# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 15:47:20 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1-[[(2~{R},4~{S})-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
 5LX  5LX  1-[[(2~{R},4~{S})-2-[2-chloranyl-4-(4-chloranylphenoxy)phenyl]-4-methyl-1,3-dioxolan-2-yl]methyl]-1,2,4-triazole  ligand  44  27  .  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_5LX
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
 5LX  C3   C   CR16  0  -0.273  -0.6347   0.3526   0.5004
 5LX  C4   C   CR16  0  -0.319   0.6705  -0.0692   0.3060
 5LX  C5   C   CR6   0   0.362   0.8975  -1.3091  -0.2742
 5LX  C6   C   CR16  0  -0.275  -0.1767  -2.0993  -0.6644
 5LX  C10  C   CR16  0  -0.299   3.7402  -0.2146  -1.1958
 5LX  C15  C   CR5   0   0.475  -3.1456   0.1350   0.3526
 5LX  C14  C   CR16  0  -0.209   4.9957  -0.4444   1.2784
 5LX  C13  C   CR6   0  -0.040   5.4978   0.4063   0.3057
 5LX  C12  C   CR6   0   0.082  -1.7364  -0.4182   0.1447
 5LX  C11  C   CR16  0  -0.210   4.8818   0.5265  -0.9307
 5LX  C9   C   CR6   0   0.302   3.2360  -1.0659  -0.2250
 5LX  C7   C   CR6   0  -0.093  -1.4676  -1.6466  -0.4582
 5LX  O8   O   O2    0  -0.508   2.1294  -1.8299  -0.5024
 5LX  O16  O   O     0  -0.490  -4.0154  -0.8231   0.8824
 5LX  O17  O   O     0  -0.487  -3.1356   1.1828   1.2670
 5LX  C18  C   CR16  0  -0.302   3.8537  -1.1841   1.0098
 5LX  CL2  CL  CL    0  -0.113  -2.7399  -2.6737  -1.0389
 5LX  C22  C   CH2   0  -0.188  -4.0336  -0.6784   2.2935
 5LX  C23  C   CR15  0  -0.014  -3.2305   0.6004   2.5644
 5LX  C25  C   CH2   0  -0.335  -3.7502   0.6281  -0.9697
 5LX  N28  N   NR5   0  -0.262  -2.8215   1.4227  -1.7271
 5LX  N29  N   N     0  -0.251  -2.5237   2.6800  -1.3849
 5LX  C30  C   CR15  0   0.003  -1.5836   3.0007  -2.2405
 5LX  N31  N   N     0  -0.459  -1.2556   2.0189  -3.1080
 5LX  C32  C   CR15  0   0.120  -2.0507   1.0384  -2.7492
 5LX  C40  C   CH3   0  -0.692  -3.8899   1.5680   3.5166
 5LX  H1   H   HCR6  0   0.276  -0.7947   1.3245   0.9464
 5LX  H2   H   HCR6  0   0.286   1.4854   0.5745   0.6078
 5LX  H3   H   HCR6  0   0.294   0.0023  -3.0591  -1.1309
 5LX  H4   H   HCR6  0   0.288   3.2537  -0.1313  -2.1591
 5LX  H5   H   HCR6  0   0.289   5.4818  -0.5308   2.2404
 5LX  H6   H   HCR6  0   0.289   5.2827   1.1899  -1.6844
 5LX  H7   H   HCR6  0   0.287   3.4522  -1.8519   1.7609
 5LX  H8   H   HCH2  0   0.236  -5.0717  -0.5901   2.6236
 5LX  H9   H   HCH2  0   0.235  -3.5854  -1.5472   2.7803
 5LX  H10  H   HCR5  0   0.240  -2.2283   0.3461   2.9303
 5LX  H11  H   HCH2  0   0.284  -4.0386  -0.2244  -1.5825
 5LX  H12  H   HCH2  0   0.297  -4.6459   1.2147  -0.7664
 5LX  H13  H   HCR5  0   0.274  -1.1226   3.9767  -2.2443
 5LX  H14  H   HCR5  0   0.300  -2.1095   0.0559  -3.1935
 5LX  H15  H   HCH3  0   0.242  -3.9935   1.1026   4.4969
 5LX  H16  H   HCH3  0   0.246  -3.2939   2.4717   3.6409
 5LX  H17  H   HCH3  0   0.235  -4.8847   1.8471   3.1670
 5LX  CL1  CL  CL    0  -0.123   6.9235   1.3327   0.6386

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
 5LX  CL1  C13  single    1.733  0.020  1.733
 5LX  C13  C11  aromatic  1.387  0.020  1.387
 5LX  C13  C14  aromatic  1.386  0.020  1.386
 5LX  C11  C10  aromatic  1.387  0.020  1.387
 5LX  C14  C18  aromatic  1.387  0.020  1.387
 5LX  C10  C9   aromatic  1.386  0.020  1.386
 5LX  C18  C9   aromatic  1.386  0.020  1.386
 5LX  C9   O8   single    1.373  0.020  1.373
 5LX  O8   C5   single    1.357  0.020  1.357
 5LX  C6   C5   aromatic  1.389  0.020  1.389
 5LX  C6   C7   aromatic  1.383  0.020  1.383
 5LX  C5   C4   aromatic  1.388  0.020  1.388
 5LX  CL2  C7   single    1.735  0.020  1.735
 5LX  C7   C12  aromatic  1.395  0.020  1.395
 5LX  C4   C3   aromatic  1.385  0.020  1.385
 5LX  C3   C12  aromatic  1.391  0.020  1.391
 5LX  C12  C15  single    1.528  0.020  1.528
 5LX  O16  C15  single    1.398  0.020  1.398
 5LX  O16  C22  single    1.419  0.020  1.419
 5LX  C15  O17  single    1.391  0.020  1.391
 5LX  C15  C25  single    1.535  0.020  1.535
 5LX  C22  C23  single    1.534  0.020  1.534
 5LX  C23  O17  single    1.425  0.020  1.425
 5LX  C23  C40  single    1.509  0.020  1.509
 5LX  N29  N28  aromatic  1.337  0.020  1.337
 5LX  N29  C30  aromatic  1.311  0.020  1.311
 5LX  C25  N28  single    1.438  0.020  1.438
 5LX  N28  C32  aromatic  1.337  0.020  1.337
 5LX  C30  N31  aromatic  1.351  0.020  1.351
 5LX  C32  N31  aromatic  1.312  0.020  1.312
 5LX  C3   H1   single    0.930  0.020  1.080
 5LX  C4   H2   single    0.930  0.020  1.080
 5LX  C6   H3   single    0.930  0.020  1.080
 5LX  C10  H4   single    0.930  0.020  1.080
 5LX  C14  H5   single    0.930  0.020  1.080
 5LX  C11  H6   single    0.930  0.020  1.080
 5LX  C18  H7   single    0.930  0.020  1.080
 5LX  C22  H8   single    0.970  0.020  1.090
 5LX  C22  H9   single    0.970  0.020  1.090
 5LX  C23  H10  single    0.970  0.020  1.090
 5LX  C25  H11  single    0.970  0.020  1.090
 5LX  C25  H12  single    0.970  0.020  1.090
 5LX  C30  H13  single    0.930  0.020  1.080
 5LX  C32  H14  single    0.930  0.020  1.080
 5LX  C40  H15  single    0.970  0.020  1.090
 5LX  C40  H16  single    0.970  0.020  1.090
 5LX  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
 5LX  H1   C3   C12  119.11  3.000
 5LX  H1   C3   C4   118.09  3.000
 5LX  C12  C3   C4   122.80  3.000
 5LX  H2   C4   C5   121.69  3.000
 5LX  H2   C4   C3   119.31  3.000
 5LX  C5   C4   C3   119.00  3.000
 5LX  O8   C5   C6   115.87  3.000
 5LX  C6   C5   C4   119.94  3.000
 5LX  O8   C5   C4   124.19  3.000
 5LX  H3   C6   C7   120.59  3.000
 5LX  H3   C6   C5   119.85  3.000
 5LX  C7   C6   C5   119.57  3.000
 5LX  H4   C10  C9   120.47  3.000
 5LX  H4   C10  C11  119.94  3.000
 5LX  C9   C10  C11  119.59  3.000
 5LX  C25  C15  O17  109.09  3.000
 5LX  C25  C15  O16  107.54  3.000
 5LX  O17  C15  O16  105.76  3.000
 5LX  C25  C15  C12  111.24  3.000
 5LX  O17  C15  C12  110.83  3.000
 5LX  O16  C15  C12  112.16  3.000
 5LX  H5   C14  C18  119.99  3.000
 5LX  H5   C14  C13  120.70  3.000
 5LX  C18  C14  C13  119.31  3.000
 5LX  CL1  C13  C11  119.38  3.000
 5LX  C11  C13  C14  121.19  3.000
 5LX  CL1  C13  C14  119.43  3.000
 5LX  C7   C12  C15  123.74  3.000
 5LX  C15  C12  C3   119.67  3.000
 5LX  C7   C12  C3   116.49  3.000
 5LX  H6   C11  C13  120.66  3.000
 5LX  H6   C11  C10  120.00  3.000
 5LX  C13  C11  C10  119.33  3.000
 5LX  C18  C9   O8   119.46  3.000
 5LX  O8   C9   C10  119.57  3.000
 5LX  C18  C9   C10  120.95  3.000
 5LX  CL2  C7   C12  121.65  3.000
 5LX  C12  C7   C6   122.18  3.000
 5LX  CL2  C7   C6   116.14  3.000
 5LX  C9   O8   C5   118.95  3.000
 5LX  C22  O16  C15  108.36  3.000
 5LX  C23  O17  C15  106.87  3.000
 5LX  H7   C18  C9   120.38  3.000
 5LX  H7   C18  C14  120.01  3.000
 5LX  C9   C18  C14  119.61  3.000
 5LX  H9   C22  H8   108.63  3.000
 5LX  H9   C22  C23  111.69  3.000
 5LX  H8   C22  C23  112.12  3.000
 5LX  H9   C22  O16  110.92  3.000
 5LX  H8   C22  O16  108.72  3.000
 5LX  C23  C22  O16  104.71  3.000
 5LX  H10  C23  C40  109.72  3.000
 5LX  H10  C23  C22  110.12  3.000
 5LX  C40  C23  C22  114.65  3.000
 5LX  H10  C23  O17  109.72  3.000
 5LX  C40  C23  O17  109.96  3.000
 5LX  C22  C23  O17  102.40  3.000
 5LX  H12  C25  H11  107.99  3.000
 5LX  H12  C25  N28  109.37  3.000
 5LX  H11  C25  N28  107.89  3.000
 5LX  H12  C25  C15  109.63  3.000
 5LX  H11  C25  C15  109.73  3.000
 5LX  N28  C25  C15  112.13  3.000
 5LX  C32  N28  N29  109.74  3.000
 5LX  C32  N28  C25  128.05  3.000
 5LX  N29  N28  C25  121.92  3.000
 5LX  C30  N29  N28  102.87  3.000
 5LX  H13  C30  N31  123.45  3.000
 5LX  H13  C30  N29  121.99  3.000
 5LX  N31  C30  N29  114.55  3.000
 5LX  C32  N31  C30  102.73  3.000
 5LX  H14  C32  N31  126.89  3.000
 5LX  H14  C32  N28  123.01  3.000
 5LX  N31  C32  N28  110.10  3.000
 5LX  H17  C40  H16  108.86  3.000
 5LX  H17  C40  H15  108.11  3.000
 5LX  H16  C40  H15  107.67  3.000
 5LX  H17  C40  C23  111.11  3.000
 5LX  H16  C40  C23  111.39  3.000
 5LX  H15  C40  C23  109.58  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
 5LX  CONST_01  C6   C5   C4   C3     0.00   0.0  0
 5LX  CONST_02  C6   C7   C12  C3     0.00   0.0  0
 5LX  CONST_03  C7   C6   C5   C4     0.00   0.0  0
 5LX  CONST_04  C7   C12  C3   C4     0.00   0.0  0
 5LX  CONST_05  C12  C7   C6   C5     0.00   0.0  0
 5LX  CONST_06  C12  C3   C4   C5     0.00   0.0  0
 5LX  CONST_07  C14  C13  C11  C10    0.00   0.0  0
 5LX  CONST_08  C14  C18  C9   C10    0.00   0.0  0
 5LX  CONST_09  C9   C10  C11  C13    0.00   0.0  0
 5LX  CONST_10  C9   C18  C14  C13    0.00   0.0  0
 5LX  CONST_11  C18  C14  C13  C11    0.00   0.0  0
 5LX  CONST_12  C18  C9   C10  C11    0.00   0.0  0
 5LX  CONST_13  N31  C30  N29  N28    0.00   0.0  0
 5LX  CONST_14  C30  N31  C32  N28    0.00   0.0  0
 5LX  CONST_15  N31  C32  N28  N29    0.00   0.0  0
 5LX  CONST_16  C32  N31  C30  N29    0.00   0.0  0
 5LX  CONST_17  C32  N28  N29  C30    0.00   0.0  0
 5LX  CONST_18  C15  C12  C3   C4   180.00   0.0  0
 5LX  CONST_19  C15  C12  C7   C6   180.00   0.0  0
 5LX  CONST_20  O8   C5   C4   C3   180.00   0.0  0
 5LX  CONST_21  CL2  C7   C12  C3   180.00   0.0  0
 5LX  CONST_22  CL2  C7   C6   C5   180.00   0.0  0
 5LX  CONST_23  CL1  C13  C11  C10  180.00   0.0  0
 5LX  CONST_24  CL2  C7   C12  C15    0.00   0.0  0
 5LX  CONST_25  O8   C9   C18  C14  180.00   0.0  0
 5LX  CONST_26  O8   C9   C10  C11  180.00   0.0  0
 5LX  CONST_27  O8   C5   C6   C7   180.00   0.0  0
 5LX  CONST_28  CL1  C13  C14  C18  180.00   0.0  0
 5LX  CONST_29  C30  N29  N28  C25  180.00   0.0  0
 5LX  CONST_30  N31  C32  N28  C25  180.00   0.0  0
 5LX  CONST_31  H3   C6   C5   C4   180.00   0.0  0
 5LX  CONST_32  H1   C3   C4   C5   180.00   0.0  0
 5LX  CONST_33  H2   C4   C5   C6   180.00   0.0  0
 5LX  CONST_34  H7   C18  C9   C10  180.00   0.0  0
 5LX  CONST_35  H6   C11  C13  C14  180.00   0.0  0
 5LX  CONST_36  H4   C10  C11  C13  180.00   0.0  0
 5LX  CONST_37  H5   C14  C13  C11  180.00   0.0  0
 5LX  CONST_38  H13  C30  N29  N28  180.00   0.0  0
 5LX  CONST_39  H14  C32  N28  N29  180.00   0.0  0
 5LX  Var_01    C23  C22  O16  C15    7.63  30.0  1
 5LX  Var_02    C10  C9   O8   C5   -88.00  30.0  2
 5LX  Var_03    N29  N28  C25  C15  -74.86  30.0  2

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
 5LX  chir_01  C15  O16  O17  C12  negativ
 5LX  chir_02  C23  O17  C40  C22  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
 5LX  plan-1  C25  0.020
 5LX  plan-1  N28  0.020
 5LX  plan-1  N29  0.020
 5LX  plan-1  C30  0.020
 5LX  plan-1  N31  0.020
 5LX  plan-1  C32  0.020
 5LX  plan-1  H13  0.020
 5LX  plan-1  H14  0.020
 5LX  plan-2  C3   0.020
 5LX  plan-2  C4   0.020
 5LX  plan-2  C5   0.020
 5LX  plan-2  C6   0.020
 5LX  plan-2  C15  0.020
 5LX  plan-2  C12  0.020
 5LX  plan-2  C7   0.020
 5LX  plan-2  O8   0.020
 5LX  plan-2  CL2  0.020
 5LX  plan-2  H1   0.020
 5LX  plan-2  H2   0.020
 5LX  plan-2  H3   0.020
 5LX  plan-3  C10  0.020
 5LX  plan-3  C14  0.020
 5LX  plan-3  C13  0.020
 5LX  plan-3  C11  0.020
 5LX  plan-3  C9   0.020
 5LX  plan-3  O8   0.020
 5LX  plan-3  C18  0.020
 5LX  plan-3  H4   0.020
 5LX  plan-3  H5   0.020
 5LX  plan-3  H6   0.020
 5LX  plan-3  H7   0.020
 5LX  plan-3  CL1  0.020

