# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 13:12:28 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (4S)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methylidene-5,6-dihydro-4H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](NC(=O)Cc1sccc1)C2=N[C@H](C(O)=O)C(=C)CS2
#
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
 THN  THN  '(4S)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methylidene-5,6-dihydro-4H-1,3-thiazine-4-carboxylic acid'  ligand  35  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_THN
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
 THN  S1    S  S2     0   0.016  -0.0914   1.5950  -2.0735
 THN  C2    C  CH2    0  -0.604  -1.0229   1.4736  -3.6349
 THN  C3    C  C      0   0.150  -1.7157   0.1573  -3.7555
 THN  C3'   C  C2     0  -0.587  -3.0202   0.0728  -4.0001
 THN  C4    C  CH1    0  -0.284  -0.8440  -1.0575  -3.6037
 THN  C4'   C  C      0   0.411   0.1763  -1.0926  -4.7922
 THN  O4A   O  OC    -1  -0.599  -0.2121  -1.6911  -5.8101
 THN  O4B   O  O      0  -0.573   1.2438  -0.4869  -4.6170
 THN  N5    N  N      0  -0.338  -0.1596  -1.1293  -2.3368
 THN  C6    C  C      0   0.099   0.1922  -0.1112  -1.6874
 THN  C7    C  CH1    0  -0.237   0.9227  -0.2682  -0.3749
 THN  C8    C  C      0   0.407   2.3224   0.4163  -0.4780
 THN  O9A   O  O      0  -0.593   3.1533  -0.2167  -1.1508
 THN  O9B   O  OC    -1  -0.586   2.4548   1.5139   0.0813
 THN  N10   N  NH1    0  -0.639   0.1115   0.2542   0.7004
 THN  C11   C  C      0   0.567   0.4928   0.1171   1.9780
 THN  O12   O  O      0  -0.487   1.4057  -0.6124   2.3298
 THN  C13   C  CH2    0  -0.681  -0.3033   0.9550   2.9688
 THN  C14   C  CR5    0  -0.109  -0.3316   0.3654   4.3352
 THN  C15   C  CR15   0  -0.242   0.3440   0.7769   5.4435
 THN  C16   C  CR15   0  -0.183   0.1025  -0.0406   6.5832
 THN  C17   C  CR15   0  -0.471  -0.7542  -1.0634   6.3188
 THN  S19   S  S2     0   0.204  -1.2724  -1.0358   4.6835
 THN  H21   H  HCH2   0   0.292  -0.3128   1.6189  -4.4486
 THN  H22   H  HCH2   0   0.288  -1.7310   2.3010  -3.6384
 THN  H3'1  H  H      0   0.239  -3.6362   0.9559  -4.1179
 THN  H3'2  H  H      0   0.240  -3.5140  -0.8852  -4.1068
 THN  H4    H  HCH1   0   0.235  -1.4745  -1.9464  -3.6768
 THN  H7    H  HCH1   0   0.264   1.0630  -1.3409  -0.2341
 THN  H10   H  HNH1   0   0.395  -0.6081   0.9277   0.4866
 THN  H131  H  HCH2   0   0.302   0.1835   1.9331   3.0240
 THN  H132  H  HCH2   0   0.286  -1.3126   1.1398   2.5923
 THN  H15   H  HCR5   0   0.262   0.9976   1.6384   5.4444
 THN  H16   H  HCR5   0   0.264   0.5476   0.1275   7.5535
 THN  H17   H  HCR5   0   0.293  -1.1120  -1.8257   6.9934

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
 THN  S1   C2    single    1.822  0.020  1.822
 THN  S1   C6    single    1.772  0.020  1.772
 THN  C2   C3    single    1.492  0.020  1.492
 THN  C2   H21   single    0.970  0.020  1.090
 THN  C2   H22   single    0.970  0.020  1.090
 THN  C3   C3'   double    1.330  0.020  1.330
 THN  C3   C4    single    1.503  0.020  1.503
 THN  C3'  H3'1  single    0.930  0.020  1.080
 THN  C3'  H3'2  single    0.930  0.020  1.080
 THN  C4   C4'   single    1.567  0.020  1.567
 THN  C4   N5    single    1.442  0.020  1.442
 THN  C4   H4    single    0.970  0.020  1.090
 THN  C4'  O4A   deloc     1.243  0.020  1.243
 THN  C4'  O4B   deloc     1.240  0.020  1.240
 THN  N5   C6    double    1.258  0.020  1.258
 THN  C6   C7    single    1.510  0.020  1.510
 THN  C7   C8    single    1.561  0.020  1.561
 THN  C7   N10   single    1.445  0.020  1.445
 THN  C7   H7    single    0.970  0.020  1.090
 THN  C8   O9A   deloc     1.242  0.020  1.242
 THN  C8   O9B   deloc     1.239  0.020  1.239
 THN  N10  C11   single    1.340  0.020  1.340
 THN  N10  H10   single    0.860  0.020  1.020
 THN  C11  O12   double    1.220  0.020  1.220
 THN  C11  C13   single    1.522  0.020  1.522
 THN  C13  C14   single    1.488  0.020  1.488
 THN  C13  H131  single    0.970  0.020  1.090
 THN  C13  H132  single    0.970  0.020  1.090
 THN  C14  C15   aromatic  1.362  0.020  1.362
 THN  C14  S19   aromatic  1.723  0.020  1.723
 THN  C15  C16   aromatic  1.423  0.020  1.423
 THN  C15  H15   single    0.930  0.020  1.080
 THN  C16  C17   aromatic  1.360  0.020  1.360
 THN  C16  H16   single    0.930  0.020  1.080
 THN  C17  S19   aromatic  1.716  0.020  1.716
 THN  C17  H17   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
 THN  C6    S1   C2    101.79  3.000
 THN  H22   C2   H21   108.67  3.000
 THN  H22   C2   C3    111.59  3.000
 THN  H21   C2   C3    111.09  3.000
 THN  H22   C2   S1    106.53  3.000
 THN  H21   C2   S1    107.32  3.000
 THN  C3    C2   S1    111.43  3.000
 THN  C4    C3   C3'   122.42  3.000
 THN  C4    C3   C2    115.82  3.000
 THN  C3'   C3   C2    121.75  3.000
 THN  H3'2  C3'  H3'1  116.82  3.000
 THN  H3'2  C3'  C3    121.43  3.000
 THN  H3'1  C3'  C3    121.74  3.000
 THN  H4    C4   N5    107.00  3.000
 THN  H4    C4   C4'   107.87  3.000
 THN  N5    C4   C4'   110.88  3.000
 THN  H4    C4   C3    108.43  3.000
 THN  N5    C4   C3    113.85  3.000
 THN  C4'   C4   C3    108.61  3.000
 THN  O4B   C4'  O4A   128.31  3.000
 THN  O4B   C4'  C4    116.27  3.000
 THN  O4A   C4'  C4    115.37  3.000
 THN  C6    N5   C4    123.11  3.000
 THN  C7    C6   N5    119.99  3.000
 THN  C7    C6   S1    111.52  3.000
 THN  N5    C6   S1    128.47  3.000
 THN  H7    C7   N10   109.37  3.000
 THN  H7    C7   C8    108.92  3.000
 THN  N10   C7   C8    113.20  3.000
 THN  H7    C7   C6    106.06  3.000
 THN  N10   C7   C6    109.73  3.000
 THN  C8    C7   C6    109.30  3.000
 THN  O9B   C8   O9A   128.63  3.000
 THN  O9B   C8   C7    117.02  3.000
 THN  O9A   C8   C7    114.32  3.000
 THN  H10   N10  C11   118.25  3.000
 THN  H10   N10  C7    118.97  3.000
 THN  C11   N10  C7    120.85  3.000
 THN  C13   C11  O12   122.18  3.000
 THN  C13   C11  N10   114.54  3.000
 THN  O12   C11  N10   123.28  3.000
 THN  H132  C13  H131  106.09  3.000
 THN  H132  C13  C14   111.45  3.000
 THN  H131  C13  C14   108.44  3.000
 THN  H132  C13  C11   110.60  3.000
 THN  H131  C13  C11   106.99  3.000
 THN  C14   C13  C11   112.91  3.000
 THN  S19   C14  C15   110.61  3.000
 THN  S19   C14  C13   121.20  3.000
 THN  C15   C14  C13   128.18  3.000
 THN  H15   C15  C16   124.02  3.000
 THN  H15   C15  C14   122.77  3.000
 THN  C16   C15  C14   113.21  3.000
 THN  H16   C16  C17   123.43  3.000
 THN  H16   C16  C15   124.04  3.000
 THN  C17   C16  C15   112.53  3.000
 THN  H17   C17  S19   120.48  3.000
 THN  H17   C17  C16   128.21  3.000
 THN  S19   C17  C16   111.31  3.000
 THN  C17   S19  C14    92.34  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
 THN  CONST_01  C17   C16  C15  C14    0.00   0.0  0
 THN  CONST_02  C16   C17  S19  C14    0.00   0.0  0
 THN  CONST_03  C17   S19  C14  C15    0.00   0.0  0
 THN  CONST_04  S19   C17  C16  C15    0.00   0.0  0
 THN  CONST_05  S19   C14  C15  C16    0.00   0.0  0
 THN  CONST_06  C16   C15  C14  C13  180.00   0.0  0
 THN  CONST_07  C17   S19  C14  C13  180.00   0.0  0
 THN  CONST_08  H16   C16  C15  C14  180.00   0.0  0
 THN  CONST_09  H17   C17  S19  C14  180.00   0.0  0
 THN  CONST_10  H15   C15  C16  C17  180.00   0.0  0
 THN  CONST_11  O12   C11  N10  C7     0.00   0.0  0
 THN  CONST_12  C13   C11  N10  C7   180.00   0.0  0
 THN  CONST_13  H10   N10  C11  O12  180.00   0.0  0
 THN  Var_01    C4    C3   C2   S1   -54.36  30.0  1
 THN  Var_02    N5    C6   S1   C2     0.30  30.0  1
 THN  Var_03    C15   C14  C13  C11  105.70  30.0  2
 THN  Var_04    H3'1  C3'  C3   C2    -0.28  30.0  2
 THN  Var_05    C14   C13  C11  N10  153.29  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
 THN  chir_01  C4  C3   C4'  N5  negativ
 THN  chir_02  C7  N10  C8   C6  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
 THN  plan-1  C13  0.020
 THN  plan-1  C14  0.020
 THN  plan-1  C15  0.020
 THN  plan-1  C16  0.020
 THN  plan-1  C17  0.020
 THN  plan-1  S19  0.020
 THN  plan-1  H15  0.020
 THN  plan-1  H16  0.020
 THN  plan-1  H17  0.020
 THN  plan-2  C7   0.020
 THN  plan-2  N10  0.020
 THN  plan-2  C11  0.020
 THN  plan-2  O12  0.020
 THN  plan-2  C13  0.020
 THN  plan-2  H10  0.020
 THN  plan-3  C4   0.020
 THN  plan-3  C4'  0.020
 THN  plan-3  O4A  0.020
 THN  plan-3  O4B  0.020
 THN  plan-4  C7   0.020
 THN  plan-4  C8   0.020
 THN  plan-4  O9A  0.020
 THN  plan-4  O9B  0.020

