# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 15:27:42 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: (2~{S},3~{S})-2-azanyl-3-[[4-[2-(4-methoxyphenyl)hydrazinyl]phenyl]methoxy]butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NNc2ccc(CO[C@@H]([C@H](N)C(O)=O)C(O)=O)cc2)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
 QM5  QM5  '(2~{S},3~{S})-2-azanyl-3-[[4-[2-(4-methoxyphenyl)hydrazinyl]phenyl]methoxy]butanedioic acid'  ligand  46  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QM5
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
 QM5  C4   C  CR16   0  -0.306  36.4538  25.0227  -15.7518
 QM5  C14  C  CR16   0  -0.331  39.5903  28.6218  -15.2119
 QM5  C5   C  CR16   0  -0.278  36.7823  23.7453  -16.1729
 QM5  C6   C  CR6    0   0.048  36.7398  23.3814  -17.5162
 QM5  C7   C  CH2    0  -0.194  37.1418  22.0008  -17.9413
 QM5  C8   C  CH1    0  -0.021  39.0059  20.5608  -17.9637
 QM5  C9   C  C      0   0.375  38.9086  19.7754  -16.6329
 QM5  C10  C  CH1    0  -0.250  40.4478  20.6031  -18.4697
 QM5  C12  C  CR6    0   0.314  37.2446  28.2741  -14.7509
 QM5  C13  C  CR16   0  -0.299  38.3612  28.0926  -15.5691
 QM5  N1   N  NH2    0  -0.819  41.3322  21.1986  -17.4774
 QM5  C3   C  CR6    0   0.322  36.0775  25.9927  -16.6844
 QM5  N3   N  NH1    0  -0.557  36.0066  27.6942  -15.0352
 QM5  C1   C  CR16   0  -0.298  36.3609  24.3540  -18.4354
 QM5  C15  C  CR6    0   0.354  39.7465  29.3489  -14.0345
 QM5  C16  C  CR16   0  -0.368  38.6333  29.5462  -13.2223
 QM5  C17  C  CR16   0  -0.323  37.4022  29.0143  -13.5817
 QM5  C2   C  CR16   0  -0.330  36.0325  25.6396  -18.0353
 QM5  O1   O  O2     0  -0.496  38.5408  21.8894  -17.8701
 QM5  O6   O  O2     0  -0.474  40.9886  29.8161  -13.7676
 QM5  H1   H  HCR6   0   0.256  36.4953  25.2721  -14.7004
 QM5  H3   H  HCR6   0   0.237  37.0814  23.0097  -15.4349
 QM5  H4   H  HCH2   0   0.195  36.7851  21.8062  -18.9640
 QM5  H5   H  HCH2   0   0.196  36.6545  21.2633  -17.2918
 QM5  H6   H  HCH1   0   0.179  38.4202  20.0088  -18.7126
 QM5  H7   H  HCH1   0   0.199  40.7219  19.5604  -18.6881
 QM5  H8   H  HCR6   0   0.266  38.2890  27.5327  -16.4921
 QM5  H9   H  HNH2   0   0.327  41.7462  20.4774  -16.9029
 QM5  H10  H  HNH2   0   0.331  42.0869  21.6539  -17.9732
 QM5  H13  H  HNH1   0   0.384  35.2166  28.1319  -14.5860
 QM5  H14  H  HCR6   0   0.244  36.3209  24.1070  -19.4904
 QM5  H15  H  HCR6   0   0.273  38.6964  30.1114  -12.3018
 QM5  H16  H  HCR6   0   0.260  36.5513  29.1801  -12.9308
 QM5  H17  H  HCH3   0   0.254  42.2334  30.8269  -12.5514
 QM5  H18  H  HCH3   0   0.222  40.5827  31.4704  -12.5659
 QM5  H19  H  HCH3   0   0.222  40.9450  29.9691  -11.6888
 QM5  H20  H  HCR6   0   0.252  35.7426  26.3776  -18.7748
 QM5  N2   N  NH1    0  -0.551  35.7217  27.2807  -16.3098
 QM5  O2   O  O      0  -0.619  39.1966  18.5627  -16.7271
 QM5  C11  C  C      0   0.412  40.5247  21.3480  -19.8293
 QM5  O4   O  OC    -1  -0.600  41.4030  22.2256  -19.9519
 QM5  O5   O  O      0  -0.611  39.7195  20.9726  -20.7040
 QM5  C18  C  CH3    0  -0.432  41.1809  30.5545  -12.5823
 QM5  H12  H  HNH1   0   0.374  35.8259  27.9845  -17.0316
 QM5  O3   O  OC    -1  -0.594  38.5713  20.3829  -15.5995
 QM5  H2   H  HCR6   0   0.257  40.4449  28.4657  -15.8590

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
 QM5  O5   C11  deloc     1.247  0.020  1.247
 QM5  O4   C11  deloc     1.248  0.020  1.248
 QM5  C11  C10  single    1.552  0.020  1.552
 QM5  O1   C8   single    1.411  0.020  1.411
 QM5  O1   C7   single    1.405  0.020  1.405
 QM5  C10  N1   single    1.456  0.020  1.456
 QM5  C10  C8   single    1.529  0.020  1.529
 QM5  C2   C1   aromatic  1.386  0.020  1.386
 QM5  C2   C3   aromatic  1.397  0.020  1.397
 QM5  C1   C6   aromatic  1.391  0.020  1.391
 QM5  C8   C9   single    1.548  0.020  1.548
 QM5  N2   C3   single    1.388  0.020  1.388
 QM5  N2   N3   single    1.370  0.020  1.370
 QM5  C3   C4   aromatic  1.397  0.020  1.397
 QM5  C6   C7   single    1.499  0.020  1.499
 QM5  C6   C5   aromatic  1.392  0.020  1.392
 QM5  C4   C5   aromatic  1.385  0.020  1.385
 QM5  C13  C14  aromatic  1.385  0.020  1.385
 QM5  C13  C12  aromatic  1.396  0.020  1.396
 QM5  N3   C12  single    1.396  0.020  1.396
 QM5  C9   O2   deloc     1.250  0.020  1.250
 QM5  C9   O3   deloc     1.245  0.020  1.245
 QM5  C14  C15  aromatic  1.393  0.020  1.393
 QM5  C12  C17  aromatic  1.393  0.020  1.393
 QM5  C15  O6   single    1.354  0.020  1.354
 QM5  C15  C16  aromatic  1.392  0.020  1.392
 QM5  C17  C16  aromatic  1.388  0.020  1.388
 QM5  O6   C18  single    1.410  0.020  1.410
 QM5  C4   H1   single    0.930  0.020  1.080
 QM5  C14  H2   single    0.930  0.020  1.080
 QM5  C5   H3   single    0.930  0.020  1.080
 QM5  C7   H4   single    0.970  0.020  1.090
 QM5  C7   H5   single    0.970  0.020  1.090
 QM5  C8   H6   single    0.970  0.020  1.090
 QM5  C10  H7   single    0.970  0.020  1.090
 QM5  C13  H8   single    0.930  0.020  1.080
 QM5  N1   H9   single    0.890  0.020  1.040
 QM5  N1   H10  single    0.890  0.020  1.040
 QM5  N2   H12  single    0.890  0.020  1.040
 QM5  N3   H13  single    0.890  0.020  1.040
 QM5  C1   H14  single    0.930  0.020  1.080
 QM5  C16  H15  single    0.930  0.020  1.080
 QM5  C17  H16  single    0.930  0.020  1.080
 QM5  C18  H17  single    0.970  0.020  1.090
 QM5  C18  H18  single    0.970  0.020  1.090
 QM5  C18  H19  single    0.970  0.020  1.090
 QM5  C2   H20  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
 QM5  H1   C4   C3   119.94  3.000
 QM5  H1   C4   C5   119.96  3.000
 QM5  C3   C4   C5   120.09  3.000
 QM5  H2   C14  C15  119.46  3.000
 QM5  H2   C14  C13  119.41  3.000
 QM5  C15  C14  C13  121.14  3.000
 QM5  H3   C5   C6   119.20  3.000
 QM5  H3   C5   C4   118.97  3.000
 QM5  C6   C5   C4   121.82  3.000
 QM5  C1   C6   C7   121.97  3.000
 QM5  C7   C6   C5   120.39  3.000
 QM5  C1   C6   C5   117.59  3.000
 QM5  H5   C7   H4   106.70  3.000
 QM5  H5   C7   O1   111.04  3.000
 QM5  H4   C7   O1   110.84  3.000
 QM5  H5   C7   C6   109.40  3.000
 QM5  H4   C7   C6   109.84  3.000
 QM5  O1   C7   C6   109.00  3.000
 QM5  H6   C8   O1   110.02  3.000
 QM5  H6   C8   C10  106.91  3.000
 QM5  O1   C8   C10  107.87  3.000
 QM5  H6   C8   C9   107.30  3.000
 QM5  C10  C8   C9   110.96  3.000
 QM5  O1   C8   C9   113.58  3.000
 QM5  O3   C9   O2   126.74  3.000
 QM5  O3   C9   C8   118.87  3.000
 QM5  O2   C9   C8   114.38  3.000
 QM5  H7   C10  N1   111.81  3.000
 QM5  H7   C10  C8   105.93  3.000
 QM5  N1   C10  C8   111.01  3.000
 QM5  H7   C10  C11  105.58  3.000
 QM5  C8   C10  C11  110.48  3.000
 QM5  N1   C10  C11  111.75  3.000
 QM5  C17  C12  N3   119.47  3.000
 QM5  C17  C12  C13  118.07  3.000
 QM5  N3   C12  C13  122.40  3.000
 QM5  H8   C13  C12  120.92  3.000
 QM5  H8   C13  C14  118.49  3.000
 QM5  C12  C13  C14  120.59  3.000
 QM5  H10  N1   H9   107.11  3.000
 QM5  H10  N1   C10  107.65  3.000
 QM5  H9   N1   C10  110.13  3.000
 QM5  C2   C3   N2   119.17  3.000
 QM5  N2   C3   C4   122.22  3.000
 QM5  C2   C3   C4   118.60  3.000
 QM5  H13  N3   N2   112.49  3.000
 QM5  H13  N3   C12  115.05  3.000
 QM5  N2   N3   C12  119.94  3.000
 QM5  H14  C1   C2   118.91  3.000
 QM5  H14  C1   C6   119.59  3.000
 QM5  C2   C1   C6   121.49  3.000
 QM5  O6   C15  C16  124.74  3.000
 QM5  C16  C15  C14  118.53  3.000
 QM5  O6   C15  C14  116.73  3.000
 QM5  H15  C16  C17  118.18  3.000
 QM5  H15  C16  C15  121.58  3.000
 QM5  C17  C16  C15  120.25  3.000
 QM5  H16  C17  C16  118.81  3.000
 QM5  H16  C17  C12  119.77  3.000
 QM5  C16  C17  C12  121.42  3.000
 QM5  H20  C2   C1   119.86  3.000
 QM5  H20  C2   C3   119.75  3.000
 QM5  C1   C2   C3   120.40  3.000
 QM5  C8   O1   C7   113.55  3.000
 QM5  C18  O6   C15  118.15  3.000
 QM5  H12  N2   N3   115.57  3.000
 QM5  H12  N2   C3   115.21  3.000
 QM5  N3   N2   C3   118.55  3.000
 QM5  O5   C11  O4   126.69  3.000
 QM5  O4   C11  C10  117.29  3.000
 QM5  O5   C11  C10  115.98  3.000
 QM5  H19  C18  H18  108.53  3.000
 QM5  H19  C18  H17  108.63  3.000
 QM5  H18  C18  H17  108.60  3.000
 QM5  H19  C18  O6   112.15  3.000
 QM5  H18  C18  O6   112.12  3.000
 QM5  H17  C18  O6   106.69  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
 QM5  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 QM5  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 QM5  CONST_03  C17  C12  C13  C14    0.00   0.0  0
 QM5  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 QM5  CONST_05  C2   C1   C6   C5     0.00   0.0  0
 QM5  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 QM5  CONST_07  C3   C2   C1   C6     0.00   0.0  0
 QM5  CONST_08  C3   C4   C5   C6     0.00   0.0  0
 QM5  CONST_09  C15  C14  C13  C12    0.00   0.0  0
 QM5  CONST_10  C15  C16  C17  C12    0.00   0.0  0
 QM5  CONST_11  C16  C15  C14  C13    0.00   0.0  0
 QM5  CONST_12  C16  C17  C12  C13    0.00   0.0  0
 QM5  CONST_13  C7   C6   C5   C4   180.00   0.0  0
 QM5  CONST_14  N3   C12  C13  C14  180.00   0.0  0
 QM5  CONST_15  N2   C3   C4   C5   180.00   0.0  0
 QM5  CONST_16  C2   C1   C6   C7   180.00   0.0  0
 QM5  CONST_17  O6   C15  C14  C13  180.00   0.0  0
 QM5  CONST_18  C1   C2   C3   N2   180.00   0.0  0
 QM5  CONST_19  C16  C17  C12  N3   180.00   0.0  0
 QM5  CONST_20  O6   C15  C16  C17  180.00   0.0  0
 QM5  CONST_21  H20  C2   C3   C4   180.00   0.0  0
 QM5  CONST_22  H15  C16  C15  C14  180.00   0.0  0
 QM5  CONST_23  H14  C1   C6   C5   180.00   0.0  0
 QM5  CONST_24  H1   C4   C5   C6   180.00   0.0  0
 QM5  CONST_25  H2   C14  C13  C12  180.00   0.0  0
 QM5  CONST_26  H16  C17  C12  C13  180.00   0.0  0
 QM5  CONST_27  H3   C5   C4   C3   180.00   0.0  0
 QM5  CONST_28  H8   C13  C14  C15  180.00   0.0  0
 QM5  CONST_29  N3   N2   C3   C4     0.00   0.0  0
 QM5  CONST_33  C2   C3   N2   N3   180.00   0.0  0
 QM5  Var_01    O1   C7   C6   C5   -74.11  30.0  2
 QM5  Var_02    H17  C18  O6   C15  179.54  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 QM5  chir_01  C8   O1  C10  C9   negativ
 QM5  chir_02  C10  N1  C8   C11  negativ

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
 QM5  plan-1  C14  0.020
 QM5  plan-1  C12  0.020
 QM5  plan-1  C13  0.020
 QM5  plan-1  N3   0.020
 QM5  plan-1  C15  0.020
 QM5  plan-1  C16  0.020
 QM5  plan-1  C17  0.020
 QM5  plan-1  O6   0.020
 QM5  plan-1  H8   0.020
 QM5  plan-1  H15  0.020
 QM5  plan-1  H16  0.020
 QM5  plan-1  H2   0.020
 QM5  plan-2  C4   0.020
 QM5  plan-2  C5   0.020
 QM5  plan-2  C6   0.020
 QM5  plan-2  C7   0.020
 QM5  plan-2  C3   0.020
 QM5  plan-2  C1   0.020
 QM5  plan-2  C2   0.020
 QM5  plan-2  H1   0.020
 QM5  plan-2  H3   0.020
 QM5  plan-2  H14  0.020
 QM5  plan-2  H20  0.020
 QM5  plan-2  N2   0.020
 QM5  plan-3  C3   0.020
 QM5  plan-3  N3   0.020
 QM5  plan-3  N2   0.020
 QM5  plan-3  H12  0.020
 QM5  plan-4  C12  0.020
 QM5  plan-4  N3   0.020
 QM5  plan-4  H13  0.020
 QM5  plan-4  N2   0.020
 QM5  plan-5  C8   0.020
 QM5  plan-5  C9   0.020
 QM5  plan-5  O2   0.020
 QM5  plan-5  O3   0.020
 QM5  plan-6  C10  0.020
 QM5  plan-6  C11  0.020
 QM5  plan-6  O4   0.020
 QM5  plan-6  O5   0.020

