.459  0.020  1.459
 561  C9   C10   single    1.545  0.020  1.545
 561  C9   H9    single    0.970  0.020  1.090
 561  N3   N1    single    1.406  0.020  1.406
 561  N3   HN3   single    0.890  0.020  1.040
 561  N1   N2    single    1.426  0.020  1.426
 561  N1   HN1   single    0.890  0.020  1.040
 561  N2   C33   single    1.456  0.020  1.456
 561  N2   C10   single    1.471  0.020  1.471
 561  C10  H101  single    0.970  0.020  1.090
 561  C10  H102  single    0.970  0.020  1.090
 561  C31  C32   single    1.523  0.020  1.523
 561  C31  C33   single    1.519  0.020  1.519
 561  C31  H311  single    0.970  0.020  1.090
 561  C31  H312  single    0.970  0.020  1.090
 561  C32  C34   single    1.512  0.020  1.512
 561  C32  H321  single    0.970  0.020  1.090
 561  C32  H322  single    0.970  0.020  1.090
 561  C33  H331  single    0.970  0.020  1.090
 561  C33  H332  single    0.970  0.020  1.090
 561  C34  N11   single    1.359  0.020  1.359
 561  C34  O11   double    1.217  0.020  1.217
 561  N11  C42   single    1.407  0.020  1.407
 561  N11  HN11  single    0.860  0.020  1.020
 561  C41  C50   aromatic  1.367  0.020  1.367
 561  C41  C46   aromatic  1.415  0.020  1.415
 561  C41  H41   single    0.930  0.020  1.080
 561  C42  C45   aromatic  1.424  0.020  1.424
 561  C42  C44   aromatic  1.371  0.020  1.371
 561  C43  C47   aromatic  1.367  0.020  1.367
 561  C43  C44   aromatic  1.408  0.020  1.408
 561  C43  H43   single    0.930  0.020  1.080
 561  C44  H44   single    0.930  0.020  1.080
 561  C45  C46   aromatic  1.421  0.020  1.421
 561  C45  C48   aromatic  1.416  0.020  1.416
 561  C46  C47   aromatic  1.414  0.020  1.414
 561  C47  H47   single    0.930  0.020  1.080
 561  C48  C49   aromatic  1.369  0.020  1.369
 561  C48  H48   single    0.930  0.020  1.080
 561  C49  C50   aromatic  1.409  0.020  1.409
 561  C49  H49   single    0.930  0.020  1.080
 561  C50  H50   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
 561  C6    C1   C3    135.82  3.000
 561  C3    C1   C2    118.56  3.000
 561  C6    C1   C2    105.62  3.000
 561  O2    C2   C5    125.93  3.000
 561  C5    C2   C1    123.98  3.000
 561  O2    C2   C1    110.10  3.000
 561  H3    C3   C4    118.86  3.000
 561  H3    C3   C1    121.40  3.000
 561  C4    C3   C1    119.74  3.000
 561  C21   C4   C7    119.83  3.000
 561  C7    C4   C3    120.16  3.000
 561  C21   C4   C3    120.02  3.000
 561  H5    C5   C7    121.02  3.000
 561  H5    C5   C2    122.19  3.000
 561  C7    C5   C2    116.79  3.000
 561  C9    C6   C8    127.98  3.000
 561  C8    C6   C1    105.48  3.000
 561  C9    C6   C1    126.53  3.000
 561  O1    C7   C5    119.13  3.000
 561  O1    C7   C4    120.10  3.000
 561  C5    C7   C4    120.77  3.000
 561  H8    C8   O2    115.64  3.000
 561  H8    C8   C6    132.31  3.000
 561  O2    C8   C6    112.06  3.000
 561  HO1   O1   C7    103.54  3.000
 561  C8    O2   C2    106.75  3.000
 561  O5    C21  O4    125.02  3.000
 561  O5    C21  C4    119.25  3.000
 561  O4    C21  C4    115.72  3.000
 561  H9    C9   C10   108.69  3.000
 561  H9    C9   N3    107.48  3.000
 561  C10   C9   N3    103.61  3.000
 561  H9    C9   C6    108.69  3.000
 561  C10   C9   C6    114.72  3.000
 561  N3    C9   C6    113.31  3.000
 561  HN3   N3   N1    106.99  3.000
 561  HN3   N3   C9    109.75  3.000
 561  N1    N3   C9    104.47  3.000
 561  HN1   N1   N2    106.75  3.000
 561  HN1   N1   N3    106.32  3.000
 561  N2    N1   N3    108.44  3.000
 561  C33   N2   C10   112.43  3.000
 561  C10   N2   N1    106.91  3.000
 561  C33   N2   N1    110.12  3.000
 561  H102  C10  H101  107.88  3.000
 561  H102  C10  N2    111.50  3.000
 561  H101  C10  N2    111.02  3.000
 561  H102  C10  C9    111.65  3.000
 561  H101  C10  C9    110.73  3.000
 561  N2    C10  C9    104.09  3.000
 561  H312  C31  H311  107.19  3.000
 561  H312  C31  C33   109.18  3.000
 561  H311  C31  C33   109.57  3.000
 561  H312  C31  C32   110.08  3.000
 561  H311  C31  C32   109.83  3.000
 561  C33   C31  C32   110.92  3.000
 561  H322  C32  H321  105.99  3.000
 561  H322  C32  C34   106.78  3.000
 561  H321  C32  C34   110.57  3.000
 561  H322  C32  C31   109.87  3.000
 561  H321  C32  C31   110.36  3.000
 561  C34   C32  C31   112.99  3.000
 561  H332  C33  H331  106.25  3.000
 561  H332  C33  C31   108.91  3.000
 561  H331  C33  C31   110.03  3.000
 561  H332  C33  N2    107.19  3.000
 561  H331  C33  N2    112.06  3.000
 561  C31   C33  N2    112.14  3.000
 561  N11   C34  O11   123.03  3.000
 561  O11   C34  C32   122.73  3.000
 561  N11   C34  C32   114.22  3.000
 561  HN11  N11  C42   117.36  3.000
 561  HN11  N11  C34   117.32  3.000
 561  C42   N11  C34   125.12  3.000
 561  H41   C41  C50   120.42  3.000
 561  H41   C41  C46   118.68  3.000
 561  C50   C41  C46   120.89  3.000
 561  C45   C42  C44   120.28  3.000
 561  C44   C42  N11   120.92  3.000
 561  C45   C42  N11   118.80  3.000
 561  H43   C43  C47   120.28  3.000
 561  H43   C43  C44   119.10  3.000
 561  C47   C43  C44   120.61  3.000
 561  H44   C44  C43   119.29  3.000
 561  H44   C44  C42   120.13  3.000
 561  C43   C44  C42   120.57  3.000
 561  C48   C45  C46   118.64  3.000
 561  C48   C45  C42   122.73  3.000
 561  C46   C45  C42   118.62  3.000
 561  C47   C46  C45   119.57  3.000
 561  C47   C46  C41   121.28  3.000
 561  C45   C46  C41   119.14  3.000
 561  H47   C47  C46   119.12  3.000
 561  H47   C47  C43   120.57  3.000
 561  C46   C47  C43   120.31  3.000
 561  H48   C48  C49   119.11  3.000
 561  H48   C48  C45   120.11  3.000
 561  C49   C48  C45   120.77  3.000
 561  H49   C49  C50   119.67  3.000
 561  H49   C49  C48   119.77  3.000
 561  C50   C49  C48   120.56  3.000
 561  H50   C50  C49   119.75  3.000
 561  H50   C50  C41   120.28  3.000
 561  C49   C50  C41   119.97  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
 561  CONST_01  O2   C8   C6   C1      0.00   0.0  0
 561  CONST_02  C7   C4   C3   C1      0.00   0.0  0
 561  CONST_03  C8   O2   C2   C1      0.00   0.0  0
 561  CONST_04  C7   C5   C2   C1      0.00   0.0  0
 561  CONST_05  C8   C6   C1   C2      0.00   0.0  0
 561  CONST_06  C4   C3   C1   C2      0.00   0.0  0
 561  CONST_07  C6   C8   O2   C2      0.00   0.0  0
 561  CONST_08  C4   C7   C5   C2      0.00   0.0  0
 561  CONST_09  C8   C6   C1   C3    180.00   0.0  0
 561  CONST_10  O2   C2   C1   C3    180.00   0.0  0
 561  CONST_11  C5   C2   C1   C3      0.00   0.0  0
 561  CONST_12  C5   C7   C4   C3      0.00   0.0  0
 561  CONST_13  C6   C1   C3   C4    180.00   0.0  0
 561  CONST_14  C6   C1   C2   C5    180.00   0.0  0
 561  CONST_15  C8   O2   C2   C5    180.00   0.0  0
 561  CONST_16  O2   C2   C1   C6      0.00   0.0  0
 561  CONST_17  O2   C2   C5   C7    180.00   0.0  0
 561  CONST_18  C48  C49  C50  C41     0.00   0.0  0
 561  CONST_19  C42  C45  C46  C41   180.00   0.0  0
 561  CONST_20  C48  C45  C46  C41     0.00   0.0  0
 561  CONST_21  C43  C47  C46  C41   180.00   0.0  0
 561  CONST_22  C47  C46  C45  C42     0.00   0.0  0
 561  CONST_23  C49  C48  C45  C42   180.00   0.0  0
 561  CONST_24  C47  C43  C44  C42     0.00   0.0  0
 561  CONST_25  C45  C46  C47  C43     0.00   0.0  0
 561  CONST_26  C45  C42  C44  C43     0.00   0.0  0
 561  CONST_27  C46  C45  C42  C44     0.00   0.0  0
 561  CONST_28  C48  C45  C42  C44   180.00   0.0  0
 561  CONST_29  C46  C47  C43  C44     0.00   0.0  0
 561  CONST_30  C50  C41  C46  C45     0.00   0.0  0
 561  CONST_31  C50  C49  C48  C45     0.00   0.0  0
 561  CONST_32  C49  C50  C41  C46     0.00   0.0  0
 561  CONST_33  C49  C48  C45  C46     0.00   0.0  0
 561  CONST_34  C50  C41  C46  C47   180.00   0.0  0
 561  CONST_35  C48  C45  C46  C47   180.00   0.0  0
 561  CONST_36  C9   C6   C1   C2    180.00   0.0  0
 561  CONST_37  C9   C6   C1   C3      0.00   0.0  0
 561  CONST_38  C9   C6   C8   O2    180.00   0.0  0
 561  CONST_39  C21  C4   C3   C1    180.00   0.0  0
 561  CONST_40  O1   C7   C5   C2    180.00   0.0  0
 561  CONST_41  O1   C7   C4   C3    180.00   0.0  0
 561  CONST_42  C21  C4   C7   C5    180.00   0.0  0
 561  CONST_43  C46  C45  C42  N11   180.00   0.0  0
 561  CONST_44  C48  C45  C42  N11     0.00   0.0  0
 561  CONST_45  C43  C44  C42  N11   180.00   0.0  0
 561  CONST_46  H8   C8   C6   C1    180.00   0.0  0
 561  CONST_47  H5   C5   C2   C1    180.00   0.0  0
 561  CONST_48  H3   C3   C1   C2    180.00   0.0  0
 561  CONST_49  H49  C49  C50  C41   180.00   0.0  0
 561  CONST_50  H47  C47  C46  C41     0.00   0.0  0
 561  CONST_51  H48  C48  C45  C42     0.00   0.0  0
 561  CONST_52  H43  C43  C44  C42   180.00   0.0  0
 561  CONST_53  H44  C44  C42  C45   180.00   0.0  0
 561  CONST_54  H41  C41  C46  C45   180.00   0.0  0
 561  CONST_55  H50  C50  C41  C46   180.00   0.0  0
 561  CONST_59  C42  N11  C34  C32   180.00   0.0  0
 561  CONST_60  C42  N11  C34  O11     0.00   0.0  0
 561  Var_01    N2   N1   N3   C9    -35.57  30.0  1
 561  Var_02    N1   N2   C10  C9     -0.93  30.0  1
 561  Var_03    C10  N2   N1   N3     22.54  30.0  1
 561  Var_04    O4   C21  C4   C3   -179.81  30.0  2
 561  Var_05    C31  C33  N2   N1    -67.97  30.0  3
 561  Var_06    C32  C31  C33  N2   -178.13  30.0  1
 561  Var_07    N11  C34  C32  C31   145.45  30.0  3
 561  Var_08    C34  C32  C31  C33   177.28  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
 561  chir_01  C9  C6  N3  C10  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
 561  plan-1  C1    0.020
 561  plan-1  C2    0.020
 561  plan-1  C3    0.020
 561  plan-1  C4    0.020
 561  plan-1  C5    0.020
 561  plan-1  C6    0.020
 561  plan-1  C7    0.020
 561  plan-1  C8    0.020
 561  plan-1  O1    0.020
 561  plan-1  O2    0.020
 561  plan-1  C21   0.020
 561  plan-1  C9    0.020
 561  plan-1  H3    0.020
 561  plan-1  H5    0.020
 561  plan-1  H8    0.020
 561  plan-2  N11   0.020
 561  plan-2  C41   0.020
 561  plan-2  C42   0.020
 561  plan-2  C43   0.020
 561  plan-2  C44   0.020
 561  plan-2  C45   0.020
 561  plan-2  C46   0.020
 561  plan-2  C47   0.020
 561  plan-2  C48   0.020
 561  plan-2  C49   0.020
 561  plan-2  C50   0.020
 561  plan-2  H43   0.020
 561  plan-2  H44   0.020
 561  plan-2  H47   0.020
 561  plan-2  H48   0.020
 561  plan-2  H49   0.020
 561  plan-2  H50   0.020
 561  plan-2  H41   0.020
 561  plan-3  C32   0.020
 561  plan-3  C34   0.020
 561  plan-3  O11   0.020
 561  plan-3  N11   0.020
 561  plan-3  C42   0.020
 561  plan-3  HN11  0.020
 561  plan-4  C4    0.020
 561  plan-4  C21   0.020
 561  plan-4  O4    0.020
 561  plan-4  O5    0.020

