# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:46:27 2021
#   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  48  27  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.312  36.0950  25.2535  -15.9300
 QM5  C14  C  CR16  0  -0.331  37.9437  30.1273  -13.4155
 QM5  C5   C  CR16  0  -0.291  36.3259  23.8912  -16.0586
 QM5  C6   C  CR6   0   0.057  36.8144  23.3400  -17.2363
 QM5  C7   C  CH2   0  -0.225  37.1042  21.8773  -17.3594
 QM5  C8   C  CH1   0  -0.035  38.9910  20.4915  -17.7905
 QM5  C9   C  C     0   0.510  38.9996  19.3573  -16.7752
 QM5  C10  C  CH1   0  -0.230  40.4189  20.7292  -18.3106
 QM5  C12  C  CR6   0   0.309  37.0591  28.6240  -15.0902
 QM5  C13  C  CR16  0  -0.321  36.8693  29.5827  -14.0897
 QM5  N1   N  NH2   0  -0.805  41.3201  21.0141  -17.2129
 QM5  C3   C  CR6   0   0.334  36.3572  26.1089  -17.0004
 QM5  N3   N  NH1   0  -0.551  35.9430  28.0631  -15.7188
 QM5  C1   C  CR16  0  -0.276  37.0798  24.2045  -18.2981
 QM5  C15  C  CR6   0   0.354  39.2490  29.7335  -13.7175
 QM5  C16  C  CR16  0  -0.373  39.4450  28.7824  -14.7103
 QM5  C17  C  CR16  0  -0.301  38.3591  28.2344  -15.3892
 QM5  C2   C  CR16  0  -0.331  36.8566  25.5632  -18.1902
 QM5  O1   O  O2    0  -0.483  38.5120  21.6994  -17.2929
 QM5  O3   O  OH1   0  -0.568  38.5651  19.7140  -15.5825
 QM5  O6   O  O2    0  -0.477  40.2383  30.3235  -13.0068
 QM5  H1   H  HCR6  0   0.259  35.7146  25.6524  -14.9999
 QM5  H3   H  HCR6  0   0.248  36.1176  23.2457  -15.2128
 QM5  H4   H  HCH2  0   0.223  36.7266  21.4926  -18.3151
 QM5  H5   H  HCH2  0   0.227  36.6001  21.3200  -16.5623
 QM5  H6   H  HCH1  0   0.275  38.3851  20.1340  -18.6358
 QM5  H7   H  HCH1  0   0.285  40.7055  19.8495  -18.9032
 QM5  H8   H  HCR6  0   0.263  35.8665  29.9084  -13.8383
 QM5  H9   H  HNH2  0   0.361  41.5487  20.1476  -16.7410
 QM5  H10  H  HNH2  0   0.364  42.2055  21.3586  -17.5610
 QM5  H13  H  HNH1  0   0.385  35.1128  28.6354  -15.6816
 QM5  H14  H  HCR6  0   0.243  37.4690  23.8087  -19.2290
 QM5  H15  H  HCR6  0   0.276  40.4363  28.4444  -14.9801
 QM5  H16  H  HCR6  0   0.265  38.5526  27.4924  -16.1526
 QM5  H17  H  HCH3  0   0.257  42.2020  30.5182  -12.6069
 QM5  H18  H  HCH3  0   0.224  41.7404  28.8810  -13.1021
 QM5  H19  H  HCH3  0   0.224  41.8585  30.1761  -14.3115
 QM5  H20  H  HCR6  0   0.258  37.0704  26.2131  -19.0309
 QM5  H21  H  HOH1  0   0.487  38.5797  18.9515  -14.9832
 QM5  N2   N  NH1   0  -0.555  36.1044  27.4680  -16.9432
 QM5  O2   O  O     0  -0.443  39.3744  18.2464  -17.0590
 QM5  C11  C  C     0   0.556  40.3020  21.8735  -19.3039
 QM5  O4   O  OH1   0  -0.576  41.0368  22.9269  -18.9990
 QM5  O5   O  O     0  -0.450  39.6063  21.8043  -20.2866
 QM5  H2   H  HCR6  0   0.261  37.7755  30.8712  -12.6463
 QM5  C18  C  CH3   0  -0.434  41.5698  29.9462  -13.2819
 QM5  H12  H  HNH1  0   0.377  36.5720  28.0287  -17.6458
 QM5  H22  H  HOH1  0   0.485  40.9343  23.6092  -19.6801

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  double    1.206  0.020  1.206
 QM5  O4   C11  single    1.320  0.020  1.320
 QM5  C11  C10  single    1.520  0.020  1.520
 QM5  O1   C8   single    1.391  0.020  1.391
 QM5  O1   C7   single    1.421  0.020  1.421
 QM5  C10  N1   single    1.449  0.020  1.449
 QM5  C10  C8   single    1.538  0.020  1.538
 QM5  C2   C1   aromatic  1.381  0.020  1.381
 QM5  C2   C3   aromatic  1.401  0.020  1.401
 QM5  C1   C6   aromatic  1.395  0.020  1.395
 QM5  C8   C9   single    1.522  0.020  1.522
 QM5  N2   C3   single    1.384  0.020  1.384
 QM5  N2   N3   single    1.371  0.020  1.371
 QM5  C3   C4   aromatic  1.395  0.020  1.395
 QM5  C6   C7   single    1.496  0.020  1.496
 QM5  C6   C5   aromatic  1.389  0.020  1.389
 QM5  C4   C5   aromatic  1.388  0.020  1.388
 QM5  C13  C14  aromatic  1.380  0.020  1.380
 QM5  C13  C12  aromatic  1.399  0.020  1.399
 QM5  N3   C12  single    1.398  0.020  1.398
 QM5  C9   O2   double    1.206  0.020  1.206
 QM5  C9   O3   single    1.319  0.020  1.319
 QM5  C14  C15  aromatic  1.396  0.020  1.396
 QM5  C12  C17  aromatic  1.390  0.020  1.390
 QM5  C15  O6   single    1.353  0.020  1.353
 QM5  C15  C16  aromatic  1.389  0.020  1.389
 QM5  C17  C16  aromatic  1.393  0.020  1.393
 QM5  O6   C18  single    1.411  0.020  1.411
 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
 QM5  O3   H21  single    0.850  0.020  0.980
 QM5  O4   H22  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
 QM5  H1   C4   C3   120.00  3.000
 QM5  H1   C4   C5   120.03  3.000
 QM5  C3   C4   C5   119.97  3.000
 QM5  H2   C14  C15  119.50  3.000
 QM5  H2   C14  C13  119.80  3.000
 QM5  C15  C14  C13  120.70  3.000
 QM5  H3   C5   C6   119.52  3.000
 QM5  H3   C5   C4   118.70  3.000
 QM5  C6   C5   C4   121.77  3.000
 QM5  C1   C6   C7   120.43  3.000
 QM5  C7   C6   C5   121.72  3.000
 QM5  C1   C6   C5   117.81  3.000
 QM5  H5   C7   H4   107.28  3.000
 QM5  H5   C7   O1   111.00  3.000
 QM5  H4   C7   O1   109.74  3.000
 QM5  H5   C7   C6   110.39  3.000
 QM5  H4   C7   C6   110.36  3.000
 QM5  O1   C7   C6   108.09  3.000
 QM5  H6   C8   O1   111.56  3.000
 QM5  H6   C8   C10  107.56  3.000
 QM5  O1   C8   C10  107.84  3.000
 QM5  H6   C8   C9   105.88  3.000
 QM5  C10  C8   C9   109.60  3.000
 QM5  O1   C8   C9   114.22  3.000
 QM5  O3   C9   O2   124.36  3.000
 QM5  O3   C9   C8   113.57  3.000
 QM5  O2   C9   C8   122.07  3.000
 QM5  H7   C10  N1   113.82  3.000
 QM5  H7   C10  C8   107.51  3.000
 QM5  N1   C10  C8   110.60  3.000
 QM5  H7   C10  C11  105.69  3.000
 QM5  C8   C10  C11  105.42  3.000
 QM5  N1   C10  C11  113.27  3.000
 QM5  C17  C12  N3   122.51  3.000
 QM5  C17  C12  C13  118.23  3.000
 QM5  N3   C12  C13  119.22  3.000
 QM5  H8   C13  C12  119.83  3.000
 QM5  H8   C13  C14  119.22  3.000
 QM5  C12  C13  C14  120.95  3.000
 QM5  H10  N1   H9   104.72  3.000
 QM5  H10  N1   C10  110.53  3.000
 QM5  H9   N1   C10  108.98  3.000
 QM5  C2   C3   N2   118.87  3.000
 QM5  N2   C3   C4   122.42  3.000
 QM5  C2   C3   C4   118.67  3.000
 QM5  H13  N3   N2   112.09  3.000
 QM5  H13  N3   C12  114.37  3.000
 QM5  N2   N3   C12  118.79  3.000
 QM5  H14  C1   C2   118.97  3.000
 QM5  H14  C1   C6   119.73  3.000
 QM5  C2   C1   C6   121.30  3.000
 QM5  O6   C15  C16  124.81  3.000
 QM5  C16  C15  C14  118.66  3.000
 QM5  O6   C15  C14  116.53  3.000
 QM5  H15  C16  C17  118.03  3.000
 QM5  H15  C16  C15  121.45  3.000
 QM5  C17  C16  C15  120.52  3.000
 QM5  H16  C17  C16  118.31  3.000
 QM5  H16  C17  C12  120.75  3.000
 QM5  C16  C17  C12  120.94  3.000
 QM5  H20  C2   C1   119.83  3.000
 QM5  H20  C2   C3   119.70  3.000
 QM5  C1   C2   C3   120.47  3.000
 QM5  C8   O1   C7   115.66  3.000
 QM5  H21  O3   C9   109.95  3.000
 QM5  C18  O6   C15  118.09  3.000
 QM5  H12  N2   N3   115.68  3.000
 QM5  H12  N2   C3   115.50  3.000
 QM5  N3   N2   C3   119.01  3.000
 QM5  O5   C11  O4   123.71  3.000
 QM5  O4   C11  C10  114.02  3.000
 QM5  O5   C11  C10  122.26  3.000
 QM5  H22  O4   C11  109.91  3.000
 QM5  H19  C18  H18  108.56  3.000
 QM5  H19  C18  H17  108.68  3.000
 QM5  H18  C18  H17  108.64  3.000
 QM5  H19  C18  O6   112.11  3.000
 QM5  H18  C18  O6   112.06  3.000
 QM5  H17  C18  O6   106.68  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_36  H21  O3   C9   C8    180.00   0.0  0
 QM5  CONST_37  H22  O4   C11  C10   180.00   0.0  0
 QM5  Var_01    O1   C7   C6   C5   -103.98  30.0  2
 QM5  Var_02    H17  C18  O6   C15  -179.40  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  O3   0.020
 QM5  plan-5  H21  0.020
 QM5  plan-5  O2   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
 QM5  plan-6  H22  0.020

