# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:55:48 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: (2S)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(N[C@@H](SC1)[C@H](NC(=O)Cc2sccc2)C(O)=O)C(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
 KCP  KCP  '(2S)-2-{(R)-carboxy[(thiophen-2-ylacetyl)amino]methyl}-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  37  23  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KCP
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
 KCP  S1    S  S2     0  -0.026   1.8284  -0.1875   1.2510
 KCP  C2    C  CH2    0  -0.598   2.3738   0.5206   2.8242
 KCP  C3    C  C      0   0.065   1.5038   0.1877   4.0089
 KCP  C3'   C  CH3    0  -0.730   2.2237   0.4534   5.3011
 KCP  C4    C  C      0   0.234   0.2409  -0.2704   3.8834
 KCP  C4'   C  C      0   0.346  -0.6630  -0.6929   5.0474
 KCP  O4A   O  OC    -1  -0.688  -1.8834  -0.7134   4.7854
 KCP  O4B   O  O      0  -0.563  -0.1348  -1.0113   6.1310
 KCP  N5    N  NH1    0  -0.700  -0.3957  -0.4384   2.6649
 KCP  C6    C  CH1    0  -0.167   0.0649   0.2416   1.5063
 KCP  C7    C  CH1    0  -0.200  -0.7526  -0.1466   0.2747
 KCP  C8    C  C      0   0.393  -2.2341   0.2807   0.4949
 KCP  O9A   O  O      0  -0.460  -2.9299  -0.5259   1.1434
 KCP  O9B   O  OC    -1  -0.715  -2.5666   1.3925   0.0610
 KCP  N10   N  NH1    0  -0.655  -0.1712   0.4828  -0.8843
 KCP  C11   C  C      0   0.553  -0.6431   0.2580  -2.1159
 KCP  O12   O  O      0  -0.396  -1.4800  -0.5957  -2.3670
 KCP  C13   C  CH2    0  -0.710  -0.0615   1.1567  -3.1979
 KCP  C14   C  CR5    0  -0.107   0.1095   0.4521  -4.4988
 KCP  C15   C  CR15   0  -0.090  -0.6267   0.5865  -5.6362
 KCP  C16   C  CR15   0  -0.216  -0.1954  -0.2703  -6.6878
 KCP  C17   C  CR15   0  -0.482   0.8611  -1.0471  -6.3272
 KCP  S19   S  S2     0   0.148   1.3523  -0.7231  -4.7155
 KCP  H21   H  HCH2   0   0.321   2.4922   1.6032   2.7123
 KCP  H22   H  HCH2   0   0.235   3.3802   0.1238   2.9900
 KCP  H3'1  H  HCH3   0   0.134   2.7862   1.3888   5.2215
 KCP  H3'2  H  HCH3   0   0.250   1.5625   0.5288   6.1564
 KCP  H3'3  H  HCH3   0   0.246   2.9612  -0.3263   5.5181
 KCP  H5    H  HNH1   0   0.340  -1.3982  -0.5509   2.7511
 KCP  H6    H  HCH1   0   0.264   0.0363   1.3367   1.6257
 KCP  H7    H  HCH1   0   0.246  -0.7017  -1.2333   0.1629
 KCP  H10   H  HNH1   0   0.365   0.4843   1.2369  -0.7506
 KCP  H131  H  HCH2   0   0.292  -0.7652   1.9812  -3.3398
 KCP  H132  H  HCH2   0   0.302   0.8769   1.6083  -2.8673
 KCP  H15   H  HCR5   0   0.250  -1.4578   1.2739  -5.7170
 KCP  H16   H  HCR5   0   0.214  -0.6545  -0.3063  -7.6654
 KCP  H17   H  HCR5   0   0.305   1.3837  -1.7811  -6.9208

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
 KCP  S1   C2    single    1.809  0.020  1.809
 KCP  S1   C6    single    1.833  0.020  1.833
 KCP  C2   C3    single    1.507  0.020  1.507
 KCP  C2   H21   single    0.970  0.020  1.090
 KCP  C2   H22   single    0.970  0.020  1.090
 KCP  C3   C3'   single    1.503  0.020  1.503
 KCP  C3   C4    double    1.349  0.020  1.349
 KCP  C3'  H3'1  single    0.970  0.020  1.090
 KCP  C3'  H3'2  single    0.970  0.020  1.090
 KCP  C3'  H3'3  single    0.970  0.020  1.090
 KCP  C4   C4'   single    1.533  0.020  1.533
 KCP  C4   N5    single    1.385  0.020  1.385
 KCP  C4'  O4A   deloc     1.248  0.020  1.248
 KCP  C4'  O4B   deloc     1.247  0.020  1.247
 KCP  N5   C6    single    1.420  0.020  1.420
 KCP  N5   H5    single    0.890  0.020  1.040
 KCP  C6   C7    single    1.528  0.020  1.528
 KCP  C6   H6    single    0.970  0.020  1.090
 KCP  C7   C8    single    1.557  0.020  1.557
 KCP  C7   N10   single    1.441  0.020  1.441
 KCP  C7   H7    single    0.970  0.020  1.090
 KCP  C8   O9A   deloc     1.247  0.020  1.247
 KCP  C8   O9B   deloc     1.239  0.020  1.239
 KCP  N10  C11   single    1.338  0.020  1.338
 KCP  N10  H10   single    0.860  0.020  1.020
 KCP  C11  O12   double    1.222  0.020  1.222
 KCP  C11  C13   single    1.522  0.020  1.522
 KCP  C13  C14   single    1.489  0.020  1.489
 KCP  C13  H131  single    0.970  0.020  1.090
 KCP  C13  H132  single    0.970  0.020  1.090
 KCP  C14  C15   aromatic  1.362  0.020  1.362
 KCP  C14  S19   aromatic  1.724  0.020  1.724
 KCP  C15  C16   aromatic  1.423  0.020  1.423
 KCP  C15  H15   single    0.930  0.020  1.080
 KCP  C16  C17   aromatic  1.360  0.020  1.360
 KCP  C16  H16   single    0.930  0.020  1.080
 KCP  C17  S19   aromatic  1.716  0.020  1.716
 KCP  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
 KCP  C6    S1   C2     94.43  3.000
 KCP  H22   C2   H21   105.94  3.000
 KCP  H22   C2   C3    109.37  3.000
 KCP  H21   C2   C3    111.18  3.000
 KCP  H22   C2   S1    105.49  3.000
 KCP  H21   C2   S1    109.31  3.000
 KCP  C3    C2   S1    115.02  3.000
 KCP  C4    C3   C3'   126.04  3.000
 KCP  C4    C3   C2    122.84  3.000
 KCP  C3'   C3   C2    111.12  3.000
 KCP  H3'3  C3'  H3'2  107.70  3.000
 KCP  H3'3  C3'  H3'1  106.07  3.000
 KCP  H3'2  C3'  H3'1  108.15  3.000
 KCP  H3'3  C3'  C3    111.54  3.000
 KCP  H3'2  C3'  C3    113.49  3.000
 KCP  H3'1  C3'  C3    109.56  3.000
 KCP  N5    C4   C4'   111.31  3.000
 KCP  N5    C4   C3    123.59  3.000
 KCP  C4'   C4   C3    125.09  3.000
 KCP  O4B   C4'  O4A   126.32  3.000
 KCP  O4B   C4'  C4    118.72  3.000
 KCP  O4A   C4'  C4    114.93  3.000
 KCP  H5    N5   C6    116.35  3.000
 KCP  H5    N5   C4    113.18  3.000
 KCP  C6    N5   C4    120.70  3.000
 KCP  H6    C6   C7    109.01  3.000
 KCP  H6    C6   N5    112.27  3.000
 KCP  C7    C6   N5    111.24  3.000
 KCP  H6    C6   S1    105.83  3.000
 KCP  C7    C6   S1    110.06  3.000
 KCP  N5    C6   S1    108.28  3.000
 KCP  H7    C7   N10   109.44  3.000
 KCP  H7    C7   C8    109.35  3.000
 KCP  N10   C7   C8    112.19  3.000
 KCP  H7    C7   C6    108.05  3.000
 KCP  N10   C7   C6    108.74  3.000
 KCP  C8    C7   C6    108.98  3.000
 KCP  O9B   C8   O9A   127.79  3.000
 KCP  O9B   C8   C7    116.87  3.000
 KCP  O9A   C8   C7    115.26  3.000
 KCP  H10   N10  C11   118.50  3.000
 KCP  H10   N10  C7    118.83  3.000
 KCP  C11   N10  C7    121.64  3.000
 KCP  C13   C11  O12   121.89  3.000
 KCP  C13   C11  N10   114.86  3.000
 KCP  O12   C11  N10   123.25  3.000
 KCP  H132  C13  H131  106.28  3.000
 KCP  H132  C13  C14   111.18  3.000
 KCP  H131  C13  C14   108.50  3.000
 KCP  H132  C13  C11   110.92  3.000
 KCP  H131  C13  C11   106.95  3.000
 KCP  C14   C13  C11   112.68  3.000
 KCP  S19   C14  C15   110.62  3.000
 KCP  S19   C14  C13   121.00  3.000
 KCP  C15   C14  C13   128.38  3.000
 KCP  H15   C15  C16   124.07  3.000
 KCP  H15   C15  C14   122.73  3.000
 KCP  C16   C15  C14   113.20  3.000
 KCP  H16   C16  C17   123.43  3.000
 KCP  H16   C16  C15   124.04  3.000
 KCP  C17   C16  C15   112.54  3.000
 KCP  H17   C17  S19   120.44  3.000
 KCP  H17   C17  C16   128.24  3.000
 KCP  S19   C17  C16   111.32  3.000
 KCP  C17   S19  C14    92.32  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
 KCP  CONST_01  C17   C16  C15  C14    0.00   0.0  0
 KCP  CONST_02  C16   C17  S19  C14    0.00   0.0  0
 KCP  CONST_03  C17   S19  C14  C15    0.00   0.0  0
 KCP  CONST_04  S19   C17  C16  C15    0.00   0.0  0
 KCP  CONST_05  S19   C14  C15  C16    0.00   0.0  0
 KCP  CONST_06  C16   C15  C14  C13  180.00   0.0  0
 KCP  CONST_07  C17   S19  C14  C13  180.00   0.0  0
 KCP  CONST_08  H16   C16  C15  C14  180.00   0.0  0
 KCP  CONST_09  H17   C17  S19  C14  180.00   0.0  0
 KCP  CONST_10  H15   C15  C16  C17  180.00   0.0  0
 KCP  CONST_11  O12   C11  N10  C7     0.00   0.0  0
 KCP  CONST_12  C13   C11  N10  C7   180.00   0.0  0
 KCP  CONST_13  H10   N10  C11  O12  180.00   0.0  0
 KCP  Var_01    C4    C3   C2   S1   -17.72  30.0  1
 KCP  Var_02    N5    C4   C3   C2    -2.19  30.0  1
 KCP  Var_03    C6    N5   C4   C3   -20.09  30.0  1
 KCP  Var_04    O4A   C4'  C4   C3   160.12  30.0  2
 KCP  Var_05    C15   C14  C13  C11  106.55  30.0  2
 KCP  Var_06    H3'1  C3'  C3   C2    41.00  30.0  3
 KCP  Var_07    C14   C13  C11  N10  144.43  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
 KCP  chir_01  C6  S1   N5  C7  positiv
 KCP  chir_02  C7  N10  C6  C8  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
 KCP  plan-1  C13  0.020
 KCP  plan-1  C14  0.020
 KCP  plan-1  C15  0.020
 KCP  plan-1  C16  0.020
 KCP  plan-1  C17  0.020
 KCP  plan-1  S19  0.020
 KCP  plan-1  H15  0.020
 KCP  plan-1  H16  0.020
 KCP  plan-1  H17  0.020
 KCP  plan-2  C7   0.020
 KCP  plan-2  N10  0.020
 KCP  plan-2  C11  0.020
 KCP  plan-2  O12  0.020
 KCP  plan-2  C13  0.020
 KCP  plan-2  H10  0.020
 KCP  plan-3  C4   0.020
 KCP  plan-3  N5   0.020
 KCP  plan-3  C6   0.020
 KCP  plan-3  H5   0.020
 KCP  plan-4  C4   0.020
 KCP  plan-4  C4'  0.020
 KCP  plan-4  O4A  0.020
 KCP  plan-4  O4B  0.020
 KCP  plan-5  C7   0.020
 KCP  plan-5  C8   0.020
 KCP  plan-5  O9A  0.020
 KCP  plan-5  O9B  0.020

