# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 11:52:04 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-[3-(3-nitrophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCc1onc(n1)c2cccc(c2)[N+]([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
 BTO  BTO  '4-[3-(3-nitrophenyl)-1,2,4-oxadiazol-5-yl]butanoic acid'  ligand  30  20  .  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_BTO
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
 BTO  C1    C  CR16   0  -0.233  -5.3755  -0.7000   5.5688
 BTO  C2    C  CR16   0  -0.264  -5.4045  -2.0480   5.8898
 BTO  C3    C  CR6    0   0.288  -4.4486  -2.8810   5.3296
 BTO  C4    C  CR16   0  -0.323  -3.4744  -2.4082   4.4660
 BTO  C5    C  CR6    0   0.017  -3.4569  -1.0552   4.1539
 BTO  C6    C  CR16   0  -0.258  -4.4113  -0.2029   4.7087
 BTO  N     N  N      1   0.329  -4.4671  -4.3011   5.6571
 BTO  O     O  O     -1  -0.373  -5.3122  -4.6928   6.4258
 BTO  O1    O  O      0  -0.373  -3.6372  -5.0127   5.1441
 BTO  C7    C  CR5    0   0.334  -2.4337  -0.5485   3.2399
 BTO  N1    N  N      0  -0.461  -1.4953  -1.3455   2.6550
 BTO  C8    C  CR5    0   0.525  -0.8118  -0.5125   1.9418
 BTO  C9    C  CH2    0  -0.558   0.3410  -0.7776   1.0515
 BTO  C10   C  CH2    0  -0.428   0.0545  -0.4410  -0.4161
 BTO  C11   C  CH2    0  -0.591  -1.1617  -1.1556  -0.9848
 BTO  C12   C  C      0   0.414  -1.0799  -2.6932  -1.0155
 BTO  O13   O  O      0  -0.607   0.0554  -3.2087  -0.9723
 BTO  O14   O  OC    -1  -0.625  -2.1646  -3.3006  -1.1221
 BTO  O15   O  O      0  -0.322  -1.2715   0.7304   2.0548
 BTO  N2    N  N      0  -0.154  -2.3360   0.7030   2.9074
 BTO  H111  H  HCH2   0   0.216  -2.0730  -0.8502  -0.4608
 BTO  H112  H  HCH2   0   0.244  -1.3081  -0.8181  -2.0175
 BTO  H101  H  HCH2   0   0.229  -0.0674   0.6395  -0.5236
 BTO  H102  H  HCH2   0   0.239   0.9427  -0.7100  -0.9881
 BTO  H91   H  HCH2   0   0.276   0.5950  -1.8307   1.1503
 BTO  H92   H  HCH2   0   0.284   1.1967  -0.1980   1.4067
 BTO  H6    H  HCR6   0   0.280  -4.4045   0.8514   4.4665
 BTO  H1    H  HCR6   0   0.287  -6.1133  -0.0349   5.9945
 BTO  H2    H  HCR6   0   0.306  -6.1603  -2.4305   6.5598
 BTO  H4    H  HCR6   0   0.300  -2.7369  -3.0708   4.0365

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
 BTO  C1   C6    aromatic  1.384  0.020  1.384
 BTO  C1   C2    aromatic  1.386  0.020  1.386
 BTO  C1   H1    single    0.930  0.020  1.080
 BTO  C2   C3    aromatic  1.386  0.020  1.386
 BTO  C2   H2    single    0.930  0.020  1.080
 BTO  C3   C4    aromatic  1.385  0.020  1.385
 BTO  C3   N     single    1.458  0.020  1.458
 BTO  C4   C5    aromatic  1.389  0.020  1.389
 BTO  C4   H4    single    0.930  0.020  1.080
 BTO  C5   C7    single    1.463  0.020  1.463
 BTO  C5   C6    aromatic  1.395  0.020  1.395
 BTO  C6   H6    single    0.930  0.020  1.080
 BTO  N    O     single    1.208  0.020  1.208
 BTO  N    O1    double    1.208  0.020  1.208
 BTO  C7   N1    aromatic  1.363  0.020  1.363
 BTO  C7   N2    aromatic  1.299  0.020  1.299
 BTO  N1   C8    aromatic  1.292  0.020  1.292
 BTO  C8   C9    single    1.480  0.020  1.480
 BTO  C8   O15   aromatic  1.330  0.020  1.330
 BTO  C9   C10   single    1.533  0.020  1.533
 BTO  C9   H91   single    0.970  0.020  1.090
 BTO  C9   H92   single    0.970  0.020  1.090
 BTO  C10  C11   single    1.521  0.020  1.521
 BTO  C10  H101  single    0.970  0.020  1.090
 BTO  C10  H102  single    0.970  0.020  1.090
 BTO  C11  C12   single    1.540  0.020  1.540
 BTO  C11  H111  single    0.970  0.020  1.090
 BTO  C11  H112  single    0.970  0.020  1.090
 BTO  C12  O13   deloc     1.248  0.020  1.248
 BTO  C12  O14   deloc     1.248  0.020  1.248
 BTO  O15  N2    aromatic  1.364  0.020  1.364

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
 BTO  H1    C1   C6    119.95  3.000
 BTO  H1    C1   C2    119.54  3.000
 BTO  C6    C1   C2    120.51  3.000
 BTO  H2    C2   C3    121.36  3.000
 BTO  H2    C2   C1    120.18  3.000
 BTO  C3    C2   C1    118.45  3.000
 BTO  N     C3   C4    118.79  3.000
 BTO  N     C3   C2    119.08  3.000
 BTO  C4    C3   C2    122.14  3.000
 BTO  H4    C4   C5    119.97  3.000
 BTO  H4    C4   C3    121.24  3.000
 BTO  C5    C4   C3    118.79  3.000
 BTO  C7    C5   C6    121.04  3.000
 BTO  C6    C5   C4    119.83  3.000
 BTO  C7    C5   C4    119.14  3.000
 BTO  H6    C6   C5    120.15  3.000
 BTO  H6    C6   C1    119.57  3.000
 BTO  C5    C6   C1    120.28  3.000
 BTO  O1    N    O     124.07  3.000
 BTO  O1    N    C3    118.03  3.000
 BTO  O     N    C3    117.90  3.000
 BTO  N2    C7   N1    113.69  3.000
 BTO  N2    C7   C5    123.13  3.000
 BTO  N1    C7   C5    123.18  3.000
 BTO  C8    N1   C7    102.95  3.000
 BTO  O15   C8   C9    119.18  3.000
 BTO  O15   C8   N1    111.89  3.000
 BTO  C9    C8   N1    128.92  3.000
 BTO  H92   C9   H91   107.52  3.000
 BTO  H92   C9   C10   109.94  3.000
 BTO  H91   C9   C10   110.07  3.000
 BTO  H92   C9   C8    108.62  3.000
 BTO  H91   C9   C8    107.50  3.000
 BTO  C10   C9   C8    113.01  3.000
 BTO  H102  C10  H101  106.46  3.000
 BTO  H102  C10  C11   109.84  3.000
 BTO  H101  C10  C11   109.79  3.000
 BTO  H102  C10  C9    107.22  3.000
 BTO  H101  C10  C9    109.41  3.000
 BTO  C11   C10  C9    113.85  3.000
 BTO  H112  C11  H111  104.71  3.000
 BTO  H112  C11  C12   107.20  3.000
 BTO  H111  C11  C12   109.41  3.000
 BTO  H112  C11  C10   108.32  3.000
 BTO  H111  C11  C10   110.83  3.000
 BTO  C12   C11  C10   115.72  3.000
 BTO  O14   C12  O13   126.37  3.000
 BTO  O14   C12  C11   116.20  3.000
 BTO  O13   C12  C11   117.40  3.000
 BTO  N2    O15  C8    107.70  3.000
 BTO  O15   N2   C7    103.78  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
 BTO  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 BTO  CONST_02  C7   C5   C6   C1   180.00   0.0  0
 BTO  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 BTO  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 BTO  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 BTO  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 BTO  CONST_07  C7   C5   C4   C3   180.00   0.0  0
 BTO  CONST_08  C6   C5   C4   C3     0.00   0.0  0
 BTO  CONST_09  N1   C7   C5   C4     0.00   0.0  0
 BTO  CONST_10  N2   C7   C5   C4   180.00   0.0  0
 BTO  CONST_11  C8   N1   C7   C5   180.00   0.0  0
 BTO  CONST_12  O15  N2   C7   C5   180.00   0.0  0
 BTO  CONST_13  N1   C7   C5   C6   180.00   0.0  0
 BTO  CONST_14  N2   C7   C5   C6     0.00   0.0  0
 BTO  CONST_15  O15  C8   N1   C7     0.00   0.0  0
 BTO  CONST_16  C8   O15  N2   C7     0.00   0.0  0
 BTO  CONST_17  O15  N2   C7   N1     0.00   0.0  0
 BTO  CONST_18  N2   O15  C8   N1     0.00   0.0  0
 BTO  CONST_19  N2   C7   N1   C8     0.00   0.0  0
 BTO  CONST_20  N    C3   C2   C1   180.00   0.0  0
 BTO  CONST_21  N    C3   C4   C5   180.00   0.0  0
 BTO  CONST_22  C9   C8   N1   C7   180.00   0.0  0
 BTO  CONST_23  N2   O15  C8   C9   180.00   0.0  0
 BTO  CONST_24  H6   C6   C1   C2   180.00   0.0  0
 BTO  CONST_25  H4   C4   C3   C2   180.00   0.0  0
 BTO  CONST_26  H1   C1   C2   C3   180.00   0.0  0
 BTO  CONST_27  H2   C2   C3   C4   180.00   0.0  0
 BTO  CONST_28  O    N    C3   C2     0.00   0.0  0
 BTO  CONST_29  O1   N    C3   C2   180.00   0.0  0
 BTO  CONST_30  O    N    C3   C4   180.00   0.0  0
 BTO  CONST_31  O1   N    C3   C4     0.00   0.0  0
 BTO  Var_01    C10  C9   C8   N1   117.04  30.0  2
 BTO  Var_02    C11  C10  C9   C8   -55.92  30.0  3
 BTO  Var_03    C12  C11  C10  C9   -62.10  30.0  3
 BTO  Var_04    O13  C12  C11  C10  -21.10  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
 BTO  plan-1  C5   0.020
 BTO  plan-1  C7   0.020
 BTO  plan-1  N1   0.020
 BTO  plan-1  C8   0.020
 BTO  plan-1  C9   0.020
 BTO  plan-1  O15  0.020
 BTO  plan-1  N2   0.020
 BTO  plan-2  C1   0.020
 BTO  plan-2  C2   0.020
 BTO  plan-2  C3   0.020
 BTO  plan-2  C4   0.020
 BTO  plan-2  C5   0.020
 BTO  plan-2  C6   0.020
 BTO  plan-2  N    0.020
 BTO  plan-2  C7   0.020
 BTO  plan-2  H6   0.020
 BTO  plan-2  H1   0.020
 BTO  plan-2  H2   0.020
 BTO  plan-2  H4   0.020
 BTO  plan-3  C3   0.020
 BTO  plan-3  N    0.020
 BTO  plan-3  O    0.020
 BTO  plan-3  O1   0.020
 BTO  plan-4  C11  0.020
 BTO  plan-4  C12  0.020
 BTO  plan-4  O13  0.020
 BTO  plan-4  O14  0.020

