# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 00:59:46 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-[3-chloro-4-({[(2,4-dichlorophenyl)carbonyl]carbamoyl}amino)phenoxy]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCOc1ccc(NC(=O)NC(=O)c2ccc(Cl)cc2Cl)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
 BN3  BN3  '4-[3-chloro-4-({[(2,4-dichlorophenyl)carbonyl]carbamoyl}amino)phenoxy]butanoic acid'  ligand  42  28  .  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_BN3
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
 BN3  C4    C   CR16   0  -0.188  -0.8437   1.3917  -6.3660
 BN3  C5    C   CR16   0  -0.283  -0.2593   1.1188  -5.1411
 BN3  C6    C   CR6    0   0.006   0.1994  -0.1561  -4.8226
 BN3  C1    C   CR6    0  -0.083   0.0462  -1.1691  -5.7660
 BN3  CL1   CL  CL     0  -0.096   0.5437  -2.7851  -5.4210
 BN3  C2    C   CR16   0  -0.149  -0.5529  -0.9247  -6.9907
 BN3  C3    C   CR6    0  -0.048  -0.9849   0.3603  -7.2794
 BN3  N1    N   NH1    0  -0.734   0.1798   0.0626  -2.4435
 BN3  C7    C   C      0   0.531   0.9010  -0.3857  -3.5205
 BN3  O1    O   O      0  -0.400   1.9883  -0.9044  -3.4606
 BN3  N2    N   NH1    0  -0.780  -0.3793   0.3911  -0.2531
 BN3  C9    C   CR6    0   0.358  -0.1548   0.4655   1.1334
 BN3  C10   C   CR16   0  -0.264   0.6037   1.4947   1.6863
 BN3  C11   C   CR16   0  -0.350   0.8167   1.5773   3.0457
 BN3  C12   C   CR6    0   0.396   0.2535   0.6290   3.9052
 BN3  O3    O   O2     0  -0.471   0.4977   0.7856   5.2126
 BN3  C15   C   CH2    0  -0.174  -0.0726  -0.1307   6.1418
 BN3  C16   C   CH2    0  -0.451   0.3440   0.2797   7.5376
 BN3  C17   C   CH2    0  -0.592  -0.2778  -0.6355   8.5802
 BN3  C13   C   CR16   0  -0.351  -0.5156  -0.4030   3.3743
 BN3  C14   C   CR6    0  -0.070  -0.6952  -0.4748   1.9997
 BN3  C8    C   C      0   0.735   0.6254   0.1064  -1.1211
 BN3  O2    O   O      0  -0.460   1.7765  -0.0671  -0.7947
 BN3  CL2   CL  CL     0  -0.099  -1.7199   0.6706  -8.8090
 BN3  CL3   CL  CL     0  -0.103  -1.6262  -1.7824   1.3561
 BN3  C18   C   C      0   0.417   0.0756  -0.3049  10.0427
 BN3  O4    O   OC    -1  -0.630  -0.3446  -1.1117  10.8980
 BN3  O5    O   O      0  -0.606   0.7351   0.7296  10.2610
 BN3  H4    H   HCR6   0   0.296  -1.1805   2.3914  -6.6003
 BN3  H5    H   HCR6   0   0.292  -0.1417   1.9256  -4.4290
 BN3  H2    H   HCR6   0   0.309  -0.6818  -1.7247  -7.7062
 BN3  HN1   H   HNH1   0   0.433  -0.7696   0.3538  -2.6278
 BN3  HN2   H   HNH1   0   0.413  -1.3359   0.3802  -0.5752
 BN3  H10   H   HCR6   0   0.276   1.0257   2.2479   1.0342
 BN3  H11   H   HCR6   0   0.273   1.4089   2.3849   3.4560
 BN3  H151  H   HCH2   0   0.222   0.2695  -1.1488   5.9232
 BN3  H152  H   HCH2   0   0.221  -1.1653  -0.1221   6.0512
 BN3  H161  H   HCH2   0   0.224   0.0366   1.3118   7.7186
 BN3  H162  H   HCH2   0   0.224   1.4335   0.2534   7.6152
 BN3  H171  H   HCH2   0   0.223   0.0023  -1.6764   8.3851
 BN3  H172  H   HCH2   0   0.227  -1.3700  -0.6124   8.4852
 BN3  H13   H   HCR6   0   0.302  -0.9679  -1.1582   4.0009

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
 BN3  C4   C5    aromatic  1.384  0.020  1.384
 BN3  C4   C3    aromatic  1.385  0.020  1.385
 BN3  C4   H4    single    0.930  0.020  1.080
 BN3  C5   C6    aromatic  1.392  0.020  1.392
 BN3  C5   H5    single    0.930  0.020  1.080
 BN3  C6   C1    aromatic  1.393  0.020  1.393
 BN3  C6   C7    single    1.497  0.020  1.497
 BN3  C1   CL1   single    1.726  0.020  1.726
 BN3  C1   C2    aromatic  1.385  0.020  1.385
 BN3  C2   C3    aromatic  1.386  0.020  1.386
 BN3  C2   H2    single    0.930  0.020  1.080
 BN3  C3   CL2   single    1.725  0.020  1.725
 BN3  N1   C7    single    1.372  0.020  1.372
 BN3  N1   C8    single    1.396  0.020  1.396
 BN3  N1   HN1   single    0.860  0.020  1.020
 BN3  C7   O1    double    1.206  0.020  1.206
 BN3  N2   C9    single    1.407  0.020  1.407
 BN3  N2   C8    single    1.358  0.020  1.358
 BN3  N2   HN2   single    0.860  0.020  1.020
 BN3  C9   C10   aromatic  1.393  0.020  1.393
 BN3  C9   C14   aromatic  1.388  0.020  1.388
 BN3  C10  C11   aromatic  1.378  0.020  1.378
 BN3  C10  H10   single    0.930  0.020  1.080
 BN3  C11  C12   aromatic  1.398  0.020  1.398
 BN3  C11  H11   single    0.930  0.020  1.080
 BN3  C12  O3    single    1.339  0.020  1.339
 BN3  C12  C13   aromatic  1.392  0.020  1.392
 BN3  O3   C15   single    1.424  0.020  1.424
 BN3  C15  C16   single    1.513  0.020  1.513
 BN3  C15  H151  single    0.970  0.020  1.090
 BN3  C15  H152  single    0.970  0.020  1.090
 BN3  C16  C17   single    1.520  0.020  1.520
 BN3  C16  H161  single    0.970  0.020  1.090
 BN3  C16  H162  single    0.970  0.020  1.090
 BN3  C17  C18   single    1.540  0.020  1.540
 BN3  C17  H171  single    0.970  0.020  1.090
 BN3  C17  H172  single    0.970  0.020  1.090
 BN3  C13  C14   aromatic  1.388  0.020  1.388
 BN3  C13  H13   single    0.930  0.020  1.080
 BN3  C14  CL3   single    1.729  0.020  1.729
 BN3  C8   O2    double    1.209  0.020  1.209
 BN3  C18  O4    deloc     1.249  0.020  1.249
 BN3  C18  O5    deloc     1.246  0.020  1.246

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
 BN3  H4    C4   C3    120.94  3.000
 BN3  H4    C4   C5    120.38  3.000
 BN3  C3    C4   C5    118.67  3.000
 BN3  H5    C5   C6    119.76  3.000
 BN3  H5    C5   C4    118.75  3.000
 BN3  C6    C5   C4    121.48  3.000
 BN3  C7    C6   C1    121.96  3.000
 BN3  C7    C6   C5    119.61  3.000
 BN3  C1    C6   C5    118.36  3.000
 BN3  C2    C1   CL1   117.82  3.000
 BN3  C2    C1   C6    121.21  3.000
 BN3  CL1   C1   C6    120.93  3.000
 BN3  H2    C2   C3    120.74  3.000
 BN3  H2    C2   C1    120.41  3.000
 BN3  C3    C2   C1    118.85  3.000
 BN3  CL2   C3   C2    118.96  3.000
 BN3  CL2   C3   C4    119.62  3.000
 BN3  C2    C3   C4    121.42  3.000
 BN3  HN1   N1   C8    117.63  3.000
 BN3  HN1   N1   C7    116.44  3.000
 BN3  C8    N1   C7    125.89  3.000
 BN3  O1    C7   N1    125.14  3.000
 BN3  O1    C7   C6    122.12  3.000
 BN3  N1    C7   C6    112.74  3.000
 BN3  HN2   N2   C8    119.67  3.000
 BN3  HN2   N2   C9    117.79  3.000
 BN3  C8    N2   C9    121.54  3.000
 BN3  C14   C9   C10   117.70  3.000
 BN3  C14   C9   N2    121.15  3.000
 BN3  C10   C9   N2    121.14  3.000
 BN3  H10   C10  C11   119.49  3.000
 BN3  H10   C10  C9    119.18  3.000
 BN3  C11   C10  C9    121.32  3.000
 BN3  H11   C11  C12   119.56  3.000
 BN3  H11   C11  C10   120.22  3.000
 BN3  C12   C11  C10   120.22  3.000
 BN3  C13   C12  O3    124.03  3.000
 BN3  C13   C12  C11   119.39  3.000
 BN3  O3    C12  C11   116.58  3.000
 BN3  C15   O3   C12   119.26  3.000
 BN3  H152  C15  H151  107.57  3.000
 BN3  H152  C15  C16   110.39  3.000
 BN3  H151  C15  C16   110.49  3.000
 BN3  H152  C15  O3    109.88  3.000
 BN3  H151  C15  O3    110.03  3.000
 BN3  C16   C15  O3    108.49  3.000
 BN3  H162  C16  H161  106.96  3.000
 BN3  H162  C16  C17   110.16  3.000
 BN3  H161  C16  C17   109.89  3.000
 BN3  H162  C16  C15   109.48  3.000
 BN3  H161  C16  C15   109.38  3.000
 BN3  C17   C16  C15   110.90  3.000
 BN3  H172  C17  H171  105.03  3.000
 BN3  H172  C17  C18   107.83  3.000
 BN3  H171  C17  C18   108.32  3.000
 BN3  H172  C17  C16   109.59  3.000
 BN3  H171  C17  C16   110.20  3.000
 BN3  C18   C17  C16   115.35  3.000
 BN3  H13   C13  C14   118.94  3.000
 BN3  H13   C13  C12   121.88  3.000
 BN3  C14   C13  C12   119.17  3.000
 BN3  CL3   C14  C13   118.51  3.000
 BN3  CL3   C14  C9    119.31  3.000
 BN3  C13   C14  C9    122.18  3.000
 BN3  O2    C8   N2    124.19  3.000
 BN3  O2    C8   N1    123.72  3.000
 BN3  N2    C8   N1    112.08  3.000
 BN3  O5    C18  O4    126.48  3.000
 BN3  O5    C18  C17   117.77  3.000
 BN3  O4    C18  C17   115.75  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
 BN3  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 BN3  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 BN3  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 BN3  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 BN3  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 BN3  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 BN3  CONST_07  C12  C11  C10  C9      0.00   0.0  0
 BN3  CONST_08  C12  C13  C14  C9      0.00   0.0  0
 BN3  CONST_09  C13  C14  C9   C10     0.00   0.0  0
 BN3  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 BN3  CONST_11  C14  C9   C10  C11     0.00   0.0  0
 BN3  CONST_12  C14  C13  C12  C11     0.00   0.0  0
 BN3  CONST_13  C7   C6   C5   C4    180.00   0.0  0
 BN3  CONST_14  CL2  C3   C4   C5    180.00   0.0  0
 BN3  CONST_15  CL1  C1   C6   C5    180.00   0.0  0
 BN3  CONST_16  CL2  C3   C2   C1    180.00   0.0  0
 BN3  CONST_17  C3   C2   C1   CL1   180.00   0.0  0
 BN3  CONST_18  C7   C6   C1   C2    180.00   0.0  0
 BN3  CONST_19  C11  C10  C9   N2    180.00   0.0  0
 BN3  CONST_20  C13  C14  C9   N2    180.00   0.0  0
 BN3  CONST_21  CL3  C14  C9   C10   180.00   0.0  0
 BN3  CONST_22  O3   C12  C11  C10   180.00   0.0  0
 BN3  CONST_23  CL3  C14  C13  C12   180.00   0.0  0
 BN3  CONST_24  C14  C13  C12  O3    180.00   0.0  0
 BN3  CONST_25  H2   C2   C3   C4    180.00   0.0  0
 BN3  CONST_26  H4   C4   C5   C6    180.00   0.0  0
 BN3  CONST_27  H5   C5   C6   C1    180.00   0.0  0
 BN3  CONST_28  H11  C11  C10  C9    180.00   0.0  0
 BN3  CONST_29  H13  C13  C14  C9    180.00   0.0  0
 BN3  CONST_30  H10  C10  C11  C12   180.00   0.0  0
 BN3  CONST_34  C8   N1   C7   C6    180.00   0.0  0
 BN3  CONST_35  O2   C8   N2   C9      0.00   0.0  0
 BN3  CONST_36  C9   N2   C8   N1    180.00   0.0  0
 BN3  CONST_37  HN1  N1   C7   C6      0.00   0.0  0
 BN3  CONST_38  O2   C8   N1   C7      0.00   0.0  0
 BN3  CONST_39  C8   N1   C7   O1      0.00   0.0  0
 BN3  CONST_40  N2   C8   N1   C7    180.00   0.0  0
 BN3  Var_01    N1   C7   C6   C5     52.88  30.0  2
 BN3  Var_02    C13  C12  O3   C15    -1.24  30.0  2
 BN3  Var_03    C16  C15  O3   C12  -179.35  30.0  3
 BN3  Var_04    C17  C16  C15  O3    177.95  30.0  3
 BN3  Var_05    C18  C17  C16  C15  -179.77  30.0  3
 BN3  Var_06    O4   C18  C17  C16  -174.63  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
 BN3  plan-1  C4   0.020
 BN3  plan-1  C5   0.020
 BN3  plan-1  C6   0.020
 BN3  plan-1  C1   0.020
 BN3  plan-1  CL1  0.020
 BN3  plan-1  C2   0.020
 BN3  plan-1  C3   0.020
 BN3  plan-1  C7   0.020
 BN3  plan-1  CL2  0.020
 BN3  plan-1  H4   0.020
 BN3  plan-1  H5   0.020
 BN3  plan-1  H2   0.020
 BN3  plan-2  N2   0.020
 BN3  plan-2  C9   0.020
 BN3  plan-2  C10  0.020
 BN3  plan-2  C11  0.020
 BN3  plan-2  C12  0.020
 BN3  plan-2  O3   0.020
 BN3  plan-2  C13  0.020
 BN3  plan-2  C14  0.020
 BN3  plan-2  CL3  0.020
 BN3  plan-2  H10  0.020
 BN3  plan-2  H11  0.020
 BN3  plan-2  H13  0.020
 BN3  plan-3  C6   0.020
 BN3  plan-3  N1   0.020
 BN3  plan-3  C7   0.020
 BN3  plan-3  O1   0.020
 BN3  plan-3  N2   0.020
 BN3  plan-3  C9   0.020
 BN3  plan-3  C8   0.020
 BN3  plan-3  O2   0.020
 BN3  plan-3  HN1  0.020
 BN3  plan-3  HN2  0.020
 BN3  plan-4  C17  0.020
 BN3  plan-4  C18  0.020
 BN3  plan-4  O4   0.020
 BN3  plan-4  O5   0.020

