# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:39:59 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1~{H}-pyrrole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H]([C@H]1CC(=C(N1)C(O)=O)SCCNC=N)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
 8YF  8YF  '(2~{R})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-4-(2-methanimidamidoethylsulfanyl)-2,3-dihydro-1~{H}-pyrrole-5-carboxylic acid'  ligand  40  21  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8YF
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
 8YF  C62  C  CH3   0  -0.698  -3.9023  -2.6007   1.1912
 8YF  C61  C  CH1   0   0.048  -3.5538  -1.5348   0.1609
 8YF  O62  O  OH1   0  -0.667  -4.2779  -0.3433   0.3834
 8YF  C6   C  CH1   0  -0.369  -2.0504  -1.2164   0.1758
 8YF  C7   C  C     0   0.552  -1.5987  -0.6114  -1.1334
 8YF  O71  O  O     0  -0.434  -2.2348   0.1829  -1.7810
 8YF  O72  O  OH1   0  -0.589  -0.4100  -1.0696  -1.5182
 8YF  C5   C  CR15  0  -0.133  -1.6096  -0.3421   1.3814
 8YF  C1   C  CH2   0  -0.454  -0.0779  -0.2978   1.5149
 8YF  N4   N  NR15  0  -0.649  -1.9611   1.0707   1.2661
 8YF  C3   C  CR5   0   0.170  -0.8559   1.6951   0.6634
 8YF  C31  C  C     0   0.482  -0.9191   3.0122   0.0483
 8YF  O31  O  O     0  -0.447   0.0440   3.5662  -0.4369
 8YF  O32  O  OH1   0  -0.602  -2.1404   3.5354   0.0691
 8YF  C2   C  CR5   0  -0.143   0.2670   0.9573   0.7621
 8YF  S21  S  S2    0   0.060   1.8513   1.4109   0.2279
 8YF  C22  C  CH2   0  -0.575   2.8083  -0.0915   0.5929
 8YF  C23  C  CH2   0  -0.276   4.2580   0.1653   0.1847
 8YF  N24  N  NH1   0  -0.590   5.1096  -0.9583   0.4693
 8YF  C25  C  C1    0   0.107   5.1045  -2.0892  -0.2706
 8YF  N26  N  N     0  -0.655   4.4210  -2.2211  -1.3393
 8YF  H1   H  HCH3  0   0.234  -3.3804  -3.5323   0.9707
 8YF  H2   H  HCH3  0   0.232  -3.6453  -2.2982   2.2074
 8YF  H3   H  HCH3  0   0.242  -4.9726  -2.8151   1.1693
 8YF  H4   H  HCH1  0   0.226  -3.7989  -1.9463  -0.8283
 8YF  H5   H  HOH1  0   0.458  -5.2174  -0.5517   0.3869
 8YF  H6   H  HCH1  0   0.287  -1.5319  -2.1715   0.2976
 8YF  H7   H  HOH1  0   0.476  -0.1355  -0.6276  -2.3358
 8YF  H8   H  HCR5  0   0.266  -2.0564  -0.7734   2.2776
 8YF  H9   H  HCH2  0   0.282   0.2196  -0.1870   2.5631
 8YF  H10  H  HCH2  0   0.272   0.4040  -1.2002   1.1414
 8YF  H11  H  HNR5  0   0.374  -2.8505   1.2292   0.8140
 8YF  H12  H  HOH1  0   0.488  -2.1362   4.4036  -0.3602
 8YF  H13  H  HCH2  0   0.274   2.7577  -0.3199   1.6575
 8YF  H14  H  HCH2  0   0.280   2.4086  -0.9308   0.0250
 8YF  H15  H  HCH2  0   0.247   4.3079   0.3930  -0.8819
 8YF  H16  H  HCH2  0   0.259   4.6507   1.0293   0.7214
 8YF  H17  H  H     0   0.235   5.7596  -2.8575   0.1432
 8YF  H18  H  H     0   0.332   4.5975  -3.1336  -1.7399
 8YF  H20  H  HNH1  0   0.398   5.5649  -0.9881   1.3645

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
 8YF  N26  C25  double  1.275  0.020  1.275
 8YF  C25  N24  single  1.351  0.020  1.351
 8YF  N24  C23  single  1.438  0.020  1.438
 8YF  C23  C22  single  1.528  0.020  1.528
 8YF  C22  S21  single  1.818  0.020  1.818
 8YF  O31  C31  double  1.212  0.020  1.212
 8YF  O32  C31  single  1.329  0.020  1.329
 8YF  S21  C2   single  1.732  0.020  1.732
 8YF  C31  C3   single  1.455  0.020  1.455
 8YF  C3   C2   double  1.347  0.020  1.347
 8YF  C3   N4   single  1.405  0.020  1.405
 8YF  C2   C1   single  1.504  0.020  1.504
 8YF  N4   C5   single  1.460  0.020  1.460
 8YF  C1   C5   single  1.538  0.020  1.538
 8YF  C5   C6   single  1.553  0.020  1.553
 8YF  O71  C7   double  1.206  0.020  1.206
 8YF  C7   C6   single  1.511  0.020  1.511
 8YF  C7   O72  single  1.331  0.020  1.331
 8YF  C6   C61  single  1.537  0.020  1.537
 8YF  C61  C62  single  1.523  0.020  1.523
 8YF  C61  O62  single  1.412  0.020  1.412
 8YF  C62  H1   single  0.970  0.020  1.090
 8YF  C62  H2   single  0.970  0.020  1.090
 8YF  C62  H3   single  0.970  0.020  1.090
 8YF  C61  H4   single  0.970  0.020  1.090
 8YF  O62  H5   single  0.850  0.020  0.980
 8YF  C6   H6   single  0.970  0.020  1.090
 8YF  O72  H7   single  0.850  0.020  0.980
 8YF  C5   H8   single  0.970  0.020  1.090
 8YF  C1   H9   single  0.970  0.020  1.090
 8YF  C1   H10  single  0.970  0.020  1.090
 8YF  N4   H11  single  0.890  0.020  1.040
 8YF  O32  H12  single  0.850  0.020  0.980
 8YF  C22  H13  single  0.970  0.020  1.090
 8YF  C22  H14  single  0.970  0.020  1.090
 8YF  C23  H15  single  0.970  0.020  1.090
 8YF  C23  H16  single  0.970  0.020  1.090
 8YF  C25  H17  single  0.930  0.020  1.080
 8YF  N26  H18  single  0.890  0.020  1.040
 8YF  N24  H20  single  0.860  0.020  1.020

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
 8YF  H3   C62  H2   107.71  3.000
 8YF  H3   C62  H1   107.30  3.000
 8YF  H2   C62  H1   108.21  3.000
 8YF  H3   C62  C61  110.38  3.000
 8YF  H2   C62  C61  112.47  3.000
 8YF  H1   C62  C61  110.59  3.000
 8YF  H4   C61  C6   107.72  3.000
 8YF  H4   C61  O62  110.09  3.000
 8YF  C6   C61  O62  108.98  3.000
 8YF  H4   C61  C62  107.21  3.000
 8YF  O62  C61  C62  111.51  3.000
 8YF  C6   C61  C62  111.24  3.000
 8YF  H5   O62  C61  108.57  3.000
 8YF  H6   C6   C5   105.70  3.000
 8YF  H6   C6   C7   107.72  3.000
 8YF  C5   C6   C7   111.24  3.000
 8YF  H6   C6   C61  106.49  3.000
 8YF  C7   C6   C61  111.53  3.000
 8YF  C5   C6   C61  113.69  3.000
 8YF  O72  C7   O71  122.86  3.000
 8YF  O72  C7   C6   112.31  3.000
 8YF  O71  C7   C6   124.82  3.000
 8YF  H7   O72  C7   109.87  3.000
 8YF  H8   C5   N4   110.42  3.000
 8YF  H8   C5   C1   110.37  3.000
 8YF  N4   C5   C1   102.63  3.000
 8YF  H8   C5   C6   107.40  3.000
 8YF  C1   C5   C6   111.48  3.000
 8YF  N4   C5   C6   114.52  3.000
 8YF  H10  C1   H9   106.96  3.000
 8YF  H10  C1   C2   114.74  3.000
 8YF  H9   C1   C2   109.41  3.000
 8YF  H10  C1   C5   112.77  3.000
 8YF  H9   C1   C5   110.88  3.000
 8YF  C2   C1   C5   102.06  3.000
 8YF  H11  N4   C3   115.51  3.000
 8YF  H11  N4   C5   113.52  3.000
 8YF  C3   N4   C5   105.93  3.000
 8YF  C2   C3   C31  124.26  3.000
 8YF  C2   C3   N4   112.38  3.000
 8YF  C31  C3   N4   123.32  3.000
 8YF  O32  C31  O31  123.81  3.000
 8YF  O32  C31  C3   112.94  3.000
 8YF  O31  C31  C3   123.25  3.000
 8YF  H12  O32  C31  110.00  3.000
 8YF  S21  C2   C3   126.60  3.000
 8YF  C3   C2   C1   107.62  3.000
 8YF  S21  C2   C1   125.64  3.000
 8YF  C22  S21  C2   101.72  3.000
 8YF  H14  C22  H13  109.31  3.000
 8YF  H14  C22  C23  109.78  3.000
 8YF  H13  C22  C23  109.89  3.000
 8YF  H14  C22  S21  109.81  3.000
 8YF  H13  C22  S21  110.17  3.000
 8YF  C23  C22  S21  107.87  3.000
 8YF  H16  C23  H15  107.41  3.000
 8YF  H16  C23  N24  107.97  3.000
 8YF  H15  C23  N24  109.22  3.000
 8YF  H16  C23  C22  110.09  3.000
 8YF  H15  C23  C22  109.84  3.000
 8YF  N24  C23  C22  112.18  3.000
 8YF  H20  N24  C25  117.69  3.000
 8YF  H20  N24  C23  117.89  3.000
 8YF  C25  N24  C23  122.90  3.000
 8YF  H17  C25  N26  124.51  3.000
 8YF  H17  C25  N24  112.30  3.000
 8YF  N26  C25  N24  123.18  3.000
 8YF  H18  N26  C25  109.36  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
 8YF  CONST_01  H12  O32  C31  C3    180.00   0.0  0
 8YF  CONST_02  N26  C25  N24  C23     0.00   0.0  0
 8YF  CONST_03  H7   O72  C7   C6    180.00   0.0  0
 8YF  CONST_04  H17  C25  N24  C23   180.00   0.0  0
 8YF  CONST_05  H18  N26  C25  N24   180.00   0.0  0
 8YF  CONST_06  H20  N24  C25  N26   180.00   0.0  0
 8YF  Var_01    C2   C3   N4   C5    -19.01  30.0  1
 8YF  Var_02    N4   C3   C2   C1     -0.52  30.0  1
 8YF  Var_03    O31  C31  C3   N4    177.79  30.0  3
 8YF  Var_04    C23  C22  S21  C2   -179.30  30.0  1
 8YF  Var_05    N24  C23  C22  S21   178.39  30.0  1
 8YF  Var_06    C25  N24  C23  C22    74.86  30.0  1

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
 8YF  chir_01  C61  C6   C62  O62  negativ
 8YF  chir_02  C6   C61  C7   C5   negativ
 8YF  chir_03  C5   N4   C1   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
 8YF  plan-1  C23  0.020
 8YF  plan-1  N24  0.020
 8YF  plan-1  C25  0.020
 8YF  plan-1  N26  0.020
 8YF  plan-1  H17  0.020
 8YF  plan-1  H18  0.020
 8YF  plan-1  H20  0.020
 8YF  plan-2  C5   0.020
 8YF  plan-2  N4   0.020
 8YF  plan-2  C3   0.020
 8YF  plan-2  H11  0.020
 8YF  plan-3  C6   0.020
 8YF  plan-3  C7   0.020
 8YF  plan-3  O71  0.020
 8YF  plan-3  O72  0.020
 8YF  plan-3  H7   0.020
 8YF  plan-4  C3   0.020
 8YF  plan-4  C31  0.020
 8YF  plan-4  O31  0.020
 8YF  plan-4  O32  0.020
 8YF  plan-4  H12  0.020

