# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 14:57:35 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-oxo-5-({4-[(E)-2-phenylethenyl]phenyl}amino)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC(=O)Nc1ccc(cc1)/C=C/c2ccccc2
#
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
 SPB  SPB  '5-oxo-5-({4-[(E)-2-phenylethenyl]phenyl}amino)pentanoic acid'  ligand  42  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SPB
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
 SPB  C1    C  CR16  0  -0.316   1.6635   0.4167  -6.4800
 SPB  C2    C  CR16  0  -0.241   1.7563   0.3918  -7.8638
 SPB  C3    C  CR16  0  -0.272   0.6698  -0.0117  -8.6272
 SPB  C4    C  CR16  0  -0.233  -0.5074  -0.3926  -7.9911
 SPB  C5    C  CR16  0  -0.335  -0.5992  -0.3684  -6.6098
 SPB  C6    C  CR6   0   0.167   0.4850   0.0442  -5.8259
 SPB  C7    C  C1    0  -0.313   0.4479   0.1002  -4.3659
 SPB  C8    C  C1    0  -0.302  -0.6309  -0.0776  -3.5905
 SPB  C9    C  CR6   0   0.152  -0.6621  -0.0328  -2.1322
 SPB  C10   C  CR16  0  -0.301  -1.8952  -0.0682  -1.4750
 SPB  C11   C  CR16  0  -0.340  -1.9812  -0.0286  -0.0971
 SPB  C12   C  CR6   0   0.361  -0.8286   0.0411   0.6894
 SPB  C13   C  CR16  0  -0.293   0.4143   0.0735   0.0481
 SPB  C14   C  CR16  0  -0.324   0.4820   0.0358  -1.3331
 SPB  N15   N  NH1   0  -0.747  -1.0071   0.0721   2.0716
 SPB  C16   C  C     0   0.561  -0.0804   0.0730   3.0687
 SPB  C17   C  CH2   0  -0.599  -0.6966   0.0920   4.4515
 SPB  C18   C  CH2   0  -0.419   0.3272   0.0780   5.5742
 SPB  C19   C  CH2   0  -0.583  -0.3714   0.1035   6.9239
 SPB  C20   C  C     0   0.552   0.5752   0.0804   8.0913
 SPB  O21   O  O     0  -0.444   1.7771   0.0225   8.0138
 SPB  O22   O  O     0  -0.464   1.1209   0.0594   2.8767
 SPB  O23   O  OH1   0  -0.597  -0.0739   0.1301   9.2511
 SPB  HC1   H  HCR6  0   0.253   2.5178   0.7336  -5.8933
 SPB  HC2   H  HCR6  0   0.257   2.6792   0.6892  -8.3447
 SPB  HC3   H  HCR6  0   0.257   0.7380  -0.0339  -9.7070
 SPB  HC4   H  HCR6  0   0.258  -1.3589  -0.7157  -8.5764
 SPB  HC5   H  HCR6  0   0.252  -1.5227  -0.6844  -6.1417
 SPB  HC7   H  H     0   0.250   1.4027   0.3271  -3.9009
 SPB  HC8   H  H     0   0.250  -1.5939  -0.2664  -4.0561
 SPB  H10C  H  HCR6  0   0.257  -2.8080  -0.1271  -2.0561
 SPB  H11C  H  HCR6  0   0.270  -2.9559  -0.0566   0.3767
 SPB  H13C  H  HCR6  0   0.282   1.3278   0.1229   0.6172
 SPB  H14C  H  HCR6  0   0.254   1.4644   0.0514  -1.7876
 SPB  H15N  H  HNH1  0   0.418  -1.9709   0.0765   2.3719
 SPB  H171  H  HCH2  0   0.276  -1.3703  -0.7662   4.5427
 SPB  H172  H  HCH2  0   0.277  -1.3368   0.9767   4.5319
 SPB  H181  H  HCH2  0   0.241   0.9919   0.9385   5.4839
 SPB  H182  H  HCH2  0   0.241   0.9523  -0.8130   5.4969
 SPB  H191  H  HCH2  0   0.280  -1.0512  -0.7491   7.0242
 SPB  H192  H  HCH2  0   0.279  -1.0051   0.9914   7.0160
 SPB  H23O  H  HOH1  0   0.479   0.5569   0.1076   9.9860

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
 SPB  C1   C2    aromatic  1.387  0.020  1.387
 SPB  C1   C6    aromatic  1.398  0.020  1.398
 SPB  C1   HC1   single    0.930  0.020  1.080
 SPB  C2   C3    aromatic  1.388  0.020  1.388
 SPB  C2   HC2   single    0.930  0.020  1.080
 SPB  C3   C4    aromatic  1.391  0.020  1.391
 SPB  C3   HC3   single    0.930  0.020  1.080
 SPB  C4   C5    aromatic  1.385  0.020  1.385
 SPB  C4   HC4   single    0.930  0.020  1.080
 SPB  C5   C6    aromatic  1.400  0.020  1.400
 SPB  C5   HC5   single    0.930  0.020  1.080
 SPB  C6   C7    single    1.462  0.020  1.462
 SPB  C7   C8    double    1.340  0.020  1.340
 SPB  C7   HC7   single    0.930  0.020  1.080
 SPB  C8   C9    single    1.459  0.020  1.459
 SPB  C8   HC8   single    0.930  0.020  1.080
 SPB  C9   C10   aromatic  1.398  0.020  1.398
 SPB  C9   C14   aromatic  1.397  0.020  1.397
 SPB  C10  C11   aromatic  1.381  0.020  1.381
 SPB  C10  H10C  single    0.930  0.020  1.080
 SPB  C11  C12   aromatic  1.397  0.020  1.397
 SPB  C11  H11C  single    0.930  0.020  1.080
 SPB  C12  C13   aromatic  1.399  0.020  1.399
 SPB  C12  N15   single    1.394  0.020  1.394
 SPB  C13  C14   aromatic  1.383  0.020  1.383
 SPB  C13  H13C  single    0.930  0.020  1.080
 SPB  C14  H14C  single    0.930  0.020  1.080
 SPB  N15  C16   single    1.361  0.020  1.361
 SPB  N15  H15N  single    0.860  0.020  1.020
 SPB  C16  C17   single    1.514  0.020  1.514
 SPB  C16  O22   double    1.217  0.020  1.217
 SPB  C17  C18   single    1.519  0.020  1.519
 SPB  C17  H171  single    0.970  0.020  1.090
 SPB  C17  H172  single    0.970  0.020  1.090
 SPB  C18  C19   single    1.520  0.020  1.520
 SPB  C18  H181  single    0.970  0.020  1.090
 SPB  C18  H182  single    0.970  0.020  1.090
 SPB  C19  C20   single    1.503  0.020  1.503
 SPB  C19  H191  single    0.970  0.020  1.090
 SPB  C19  H192  single    0.970  0.020  1.090
 SPB  C20  O21   double    1.206  0.020  1.206
 SPB  C20  O23   single    1.330  0.020  1.330
 SPB  O23  H23O  single    0.850  0.020  0.980

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
 SPB  HC1   C1   C6    119.28  3.000
 SPB  HC1   C1   C2    119.50  3.000
 SPB  C6    C1   C2    121.22  3.000
 SPB  HC2   C2   C3    120.20  3.000
 SPB  HC2   C2   C1    119.70  3.000
 SPB  C3    C2   C1    120.10  3.000
 SPB  HC3   C3   C4    120.26  3.000
 SPB  HC3   C3   C2    120.36  3.000
 SPB  C4    C3   C2    119.38  3.000
 SPB  HC4   C4   C5    119.50  3.000
 SPB  HC4   C4   C3    120.01  3.000
 SPB  C5    C4   C3    120.50  3.000
 SPB  HC5   C5   C6    120.30  3.000
 SPB  HC5   C5   C4    118.87  3.000
 SPB  C6    C5   C4    120.82  3.000
 SPB  C7    C6   C5    123.44  3.000
 SPB  C7    C6   C1    118.58  3.000
 SPB  C5    C6   C1    117.98  3.000
 SPB  HC7   C7   C8    119.19  3.000
 SPB  HC7   C7   C6    114.42  3.000
 SPB  C8    C7   C6    126.38  3.000
 SPB  HC8   C8   C9    114.50  3.000
 SPB  HC8   C8   C7    119.26  3.000
 SPB  C9    C8   C7    126.24  3.000
 SPB  C14   C9   C10   117.05  3.000
 SPB  C14   C9   C8    123.75  3.000
 SPB  C10   C9   C8    119.20  3.000
 SPB  H10C  C10  C11   118.96  3.000
 SPB  H10C  C10  C9    119.49  3.000
 SPB  C11   C10  C9    121.55  3.000
 SPB  H11C  C11  C12   119.80  3.000
 SPB  H11C  C11  C10   119.42  3.000
 SPB  C12   C11  C10   120.78  3.000
 SPB  N15   C12  C13   124.59  3.000
 SPB  N15   C12  C11   116.98  3.000
 SPB  C13   C12  C11   118.43  3.000
 SPB  H13C  C13  C14   119.16  3.000
 SPB  H13C  C13  C12   120.81  3.000
 SPB  C14   C13  C12   120.03  3.000
 SPB  H14C  C14  C13   117.59  3.000
 SPB  H14C  C14  C9    120.25  3.000
 SPB  C13   C14  C9    122.16  3.000
 SPB  H15N  N15  C16   115.60  3.000
 SPB  H15N  N15  C12   114.66  3.000
 SPB  C16   N15  C12   129.73  3.000
 SPB  O22   C16  C17   123.11  3.000
 SPB  O22   C16  N15   123.82  3.000
 SPB  C17   C16  N15   113.07  3.000
 SPB  H172  C17  H171  105.51  3.000
 SPB  H172  C17  C18   110.31  3.000
 SPB  H171  C17  C18   110.23  3.000
 SPB  H172  C17  C16   108.37  3.000
 SPB  H171  C17  C16   108.46  3.000
 SPB  C18   C17  C16   113.61  3.000
 SPB  H182  C18  H181  106.80  3.000
 SPB  H182  C18  C19   109.87  3.000
 SPB  H181  C18  C19   109.90  3.000
 SPB  H182  C18  C17   109.95  3.000
 SPB  H181  C18  C17   110.00  3.000
 SPB  C19   C18  C17   110.26  3.000
 SPB  H192  C19  H191  105.34  3.000
 SPB  H192  C19  C20   108.16  3.000
 SPB  H191  C19  C20   107.93  3.000
 SPB  H192  C19  C18   110.75  3.000
 SPB  H191  C19  C18   110.71  3.000
 SPB  C20   C19  C18   113.57  3.000
 SPB  O23   C20  O21   122.98  3.000
 SPB  O23   C20  C19   111.67  3.000
 SPB  O21   C20  C19   125.35  3.000
 SPB  H23O  O23  C20   110.05  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
 SPB  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 SPB  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 SPB  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 SPB  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 SPB  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 SPB  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 SPB  CONST_07  C12   C11  C10  C9     0.00   0.0  0
 SPB  CONST_08  C12   C13  C14  C9     0.00   0.0  0
 SPB  CONST_09  C13   C14  C9   C10    0.00   0.0  0
 SPB  CONST_10  C13   C12  C11  C10    0.00   0.0  0
 SPB  CONST_11  C14   C9   C10  C11    0.00   0.0  0
 SPB  CONST_12  C14   C13  C12  C11    0.00   0.0  0
 SPB  CONST_13  C7    C6   C1   C2   180.00   0.0  0
 SPB  CONST_14  C7    C6   C5   C4   180.00   0.0  0
 SPB  CONST_15  C11   C10  C9   C8   180.00   0.0  0
 SPB  CONST_16  C13   C14  C9   C8   180.00   0.0  0
 SPB  CONST_17  N15   C12  C11  C10  180.00   0.0  0
 SPB  CONST_18  N15   C12  C13  C14  180.00   0.0  0
 SPB  CONST_19  HC3   C3   C2   C1   180.00   0.0  0
 SPB  CONST_20  HC5   C5   C6   C1   180.00   0.0  0
 SPB  CONST_21  HC4   C4   C3   C2   180.00   0.0  0
 SPB  CONST_22  HC1   C1   C2   C3   180.00   0.0  0
 SPB  CONST_23  HC2   C2   C3   C4   180.00   0.0  0
 SPB  CONST_24  H11C  C11  C10  C9   180.00   0.0  0
 SPB  CONST_25  H13C  C13  C14  C9   180.00   0.0  0
 SPB  CONST_26  H14C  C14  C9   C10  180.00   0.0  0
 SPB  CONST_27  H10C  C10  C11  C12  180.00   0.0  0
 SPB  CONST_28  C16   N15  C12  C11  180.00   0.0  0
 SPB  CONST_29  C16   N15  C12  C13    0.00   0.0  0
 SPB  CONST_30  H15N  N15  C12  C11    0.00   0.0  0
 SPB  CONST_31  C17   C16  N15  C12  180.00   0.0  0
 SPB  CONST_32  O22   C16  N15  C12    0.00   0.0  0
 SPB  CONST_33  H23O  O23  C20  C19  180.00   0.0  0
 SPB  Var_01    C9    C8   C7   C6   179.41   0.0  2
 SPB  Var_02    C8    C7   C6   C1   172.21  30.0  2
 SPB  Var_03    C10   C9   C8   C7   171.87  30.0  2
 SPB  Var_04    C18   C17  C16  N15  179.38  30.0  3
 SPB  Var_05    C19   C18  C17  C16  179.80  30.0  3
 SPB  Var_06    C20   C19  C18  C17  179.54  30.0  3
 SPB  Var_07    O21   C20  C19  C18   -1.31  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
 SPB  plan-1  C1    0.020
 SPB  plan-1  C2    0.020
 SPB  plan-1  C3    0.020
 SPB  plan-1  C4    0.020
 SPB  plan-1  C5    0.020
 SPB  plan-1  C6    0.020
 SPB  plan-1  C7    0.020
 SPB  plan-1  HC1   0.020
 SPB  plan-1  HC2   0.020
 SPB  plan-1  HC3   0.020
 SPB  plan-1  HC4   0.020
 SPB  plan-1  HC5   0.020
 SPB  plan-2  C8    0.020
 SPB  plan-2  C9    0.020
 SPB  plan-2  C10   0.020
 SPB  plan-2  C11   0.020
 SPB  plan-2  C12   0.020
 SPB  plan-2  C13   0.020
 SPB  plan-2  C14   0.020
 SPB  plan-2  N15   0.020
 SPB  plan-2  H10C  0.020
 SPB  plan-2  H11C  0.020
 SPB  plan-2  H13C  0.020
 SPB  plan-2  H14C  0.020
 SPB  plan-3  C12   0.020
 SPB  plan-3  N15   0.020
 SPB  plan-3  C16   0.020
 SPB  plan-3  C17   0.020
 SPB  plan-3  O22   0.020
 SPB  plan-3  H15N  0.020
 SPB  plan-4  C19   0.020
 SPB  plan-4  C20   0.020
 SPB  plan-4  O21   0.020
 SPB  plan-4  O23   0.020
 SPB  plan-4  H23O  0.020
 SPB  plan-5  C6    0.020
 SPB  plan-5  C7    0.020
 SPB  plan-5  C8    0.020
 SPB  plan-5  C9    0.020
 SPB  plan-5  HC7   0.020
 SPB  plan-5  HC8   0.020

