# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 22:01:02 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 1-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)c2cnc(N)c(n2)N3CCC(CC3)C(O)=O
#
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
 BX1  BX1  '1-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic acid'  ligand  51  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BX1
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
 BX1  C01   C  CH3    0  -0.440  -5.5214   2.5196  -0.3271
 BX1  O02   O  O2     0  -0.466  -5.4001   1.1127  -0.2612
 BX1  C03   C  CR6    0   0.367  -4.1768   0.5801  -0.0954
 BX1  C04   C  CR16   0  -0.517  -3.0059   1.3241   0.0152
 BX1  C05   C  CR6    0   0.102  -1.7817   0.6789   0.1828
 BX1  C06   C  CR6    0   0.184  -0.5328   1.4496   0.3236
 BX1  C07   C  CR16   0  -0.147  -0.4950   2.7728   0.7145
 BX1  N08   N  N      0  -0.409   0.6467   3.4607   0.7780
 BX1  C09   C  CR6    0   0.379   1.7705   2.8381   0.4925
 BX1  N10   N  NH2    0  -0.824   2.9378   3.5379   0.5047
 BX1  C11   C  CR6    0   0.381   1.7590   1.4388   0.1855
 BX1  N12   N  NT     0  -0.509   2.9573   0.7921  -0.0825
 BX1  C13   C  CH2    0  -0.329   3.8727   0.6515   1.0547
 BX1  C14   C  CH2    0  -0.417   5.2714   0.3135   0.5718
 BX1  C15   C  CH1    0  -0.404   5.2695  -0.9535  -0.2794
 BX1  C16   C  C      0   0.424   5.0583  -2.2414   0.5580
 BX1  O17   O  O      0  -0.611   5.4846  -2.2303   1.7311
 BX1  O18   O  OC    -1  -0.609   4.5195  -3.2108  -0.0136
 BX1  C19   C  CH2    0  -0.416   4.2493  -0.7943  -1.4034
 BX1  C20   C  CH2    0  -0.290   2.8722  -0.4294  -0.8713
 BX1  N21   N  N      0  -0.421   0.6219   0.8043   0.0872
 BX1  C22   C  CR16   0  -0.475  -1.7294  -0.7126   0.2215
 BX1  C23   C  CR6    0   0.364  -2.8986  -1.4577   0.1097
 BX1  O24   O  O2     0  -0.465  -2.9465  -2.8011   0.1443
 BX1  C25   C  CH3    0  -0.439  -1.7398  -3.5120   0.3367
 BX1  C26   C  CR6    0   0.164  -4.1307  -0.8153  -0.0381
 BX1  O27   O  O2     0  -0.481  -5.2763  -1.5417  -0.1134
 BX1  C28   C  CH3    0  -0.408  -5.6538  -1.9094  -1.4336
 BX1  H011  H  HCH3   0   0.229  -4.9663   2.9390  -1.1701
 BX1  H012  H  HCH3   0   0.262  -6.5788   2.7304  -0.4659
 BX1  H013  H  HCH3   0   0.228  -5.1847   3.0034   0.5936
 BX1  H04   H  HCR6   0   0.269  -3.0426   2.4016  -0.0568
 BX1  H22   H  HCR6   0   0.270  -0.7695  -1.1934   0.3454
 BX1  H07   H  HCR6   0   0.255  -1.3934   3.3172   0.9793
 BX1  H101  H  HNH2   0   0.389   2.8437   4.5408   0.4662
 BX1  H102  H  HNH2   0   0.390   3.6782   3.1727  -0.0744
 BX1  H131  H  HCH2   0   0.252   3.8830   1.5763   1.6317
 BX1  H132  H  HCH2   0   0.224   3.5118  -0.1385   1.7282
 BX1  H201  H  HCH2   0   0.206   2.4668  -1.2617  -0.2811
 BX1  H202  H  HCH2   0   0.235   2.1797  -0.2629  -1.6971
 BX1  H141  H  HCH2   0   0.212   5.6544   1.1551  -0.0145
 BX1  H142  H  HCH2   0   0.226   5.9300   0.1976   1.4318
 BX1  H15   H  HCH1   0   0.237   6.2632  -1.0559  -0.7361
 BX1  H191  H  HCH2   0   0.209   4.5782  -0.0086  -2.0908
 BX1  H192  H  HCH2   0   0.224   4.1763  -1.7143  -1.9828
 BX1  H251  H  HCH3   0   0.262  -2.0032  -4.5666   0.3525
 BX1  H252  H  HCH3   0   0.227  -1.0280  -3.3399  -0.4748
 BX1  H253  H  HCH3   0   0.229  -1.2609  -3.2538   1.2845
 BX1  H281  H  HCH3   0   0.220  -5.8542  -1.0348  -2.0573
 BX1  H282  H  HCH3   0   0.221  -4.8889  -2.5201  -1.9194
 BX1  H283  H  HCH3   0   0.236  -6.5680  -2.4951  -1.3548

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
 BX1  C01  O02   single    1.414  0.020  1.414
 BX1  O02  C03   single    1.344  0.020  1.344
 BX1  C03  C04   aromatic  1.392  0.020  1.392
 BX1  C03  C26   aromatic  1.397  0.020  1.397
 BX1  C04  C05   aromatic  1.394  0.020  1.394
 BX1  C05  C06   single    1.474  0.020  1.474
 BX1  C05  C22   aromatic  1.393  0.020  1.393
 BX1  C06  C07   aromatic  1.380  0.020  1.380
 BX1  C06  N21   aromatic  1.344  0.020  1.344
 BX1  C07  N08   aromatic  1.334  0.020  1.334
 BX1  N08  C09   aromatic  1.316  0.020  1.316
 BX1  C09  N10   single    1.361  0.020  1.361
 BX1  C09  C11   aromatic  1.433  0.020  1.433
 BX1  C11  N12   single    1.388  0.020  1.388
 BX1  C11  N21   aromatic  1.306  0.020  1.306
 BX1  N12  C13   single    1.467  0.020  1.467
 BX1  N12  C20   single    1.457  0.020  1.457
 BX1  C13  C14   single    1.518  0.020  1.518
 BX1  C14  C15   single    1.526  0.020  1.526
 BX1  C15  C16   single    1.551  0.020  1.551
 BX1  C15  C19   single    1.526  0.020  1.526
 BX1  C16  O17   deloc     1.248  0.020  1.248
 BX1  C16  O18   deloc     1.248  0.020  1.248
 BX1  C19  C20   single    1.521  0.020  1.521
 BX1  C22  C23   aromatic  1.391  0.020  1.391
 BX1  C23  O24   single    1.345  0.020  1.345
 BX1  C23  C26   aromatic  1.397  0.020  1.397
 BX1  O24  C25   single    1.414  0.020  1.414
 BX1  C26  O27   single    1.359  0.020  1.359
 BX1  O27  C28   single    1.421  0.020  1.421
 BX1  C01  H011  single    0.970  0.020  1.090
 BX1  C01  H012  single    0.970  0.020  1.090
 BX1  C01  H013  single    0.970  0.020  1.090
 BX1  C04  H04   single    0.930  0.020  1.080
 BX1  C22  H22   single    0.930  0.020  1.080
 BX1  C07  H07   single    0.930  0.020  1.080
 BX1  N10  H101  single    0.890  0.020  1.040
 BX1  N10  H102  single    0.890  0.020  1.040
 BX1  C13  H131  single    0.970  0.020  1.090
 BX1  C13  H132  single    0.970  0.020  1.090
 BX1  C20  H201  single    0.970  0.020  1.090
 BX1  C20  H202  single    0.970  0.020  1.090
 BX1  C14  H141  single    0.970  0.020  1.090
 BX1  C14  H142  single    0.970  0.020  1.090
 BX1  C15  H15   single    0.970  0.020  1.090
 BX1  C19  H191  single    0.970  0.020  1.090
 BX1  C19  H192  single    0.970  0.020  1.090
 BX1  C25  H251  single    0.970  0.020  1.090
 BX1  C25  H252  single    0.970  0.020  1.090
 BX1  C25  H253  single    0.970  0.020  1.090
 BX1  C28  H281  single    0.970  0.020  1.090
 BX1  C28  H282  single    0.970  0.020  1.090
 BX1  C28  H283  single    0.970  0.020  1.090

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
 BX1  H013  C01  H012  108.75  3.000
 BX1  H013  C01  H011  108.86  3.000
 BX1  H012  C01  H011  108.73  3.000
 BX1  H013  C01  O02   112.01  3.000
 BX1  H012  C01  O02   106.41  3.000
 BX1  H011  C01  O02   111.98  3.000
 BX1  C03   O02  C01   118.56  3.000
 BX1  C26   C03  C04   120.19  3.000
 BX1  C26   C03  O02   115.51  3.000
 BX1  C04   C03  O02   124.30  3.000
 BX1  H04   C04  C05   119.96  3.000
 BX1  H04   C04  C03   119.95  3.000
 BX1  C05   C04  C03   120.07  3.000
 BX1  C22   C05  C06   119.19  3.000
 BX1  C22   C05  C04   119.91  3.000
 BX1  C06   C05  C04   120.90  3.000
 BX1  N21   C06  C07   119.12  3.000
 BX1  N21   C06  C05   117.40  3.000
 BX1  C07   C06  C05   123.46  3.000
 BX1  H07   C07  N08   116.03  3.000
 BX1  H07   C07  C06   121.89  3.000
 BX1  N08   C07  C06   122.08  3.000
 BX1  C09   N08  C07   118.45  3.000
 BX1  C11   C09  N10   120.73  3.000
 BX1  C11   C09  N08   120.11  3.000
 BX1  N10   C09  N08   119.15  3.000
 BX1  H102  N10  H101  114.01  3.000
 BX1  H102  N10  C09   116.00  3.000
 BX1  H101  N10  C09   115.54  3.000
 BX1  N21   C11  N12   120.73  3.000
 BX1  N21   C11  C09   119.85  3.000
 BX1  N12   C11  C09   119.31  3.000
 BX1  C20   N12  C13   112.08  3.000
 BX1  C20   N12  C11   116.42  3.000
 BX1  C13   N12  C11   115.71  3.000
 BX1  H132  C13  H131  106.76  3.000
 BX1  H132  C13  C14   109.73  3.000
 BX1  H131  C13  C14   110.41  3.000
 BX1  H132  C13  N12   109.83  3.000
 BX1  H131  C13  N12   109.57  3.000
 BX1  C14   C13  N12   110.48  3.000
 BX1  H142  C14  H141  107.03  3.000
 BX1  H142  C14  C15   110.65  3.000
 BX1  H141  C14  C15   109.87  3.000
 BX1  H142  C14  C13   109.25  3.000
 BX1  H141  C14  C13   108.76  3.000
 BX1  C15   C14  C13   111.17  3.000
 BX1  H15   C15  C19   107.95  3.000
 BX1  H15   C15  C16   105.68  3.000
 BX1  C19   C15  C16   113.16  3.000
 BX1  H15   C15  C14   107.94  3.000
 BX1  C19   C15  C14   108.96  3.000
 BX1  C16   C15  C14   112.86  3.000
 BX1  O18   C16  O17   125.80  3.000
 BX1  O18   C16  C15   117.17  3.000
 BX1  O17   C16  C15   116.98  3.000
 BX1  H192  C19  H191  106.99  3.000
 BX1  H192  C19  C20   109.14  3.000
 BX1  H191  C19  C20   108.64  3.000
 BX1  H192  C19  C15   110.39  3.000
 BX1  H191  C19  C15   109.67  3.000
 BX1  C20   C19  C15   111.88  3.000
 BX1  H202  C20  H201  106.75  3.000
 BX1  H202  C20  C19   110.29  3.000
 BX1  H201  C20  C19   109.91  3.000
 BX1  H202  C20  N12   108.61  3.000
 BX1  H201  C20  N12   111.48  3.000
 BX1  C19   C20  N12   109.75  3.000
 BX1  C11   N21  C06   120.11  3.000
 BX1  H22   C22  C23   121.16  3.000
 BX1  H22   C22  C05   118.75  3.000
 BX1  C23   C22  C05   120.09  3.000
 BX1  C26   C23  O24   115.50  3.000
 BX1  C26   C23  C22   120.23  3.000
 BX1  O24   C23  C22   124.27  3.000
 BX1  C25   O24  C23   118.39  3.000
 BX1  H253  C25  H252  108.75  3.000
 BX1  H253  C25  H251  108.83  3.000
 BX1  H252  C25  H251  108.74  3.000
 BX1  H253  C25  O24   111.92  3.000
 BX1  H252  C25  O24   112.06  3.000
 BX1  H251  C25  O24   106.44  3.000
 BX1  O27   C26  C23   120.24  3.000
 BX1  O27   C26  C03   120.25  3.000
 BX1  C23   C26  C03   119.51  3.000
 BX1  C28   O27  C26   114.44  3.000
 BX1  H283  C28  H282  108.62  3.000
 BX1  H283  C28  H281  108.54  3.000
 BX1  H282  C28  H281  108.79  3.000
 BX1  H283  C28  O27   107.15  3.000
 BX1  H282  C28  O27   111.82  3.000
 BX1  H281  C28  O27   111.82  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
 BX1  CONST_01  C06   C05  C04  C03   180.00   0.0  0
 BX1  CONST_02  C22   C05  C04  C03     0.00   0.0  0
 BX1  CONST_03  C22   C23  C26  C03     0.00   0.0  0
 BX1  CONST_04  C23   C26  C03  C04     0.00   0.0  0
 BX1  CONST_07  C23   C22  C05  C04     0.00   0.0  0
 BX1  CONST_08  C26   C03  C04  C05     0.00   0.0  0
 BX1  CONST_09  N08   C07  C06  C05   180.00   0.0  0
 BX1  CONST_10  C11   N21  C06  C05   180.00   0.0  0
 BX1  CONST_11  C26   C23  C22  C05     0.00   0.0  0
 BX1  CONST_12  C23   C22  C05  C06   180.00   0.0  0
 BX1  CONST_13  C09   N08  C07  C06     0.00   0.0  0
 BX1  CONST_14  C09   C11  N21  C06     0.00   0.0  0
 BX1  CONST_16  C11   N21  C06  C07     0.00   0.0  0
 BX1  CONST_17  C11   C09  N08  C07     0.00   0.0  0
 BX1  CONST_18  N21   C06  C07  N08     0.00   0.0  0
 BX1  CONST_19  N21   C11  C09  N08     0.00   0.0  0
 BX1  CONST_21  N12   C11  N21  C06   180.00   0.0  0
 BX1  CONST_22  N12   C11  C09  N08   180.00   0.0  0
 BX1  CONST_23  C05   C04  C03  O02   180.00   0.0  0
 BX1  CONST_24  C23   C26  C03  O02   180.00   0.0  0
 BX1  CONST_25  O24   C23  C26  C03   180.00   0.0  0
 BX1  CONST_26  O27   C26  C03  C04   180.00   0.0  0
 BX1  CONST_27  O24   C23  C22  C05   180.00   0.0  0
 BX1  CONST_28  N10   C09  N08  C07   180.00   0.0  0
 BX1  CONST_29  N12   C11  C09  N10     0.00   0.0  0
 BX1  CONST_30  N21   C11  C09  N10   180.00   0.0  0
 BX1  CONST_31  O27   C26  C23  C22   180.00   0.0  0
 BX1  CONST_32  H22   C22  C05  C04   180.00   0.0  0
 BX1  CONST_33  H07   C07  C06  C05     0.00   0.0  0
 BX1  CONST_34  H04   C04  C05  C06     0.00   0.0  0
 BX1  Var_01    C13   N12  C11  C09    68.34  30.0  2
 BX1  Var_02    C14   C13  N12  C11  -163.46  30.0  1
 BX1  Var_03    C19   C20  N12  C11   164.18  30.0  1
 BX1  Var_04    C15   C14  C13  N12   -56.68  30.0  1
 BX1  Var_05    C15   C19  C20  N12    56.95  30.0  1
 BX1  Var_06    C04   C03  O02  C01    -0.12  30.0  2
 BX1  Var_07    C26   C23  O24  C25  -177.92  30.0  2
 BX1  Var_08    H011  C01  O02  C03    61.08  30.0  3
 BX1  Var_09    H251  C25  O24  C23   178.88  30.0  3
 BX1  Var_10    H281  C28  O27  C26   -62.11  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
 BX1  chir_01  C15  C14  C16  C19  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
 BX1  plan-1  O02   0.020
 BX1  plan-1  C03   0.020
 BX1  plan-1  C04   0.020
 BX1  plan-1  C05   0.020
 BX1  plan-1  C06   0.020
 BX1  plan-1  C22   0.020
 BX1  plan-1  C23   0.020
 BX1  plan-1  O24   0.020
 BX1  plan-1  C26   0.020
 BX1  plan-1  O27   0.020
 BX1  plan-1  H04   0.020
 BX1  plan-1  H22   0.020
 BX1  plan-2  C05   0.020
 BX1  plan-2  C06   0.020
 BX1  plan-2  C07   0.020
 BX1  plan-2  N08   0.020
 BX1  plan-2  C09   0.020
 BX1  plan-2  N10   0.020
 BX1  plan-2  C11   0.020
 BX1  plan-2  N12   0.020
 BX1  plan-2  N21   0.020
 BX1  plan-2  H07   0.020
 BX1  plan-3  C09   0.020
 BX1  plan-3  N10   0.020
 BX1  plan-3  H101  0.020
 BX1  plan-3  H102  0.020
 BX1  plan-4  C15   0.020
 BX1  plan-4  C16   0.020
 BX1  plan-4  O17   0.020
 BX1  plan-4  O18   0.020

