# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 18:44:29 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(Cl)c1C(=O)NCc2ccc3OCOc3c2
#
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
 BXB  BXB  N-(1,3-benzodioxol-5-ylmethyl)-2,6-dichlorobenzamide  ligand  32  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BXB
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
 BXB  C1    C   CR6   0   0.098   2.4397   0.1783   0.0339
 BXB  C2    C   CR6   0  -0.086   3.4890  -0.6871  -0.2479
 BXB  C3    C   CR16  0  -0.191   4.4462  -0.3852  -1.2022
 BXB  C4    C   CR16  0  -0.276   4.3541   0.8161  -1.8878
 BXB  C5    C   CR16  0  -0.192   3.3204   1.7035  -1.6303
 BXB  C6    C   CR6   0  -0.090   2.3782   1.3740  -0.6704
 BXB  C7    C   C     0   0.482   1.4397  -0.1349   1.1137
 BXB  N8    N   NH1   0  -0.593   0.3880  -0.8371   0.6816
 BXB  O9    O   O     0  -0.455   1.6158   0.2477   2.2568
 BXB  CL10  CL  CL    0  -0.101   3.5919  -2.1846   0.6121
 BXB  CL11  CL  CL    0  -0.099   1.0829   2.4741  -0.3465
 BXB  C12   C   CH2   0  -0.349  -0.7159  -1.2570   1.5188
 BXB  C13   C   CR6   0   0.076  -2.0435  -0.9482   0.8792
 BXB  C14   C   CR16  0  -0.327  -2.9762  -1.9556   0.6923
 BXB  C15   C   CR16  0  -0.331  -4.2309  -1.7075   0.1176
 BXB  C16   C   CR56  0   0.293  -4.4921  -0.4161  -0.2602
 BXB  C17   C   CR56  0   0.315  -3.5615   0.5976  -0.0813
 BXB  C18   C   CR16  0  -0.367  -2.3336   0.3690   0.4818
 BXB  O19   O   O     0  -0.487  -4.0694   1.7628  -0.5469
 BXB  C20   C   CH2   0   0.074  -5.3916   1.4877  -0.9930
 BXB  O21   O   O     0  -0.486  -5.6041   0.0896  -0.8434
 BXB  H3    H   HCR6  0   0.292   5.2508  -1.0772  -1.4072
 BXB  H4    H   HCR6  0   0.286   5.0969   1.0625  -2.6339
 BXB  H5    H   HCR6  0   0.291   3.2504   2.6381  -2.1688
 BXB  HN8   H   HNH1  0   0.414   0.3717  -1.1260  -0.2846
 BXB  H12   H   HCH2  0   0.270  -0.6429  -2.3279   1.7216
 BXB  H12A  H   HCH2  0   0.271  -0.6216  -0.7453   2.4764
 BXB  H14   H   HCR6  0   0.258  -2.7316  -2.9662   0.9940
 BXB  H15   H   HCR6  0   0.273  -4.9500  -2.5021  -0.0262
 BXB  H18   H   HCR6  0   0.259  -1.6153   1.1690   0.6101
 BXB  H20   H   HCH2  0   0.238  -6.1112   2.0395  -0.3823
 BXB  H20A  H   HCH2  0   0.241  -5.4925   1.7666  -2.0438

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
 BXB  C1   C2    aromatic  1.389  0.020  1.389
 BXB  C1   C6    aromatic  1.389  0.020  1.389
 BXB  C1   C7    single    1.505  0.020  1.505
 BXB  C2   C3    aromatic  1.385  0.020  1.385
 BXB  C2   CL10  single    1.730  0.020  1.730
 BXB  C3   C4    aromatic  1.386  0.020  1.386
 BXB  C4   C5    aromatic  1.386  0.020  1.386
 BXB  C5   C6    aromatic  1.385  0.020  1.385
 BXB  C6   CL11  single    1.730  0.020  1.730
 BXB  C7   N8    single    1.336  0.020  1.336
 BXB  C7   O9    double    1.218  0.020  1.218
 BXB  N8   C12   single    1.448  0.020  1.448
 BXB  C12  C13   single    1.506  0.020  1.506
 BXB  C13  C14   aromatic  1.386  0.020  1.386
 BXB  C13  C18   aromatic  1.406  0.020  1.406
 BXB  C14  C15   aromatic  1.402  0.020  1.402
 BXB  C15  C16   aromatic  1.371  0.020  1.371
 BXB  C16  C17   aromatic  1.388  0.020  1.388
 BXB  C16  O21   single    1.354  0.020  1.354
 BXB  C17  C18   aromatic  1.370  0.020  1.370
 BXB  C17  O19   single    1.354  0.020  1.354
 BXB  O19  C20   single    1.422  0.020  1.422
 BXB  C20  O21   single    1.422  0.020  1.422
 BXB  C3   H3    single    0.930  0.020  1.080
 BXB  C4   H4    single    0.930  0.020  1.080
 BXB  C5   H5    single    0.930  0.020  1.080
 BXB  N8   HN8   single    0.860  0.020  1.020
 BXB  C12  H12   single    0.970  0.020  1.090
 BXB  C12  H12A  single    0.970  0.020  1.090
 BXB  C14  H14   single    0.930  0.020  1.080
 BXB  C15  H15   single    0.930  0.020  1.080
 BXB  C18  H18   single    0.930  0.020  1.080
 BXB  C20  H20   single    0.970  0.020  1.090
 BXB  C20  H20A  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
 BXB  C7    C1   C6   120.91  3.000
 BXB  C7    C1   C2   121.20  3.000
 BXB  C6    C1   C2   117.83  3.000
 BXB  CL10  C2   C3   119.35  3.000
 BXB  CL10  C2   C1   118.91  3.000
 BXB  C3    C2   C1   121.74  3.000
 BXB  H3    C3   C4   120.70  3.000
 BXB  H3    C3   C2   120.37  3.000
 BXB  C4    C3   C2   118.93  3.000
 BXB  H4    C4   C5   119.64  3.000
 BXB  H4    C4   C3   119.54  3.000
 BXB  C5    C4   C3   120.82  3.000
 BXB  H5    C5   C6   120.46  3.000
 BXB  H5    C5   C4   120.61  3.000
 BXB  C6    C5   C4   118.93  3.000
 BXB  CL11  C6   C5   119.20  3.000
 BXB  CL11  C6   C1   119.05  3.000
 BXB  C5    C6   C1   121.75  3.000
 BXB  O9    C7   N8   125.60  3.000
 BXB  O9    C7   C1   120.80  3.000
 BXB  N8    C7   C1   113.60  3.000
 BXB  HN8   N8   C12  117.29  3.000
 BXB  HN8   N8   C7   118.23  3.000
 BXB  C12   N8   C7   124.44  3.000
 BXB  H12A  C12  H12  106.94  3.000
 BXB  H12A  C12  C13  110.69  3.000
 BXB  H12   C12  C13  109.80  3.000
 BXB  H12A  C12  N8   107.82  3.000
 BXB  H12   C12  N8   109.92  3.000
 BXB  C13   C12  N8   111.54  3.000
 BXB  C18   C13  C14  120.27  3.000
 BXB  C18   C13  C12  119.61  3.000
 BXB  C14   C13  C12  120.12  3.000
 BXB  H14   C14  C15  118.78  3.000
 BXB  H14   C14  C13  119.28  3.000
 BXB  C15   C14  C13  121.94  3.000
 BXB  H15   C15  C16  121.93  3.000
 BXB  H15   C15  C14  121.31  3.000
 BXB  C16   C15  C14  116.76  3.000
 BXB  O21   C16  C17  109.49  3.000
 BXB  O21   C16  C15  128.85  3.000
 BXB  C17   C16  C15  121.66  3.000
 BXB  O19   C17  C18  128.41  3.000
 BXB  O19   C17  C16  109.44  3.000
 BXB  C18   C17  C16  122.15  3.000
 BXB  H18   C18  C17  121.33  3.000
 BXB  H18   C18  C13  121.45  3.000
 BXB  C17   C18  C13  117.22  3.000
 BXB  C20   O19  C17  106.87  3.000
 BXB  H20A  C20  H20  110.36  3.000
 BXB  H20A  C20  O21  109.79  3.000
 BXB  H20   C20  O21  109.83  3.000
 BXB  H20A  C20  O19  109.77  3.000
 BXB  H20   C20  O19  109.82  3.000
 BXB  O21   C20  O19  107.22  3.000
 BXB  C20   O21  C16  106.85  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
 BXB  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 BXB  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 BXB  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 BXB  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 BXB  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 BXB  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 BXB  CONST_07  C16   C15  C14  C13    0.00   0.0  0
 BXB  CONST_08  C16   C17  C18  C13    0.00   0.0  0
 BXB  CONST_09  C17   C18  C13  C14    0.00   0.0  0
 BXB  CONST_10  C17   C16  C15  C14    0.00   0.0  0
 BXB  CONST_11  C18   C13  C14  C15    0.00   0.0  0
 BXB  CONST_12  C18   C17  C16  C15    0.00   0.0  0
 BXB  CONST_13  CL11  C6   C1   C2   180.00   0.0  0
 BXB  CONST_14  C7    C1   C2   C3   180.00   0.0  0
 BXB  CONST_15  CL10  C2   C3   C4   180.00   0.0  0
 BXB  CONST_16  CL11  C6   C5   C4   180.00   0.0  0
 BXB  CONST_17  C7    C1   C6   C5   180.00   0.0  0
 BXB  CONST_18  CL10  C2   C1   C6   180.00   0.0  0
 BXB  CONST_19  C15   C14  C13  C12  180.00   0.0  0
 BXB  CONST_20  C17   C18  C13  C12  180.00   0.0  0
 BXB  CONST_21  H3    C3   C2   C1   180.00   0.0  0
 BXB  CONST_22  H5    C5   C6   C1   180.00   0.0  0
 BXB  CONST_23  H4    C4   C3   C2   180.00   0.0  0
 BXB  CONST_24  H15   C15  C14  C13  180.00   0.0  0
 BXB  CONST_25  H18   C18  C13  C14  180.00   0.0  0
 BXB  CONST_26  H14   C14  C15  C16  180.00   0.0  0
 BXB  CONST_27  C12   N8   C7   C1   180.00   0.0  0
 BXB  CONST_28  HN8   N8   C7   C1     0.00   0.0  0
 BXB  CONST_29  C12   N8   C7   O9     0.00   0.0  0
 BXB  Var_01    O19   C20  O21  C16    3.59  30.0  1
 BXB  Var_02    O21   C20  O19  C17   -3.55  30.0  1
 BXB  Var_03    N8    C7   C1   C2   -89.58  30.0  2
 BXB  Var_04    C14   C13  C12  N8   125.04  30.0  2
 BXB  Var_05    C13   C12  N8   C7   132.26  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
 BXB  plan-1  C1    0.020
 BXB  plan-1  C2    0.020
 BXB  plan-1  C3    0.020
 BXB  plan-1  C4    0.020
 BXB  plan-1  C5    0.020
 BXB  plan-1  C6    0.020
 BXB  plan-1  C7    0.020
 BXB  plan-1  CL10  0.020
 BXB  plan-1  CL11  0.020
 BXB  plan-1  H3    0.020
 BXB  plan-1  H4    0.020
 BXB  plan-1  H5    0.020
 BXB  plan-2  C12   0.020
 BXB  plan-2  C13   0.020
 BXB  plan-2  C14   0.020
 BXB  plan-2  C15   0.020
 BXB  plan-2  C16   0.020
 BXB  plan-2  C17   0.020
 BXB  plan-2  C18   0.020
 BXB  plan-2  O19   0.020
 BXB  plan-2  O21   0.020
 BXB  plan-2  H14   0.020
 BXB  plan-2  H15   0.020
 BXB  plan-2  H18   0.020
 BXB  plan-3  C1    0.020
 BXB  plan-3  C7    0.020
 BXB  plan-3  N8    0.020
 BXB  plan-3  O9    0.020
 BXB  plan-3  C12   0.020
 BXB  plan-3  HN8   0.020

