# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:13:28 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  39  20  .  2021-08-11  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_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   0.197  -1.4643   0.8824   1.4956
 IM2  C2    C  CR5   0  -0.144   0.0338  -0.8745  -0.4176
 IM2  C6    C  CH1   0  -0.379  -2.1748   1.3371   0.2443
 IM2  C5    C  CR15  0  -0.143  -1.8557   0.4255  -0.9667
 IM2  C3    C  CR5   0   0.161  -1.0915  -1.5927  -0.2191
 IM2  O7    O  O     0  -0.381  -0.5099   1.4534   1.9696
 IM2  C61   C  CH1   0   0.045  -3.6738   1.5319   0.5245
 IM2  O62   O  OH1   0  -0.668  -4.2190   0.2830   0.9101
 IM2  C62   C  CH3   0  -0.703  -4.4180   2.1352  -0.6567
 IM2  N4    N  NR15  0  -0.648  -2.2235  -0.9780  -0.7815
 IM2  C31   C  C     0   0.486  -1.1273  -2.8913   0.4395
 IM2  O31   O  O     0  -0.444  -0.1440  -3.4263   0.9039
 IM2  O32   O  OH1   0  -0.601  -2.3474  -3.4142   0.4826
 IM2  C22   C  CH2   0  -0.575   2.6092   0.1017  -0.5352
 IM2  C23   C  CH2   0  -0.275   4.0775  -0.1705  -0.2105
 IM2  N24   N  NH1   0  -0.590   4.9362   0.8992  -0.6419
 IM2  C25   C  C1    0   0.107   5.0210   2.0790   0.0117
 IM2  N26   N  N     0  -0.656   4.4154   2.3110   1.1098
 IM2  C1    C  CH2   0  -0.460  -0.3391   0.3552  -1.1976
 IM2  H71   H  H     0   0.195  -1.8881  -0.0030   1.9988
 IM2  H61A  H  HCH1  0   0.275  -1.7712   2.3236  -0.0064
 IM2  H51   H  HCR5  0   0.273  -2.3587   0.8396  -1.8407
 IM2  H61   H  HCH1  0   0.229  -3.7482   2.2433   1.3592
 IM2  HO6   H  HOH1  0   0.461  -5.1582   0.3983   1.0877
 IM2  H621  H  HCH3  0   0.236  -4.4593   1.4560  -1.5084
 IM2  H622  H  HCH3  0   0.247  -5.4441   2.3743  -0.3717
 IM2  H623  H  HCH3  0   0.236  -3.9440   3.0624  -0.9791
 IM2  H41   H  HNR5  0   0.372  -3.0813  -1.0945  -0.2580
 IM2  H321  H  HOH1  0   0.489  -2.3282  -4.2673   0.9412
 IM2  H221  H  HCH2  0   0.276   2.4839   0.2341  -1.6100
 IM2  H222  H  HCH2  0   0.281   2.2816   1.0037  -0.0202
 IM2  H231  H  HCH2  0   0.247   4.1971  -0.3157   0.8651
 IM2  H232  H  HCH2  0   0.260   4.4066  -1.0862  -0.7023
 IM2  H241  H  HNH1  0   0.398   5.3374   0.8419  -1.5612
 IM2  H25   H  H     0   0.236   5.6727   2.7900  -0.4985
 IM2  H26   H  H     0   0.332   4.6482   3.2413   1.4336
 IM2  H11   H  HCH2  0   0.272   0.1712   1.2642  -0.8786
 IM2  H12   H  HCH2  0   0.288  -0.1031   0.2063  -2.2563
 IM2  S21   S  S2    0   0.068   1.6413  -1.3274   0.0385

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  1.509  0.020  1.509
 IM2  C7   O7    double  1.209  0.020  1.209
 IM2  C7   H71   single  0.930  0.020  1.080
 IM2  C2   C3    double  1.350  0.020  1.350
 IM2  C2   S21   single  1.731  0.020  1.731
 IM2  C2   C1    single  1.503  0.020  1.503
 IM2  C6   C5    single  1.549  0.020  1.549
 IM2  C6   C61   single  1.537  0.020  1.537
 IM2  C6   H61A  single  0.970  0.020  1.090
 IM2  C5   N4    single  1.463  0.020  1.463
 IM2  C5   C1    single  1.536  0.020  1.536
 IM2  C5   H51   single  0.970  0.020  1.090
 IM2  C3   N4    single  1.406  0.020  1.406
 IM2  C3   C31   single  1.457  0.020  1.457
 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   double  1.212  0.020  1.212
 IM2  C31  O32   single  1.328  0.020  1.328
 IM2  O32  H321  single  0.850  0.020  0.980
 IM2  S21  C22   single  1.819  0.020  1.819
 IM2  C22  C23   single  1.528  0.020  1.528
 IM2  C22  H221  single  0.970  0.020  1.090
 IM2  C22  H222  single  0.970  0.020  1.090
 IM2  C23  N24   single  1.438  0.020  1.438
 IM2  C23  H231  single  0.970  0.020  1.090
 IM2  C23  H232  single  0.970  0.020  1.090
 IM2  N24  C25   single  1.351  0.020  1.351
 IM2  N24  H241  single  0.860  0.020  1.020
 IM2  C25  N26   double  1.275  0.020  1.275
 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    120.23  3.000
 IM2  H71   C7   C6    116.06  3.000
 IM2  O7    C7   C6    123.68  3.000
 IM2  C1    C2   S21   125.53  3.000
 IM2  C1    C2   C3    107.75  3.000
 IM2  S21   C2   C3    126.60  3.000
 IM2  H61A  C6   C61   106.68  3.000
 IM2  H61A  C6   C5    105.98  3.000
 IM2  C61   C6   C5    114.70  3.000
 IM2  H61A  C6   C7    106.73  3.000
 IM2  C61   C6   C7    110.25  3.000
 IM2  C5    C6   C7    111.96  3.000
 IM2  H51   C5   C1    110.64  3.000
 IM2  H51   C5   N4    110.49  3.000
 IM2  C1    C5   N4    102.91  3.000
 IM2  H51   C5   C6    107.95  3.000
 IM2  C1    C5   C6    110.36  3.000
 IM2  N4    C5   C6    114.45  3.000
 IM2  C31   C3   N4    123.44  3.000
 IM2  C31   C3   C2    124.16  3.000
 IM2  N4    C3   C2    112.33  3.000
 IM2  H61   C61  C62   107.45  3.000
 IM2  H61   C61  O62   109.75  3.000
 IM2  C62   C61  O62   111.90  3.000
 IM2  H61   C61  C6    106.64  3.000
 IM2  C62   C61  C6    112.70  3.000
 IM2  O62   C61  C6    108.26  3.000
 IM2  HO6   O62  C61   108.67  3.000
 IM2  H623  C62  H622  107.44  3.000
 IM2  H623  C62  H621  108.38  3.000
 IM2  H622  C62  H621  107.75  3.000
 IM2  H623  C62  C61   110.76  3.000
 IM2  H622  C62  C61   110.13  3.000
 IM2  H621  C62  C61   112.22  3.000
 IM2  H41   N4   C3    115.18  3.000
 IM2  H41   N4   C5    112.91  3.000
 IM2  C3    N4   C5    105.54  3.000
 IM2  O32   C31  O31   124.00  3.000
 IM2  O32   C31  C3    112.85  3.000
 IM2  O31   C31  C3    123.15  3.000
 IM2  H321  O32  C31   110.11  3.000
 IM2  H222  C22  H221  109.33  3.000
 IM2  H222  C22  C23   109.64  3.000
 IM2  H221  C22  C23   109.97  3.000
 IM2  H222  C22  S21   109.97  3.000
 IM2  H221  C22  S21   110.20  3.000
 IM2  C23   C22  S21   107.72  3.000
 IM2  H232  C23  H231  107.44  3.000
 IM2  H232  C23  N24   108.01  3.000
 IM2  H231  C23  N24   109.21  3.000
 IM2  H232  C23  C22   110.10  3.000
 IM2  H231  C23  C22   109.77  3.000
 IM2  N24   C23  C22   112.18  3.000
 IM2  H241  N24  C25   117.86  3.000
 IM2  H241  N24  C23   118.07  3.000
 IM2  C25   N24  C23   122.81  3.000
 IM2  H25   C25  N26   124.59  3.000
 IM2  H25   C25  N24   112.34  3.000
 IM2  N26   C25  N24   123.06  3.000
 IM2  H26   N26  C25   109.47  3.000
 IM2  H12   C1   H11   107.19  3.000
 IM2  H12   C1   C5    111.37  3.000
 IM2  H11   C1   C5    112.34  3.000
 IM2  H12   C1   C2    109.69  3.000
 IM2  H11   C1   C2    114.46  3.000
 IM2  C5    C1   C2    101.80  3.000
 IM2  C22   S21  C2    101.86  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  H321  O32  C31  C3    180.00   0.0  0
 IM2  CONST_02  N26   C25  N24  C23     0.00   0.0  0
 IM2  CONST_03  H25   C25  N24  C23   180.00   0.0  0
 IM2  CONST_04  H26   N26  C25  N24   180.00   0.0  0
 IM2  CONST_05  H241  N24  C25  N26   180.00   0.0  0
 IM2  Var_01    C5    N4   C3   C2    -19.40  30.0  1
 IM2  Var_02    C3    C2   C1   C5     18.62  30.0  1
 IM2  Var_03    C1    C2   C3   N4     -0.32  30.0  1
 IM2  Var_04    O31   C31  C3   C2      2.17  30.0  2
 IM2  Var_05    C23   C22  S21  C2   -179.25  30.0  3
 IM2  Var_06    N24   C23  C22  S21   179.26  30.0  3
 IM2  Var_07    C25   N24  C23  C22    75.34  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-3  H321  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

