# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 03:30:59 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2E)-3-(3,4-dihydroxyphenyl)-N-[2-(4-hydroxyphenyl)ethyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(CCNC(=O)\C=C\c2ccc(O)c(O)c2)cc1
#
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
 Y13  Y13  (2E)-3-(3,4-dihydroxyphenyl)-N-[2-(4-hydroxyphenyl)ethyl]prop-2-enamide  ligand  39  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y13
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
 Y13  C2   C  CR6   0   0.337   7.2826  -0.0413  -0.2373
 Y13  O16  O  OH1   0  -0.635   8.6145  -0.2572  -0.2013
 Y13  C1   C  CR16  0  -0.370   6.3978  -0.8935  -0.8926
 Y13  C6   C  CR16  0  -0.292   5.0387  -0.6138  -0.8935
 Y13  C5   C  CR6   0   0.100   4.5248   0.5092  -0.2513
 Y13  C7   C  CH2   0  -0.518   3.0464   0.7751  -0.2167
 Y13  C8   C  CH2   0  -0.277   2.3702  -0.0058   0.9156
 Y13  N9   N  NH1   0  -0.656   0.9545   0.2554   1.0255
 Y13  C10  C  C     0   0.571   0.0339  -0.3116   0.2238
 Y13  C11  C  C1    0  -0.434  -1.3546   0.1257   0.4881
 Y13  C12  C  C1    0  -0.229  -2.3696  -0.3120  -0.2647
 Y13  C13  C  CR6   0   0.141  -3.7799   0.0221  -0.1180
 Y13  C14  C  CR16  0  -0.330  -4.2844   0.7849   0.9358
 Y13  C15  C  CR16  0  -0.321  -5.6373   1.0638   1.0207
 Y13  C16  C  CR6   0   0.289  -6.5232   0.5939   0.0594
 Y13  O19  O  OH1   0  -0.625  -7.8311   0.8850   0.1763
 Y13  C17  C  CR6   0   0.278  -6.0295  -0.1723  -1.0052
 Y13  O23  O  OH1   0  -0.643  -6.9430  -0.5964  -1.9068
 Y13  C18  C  CR16  0  -0.434  -4.6777  -0.4515  -1.0816
 Y13  O27  O  O     0  -0.507   0.3283  -1.1283  -0.6438
 Y13  C4   C  CR16  0  -0.296   5.4261   1.3487   0.3998
 Y13  C3   C  CR16  0  -0.323   6.7873   1.0875   0.4106
 Y13  H16  H  HOH1  0   0.473   8.8363  -1.0622  -0.6818
 Y13  H1   H  HCR6  0   0.268   6.7662  -1.7758  -1.4043
 Y13  H6   H  HCR6  0   0.250   4.3678  -1.2884  -1.4133
 Y13  H71  H  HCH2  0   0.244   2.8586   1.8419  -0.0749
 Y13  H72  H  HCH2  0   0.249   2.5892   0.4917  -1.1669
 Y13  H81  H  HCH2  0   0.243   2.5299  -1.0758   0.7719
 Y13  H82  H  HCH2  0   0.255   2.8268   0.2611   1.8689
 Y13  HN9  H  HNH1  0   0.402   0.6573   0.9543   1.6862
 Y13  H11  H  H     0   0.266  -1.5161   0.8172   1.3079
 Y13  H12  H  H     0   0.256  -2.1348  -0.9875  -1.0823
 Y13  H14  H  HCR6  0   0.255  -3.6283   1.1654   1.7073
 Y13  H15  H  HCR6  0   0.271  -6.0213   1.6514   1.8453
 Y13  H19  H  HOH1  0   0.476  -8.3335   0.4952  -0.5491
 Y13  H23  H  HOH1  0   0.483  -6.5239  -1.1075  -2.6078
 Y13  H18  H  HCR6  0   0.276  -4.3066  -1.0452  -1.9110
 Y13  H4   H  HCR6  0   0.248   5.0612   2.2347   0.9066
 Y13  H3   H  HCR6  0   0.260   7.4684   1.7588   0.9190

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
 Y13  C2   O16  single    1.350  0.020  1.350
 Y13  C2   C1   aromatic  1.392  0.020  1.392
 Y13  C2   C3   aromatic  1.393  0.020  1.393
 Y13  O16  H16  single    0.850  0.020  0.980
 Y13  C1   C6   aromatic  1.388  0.020  1.388
 Y13  C1   H1   single    0.930  0.020  1.080
 Y13  C6   C5   aromatic  1.392  0.020  1.392
 Y13  C6   H6   single    0.930  0.020  1.080
 Y13  C5   C7   single    1.503  0.020  1.503
 Y13  C5   C4   aromatic  1.393  0.020  1.393
 Y13  C7   C8   single    1.533  0.020  1.533
 Y13  C7   H71  single    0.970  0.020  1.090
 Y13  C7   H72  single    0.970  0.020  1.090
 Y13  C8   N9   single    1.444  0.020  1.444
 Y13  C8   H81  single    0.970  0.020  1.090
 Y13  C8   H82  single    0.970  0.020  1.090
 Y13  N9   C10  single    1.346  0.020  1.346
 Y13  N9   HN9  single    0.860  0.020  1.020
 Y13  C10  C11  single    1.480  0.020  1.480
 Y13  C10  O27  double    1.227  0.020  1.227
 Y13  C11  C12  double    1.337  0.020  1.337
 Y13  C11  H11  single    0.930  0.020  1.080
 Y13  C12  C13  single    1.457  0.020  1.457
 Y13  C12  H12  single    0.930  0.020  1.080
 Y13  C13  C14  aromatic  1.395  0.020  1.395
 Y13  C13  C18  aromatic  1.400  0.020  1.400
 Y13  C14  C15  aromatic  1.384  0.020  1.384
 Y13  C14  H14  single    0.930  0.020  1.080
 Y13  C15  C16  aromatic  1.389  0.020  1.389
 Y13  C15  H15  single    0.930  0.020  1.080
 Y13  C16  O19  single    1.345  0.020  1.345
 Y13  C16  C17  aromatic  1.402  0.020  1.402
 Y13  O19  H19  single    0.850  0.020  0.980
 Y13  C17  O23  single    1.352  0.020  1.352
 Y13  C17  C18  aromatic  1.382  0.020  1.382
 Y13  O23  H23  single    0.850  0.020  0.980
 Y13  C18  H18  single    0.930  0.020  1.080
 Y13  C4   C3   aromatic  1.386  0.020  1.386
 Y13  C4   H4   single    0.930  0.020  1.080
 Y13  C3   H3   single    0.930  0.020  1.080

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
 Y13  C3   C2   C1   119.28  3.000
 Y13  C3   C2   O16  117.92  3.000
 Y13  C1   C2   O16  122.80  3.000
 Y13  H16  O16  C2   110.33  3.000
 Y13  H1   C1   C6   119.76  3.000
 Y13  H1   C1   C2   120.28  3.000
 Y13  C6   C1   C2   119.96  3.000
 Y13  H6   C6   C5   119.65  3.000
 Y13  H6   C6   C1   118.75  3.000
 Y13  C5   C6   C1   121.60  3.000
 Y13  C4   C5   C7   121.28  3.000
 Y13  C4   C5   C6   117.57  3.000
 Y13  C7   C5   C6   121.11  3.000
 Y13  H72  C7   H71  107.12  3.000
 Y13  H72  C7   C8   109.02  3.000
 Y13  H71  C7   C8   109.01  3.000
 Y13  H72  C7   C5   110.24  3.000
 Y13  H71  C7   C5   110.18  3.000
 Y13  C8   C7   C5   111.16  3.000
 Y13  H82  C8   H81  107.09  3.000
 Y13  H82  C8   N9   107.45  3.000
 Y13  H81  C8   N9   109.32  3.000
 Y13  H82  C8   C7   109.66  3.000
 Y13  H81  C8   C7   109.74  3.000
 Y13  N9   C8   C7   113.37  3.000
 Y13  HN9  N9   C10  118.78  3.000
 Y13  HN9  N9   C8   117.71  3.000
 Y13  C10  N9   C8   123.31  3.000
 Y13  O27  C10  C11  123.24  3.000
 Y13  O27  C10  N9   122.50  3.000
 Y13  C11  C10  N9   114.26  3.000
 Y13  H11  C11  C12  121.41  3.000
 Y13  H11  C11  C10  117.60  3.000
 Y13  C12  C11  C10  120.99  3.000
 Y13  H12  C12  C13  115.32  3.000
 Y13  H12  C12  C11  117.60  3.000
 Y13  C13  C12  C11  127.08  3.000
 Y13  C18  C13  C14  118.23  3.000
 Y13  C18  C13  C12  118.30  3.000
 Y13  C14  C13  C12  123.47  3.000
 Y13  H14  C14  C15  118.57  3.000
 Y13  H14  C14  C13  120.77  3.000
 Y13  C15  C14  C13  120.66  3.000
 Y13  H15  C15  C16  118.97  3.000
 Y13  H15  C15  C14  120.18  3.000
 Y13  C16  C15  C14  120.85  3.000
 Y13  C17  C16  O19  121.80  3.000
 Y13  C17  C16  C15  119.08  3.000
 Y13  O19  C16  C15  119.13  3.000
 Y13  H19  O19  C16  110.71  3.000
 Y13  C18  C17  O23  124.10  3.000
 Y13  C18  C17  C16  119.79  3.000
 Y13  O23  C17  C16  116.11  3.000
 Y13  H23  O23  C17  110.96  3.000
 Y13  H18  C18  C17  119.15  3.000
 Y13  H18  C18  C13  119.46  3.000
 Y13  C17  C18  C13  121.39  3.000
 Y13  H4   C4   C3   118.75  3.000
 Y13  H4   C4   C5   119.55  3.000
 Y13  C3   C4   C5   121.70  3.000
 Y13  H3   C3   C4   120.29  3.000
 Y13  H3   C3   C2   119.81  3.000
 Y13  C4   C3   C2   119.90  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
 Y13  CONST_01  C5   C6   C1   C2     0.00   0.0  0
 Y13  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 Y13  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 Y13  CONST_04  C4   C5   C6   C1     0.00   0.0  0
 Y13  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 Y13  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 Y13  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 Y13  CONST_08  C16  C17  C18  C13    0.00   0.0  0
 Y13  CONST_09  C17  C18  C13  C14    0.00   0.0  0
 Y13  CONST_10  C17  C16  C15  C14    0.00   0.0  0
 Y13  CONST_11  C18  C13  C14  C15    0.00   0.0  0
 Y13  CONST_12  C18  C17  C16  C15    0.00   0.0  0
 Y13  CONST_13  C6   C1   C2   O16  180.00   0.0  0
 Y13  CONST_14  C4   C3   C2   O16  180.00   0.0  0
 Y13  CONST_15  C7   C5   C6   C1   180.00   0.0  0
 Y13  CONST_16  C3   C4   C5   C7   180.00   0.0  0
 Y13  CONST_17  C15  C14  C13  C12  180.00   0.0  0
 Y13  CONST_18  C17  C18  C13  C12  180.00   0.0  0
 Y13  CONST_19  O23  C17  C18  C13  180.00   0.0  0
 Y13  CONST_20  O19  C16  C15  C14  180.00   0.0  0
 Y13  CONST_21  O23  C17  C16  C15  180.00   0.0  0
 Y13  CONST_22  C18  C17  C16  O19  180.00   0.0  0
 Y13  CONST_23  H6   C6   C1   C2   180.00   0.0  0
 Y13  CONST_24  H4   C4   C3   C2   180.00   0.0  0
 Y13  CONST_25  H3   C3   C2   C1   180.00   0.0  0
 Y13  CONST_26  H1   C1   C6   C5   180.00   0.0  0
 Y13  CONST_27  H15  C15  C14  C13  180.00   0.0  0
 Y13  CONST_28  H18  C18  C13  C14  180.00   0.0  0
 Y13  CONST_29  H14  C14  C15  C16  180.00   0.0  0
 Y13  CONST_30  C11  C10  N9   C8   180.00   0.0  0
 Y13  CONST_31  O27  C10  N9   C8     0.00   0.0  0
 Y13  CONST_32  HN9  N9   C10  C11    0.00   0.0  0
 Y13  Var_01    C8   C7   C5   C6    83.25  30.0  2
 Y13  Var_02    C14  C13  C12  C11   -5.69  30.0  2
 Y13  Var_03    C13  C12  C11  C10  179.52   0.0  2
 Y13  Var_04    N9   C8   C7   C5   177.72  30.0  3
 Y13  Var_05    C10  N9   C8   C7    79.37  30.0  3
 Y13  Var_06    C12  C11  C10  N9   177.30  30.0  2

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
 Y13  plan-1  C2   0.020
 Y13  plan-1  O16  0.020
 Y13  plan-1  C1   0.020
 Y13  plan-1  C6   0.020
 Y13  plan-1  C5   0.020
 Y13  plan-1  C7   0.020
 Y13  plan-1  C4   0.020
 Y13  plan-1  C3   0.020
 Y13  plan-1  H1   0.020
 Y13  plan-1  H6   0.020
 Y13  plan-1  H4   0.020
 Y13  plan-1  H3   0.020
 Y13  plan-2  C12  0.020
 Y13  plan-2  C13  0.020
 Y13  plan-2  C14  0.020
 Y13  plan-2  C15  0.020
 Y13  plan-2  C16  0.020
 Y13  plan-2  O19  0.020
 Y13  plan-2  C17  0.020
 Y13  plan-2  O23  0.020
 Y13  plan-2  C18  0.020
 Y13  plan-2  H14  0.020
 Y13  plan-2  H15  0.020
 Y13  plan-2  H18  0.020
 Y13  plan-3  C8   0.020
 Y13  plan-3  N9   0.020
 Y13  plan-3  C10  0.020
 Y13  plan-3  C11  0.020
 Y13  plan-3  O27  0.020
 Y13  plan-3  HN9  0.020
 Y13  plan-4  C10  0.020
 Y13  plan-4  C11  0.020
 Y13  plan-4  C12  0.020
 Y13  plan-4  C13  0.020
 Y13  plan-4  H11  0.020
 Y13  plan-4  H12  0.020

