# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:06:11 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 1,3-dichloro-2-({4-[(2-chloro-4-methoxyphenoxy)methyl]benzyl}oxy)benzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(OCc2ccc(COc3c(Cl)cccc3Cl)cc2)c(Cl)c1
#
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
 SC4  SC4  1,3-dichloro-2-({4-[(2-chloro-4-methoxyphenoxy)methyl]benzyl}oxy)benzene  ligand  44  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SC4
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
 SC4  C1    C   CR16  0  -0.326   0.0271   1.8409   6.5127
 SC4  C2    C   CR16  0  -0.373  -0.0082   1.7088   5.1350
 SC4  C3    C   CR6   0   0.434  -0.0075   0.4524   4.5321
 SC4  C4    C   CR6   0  -0.144   0.0323  -0.6601   5.3690
 SC4  CL1   CL  CL    0  -0.110   0.0395  -2.2374   4.6590
 SC4  C5    C   CR16  0  -0.334   0.0673  -0.5452   6.7499
 SC4  C6    C   CR6   0   0.366   0.0639   0.7181   7.3347
 SC4  O1    O   O2    0  -0.455  -0.0428   0.2263   3.2062
 SC4  C7    C   CH2   0  -0.271  -0.0689   1.3473   2.3324
 SC4  C10   C   CR16  0  -0.267   1.0504   0.0285  -1.0351
 SC4  C11   C   CR6   0   0.077  -0.1644  -0.2624  -1.6496
 SC4  C12   C   CR16  0  -0.282  -1.3460  -0.0027  -0.9649
 SC4  C13   C   CR16  0  -0.277  -1.3153   0.5252   0.3178
 SC4  C8    C   CR6   0   0.095  -0.1024   0.8131   0.9332
 SC4  C9    C   CR16  0  -0.280   1.0805   0.5569   0.2455
 SC4  O3    O   O2    0  -0.473   0.0946   0.9367   8.6644
 SC4  C21   C   CH3   0  -0.440   0.1240  -0.1793   9.5306
 SC4  O2    O   O2    0  -0.463   0.0007   0.3264  -3.9292
 SC4  C16   C   CR6   0  -0.142  -1.0973  -0.0447  -6.0170
 SC4  C17   C   CR16  0  -0.218  -1.0430  -0.3298  -7.3716
 SC4  C18   C   CR16  0  -0.277   0.1863  -0.5785  -7.9624
 SC4  C19   C   CR16  0  -0.218   1.3518  -0.5369  -7.2127
 SC4  C20   C   CR6   0  -0.142   1.2755  -0.2509  -5.8594
 SC4  C15   C   CR6   0   0.490   0.0563   0.0102  -5.2375
 SC4  H1    H   HCR6  0   0.272   0.0257   2.8295   6.9538
 SC4  H2    H   HCR6  0   0.294  -0.0368   2.6076   4.5344
 SC4  H5    H   HCR6  0   0.298   0.0974  -1.4468   7.3458
 SC4  H71   H   HCH2  0   0.245  -0.9512   1.9658   2.5288
 SC4  H72   H   HCH2  0   0.246   0.8170   1.9727   2.4859
 SC4  H10   H   HCR6  0   0.252   1.9794  -0.1638  -1.5584
 SC4  H12   H   HCR6  0   0.256  -2.2987  -0.2167  -1.4340
 SC4  H13   H   HCR6  0   0.257  -2.2451   0.7213   0.8378
 SC4  H9    H   HCR6  0   0.258   2.0333   0.7764   0.7119
 SC4  H211  H   HCH3  0   0.262   0.1395   0.2155  10.5432
 SC4  H212  H   HCH3  0   0.229  -0.7604  -0.8116   9.4140
 SC4  H213  H   HCH3  0   0.229   1.0165  -0.7927   9.3798
 SC4  H141  H   HCH2  0   0.246   0.6017  -1.5289  -3.2019
 SC4  H142  H   HCH2  0   0.247  -1.1490  -1.2761  -3.2628
 SC4  H17   H   HCR6  0   0.289  -1.9513  -0.3614  -7.9571
 SC4  H18   H   HCR6  0   0.281   0.2373  -0.7988  -9.0196
 SC4  H19   H   HCR6  0   0.289   2.3106  -0.7300  -7.6733
 SC4  C14   C   CH2   0  -0.244  -0.1924  -0.7929  -3.0476
 SC4  CL2   CL  CL    0  -0.087  -2.6152   0.2826  -5.2622
 SC4  CL3   CL  CL    0  -0.086   2.7142  -0.1809  -4.9082

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
 SC4  C1   C2    aromatic  1.384  0.020  1.384
 SC4  C1   C6    aromatic  1.392  0.020  1.392
 SC4  C1   H1    single    0.930  0.020  1.080
 SC4  C2   C3    aromatic  1.393  0.020  1.393
 SC4  C2   H2    single    0.930  0.020  1.080
 SC4  C3   C4    aromatic  1.393  0.020  1.393
 SC4  C3   O1    single    1.346  0.020  1.346
 SC4  C4   CL1   single    1.730  0.020  1.730
 SC4  C4   C5    aromatic  1.386  0.020  1.386
 SC4  CL2  C16   single    1.727  0.020  1.727
 SC4  CL3  C20   single    1.726  0.020  1.726
 SC4  C5   C6    aromatic  1.392  0.020  1.392
 SC4  C5   H5    single    0.930  0.020  1.080
 SC4  C6   O3    single    1.348  0.020  1.348
 SC4  O1   C7    single    1.422  0.020  1.422
 SC4  C7   C8    single    1.498  0.020  1.498
 SC4  C7   H71   single    0.970  0.020  1.090
 SC4  C7   H72   single    0.970  0.020  1.090
 SC4  C10  C11   aromatic  1.392  0.020  1.392
 SC4  C10  C9    aromatic  1.386  0.020  1.386
 SC4  C10  H10   single    0.930  0.020  1.080
 SC4  C11  C12   aromatic  1.390  0.020  1.390
 SC4  C11  C14   single    1.496  0.020  1.496
 SC4  C12  C13   aromatic  1.387  0.020  1.387
 SC4  C12  H12   single    0.930  0.020  1.080
 SC4  C13  C8    aromatic  1.390  0.020  1.390
 SC4  C13  H13   single    0.930  0.020  1.080
 SC4  C8   C9    aromatic  1.392  0.020  1.392
 SC4  C9   H9    single    0.930  0.020  1.080
 SC4  O3   C21   single    1.413  0.020  1.413
 SC4  C21  H211  single    0.970  0.020  1.090
 SC4  C21  H212  single    0.970  0.020  1.090
 SC4  C21  H213  single    0.970  0.020  1.090
 SC4  C14  O2    single    1.438  0.020  1.438
 SC4  C14  H141  single    0.970  0.020  1.090
 SC4  C14  H142  single    0.970  0.020  1.090
 SC4  O2   C15   single    1.347  0.020  1.347
 SC4  C16  C17   aromatic  1.385  0.020  1.385
 SC4  C16  C15   aromatic  1.393  0.020  1.393
 SC4  C17  C18   aromatic  1.386  0.020  1.386
 SC4  C17  H17   single    0.930  0.020  1.080
 SC4  C18  C19   aromatic  1.386  0.020  1.386
 SC4  C18  H18   single    0.930  0.020  1.080
 SC4  C19  C20   aromatic  1.385  0.020  1.385
 SC4  C19  H19   single    0.930  0.020  1.080
 SC4  C20  C15   aromatic  1.393  0.020  1.393

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
 SC4  H1    C1   C6    119.74  3.000
 SC4  H1    C1   C2    119.51  3.000
 SC4  C6    C1   C2    120.75  3.000
 SC4  H2    C2   C3    120.60  3.000
 SC4  H2    C2   C1    118.29  3.000
 SC4  C3    C2   C1    121.10  3.000
 SC4  O1    C3   C4    117.30  3.000
 SC4  O1    C3   C2    125.30  3.000
 SC4  C4    C3   C2    117.40  3.000
 SC4  C5    C4   CL1   118.97  3.000
 SC4  C5    C4   C3    122.22  3.000
 SC4  CL1   C4   C3    118.81  3.000
 SC4  H5    C5   C6    121.69  3.000
 SC4  H5    C5   C4    118.73  3.000
 SC4  C6    C5   C4    119.58  3.000
 SC4  O3    C6   C5    124.16  3.000
 SC4  O3    C6   C1    116.90  3.000
 SC4  C5    C6   C1    118.94  3.000
 SC4  C7    O1   C3    118.27  3.000
 SC4  H72   C7   H71   107.70  3.000
 SC4  H72   C7   C8    110.65  3.000
 SC4  H71   C7   C8    110.54  3.000
 SC4  H72   C7   O1    110.44  3.000
 SC4  H71   C7   O1    110.48  3.000
 SC4  C8    C7   O1    107.05  3.000
 SC4  H10   C10  C9    119.69  3.000
 SC4  H10   C10  C11   119.87  3.000
 SC4  C9    C10  C11   120.44  3.000
 SC4  C14   C11  C12   120.71  3.000
 SC4  C14   C11  C10   120.21  3.000
 SC4  C12   C11  C10   119.03  3.000
 SC4  H12   C12  C13   119.67  3.000
 SC4  H12   C12  C11   119.83  3.000
 SC4  C13   C12  C11   120.50  3.000
 SC4  H13   C13  C8    119.92  3.000
 SC4  H13   C13  C12   119.58  3.000
 SC4  C8    C13  C12   120.49  3.000
 SC4  C9    C8   C13   118.98  3.000
 SC4  C9    C8   C7    120.53  3.000
 SC4  C13   C8   C7    120.45  3.000
 SC4  H9    C9   C8    119.83  3.000
 SC4  H9    C9   C10   119.62  3.000
 SC4  C8    C9   C10   120.55  3.000
 SC4  C21   O3   C6    118.50  3.000
 SC4  H213  C21  H212  108.74  3.000
 SC4  H213  C21  H211  108.70  3.000
 SC4  H212  C21  H211  108.72  3.000
 SC4  H213  C21  O3    112.05  3.000
 SC4  H212  C21  O3    112.00  3.000
 SC4  H211  C21  O3    106.52  3.000
 SC4  C15   O2   C14   114.72  3.000
 SC4  C15   C16  C17   121.51  3.000
 SC4  C15   C16  CL2   118.42  3.000
 SC4  C17   C16  CL2   120.06  3.000
 SC4  H17   C17  C18   120.59  3.000
 SC4  H17   C17  C16   120.17  3.000
 SC4  C18   C17  C16   119.23  3.000
 SC4  H18   C18  C19   119.69  3.000
 SC4  H18   C18  C17   119.67  3.000
 SC4  C19   C18  C17   120.63  3.000
 SC4  H19   C19  C20   120.13  3.000
 SC4  H19   C19  C18   120.64  3.000
 SC4  C20   C19  C18   119.22  3.000
 SC4  C15   C20  C19   121.53  3.000
 SC4  C15   C20  CL3   118.41  3.000
 SC4  C19   C20  CL3   120.06  3.000
 SC4  C20   C15  C16   117.87  3.000
 SC4  C20   C15  O2    120.90  3.000
 SC4  C16   C15  O2    121.22  3.000
 SC4  H142  C14  H141  108.07  3.000
 SC4  H142  C14  O2    109.94  3.000
 SC4  H141  C14  O2    109.87  3.000
 SC4  H142  C14  C11   110.93  3.000
 SC4  H141  C14  C11   110.92  3.000
 SC4  O2    C14  C11   107.13  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
 SC4  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 SC4  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 SC4  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 SC4  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 SC4  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 SC4  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 SC4  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 SC4  CONST_08  C13   C8   C9   C10     0.00   0.0  0
 SC4  CONST_09  C8    C9   C10  C11     0.00   0.0  0
 SC4  CONST_10  C8    C13  C12  C11     0.00   0.0  0
 SC4  CONST_11  C9    C10  C11  C12     0.00   0.0  0
 SC4  CONST_12  C9    C8   C13  C12     0.00   0.0  0
 SC4  CONST_13  C19   C18  C17  C16     0.00   0.0  0
 SC4  CONST_14  C19   C20  C15  C16     0.00   0.0  0
 SC4  CONST_15  C20   C15  C16  C17     0.00   0.0  0
 SC4  CONST_16  C20   C19  C18  C17     0.00   0.0  0
 SC4  CONST_17  C15   C16  C17  C18     0.00   0.0  0
 SC4  CONST_18  C15   C20  C19  C18     0.00   0.0  0
 SC4  CONST_19  O1    C3   C2   C1    180.00   0.0  0
 SC4  CONST_20  O3    C6   C1   C2    180.00   0.0  0
 SC4  CONST_21  CL1   C4   C3   C2    180.00   0.0  0
 SC4  CONST_22  O3    C6   C5   C4    180.00   0.0  0
 SC4  CONST_23  C6    C5   C4   CL1   180.00   0.0  0
 SC4  CONST_24  C18   C17  C16  CL2   180.00   0.0  0
 SC4  CONST_25  C20   C15  C16  CL2   180.00   0.0  0
 SC4  CONST_26  C18   C19  C20  CL3   180.00   0.0  0
 SC4  CONST_27  C16   C15  C20  CL3   180.00   0.0  0
 SC4  CONST_28  O1    C3   C4   C5    180.00   0.0  0
 SC4  CONST_29  C12   C13  C8   C7    180.00   0.0  0
 SC4  CONST_30  C10   C9   C8   C7    180.00   0.0  0
 SC4  CONST_31  C14   C11  C12  C13   180.00   0.0  0
 SC4  CONST_32  C14   C11  C10  C9    180.00   0.0  0
 SC4  CONST_33  C17   C16  C15  O2    180.00   0.0  0
 SC4  CONST_34  C19   C20  C15  O2    180.00   0.0  0
 SC4  CONST_35  H5    C5   C6   C1    180.00   0.0  0
 SC4  CONST_36  H1    C1   C2   C3    180.00   0.0  0
 SC4  CONST_37  H2    C2   C3   C4    180.00   0.0  0
 SC4  CONST_38  H12   C12  C11  C10   180.00   0.0  0
 SC4  CONST_39  H9    C9   C10  C11   180.00   0.0  0
 SC4  CONST_40  H13   C13  C12  C11   180.00   0.0  0
 SC4  CONST_41  H10   C10  C11  C12   180.00   0.0  0
 SC4  CONST_42  H18   C18  C17  C16   180.00   0.0  0
 SC4  CONST_43  H19   C19  C18  C17   180.00   0.0  0
 SC4  CONST_44  H17   C17  C18  C19   180.00   0.0  0
 SC4  Var_01    C8    C7   O1   C3    179.88  30.0  3
 SC4  Var_02    C13   C8   C7   O1     88.34  30.0  2
 SC4  Var_03    O2    C14  C11  C10   -79.01  30.0  2
 SC4  Var_04    C16   C15  O2   C14    88.84  30.0  2
 SC4  Var_05    H211  C21  O3   C6   -179.66  30.0  3

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
 SC4  plan-1  C1   0.020
 SC4  plan-1  C2   0.020
 SC4  plan-1  C3   0.020
 SC4  plan-1  C4   0.020
 SC4  plan-1  CL1  0.020
 SC4  plan-1  C5   0.020
 SC4  plan-1  C6   0.020
 SC4  plan-1  O1   0.020
 SC4  plan-1  O3   0.020
 SC4  plan-1  H1   0.020
 SC4  plan-1  H2   0.020
 SC4  plan-1  H5   0.020
 SC4  plan-2  C7   0.020
 SC4  plan-2  C10  0.020
 SC4  plan-2  C11  0.020
 SC4  plan-2  C12  0.020
 SC4  plan-2  C13  0.020
 SC4  plan-2  C8   0.020
 SC4  plan-2  C9   0.020
 SC4  plan-2  H10  0.020
 SC4  plan-2  H12  0.020
 SC4  plan-2  H13  0.020
 SC4  plan-2  H9   0.020
 SC4  plan-2  C14  0.020
 SC4  plan-3  O2   0.020
 SC4  plan-3  C16  0.020
 SC4  plan-3  C17  0.020
 SC4  plan-3  C18  0.020
 SC4  plan-3  C19  0.020
 SC4  plan-3  C20  0.020
 SC4  plan-3  C15  0.020
 SC4  plan-3  H17  0.020
 SC4  plan-3  H18  0.020
 SC4  plan-3  H19  0.020
 SC4  plan-3  CL2  0.020
 SC4  plan-3  CL3  0.020

