# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 17:12:08 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  38  21  .  2021-08-06  2022-09-16
;
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  -0.700  -3.9260  -2.1422   2.0991
 8YF  C61  C  CH1    0   0.052  -3.7704  -1.3364   0.8137
 8YF  O62  O  OH1    0  -0.671  -4.3374  -0.0479   0.9718
 8YF  C6   C  CH1    0  -0.361  -2.2992  -1.2299   0.3856
 8YF  C7   C  C      0   0.426  -2.1126  -0.9811  -1.1252
 8YF  O71  O  O      0  -0.604  -2.9104  -0.1988  -1.6796
 8YF  O72  O  OC    -1  -0.616  -1.1775  -1.5950  -1.6813
 8YF  C5   C  CR15   0  -0.100  -1.4875  -0.2317   1.2349
 8YF  C1   C  CH2    0  -0.451   0.0356  -0.3797   1.0036
 8YF  N4   N  NR15   0  -0.657  -1.7458   1.1786   0.9258
 8YF  C3   C  CR5    0   0.124  -0.7040   1.6239   0.1005
 8YF  C31  C  C      0   0.356  -0.8069   2.9227  -0.6321
 8YF  O31  O  O      0  -0.594   0.2059   3.2611  -1.2826
 8YF  O32  O  OC    -1  -0.609  -1.8823   3.5482  -0.5346
 8YF  C2   C  CR5    0  -0.156   0.3438   0.7897   0.1127
 8YF  S21  S  S2     0   0.000   1.8798   1.0673  -0.6793
 8YF  C22  C  CH2    0  -0.564   2.7725  -0.4672  -0.2798
 8YF  C23  C  CH2    0  -0.273   4.2201  -0.3028  -0.7350
 8YF  N24  N  NH1    0  -0.589   5.0172  -1.4754  -0.4859
 8YF  C25  C  C1     0   0.107   5.5285  -1.7732   0.7274
 8YF  N26  N  N      0  -0.661   5.4228  -1.0043   1.7406
 8YF  H1   H  HCH3   0   0.223  -3.5463  -3.1567   1.9706
 8YF  H2   H  HCH3   0   0.224  -3.3928  -1.6854   2.9349
 8YF  H3   H  HCH3   0   0.228  -4.9784  -2.2226   2.3833
 8YF  H4   H  HCH1   0   0.194  -4.3061  -1.8823   0.0230
 8YF  H5   H  HOH1   0   0.445  -5.2397  -0.1570   1.2870
 8YF  H6   H  HCH1   0   0.213  -1.8663  -2.2118   0.6076
 8YF  H8   H  HCR5   0   0.217  -1.7153  -0.4271   2.2874
 8YF  H9   H  HCH2   0   0.234   0.5894  -0.3087   1.9469
 8YF  H10  H  HCH2   0   0.244   0.2885  -1.3430   0.5593
 8YF  H11  H  HNR5   0   0.353  -2.6587   1.3337   0.5237
 8YF  H13  H  HCH2   0   0.263   2.7505  -0.6556   0.7933
 8YF  H14  H  HCH2   0   0.256   2.3132  -1.3157  -0.7892
 8YF  H15  H  HCH2   0   0.251   4.2572  -0.0900  -1.8045
 8YF  H16  H  HCH2   0   0.240   4.6710   0.5470  -0.2198
 8YF  H17  H  H      0   0.232   6.0528  -2.7305   0.7321
 8YF  H18  H  H      0   0.330   5.9176  -1.4119   2.5237
 8YF  H20  H  HNH1   0   0.396   5.0416  -2.1892  -1.1922

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  1.276  0.020  1.276
 8YF  C25  N24  single  1.350  0.020  1.350
 8YF  N24  C23  single  1.440  0.020  1.440
 8YF  C23  C22  single  1.526  0.020  1.526
 8YF  C22  S21  single  1.820  0.020  1.820
 8YF  O31  C31  deloc   1.250  0.020  1.250
 8YF  O32  C31  deloc   1.248  0.020  1.248
 8YF  S21  C2   single  1.750  0.020  1.750
 8YF  C31  C3   single  1.495  0.020  1.495
 8YF  C3   C2   double  1.339  0.020  1.339
 8YF  C3   N4   single  1.402  0.020  1.402
 8YF  C2   C1   single  1.502  0.020  1.502
 8YF  N4   C5   single  1.467  0.020  1.467
 8YF  C1   C5   single  1.548  0.020  1.548
 8YF  C5   C6   single  1.542  0.020  1.542
 8YF  O71  C7   deloc   1.247  0.020  1.247
 8YF  C7   C6   single  1.542  0.020  1.542
 8YF  C7   O72  deloc   1.249  0.020  1.249
 8YF  C6   C61  single  1.536  0.020  1.536
 8YF  C61  C62  single  1.525  0.020  1.525
 8YF  C61  O62  single  1.417  0.020  1.417
 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  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  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   107.58  3.000
 8YF  H3   C62  H1   107.29  3.000
 8YF  H2   C62  H1   108.02  3.000
 8YF  H3   C62  C61  110.87  3.000
 8YF  H2   C62  C61  111.99  3.000
 8YF  H1   C62  C61  110.89  3.000
 8YF  H4   C61  C6   107.49  3.000
 8YF  H4   C61  O62  109.67  3.000
 8YF  C6   C61  O62  110.58  3.000
 8YF  H4   C61  C62  107.09  3.000
 8YF  O62  C61  C62  110.22  3.000
 8YF  C6   C61  C62  111.67  3.000
 8YF  H5   O62  C61  107.99  3.000
 8YF  H6   C6   C5   105.11  3.000
 8YF  H6   C6   C7   107.17  3.000
 8YF  C5   C6   C7   111.81  3.000
 8YF  H6   C6   C61  105.06  3.000
 8YF  C7   C6   C61  113.58  3.000
 8YF  C5   C6   C61  113.31  3.000
 8YF  O72  C7   O71  126.10  3.000
 8YF  O72  C7   C6   116.57  3.000
 8YF  O71  C7   C6   117.33  3.000
 8YF  H8   C5   N4   109.73  3.000
 8YF  H8   C5   C1   109.36  3.000
 8YF  N4   C5   C1   103.52  3.000
 8YF  H8   C5   C6   107.73  3.000
 8YF  C1   C5   C6   111.96  3.000
 8YF  N4   C5   C6   114.44  3.000
 8YF  H10  C1   H9   106.90  3.000
 8YF  H10  C1   C2   113.48  3.000
 8YF  H9   C1   C2   110.88  3.000
 8YF  H10  C1   C5   111.93  3.000
 8YF  H9   C1   C5   111.25  3.000
 8YF  C2   C1   C5   102.48  3.000
 8YF  H11  N4   C3   112.88  3.000
 8YF  H11  N4   C5   113.01  3.000
 8YF  C3   N4   C5   107.37  3.000
 8YF  C2   C3   C31  126.84  3.000
 8YF  C2   C3   N4   112.22  3.000
 8YF  C31  C3   N4   120.89  3.000
 8YF  O32  C31  O31  127.09  3.000
 8YF  O32  C31  C3   117.17  3.000
 8YF  O31  C31  C3   115.74  3.000
 8YF  S21  C2   C3   125.70  3.000
 8YF  C3   C2   C1   109.25  3.000
 8YF  S21  C2   C1   124.89  3.000
 8YF  C22  S21  C2   101.38  3.000
 8YF  H14  C22  H13  108.47  3.000
 8YF  H14  C22  C23  110.11  3.000
 8YF  H13  C22  C23  109.35  3.000
 8YF  H14  C22  S21  110.29  3.000
 8YF  H13  C22  S21  110.61  3.000
 8YF  C23  C22  S21  108.00  3.000
 8YF  H16  C23  H15  107.27  3.000
 8YF  H16  C23  N24  108.90  3.000
 8YF  H15  C23  N24  108.03  3.000
 8YF  H16  C23  C22  109.57  3.000
 8YF  H15  C23  C22  110.21  3.000
 8YF  N24  C23  C22  112.69  3.000
 8YF  H20  N24  C25  117.78  3.000
 8YF  H20  N24  C23  118.08  3.000
 8YF  C25  N24  C23  123.02  3.000
 8YF  H17  C25  N26  124.39  3.000
 8YF  H17  C25  N24  112.29  3.000
 8YF  N26  C25  N24  123.31  3.000
 8YF  H18  N26  C25  109.34  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
 8YF  CONST_01  N26  C25  N24  C23     0.00   0.0  0
 8YF  CONST_02  H17  C25  N24  C23   180.00   0.0  0
 8YF  CONST_03  H18  N26  C25  N24   180.00   0.0  0
 8YF  CONST_04  H20  N24  C25  N26   180.00   0.0  0
 8YF  Var_01    C2   C3   N4   C5    -15.45  30.0  1
 8YF  Var_02    N4   C3   C2   C1      1.08  30.0  1
 8YF  Var_03    O31  C31  C3   N4    176.26  30.0  2
 8YF  Var_04    C23  C22  S21  C2   -172.01  30.0  1
 8YF  Var_05    N24  C23  C22  S21  -179.01  30.0  1
 8YF  Var_06    C25  N24  C23  C22   -79.36  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-4  C3   0.020
 8YF  plan-4  C31  0.020
 8YF  plan-4  O31  0.020
 8YF  plan-4  O32  0.020

