# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 00:39:11 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (1~{R},2~{R})-2-phenyl-~{N}-(1,3-thiazol-2-yl)cyclopropane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1sccn1)[C@@H]2C[C@H]2c3ccccc3
#
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
 3IR  3IR  "(1~{R},2~{R})-2-phenyl-~{N}-(1,3-thiazol-2-yl)cyclopropane-1-carboxamide"  ligand  29  17  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3IR
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
 3IR  C1   C  C     0   0.565  -125.7383  -7.6560  14.3556
 3IR  C2   C  CR5   0   0.285  -123.5090  -7.0018  15.2726
 3IR  C3   C  CR15  0  -0.021  -121.6377  -6.4959  16.2915
 3IR  C4   C  CR15  0  -0.492  -122.1969  -5.2631  16.3240
 3IR  C5   C  CH1   0  -0.445  -126.4662  -6.7148  15.2415
 3IR  C10  C  CR16  0  -0.237  -126.5043  -1.7899  15.0940
 3IR  C11  C  CR16  0  -0.271  -126.7096  -1.6375  16.4578
 3IR  C12  C  CR16  0  -0.234  -127.0497  -2.7457  17.2242
 3IR  C13  C  CR16  0  -0.346  -127.1819  -3.9937  16.6334
 3IR  C6   C  CH2   0  -0.448  -127.9454  -6.5820  15.0957
 3IR  C7   C  CH1   0  -0.353  -127.0813  -5.4767  14.5945
 3IR  C8   C  CR6   0   0.226  -126.9745  -4.1584  15.2642
 3IR  C9   C  CR16  0  -0.319  -126.6349  -3.0403  14.5051
 3IR  N1   N  NH1   0  -0.694  -124.3854  -7.7834  14.5501
 3IR  N2   N  N     0  -0.399  -122.3811  -7.4736  15.6966
 3IR  O1   O  O     0  -0.440  -126.2849  -8.3066  13.4873
 3IR  S1   S  S2    0   0.219  -123.7328  -5.3043  15.5536
 3IR  H2   H  HCR5  0   0.275  -120.6717  -6.7427  16.7081
 3IR  H3   H  HCR5  0   0.307  -121.8165  -4.3587  16.7709
 3IR  H4   H  HCH1  0   0.312  -126.0679  -6.5781  16.2407
 3IR  H9   H  HCR6  0   0.254  -126.2400  -0.9351  14.4848
 3IR  H10  H  HCR6  0   0.253  -126.6068  -0.6646  16.9206
 3IR  H11  H  HCR6  0   0.255  -127.2135  -2.6384  18.2888
 3IR  H12  H  HCR6  0   0.250  -127.4480  -4.8397  17.2566
 3IR  H5   H  HCH2  0   0.274  -128.5090  -6.4212  16.0059
 3IR  H6   H  HCH2  0   0.275  -128.4419  -7.2018  14.3613
 3IR  H7   H  HCH1  0   0.282  -126.9677  -5.4333  13.5164
 3IR  H8   H  HCR6  0   0.251  -126.4683  -3.1512  13.4401
 3IR  H1   H  HNH1  0   0.418  -123.9442  -8.5346  14.0335

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
 3IR  O1   C1   double    1.215  0.020  1.215
 3IR  C1   N1   single    1.373  0.020  1.373
 3IR  C1   C5   single    1.483  0.020  1.483
 3IR  N1   C2   single    1.379  0.020  1.379
 3IR  C7   C5   single    1.526  0.020  1.526
 3IR  C7   C8   single    1.483  0.020  1.483
 3IR  C7   C6   single    1.490  0.020  1.490
 3IR  C9   C8   aromatic  1.393  0.020  1.393
 3IR  C9   C10  aromatic  1.388  0.020  1.388
 3IR  C5   C6   single    1.492  0.020  1.492
 3IR  C8   C13  aromatic  1.395  0.020  1.395
 3IR  C2   S1   aromatic  1.735  0.020  1.735
 3IR  C2   N2   aromatic  1.294  0.020  1.294
 3IR  C10  C11  aromatic  1.388  0.020  1.388
 3IR  S1   C4   aromatic  1.719  0.020  1.719
 3IR  C13  C12  aromatic  1.387  0.020  1.387
 3IR  C11  C12  aromatic  1.390  0.020  1.390
 3IR  N2   C3   aromatic  1.365  0.020  1.365
 3IR  C4   C3   aromatic  1.354  0.020  1.354
 3IR  C3   H2   single    0.930  0.020  1.080
 3IR  C4   H3   single    0.930  0.020  1.080
 3IR  C5   H4   single    0.970  0.020  1.090
 3IR  C10  H9   single    0.930  0.020  1.080
 3IR  C11  H10  single    0.930  0.020  1.080
 3IR  C12  H11  single    0.930  0.020  1.080
 3IR  C13  H12  single    0.930  0.020  1.080
 3IR  C6   H5   single    0.970  0.020  1.090
 3IR  C6   H6   single    0.970  0.020  1.090
 3IR  C7   H7   single    0.970  0.020  1.090
 3IR  C9   H8   single    0.930  0.020  1.080
 3IR  N1   H1   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
 3IR  O1   C1   N1   119.67  3.000
 3IR  N1   C1   C5   117.25  3.000
 3IR  O1   C1   C5   123.08  3.000
 3IR  S1   C2   N2   114.59  3.000
 3IR  N2   C2   N1   121.27  3.000
 3IR  S1   C2   N1   123.88  3.000
 3IR  H2   C3   N2   119.43  3.000
 3IR  H2   C3   C4   124.61  3.000
 3IR  N2   C3   C4   115.96  3.000
 3IR  H3   C4   S1   121.41  3.000
 3IR  H3   C4   C3   128.90  3.000
 3IR  S1   C4   C3   109.66  3.000
 3IR  H4   C5   C7   115.88  3.000
 3IR  H4   C5   C6   116.29  3.000
 3IR  C7   C5   C6    59.13  3.000
 3IR  H4   C5   C1   116.75  3.000
 3IR  C6   C5   C1   118.98  3.000
 3IR  C7   C5   C1   117.34  3.000
 3IR  H9   C10  C9   119.71  3.000
 3IR  H9   C10  C11  120.17  3.000
 3IR  C9   C10  C11  120.13  3.000
 3IR  H10  C11  C12  120.28  3.000
 3IR  H10  C11  C10  120.33  3.000
 3IR  C12  C11  C10  119.38  3.000
 3IR  H11  C12  C13  119.58  3.000
 3IR  H11  C12  C11  120.03  3.000
 3IR  C13  C12  C11  120.39  3.000
 3IR  H12  C13  C8   120.59  3.000
 3IR  H12  C13  C12  118.73  3.000
 3IR  C8   C13  C12  120.68  3.000
 3IR  H6   C6   H5   114.65  3.000
 3IR  H6   C6   C7   117.58  3.000
 3IR  H5   C6   C7   118.33  3.000
 3IR  H6   C6   C5   118.06  3.000
 3IR  H5   C6   C5   116.55  3.000
 3IR  C7   C6   C5    61.57  3.000
 3IR  H7   C7   C8   113.94  3.000
 3IR  H7   C7   C6   115.13  3.000
 3IR  C8   C7   C6   123.34  3.000
 3IR  H7   C7   C5   114.30  3.000
 3IR  C6   C7   C5    59.30  3.000
 3IR  C8   C7   C5   120.05  3.000
 3IR  C9   C8   C7   119.01  3.000
 3IR  C9   C8   C13  118.45  3.000
 3IR  C7   C8   C13  122.53  3.000
 3IR  H8   C9   C8   119.39  3.000
 3IR  H8   C9   C10  119.64  3.000
 3IR  C8   C9   C10  120.97  3.000
 3IR  H1   N1   C2   114.26  3.000
 3IR  H1   N1   C1   115.20  3.000
 3IR  C2   N1   C1   130.40  3.000
 3IR  C3   N2   C2   110.88  3.000
 3IR  C4   S1   C2    88.90  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
 3IR  CONST_01  C3   C4   S1   C2      0.00   0.0  0
 3IR  CONST_02  C4   C3   N2   C2      0.00   0.0  0
 3IR  CONST_03  S1   C2   N2   C3      0.00   0.0  0
 3IR  CONST_04  N2   C2   S1   C4      0.00   0.0  0
 3IR  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 3IR  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 3IR  CONST_07  C8   C9   C10  C11     0.00   0.0  0
 3IR  CONST_08  C8   C13  C12  C11     0.00   0.0  0
 3IR  CONST_09  C9   C8   C13  C12     0.00   0.0  0
 3IR  CONST_10  C9   C10  C11  C12     0.00   0.0  0
 3IR  CONST_11  S1   C4   C3   N2      0.00   0.0  0
 3IR  CONST_12  C7   C8   C9   C10   180.00   0.0  0
 3IR  CONST_13  C7   C8   C13  C12   180.00   0.0  0
 3IR  CONST_14  N1   C2   N2   C3    180.00   0.0  0
 3IR  CONST_15  N1   C2   S1   C4    180.00   0.0  0
 3IR  CONST_16  H3   C4   S1   C2    180.00   0.0  0
 3IR  CONST_17  H2   C3   N2   C2    180.00   0.0  0
 3IR  CONST_18  H11  C12  C11  C10   180.00   0.0  0
 3IR  CONST_19  H8   C9   C10  C11   180.00   0.0  0
 3IR  CONST_20  H12  C13  C12  C11   180.00   0.0  0
 3IR  CONST_21  H9   C10  C11  C12   180.00   0.0  0
 3IR  CONST_22  H8   C9   C8   C13   180.00   0.0  0
 3IR  CONST_23  H10  C11  C12  C13   180.00   0.0  0
 3IR  CONST_24  H8   C9   C8   C7      0.00   0.0  0
 3IR  CONST_25  H12  C13  C8   C7      0.00   0.0  0
 3IR  CONST_26  H9   C10  C9   C8    180.00   0.0  0
 3IR  CONST_27  H11  C12  C13  C8    180.00   0.0  0
 3IR  CONST_28  H12  C13  C8   C9    180.00   0.0  0
 3IR  CONST_29  H10  C11  C10  C9    180.00   0.0  0
 3IR  CONST_30  H3   C4   C3   N2    180.00   0.0  0
 3IR  CONST_31  H2   C3   C4   S1    180.00   0.0  0
 3IR  CONST_32  C5   C1   N1   C2      0.00   0.0  0
 3IR  CONST_37  O1   C1   N1   C2    180.00   0.0  0
 3IR  CONST_38  H1   N1   C1   C5    180.00   0.0  0
 3IR  CONST_39  H1   N1   C1   O1      0.00   0.0  0
 3IR  Var_01    C9   C8   C7   C5    135.58  30.0  2
 3IR  Var_02    C13  C8   C7   C5    -43.45  30.0  2
 3IR  Var_03    C8   C7   C6   C5   -107.84  30.0  1
 3IR  Var_04    C6   C7   C8   C13    27.55  30.0  2
 3IR  Var_05    C9   C8   C7   C6   -153.42  30.0  2
 3IR  Var_06    C8   C7   C5   C1   -137.69  30.0  1
 3IR  Var_07    C6   C7   C5   C1    109.05  30.0  1
 3IR  Var_08    H5   C6   C7   C5    106.60  30.0  1
 3IR  Var_09    H6   C6   C7   C5   -108.71  30.0  1
 3IR  Var_10    H7   C7   C6   C5    104.48  30.0  1
 3IR  Var_11    H7   C7   C8   C13   175.56  30.0  2
 3IR  Var_12    H4   C5   C7   C6   -106.48  30.0  1
 3IR  Var_13    H4   C5   C7   C8      6.78  30.0  1
 3IR  Var_14    H5   C6   C7   C8     -1.25  30.0  1
 3IR  Var_15    H6   C6   C7   C8    143.45  30.0  1
 3IR  Var_16    H7   C7   C8   C9     -5.40  30.0  2
 3IR  Var_17    O1   C1   C5   C6      1.86  30.0  2
 3IR  Var_18    N1   C1   C5   C6   -177.87  30.0  2
 3IR  Var_19    O1   C1   C5   C7    -66.18  30.0  2
 3IR  Var_20    N1   C1   C5   C7    114.08  30.0  2
 3IR  Var_21    H7   C7   C5   C1      3.16  30.0  1
 3IR  Var_22    H5   C6   C5   C1    144.27  30.0  1
 3IR  Var_23    H6   C6   C5   C1      1.64  30.0  1
 3IR  Var_24    H4   C5   C1   N1    -30.08  30.0  3
 3IR  Var_25    H4   C5   C1   O1    149.65  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
 3IR  chir_01  C5  C1  C7  C6  both
 3IR  chir_02  C7  C5  C8  C6  both

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
 3IR  plan-1  C2   0.020
 3IR  plan-1  C3   0.020
 3IR  plan-1  C4   0.020
 3IR  plan-1  N1   0.020
 3IR  plan-1  N2   0.020
 3IR  plan-1  S1   0.020
 3IR  plan-1  H2   0.020
 3IR  plan-1  H3   0.020
 3IR  plan-2  C10  0.020
 3IR  plan-2  C11  0.020
 3IR  plan-2  C12  0.020
 3IR  plan-2  C13  0.020
 3IR  plan-2  C7   0.020
 3IR  plan-2  C8   0.020
 3IR  plan-2  C9   0.020
 3IR  plan-2  H9   0.020
 3IR  plan-2  H10  0.020
 3IR  plan-2  H11  0.020
 3IR  plan-2  H12  0.020
 3IR  plan-2  H8   0.020
 3IR  plan-3  C1   0.020
 3IR  plan-3  C2   0.020
 3IR  plan-3  C5   0.020
 3IR  plan-3  N1   0.020
 3IR  plan-3  O1   0.020
 3IR  plan-3  H1   0.020

