# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 00:09:55 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 2-chloro-N-[3-(4-{[(2Z)-2-cyano-3-cyclopropyl-3-hydroxyprop-2-enoyl]amino}phenoxy)phenyl]-4-methyl-1,3-thiazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(Cl)sc1C(=O)Nc2cccc(Oc3ccc(NC(=O)\C(C#N)=C(/O)C4CC4)cc3)c2
#
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
 3V1  3V1  2-chloro-N-[3-(4-{[(2Z)-2-cyano-3-cyclopropyl-3-hydroxyprop-2-enoyl]amino}phenoxy)phenyl]-4-methyl-1,3-thiazole-5-carboxamide  ligand  53  34  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3V1
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
 3V1  C1    C   CR6   0   0.393    1.0172   1.0411   0.1082
 3V1  C2    C   CR16  0  -0.357    0.5612   1.7012  -1.0242
 3V1  C3    C   CR16  0  -0.234    1.5012   2.1823  -1.9270
 3V1  C4    C   CR16  0  -0.365    2.8555   2.0108  -1.7172
 3V1  C5    C   CR6   0   0.398    3.3016   1.3412  -0.5738
 3V1  C6    C   CR16  0  -0.413    2.3765   0.8542   0.3439
 3V1  N7    N   NH1   0  -0.767    4.6872   1.2207  -0.4216
 3V1  C8    C   C     0   0.543    5.3773   0.4498   0.4599
 3V1  O9    O   O     0  -0.442    4.8640  -0.3170   1.2530
 3V1  C10   C   CR5   0  -0.430    6.8452   0.5994   0.3992
 3V1  S11   S   S2    0   0.316    7.6325   2.0569  -0.0960
 3V1  C12   C   CR5   0   0.024    9.1315   1.2915   0.2081
 3V1  N13   N   N     0  -0.349    9.0733   0.0825   0.6389
 3V1  C14   C   CR5   0   0.383    7.7787  -0.3363   0.7631
 3V1  C15   C   CH3   0  -0.725    7.5181  -1.7197   1.2531
 3V1  CL16  CL  CL    0  -0.036   10.5909   2.1275  -0.0434
 3V1  O17   O   O2    0  -0.515    0.1925   0.5492   1.0738
 3V1  C18   C   CR6   0   0.292   -1.1540   0.4548   0.8233
 3V1  C19   C   CR16  0  -0.299   -2.0215   1.3585   1.4138
 3V1  C20   C   CR16  0  -0.352   -3.3847   1.2275   1.2128
 3V1  C21   C   CR6   0   0.383   -3.9002   0.2087   0.4099
 3V1  C22   C   CR16  0  -0.305   -3.0141  -0.6883  -0.1903
 3V1  C23   C   CR16  0  -0.292   -1.6498  -0.5617   0.0229
 3V1  N24   N   NH1   0  -0.783   -5.2879   0.1822   0.2354
 3V1  C25   C   C     0   0.604   -6.0600  -0.8702  -0.1600
 3V1  O26   O   O     0  -0.453   -5.6016  -1.9652  -0.4253
 3V1  C27   C   C     0  -0.298   -7.5103  -0.5638  -0.2482
 3V1  C28   C   CSP   0  -0.004   -7.9167   0.7880  -0.1472
 3V1  N29   N   NS    0  -0.258   -8.1987   1.9056  -0.0593
 3V1  C30   C   C     0   0.499   -8.4814  -1.5189  -0.4419
 3V1  O31   O   OH1   0  -0.549   -8.1241  -2.7781  -0.5299
 3V1  C32   C   CH1   0  -0.439   -9.9028  -1.1682  -0.5491
 3V1  C33   C   CH2   0  -0.474  -10.8037  -1.9136  -1.5117
 3V1  C34   C   CH2   0  -0.479  -10.9770  -2.1104  -0.0540
 3V1  H1    H   HCR6  0   0.278   -0.4933   1.8478  -1.2126
 3V1  H2    H   HCR6  0   0.268    1.1636   2.7011  -2.8143
 3V1  H3    H   HCR6  0   0.272    3.5689   2.3944  -2.4362
 3V1  H4    H   HCR6  0   0.291    2.6836   0.3363   1.2382
 3V1  H5    H   HNH1  0   0.422    5.2184   1.6747  -1.1503
 3V1  H6    H   HCH3  0   0.264    7.2771  -1.7156   2.3166
 3V1  H7    H   HCH3  0   0.257    6.6850  -2.1845   0.7314
 3V1  H8    H   HCH3  0   0.256    8.4058  -2.3322   1.1119
 3V1  H9    H   HCR6  0   0.276   -1.6402   2.1569   2.0374
 3V1  H10   H   HCR6  0   0.277   -4.0569   1.9321   1.6882
 3V1  H11   H   HCR6  0   0.282   -3.3679  -1.4848  -0.8233
 3V1  H12   H   HCR6  0   0.278   -0.9736  -1.2671  -0.4437
 3V1  H13   H   HNH1  0   0.422   -5.7582   1.0145   0.5578
 3V1  H14   H   HOH1  0   0.498   -8.8759  -3.3721  -0.6526
 3V1  H15   H   HCH1  0   0.309  -10.1235  -0.1170  -0.4310
 3V1  H16   H   HCH2  0   0.292  -11.5191  -1.3057  -2.0476
 3V1  H17   H   HCH2  0   0.277  -10.3785  -2.7167  -2.1018
 3V1  H18   H   HCH2  0   0.273  -10.6843  -3.0555   0.3887
 3V1  H19   H   HCH2  0   0.293  -11.8149  -1.6405   0.4419

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
 3V1  N29   C28  triple    1.156  0.020  1.156
 3V1  C28   C27  single    1.415  0.020  1.415
 3V1  O26   C25  double    1.216  0.020  1.216
 3V1  CL16  C12  single    1.701  0.020  1.701
 3V1  N13   C12  aromatic  1.285  0.020  1.285
 3V1  N13   C14  aromatic  1.366  0.020  1.366
 3V1  C12   S11  aromatic  1.710  0.020  1.710
 3V1  C15   C14  single    1.491  0.020  1.491
 3V1  C14   C10  aromatic  1.371  0.020  1.371
 3V1  C27   C25  single    1.485  0.020  1.485
 3V1  C27   C30  double    1.376  0.020  1.376
 3V1  C25   N24  single    1.364  0.020  1.364
 3V1  O9    C8   double    1.217  0.020  1.217
 3V1  C20   C19  aromatic  1.384  0.020  1.384
 3V1  C20   C21  aromatic  1.396  0.020  1.396
 3V1  C19   C18  aromatic  1.385  0.020  1.385
 3V1  S11   C10  aromatic  1.729  0.020  1.729
 3V1  C10   C8   single    1.477  0.020  1.477
 3V1  C8    N7   single    1.359  0.020  1.359
 3V1  C32   C30  single    1.468  0.020  1.468
 3V1  C32   C34  single    1.512  0.020  1.512
 3V1  C32   C33  single    1.515  0.020  1.515
 3V1  C30   O31  single    1.312  0.020  1.312
 3V1  N24   C21  single    1.399  0.020  1.399
 3V1  C21   C22  aromatic  1.396  0.020  1.396
 3V1  C18   O17  single    1.373  0.020  1.373
 3V1  C18   C23  aromatic  1.385  0.020  1.385
 3V1  O17   C1   single    1.362  0.020  1.362
 3V1  C6    C1   aromatic  1.392  0.020  1.392
 3V1  C6    C5   aromatic  1.391  0.020  1.391
 3V1  N7    C5   single    1.399  0.020  1.399
 3V1  C34   C33  single    1.481  0.020  1.481
 3V1  C1    C2   aromatic  1.388  0.020  1.388
 3V1  C5    C4   aromatic  1.398  0.020  1.398
 3V1  C22   C23  aromatic  1.387  0.020  1.387
 3V1  C2    C3   aromatic  1.389  0.020  1.389
 3V1  C4    C3   aromatic  1.381  0.020  1.381
 3V1  C2    H1   single    0.930  0.020  1.080
 3V1  C3    H2   single    0.930  0.020  1.080
 3V1  C4    H3   single    0.930  0.020  1.080
 3V1  C6    H4   single    0.930  0.020  1.080
 3V1  N7    H5   single    0.860  0.020  1.020
 3V1  C15   H6   single    0.970  0.020  1.090
 3V1  C15   H7   single    0.970  0.020  1.090
 3V1  C15   H8   single    0.970  0.020  1.090
 3V1  C19   H9   single    0.930  0.020  1.080
 3V1  C20   H10  single    0.930  0.020  1.080
 3V1  C22   H11  single    0.930  0.020  1.080
 3V1  C23   H12  single    0.930  0.020  1.080
 3V1  N24   H13  single    0.860  0.020  1.020
 3V1  O31   H14  single    0.850  0.020  0.980
 3V1  C32   H15  single    0.970  0.020  1.090
 3V1  C33   H16  single    0.970  0.020  1.090
 3V1  C33   H17  single    0.970  0.020  1.090
 3V1  C34   H18  single    0.970  0.020  1.090
 3V1  C34   H19  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
 3V1  O17   C1   C6   115.01  3.000
 3V1  C6    C1   C2   121.52  3.000
 3V1  O17   C1   C2   123.46  3.000
 3V1  H1    C2   C3   119.98  3.000
 3V1  H1    C2   C1   121.81  3.000
 3V1  C3    C2   C1   118.21  3.000
 3V1  H2    C3   C4   119.35  3.000
 3V1  H2    C3   C2   119.20  3.000
 3V1  C4    C3   C2   121.45  3.000
 3V1  H3    C4   C5   120.15  3.000
 3V1  H3    C4   C3   120.07  3.000
 3V1  C5    C4   C3   119.77  3.000
 3V1  N7    C5   C6   123.83  3.000
 3V1  N7    C5   C4   116.50  3.000
 3V1  C6    C5   C4   119.67  3.000
 3V1  H4    C6   C5   121.73  3.000
 3V1  H4    C6   C1   118.88  3.000
 3V1  C5    C6   C1   119.39  3.000
 3V1  H5    N7   C8   117.13  3.000
 3V1  H5    N7   C5   113.82  3.000
 3V1  C8    N7   C5   128.48  3.000
 3V1  C10   C8   O9   120.66  3.000
 3V1  C10   C8   N7   114.87  3.000
 3V1  O9    C8   N7   124.47  3.000
 3V1  C14   C10  S11  109.96  3.000
 3V1  S11   C10  C8   123.35  3.000
 3V1  C14   C10  C8   126.64  3.000
 3V1  C12   S11  C10   88.33  3.000
 3V1  CL16  C12  N13  123.44  3.000
 3V1  N13   C12  S11  116.17  3.000
 3V1  CL16  C12  S11  120.39  3.000
 3V1  C14   N13  C12  111.22  3.000
 3V1  C15   C14  N13  118.69  3.000
 3V1  C15   C14  C10  126.99  3.000
 3V1  N13   C14  C10  114.32  3.000
 3V1  H8    C15  H7   108.81  3.000
 3V1  H8    C15  H6   108.00  3.000
 3V1  H7    C15  H6   107.47  3.000
 3V1  H8    C15  C14  109.71  3.000
 3V1  H7    C15  C14  111.90  3.000
 3V1  H6    C15  C14  110.83  3.000
 3V1  C18   O17  C1   119.31  3.000
 3V1  C23   C18  C19  120.06  3.000
 3V1  C23   C18  O17  120.46  3.000
 3V1  C19   C18  O17  119.45  3.000
 3V1  H9    C19  C20  120.02  3.000
 3V1  H9    C19  C18  120.42  3.000
 3V1  C20   C19  C18  119.56  3.000
 3V1  H10   C20  C21  119.86  3.000
 3V1  H10   C20  C19  119.06  3.000
 3V1  C21   C20  C19  121.08  3.000
 3V1  N24   C21  C22  124.31  3.000
 3V1  C22   C21  C20  118.80  3.000
 3V1  N24   C21  C20  116.86  3.000
 3V1  H11   C22  C23  118.75  3.000
 3V1  H11   C22  C21  121.28  3.000
 3V1  C23   C22  C21  119.97  3.000
 3V1  H12   C23  C22  119.26  3.000
 3V1  H12   C23  C18  120.22  3.000
 3V1  C22   C23  C18  120.53  3.000
 3V1  H13   N24  C25  117.73  3.000
 3V1  H13   N24  C21  114.02  3.000
 3V1  C25   N24  C21  127.76  3.000
 3V1  C27   C25  O26  122.74  3.000
 3V1  C27   C25  N24  114.26  3.000
 3V1  O26   C25  N24  123.00  3.000
 3V1  C30   C27  C28  118.07  3.000
 3V1  C30   C27  C25  123.68  3.000
 3V1  C28   C27  C25  118.25  3.000
 3V1  N29   C28  C27  180.00  3.000
 3V1  C32   C30  O31  119.22  3.000
 3V1  O31   C30  C27  118.92  3.000
 3V1  C32   C30  C27  121.87  3.000
 3V1  H14   O31  C30  112.76  3.000
 3V1  H15   C32  C34  115.17  3.000
 3V1  H15   C32  C33  115.26  3.000
 3V1  C34   C32  C33   58.59  3.000
 3V1  H15   C32  C30  114.97  3.000
 3V1  C33   C32  C30  120.32  3.000
 3V1  C34   C32  C30  121.01  3.000
 3V1  H17   C33  H16  113.99  3.000
 3V1  H17   C33  C34  118.91  3.000
 3V1  H16   C33  C34  119.03  3.000
 3V1  H17   C33  C32  118.52  3.000
 3V1  H16   C33  C32  115.60  3.000
 3V1  C34   C33  C32   60.62  3.000
 3V1  H19   C34  H18  113.64  3.000
 3V1  H19   C34  C33  118.97  3.000
 3V1  H18   C34  C33  119.09  3.000
 3V1  H19   C34  C32  115.46  3.000
 3V1  H18   C34  C32  119.02  3.000
 3V1  C33   C34  C32   60.78  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
 3V1  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 3V1  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 3V1  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 3V1  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 3V1  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 3V1  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 3V1  CONST_07  C12   N13  C14  C10     0.00   0.0  0
 3V1  CONST_08  N13   C12  S11  C10     0.00   0.0  0
 3V1  CONST_09  C14   N13  C12  S11     0.00   0.0  0
 3V1  CONST_10  N13   C14  C10  S11     0.00   0.0  0
 3V1  CONST_11  C14   C10  S11  C12     0.00   0.0  0
 3V1  CONST_12  C21   C20  C19  C18     0.00   0.0  0
 3V1  CONST_13  C21   C22  C23  C18     0.00   0.0  0
 3V1  CONST_14  C22   C21  C20  C19     0.00   0.0  0
 3V1  CONST_15  C22   C23  C18  C19     0.00   0.0  0
 3V1  CONST_16  C23   C18  C19  C20     0.00   0.0  0
 3V1  CONST_17  C23   C22  C21  C20     0.00   0.0  0
 3V1  CONST_18  N7    C5   C6   C1    180.00   0.0  0
 3V1  CONST_19  O17   C1   C2   C3    180.00   0.0  0
 3V1  CONST_20  N7    C5   C4   C3    180.00   0.0  0
 3V1  CONST_21  O17   C1   C6   C5    180.00   0.0  0
 3V1  CONST_22  N13   C14  C10  C8    180.00   0.0  0
 3V1  CONST_23  C12   S11  C10  C8    180.00   0.0  0
 3V1  CONST_24  CL16  C12  S11  C10   180.00   0.0  0
 3V1  CONST_25  C15   C14  C10  S11   180.00   0.0  0
 3V1  CONST_26  C15   C14  N13  C12   180.00   0.0  0
 3V1  CONST_27  CL16  C12  N13  C14   180.00   0.0  0
 3V1  CONST_28  C20   C19  C18  O17   180.00   0.0  0
 3V1  CONST_29  C22   C23  C18  O17   180.00   0.0  0
 3V1  CONST_30  N24   C21  C20  C19   180.00   0.0  0
 3V1  CONST_31  N24   C21  C22  C23   180.00   0.0  0
 3V1  CONST_32  H2    C3   C2   C1    180.00   0.0  0
 3V1  CONST_33  H4    C6   C1   C2    180.00   0.0  0
 3V1  CONST_34  H3    C4   C3   C2    180.00   0.0  0
 3V1  CONST_35  H1    C2   C3   C4    180.00   0.0  0
 3V1  CONST_36  H10   C20  C19  C18   180.00   0.0  0
 3V1  CONST_37  H11   C22  C23  C18   180.00   0.0  0
 3V1  CONST_38  H12   C23  C18  C19   180.00   0.0  0
 3V1  CONST_39  H9    C19  C20  C21   180.00   0.0  0
 3V1  CONST_40  C10   C8   N7   C5    180.00   0.0  0
 3V1  CONST_41  C8    N7   C5   C4    180.00   0.0  0
 3V1  CONST_42  C8    N7   C5   C6      0.00   0.0  0
 3V1  CONST_45  H5    N7   C5   C4      0.00   0.0  0
 3V1  CONST_46  H13   N24  C21  C20     0.00   0.0  0
 3V1  CONST_47  O9    C8   N7   C5      0.00   0.0  0
 3V1  CONST_48  O26   C25  N24  C21     0.00   0.0  0
 3V1  CONST_49  C27   C25  N24  C21   180.00   0.0  0
 3V1  Var_01    C19   C18  O17  C1   -105.69  30.0  3
 3V1  Var_02    C33   C34  C32  C30  -108.85  30.0  1
 3V1  Var_03    H16   C33  C34  C32  -104.75  30.0  1
 3V1  Var_04    C14   C10  C8   N7   -153.94  30.0  2
 3V1  Var_05    C34   C32  C30  C27  -147.79  30.0  3
 3V1  Var_06    H6    C15  C14  C10   -81.67  30.0  2
 3V1  Var_07    C32   C30  C27  C25  -178.79   0.0  2
 3V1  Var_08    C28   C27  C25  N24    10.47  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
 3V1  chir_01  C32  C30  C34  C33  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
 3V1  plan-1  C25   0.020
 3V1  plan-1  C27   0.020
 3V1  plan-1  C28   0.020
 3V1  plan-1  C30   0.020
 3V1  plan-1  O31   0.020
 3V1  plan-1  C32   0.020
 3V1  plan-2  C8    0.020
 3V1  plan-2  C10   0.020
 3V1  plan-2  S11   0.020
 3V1  plan-2  C12   0.020
 3V1  plan-2  N13   0.020
 3V1  plan-2  C14   0.020
 3V1  plan-2  C15   0.020
 3V1  plan-2  CL16  0.020
 3V1  plan-3  C1    0.020
 3V1  plan-3  C2    0.020
 3V1  plan-3  C3    0.020
 3V1  plan-3  C4    0.020
 3V1  plan-3  C5    0.020
 3V1  plan-3  C6    0.020
 3V1  plan-3  N7    0.020
 3V1  plan-3  O17   0.020
 3V1  plan-3  H1    0.020
 3V1  plan-3  H2    0.020
 3V1  plan-3  H3    0.020
 3V1  plan-3  H4    0.020
 3V1  plan-4  O17   0.020
 3V1  plan-4  C18   0.020
 3V1  plan-4  C19   0.020
 3V1  plan-4  C20   0.020
 3V1  plan-4  C21   0.020
 3V1  plan-4  C22   0.020
 3V1  plan-4  C23   0.020
 3V1  plan-4  N24   0.020
 3V1  plan-4  H9    0.020
 3V1  plan-4  H10   0.020
 3V1  plan-4  H11   0.020
 3V1  plan-4  H12   0.020
 3V1  plan-5  C21   0.020
 3V1  plan-5  N24   0.020
 3V1  plan-5  C25   0.020
 3V1  plan-5  O26   0.020
 3V1  plan-5  C27   0.020
 3V1  plan-5  H13   0.020
 3V1  plan-6  C5    0.020
 3V1  plan-6  N7    0.020
 3V1  plan-6  C8    0.020
 3V1  plan-6  O9    0.020
 3V1  plan-6  C10   0.020
 3V1  plan-6  H5    0.020

