# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:53:20 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]-2-methoxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)c2cnc(N)c(n2)c3ccc(C(O)=O)c(OC)c3
#
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
 5R1  5R1  '4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]-2-methoxybenzoic acid'  ligand  50  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5R1
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
 5R1  C01   C  CH3    0  -0.438  -2.8355  -2.8479   1.4320
 5R1  O02   O  O2     0  -0.456  -3.9206  -2.2334   0.7707
 5R1  C03   C  CR6    0   0.381  -3.7631  -0.9867   0.2858
 5R1  C04   C  CR16   0  -0.431  -2.5914  -0.2573   0.4543
 5R1  C05   C  CR6    0   0.064  -2.4612   1.0263  -0.0785
 5R1  C06   C  CR6    0   0.122  -1.1785   1.7364   0.1084
 5R1  N07   N  N      0  -0.401  -0.0822   1.0221  -0.0081
 5R1  C08   C  CR6    0   0.184   1.1206   1.5762   0.1488
 5R1  C09   C  CR6    0   0.096   2.2989   0.6974   0.0099
 5R1  C10   C  CR16   0  -0.533   3.5911   1.2192  -0.0195
 5R1  C11   C  CR6    0   0.377   4.6837   0.3653  -0.1403
 5R1  O12   O  O2     0  -0.466   5.9636   0.7733  -0.1771
 5R1  C13   C  CH3    0  -0.441   6.2361   2.1584  -0.1068
 5R1  C14   C  CR6    0   0.163   4.4909  -1.0148  -0.2463
 5R1  O15   O  O2     0  -0.480   5.5548  -1.8442  -0.4027
 5R1  C16   C  CH3    0  -0.409   6.1146  -2.3165   0.8158
 5R1  C17   C  CR6    0   0.371   3.1936  -1.5324  -0.2137
 5R1  O18   O  O2     0  -0.465   3.0987  -2.8699  -0.3105
 5R1  C19   C  CH3    0  -0.439   1.8104  -3.4516  -0.3370
 5R1  C20   C  CR16   0  -0.478   2.1035  -0.6779  -0.0938
 5R1  C21   C  CR16   0  -0.119   1.1885   2.9311   0.4475
 5R1  N22   N  N      0  -0.408   0.1062   3.6770   0.5995
 5R1  C23   C  CR6    0   0.400  -1.0868   3.1156   0.4448
 5R1  N24   N  NH2    0  -0.831  -2.1734   3.9093   0.6119
 5R1  C25   C  CR16   0  -0.333  -3.5100   1.5621  -0.8172
 5R1  C26   C  CR16   0  -0.263  -4.6626   0.8116  -1.0095
 5R1  C27   C  CR6    0  -0.154  -4.8307  -0.4480  -0.4527
 5R1  C28   C  C      0   0.376  -6.1552  -1.1727  -0.6561
 5R1  O29   O  O      0  -0.593  -6.6632  -1.7066   0.3446
 5R1  O30   O  OC    -1  -0.599  -6.6251  -1.1268  -1.8085
 5R1  H011  H  HCH3   0   0.217  -1.9556  -2.9345   0.7877
 5R1  H012  H  HCH3   0   0.227  -2.5493  -2.3149   2.3427
 5R1  H013  H  HCH3   0   0.261  -3.1666  -3.8472   1.7042
 5R1  H04   H  HCR6   0   0.270  -1.7561  -0.6660   1.0061
 5R1  H25   H  HCR6   0   0.258  -3.4242   2.5367  -1.2797
 5R1  H21   H  HCR6   0   0.264   2.1336   3.4406   0.5935
 5R1  H10   H  HCR6   0   0.271   3.7452   2.2863   0.0418
 5R1  H20   H  HCR6   0   0.272   1.0931  -1.0599  -0.0751
 5R1  H131  H  HCH3   0   0.229   5.8807   2.6001   0.8279
 5R1  H132  H  HCH3   0   0.262   7.3174   2.2609  -0.1516
 5R1  H133  H  HCH3   0   0.230   5.7972   2.7052  -0.9454
 5R1  H161  H  HCH3   0   0.222   5.3816  -2.8621   1.4147
 5R1  H162  H  HCH3   0   0.237   6.9257  -2.9943   0.5549
 5R1  H163  H  HCH3   0   0.222   6.5213  -1.5003   1.4173
 5R1  H191  H  HCH3   0   0.225   1.2485  -3.2469   0.5782
 5R1  H192  H  HCH3   0   0.230   1.2269  -3.1077  -1.1947
 5R1  H193  H  HCH3   0   0.263   1.9592  -4.5251  -0.4220
 5R1  H241  H  HNH2   0   0.400  -3.0587   3.4798   0.8243
 5R1  H242  H  HNH2   0   0.393  -2.0102   4.7864   1.0803
 5R1  H26   H  HCR6   0   0.250  -5.4615   1.2248  -1.6115

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
 5R1  C01  O02   single    1.412  0.020  1.412
 5R1  O02  C03   single    1.347  0.020  1.347
 5R1  C03  C04   aromatic  1.390  0.020  1.390
 5R1  C03  C27   aromatic  1.405  0.020  1.405
 5R1  C04  C05   aromatic  1.396  0.020  1.396
 5R1  C05  C06   single    1.478  0.020  1.478
 5R1  C05  C25   aromatic  1.390  0.020  1.390
 5R1  C06  N07   aromatic  1.314  0.020  1.314
 5R1  C06  C23   aromatic  1.423  0.020  1.423
 5R1  N07  C08   aromatic  1.334  0.020  1.334
 5R1  C08  C09   single    1.476  0.020  1.476
 5R1  C08  C21   aromatic  1.389  0.020  1.389
 5R1  C09  C10   aromatic  1.394  0.020  1.394
 5R1  C09  C20   aromatic  1.393  0.020  1.393
 5R1  C10  C11   aromatic  1.392  0.020  1.392
 5R1  C11  O12   single    1.344  0.020  1.344
 5R1  C11  C14   aromatic  1.398  0.020  1.398
 5R1  O12  C13   single    1.413  0.020  1.413
 5R1  C14  O15   single    1.358  0.020  1.358
 5R1  C14  C17   aromatic  1.397  0.020  1.397
 5R1  O15  C16   single    1.422  0.020  1.422
 5R1  C17  O18   single    1.344  0.020  1.344
 5R1  C17  C20   aromatic  1.390  0.020  1.390
 5R1  O18  C19   single    1.414  0.020  1.414
 5R1  C21  N22   aromatic  1.323  0.020  1.323
 5R1  N22  C23   aromatic  1.328  0.020  1.328
 5R1  C23  N24   single    1.356  0.020  1.356
 5R1  C25  C26   aromatic  1.389  0.020  1.389
 5R1  C26  C27   aromatic  1.387  0.020  1.387
 5R1  C27  C28   single    1.523  0.020  1.523
 5R1  C28  O29   deloc     1.243  0.020  1.243
 5R1  C28  O30   deloc     1.245  0.020  1.245
 5R1  C01  H011  single    0.970  0.020  1.090
 5R1  C01  H012  single    0.970  0.020  1.090
 5R1  C01  H013  single    0.970  0.020  1.090
 5R1  C04  H04   single    0.930  0.020  1.080
 5R1  C25  H25   single    0.930  0.020  1.080
 5R1  C21  H21   single    0.930  0.020  1.080
 5R1  C10  H10   single    0.930  0.020  1.080
 5R1  C20  H20   single    0.930  0.020  1.080
 5R1  C13  H131  single    0.970  0.020  1.090
 5R1  C13  H132  single    0.970  0.020  1.090
 5R1  C13  H133  single    0.970  0.020  1.090
 5R1  C16  H161  single    0.970  0.020  1.090
 5R1  C16  H162  single    0.970  0.020  1.090
 5R1  C16  H163  single    0.970  0.020  1.090
 5R1  C19  H191  single    0.970  0.020  1.090
 5R1  C19  H192  single    0.970  0.020  1.090
 5R1  C19  H193  single    0.970  0.020  1.090
 5R1  N24  H241  single    0.890  0.020  1.040
 5R1  N24  H242  single    0.890  0.020  1.040
 5R1  C26  H26   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
 5R1  H013  C01  H012  108.62  3.000
 5R1  H013  C01  H011  108.64  3.000
 5R1  H012  C01  H011  108.58  3.000
 5R1  H013  C01  O02   106.46  3.000
 5R1  H012  C01  O02   112.29  3.000
 5R1  H011  C01  O02   112.14  3.000
 5R1  C03   O02  C01   118.80  3.000
 5R1  C27   C03  C04   120.18  3.000
 5R1  C27   C03  O02   117.07  3.000
 5R1  C04   C03  O02   122.72  3.000
 5R1  H04   C04  C05   118.05  3.000
 5R1  H04   C04  C03   120.97  3.000
 5R1  C05   C04  C03   120.98  3.000
 5R1  C25   C05  C06   122.46  3.000
 5R1  C25   C05  C04   119.13  3.000
 5R1  C06   C05  C04   118.33  3.000
 5R1  C23   C06  N07   119.63  3.000
 5R1  C23   C06  C05   123.48  3.000
 5R1  N07   C06  C05   116.86  3.000
 5R1  C08   N07  C06   121.09  3.000
 5R1  C21   C08  C09   124.18  3.000
 5R1  C21   C08  N07   118.34  3.000
 5R1  C09   C08  N07   117.48  3.000
 5R1  C20   C09  C10   119.87  3.000
 5R1  C20   C09  C08   118.86  3.000
 5R1  C10   C09  C08   121.27  3.000
 5R1  H10   C10  C11   119.94  3.000
 5R1  H10   C10  C09   120.06  3.000
 5R1  C11   C10  C09   120.00  3.000
 5R1  C14   C11  O12   115.41  3.000
 5R1  C14   C11  C10   120.27  3.000
 5R1  O12   C11  C10   124.32  3.000
 5R1  C13   O12  C11   118.67  3.000
 5R1  H133  C13  H132  108.70  3.000
 5R1  H133  C13  H131  108.86  3.000
 5R1  H132  C13  H131  108.69  3.000
 5R1  H133  C13  O12   112.00  3.000
 5R1  H132  C13  O12   106.39  3.000
 5R1  H131  C13  O12   112.08  3.000
 5R1  C17   C14  O15   120.26  3.000
 5R1  C17   C14  C11   119.48  3.000
 5R1  O15   C14  C11   120.25  3.000
 5R1  C16   O15  C14   114.38  3.000
 5R1  H163  C16  H162  108.64  3.000
 5R1  H163  C16  H161  108.73  3.000
 5R1  H162  C16  H161  108.69  3.000
 5R1  H163  C16  O15   111.73  3.000
 5R1  H162  C16  O15   107.14  3.000
 5R1  H161  C16  O15   111.81  3.000
 5R1  C20   C17  O18   124.22  3.000
 5R1  C20   C17  C14   120.16  3.000
 5R1  O18   C17  C14   115.62  3.000
 5R1  C19   O18  C17   118.36  3.000
 5R1  H193  C19  H192  108.81  3.000
 5R1  H193  C19  H191  108.70  3.000
 5R1  H192  C19  H191  108.88  3.000
 5R1  H193  C19  O18   106.45  3.000
 5R1  H192  C19  O18   111.82  3.000
 5R1  H191  C19  O18   112.06  3.000
 5R1  H20   C20  C17   121.16  3.000
 5R1  H20   C20  C09   118.62  3.000
 5R1  C17   C20  C09   120.22  3.000
 5R1  H21   C21  N22   115.65  3.000
 5R1  H21   C21  C08   122.03  3.000
 5R1  N22   C21  C08   122.31  3.000
 5R1  C23   N22  C21   118.90  3.000
 5R1  N24   C23  N22   117.27  3.000
 5R1  N24   C23  C06   123.03  3.000
 5R1  N22   C23  C06   119.70  3.000
 5R1  H242  N24  H241  114.57  3.000
 5R1  H242  N24  C23   115.91  3.000
 5R1  H241  N24  C23   118.75  3.000
 5R1  H25   C25  C26   119.56  3.000
 5R1  H25   C25  C05   120.96  3.000
 5R1  C26   C25  C05   119.43  3.000
 5R1  H26   C26  C27   118.71  3.000
 5R1  H26   C26  C25   118.90  3.000
 5R1  C27   C26  C25   122.39  3.000
 5R1  C28   C27  C26   118.92  3.000
 5R1  C28   C27  C03   123.25  3.000
 5R1  C26   C27  C03   117.82  3.000
 5R1  O30   C28  O29   127.36  3.000
 5R1  O30   C28  C27   115.72  3.000
 5R1  O29   C28  C27   116.88  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
 5R1  CONST_01  C06   C05  C04  C03  180.00   0.0  0
 5R1  CONST_02  C25   C05  C04  C03    0.00   0.0  0
 5R1  CONST_03  C25   C26  C27  C03    0.00   0.0  0
 5R1  CONST_04  C26   C27  C03  C04    0.00   0.0  0
 5R1  CONST_07  C26   C25  C05  C04    0.00   0.0  0
 5R1  CONST_08  C27   C03  C04  C05    0.00   0.0  0
 5R1  CONST_09  C08   N07  C06  C05  180.00   0.0  0
 5R1  CONST_10  N22   C23  C06  C05  180.00   0.0  0
 5R1  CONST_11  C27   C26  C25  C05    0.00   0.0  0
 5R1  CONST_12  C26   C25  C05  C06  180.00   0.0  0
 5R1  CONST_13  C09   C08  N07  C06  180.00   0.0  0
 5R1  CONST_14  C21   C08  N07  C06    0.00   0.0  0
 5R1  CONST_15  C21   N22  C23  C06    0.00   0.0  0
 5R1  CONST_17  N22   C23  C06  N07    0.00   0.0  0
 5R1  CONST_18  C10   C09  C08  N07  180.00   0.0  0
 5R1  CONST_19  C20   C09  C08  N07    0.00   0.0  0
 5R1  CONST_20  N22   C21  C08  N07    0.00   0.0  0
 5R1  CONST_21  C23   C06  N07  C08    0.00   0.0  0
 5R1  CONST_22  C11   C10  C09  C08  180.00   0.0  0
 5R1  CONST_23  C17   C20  C09  C08  180.00   0.0  0
 5R1  CONST_24  C23   N22  C21  C08    0.00   0.0  0
 5R1  CONST_25  N22   C21  C08  C09  180.00   0.0  0
 5R1  CONST_26  C14   C11  C10  C09    0.00   0.0  0
 5R1  CONST_27  C14   C17  C20  C09    0.00   0.0  0
 5R1  CONST_28  C21   C08  C09  C10    0.00   0.0  0
 5R1  CONST_29  C17   C20  C09  C10    0.00   0.0  0
 5R1  CONST_30  C17   C14  C11  C10    0.00   0.0  0
 5R1  CONST_31  C20   C09  C10  C11    0.00   0.0  0
 5R1  CONST_32  C20   C17  C14  C11    0.00   0.0  0
 5R1  CONST_33  C21   C08  C09  C20  180.00   0.0  0
 5R1  CONST_35  C05   C04  C03  O02  180.00   0.0  0
 5R1  CONST_36  C26   C27  C03  O02  180.00   0.0  0
 5R1  CONST_37  C28   C27  C03  C04  180.00   0.0  0
 5R1  CONST_38  N24   C23  C06  C05    0.00   0.0  0
 5R1  CONST_39  N24   C23  C06  N07  180.00   0.0  0
 5R1  CONST_40  O12   C11  C10  C09  180.00   0.0  0
 5R1  CONST_41  O18   C17  C20  C09  180.00   0.0  0
 5R1  CONST_42  O15   C14  C11  C10  180.00   0.0  0
 5R1  CONST_43  O18   C17  C14  C11  180.00   0.0  0
 5R1  CONST_44  C17   C14  C11  O12  180.00   0.0  0
 5R1  CONST_45  C20   C17  C14  O15  180.00   0.0  0
 5R1  CONST_46  N24   C23  N22  C21  180.00   0.0  0
 5R1  CONST_47  C28   C27  C26  C25  180.00   0.0  0
 5R1  CONST_48  H26   C26  C27  C03  180.00   0.0  0
 5R1  CONST_49  H25   C25  C05  C04  180.00   0.0  0
 5R1  CONST_50  H04   C04  C05  C06    0.00   0.0  0
 5R1  CONST_51  H21   C21  C08  N07  180.00   0.0  0
 5R1  CONST_52  H10   C10  C09  C08    0.00   0.0  0
 5R1  CONST_53  H20   C20  C09  C08    0.00   0.0  0
 5R1  Var_01    C04   C03  O02  C01   -2.56  30.0  2
 5R1  Var_02    O29   C28  C27  C03   45.24  30.0  2
 5R1  Var_03    C14   C11  O12  C13  178.54  30.0  2
 5R1  Var_04    C17   C14  O15  C16  -91.06  30.0  2
 5R1  Var_05    C20   C17  O18  C19    2.17  30.0  2
 5R1  Var_06    H011  C01  O02  C03  -59.31  30.0  3
 5R1  Var_07    H131  C13  O12  C11   61.28  30.0  3
 5R1  Var_08    H161  C16  O15  C14   58.88  30.0  3
 5R1  Var_09    H191  C19  O18  C17  -61.53  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
 5R1  plan-1  O02   0.020
 5R1  plan-1  C03   0.020
 5R1  plan-1  C04   0.020
 5R1  plan-1  C05   0.020
 5R1  plan-1  C06   0.020
 5R1  plan-1  C25   0.020
 5R1  plan-1  C26   0.020
 5R1  plan-1  C27   0.020
 5R1  plan-1  C28   0.020
 5R1  plan-1  H04   0.020
 5R1  plan-1  H25   0.020
 5R1  plan-1  H26   0.020
 5R1  plan-2  C05   0.020
 5R1  plan-2  C06   0.020
 5R1  plan-2  N07   0.020
 5R1  plan-2  C08   0.020
 5R1  plan-2  C09   0.020
 5R1  plan-2  C21   0.020
 5R1  plan-2  N22   0.020
 5R1  plan-2  C23   0.020
 5R1  plan-2  N24   0.020
 5R1  plan-2  H21   0.020
 5R1  plan-3  C08   0.020
 5R1  plan-3  C09   0.020
 5R1  plan-3  C10   0.020
 5R1  plan-3  C11   0.020
 5R1  plan-3  O12   0.020
 5R1  plan-3  C14   0.020
 5R1  plan-3  O15   0.020
 5R1  plan-3  C17   0.020
 5R1  plan-3  O18   0.020
 5R1  plan-3  C20   0.020
 5R1  plan-3  H10   0.020
 5R1  plan-3  H20   0.020
 5R1  plan-4  C23   0.020
 5R1  plan-4  N24   0.020
 5R1  plan-4  H241  0.020
 5R1  plan-4  H242  0.020
 5R1  plan-5  C27   0.020
 5R1  plan-5  C28   0.020
 5R1  plan-5  O29   0.020
 5R1  plan-5  O30   0.020

