# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:15:52 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-[[(2~{R},4~{R})-2-[2-chloranyl-4-(4-chloranylphenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CO[C@@](Cn2cncn2)(O1)c3ccc(Oc4ccc(Cl)cc4)cc3Cl
#
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
 5LY  5LY  1-[[(2~{R},4~{R})-2-[2-chloranyl-4-(4-chloranylphenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole  ligand  44  27  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5LY
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
 5LY  C4   C   CR16  0  -0.299   0.7127   2.4617   0.0820
 5LY  C5   C   CR6   0   0.364   1.7083   1.4956   0.1096
 5LY  C7   C   CR6   0  -0.076   0.0255  -0.2043  -0.0473
 5LY  C13  C   CR6   0  -0.040   6.1299  -0.7210   0.4109
 5LY  C22  C   CH2   0  -0.194  -3.4076  -1.6259  -0.9703
 5LY  C25  C   CH2   0  -0.304  -3.3728   1.5919  -0.2835
 5LY  C23  C   CH1   0  -0.018  -3.7116  -1.4776   0.5232
 5LY  C14  C   CR16  0  -0.210   5.4808  -0.3394   1.5752
 5LY  C12  C   CR6   0   0.194  -1.0055   0.7344  -0.0748
 5LY  C11  C   CR16  0  -0.210   5.7317  -0.2356  -0.8251
 5LY  C9   C   CR6   0   0.297   4.0129   1.0285   0.2655
 5LY  C30  C   CR15  0   0.001  -6.6290   0.6651  -1.0044
 5LY  C32  C   CR15  0   0.102  -5.6395   1.3037   0.7115
 5LY  C3   C   CR16  0  -0.334  -0.6091   2.0709  -0.0085
 5LY  C6   C   CR16  0  -0.285   1.3630   0.1536   0.0443
 5LY  O8   O   O2    0  -0.506   2.9862   1.9381   0.1947
 5LY  C10  C   CR16  0  -0.300   4.6609   0.6430  -0.8971
 5LY  C15  C   CT    0   0.418  -2.4756   0.3380  -0.1815
 5LY  O16  O   O2    0  -0.498  -2.6719  -0.4653  -1.3121
 5LY  O17  O   O2    0  -0.499  -2.8347  -0.4278   0.9302
 5LY  C18  C   CR16  0  -0.299   4.4122   0.5409   1.5000
 5LY  CL2  CL  CL    0  -0.103  -0.2750  -1.9057  -0.1348
 5LY  N28  N   NR5   0  -0.277  -4.7749   1.2722  -0.3084
 5LY  N29  N   N     0  -0.248  -5.4011   0.8666  -1.4177
 5LY  N31  N   N     0  -0.455  -6.8285   0.9231   0.3067
 5LY  H1   H   HCR6  0   0.281   0.9674   3.5121   0.1300
 5LY  H2   H   HCH2  0   0.228  -2.8064  -2.5145  -1.1787
 5LY  H3   H   HCH2  0   0.237  -4.3209  -1.6787  -1.5645
 5LY  H4   H   HCH2  0   0.283  -3.2179   2.2389   0.5783
 5LY  H5   H   HCH2  0   0.292  -3.1357   2.1612  -1.1815
 5LY  H6   H   HCH1  0   0.237  -4.7524  -1.1706   0.6690
 5LY  H7   H   HCR6  0   0.290   5.8012  -0.7200   2.5352
 5LY  H8   H   HCR6  0   0.289   6.2465  -0.5357  -1.7274
 5LY  H10  H   HCR5  0   0.305  -5.3602   1.6075   1.7089
 5LY  H11  H   HCR6  0   0.278  -1.3430   2.8618  -0.0265
 5LY  H12  H   HCR6  0   0.302   2.1156  -0.6226   0.0572
 5LY  H13  H   HCR6  0   0.288   4.3405   1.0286  -1.8563
 5LY  H14  H   HCR6  0   0.289   3.9008   0.8484   2.4029
 5LY  C40  C   CH3   0  -0.682  -3.4710  -2.7195   1.3502
 5LY  CL1  CL  CL    0  -0.122   7.4651  -1.8201   0.5035
 5LY  H9   H   HCR5  0   0.275  -7.4086   0.3299  -1.6715
 5LY  H15  H   HCH3  0   0.229  -2.4439  -3.0705   1.2655
 5LY  H16  H   HCH3  0   0.243  -3.6942  -2.5393   2.4018
 5LY  H17  H   HCH3  0   0.238  -4.1332  -3.5152   1.0068

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
 5LY  CL1  C13  single    1.732  0.020  1.732
 5LY  C14  C13  aromatic  1.387  0.020  1.387
 5LY  C14  C18  aromatic  1.387  0.020  1.387
 5LY  C13  C11  aromatic  1.386  0.020  1.386
 5LY  C18  C9   aromatic  1.386  0.020  1.386
 5LY  C11  C10  aromatic  1.387  0.020  1.387
 5LY  C9   C10  aromatic  1.386  0.020  1.386
 5LY  C9   O8   single    1.374  0.020  1.374
 5LY  O8   C5   single    1.355  0.020  1.355
 5LY  C6   C5   aromatic  1.387  0.020  1.387
 5LY  C6   C7   aromatic  1.388  0.020  1.388
 5LY  C5   C4   aromatic  1.388  0.020  1.388
 5LY  CL2  C7   single    1.730  0.020  1.730
 5LY  C7   C12  aromatic  1.395  0.020  1.395
 5LY  C4   C3   aromatic  1.381  0.020  1.381
 5LY  C12  C3   aromatic  1.396  0.020  1.396
 5LY  C12  C15  single    1.526  0.020  1.526
 5LY  O16  C22  single    1.416  0.020  1.416
 5LY  O16  C15  single    1.401  0.020  1.401
 5LY  C22  C23  single    1.531  0.020  1.531
 5LY  C15  O17  single    1.397  0.020  1.397
 5LY  C15  C25  single    1.545  0.020  1.545
 5LY  O17  C23  single    1.427  0.020  1.427
 5LY  N29  N28  aromatic  1.337  0.020  1.337
 5LY  N29  C30  aromatic  1.311  0.020  1.311
 5LY  C25  N28  single    1.438  0.020  1.438
 5LY  C23  C40  single    1.511  0.020  1.511
 5LY  N28  C32  aromatic  1.337  0.020  1.337
 5LY  C30  N31  aromatic  1.351  0.020  1.351
 5LY  C32  N31  aromatic  1.312  0.020  1.312
 5LY  C4   H1   single    0.930  0.020  1.080
 5LY  C22  H2   single    0.970  0.020  1.090
 5LY  C22  H3   single    0.970  0.020  1.090
 5LY  C25  H4   single    0.970  0.020  1.090
 5LY  C25  H5   single    0.970  0.020  1.090
 5LY  C23  H6   single    0.970  0.020  1.090
 5LY  C14  H7   single    0.930  0.020  1.080
 5LY  C11  H8   single    0.930  0.020  1.080
 5LY  C30  H9   single    0.930  0.020  1.080
 5LY  C32  H10  single    0.930  0.020  1.080
 5LY  C3   H11  single    0.930  0.020  1.080
 5LY  C6   H12  single    0.930  0.020  1.080
 5LY  C10  H13  single    0.930  0.020  1.080
 5LY  C18  H14  single    0.930  0.020  1.080
 5LY  C40  H15  single    0.970  0.020  1.090
 5LY  C40  H16  single    0.970  0.020  1.090
 5LY  C40  H17  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
 5LY  H1   C4   C3   120.19  3.000
 5LY  H1   C4   C5   120.41  3.000
 5LY  C3   C4   C5   119.40  3.000
 5LY  O8   C5   C6   123.61  3.000
 5LY  C6   C5   C4   119.61  3.000
 5LY  O8   C5   C4   116.78  3.000
 5LY  CL2  C7   C6   115.11  3.000
 5LY  CL2  C7   C12  122.19  3.000
 5LY  C6   C7   C12  122.70  3.000
 5LY  CL1  C13  C11  119.43  3.000
 5LY  C11  C13  C14  121.19  3.000
 5LY  CL1  C13  C14  119.38  3.000
 5LY  H3   C22  H2   108.50  3.000
 5LY  H3   C22  O16  110.07  3.000
 5LY  H2   C22  O16  109.54  3.000
 5LY  H3   C22  C23  111.71  3.000
 5LY  H2   C22  C23  111.96  3.000
 5LY  O16  C22  C23  105.02  3.000
 5LY  H5   C25  H4   108.11  3.000
 5LY  H5   C25  N28  108.30  3.000
 5LY  H4   C25  N28  106.53  3.000
 5LY  H5   C25  C15  110.62  3.000
 5LY  H4   C25  C15  110.33  3.000
 5LY  N28  C25  C15  112.76  3.000
 5LY  H6   C23  C40  107.99  3.000
 5LY  H6   C23  O17  109.87  3.000
 5LY  C40  C23  O17  110.53  3.000
 5LY  H6   C23  C22  110.22  3.000
 5LY  C40  C23  C22  114.99  3.000
 5LY  O17  C23  C22  103.14  3.000
 5LY  H7   C14  C18  120.00  3.000
 5LY  H7   C14  C13  120.66  3.000
 5LY  C18  C14  C13  119.34  3.000
 5LY  C15  C12  C3   121.71  3.000
 5LY  C15  C12  C7   122.59  3.000
 5LY  C3   C12  C7   115.71  3.000
 5LY  H8   C11  C10  120.01  3.000
 5LY  H8   C11  C13  120.66  3.000
 5LY  C10  C11  C13  119.33  3.000
 5LY  C18  C9   C10  120.97  3.000
 5LY  C10  C9   O8   119.38  3.000
 5LY  C18  C9   O8   119.61  3.000
 5LY  H9   C30  N31  123.53  3.000
 5LY  H9   C30  N29  121.96  3.000
 5LY  N31  C30  N29  114.51  3.000
 5LY  H10  C32  N31  126.95  3.000
 5LY  H10  C32  N28  122.96  3.000
 5LY  N31  C32  N28  110.10  3.000
 5LY  H11  C3   C12  120.53  3.000
 5LY  H11  C3   C4   116.39  3.000
 5LY  C12  C3   C4   123.08  3.000
 5LY  H12  C6   C7   119.11  3.000
 5LY  H12  C6   C5   121.38  3.000
 5LY  C7   C6   C5   119.50  3.000
 5LY  C9   O8   C5   119.48  3.000
 5LY  H13  C10  C9   120.40  3.000
 5LY  H13  C10  C11  120.02  3.000
 5LY  C9   C10  C11  119.59  3.000
 5LY  O17  C15  O16  106.97  3.000
 5LY  O17  C15  C12  109.53  3.000
 5LY  O16  C15  C12  109.90  3.000
 5LY  O17  C15  C25  110.38  3.000
 5LY  O16  C15  C25  109.31  3.000
 5LY  C12  C15  C25  110.68  3.000
 5LY  C15  O16  C22  110.36  3.000
 5LY  C15  O17  C23  109.53  3.000
 5LY  H14  C18  C9   120.46  3.000
 5LY  H14  C18  C14  119.95  3.000
 5LY  C9   C18  C14  119.58  3.000
 5LY  N29  N28  C32  109.70  3.000
 5LY  C32  N28  C25  127.72  3.000
 5LY  N29  N28  C25  122.57  3.000
 5LY  N28  N29  C30  102.93  3.000
 5LY  C32  N31  C30  102.76  3.000
 5LY  H17  C40  H16  107.46  3.000
 5LY  H17  C40  H15  108.24  3.000
 5LY  H16  C40  H15  108.76  3.000
 5LY  H17  C40  C23  109.30  3.000
 5LY  H16  C40  C23  111.07  3.000
 5LY  H15  C40  C23  111.87  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
 5LY  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 5LY  CONST_02  C7   C12  C3   C4      0.00   0.0  0
 5LY  CONST_03  C12  C7   C6   C5      0.00   0.0  0
 5LY  CONST_04  C12  C3   C4   C5      0.00   0.0  0
 5LY  CONST_05  C9   C18  C14  C13     0.00   0.0  0
 5LY  CONST_06  C9   C10  C11  C13     0.00   0.0  0
 5LY  CONST_07  C10  C11  C13  C14     0.00   0.0  0
 5LY  CONST_08  C10  C9   C18  C14     0.00   0.0  0
 5LY  CONST_09  C18  C14  C13  C11     0.00   0.0  0
 5LY  CONST_10  C18  C9   C10  C11     0.00   0.0  0
 5LY  CONST_11  C32  N28  N29  C30     0.00   0.0  0
 5LY  CONST_12  N28  C32  N31  C30     0.00   0.0  0
 5LY  CONST_13  N29  C30  N31  C32     0.00   0.0  0
 5LY  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 5LY  CONST_15  C6   C7   C12  C3      0.00   0.0  0
 5LY  CONST_16  N31  C30  N29  N28     0.00   0.0  0
 5LY  CONST_17  N31  C32  N28  N29     0.00   0.0  0
 5LY  CONST_18  C15  C12  C3   C4    180.00   0.0  0
 5LY  CONST_19  C15  C12  C7   C6    180.00   0.0  0
 5LY  CONST_20  CL2  C7   C6   C5    180.00   0.0  0
 5LY  CONST_21  O8   C5   C6   C7    180.00   0.0  0
 5LY  CONST_22  C30  N29  N28  C25   180.00   0.0  0
 5LY  CONST_23  N31  C32  N28  C25   180.00   0.0  0
 5LY  CONST_24  O8   C9   C18  C14   180.00   0.0  0
 5LY  CONST_25  O8   C9   C10  C11   180.00   0.0  0
 5LY  CONST_26  O8   C5   C4   C3    180.00   0.0  0
 5LY  CONST_27  CL2  C7   C12  C3    180.00   0.0  0
 5LY  CONST_28  CL1  C13  C11  C10   180.00   0.0  0
 5LY  CONST_29  CL2  C7   C12  C15     0.00   0.0  0
 5LY  CONST_30  CL1  C13  C14  C18   180.00   0.0  0
 5LY  CONST_31  H12  C6   C5   C4    180.00   0.0  0
 5LY  CONST_32  H11  C3   C4   C5    180.00   0.0  0
 5LY  CONST_33  H14  C18  C14  C13   180.00   0.0  0
 5LY  CONST_34  H13  C10  C11  C13   180.00   0.0  0
 5LY  CONST_35  H8   C11  C13  C14   180.00   0.0  0
 5LY  CONST_36  H1   C4   C3   C12   180.00   0.0  0
 5LY  CONST_37  H7   C14  C13  C11   180.00   0.0  0
 5LY  CONST_38  H10  C32  N31  C30   180.00   0.0  0
 5LY  CONST_39  H9   C30  N31  C32   180.00   0.0  0
 5LY  Var_01    C18  C9   O8   C5    -87.70  30.0  1
 5LY  Var_02    C6   C5   O8   C9     -2.20  30.0  2
 5LY  Var_03    C15  C25  N28  C32    98.48  30.0  2
 5LY  Var_04    H2   C22  O16  C15  -118.88  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
 5LY  chir_01  C23  C22  O17  C40  positiv
 5LY  chir_02  C15  O16  O17  C12  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
 5LY  plan-1  C25  0.020
 5LY  plan-1  C30  0.020
 5LY  plan-1  C32  0.020
 5LY  plan-1  N28  0.020
 5LY  plan-1  N29  0.020
 5LY  plan-1  N31  0.020
 5LY  plan-1  H10  0.020
 5LY  plan-1  H9   0.020
 5LY  plan-2  C13  0.020
 5LY  plan-2  C14  0.020
 5LY  plan-2  C11  0.020
 5LY  plan-2  C9   0.020
 5LY  plan-2  O8   0.020
 5LY  plan-2  C10  0.020
 5LY  plan-2  C18  0.020
 5LY  plan-2  H7   0.020
 5LY  plan-2  H8   0.020
 5LY  plan-2  H13  0.020
 5LY  plan-2  H14  0.020
 5LY  plan-2  CL1  0.020
 5LY  plan-3  C4   0.020
 5LY  plan-3  C5   0.020
 5LY  plan-3  C7   0.020
 5LY  plan-3  C12  0.020
 5LY  plan-3  C3   0.020
 5LY  plan-3  C6   0.020
 5LY  plan-3  O8   0.020
 5LY  plan-3  C15  0.020
 5LY  plan-3  CL2  0.020
 5LY  plan-3  H1   0.020
 5LY  plan-3  H11  0.020
 5LY  plan-3  H12  0.020

