# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:08:58 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (2R)-2-[(1R)-2-oxo-1-{[(thiophen-2-yl)acetyl]amino}ethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=N[C@H](SCC1)[C@H](NC(=O)Cc2sccc2)C=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
 NCF  NCF  '(2R)-2-[(1R)-2-oxo-1-{[(thiophen-2-yl)acetyl]amino}ethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  34  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NCF
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
 NCF  S1    S  S2     0  -0.025  -3.3838   1.7100  -0.8408
 NCF  C2    C  CH2    0  -0.578  -4.6688   1.1685   0.3144
 NCF  C3    C  CH2    0  -0.478  -4.7121  -0.3446   0.3704
 NCF  C4    C  C      0   0.081  -3.3749  -0.9974   0.5940
 NCF  C4'   C  C      0   0.391  -3.3943  -2.4887   0.9875
 NCF  O4A   O  OC    -1  -0.581  -2.3494  -2.9632   1.4533
 NCF  O4B   O  O      0  -0.586  -4.4766  -3.0678   0.7809
 NCF  N5    N  N      0  -0.345  -2.2403  -0.4489   0.4746
 NCF  C6    C  CH1    0  -0.253  -2.0240   0.9021   0.0691
 NCF  C7    C  CH1    0  -0.140  -0.7702   0.9535  -0.8216
 NCF  C8    C  C1     0   0.157  -0.3869   2.4129  -1.0396
 NCF  O9    O  O      0  -0.369   0.0717   3.1015  -0.1670
 NCF  N10   N  NH1    0  -0.646   0.2889   0.2379  -0.1607
 NCF  C11   C  C      0   0.583   1.5274   0.2474  -0.6701
 NCF  O12   O  O      0  -0.484   1.8350   0.9606  -1.6151
 NCF  C13   C  CH2    0  -0.642   2.5138  -0.7011  -0.0233
 NCF  C14   C  CR5    0  -0.134   3.8749  -0.1170   0.1557
 NCF  C15   C  CR15   0  -0.235   4.6204  -0.1213   1.2975
 NCF  C16   C  CR15   0  -0.187   5.9075   0.4594   1.1288
 NCF  C17   C  CR15   0  -0.476   6.1181   0.8886  -0.1448
 NCF  S19   S  S2     0   0.218   4.7496   0.6087  -1.1403
 NCF  H2C1  H  HCH2   0   0.278  -4.4678   1.5998   1.2967
 NCF  H2C2  H  HCH2   0   0.297  -5.6146   1.5768  -0.0379
 NCF  H3C1  H  HCH2   0   0.268  -5.3834  -0.6560   1.1742
 NCF  H3C2  H  HCH2   0   0.268  -5.1459  -0.7442  -0.5496
 NCF  H6    H  HCH1   0   0.299  -1.8156   1.4894   0.9713
 NCF  H7    H  HCH1   0   0.286  -1.0032   0.5010  -1.7923
 NCF  H8    H  H      0   0.218  -0.6073   2.8121  -2.0428
 NCF  H10   H  HNH1   0   0.410   0.0084  -0.4618   0.5137
 NCF  H131  H  HCH2   0   0.286   2.1493  -1.0433   0.9459
 NCF  H132  H  HCH2   0   0.304   2.5598  -1.5866  -0.6674
 NCF  H15   H  HCR5   0   0.262   4.2598  -0.5328   2.2305
 NCF  H16   H  HCR5   0   0.263   6.6352   0.5554   1.9216
 NCF  H17   H  HCR5   0   0.291   6.9924   1.3778  -0.5458

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
 NCF  S1   C2    single    1.811  0.020  1.811
 NCF  S1   C6    single    1.825  0.020  1.825
 NCF  C2   C3    single    1.515  0.020  1.515
 NCF  C2   H2C1  single    0.970  0.020  1.090
 NCF  C2   H2C2  single    0.970  0.020  1.090
 NCF  C3   C4    single    1.505  0.020  1.505
 NCF  C3   H3C1  single    0.970  0.020  1.090
 NCF  C3   H3C2  single    0.970  0.020  1.090
 NCF  C4   C4'   single    1.542  0.020  1.542
 NCF  C4   N5    double    1.266  0.020  1.266
 NCF  C4'  O4A   deloc     1.238  0.020  1.238
 NCF  C4'  O4B   deloc     1.245  0.020  1.245
 NCF  N5   C6    single    1.427  0.020  1.427
 NCF  C6   C7    single    1.539  0.020  1.539
 NCF  C6   H6    single    0.970  0.020  1.090
 NCF  C7   C8    single    1.525  0.020  1.525
 NCF  C7   N10   single    1.439  0.020  1.439
 NCF  C7   H7    single    0.970  0.020  1.090
 NCF  C8   O9    double    1.202  0.020  1.202
 NCF  C8   H8    single    0.930  0.020  1.080
 NCF  N10  C11   single    1.339  0.020  1.339
 NCF  N10  H10   single    0.860  0.020  1.020
 NCF  C11  O12   double    1.223  0.020  1.223
 NCF  C11  C13   single    1.514  0.020  1.514
 NCF  C13  C14   single    1.492  0.020  1.492
 NCF  C13  H131  single    0.970  0.020  1.090
 NCF  C13  H132  single    0.970  0.020  1.090
 NCF  C14  C15   aromatic  1.364  0.020  1.364
 NCF  C14  S19   aromatic  1.724  0.020  1.724
 NCF  C15  C16   aromatic  1.422  0.020  1.422
 NCF  C15  H15   single    0.930  0.020  1.080
 NCF  C16  C17   aromatic  1.360  0.020  1.360
 NCF  C16  H16   single    0.930  0.020  1.080
 NCF  C17  S19   aromatic  1.715  0.020  1.715
 NCF  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
 NCF  C6    S1   C2     94.49  3.000
 NCF  H2C2  C2   H2C1  107.63  3.000
 NCF  H2C2  C2   C3    111.21  3.000
 NCF  H2C1  C2   C3    111.51  3.000
 NCF  H2C2  C2   S1    107.33  3.000
 NCF  H2C1  C2   S1    108.98  3.000
 NCF  C3    C2   S1    110.04  3.000
 NCF  H3C2  C3   H3C1  105.74  3.000
 NCF  H3C2  C3   C4    108.62  3.000
 NCF  H3C1  C3   C4    108.24  3.000
 NCF  H3C2  C3   C2    110.22  3.000
 NCF  H3C1  C3   C2    109.24  3.000
 NCF  C4    C3   C2    114.42  3.000
 NCF  N5    C4   C4'   117.02  3.000
 NCF  N5    C4   C3    126.48  3.000
 NCF  C4'   C4   C3    116.50  3.000
 NCF  O4B   C4'  O4A   128.15  3.000
 NCF  O4B   C4'  C4    114.73  3.000
 NCF  O4A   C4'  C4    117.12  3.000
 NCF  C6    N5   C4    124.95  3.000
 NCF  H6    C6   C7    107.68  3.000
 NCF  H6    C6   N5    107.58  3.000
 NCF  C7    C6   N5    108.64  3.000
 NCF  H6    C6   S1    108.35  3.000
 NCF  C7    C6   S1    107.68  3.000
 NCF  N5    C6   S1    116.61  3.000
 NCF  H7    C7   N10   110.97  3.000
 NCF  H7    C7   C8    108.79  3.000
 NCF  N10   C7   C8    110.89  3.000
 NCF  H7    C7   C6    109.01  3.000
 NCF  N10   C7   C6    108.49  3.000
 NCF  C8    C7   C6    108.64  3.000
 NCF  H8    C8   O9    121.97  3.000
 NCF  H8    C8   C7    115.26  3.000
 NCF  O9    C8   C7    122.70  3.000
 NCF  H10   N10  C11   121.00  3.000
 NCF  H10   N10  C7    116.49  3.000
 NCF  C11   N10  C7    120.16  3.000
 NCF  C13   C11  O12   122.12  3.000
 NCF  C13   C11  N10   115.82  3.000
 NCF  O12   C11  N10   122.05  3.000
 NCF  H132  C13  H131  106.43  3.000
 NCF  H132  C13  C14   110.40  3.000
 NCF  H131  C13  C14   108.73  3.000
 NCF  H132  C13  C11   106.41  3.000
 NCF  H131  C13  C11   111.02  3.000
 NCF  C14   C13  C11   113.61  3.000
 NCF  S19   C14  C15   110.70  3.000
 NCF  S19   C14  C13   122.52  3.000
 NCF  C15   C14  C13   126.73  3.000
 NCF  H15   C15  C16   124.01  3.000
 NCF  H15   C15  C14   122.77  3.000
 NCF  C16   C15  C14   113.22  3.000
 NCF  H16   C16  C17   123.69  3.000
 NCF  H16   C16  C15   123.98  3.000
 NCF  C17   C16  C15   112.33  3.000
 NCF  H17   C17  S19   120.31  3.000
 NCF  H17   C17  C16   128.05  3.000
 NCF  S19   C17  C16   111.62  3.000
 NCF  C17   S19  C14    92.13  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
 NCF  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 NCF  CONST_02  C16  C17  S19  C14     0.00   0.0  0
 NCF  CONST_03  C17  S19  C14  C15     0.00   0.0  0
 NCF  CONST_04  S19  C17  C16  C15     0.00   0.0  0
 NCF  CONST_05  S19  C14  C15  C16     0.00   0.0  0
 NCF  CONST_06  C16  C15  C14  C13   180.00   0.0  0
 NCF  CONST_07  C17  S19  C14  C13   180.00   0.0  0
 NCF  CONST_08  H16  C16  C15  C14   180.00   0.0  0
 NCF  CONST_09  H17  C17  S19  C14   180.00   0.0  0
 NCF  CONST_10  H15  C15  C16  C17   180.00   0.0  0
 NCF  CONST_11  O12  C11  N10  C7      0.00   0.0  0
 NCF  CONST_12  C13  C11  N10  C7    180.00   0.0  0
 NCF  CONST_13  H10  N10  C11  O12   180.00   0.0  0
 NCF  Var_01    C4   C3   C2   S1     50.19  30.0  1
 NCF  Var_02    N5   C4   C3   C2    -14.85  30.0  1
 NCF  Var_03    O4A  C4'  C4   C3   -164.74  30.0  2
 NCF  Var_04    C15  C14  C13  C11   130.46  30.0  2
 NCF  Var_05    C14  C13  C11  N10  -139.41  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
 NCF  chir_01  C6  S1   N5  C7  negativ
 NCF  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
 NCF  plan-1  C13  0.020
 NCF  plan-1  C14  0.020
 NCF  plan-1  C15  0.020
 NCF  plan-1  C16  0.020
 NCF  plan-1  C17  0.020
 NCF  plan-1  S19  0.020
 NCF  plan-1  H15  0.020
 NCF  plan-1  H16  0.020
 NCF  plan-1  H17  0.020
 NCF  plan-2  C7   0.020
 NCF  plan-2  N10  0.020
 NCF  plan-2  C11  0.020
 NCF  plan-2  O12  0.020
 NCF  plan-2  C13  0.020
 NCF  plan-2  H10  0.020
 NCF  plan-3  C4   0.020
 NCF  plan-3  C4'  0.020
 NCF  plan-3  O4A  0.020
 NCF  plan-3  O4B  0.020
 NCF  plan-4  C7   0.020
 NCF  plan-4  C8   0.020
 NCF  plan-4  O9   0.020
 NCF  plan-4  H8   0.020

