# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 16:10:28 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: N-(2-{4-[(2,4-dioxo-3,4-dihydro-2H-1lambda~4~,3-thiazol-5-yl)methyl]phenoxy}ethyl)-5-[(3R)-1,2-dithiolan-3-yl]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCCC[C@@H]1CCSS1)NCCOc2ccc(CC3=[SH]C(=O)NC3=O)cc2
#
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
 GBV  GBV  N-(2-{4-[(2,4-dioxo-3,4-dihydro-2H-1lambda~4~,3-thiazol-5-yl)methyl]phenoxy}ethyl)-5-[(3R)-1,2-dithiolan-3-yl]pentanamide  ligand  55  29  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GBV
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
 GBV  C17  C  CH2   0  -0.333   0.3459  -2.6007   0.3829
 GBV  C21  C  CH2   0  -0.558   3.3373  -0.2767   0.1751
 GBV  C22  C  CH2   0  -0.418   4.7362  -0.8925   0.1649
 GBV  C24  C  CH2   0  -0.399   7.1641  -0.5426  -0.4708
 GBV  C26  C  CH2   0  -0.427   9.5959  -0.2553  -1.1790
 GBV  C01  C  CR16  0  -0.298  -4.0060   1.0389  -1.4817
 GBV  C02  C  CR16  0  -0.337  -2.8842   0.2261  -1.4829
 GBV  C03  C  CR6   0   0.376  -2.5056  -0.4463  -0.3224
 GBV  C04  C  CR16  0  -0.369  -3.2713  -0.2931   0.8331
 GBV  C05  C  CR16  0  -0.268  -4.3943   0.5226   0.8107
 GBV  C06  C  CR6   0   0.077  -4.7799   1.2060  -0.3367
 GBV  C07  C  CH2   0  -0.522  -6.0167   2.0715  -0.3429
 GBV  C08  C  CR5   0  -0.391  -7.2655   1.3091  -0.0424
 GBV  C09  C  CR5   0   0.554  -8.1255   1.5130   1.0335
 GBV  C12  C  CR5   0   0.461  -9.0511  -0.5716   0.2968
 GBV  C16  C  CH2   0  -0.183  -0.9366  -1.8845   0.7502
 GBV  C19  C  C     0   0.538   2.3239  -1.2048   0.8053
 GBV  C23  C  CH2   0  -0.423   5.7769   0.0771  -0.3797
 GBV  C25  C  CH1   0  -0.373   8.2190   0.3956  -1.0425
 GBV  C27  C  CH2   0  -0.562  10.3644  -0.1589   0.1277
 GBV  N11  N  NR15  0  -0.666  -9.0954   0.4485   1.1375
 GBV  N18  N  NH1   0  -0.621   1.3971  -1.7036  -0.0314
 GBV  O10  O  O     0  -0.503  -8.1396   2.4056   1.8737
 GBV  O13  O  O     0  -0.363  -9.7178  -1.5476   0.1464
 GBV  O15  O  O2    0  -0.476  -1.4028  -1.2178  -0.4084
 GBV  O20  O  O     0  -0.506   2.3729  -1.4974   1.9936
 GBV  S14  S  S3    0   0.145  -7.5785  -0.1921  -0.8255
 GBV  S28  S  S2    0  -0.058  10.4042   1.6025   0.5570
 GBV  S29  S  S2    0  -0.073   8.3888   1.8822   0.0542
 GBV  H1   H  HCH2  0   0.261   0.6788  -3.1715   1.2487
 GBV  H2   H  HCH2  0   0.263   0.1590  -3.3144  -0.4207
 GBV  H3   H  HCH2  0   0.257   3.3502   0.6466   0.7603
 GBV  H4   H  HCH2  0   0.246   3.0493  -0.0043  -0.8429
 GBV  H5   H  HCH2  0   0.231   5.0129  -1.1952   1.1778
 GBV  H6   H  HCH2  0   0.228   4.7267  -1.8018  -0.4439
 GBV  H7   H  HCH2  0   0.232   7.4822  -0.9035   0.5122
 GBV  H8   H  HCH2  0   0.239   7.1194  -1.4177  -1.1277
 GBV  H10  H  HCH2  0   0.265  10.1668   0.2395  -1.9654
 GBV  H12  H  HCR6  0   0.249  -4.2832   1.5534  -2.3948
 GBV  H13  H  HCR6  0   0.258  -2.2961   0.1070  -2.3847
 GBV  H14  H  HCR6  0   0.276  -3.0114  -0.7997   1.7530
 GBV  H15  H  HCR6  0   0.251  -4.9828   0.6226   1.7157
 GBV  H16  H  HCH2  0   0.268  -5.9327   2.8504   0.4197
 GBV  H17  H  HCH2  0   0.255  -6.0780   2.5986  -1.3001
 GBV  H18  H  HCH2  0   0.234  -1.6720  -2.6154   1.1049
 GBV  H19  H  HCH2  0   0.230  -0.7515  -1.1713   1.5606
 GBV  H20  H  HCH2  0   0.222   5.4715   0.4243  -1.3725
 GBV  H21  H  HCH2  0   0.223   5.8053   0.9632   0.2637
 GBV  H22  H  HCH1  0   0.292   7.8905   0.7608  -2.0179
 GBV  H24  H  HCH2  0   0.279   9.8966  -0.7329   0.9282
 GBV  H25  H  HCH2  0   0.300  11.3983  -0.4874   0.0185
 GBV  H26  H  HNR5  0   0.441  -9.7869   0.4641   1.8774
 GBV  H27  H  HNH1  0   0.402   1.3980  -1.3952  -0.9890
 GBV  H11  H  HSH1  0   0.309  -8.3764   0.0563  -1.8974
 GBV  H9   H  HCH2  0   0.268   9.4721  -1.3009  -1.4711

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
 GBV  S28  S29  single    2.096  0.020  2.096
 GBV  S28  C27  single    1.813  0.020  1.813
 GBV  S29  C25  single    1.855  0.020  1.855
 GBV  C27  C26  single    1.519  0.020  1.519
 GBV  C25  C24  single    1.523  0.020  1.523
 GBV  C24  C23  single    1.522  0.020  1.522
 GBV  C22  C21  single    1.528  0.020  1.528
 GBV  C22  C23  single    1.523  0.020  1.523
 GBV  C21  C19  single    1.512  0.020  1.512
 GBV  O20  C19  double    1.225  0.020  1.225
 GBV  C19  N18  single    1.345  0.020  1.345
 GBV  N18  C17  single    1.443  0.020  1.443
 GBV  C17  C16  single    1.514  0.020  1.514
 GBV  C16  O15  single    1.416  0.020  1.416
 GBV  O15  C03  single    1.349  0.020  1.349
 GBV  C03  C02  aromatic  1.394  0.020  1.394
 GBV  C03  C04  aromatic  1.395  0.020  1.395
 GBV  C02  C01  aromatic  1.385  0.020  1.385
 GBV  C04  C05  aromatic  1.388  0.020  1.388
 GBV  C01  C06  aromatic  1.392  0.020  1.392
 GBV  C05  C06  aromatic  1.390  0.020  1.390
 GBV  C06  C07  single    1.510  0.020  1.510
 GBV  C07  C08  single    1.494  0.020  1.494
 GBV  S14  C08  double    1.722  0.020  1.722
 GBV  S14  C12  single    1.890  0.020  1.890
 GBV  C08  C09  single    1.392  0.020  1.392
 GBV  C12  O13  double    1.191  0.020  1.191
 GBV  C12  N11  single    1.323  0.020  1.323
 GBV  C09  N11  single    1.444  0.020  1.444
 GBV  C09  O10  double    1.226  0.020  1.226
 GBV  C17  H1   single    0.970  0.020  1.090
 GBV  C17  H2   single    0.970  0.020  1.090
 GBV  C21  H3   single    0.970  0.020  1.090
 GBV  C21  H4   single    0.970  0.020  1.090
 GBV  C22  H5   single    0.970  0.020  1.090
 GBV  C22  H6   single    0.970  0.020  1.090
 GBV  C24  H7   single    0.970  0.020  1.090
 GBV  C24  H8   single    0.970  0.020  1.090
 GBV  C26  H9   single    0.970  0.020  1.090
 GBV  C26  H10  single    0.970  0.020  1.090
 GBV  C01  H12  single    0.930  0.020  1.080
 GBV  C02  H13  single    0.930  0.020  1.080
 GBV  C04  H14  single    0.930  0.020  1.080
 GBV  C05  H15  single    0.930  0.020  1.080
 GBV  C07  H16  single    0.970  0.020  1.090
 GBV  C07  H17  single    0.970  0.020  1.090
 GBV  C16  H18  single    0.970  0.020  1.090
 GBV  C16  H19  single    0.970  0.020  1.090
 GBV  C23  H20  single    0.970  0.020  1.090
 GBV  C23  H21  single    0.970  0.020  1.090
 GBV  C25  H22  single    0.970  0.020  1.090
 GBV  C27  H24  single    0.970  0.020  1.090
 GBV  C27  H25  single    0.970  0.020  1.090
 GBV  N11  H26  single    0.860  0.020  1.020
 GBV  N18  H27  single    0.860  0.020  1.020
 GBV  C26  C25  single    1.529  0.020  1.529
 GBV  S14  H11  single    1.200  0.020  1.300

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
 GBV  H2   C17  H1   107.16  3.000
 GBV  H2   C17  N18  108.67  3.000
 GBV  H1   C17  N18  109.36  3.000
 GBV  H2   C17  C16  110.06  3.000
 GBV  H1   C17  C16  108.30  3.000
 GBV  N18  C17  C16  113.12  3.000
 GBV  H4   C21  H3   106.94  3.000
 GBV  H4   C21  C19  111.40  3.000
 GBV  H3   C21  C19  107.65  3.000
 GBV  H4   C21  C22  109.61  3.000
 GBV  H3   C21  C22  109.45  3.000
 GBV  C19  C21  C22  111.65  3.000
 GBV  H6   C22  H5   106.72  3.000
 GBV  H6   C22  C23  109.63  3.000
 GBV  H5   C22  C23  109.55  3.000
 GBV  H6   C22  C21  109.31  3.000
 GBV  H5   C22  C21  109.70  3.000
 GBV  C23  C22  C21  111.80  3.000
 GBV  H8   C24  H7   106.69  3.000
 GBV  H8   C24  C25  107.18  3.000
 GBV  H7   C24  C25  109.81  3.000
 GBV  H8   C24  C23  108.91  3.000
 GBV  H7   C24  C23  110.21  3.000
 GBV  C25  C24  C23  113.76  3.000
 GBV  H10  C26  H9   107.50  3.000
 GBV  H10  C26  C27  109.07  3.000
 GBV  H9   C26  C27  110.37  3.000
 GBV  H10  C26  C25  110.03  3.000
 GBV  H9   C26  C25  109.22  3.000
 GBV  C27  C26  C25  110.60  3.000
 GBV  H12  C01  C06  119.58  3.000
 GBV  H12  C01  C02  119.00  3.000
 GBV  C06  C01  C02  121.42  3.000
 GBV  H13  C02  C03  119.52  3.000
 GBV  H13  C02  C01  120.32  3.000
 GBV  C03  C02  C01  120.16  3.000
 GBV  O15  C03  C04  124.38  3.000
 GBV  C04  C03  C02  119.19  3.000
 GBV  O15  C03  C02  116.43  3.000
 GBV  H14  C04  C05  118.90  3.000
 GBV  H14  C04  C03  121.40  3.000
 GBV  C05  C04  C03  119.69  3.000
 GBV  H15  C05  C06  119.55  3.000
 GBV  H15  C05  C04  118.67  3.000
 GBV  C06  C05  C04  121.78  3.000
 GBV  C07  C06  C05  120.83  3.000
 GBV  C07  C06  C01  121.39  3.000
 GBV  C05  C06  C01  117.76  3.000
 GBV  H17  C07  H16  105.74  3.000
 GBV  H17  C07  C08  112.02  3.000
 GBV  H16  C07  C08  106.71  3.000
 GBV  H17  C07  C06  109.00  3.000
 GBV  H16  C07  C06  110.04  3.000
 GBV  C08  C07  C06  113.05  3.000
 GBV  S14  C08  C09  111.52  3.000
 GBV  C09  C08  C07  126.66  3.000
 GBV  S14  C08  C07  120.36  3.000
 GBV  O10  C09  N11  118.67  3.000
 GBV  O10  C09  C08  130.04  3.000
 GBV  N11  C09  C08  111.27  3.000
 GBV  S14  C12  O13  121.70  3.000
 GBV  O13  C12  N11  133.89  3.000
 GBV  S14  C12  N11  104.40  3.000
 GBV  H19  C16  H18  107.95  3.000
 GBV  H19  C16  O15  110.77  3.000
 GBV  H18  C16  O15  110.98  3.000
 GBV  H19  C16  C17  110.14  3.000
 GBV  H18  C16  C17  109.36  3.000
 GBV  O15  C16  C17  107.65  3.000
 GBV  O20  C19  N18  122.87  3.000
 GBV  N18  C19  C21  115.49  3.000
 GBV  O20  C19  C21  121.62  3.000
 GBV  H21  C23  H20  106.45  3.000
 GBV  H21  C23  C24  109.93  3.000
 GBV  H20  C23  C24  109.21  3.000
 GBV  H21  C23  C22  108.82  3.000
 GBV  H20  C23  C22  109.60  3.000
 GBV  C24  C23  C22  112.64  3.000
 GBV  H22  C25  S29  106.71  3.000
 GBV  H22  C25  C26  109.49  3.000
 GBV  S29  C25  C26  108.15  3.000
 GBV  C26  C25  C24  113.26  3.000
 GBV  H22  C25  C24  109.44  3.000
 GBV  S29  C25  C24  109.58  3.000
 GBV  H25  C27  H24  108.77  3.000
 GBV  H25  C27  S28  107.19  3.000
 GBV  H24  C27  S28  110.30  3.000
 GBV  H25  C27  C26  111.99  3.000
 GBV  H24  C27  C26  112.40  3.000
 GBV  S28  C27  C26  106.05  3.000
 GBV  H26  N11  C12  119.94  3.000
 GBV  H26  N11  C09  120.00  3.000
 GBV  C12  N11  C09  120.02  3.000
 GBV  H27  N18  C19  118.56  3.000
 GBV  H27  N18  C17  117.68  3.000
 GBV  C19  N18  C17  123.66  3.000
 GBV  C16  O15  C03  119.11  3.000
 GBV  H11  S14  C12   92.73  3.000
 GBV  H11  S14  C08  107.82  3.000
 GBV  C12  S14  C08   92.67  3.000
 GBV  S29  S28  C27   92.96  3.000
 GBV  S28  S29  C25   97.06  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
 GBV  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 GBV  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 GBV  CONST_03  C05  C04  C03  C02     0.00   0.0  0
 GBV  CONST_04  C05  C06  C01  C02     0.00   0.0  0
 GBV  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 GBV  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 GBV  CONST_07  C12  N11  C09  C08     0.00   0.0  0
 GBV  CONST_08  O15  C03  C02  C01   180.00   0.0  0
 GBV  CONST_09  C07  C06  C01  C02   180.00   0.0  0
 GBV  CONST_10  C07  C06  C05  C04   180.00   0.0  0
 GBV  CONST_11  O15  C03  C04  C05   180.00   0.0  0
 GBV  CONST_12  O10  C09  N11  C12   180.00   0.0  0
 GBV  CONST_13  H15  C05  C06  C01   180.00   0.0  0
 GBV  CONST_14  H14  C04  C03  C02   180.00   0.0  0
 GBV  CONST_15  H12  C01  C02  C03   180.00   0.0  0
 GBV  CONST_16  H13  C02  C03  C04   180.00   0.0  0
 GBV  CONST_17  H26  N11  C09  C08   180.00   0.0  0
 GBV  CONST_18  C21  C19  N18  C17   180.00   0.0  0
 GBV  CONST_19  O20  C19  N18  C17     0.00   0.0  0
 GBV  CONST_20  H27  N18  C19  C21     0.00   0.0  0
 GBV  Var_01    S28  C27  C26  C25   -55.30  30.0  1
 GBV  Var_02    C08  C07  C06  C01   117.70  30.0  2
 GBV  Var_03    S14  C08  C07  C06   -46.45  30.0  3
 GBV  Var_04    C25  C24  C23  C22   178.68  30.0  1
 GBV  Var_05    H18  C16  O15  C03    63.66  30.0  2
 GBV  Var_06    C24  C23  C22  C21  -176.82  30.0  3
 GBV  Var_07    O20  C19  C21  C22    66.17  30.0  3
 GBV  Var_08    C19  N18  C17  C16    92.99  30.0  2
 GBV  Var_09    C23  C22  C21  C19  -176.00  30.0  2
 GBV  Var_10    O15  C16  C17  N18    62.33  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
 GBV  chir_01  C25  S29  C24  C26  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
 GBV  plan-1  C07  0.020
 GBV  plan-1  C08  0.020
 GBV  plan-1  C09  0.020
 GBV  plan-1  C12  0.020
 GBV  plan-1  N11  0.020
 GBV  plan-1  O10  0.020
 GBV  plan-1  O13  0.020
 GBV  plan-1  S14  0.020
 GBV  plan-1  H26  0.020
 GBV  plan-1  H11  0.020
 GBV  plan-2  C01  0.020
 GBV  plan-2  C02  0.020
 GBV  plan-2  C03  0.020
 GBV  plan-2  C04  0.020
 GBV  plan-2  C05  0.020
 GBV  plan-2  C06  0.020
 GBV  plan-2  C07  0.020
 GBV  plan-2  O15  0.020
 GBV  plan-2  H12  0.020
 GBV  plan-2  H13  0.020
 GBV  plan-2  H14  0.020
 GBV  plan-2  H15  0.020
 GBV  plan-3  C17  0.020
 GBV  plan-3  C21  0.020
 GBV  plan-3  C19  0.020
 GBV  plan-3  N18  0.020
 GBV  plan-3  O20  0.020
 GBV  plan-3  H27  0.020

