# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:16:18 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (7S)-2-[(carboxycarbonyl)amino]-7-{[(1,1-dioxido-1,2-benzisothiazol-3-yl)oxy]methyl}-4,7-dihydro-5H-thieno[2,3-c]pyran-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)Nc1sc2[C@H](COC3=N[S](=O)(=O)c4ccccc34)OCCc2c1C(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
 DBD  DBD  '(7S)-2-[(carboxycarbonyl)amino]-7-{[(1,1-dioxido-1,2-benzisothiazol-3-yl)oxy]methyl}-4,7-dihydro-5H-thieno[2,3-c]pyran-3-carboxylic acid'  ligand  45  31  .  2021-08-08  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DBD
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
 DBD  O1    O  O2    0  -0.482  -2.6255   0.0665  -0.5183
 DBD  C2    C  CH1   0   0.007  -1.4262  -0.5792  -0.1883
 DBD  C3    C  CR5   0  -0.332  -1.0985  -0.3407   1.2589
 DBD  C4    C  CR5   0   0.231  -1.9712   0.1681   2.1647
 DBD  C5    C  CH2   0  -0.517  -3.3791   0.4738   1.7490
 DBD  C6    C  CH2   0  -0.201  -3.6612  -0.1906   0.4104
 DBD  S7    S  S2    0   0.288   0.4403  -0.7225   1.9426
 DBD  C8    C  CR5   0   0.118  -0.0756  -0.1668   3.4837
 DBD  C9    C  CR5   0  -0.121  -1.3787   0.2920   3.4676
 DBD  C10   C  C     0   0.545  -1.9908   0.8431   4.6776
 DBD  O11   O  O     0  -0.470  -1.4415   0.8615   5.7634
 DBD  O12   O  OH1   0  -0.584  -3.1995   1.3381   4.4860
 DBD  N13   N  NH1   0  -0.708   0.7519  -0.1893   4.5760
 DBD  C14   C  C     0   0.453   2.0238  -0.6318   4.5575
 DBD  C15   C  C     0   0.465   2.6947  -0.5314   5.9271
 DBD  O16   O  O     0  -0.402   2.1284  -0.0913   6.8914
 DBD  O17   O  OH1   0  -0.561   3.9227  -0.9800   5.8788
 DBD  O18   O  O     0  -0.413   2.5872  -1.0640   3.5765
 DBD  C19   C  CH2   0  -0.200  -0.3412  -0.0145  -1.0820
 DBD  O20   O  O2    0  -0.423  -0.7018  -0.3379  -2.4313
 DBD  C21   C  CR5   0   0.544   0.0860   0.0462  -3.3878
 DBD  C22   C  CR56  0   0.110  -0.3125  -0.2771  -4.7697
 DBD  C23   C  CR56  0  -0.211   0.6357   0.2134  -5.6493
 DBD  S24   S  S     0   1.390   1.8984   1.0023  -4.6815
 DBD  N25   N  N     0  -0.600   1.1853   0.6886  -3.2096
 DBD  C26   C  CR16  0  -0.286  -1.4248  -0.9513  -5.2372
 DBD  C27   C  CR16  0  -0.232  -1.5479  -1.1143  -6.6135
 DBD  C28   C  CR16  0  -0.238  -0.5862  -0.6164  -7.4866
 DBD  C29   C  CR16  0  -0.280   0.5343   0.0633  -7.0130
 DBD  O30   O  OS    0  -0.637   1.9135   2.4340  -4.9107
 DBD  O31   O  OS    0  -0.637   3.1506   0.2774  -4.7780
 DBD  H2    H  HCH1  0   0.260  -1.5086  -1.6633  -0.3690
 DBD  H51   H  HCH2  0   0.260  -3.5347   1.5536   1.6845
 DBD  H52   H  HCH2  0   0.260  -4.0936   0.0956   2.4802
 DBD  H61   H  HCH2  0   0.253  -4.5800   0.1999  -0.0260
 DBD  H62   H  HCH2  0   0.220  -3.7894  -1.2718   0.5481
 DBD  H12   H  HOH1  0   0.492  -3.5553   1.6778   5.3217
 DBD  H13   H  HNH1  0   0.444   0.3393   0.1471   5.4437
 DBD  H17   H  HOH1  0   0.502   4.3435  -0.9202   6.7512
 DBD  H191  H  HCH2  0   0.276  -0.2648   1.0688  -0.9655
 DBD  H192  H  HCH2  0   0.267   0.6290  -0.4605  -0.8517
 DBD  H26   H  HCR6  0   0.282  -2.1765  -1.3412  -4.5644
 DBD  H27   H  HCR6  0   0.287  -2.4069  -1.6363  -7.0117
 DBD  H28   H  HCR6  0   0.288  -0.7093  -0.7586  -8.5515
 DBD  H29   H  HCR6  0   0.296   1.2826   0.4505  -7.6910

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
 DBD  O1   C2    single    1.402  0.020  1.402
 DBD  O1   C6    single    1.415  0.020  1.415
 DBD  C2   C3    single    1.503  0.020  1.503
 DBD  C2   C19   single    1.515  0.020  1.515
 DBD  C2   H2    single    0.970  0.020  1.090
 DBD  C3   C4    aromatic  1.357  0.020  1.357
 DBD  C3   S7    aromatic  1.727  0.020  1.727
 DBD  C4   C5    single    1.499  0.020  1.499
 DBD  C4   C9    aromatic  1.437  0.020  1.437
 DBD  C5   C6    single    1.521  0.020  1.521
 DBD  C5   H51   single    0.970  0.020  1.090
 DBD  C5   H52   single    0.970  0.020  1.090
 DBD  C6   H61   single    0.970  0.020  1.090
 DBD  C6   H62   single    0.970  0.020  1.090
 DBD  S7   C8    aromatic  1.718  0.020  1.718
 DBD  C8   C9    aromatic  1.382  0.020  1.382
 DBD  C8   N13   single    1.371  0.020  1.371
 DBD  C9   C10   single    1.464  0.020  1.464
 DBD  C10  O11   double    1.217  0.020  1.217
 DBD  C10  O12   single    1.320  0.020  1.320
 DBD  O12  H12   single    0.850  0.020  0.980
 DBD  N13  C14   single    1.347  0.020  1.347
 DBD  N13  H13   single    0.860  0.020  1.020
 DBD  C14  C15   single    1.528  0.020  1.528
 DBD  C14  O18   double    1.211  0.020  1.211
 DBD  C15  O16   double    1.202  0.020  1.202
 DBD  C15  O17   single    1.308  0.020  1.308
 DBD  O17  H17   single    0.850  0.020  0.980
 DBD  C19  O20   single    1.434  0.020  1.434
 DBD  C19  H191  single    0.970  0.020  1.090
 DBD  C19  H192  single    0.970  0.020  1.090
 DBD  O20  C21   single    1.297  0.020  1.297
 DBD  C21  C22   single    1.474  0.020  1.474
 DBD  C21  N25   double    1.286  0.020  1.286
 DBD  C22  C23   aromatic  1.383  0.020  1.383
 DBD  C22  C26   aromatic  1.382  0.020  1.382
 DBD  C23  S24   single    1.776  0.020  1.776
 DBD  C23  C29   aromatic  1.376  0.020  1.376
 DBD  S24  N25   single    1.665  0.020  1.665
 DBD  S24  O30   double    1.450  0.020  1.450
 DBD  S24  O31   double    1.450  0.020  1.450
 DBD  C26  C27   aromatic  1.391  0.020  1.391
 DBD  C26  H26   single    0.930  0.020  1.080
 DBD  C27  C28   aromatic  1.391  0.020  1.391
 DBD  C27  H27   single    0.930  0.020  1.080
 DBD  C28  C29   aromatic  1.393  0.020  1.393
 DBD  C28  H28   single    0.930  0.020  1.080
 DBD  C29  H29   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
 DBD  C6    O1   C2    112.84  3.000
 DBD  H2    C2   C19   108.88  3.000
 DBD  H2    C2   C3    109.28  3.000
 DBD  C19   C2   C3    110.66  3.000
 DBD  H2    C2   O1    110.53  3.000
 DBD  C19   C2   O1    107.59  3.000
 DBD  C3    C2   O1    109.89  3.000
 DBD  S7    C3   C4    113.07  3.000
 DBD  S7    C3   C2    122.72  3.000
 DBD  C4    C3   C2    124.21  3.000
 DBD  C9    C4   C5    128.40  3.000
 DBD  C9    C4   C3    111.87  3.000
 DBD  C5    C4   C3    119.69  3.000
 DBD  H52   C5   H51   106.80  3.000
 DBD  H52   C5   C6    108.50  3.000
 DBD  H51   C5   C6    110.69  3.000
 DBD  H52   C5   C4    111.02  3.000
 DBD  H51   C5   C4    110.58  3.000
 DBD  C6    C5   C4    109.22  3.000
 DBD  H62   C6   H61   107.75  3.000
 DBD  H62   C6   C5    109.97  3.000
 DBD  H61   C6   C5    110.64  3.000
 DBD  H62   C6   O1    110.30  3.000
 DBD  H61   C6   O1    106.82  3.000
 DBD  C5    C6   O1    111.26  3.000
 DBD  C8    S7   C3     90.92  3.000
 DBD  N13   C8   C9    125.75  3.000
 DBD  N13   C8   S7    121.90  3.000
 DBD  C9    C8   S7    112.35  3.000
 DBD  C10   C9   C8    120.65  3.000
 DBD  C10   C9   C4    127.57  3.000
 DBD  C8    C9   C4    111.77  3.000
 DBD  O12   C10  O11   122.49  3.000
 DBD  O12   C10  C9    113.83  3.000
 DBD  O11   C10  C9    123.68  3.000
 DBD  H12   O12  C10   110.01  3.000
 DBD  H13   N13  C14   120.21  3.000
 DBD  H13   N13  C8    115.41  3.000
 DBD  C14   N13  C8    124.38  3.000
 DBD  O18   C14  C15   123.04  3.000
 DBD  O18   C14  N13   124.59  3.000
 DBD  C15   C14  N13   112.37  3.000
 DBD  O17   C15  O16   126.70  3.000
 DBD  O17   C15  C14   110.88  3.000
 DBD  O16   C15  C14   122.43  3.000
 DBD  H17   O17  C15   110.65  3.000
 DBD  H192  C19  H191  108.68  3.000
 DBD  H192  C19  O20   109.25  3.000
 DBD  H191  C19  O20   109.98  3.000
 DBD  H192  C19  C2    111.08  3.000
 DBD  H191  C19  C2    110.91  3.000
 DBD  O20   C19  C2    106.92  3.000
 DBD  C21   O20  C19   118.32  3.000
 DBD  N25   C21  C22   118.08  3.000
 DBD  N25   C21  O20   124.40  3.000
 DBD  C22   C21  O20   117.52  3.000
 DBD  C26   C22  C23   120.64  3.000
 DBD  C26   C22  C21   129.91  3.000
 DBD  C23   C22  C21   109.45  3.000
 DBD  C29   C23  S24   129.88  3.000
 DBD  C29   C23  C22   122.76  3.000
 DBD  S24   C23  C22   107.36  3.000
 DBD  O31   S24  O30   118.30  3.000
 DBD  O31   S24  N25   109.54  3.000
 DBD  O30   S24  N25   109.27  3.000
 DBD  O31   S24  C23   110.84  3.000
 DBD  O30   S24  C23   111.09  3.000
 DBD  N25   S24  C23    95.37  3.000
 DBD  S24   N25  C21   109.74  3.000
 DBD  H26   C26  C27   120.77  3.000
 DBD  H26   C26  C22   121.66  3.000
 DBD  C27   C26  C22   117.57  3.000
 DBD  H27   C27  C28   119.40  3.000
 DBD  H27   C27  C26   119.42  3.000
 DBD  C28   C27  C26   121.18  3.000
 DBD  H28   C28  C29   119.36  3.000
 DBD  H28   C28  C27   119.49  3.000
 DBD  C29   C28  C27   121.15  3.000
 DBD  H29   C29  C28   121.20  3.000
 DBD  H29   C29  C23   122.10  3.000
 DBD  C28   C29  C23   116.70  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
 DBD  CONST_01  C8    C9   C4   C3      0.00   0.0  0
 DBD  CONST_02  C9    C8   S7   C3      0.00   0.0  0
 DBD  CONST_03  C8    S7   C3   C4      0.00   0.0  0
 DBD  CONST_04  S7    C8   C9   C4      0.00   0.0  0
 DBD  CONST_05  C9    C4   C3   S7      0.00   0.0  0
 DBD  CONST_06  C28   C29  C23  C22     0.00   0.0  0
 DBD  CONST_07  C28   C27  C26  C22     0.00   0.0  0
 DBD  CONST_08  C27   C26  C22  C23     0.00   0.0  0
 DBD  CONST_09  C27   C28  C29  C23     0.00   0.0  0
 DBD  CONST_10  C29   C23  C22  C26     0.00   0.0  0
 DBD  CONST_11  C29   C28  C27  C26     0.00   0.0  0
 DBD  CONST_12  C10   C9   C4   C3    180.00   0.0  0
 DBD  CONST_13  N13   C8   S7   C3    180.00   0.0  0
 DBD  CONST_14  N13   C8   C9   C4    180.00   0.0  0
 DBD  CONST_15  C10   C9   C4   C5      0.00   0.0  0
 DBD  CONST_16  C10   C9   C8   S7    180.00   0.0  0
 DBD  CONST_17  H26   C26  C22  C21     0.00   0.0  0
 DBD  CONST_18  H29   C29  C23  C22   180.00   0.0  0
 DBD  CONST_19  H27   C27  C26  C22   180.00   0.0  0
 DBD  CONST_20  H28   C28  C29  C23   180.00   0.0  0
 DBD  CONST_21  C14   N13  C8   S7      0.00   0.0  0
 DBD  CONST_22  C14   N13  C8   C9    180.00   0.0  0
 DBD  CONST_23  H13   N13  C8   S7    180.00   0.0  0
 DBD  CONST_24  C15   C14  N13  C8    180.00   0.0  0
 DBD  CONST_25  O18   C14  N13  C8      0.00   0.0  0
 DBD  CONST_26  H12   O12  C10  C9    180.00   0.0  0
 DBD  CONST_27  H17   O17  C15  C14   180.00   0.0  0
 DBD  Var_01    C4    C5   C6   O1    -48.10  30.0  1
 DBD  Var_02    C5    C6   O1   C2     69.17  30.0  1
 DBD  Var_03    C6    C5   C4   C3     14.24  30.0  1
 DBD  Var_04    O11   C10  C9   C4    176.71  30.0  2
 DBD  Var_05    C22   C21  O20  C19  -179.06  30.0  3
 DBD  Var_06    H191  C19  O20  C21    59.52  30.0  1
 DBD  Var_07    O16   C15  C14  N13    -0.61  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
 DBD  chir_01  C2  O1  C3  C19  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
 DBD  plan-1  C2   0.020
 DBD  plan-1  C3   0.020
 DBD  plan-1  C4   0.020
 DBD  plan-1  C5   0.020
 DBD  plan-1  S7   0.020
 DBD  plan-1  C8   0.020
 DBD  plan-1  C9   0.020
 DBD  plan-1  C10  0.020
 DBD  plan-1  N13  0.020
 DBD  plan-2  O20  0.020
 DBD  plan-2  C21  0.020
 DBD  plan-2  C22  0.020
 DBD  plan-2  C23  0.020
 DBD  plan-2  S24  0.020
 DBD  plan-2  N25  0.020
 DBD  plan-2  C26  0.020
 DBD  plan-2  C27  0.020
 DBD  plan-2  C28  0.020
 DBD  plan-2  C29  0.020
 DBD  plan-2  O30  0.020
 DBD  plan-2  O31  0.020
 DBD  plan-2  H26  0.020
 DBD  plan-2  H27  0.020
 DBD  plan-2  H28  0.020
 DBD  plan-2  H29  0.020
 DBD  plan-3  C8   0.020
 DBD  plan-3  N13  0.020
 DBD  plan-3  C14  0.020
 DBD  plan-3  C15  0.020
 DBD  plan-3  O18  0.020
 DBD  plan-3  H13  0.020
 DBD  plan-4  C9   0.020
 DBD  plan-4  C10  0.020
 DBD  plan-4  O11  0.020
 DBD  plan-4  O12  0.020
 DBD  plan-4  H12  0.020
 DBD  plan-5  C14  0.020
 DBD  plan-5  C15  0.020
 DBD  plan-5  O16  0.020
 DBD  plan-5  O17  0.020
 DBD  plan-5  H17  0.020

