# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 19:04:46 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 5-[3-({[(2,4-dichlorophenyl)carbonyl]carbamoyl}amino)-2-methylphenoxy]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(NC(=O)NC(=O)c2ccc(Cl)cc2Cl)cccc1OCCCCC(O)=O
#
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
 BN5  BN5  '5-[3-({[(2,4-dichlorophenyl)carbonyl]carbamoyl}amino)-2-methylphenoxy]pentanoic acid'  ligand  49  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BN5
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
 BN5  C4    C   CR16  0  -0.188   2.6362   0.4458    5.6100
 BN5  C5    C   CR16  0  -0.284   1.7195   0.5921    4.5831
 BN5  C6    C   CR6   0   0.010   0.3510   0.4706    4.8062
 BN5  C1    C   CR6   0  -0.084  -0.0848   0.1850    6.0982
 BN5  CL1   CL  CL    0  -0.096  -1.7618  -0.0310    6.4439
 BN5  C2    C   CR16  0  -0.149   0.8144   0.0171    7.1383
 BN5  C3    C   CR6   0  -0.048   2.1690   0.1584    6.8816
 BN5  N1    N   NH1   0  -0.737  -0.3071  -0.0032    2.5580
 BN5  C7    C   C     0   0.529  -0.6099   0.7184    3.6846
 BN5  O1    O   O     0  -0.400  -1.5300   1.4910    3.7911
 BN5  N2    N   NH1   0  -0.789  -0.4046  -0.7333    0.3948
 BN5  C9    C   CR6   0   0.301  -0.9050  -0.8281   -0.9244
 BN5  C10   C   CR16  0  -0.294  -2.2070  -1.2851   -1.1217
 BN5  C11   C   CR16  0  -0.263  -2.6952  -1.4017   -2.4071
 BN5  C12   C   CR16  0  -0.384  -1.8963  -1.0885   -3.5004
 BN5  C16   C   CH2   0  -0.168  -0.2172  -0.3417   -5.6314
 BN5  C17   C   CH2   0  -0.456   0.9109   0.1144   -6.5323
 BN5  C18   C   CH2   0  -0.430   0.4639   0.1650   -7.9885
 BN5  C19   C   CH2   0  -0.579   1.5958   0.6018   -8.9030
 BN5  C20   C   C     0   0.551   1.1992   0.6883  -10.3506
 BN5  O5    O   OH1   0  -0.598   2.2115   1.0824  -11.1183
 BN5  O4    O   O     0  -0.445   0.1045   0.4357  -10.7886
 BN5  C13   C   CR6   0   0.362  -0.5942  -0.6476   -3.2952
 BN5  C14   C   CR6   0  -0.048  -0.0813  -0.4882   -1.9952
 BN5  C8    C   C     0   0.738  -0.9628   0.0793    1.3268
 BN5  O2    O   O     0  -0.464  -1.9181   0.7933    1.1245
 BN5  CL2   CL  CL    0  -0.099   3.2896  -0.0364    8.1788
 BN5  H4    H   HCR6  0   0.296   3.6939   0.5558    5.4176
 BN5  H5    H   HCR6  0   0.292   2.0837   0.8266    3.5909
 BN5  H2    H   HCR6  0   0.310   0.4621  -0.2219    8.1318
 BN5  HN1   H   HNH1  0   0.432   0.4403  -0.6767    2.6467
 BN5  HN2   H   HNH1  0   0.416   0.4585  -1.2117    0.6028
 BN5  H10   H   HCR6  0   0.258  -2.8197  -1.5596   -0.2738
 BN5  H11   H   HCR6  0   0.260  -3.7045  -1.7542   -2.5729
 BN5  H151  H   HCH3  0   0.251   2.0582  -0.7545   -1.9729
 BN5  H152  H   HCH3  0   0.251   1.5379   0.8385   -2.4913
 BN5  H153  H   HCH3  0   0.240   1.4649   0.4034   -0.7918
 BN5  H12   H   HCR6  0   0.280  -2.2997  -1.2061   -4.4964
 BN5  H161  H   HCH2  0   0.222  -0.5449  -1.3483   -5.9166
 BN5  H162  H   HCH2  0   0.222  -1.0804   0.3268   -5.7320
 BN5  H171  H   HCH2  0   0.234   1.2526   1.1041   -6.2160
 BN5  H172  H   HCH2  0   0.234   1.7593  -0.5681   -6.4272
 BN5  H181  H   HCH2  0   0.234   0.0990  -0.8186   -8.2954
 BN5  H182  H   HCH2  0   0.234  -0.3773   0.8556   -8.0881
 BN5  H191  H   HCH2  0   0.278   1.9835   1.5790   -8.5976
 BN5  H192  H   HCH2  0   0.279   2.4434  -0.0866   -8.8251
 BN5  HO5   H   HOH1  0   0.478   1.9258   1.1262  -12.0429
 BN5  C15   C   CH3   0  -0.718   1.3142   0.0267   -1.8009
 BN5  O3    O   O2    0  -0.471   0.2534  -0.3335   -4.2933

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
 BN5  C4   C5    aromatic  1.384  0.020  1.384
 BN5  C4   C3    aromatic  1.385  0.020  1.385
 BN5  C4   H4    single    0.930  0.020  1.080
 BN5  C5   C6    aromatic  1.392  0.020  1.392
 BN5  C5   H5    single    0.930  0.020  1.080
 BN5  C6   C1    aromatic  1.393  0.020  1.393
 BN5  C6   C7    single    1.498  0.020  1.498
 BN5  C1   CL1   single    1.726  0.020  1.726
 BN5  C1   C2    aromatic  1.385  0.020  1.385
 BN5  C2   C3    aromatic  1.386  0.020  1.386
 BN5  C2   H2    single    0.930  0.020  1.080
 BN5  C3   CL2   single    1.725  0.020  1.725
 BN5  N1   C7    single    1.372  0.020  1.372
 BN5  N1   C8    single    1.397  0.020  1.397
 BN5  N1   HN1   single    0.860  0.020  1.020
 BN5  C7   O1    double    1.206  0.020  1.206
 BN5  N2   C9    single    1.414  0.020  1.414
 BN5  N2   C8    single    1.357  0.020  1.357
 BN5  N2   HN2   single    0.860  0.020  1.020
 BN5  C9   C10   aromatic  1.394  0.020  1.394
 BN5  C9   C14   aromatic  1.393  0.020  1.393
 BN5  C10  C11   aromatic  1.380  0.020  1.380
 BN5  C10  H10   single    0.930  0.020  1.080
 BN5  C11  C12   aromatic  1.390  0.020  1.390
 BN5  C11  H11   single    0.930  0.020  1.080
 BN5  C15  C14   single    1.500  0.020  1.500
 BN5  C15  H151  single    0.970  0.020  1.090
 BN5  C15  H152  single    0.970  0.020  1.090
 BN5  C15  H153  single    0.970  0.020  1.090
 BN5  C12  C13   aromatic  1.390  0.020  1.390
 BN5  C12  H12   single    0.930  0.020  1.080
 BN5  O3   C16   single    1.419  0.020  1.419
 BN5  O3   C13   single    1.347  0.020  1.347
 BN5  C16  C17   single    1.514  0.020  1.514
 BN5  C16  H161  single    0.970  0.020  1.090
 BN5  C16  H162  single    0.970  0.020  1.090
 BN5  C17  C18   single    1.524  0.020  1.524
 BN5  C17  H171  single    0.970  0.020  1.090
 BN5  C17  H172  single    0.970  0.020  1.090
 BN5  C18  C19   single    1.519  0.020  1.519
 BN5  C18  H181  single    0.970  0.020  1.090
 BN5  C18  H182  single    0.970  0.020  1.090
 BN5  C19  C20   single    1.503  0.020  1.503
 BN5  C19  H191  single    0.970  0.020  1.090
 BN5  C19  H192  single    0.970  0.020  1.090
 BN5  C20  O5    single    1.330  0.020  1.330
 BN5  C20  O4    double    1.206  0.020  1.206
 BN5  O5   HO5   single    0.850  0.020  0.980
 BN5  C13  C14   aromatic  1.407  0.020  1.407
 BN5  C8   O2    double    1.210  0.020  1.210

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
 BN5  H4    C4   C3    120.98  3.000
 BN5  H4    C4   C5    120.35  3.000
 BN5  C3    C4   C5    118.67  3.000
 BN5  H5    C5   C6    119.78  3.000
 BN5  H5    C5   C4    118.68  3.000
 BN5  C6    C5   C4    121.53  3.000
 BN5  C7    C6   C1    121.86  3.000
 BN5  C7    C6   C5    119.76  3.000
 BN5  C1    C6   C5    118.31  3.000
 BN5  C2    C1   CL1   117.73  3.000
 BN5  C2    C1   C6    121.21  3.000
 BN5  CL1   C1   C6    121.03  3.000
 BN5  H2    C2   C3    120.75  3.000
 BN5  H2    C2   C1    120.36  3.000
 BN5  C3    C2   C1    118.89  3.000
 BN5  CL2   C3   C2    118.95  3.000
 BN5  CL2   C3   C4    119.65  3.000
 BN5  C2    C3   C4    121.39  3.000
 BN5  HN1   N1   C8    117.65  3.000
 BN5  HN1   N1   C7    116.23  3.000
 BN5  C8    N1   C7    126.08  3.000
 BN5  O1    C7   N1    125.30  3.000
 BN5  O1    C7   C6    121.96  3.000
 BN5  N1    C7   C6    112.73  3.000
 BN5  HN2   N2   C8    119.64  3.000
 BN5  HN2   N2   C9    117.61  3.000
 BN5  C8    N2   C9    122.37  3.000
 BN5  C14   C9   C10   121.57  3.000
 BN5  C14   C9   N2    119.44  3.000
 BN5  C10   C9   N2    118.98  3.000
 BN5  H10   C10  C11   120.56  3.000
 BN5  H10   C10  C9    120.09  3.000
 BN5  C11   C10  C9    119.34  3.000
 BN5  H11   C11  C12   119.28  3.000
 BN5  H11   C11  C10   120.02  3.000
 BN5  C12   C11  C10   120.69  3.000
 BN5  H12   C12  C13   121.33  3.000
 BN5  H12   C12  C11   119.07  3.000
 BN5  C13   C12  C11   119.60  3.000
 BN5  H162  C16  H161  107.50  3.000
 BN5  H162  C16  C17   110.39  3.000
 BN5  H161  C16  C17   110.16  3.000
 BN5  H162  C16  O3    110.14  3.000
 BN5  H161  C16  O3    110.48  3.000
 BN5  C17   C16  O3    108.20  3.000
 BN5  H172  C17  H171  107.12  3.000
 BN5  H172  C17  C18   109.87  3.000
 BN5  H171  C17  C18   109.75  3.000
 BN5  H172  C17  C16   109.44  3.000
 BN5  H171  C17  C16   109.48  3.000
 BN5  C18   C17  C16   111.10  3.000
 BN5  H182  C18  H181  106.62  3.000
 BN5  H182  C18  C19   109.69  3.000
 BN5  H181  C18  C19   109.78  3.000
 BN5  H182  C18  C17   109.50  3.000
 BN5  H181  C18  C17   109.65  3.000
 BN5  C19   C18  C17   111.48  3.000
 BN5  H192  C19  H191  105.50  3.000
 BN5  H192  C19  C20   108.00  3.000
 BN5  H191  C19  C20   108.10  3.000
 BN5  H192  C19  C18   110.68  3.000
 BN5  H191  C19  C18   110.64  3.000
 BN5  C20   C19  C18   113.55  3.000
 BN5  O4    C20  O5    122.91  3.000
 BN5  O4    C20  C19   125.25  3.000
 BN5  O5    C20  C19   111.84  3.000
 BN5  HO5   O5   C20   109.87  3.000
 BN5  C14   C13  O3    115.41  3.000
 BN5  C14   C13  C12   120.93  3.000
 BN5  O3    C13  C12   123.66  3.000
 BN5  C13   C14  C15   119.86  3.000
 BN5  C13   C14  C9    117.85  3.000
 BN5  C15   C14  C9    122.29  3.000
 BN5  O2    C8   N2    124.30  3.000
 BN5  O2    C8   N1    123.56  3.000
 BN5  N2    C8   N1    112.14  3.000
 BN5  H153  C15  H152  107.55  3.000
 BN5  H153  C15  H151  107.42  3.000
 BN5  H152  C15  H151  107.06  3.000
 BN5  H153  C15  C14   111.59  3.000
 BN5  H152  C15  C14   111.40  3.000
 BN5  H151  C15  C14   111.58  3.000
 BN5  C13   O3   C16   119.27  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
 BN5  CONST_01  C1    C6   C5   C4      0.00   0.0  0
 BN5  CONST_02  C1    C2   C3   C4      0.00   0.0  0
 BN5  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 BN5  CONST_04  C2    C1   C6   C5      0.00   0.0  0
 BN5  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 BN5  CONST_06  C3    C2   C1   C6      0.00   0.0  0
 BN5  CONST_07  C12   C11  C10  C9      0.00   0.0  0
 BN5  CONST_08  C12   C13  C14  C9      0.00   0.0  0
 BN5  CONST_09  C13   C14  C9   C10     0.00   0.0  0
 BN5  CONST_10  C13   C12  C11  C10     0.00   0.0  0
 BN5  CONST_11  C14   C9   C10  C11     0.00   0.0  0
 BN5  CONST_12  C14   C13  C12  C11     0.00   0.0  0
 BN5  CONST_13  C7    C6   C5   C4    180.00   0.0  0
 BN5  CONST_14  CL2   C3   C4   C5    180.00   0.0  0
 BN5  CONST_15  CL1   C1   C6   C5    180.00   0.0  0
 BN5  CONST_16  CL2   C3   C2   C1    180.00   0.0  0
 BN5  CONST_17  C3    C2   C1   CL1   180.00   0.0  0
 BN5  CONST_18  C7    C6   C1   C2    180.00   0.0  0
 BN5  CONST_19  C11   C10  C9   N2    180.00   0.0  0
 BN5  CONST_20  C13   C14  C9   N2    180.00   0.0  0
 BN5  CONST_21  O3    C13  C14  C9    180.00   0.0  0
 BN5  CONST_22  C15   C14  C9   C10   180.00   0.0  0
 BN5  CONST_23  O3    C13  C12  C11   180.00   0.0  0
 BN5  CONST_24  C12   C13  C14  C15   180.00   0.0  0
 BN5  CONST_25  H2    C2   C3   C4    180.00   0.0  0
 BN5  CONST_26  H4    C4   C5   C6    180.00   0.0  0
 BN5  CONST_27  H5    C5   C6   C1    180.00   0.0  0
 BN5  CONST_28  H11   C11  C10  C9    180.00   0.0  0
 BN5  CONST_29  H12   C12  C11  C10   180.00   0.0  0
 BN5  CONST_30  H10   C10  C11  C12   180.00   0.0  0
 BN5  CONST_34  C8    N1   C7   C6    180.00   0.0  0
 BN5  CONST_35  O2    C8   N2   C9      0.00   0.0  0
 BN5  CONST_36  C9    N2   C8   N1    180.00   0.0  0
 BN5  CONST_37  HN1   N1   C7   C6      0.00   0.0  0
 BN5  CONST_38  O2    C8   N1   C7      0.00   0.0  0
 BN5  CONST_39  C8    N1   C7   O1      0.00   0.0  0
 BN5  CONST_40  N2    C8   N1   C7    180.00   0.0  0
 BN5  CONST_41  HO5   O5   C20  C19   180.00   0.0  0
 BN5  Var_01    N1    C7   C6   C5     51.85  30.0  2
 BN5  Var_02    C14   C13  O3   C16  -174.06  30.0  2
 BN5  Var_03    H151  C15  C14  C9    101.20  30.0  2
 BN5  Var_04    H161  C16  O3   C13   -62.24  30.0  3
 BN5  Var_05    C18   C17  C16  O3   -178.52  30.0  3
 BN5  Var_06    C19   C18  C17  C16  -179.15  30.0  3
 BN5  Var_07    C20   C19  C18  C17  -179.11  30.0  3
 BN5  Var_08    O5    C20  C19  C18   179.55  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
 BN5  plan-1  C4   0.020
 BN5  plan-1  C5   0.020
 BN5  plan-1  C6   0.020
 BN5  plan-1  C1   0.020
 BN5  plan-1  CL1  0.020
 BN5  plan-1  C2   0.020
 BN5  plan-1  C3   0.020
 BN5  plan-1  C7   0.020
 BN5  plan-1  CL2  0.020
 BN5  plan-1  H4   0.020
 BN5  plan-1  H5   0.020
 BN5  plan-1  H2   0.020
 BN5  plan-2  N2   0.020
 BN5  plan-2  C9   0.020
 BN5  plan-2  C10  0.020
 BN5  plan-2  C11  0.020
 BN5  plan-2  C12  0.020
 BN5  plan-2  C13  0.020
 BN5  plan-2  C14  0.020
 BN5  plan-2  H10  0.020
 BN5  plan-2  H11  0.020
 BN5  plan-2  H12  0.020
 BN5  plan-2  C15  0.020
 BN5  plan-2  O3   0.020
 BN5  plan-3  C6   0.020
 BN5  plan-3  N1   0.020
 BN5  plan-3  C7   0.020
 BN5  plan-3  O1   0.020
 BN5  plan-3  N2   0.020
 BN5  plan-3  C9   0.020
 BN5  plan-3  C8   0.020
 BN5  plan-3  O2   0.020
 BN5  plan-3  HN1  0.020
 BN5  plan-3  HN2  0.020
 BN5  plan-4  C19  0.020
 BN5  plan-4  C20  0.020
 BN5  plan-4  O5   0.020
 BN5  plan-4  O4   0.020
 BN5  plan-4  HO5  0.020

