# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 04:11:53 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  35  21  .  2021-08-15  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_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   0.002  -3.3635   1.7040  -0.8181
 NCF  C2    C  CH2   0  -0.582  -4.7278   1.0543   0.1792
 NCF  C3    C  CH2   0  -0.483  -4.7593  -0.4584   0.1028
 NCF  C4    C  C     0   0.128  -3.4202  -1.1012   0.3140
 NCF  C4'   C  C     0   0.535  -3.4532  -2.5986   0.5084
 NCF  O4A   O  OH1   0  -0.572  -2.2698  -3.1187   0.7588
 NCF  O4B   O  O     0  -0.418  -4.4760  -3.2300   0.4244
 NCF  N5    N  N     0  -0.326  -2.2828  -0.5558   0.3335
 NCF  C6    C  CH1   0  -0.266  -2.0686   0.8430   0.1270
 NCF  C7    C  CH1   0  -0.134  -0.7314   1.0381  -0.6024
 NCF  C8    C  C1    0   0.156  -0.3993   2.5298  -0.6124
 NCF  O9    O  O     0  -0.367  -0.1523   3.1413   0.3928
 NCF  N10   N  NH1   0  -0.651   0.2883   0.3007   0.0958
 NCF  C11   C  C     0   0.586   1.5782   0.4535  -0.2464
 NCF  O12   O  O     0  -0.477   1.9342   1.3107  -1.0392
 NCF  C13   C  CH2   0  -0.674   2.5339  -0.5157   0.4272
 NCF  C14   C  CR5   0  -0.120   3.9663  -0.1665   0.2271
 NCF  C15   C  CR15  0  -0.232   4.8281   0.3778   1.1316
 NCF  C16   C  CR15  0  -0.185   6.1322   0.5889   0.6036
 NCF  C17   C  CR15  0  -0.471   6.2368   0.2011  -0.6963
 NCF  S19   S  S2    0   0.208   4.7510  -0.4199  -1.2839
 NCF  H2C1  H  HCH2  0   0.290  -4.6143   1.4018   1.2068
 NCF  H2C2  H  HCH2  0   0.308  -5.6488   1.4793  -0.2152
 NCF  H3C1  H  HCH2  0   0.289  -5.4528  -0.8427   0.8546
 NCF  H3C2  H  HCH2  0   0.289  -5.1513  -0.7825  -0.8650
 NCF  H4A   H  HOH1  0   0.490  -2.3487  -4.0794   0.8596
 NCF  H6    H  HCH1  0   0.319  -1.9836   1.3066   1.1168
 NCF  H7    H  HCH1  0   0.291  -0.8329   0.6916  -1.6370
 NCF  H8    H  H     0   0.222  -0.4556   3.0199  -1.5967
 NCF  H10   H  HNH1  0   0.411  -0.0087  -0.5090   0.6228
 NCF  H131  H  HCH2  0   0.305   2.3188  -0.5454   1.4977
 NCF  H132  H  HCH2  0   0.308   2.3152  -1.5194   0.0494
 NCF  H15   H  HCR5  0   0.263   4.5413   0.6175   2.1465
 NCF  H16   H  HCR5  0   0.265   6.9530   1.0068   1.1685
 NCF  H17   H  HCR5  0   0.293   7.1028   0.2449  -1.3384

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    1.810  0.020  1.810
 NCF  S1   C6    single    1.820  0.020  1.820
 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    1.500  0.020  1.500
 NCF  C3   H3C1  single    0.970  0.020  1.090
 NCF  C3   H3C2  single    0.970  0.020  1.090
 NCF  C4   C4'   single    1.510  0.020  1.510
 NCF  C4   N5    double    1.261  0.020  1.261
 NCF  C4'  O4A   single    1.317  0.020  1.317
 NCF  C4'  O4B   double    1.205  0.020  1.205
 NCF  O4A  H4A   single    0.850  0.020  0.980
 NCF  N5   C6    single    1.430  0.020  1.430
 NCF  C6   C7    single    1.536  0.020  1.536
 NCF  C6   H6    single    0.970  0.020  1.090
 NCF  C7   C8    single    1.528  0.020  1.528
 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    1.343  0.020  1.343
 NCF  N10  H10   single    0.860  0.020  1.020
 NCF  C11  O12   double    1.221  0.020  1.221
 NCF  C11  C13   single    1.519  0.020  1.519
 NCF  C13  C14   single    1.488  0.020  1.488
 NCF  C13  H131  single    0.970  0.020  1.090
 NCF  C13  H132  single    0.970  0.020  1.090
 NCF  C14  C15   aromatic  1.363  0.020  1.363
 NCF  C14  S19   aromatic  1.721  0.020  1.721
 NCF  C15  C16   aromatic  1.423  0.020  1.423
 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  1.714  0.020  1.714
 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     94.61  3.000
 NCF  H2C2  C2   H2C1  107.76  3.000
 NCF  H2C2  C2   C3    110.73  3.000
 NCF  H2C1  C2   C3    111.58  3.000
 NCF  H2C2  C2   S1    107.34  3.000
 NCF  H2C1  C2   S1    109.04  3.000
 NCF  C3    C2   S1    110.26  3.000
 NCF  H3C2  C3   H3C1  106.10  3.000
 NCF  H3C2  C3   C4    108.52  3.000
 NCF  H3C1  C3   C4    108.60  3.000
 NCF  H3C2  C3   C2    110.37  3.000
 NCF  H3C1  C3   C2    109.25  3.000
 NCF  C4    C3   C2    113.71  3.000
 NCF  N5    C4   C4'   116.51  3.000
 NCF  N5    C4   C3    128.44  3.000
 NCF  C4'   C4   C3    115.04  3.000
 NCF  O4B   C4'  O4A   124.70  3.000
 NCF  O4B   C4'  C4    121.95  3.000
 NCF  O4A   C4'  C4    113.35  3.000
 NCF  H4A   O4A  C4'   109.77  3.000
 NCF  C6    N5   C4    123.76  3.000
 NCF  H6    C6   C7    107.92  3.000
 NCF  H6    C6   N5    107.15  3.000
 NCF  C7    C6   N5    108.86  3.000
 NCF  H6    C6   S1    108.91  3.000
 NCF  C7    C6   S1    108.23  3.000
 NCF  N5    C6   S1    115.54  3.000
 NCF  H7    C7   N10   111.20  3.000
 NCF  H7    C7   C8    108.82  3.000
 NCF  N10   C7   C8    110.45  3.000
 NCF  H7    C7   C6    109.13  3.000
 NCF  N10   C7   C6    108.75  3.000
 NCF  C8    C7   C6    108.44  3.000
 NCF  H8    C8   O9    122.11  3.000
 NCF  H8    C8   C7    115.42  3.000
 NCF  O9    C8   C7    122.39  3.000
 NCF  H10   N10  C11   120.41  3.000
 NCF  H10   N10  C7    117.08  3.000
 NCF  C11   N10  C7    119.90  3.000
 NCF  C13   C11  O12   123.55  3.000
 NCF  C13   C11  N10   114.75  3.000
 NCF  O12   C11  N10   121.70  3.000
 NCF  H132  C13  H131  105.90  3.000
 NCF  H132  C13  C14   111.17  3.000
 NCF  H131  C13  C14   109.13  3.000
 NCF  H132  C13  C11   107.84  3.000
 NCF  H131  C13  C11   109.16  3.000
 NCF  C14   C13  C11   113.35  3.000
 NCF  S19   C14  C15   110.68  3.000
 NCF  S19   C14  C13   121.49  3.000
 NCF  C15   C14  C13   127.82  3.000
 NCF  H15   C15  C16   123.95  3.000
 NCF  H15   C15  C14   122.94  3.000
 NCF  C16   C15  C14   113.11  3.000
 NCF  H16   C16  C17   123.46  3.000
 NCF  H16   C16  C15   124.03  3.000
 NCF  C17   C16  C15   112.51  3.000
 NCF  H17   C17  S19   120.43  3.000
 NCF  H17   C17  C16   128.22  3.000
 NCF  S19   C17  C16   111.35  3.000
 NCF  C17   S19  C14    92.35  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  H4A  O4A  C4'  C4    180.00   0.0  0
 NCF  CONST_12  O12  C11  N10  C7      0.00   0.0  0
 NCF  CONST_13  C13  C11  N10  C7    180.00   0.0  0
 NCF  CONST_14  H10  N10  C11  O12   180.00   0.0  0
 NCF  Var_01    C4   C3   C2   S1     47.48  30.0  1
 NCF  Var_02    N5   C4   C3   C2    -12.11  30.0  1
 NCF  Var_03    O4A  C4'  C4   C3   -176.72  30.0  2
 NCF  Var_04    C15  C14  C13  C11   105.55  30.0  2
 NCF  Var_05    C14  C13  C11  N10  -169.39  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-3  H4A  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

