# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:07:04 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: (4R)-4-hydroxy-2-(thiophen-2-ylmethyl)-3,4-dihydro-2H-thieno[3,2-e][1,2]thiazine-6-sulfonamide 1,1-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)c1sc2c(c1)[C@@H](O)CN(Cc3sccc3)[S]2(=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
 AL3  AL3  '(4R)-4-hydroxy-2-(thiophen-2-ylmethyl)-3,4-dihydro-2H-thieno[3,2-e][1,2]thiazine-6-sulfonamide 1,1-dioxide'  ligand  34  22  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AL3
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
 AL3  C3    C  CR5   0  -0.426  -0.0374   0.1027   3.0557
 AL3  O5    O  OH1   0  -0.653  -3.2792   0.2641   0.3473
 AL3  C9    C  CH2   0  -0.373  -1.7134  -0.2011  -1.3767
 AL3  C10   C  CH1   0   0.011  -2.1651  -0.5304   0.0428
 AL3  C12   C  CR5   0  -0.152   0.1152  -0.5232  -4.0567
 AL3  C13   C  CR15  0  -0.215   1.3479  -0.3470  -4.6101
 AL3  C14   C  CR15  0  -0.183   1.3839   0.7060  -5.5641
 AL3  C15   C  CR15  0  -0.462   0.1768   1.3168  -5.7110
 AL3  O1A   O  OS    0  -0.631  -1.0735   0.8096   5.3010
 AL3  O2A   O  OS    0  -0.653   1.3987   1.1430   4.9476
 AL3  N21   N  NC2   0  -0.880   0.5756  -1.1714   5.2847
 AL3  S1    S  S     0   1.376   0.1980   0.3442   4.7790
 AL3  C4    C  CR15  0  -0.172  -1.2225  -0.1057   2.4220
 AL3  C5    C  CR5   0   0.276  -1.0474  -0.2856   1.0255
 AL3  C6    C  CR5   0  -0.536   0.2711  -0.2004   0.6848
 AL3  S2    S  S2    0   0.386   1.3164   0.1014   2.0058
 AL3  S7    S  S     0   1.418   0.8747  -0.2400  -0.9648
 AL3  O3B   O  OS    0  -0.627   1.1238   1.1337  -1.3671
 AL3  O4B   O  OS    0  -0.637   1.9692  -1.1865  -1.0769
 AL3  N8    N  N     0  -0.585  -0.4641  -0.9087  -1.6631
 AL3  S16   S  S2    0   0.212  -1.0123   0.6094  -4.7007
 AL3  HO5   H  HOH1  0   0.471  -3.9323  -0.2705   0.8067
 AL3  H91   H  HCH2  0   0.298  -2.4645  -0.5561  -2.0816
 AL3  H92   H  HCH2  0   0.275  -1.6259   0.8826  -1.5090
 AL3  H10   H  HCH1  0   0.270  -2.4115  -1.5980   0.0821
 AL3  H111  H  HCH2  0   0.304   0.4976  -2.2708  -2.9222
 AL3  H112  H  HCH2  0   0.307  -1.2012  -2.0103  -3.2272
 AL3  H13   H  HCR5  0   0.268   2.2038  -0.9529  -4.3453
 AL3  H14   H  HCR5  0   0.269   2.2673   0.9937  -6.1158
 AL3  H15   H  HCR5  0   0.297  -0.0798   2.1386  -6.3617
 AL3  HNL1  H  HNC2  0   0.428   1.2084  -1.1642   6.0785
 AL3  HNL2  H  HNC2  0   0.424  -0.2369  -1.7505   5.4679
 AL3  H4    H  HCR5  0   0.306  -2.1781  -0.1314   2.9255
 AL3  C11   C  CH2   0  -0.414  -0.2680  -1.4987  -2.9911

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
 AL3  C3   S1    single    1.756  0.020  1.756
 AL3  C3   C4    aromatic  1.360  0.020  1.360
 AL3  C3   S2    aromatic  1.713  0.020  1.713
 AL3  O5   C10   single    1.402  0.020  1.402
 AL3  O5   HO5   single    0.850  0.020  0.980
 AL3  C9   C10   single    1.526  0.020  1.526
 AL3  C9   N8    single    1.464  0.020  1.464
 AL3  C9   H91   single    0.970  0.020  1.090
 AL3  C9   H92   single    0.970  0.020  1.090
 AL3  C10  C5    single    1.508  0.020  1.508
 AL3  C10  H10   single    0.970  0.020  1.090
 AL3  C11  C12   single    1.495  0.020  1.495
 AL3  C11  N8    single    1.466  0.020  1.466
 AL3  C11  H111  single    0.970  0.020  1.090
 AL3  C11  H112  single    0.970  0.020  1.090
 AL3  C12  C13   aromatic  1.363  0.020  1.363
 AL3  C12  S16   aromatic  1.723  0.020  1.723
 AL3  C13  C14   aromatic  1.421  0.020  1.421
 AL3  C13  H13   single    0.930  0.020  1.080
 AL3  C14  C15   aromatic  1.361  0.020  1.361
 AL3  C14  H14   single    0.930  0.020  1.080
 AL3  C15  S16   aromatic  1.713  0.020  1.713
 AL3  C15  H15   single    0.930  0.020  1.080
 AL3  O1A  S1    double    1.451  0.020  1.451
 AL3  O2A  S1    double    1.452  0.020  1.452
 AL3  N21  S1    single    1.642  0.020  1.642
 AL3  N21  HNL1  single    0.890  0.020  1.040
 AL3  N21  HNL2  single    0.890  0.020  1.040
 AL3  C4   C5    aromatic  1.419  0.020  1.419
 AL3  C4   H4    single    0.930  0.020  1.080
 AL3  C5   C6    aromatic  1.365  0.020  1.365
 AL3  C6   S2    aromatic  1.711  0.020  1.711
 AL3  C6   S7    single    1.757  0.020  1.757
 AL3  S7   O3B   double    1.453  0.020  1.453
 AL3  S7   O4B   double    1.451  0.020  1.451
 AL3  S7   N8    single    1.651  0.020  1.651

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
 AL3  S2    C3   C4    113.76  3.000
 AL3  S2    C3   S1    119.71  3.000
 AL3  C4    C3   S1    126.52  3.000
 AL3  HO5   O5   C10   109.19  3.000
 AL3  H92   C9   H91   107.42  3.000
 AL3  H92   C9   N8    112.73  3.000
 AL3  H91   C9   N8    107.71  3.000
 AL3  H92   C9   C10   110.47  3.000
 AL3  H91   C9   C10   109.12  3.000
 AL3  N8    C9   C10   109.29  3.000
 AL3  H10   C10  C5    107.53  3.000
 AL3  H10   C10  C9    108.07  3.000
 AL3  C5    C10  C9    110.60  3.000
 AL3  H10   C10  O5    111.44  3.000
 AL3  C5    C10  O5    110.82  3.000
 AL3  C9    C10  O5    108.36  3.000
 AL3  S16   C12  C13   110.80  3.000
 AL3  S16   C12  C11   121.85  3.000
 AL3  C13   C12  C11   127.29  3.000
 AL3  H13   C13  C14   124.01  3.000
 AL3  H13   C13  C12   122.95  3.000
 AL3  C14   C13  C12   113.04  3.000
 AL3  H14   C14  C15   123.41  3.000
 AL3  H14   C14  C13   124.10  3.000
 AL3  C15   C14  C13   112.49  3.000
 AL3  H15   C15  S16   120.33  3.000
 AL3  H15   C15  C14   128.16  3.000
 AL3  S16   C15  C14   111.51  3.000
 AL3  HNL2  N21  HNL1  111.22  3.000
 AL3  HNL2  N21  S1    113.48  3.000
 AL3  HNL1  N21  S1    112.20  3.000
 AL3  N21   S1   O2A   106.37  3.000
 AL3  N21   S1   O1A   112.75  3.000
 AL3  O2A   S1   O1A   120.42  3.000
 AL3  N21   S1   C3    101.90  3.000
 AL3  O2A   S1   C3    107.49  3.000
 AL3  O1A   S1   C3    106.24  3.000
 AL3  H4    C4   C5    124.39  3.000
 AL3  H4    C4   C3    123.87  3.000
 AL3  C5    C4   C3    111.75  3.000
 AL3  C6    C5   C4    110.92  3.000
 AL3  C6    C5   C10   124.30  3.000
 AL3  C4    C5   C10   124.78  3.000
 AL3  S7    C6   S2    121.26  3.000
 AL3  S7    C6   C5    124.40  3.000
 AL3  S2    C6   C5    114.11  3.000
 AL3  C6    S2   C3     89.46  3.000
 AL3  N8    S7   O4B   108.34  3.000
 AL3  N8    S7   O3B   113.88  3.000
 AL3  O4B   S7   O3B   117.77  3.000
 AL3  N8    S7   C6     97.33  3.000
 AL3  O4B   S7   C6    110.26  3.000
 AL3  O3B   S7   C6    107.31  3.000
 AL3  S7    N8   C11   115.94  3.000
 AL3  S7    N8   C9    114.42  3.000
 AL3  C11   N8   C9    119.06  3.000
 AL3  C15   S16  C12    92.16  3.000
 AL3  H112  C11  H111  106.41  3.000
 AL3  H112  C11  N8    105.70  3.000
 AL3  H111  C11  N8    108.78  3.000
 AL3  H112  C11  C12   111.80  3.000
 AL3  H111  C11  C12   109.11  3.000
 AL3  N8    C11  C12   114.67  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
 AL3  CONST_01  C6    C5   C4   C3     0.00   0.0  0
 AL3  CONST_02  C5    C6   S2   C3     0.00   0.0  0
 AL3  CONST_03  C15   C14  C13  C12    0.00   0.0  0
 AL3  CONST_04  C14   C15  S16  C12    0.00   0.0  0
 AL3  CONST_05  C15   S16  C12  C13    0.00   0.0  0
 AL3  CONST_06  S16   C15  C14  C13    0.00   0.0  0
 AL3  CONST_07  S16   C12  C13  C14    0.00   0.0  0
 AL3  CONST_08  C6    S2   C3   C4     0.00   0.0  0
 AL3  CONST_09  S2    C6   C5   C4     0.00   0.0  0
 AL3  CONST_10  S2    C3   C4   C5     0.00   0.0  0
 AL3  CONST_11  C14   C13  C12  C11  180.00   0.0  0
 AL3  CONST_12  C15   S16  C12  C11  180.00   0.0  0
 AL3  CONST_13  C5    C4   C3   S1   180.00   0.0  0
 AL3  CONST_14  C6    S2   C3   S1   180.00   0.0  0
 AL3  CONST_15  H4    C4   C5   C10    0.00   0.0  0
 AL3  CONST_16  H14   C14  C13  C12  180.00   0.0  0
 AL3  CONST_17  H15   C15  S16  C12  180.00   0.0  0
 AL3  CONST_18  H13   C13  C14  C15  180.00   0.0  0
 AL3  Var_01    C6    S7   N8   C9    53.24  30.0  1
 AL3  Var_02    S7    N8   C9   C10  -76.37  30.0  1
 AL3  Var_03    N8    S7   C6   C5   -18.69  30.0  1
 AL3  Var_04    C12   C11  N8   C9    78.39  30.0  3
 AL3  Var_05    N8    C11  C12  C13  104.74  30.0  2
 AL3  Var_06    C4    C3   S1   O1A  -22.41  30.0  2
 AL3  Var_07    HNL1  N21  S1   C3   148.69  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
 AL3  chir_01  C10  O5  C9  C5  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
 AL3  plan-1  C12  0.020
 AL3  plan-1  C13  0.020
 AL3  plan-1  C14  0.020
 AL3  plan-1  C15  0.020
 AL3  plan-1  S16  0.020
 AL3  plan-1  H13  0.020
 AL3  plan-1  H14  0.020
 AL3  plan-1  H15  0.020
 AL3  plan-1  C11  0.020
 AL3  plan-2  C3   0.020
 AL3  plan-2  C10  0.020
 AL3  plan-2  S1   0.020
 AL3  plan-2  C4   0.020
 AL3  plan-2  C5   0.020
 AL3  plan-2  C6   0.020
 AL3  plan-2  S2   0.020
 AL3  plan-2  S7   0.020
 AL3  plan-2  H4   0.020
 AL3  plan-3  C9   0.020
 AL3  plan-3  S7   0.020
 AL3  plan-3  N8   0.020
 AL3  plan-3  C11  0.020

