# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 10:31:05 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (5R)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](C=O)[C@H]1CC(=C(N1)C(O)=O)SCCNC=N
#
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
 IM2  IM2  '(5R)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acid'  ligand  38  20  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IM2
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
 IM2  C7    C  C1     0   0.209  -1.3245   1.7041   0.4840
 IM2  C2    C  CR5    0  -0.247  -0.0919  -0.5487  -1.2241
 IM2  C6    C  CH1    0  -0.379  -2.4995   1.4948  -0.4354
 IM2  C5    C  CR15   0  -0.130  -2.3268   0.2308  -1.3089
 IM2  C3    C  CR5    0   0.218  -0.8476  -1.2650  -0.3634
 IM2  O7    O  O      0  -0.391  -0.5911   2.6641   0.4229
 IM2  C61   C  CH1    0   0.047  -3.8113   1.5498   0.3695
 IM2  O62   O  OH1    0  -0.667  -3.7628   0.5522   1.3726
 IM2  C62   C  CH3    0  -0.703  -5.0462   1.4086  -0.5068
 IM2  N4    N  NR15   0  -0.632  -2.1906  -1.0016  -0.5437
 IM2  C31   C  C      0   0.355  -0.4495  -2.2606   0.7102
 IM2  O31   O  O      0  -0.563   0.7593  -2.3607   0.9737
 IM2  O32   O  OC    -1  -0.598  -1.3984  -2.8737   1.2371
 IM2  C22   C  CH2    0  -0.575   2.3010   0.3374  -0.1358
 IM2  C23   C  CH2    0  -0.231   3.8184   0.3058  -0.2030
 IM2  N24   N  NH1    0  -0.598   4.3725   1.0891   0.8740
 IM2  C25   C  C1     0   0.108   5.6977   1.2229   1.0687
 IM2  N26   N  N      0  -0.669   6.5678   0.6437   0.3344
 IM2  C1    C  CH2    0  -0.446  -1.0078   0.2708  -2.0999
 IM2  H71   H  H      0   0.194  -1.1776   0.9418   1.2656
 IM2  H61A  H  HCH1   0   0.266  -2.5250   2.3468  -1.1227
 IM2  H51   H  HCR5   0   0.261  -3.1834   0.1754  -1.9823
 IM2  H61   H  HCH1   0   0.225  -3.8487   2.5445   0.8363
 IM2  HO6   H  HOH1   0   0.458  -4.5850   0.5815   1.8726
 IM2  H621  H  HCH3   0   0.235  -5.1182   0.4180  -0.9569
 IM2  H622  H  HCH3   0   0.245  -5.9493   1.5700   0.0853
 IM2  H623  H  HCH3   0   0.235  -5.0436   2.1478  -1.3086
 IM2  H41   H  HNR5   0   0.367  -2.7840  -1.1174   0.2642
 IM2  H221  H  HCH2   0   0.260   1.9356   1.3633  -0.2022
 IM2  H222  H  HCH2   0   0.272   1.9433  -0.1090   0.7910
 IM2  H231  H  HCH2   0   0.231   4.1711  -0.7276  -0.1344
 IM2  H232  H  HCH2   0   0.227   4.1619   0.6909  -1.1694
 IM2  H241  H  HNH1   0   0.398   3.7503   1.6150   1.4622
 IM2  H25   H  H      0   0.232   5.9335   1.8696   1.9158
 IM2  H26   H  H      0   0.329   7.4952   0.8773   0.6659
 IM2  H11   H  HCH2   0   0.242  -0.6525   1.2894  -2.2743
 IM2  H12   H  HCH2   0   0.250  -1.1310  -0.1912  -3.0861
 IM2  S21   S  S2     0  -0.036   1.6273  -0.6382  -1.5145

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
 IM2  C7   C6    single  1.507  0.020  1.507
 IM2  C7   O7    double  1.210  0.020  1.210
 IM2  C7   H71   single  0.930  0.020  1.080
 IM2  C2   C3    double  1.351  0.020  1.351
 IM2  C2   S21   single  1.746  0.020  1.746
 IM2  C2   C1    single  1.509  0.020  1.509
 IM2  C6   C5    single  1.546  0.020  1.546
 IM2  C6   C61   single  1.540  0.020  1.540
 IM2  C6   H61A  single  0.970  0.020  1.090
 IM2  C5   N4    single  1.457  0.020  1.457
 IM2  C5   C1    single  1.539  0.020  1.539
 IM2  C5   H51   single  0.970  0.020  1.090
 IM2  C3   N4    single  1.380  0.020  1.380
 IM2  C3   C31   single  1.517  0.020  1.517
 IM2  C61  O62   single  1.416  0.020  1.416
 IM2  C61  C62   single  1.521  0.020  1.521
 IM2  C61  H61   single  0.970  0.020  1.090
 IM2  O62  HO6   single  0.850  0.020  0.980
 IM2  C62  H621  single  0.970  0.020  1.090
 IM2  C62  H622  single  0.970  0.020  1.090
 IM2  C62  H623  single  0.970  0.020  1.090
 IM2  N4   H41   single  0.890  0.020  1.040
 IM2  C31  O31   deloc   1.241  0.020  1.241
 IM2  C31  O32   deloc   1.247  0.020  1.247
 IM2  S21  C22   single  1.818  0.020  1.818
 IM2  C22  C23   single  1.519  0.020  1.519
 IM2  C22  H221  single  0.970  0.020  1.090
 IM2  C22  H222  single  0.970  0.020  1.090
 IM2  C23  N24   single  1.442  0.020  1.442
 IM2  C23  H231  single  0.970  0.020  1.090
 IM2  C23  H232  single  0.970  0.020  1.090
 IM2  N24  C25   single  1.346  0.020  1.346
 IM2  N24  H241  single  0.860  0.020  1.020
 IM2  C25  N26   double  1.277  0.020  1.277
 IM2  C25  H25   single  0.930  0.020  1.080
 IM2  N26  H26   single  0.890  0.020  1.040
 IM2  C1   H11   single  0.970  0.020  1.090
 IM2  C1   H12   single  0.970  0.020  1.090

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
 IM2  H71   C7   O7    120.27  3.000
 IM2  H71   C7   C6    116.16  3.000
 IM2  O7    C7   C6    123.53  3.000
 IM2  C1    C2   S21   121.94  3.000
 IM2  C1    C2   C3    108.55  3.000
 IM2  S21   C2   C3    129.02  3.000
 IM2  H61A  C6   C61   106.28  3.000
 IM2  H61A  C6   C5    106.51  3.000
 IM2  C61   C6   C5    114.81  3.000
 IM2  H61A  C6   C7    107.05  3.000
 IM2  C61   C6   C7    109.90  3.000
 IM2  C5    C6   C7    111.79  3.000
 IM2  H51   C5   C1    110.92  3.000
 IM2  H51   C5   N4    110.77  3.000
 IM2  C1    C5   N4    102.23  3.000
 IM2  H51   C5   C6    107.61  3.000
 IM2  C1    C5   C6    111.41  3.000
 IM2  N4    C5   C6    113.91  3.000
 IM2  C31   C3   N4    118.22  3.000
 IM2  C31   C3   C2    130.69  3.000
 IM2  N4    C3   C2    111.09  3.000
 IM2  H61   C61  C62   107.52  3.000
 IM2  H61   C61  O62   109.75  3.000
 IM2  C62   C61  O62   111.76  3.000
 IM2  H61   C61  C6    106.45  3.000
 IM2  C62   C61  C6    112.78  3.000
 IM2  O62   C61  C6    108.42  3.000
 IM2  HO6   O62  C61   108.50  3.000
 IM2  H623  C62  H622  107.49  3.000
 IM2  H623  C62  H621  108.20  3.000
 IM2  H622  C62  H621  107.67  3.000
 IM2  H623  C62  C61   111.02  3.000
 IM2  H622  C62  C61   110.21  3.000
 IM2  H621  C62  C61   112.07  3.000
 IM2  H41   N4   C3    116.46  3.000
 IM2  H41   N4   C5    117.56  3.000
 IM2  C3    N4   C5    108.72  3.000
 IM2  O32   C31  O31   127.73  3.000
 IM2  O32   C31  C3    114.97  3.000
 IM2  O31   C31  C3    117.30  3.000
 IM2  H222  C22  H221  109.10  3.000
 IM2  H222  C22  C23   110.92  3.000
 IM2  H221  C22  C23   110.57  3.000
 IM2  H222  C22  S21   107.68  3.000
 IM2  H221  C22  S21   109.53  3.000
 IM2  C23   C22  S21   108.99  3.000
 IM2  H232  C23  H231  106.64  3.000
 IM2  H232  C23  N24   110.32  3.000
 IM2  H231  C23  N24   110.01  3.000
 IM2  H232  C23  C22   110.18  3.000
 IM2  H231  C23  C22   109.80  3.000
 IM2  N24   C23  C22   109.84  3.000
 IM2  H241  N24  C25   118.23  3.000
 IM2  H241  N24  C23   118.91  3.000
 IM2  C25   N24  C23   122.70  3.000
 IM2  H25   C25  N26   124.58  3.000
 IM2  H25   C25  N24   112.57  3.000
 IM2  N26   C25  N24   122.85  3.000
 IM2  H26   N26  C25   109.34  3.000
 IM2  H12   C1   H11   106.61  3.000
 IM2  H12   C1   C5    110.81  3.000
 IM2  H11   C1   C5    112.64  3.000
 IM2  H12   C1   C2    111.20  3.000
 IM2  H11   C1   C2    113.66  3.000
 IM2  C5    C1   C2    101.99  3.000
 IM2  C22   S21  C2    102.19  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
 IM2  CONST_01  N26   C25  N24  C23    0.00   0.0  0
 IM2  CONST_02  H25   C25  N24  C23  180.00   0.0  0
 IM2  CONST_03  H26   N26  C25  N24  180.00   0.0  0
 IM2  CONST_04  H241  N24  C25  N26  180.00   0.0  0
 IM2  Var_01    C5    N4   C3   C2   -16.72  30.0  1
 IM2  Var_02    C3    C2   C1   C5    16.96  30.0  1
 IM2  Var_03    C1    C2   C3   N4    -1.10  30.0  1
 IM2  Var_04    O31   C31  C3   C2     8.85  30.0  2
 IM2  Var_05    C23   C22  S21  C2   177.34  30.0  3
 IM2  Var_06    N24   C23  C22  S21  179.28  30.0  3
 IM2  Var_07    C25   N24  C23  C22  179.12  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
 IM2  chir_01  C6   C7   C5  C61  negativ
 IM2  chir_02  C5   N4   C1  C6   positiv
 IM2  chir_03  C61  O62  C6  C62  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
 IM2  plan-1  C23   0.020
 IM2  plan-1  N24   0.020
 IM2  plan-1  C25   0.020
 IM2  plan-1  N26   0.020
 IM2  plan-1  H241  0.020
 IM2  plan-1  H25   0.020
 IM2  plan-1  H26   0.020
 IM2  plan-2  C5    0.020
 IM2  plan-2  C3    0.020
 IM2  plan-2  N4    0.020
 IM2  plan-2  H41   0.020
 IM2  plan-3  C3    0.020
 IM2  plan-3  C31   0.020
 IM2  plan-3  O31   0.020
 IM2  plan-3  O32   0.020
 IM2  plan-4  C7    0.020
 IM2  plan-4  C6    0.020
 IM2  plan-4  O7    0.020
 IM2  plan-4  H71   0.020

