# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 06:07:40 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-[6-(3,4,5-trimethoxyanilino)pyrazin-2-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Nc2cncc(n2)c3ccc(cc3)C(N)=O)cc(OC)c1OC
#
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
 ZHY  ZHY  "4-[6-(3,4,5-trimethoxyanilino)pyrazin-2-yl]benzamide"
  ligand  48  28  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZHY
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
 ZHY  C1   C  CR16  0  -0.159  -15.3974  13.9538  29.2538
 ZHY  C2   C  CR16  0  -0.295  -15.4299  12.3074  26.7482
 ZHY  C3   C  CR16  0  -0.277  -17.3081  11.1659  27.7065
 ZHY  C4   C  CR6   0   0.065  -16.4032  12.2271  27.7430
 ZHY  C5   C  CR6   0   0.231  -16.4997  13.2419  28.8084
 ZHY  C6   C  CR6   0   0.485  -17.8266  14.3299  30.3109
 ZHY  C7   C  CR16  0  -0.264  -15.3523  11.3450  25.7548
 ZHY  O1   O  O2    0  -0.479  -24.1563  12.5454  30.3499
 ZHY  O2   O  O2    0  -0.464  -22.2655  11.7182  28.6657
 ZHY  C9   C  CR16  0  -0.252  -17.2355  10.2106  26.7104
 ZHY  C02  C  CR16  0  -0.548  -21.2917  14.4743  31.5686
 ZHY  C06  C  CR16  0  -0.522  -20.5811  13.0907  29.7142
 ZHY  C    C  CR16  0  -0.165  -16.6973  15.0651  30.7447
 ZHY  C8   C  CR6   0  -0.044  -16.2499  10.2808  25.7282
 ZHY  C10  C  CR6   0   0.421  -20.2877  14.0254  30.7049
 ZHY  C03  C  CR6   0   0.351  -22.5870  13.9894  31.4400
 ZHY  C05  C  CR6   0   0.375  -21.8865  12.6138  29.5943
 ZHY  C04  C  CR6   0   0.150  -22.8947  13.0451  30.4559
 ZHY  C01  C  C     0   0.486  -16.2362   9.2270  24.6653
 ZHY  C13  C  CH3   0  -0.438  -23.3789  15.3366  33.2233
 ZHY  C11  C  CH3   0  -0.440  -21.2950  11.2063  27.7760
 ZHY  C12  C  CH3   0  -0.406  -25.0035  13.2804  29.4787
 ZHY  N5   N  N     0  -0.339  -15.5154  14.8660  30.2208
 ZHY  N    N  N     0  -0.464  -17.7049  13.4340  29.3501
 ZHY  N1   N  NH2   0  -0.812  -15.0739   9.0453  24.0187
 ZHY  N8   N  NH1   0  -0.802  -19.0258  14.5766  30.9070
 ZHY  O02  O  O     0  -0.470  -17.2434   8.5822  24.4112
 ZHY  O    O  O2    0  -0.462  -23.6102  14.3624  32.2265
 ZHY  H1   H  HCR6  0   0.267  -14.4059  13.7859  28.8539
 ZHY  H2   H  HCR6  0   0.262  -14.7400  13.1406  26.7217
 ZHY  H3   H  HCR6  0   0.262  -18.0703  11.0818  28.4694
 ZHY  H4   H  HCR6  0   0.263  -14.6000  11.4662  24.9860
 ZHY  H5   H  HCR6  0   0.263  -17.9460   9.3949  26.7006
 ZHY  H6   H  HCR6  0   0.289  -21.0472  15.2004  32.3335
 ZHY  H7   H  HCR6  0   0.319  -19.8021  12.7531  29.0531
 ZHY  H8   H  HCR6  0   0.281  -16.7897  15.8107  31.5287
 ZHY  H9   H  HCH3  0   0.260  -24.3318  15.4992  33.7208
 ZHY  H10  H  HCH3  0   0.228  -22.6491  15.0000  33.9641
 ZHY  H11  H  HCH3  0   0.228  -23.0380  16.2841  32.7977
 ZHY  H12  H  HCH3  0   0.260  -21.8175  10.5196  27.1142
 ZHY  H13  H  HCH3  0   0.227  -20.8322  11.9914  27.1723
 ZHY  H14  H  HCH3  0   0.229  -20.5088  10.6570  28.3008
 ZHY  H15  H  HCH3  0   0.233  -25.9767  12.7919  29.4873
 ZHY  H16  H  HCH3  0   0.218  -25.1307  14.3146  29.8088
 ZHY  H17  H  HCH3  0   0.218  -24.6258  13.2848  28.4530
 ZHY  H18  H  HNH2  0   0.404  -15.0073   8.3241  23.3186
 ZHY  H19  H  HNH2  0   0.411  -14.2094   9.4538  24.3284
 ZHY  H20  H  HNH1  0   0.418  -18.9916  15.2718  31.6370

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
 ZHY  N1   C01  single    1.342  0.020  1.342
 ZHY  O02  C01  double    1.223  0.020  1.223
 ZHY  C01  C8   single    1.497  0.020  1.497
 ZHY  C7   C8   aromatic  1.392  0.020  1.392
 ZHY  C7   C2   aromatic  1.385  0.020  1.385
 ZHY  C8   C9   aromatic  1.393  0.020  1.393
 ZHY  C2   C4   aromatic  1.394  0.020  1.394
 ZHY  C9   C3   aromatic  1.382  0.020  1.382
 ZHY  C11  O2   single    1.413  0.020  1.413
 ZHY  C4   C3   aromatic  1.395  0.020  1.395
 ZHY  C4   C5   single    1.475  0.020  1.475
 ZHY  O2   C05  single    1.345  0.020  1.345
 ZHY  C5   C1   aromatic  1.386  0.020  1.386
 ZHY  C5   N    aromatic  1.335  0.020  1.335
 ZHY  C1   N5   aromatic  1.335  0.020  1.335
 ZHY  C05  C06  aromatic  1.395  0.020  1.395
 ZHY  C05  C04  aromatic  1.395  0.020  1.395
 ZHY  N    C6   aromatic  1.319  0.020  1.319
 ZHY  C06  C10  aromatic  1.393  0.020  1.393
 ZHY  C12  O1   single    1.420  0.020  1.420
 ZHY  N5   C    aromatic  1.308  0.020  1.308
 ZHY  O1   C04  single    1.361  0.020  1.361
 ZHY  C6   C    aromatic  1.416  0.020  1.416
 ZHY  C6   N8   single    1.362  0.020  1.362
 ZHY  C04  C03  aromatic  1.398  0.020  1.398
 ZHY  C10  N8   single    1.392  0.020  1.392
 ZHY  C10  C02  aromatic  1.398  0.020  1.398
 ZHY  C03  C02  aromatic  1.389  0.020  1.389
 ZHY  C03  O    single    1.343  0.020  1.343
 ZHY  O    C13  single    1.413  0.020  1.413
 ZHY  C1   H1   single    0.930  0.020  1.080
 ZHY  C2   H2   single    0.930  0.020  1.080
 ZHY  C3   H3   single    0.930  0.020  1.080
 ZHY  C7   H4   single    0.930  0.020  1.080
 ZHY  C9   H5   single    0.930  0.020  1.080
 ZHY  C02  H6   single    0.930  0.020  1.080
 ZHY  C06  H7   single    0.930  0.020  1.080
 ZHY  C    H8   single    0.930  0.020  1.080
 ZHY  C13  H9   single    0.970  0.020  1.090
 ZHY  C13  H10  single    0.970  0.020  1.090
 ZHY  C13  H11  single    0.970  0.020  1.090
 ZHY  C11  H12  single    0.970  0.020  1.090
 ZHY  C11  H13  single    0.970  0.020  1.090
 ZHY  C11  H14  single    0.970  0.020  1.090
 ZHY  C12  H15  single    0.970  0.020  1.090
 ZHY  C12  H16  single    0.970  0.020  1.090
 ZHY  C12  H17  single    0.970  0.020  1.090
 ZHY  N1   H18  single    0.860  0.020  1.020
 ZHY  N1   H19  single    0.860  0.020  1.020
 ZHY  N8   H20  single    0.860  0.020  1.020

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
 ZHY  H1   C1   N5   117.05  3.000
 ZHY  H1   C1   C5   122.02  3.000
 ZHY  N5   C1   C5   120.91  3.000
 ZHY  H2   C2   C7   118.79  3.000
 ZHY  H2   C2   C4   120.47  3.000
 ZHY  C7   C2   C4   120.71  3.000
 ZHY  H3   C3   C9   119.44  3.000
 ZHY  H3   C3   C4   119.85  3.000
 ZHY  C9   C3   C4   120.70  3.000
 ZHY  C5   C4   C3   120.00  3.000
 ZHY  C5   C4   C2   121.44  3.000
 ZHY  C3   C4   C2   118.56  3.000
 ZHY  N    C5   C4   116.82  3.000
 ZHY  N    C5   C1   120.91  3.000
 ZHY  C4   C5   C1   122.26  3.000
 ZHY  N8   C6   N    121.54  3.000
 ZHY  N8   C6   C    118.31  3.000
 ZHY  N    C6   C    120.15  3.000
 ZHY  H4   C7   C8   121.33  3.000
 ZHY  H4   C7   C2   118.06  3.000
 ZHY  C8   C7   C2   120.57  3.000
 ZHY  C12  O1   C04  114.25  3.000
 ZHY  C11  O2   C05  118.87  3.000
 ZHY  H5   C9   C8   119.75  3.000
 ZHY  H5   C9   C3   119.55  3.000
 ZHY  C8   C9   C3   120.69  3.000
 ZHY  H6   C02  C03  120.67  3.000
 ZHY  H6   C02  C10  119.31  3.000
 ZHY  C03  C02  C10  120.02  3.000
 ZHY  H7   C06  C05  121.16  3.000
 ZHY  H7   C06  C10  119.66  3.000
 ZHY  C05  C06  C10  119.18  3.000
 ZHY  H8   C    N5   118.07  3.000
 ZHY  H8   C    C6   120.66  3.000
 ZHY  N5   C    C6   121.27  3.000
 ZHY  C01  C8   C9   118.14  3.000
 ZHY  C9   C8   C7   118.75  3.000
 ZHY  C01  C8   C7   123.08  3.000
 ZHY  N8   C10  C06  124.05  3.000
 ZHY  N8   C10  C02  115.73  3.000
 ZHY  C06  C10  C02  120.22  3.000
 ZHY  O    C03  C04  115.60  3.000
 ZHY  O    C03  C02  123.99  3.000
 ZHY  C04  C03  C02  120.41  3.000
 ZHY  C04  C05  C06  121.18  3.000
 ZHY  C04  C05  O2   115.40  3.000
 ZHY  C06  C05  O2   123.42  3.000
 ZHY  C05  C04  C03  118.99  3.000
 ZHY  C03  C04  O1   120.45  3.000
 ZHY  C05  C04  O1   120.56  3.000
 ZHY  O02  C01  N1   122.80  3.000
 ZHY  O02  C01  C8   120.76  3.000
 ZHY  N1   C01  C8   116.44  3.000
 ZHY  H11  C13  H10  108.81  3.000
 ZHY  H11  C13  H9   108.77  3.000
 ZHY  H10  C13  H9   108.73  3.000
 ZHY  H11  C13  O    111.97  3.000
 ZHY  H10  C13  O    112.03  3.000
 ZHY  H9   C13  O    106.41  3.000
 ZHY  H14  C11  H13  108.75  3.000
 ZHY  H14  C11  H12  108.69  3.000
 ZHY  H13  C11  H12  108.72  3.000
 ZHY  H14  C11  O2   111.94  3.000
 ZHY  H13  C11  O2   112.24  3.000
 ZHY  H12  C11  O2   106.39  3.000
 ZHY  H17  C12  H16  108.65  3.000
 ZHY  H17  C12  H15  108.54  3.000
 ZHY  H16  C12  H15  108.54  3.000
 ZHY  H17  C12  O1   111.82  3.000
 ZHY  H16  C12  O1   111.95  3.000
 ZHY  H15  C12  O1   107.23  3.000
 ZHY  C    N5   C1   118.30  3.000
 ZHY  C6   N    C5   118.45  3.000
 ZHY  H19  N1   H18  116.63  3.000
 ZHY  H19  N1   C01  122.77  3.000
 ZHY  H18  N1   C01  119.27  3.000
 ZHY  H20  N8   C10  114.13  3.000
 ZHY  H20  N8   C6   114.32  3.000
 ZHY  C10  N8   C6   131.54  3.000
 ZHY  C13  O    C03  118.68  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
 ZHY  CONST_03  C6   N    C5   C1      0.00   0.0  0
 ZHY  CONST_04  C6   C    N5   C1      0.00   0.0  0
 ZHY  CONST_05  C9   C8   C7   C2      0.00   0.0  0
 ZHY  CONST_06  C9   C3   C4   C2      0.00   0.0  0
 ZHY  CONST_08  C7   C8   C9   C3      0.00   0.0  0
 ZHY  CONST_09  C7   C2   C4   C3      0.00   0.0  0
 ZHY  CONST_11  C8   C7   C2   C4      0.00   0.0  0
 ZHY  CONST_12  C8   C9   C3   C4      0.00   0.0  0
 ZHY  CONST_13  N5   C1   C5   C4    180.00   0.0  0
 ZHY  CONST_14  C6   N    C5   C4    180.00   0.0  0
 ZHY  CONST_15  C7   C2   C4   C5    180.00   0.0  0
 ZHY  CONST_16  C9   C3   C4   C5    180.00   0.0  0
 ZHY  CONST_17  C    N5   C1   C5      0.00   0.0  0
 ZHY  CONST_18  C    C6   N    C5      0.00   0.0  0
 ZHY  CONST_19  C05  C06  C10  C02     0.00   0.0  0
 ZHY  CONST_20  C05  C04  C03  C02     0.00   0.0  0
 ZHY  CONST_21  C03  C04  C05  C06     0.00   0.0  0
 ZHY  CONST_22  C03  C02  C10  C06     0.00   0.0  0
 ZHY  CONST_23  C04  C05  C06  C10     0.00   0.0  0
 ZHY  CONST_24  C04  C03  C02  C10     0.00   0.0  0
 ZHY  CONST_25  N    C5   C1   N5      0.00   0.0  0
 ZHY  CONST_26  N    C6   C    N5      0.00   0.0  0
 ZHY  CONST_27  C01  C8   C7   C2    180.00   0.0  0
 ZHY  CONST_28  C01  C8   C9   C3    180.00   0.0  0
 ZHY  CONST_29  N8   C6   N    C5    180.00   0.0  0
 ZHY  CONST_30  C06  C05  C04  O1    180.00   0.0  0
 ZHY  CONST_31  C02  C03  C04  O1    180.00   0.0  0
 ZHY  CONST_32  C10  C06  C05  O2    180.00   0.0  0
 ZHY  CONST_33  C03  C04  C05  O2    180.00   0.0  0
 ZHY  CONST_34  O    C03  C02  C10   180.00   0.0  0
 ZHY  CONST_35  N8   C10  C02  C03   180.00   0.0  0
 ZHY  CONST_36  N8   C10  C06  C05   180.00   0.0  0
 ZHY  CONST_37  O    C03  C04  C05   180.00   0.0  0
 ZHY  CONST_38  N8   C6   C    N5    180.00   0.0  0
 ZHY  CONST_39  H8   C    N5   C1    180.00   0.0  0
 ZHY  CONST_40  H3   C3   C4   C2    180.00   0.0  0
 ZHY  CONST_41  H2   C2   C4   C3    180.00   0.0  0
 ZHY  CONST_42  H4   C7   C2   C4    180.00   0.0  0
 ZHY  CONST_43  H5   C9   C3   C4    180.00   0.0  0
 ZHY  CONST_44  H1   C1   C5   C4      0.00   0.0  0
 ZHY  CONST_45  H2   C2   C4   C5      0.00   0.0  0
 ZHY  CONST_46  H3   C3   C4   C5      0.00   0.0  0
 ZHY  CONST_47  H5   C9   C8   C7    180.00   0.0  0
 ZHY  CONST_48  H4   C7   C8   C9    180.00   0.0  0
 ZHY  CONST_49  H7   C06  C10  C02   180.00   0.0  0
 ZHY  CONST_50  H6   C02  C10  C06   180.00   0.0  0
 ZHY  CONST_51  H1   C1   N5   C     180.00   0.0  0
 ZHY  CONST_52  H2   C2   C7   C8    180.00   0.0  0
 ZHY  CONST_53  H3   C3   C9   C8    180.00   0.0  0
 ZHY  CONST_54  H7   C06  C05  C04   180.00   0.0  0
 ZHY  CONST_55  H6   C02  C03  C04   180.00   0.0  0
 ZHY  CONST_56  H1   C1   C5   N     180.00   0.0  0
 ZHY  CONST_57  H8   C    C6   N     180.00   0.0  0
 ZHY  CONST_58  H18  N1   C01  C8    180.00   0.0  0
 ZHY  CONST_59  H19  N1   C01  C8      0.00   0.0  0
 ZHY  CONST_60  H18  N1   C01  O02     0.00   0.0  0
 ZHY  CONST_61  H19  N1   C01  O02   180.00   0.0  0
 ZHY  Var_01    C06  C10  N8   C6     -4.04  30.0  2
 ZHY  Var_02    C02  C10  N8   C6    176.35  30.0  2
 ZHY  Var_03    C10  N8   C6   C    -179.83  30.0  2
 ZHY  Var_04    N    C6   N8   C10     0.33  30.0  2
 ZHY  Var_05    N1   C01  C8   C7     23.43  30.0  2
 ZHY  Var_06    O02  C01  C8   C7   -156.23  30.0  2
 ZHY  Var_07    N1   C01  C8   C9   -158.63  30.0  2
 ZHY  Var_08    O02  C01  C8   C9     21.72  30.0  2
 ZHY  Var_09    C13  O    C03  C02     2.03  30.0  2
 ZHY  Var_10    C11  O2   C05  C06     1.28  30.0  2
 ZHY  Var_11    C12  O1   C04  C03    90.39  30.0  2
 ZHY  Var_12    C12  O1   C04  C05   -90.25  30.0  2
 ZHY  Var_13    C11  O2   C05  C04  -178.42  30.0  2
 ZHY  Var_14    C13  O    C03  C04  -178.57  30.0  2
 ZHY  Var_15    H20  N8   C10  C02    -2.42  30.0  2
 ZHY  Var_16    H20  N8   C10  C06   177.19  30.0  2
 ZHY  Var_17    H20  N8   C6   C      -1.05  30.0  2
 ZHY  Var_18    H20  N8   C6   N     179.11  30.0  2
 ZHY  Var_19    H9   C13  O    C03   178.92  30.0  3
 ZHY  Var_20    H10  C13  O    C03   -62.37  30.0  3
 ZHY  Var_21    H11  C13  O    C03    60.20  30.0  3
 ZHY  Var_22    H12  C11  O2   C05  -179.30  30.0  3
 ZHY  Var_23    H13  C11  O2   C05   -60.51  30.0  3
 ZHY  Var_24    H14  C11  O2   C05    62.11  30.0  3
 ZHY  Var_25    H15  C12  O1   C04  -179.44  30.0  3
 ZHY  Var_26    H16  C12  O1   C04   -60.49  30.0  3
 ZHY  Var_27    H17  C12  O1   C04    61.70  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
 ZHY  plan-1  C1   0.020
 ZHY  plan-1  C4   0.020
 ZHY  plan-1  C5   0.020
 ZHY  plan-1  C6   0.020
 ZHY  plan-1  C    0.020
 ZHY  plan-1  N5   0.020
 ZHY  plan-1  N    0.020
 ZHY  plan-1  N8   0.020
 ZHY  plan-1  H1   0.020
 ZHY  plan-1  H8   0.020
 ZHY  plan-2  C2   0.020
 ZHY  plan-2  C3   0.020
 ZHY  plan-2  C4   0.020
 ZHY  plan-2  C5   0.020
 ZHY  plan-2  C7   0.020
 ZHY  plan-2  C9   0.020
 ZHY  plan-2  C8   0.020
 ZHY  plan-2  C01  0.020
 ZHY  plan-2  H2   0.020
 ZHY  plan-2  H3   0.020
 ZHY  plan-2  H4   0.020
 ZHY  plan-2  H5   0.020
 ZHY  plan-3  O1   0.020
 ZHY  plan-3  O2   0.020
 ZHY  plan-3  C02  0.020
 ZHY  plan-3  C06  0.020
 ZHY  plan-3  C10  0.020
 ZHY  plan-3  C03  0.020
 ZHY  plan-3  C05  0.020
 ZHY  plan-3  C04  0.020
 ZHY  plan-3  N8   0.020
 ZHY  plan-3  O    0.020
 ZHY  plan-3  H6   0.020
 ZHY  plan-3  H7   0.020
 ZHY  plan-4  C8   0.020
 ZHY  plan-4  C01  0.020
 ZHY  plan-4  N1   0.020
 ZHY  plan-4  O02  0.020
 ZHY  plan-4  H18  0.020
 ZHY  plan-4  H19  0.020

