# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 11:39:26 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2S)-N-(4-cyano-3-iodophenyl)-3-(4-cyanophenoxy)-2-hydroxy-2-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(COc1ccc(cc1)C#N)C(=O)Nc2ccc(C#N)c(I)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
 3B6  3B6  (2S)-N-(4-cyano-3-iodophenyl)-3-(4-cyanophenoxy)-2-hydroxy-2-methylpropanamide  ligand  39  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3B6
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
 3B6  C5    C  CR16  0  -0.325  -2.3035  -0.3791  -0.9628
 3B6  C4    C  CR6   0  -0.225  -3.5700   0.1519  -1.0713
 3B6  I7    I  I     0   0.132  -4.9912  -0.8380  -2.2470
 3B6  C3    C  CR6   0   0.054  -3.8993   1.3359  -0.4033
 3B6  C8    C  CSP   0   0.034  -5.1934   1.9203  -0.4920
 3B6  N8    N  NS    0  -0.240  -6.2319   2.4176  -0.5461
 3B6  C2    C  CR16  0  -0.221  -2.9231   1.9596   0.3730
 3B6  C1    C  CR16  0  -0.309  -1.6512   1.4366   0.4916
 3B6  C6    C  CR6   0   0.423  -1.3284   0.2566  -0.1826
 3B6  N9    N  NH1   0  -0.745  -0.0851  -0.3531  -0.1435
 3B6  C10   C  C     0   0.537   1.0258   0.0109   0.5447
 3B6  O10   O  O     0  -0.445   1.1087   0.9823   1.2693
 3B6  C11   C  CT    0   0.049   2.2063  -0.9646   0.3744
 3B6  O11   O  OH1   0  -0.654   2.0334  -1.8049  -0.7405
 3B6  C12   C  CH3   0  -0.661   2.2340  -1.8616   1.6108
 3B6  C13   C  CH2   0  -0.196   3.4781  -0.1249   0.2435
 3B6  O14   O  O2    0  -0.462   4.5647  -1.0224   0.1357
 3B6  C16   C  CR6   0   0.419   5.8018  -0.5386  -0.0164
 3B6  C17   C  CR16  0  -0.338   6.8223  -1.4910  -0.1183
 3B6  C18   C  CR16  0  -0.222   8.1297  -1.0923  -0.2792
 3B6  C19   C  CR6   0  -0.024   8.4439   0.2693  -0.3420
 3B6  C22   C  CSP   0   0.050   9.7947   0.6847  -0.5132
 3B6  N22   N  NS    0  -0.261  10.8889   1.0187  -0.6581
 3B6  C20   C  CR16  0  -0.222   7.4285   1.2166  -0.2394
 3B6  C21   C  CR16  0  -0.372   6.1124   0.8205  -0.0771
 3B6  H5    H  HCR6  0   0.307  -2.0500  -1.2971  -1.4773
 3B6  H2    H  HCR6  0   0.295  -3.1683   2.8756   0.8929
 3B6  H1    H  HCR6  0   0.303  -0.9294   1.9489   1.1036
 3B6  HN9   H  HNH1  0   0.426   0.0145  -1.1906  -0.7022
 3B6  HO11  H  HOH1  0   0.465   2.2082  -1.3150  -1.5533
 3B6  H12   H  HCH3  0   0.254   1.3102  -2.4366   1.6856
 3B6  H12A  H  HCH3  0   0.260   3.0662  -2.5613   1.5564
 3B6  H12B  H  HCH3  0   0.248   2.3388  -1.2692   2.5182
 3B6  H13   H  HCH2  0   0.260   3.4156   0.5103  -0.6493
 3B6  H13A  H  HCH2  0   0.259   3.5954   0.5270   1.1122
 3B6  H17   H  HCR6  0   0.281   6.5765  -2.5437  -0.0693
 3B6  H18   H  HCR6  0   0.284   8.9124  -1.8345  -0.3564
 3B6  H20   H  HCR6  0   0.286   7.6621   2.2715  -0.2875
 3B6  H21   H  HCR6  0   0.298   5.3502   1.5826  -0.0028

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
 3B6  C5   C4    aromatic  1.378  0.020  1.378
 3B6  C5   C6    aromatic  1.401  0.020  1.401
 3B6  C4   I7    single    2.093  0.020  2.093
 3B6  C4   C3    aromatic  1.399  0.020  1.399
 3B6  C3   C8    single    1.423  0.020  1.423
 3B6  C3   C2    aromatic  1.394  0.020  1.394
 3B6  C8   N8    triple    1.153  0.020  1.153
 3B6  C2   C1    aromatic  1.380  0.020  1.380
 3B6  C1   C6    aromatic  1.397  0.020  1.397
 3B6  C6   N9    single    1.385  0.020  1.385
 3B6  N9   C10   single    1.357  0.020  1.357
 3B6  C10  O10   double    1.215  0.020  1.215
 3B6  C10  C11   single    1.541  0.020  1.541
 3B6  C11  O11   single    1.407  0.020  1.407
 3B6  C11  C12   single    1.528  0.020  1.528
 3B6  C11  C13   single    1.530  0.020  1.530
 3B6  C13  O14   single    1.413  0.020  1.413
 3B6  O14  C16   single    1.337  0.020  1.337
 3B6  C16  C17   aromatic  1.400  0.020  1.400
 3B6  C16  C21   aromatic  1.395  0.020  1.395
 3B6  C17  C18   aromatic  1.376  0.020  1.376
 3B6  C18  C19   aromatic  1.399  0.020  1.399
 3B6  C19  C22   single    1.424  0.020  1.424
 3B6  C19  C20   aromatic  1.392  0.020  1.392
 3B6  C22  N22   triple    1.153  0.020  1.153
 3B6  C20  C21   aromatic  1.384  0.020  1.384
 3B6  C5   H5    single    0.930  0.020  1.080
 3B6  C2   H2    single    0.930  0.020  1.080
 3B6  C1   H1    single    0.930  0.020  1.080
 3B6  N9   HN9   single    0.860  0.020  1.020
 3B6  O11  HO11  single    0.850  0.020  0.980
 3B6  C12  H12   single    0.970  0.020  1.090
 3B6  C12  H12A  single    0.970  0.020  1.090
 3B6  C12  H12B  single    0.970  0.020  1.090
 3B6  C13  H13   single    0.970  0.020  1.090
 3B6  C13  H13A  single    0.970  0.020  1.090
 3B6  C17  H17   single    0.930  0.020  1.080
 3B6  C18  H18   single    0.930  0.020  1.080
 3B6  C20  H20   single    0.930  0.020  1.080
 3B6  C21  H21   single    0.930  0.020  1.080

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
 3B6  H5    C5   C6    119.10  3.000
 3B6  H5    C5   C4    120.31  3.000
 3B6  C6    C5   C4    120.58  3.000
 3B6  C3    C4   I7    120.58  3.000
 3B6  C3    C4   C5    120.33  3.000
 3B6  I7    C4   C5    119.09  3.000
 3B6  C2    C3   C8    119.19  3.000
 3B6  C2    C3   C4    118.67  3.000
 3B6  C8    C3   C4    122.14  3.000
 3B6  N8    C8   C3    180.00  3.000
 3B6  H2    C2   C1    119.24  3.000
 3B6  H2    C2   C3    119.20  3.000
 3B6  C1    C2   C3    121.56  3.000
 3B6  H1    C1   C6    121.44  3.000
 3B6  H1    C1   C2    119.11  3.000
 3B6  C6    C1   C2    119.44  3.000
 3B6  N9    C6   C1    124.44  3.000
 3B6  N9    C6   C5    116.14  3.000
 3B6  C1    C6   C5    119.42  3.000
 3B6  HN9   N9   C10   114.94  3.000
 3B6  HN9   N9   C6    115.92  3.000
 3B6  C10   N9   C6    129.14  3.000
 3B6  C11   C10  O10   121.32  3.000
 3B6  C11   C10  N9    113.67  3.000
 3B6  O10   C10  N9    124.97  3.000
 3B6  C13   C11  C12   112.12  3.000
 3B6  C13   C11  O11   111.24  3.000
 3B6  C12   C11  O11   107.03  3.000
 3B6  C13   C11  C10   107.39  3.000
 3B6  C12   C11  C10   107.23  3.000
 3B6  O11   C11  C10   111.81  3.000
 3B6  HO11  O11  C11   110.00  3.000
 3B6  H12B  C12  H12A  108.53  3.000
 3B6  H12B  C12  H12   108.13  3.000
 3B6  H12A  C12  H12   108.18  3.000
 3B6  H12B  C12  C11   110.91  3.000
 3B6  H12A  C12  C11   110.54  3.000
 3B6  H12   C12  C11   110.46  3.000
 3B6  H13A  C13  H13   107.92  3.000
 3B6  H13A  C13  O14   110.92  3.000
 3B6  H13   C13  O14   110.44  3.000
 3B6  H13A  C13  C11   110.41  3.000
 3B6  H13   C13  C11   109.88  3.000
 3B6  O14   C13  C11   107.29  3.000
 3B6  C16   O14  C13   119.35  3.000
 3B6  C21   C16  C17   119.82  3.000
 3B6  C21   C16  O14   124.29  3.000
 3B6  C17   C16  O14   115.90  3.000
 3B6  H17   C17  C18   120.19  3.000
 3B6  H17   C17  C16   119.54  3.000
 3B6  C18   C17  C16   120.27  3.000
 3B6  H18   C18  C19   120.15  3.000
 3B6  H18   C18  C17   119.81  3.000
 3B6  C19   C18  C17   120.04  3.000
 3B6  C20   C19  C22   120.15  3.000
 3B6  C20   C19  C18   119.68  3.000
 3B6  C22   C19  C18   120.17  3.000
 3B6  N22   C22  C19   180.00  3.000
 3B6  H20   C20  C21   119.33  3.000
 3B6  H20   C20  C19   120.18  3.000
 3B6  C21   C20  C19   120.49  3.000
 3B6  H21   C21  C20   118.49  3.000
 3B6  H21   C21  C16   121.80  3.000
 3B6  C20   C21  C16   119.70  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
 3B6  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 3B6  CONST_02  C2   C1   C6   C5      0.00   0.0  0
 3B6  CONST_03  C1   C6   C5   C4      0.00   0.0  0
 3B6  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 3B6  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 3B6  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 3B6  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 3B6  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 3B6  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 3B6  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 3B6  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 3B6  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 3B6  CONST_13  C8   C3   C4   C5    180.00   0.0  0
 3B6  CONST_14  N9   C6   C5   C4    180.00   0.0  0
 3B6  CONST_15  C6   C5   C4   I7    180.00   0.0  0
 3B6  CONST_16  C2   C3   C4   I7    180.00   0.0  0
 3B6  CONST_17  C1   C2   C3   C8    180.00   0.0  0
 3B6  CONST_18  N9   C6   C1   C2    180.00   0.0  0
 3B6  CONST_19  C18  C17  C16  O14   180.00   0.0  0
 3B6  CONST_20  C20  C21  C16  O14   180.00   0.0  0
 3B6  CONST_21  C22  C19  C18  C17   180.00   0.0  0
 3B6  CONST_22  C21  C20  C19  C22   180.00   0.0  0
 3B6  CONST_23  H1   C1   C6   C5    180.00   0.0  0
 3B6  CONST_24  H2   C2   C3   C4    180.00   0.0  0
 3B6  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 3B6  CONST_26  H18  C18  C17  C16   180.00   0.0  0
 3B6  CONST_27  H20  C20  C21  C16   180.00   0.0  0
 3B6  CONST_28  H21  C21  C16  C17   180.00   0.0  0
 3B6  CONST_29  H17  C17  C18  C19   180.00   0.0  0
 3B6  CONST_30  C10  N9   C6   C5    180.00   0.0  0
 3B6  CONST_31  C10  N9   C6   C1      0.00   0.0  0
 3B6  CONST_32  HN9  N9   C6   C5      0.00   0.0  0
 3B6  CONST_33  O10  C10  N9   C6      0.00   0.0  0
 3B6  CONST_34  C11  C10  N9   C6    180.00   0.0  0
 3B6  Var_01    C17  C16  O14  C13  -179.87  30.0  2
 3B6  Var_02    H13  C13  O14  C16    59.02  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
 3B6  chir_01  C11  O11  C12  C13  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
 3B6  plan-1  C5   0.020
 3B6  plan-1  C4   0.020
 3B6  plan-1  I7   0.020
 3B6  plan-1  C3   0.020
 3B6  plan-1  C8   0.020
 3B6  plan-1  N8   0.020
 3B6  plan-1  C2   0.020
 3B6  plan-1  C1   0.020
 3B6  plan-1  C6   0.020
 3B6  plan-1  N9   0.020
 3B6  plan-1  H5   0.020
 3B6  plan-1  H2   0.020
 3B6  plan-1  H1   0.020
 3B6  plan-2  O14  0.020
 3B6  plan-2  C16  0.020
 3B6  plan-2  C17  0.020
 3B6  plan-2  C18  0.020
 3B6  plan-2  C19  0.020
 3B6  plan-2  C22  0.020
 3B6  plan-2  N22  0.020
 3B6  plan-2  C20  0.020
 3B6  plan-2  C21  0.020
 3B6  plan-2  H17  0.020
 3B6  plan-2  H18  0.020
 3B6  plan-2  H20  0.020
 3B6  plan-2  H21  0.020
 3B6  plan-3  C6   0.020
 3B6  plan-3  N9   0.020
 3B6  plan-3  C10  0.020
 3B6  plan-3  O10  0.020
 3B6  plan-3  C11  0.020
 3B6  plan-3  HN9  0.020

