# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 17:08:12 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 8-(3-aminopropyl)-6-[2-chloro-4-(3-methyl-2-oxopyrazin-1(2H)-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncc2C=C(C(=O)N(CCCN)c2n1)c3ccc(cc3Cl)N4C=CN=C(C)C4=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
 6BZ  6BZ  8-(3-aminopropyl)-6-[2-chloro-4-(3-methyl-2-oxopyrazin-1(2H)-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  54  32  .  2021-08-05  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6BZ
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
 6BZ  C14  C   CR16  0  -0.198   2.8331  -0.2839  -0.9478
 6BZ  C6   C   CR16  0  -0.012   5.5859   1.0419  -1.2459
 6BZ  C11  C   CR16  0  -0.319   1.5838   1.2152   1.0169
 6BZ  C7   C   CR16  0  -0.192   6.9287   1.0300  -1.3741
 6BZ  C9   C   CR6   0   0.278   3.5809   0.4536  -0.0449
 6BZ  C10  C   CR16  0  -0.230   2.9662   1.2089   0.9395
 6BZ  C12  C   CR6   0   0.189   0.7984   0.4868   0.1261
 6BZ  C13  C   CR6   0  -0.110   1.4510  -0.2528  -0.8572
 6BZ  C3   C   CR6   0   0.525   5.7503  -0.1805   0.8153
 6BZ  C2   C   CR6   0   0.091   7.1988  -0.1338   0.5832
 6BZ  O4   O   O     0  -0.466   5.2309  -0.7264   1.7749
 6BZ  N5   N   NR6   0  -0.591   5.0028   0.4482  -0.1624
 6BZ  N8   N   N     0  -0.349   7.7294   0.4372  -0.4465
 6BZ  CL1  CL  CL    0  -0.112   0.5307  -1.1251  -2.0305
 6BZ  C16  C   CR6   0  -0.212  -0.6722   0.5437   0.2159
 6BZ  C17  C   CR16  0  -0.166  -1.3556   1.6854  -0.0154
 6BZ  C18  C   CR66  0  -0.108  -2.7685   1.7061   0.0791
 6BZ  C19  C   CR16  0  -0.035  -3.5684   2.8208  -0.1693
 6BZ  N20  N   N     0  -0.466  -4.8777   2.8056  -0.0964
 6BZ  C21  C   CR6   0   0.610  -5.4378   1.6250   0.2349
 6BZ  N22  N   N     0  -0.507  -4.7785   0.4912   0.4921
 6BZ  C23  C   CR66  0   0.564  -3.4624   0.5296   0.4208
 6BZ  N24  N   NR6   0  -0.595  -2.7569  -0.6110   0.6926
 6BZ  C25  C   CR6   0   0.570  -1.3695  -0.6772   0.6043
 6BZ  O26  O   O     0  -0.458  -0.7811  -1.7157   0.8546
 6BZ  C27  C   CH2   0  -0.311  -3.4817  -1.8333   1.0419
 6BZ  C28  C   CH2   0  -0.443  -3.8507  -2.6509  -0.1869
 6BZ  C29  C   CH2   0  -0.276  -4.6620  -3.8820   0.1886
 6BZ  N30  N   NH2   0  -0.799  -4.9792  -4.6666  -0.9948
 6BZ  N31  N   NH1   0  -0.635  -6.7693   1.5819   0.3109
 6BZ  C32  C   CH3   0  -0.511  -7.6314   2.7117   0.0674
 6BZ  H1   H   HCR6  0   0.298   3.3208  -0.8677  -1.7175
 6BZ  H2   H   HCR6  0   0.323   4.9273   1.5125  -1.9607
 6BZ  H3   H   HCR6  0   0.272   1.0958   1.7953   1.7889
 6BZ  H4   H   HCR6  0   0.277   7.4060   1.4991  -2.2218
 6BZ  H5   H   HCR6  0   0.280   3.5555   1.7894   1.6357
 6BZ  H6   H   HCH3  0   0.255   7.8385  -1.8621   1.6725
 6BZ  H7   H   HCH3  0   0.254   9.1095  -0.6726   1.3473
 6BZ  H8   H   HCH3  0   0.254   7.8898  -0.3747   2.5972
 6BZ  H9   H   HCR6  0   0.279  -0.8344   2.5929  -0.2988
 6BZ  H10  H   HCR6  0   0.280  -3.1004   3.7630  -0.4393
 6BZ  H11  H   HCH2  0   0.265  -2.8559  -2.4136   1.7158
 6BZ  H12  H   HCH2  0   0.264  -4.3749  -1.5419   1.5886
 6BZ  H13  H   HCH2  0   0.231  -4.4303  -2.0276  -0.8747
 6BZ  H14  H   HCH2  0   0.231  -2.9465  -2.9619  -0.7161
 6BZ  H15  H   HCH2  0   0.218  -4.0730  -4.5084   0.8647
 6BZ  H16  H   HCH2  0   0.193  -5.5483  -3.5642   0.7573
 6BZ  H17  H   HNH2  0   0.347  -5.5079  -5.4859  -0.7243
 6BZ  H18  H   HNH2  0   0.339  -5.5954  -4.1320  -1.5950
 6BZ  H20  H   HNH1  0   0.404  -7.1825   0.7011   0.5666
 6BZ  H21  H   HCH3  0   0.239  -7.4536   3.5196   0.7779
 6BZ  H22  H   HCH3  0   0.239  -7.5037   3.1098  -0.9393
 6BZ  H23  H   HCH3  0   0.254  -8.6593   2.3785   0.1768
 6BZ  C1   C   CH3   0  -0.720   8.0603  -0.7954   1.6047

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
 6BZ  N31  C32  single    1.442  0.020  1.442
 6BZ  N31  C21  single    1.334  0.020  1.334
 6BZ  N20  C21  aromatic  1.348  0.020  1.348
 6BZ  N20  C19  aromatic  1.311  0.020  1.311
 6BZ  C21  N22  aromatic  1.337  0.020  1.337
 6BZ  C19  C18  aromatic  1.394  0.020  1.394
 6BZ  N22  C23  aromatic  1.319  0.020  1.319
 6BZ  C18  C23  aromatic  1.408  0.020  1.408
 6BZ  C18  C17  single    1.416  0.020  1.416
 6BZ  C23  N24  single    1.368  0.020  1.368
 6BZ  C17  C16  double    1.350  0.020  1.350
 6BZ  N24  C27  single    1.463  0.020  1.463
 6BZ  N24  C25  single    1.392  0.020  1.392
 6BZ  C16  C25  single    1.459  0.020  1.459
 6BZ  C16  C12  single    1.475  0.020  1.475
 6BZ  C28  C27  single    1.521  0.020  1.521
 6BZ  C28  C29  single    1.522  0.020  1.522
 6BZ  C25  O26  double    1.220  0.020  1.220
 6BZ  C12  C11  aromatic  1.393  0.020  1.393
 6BZ  C12  C13  aromatic  1.393  0.020  1.393
 6BZ  CL1  C13  single    1.728  0.020  1.728
 6BZ  C29  N30  single    1.455  0.020  1.455
 6BZ  C11  C10  aromatic  1.385  0.020  1.385
 6BZ  C13  C14  aromatic  1.385  0.020  1.385
 6BZ  C10  C9   aromatic  1.385  0.020  1.385
 6BZ  C14  C9   aromatic  1.385  0.020  1.385
 6BZ  C9   N5   single    1.427  0.020  1.427
 6BZ  C6   N5   single    1.366  0.020  1.366
 6BZ  C6   C7   double    1.349  0.020  1.349
 6BZ  N5   C3   single    1.382  0.020  1.382
 6BZ  C7   N8   single    1.361  0.020  1.361
 6BZ  C3   O4   double    1.220  0.020  1.220
 6BZ  C3   C2   single    1.468  0.020  1.468
 6BZ  N8   C2   double    1.291  0.020  1.291
 6BZ  C2   C1   single    1.491  0.020  1.491
 6BZ  C14  H1   single    0.930  0.020  1.080
 6BZ  C6   H2   single    0.930  0.020  1.080
 6BZ  C11  H3   single    0.930  0.020  1.080
 6BZ  C7   H4   single    0.930  0.020  1.080
 6BZ  C10  H5   single    0.930  0.020  1.080
 6BZ  C1   H6   single    0.970  0.020  1.090
 6BZ  C1   H7   single    0.970  0.020  1.090
 6BZ  C1   H8   single    0.970  0.020  1.090
 6BZ  C17  H9   single    0.930  0.020  1.080
 6BZ  C19  H10  single    0.930  0.020  1.080
 6BZ  C27  H11  single    0.970  0.020  1.090
 6BZ  C27  H12  single    0.970  0.020  1.090
 6BZ  C28  H13  single    0.970  0.020  1.090
 6BZ  C28  H14  single    0.970  0.020  1.090
 6BZ  C29  H15  single    0.970  0.020  1.090
 6BZ  C29  H16  single    0.970  0.020  1.090
 6BZ  N30  H17  single    0.890  0.020  1.040
 6BZ  N30  H18  single    0.890  0.020  1.040
 6BZ  N31  H20  single    0.860  0.020  1.020
 6BZ  C32  H21  single    0.970  0.020  1.090
 6BZ  C32  H22  single    0.970  0.020  1.090
 6BZ  C32  H23  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
 6BZ  H1   C14  C13  120.54  3.000
 6BZ  H1   C14  C9   120.50  3.000
 6BZ  C13  C14  C9   118.95  3.000
 6BZ  H2   C6   N5   117.01  3.000
 6BZ  H2   C6   C7   123.23  3.000
 6BZ  N5   C6   C7   119.76  3.000
 6BZ  H3   C11  C12  118.84  3.000
 6BZ  H3   C11  C10  119.51  3.000
 6BZ  C12  C11  C10  121.65  3.000
 6BZ  H4   C7   N8   117.65  3.000
 6BZ  H4   C7   C6   120.70  3.000
 6BZ  N8   C7   C6   121.64  3.000
 6BZ  N5   C9   C10  120.20  3.000
 6BZ  N5   C9   C14  118.84  3.000
 6BZ  C10  C9   C14  120.94  3.000
 6BZ  H5   C10  C9   120.57  3.000
 6BZ  H5   C10  C11  120.39  3.000
 6BZ  C9   C10  C11  119.04  3.000
 6BZ  C16  C12  C13  122.06  3.000
 6BZ  C13  C12  C11  117.71  3.000
 6BZ  C16  C12  C11  120.21  3.000
 6BZ  CL1  C13  C12  119.87  3.000
 6BZ  CL1  C13  C14  118.41  3.000
 6BZ  C12  C13  C14  121.70  3.000
 6BZ  N5   C3   O4   121.98  3.000
 6BZ  O4   C3   C2   123.97  3.000
 6BZ  N5   C3   C2   114.05  3.000
 6BZ  N8   C2   C1   120.33  3.000
 6BZ  C1   C2   C3   116.60  3.000
 6BZ  N8   C2   C3   123.07  3.000
 6BZ  C3   N5   C9   118.85  3.000
 6BZ  C3   N5   C6   121.86  3.000
 6BZ  C9   N5   C6   119.28  3.000
 6BZ  C2   N8   C7   119.62  3.000
 6BZ  C25  C16  C17  120.75  3.000
 6BZ  C25  C16  C12  117.43  3.000
 6BZ  C17  C16  C12  121.79  3.000
 6BZ  H9   C17  C18  118.99  3.000
 6BZ  H9   C17  C16  120.61  3.000
 6BZ  C18  C17  C16  120.38  3.000
 6BZ  C23  C18  C19  115.37  3.000
 6BZ  C23  C18  C17  119.71  3.000
 6BZ  C19  C18  C17  124.90  3.000
 6BZ  H10  C19  N20  117.01  3.000
 6BZ  H10  C19  C18  119.37  3.000
 6BZ  N20  C19  C18  123.61  3.000
 6BZ  C21  N20  C19  116.02  3.000
 6BZ  N31  C21  N22  116.99  3.000
 6BZ  N22  C21  N20  125.82  3.000
 6BZ  N31  C21  N20  117.19  3.000
 6BZ  C23  N22  C21  117.21  3.000
 6BZ  N24  C23  N22  118.66  3.000
 6BZ  N24  C23  C18  119.38  3.000
 6BZ  N22  C23  C18  121.97  3.000
 6BZ  C27  N24  C25  117.98  3.000
 6BZ  C25  N24  C23  122.75  3.000
 6BZ  C27  N24  C23  119.23  3.000
 6BZ  O26  C25  N24  120.56  3.000
 6BZ  O26  C25  C16  122.46  3.000
 6BZ  N24  C25  C16  116.97  3.000
 6BZ  H12  C27  H11  107.71  3.000
 6BZ  H12  C27  C28  110.55  3.000
 6BZ  H11  C27  C28  110.69  3.000
 6BZ  H12  C27  N24  107.65  3.000
 6BZ  H11  C27  N24  107.98  3.000
 6BZ  C28  C27  N24  112.10  3.000
 6BZ  H14  C28  H13  107.22  3.000
 6BZ  H14  C28  C29  109.29  3.000
 6BZ  H13  C28  C29  109.48  3.000
 6BZ  H14  C28  C27  110.08  3.000
 6BZ  H13  C28  C27  109.27  3.000
 6BZ  C29  C28  C27  111.40  3.000
 6BZ  H16  C29  H15  106.25  3.000
 6BZ  H16  C29  N30  113.62  3.000
 6BZ  H15  C29  N30  108.14  3.000
 6BZ  H16  C29  C28  108.87  3.000
 6BZ  H15  C29  C28  109.19  3.000
 6BZ  N30  C29  C28  110.60  3.000
 6BZ  H18  N30  H17  105.54  3.000
 6BZ  H18  N30  C29  109.27  3.000
 6BZ  H17  N30  C29  109.46  3.000
 6BZ  H20  N31  C32  118.91  3.000
 6BZ  H20  N31  C21  116.91  3.000
 6BZ  C32  N31  C21  124.17  3.000
 6BZ  H23  C32  H22  108.42  3.000
 6BZ  H23  C32  H21  108.42  3.000
 6BZ  H22  C32  H21  108.19  3.000
 6BZ  H23  C32  N31  107.97  3.000
 6BZ  H22  C32  N31  111.84  3.000
 6BZ  H21  C32  N31  111.90  3.000
 6BZ  H8   C1   H7   108.82  3.000
 6BZ  H8   C1   H6   106.76  3.000
 6BZ  H7   C1   H6   108.73  3.000
 6BZ  H8   C1   C2   111.21  3.000
 6BZ  H7   C1   C2   110.19  3.000
 6BZ  H6   C1   C2   111.02  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
 6BZ  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 6BZ  CONST_02  C11  C10  C9   C14     0.00   0.0  0
 6BZ  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 6BZ  CONST_04  C12  C13  C14  C9      0.00   0.0  0
 6BZ  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 6BZ  CONST_06  C13  C14  C9   C10     0.00   0.0  0
 6BZ  CONST_07  C21  N20  C19  C18     0.00   0.0  0
 6BZ  CONST_08  C21  N22  C23  C18     0.00   0.0  0
 6BZ  CONST_09  N22  C21  N20  C19     0.00   0.0  0
 6BZ  CONST_10  N22  C23  C18  C19     0.00   0.0  0
 6BZ  CONST_11  C23  N22  C21  N20     0.00   0.0  0
 6BZ  CONST_12  C23  C18  C19  N20     0.00   0.0  0
 6BZ  CONST_13  C16  C12  C13  C14   180.00   0.0  0
 6BZ  CONST_14  N5   C9   C10  C11   180.00   0.0  0
 6BZ  CONST_15  C16  C12  C11  C10   180.00   0.0  0
 6BZ  CONST_16  N5   C9   C14  C13   180.00   0.0  0
 6BZ  CONST_17  C2   C3   N5   C6      0.00   0.0  0
 6BZ  CONST_18  C2   C3   N5   C9    180.00   0.0  0
 6BZ  CONST_19  C23  N24  C25  C16     0.00   0.0  0
 6BZ  CONST_20  CL1  C13  C12  C11   180.00   0.0  0
 6BZ  CONST_21  CL1  C13  C14  C9    180.00   0.0  0
 6BZ  CONST_22  C16  C12  C13  CL1     0.00   0.0  0
 6BZ  CONST_23  N31  C21  N20  C19   180.00   0.0  0
 6BZ  CONST_24  N31  C21  N22  C23   180.00   0.0  0
 6BZ  CONST_25  O4   C3   N5   C6    180.00   0.0  0
 6BZ  CONST_26  O4   C3   N5   C9      0.00   0.0  0
 6BZ  CONST_27  C27  N24  C25  C16   180.00   0.0  0
 6BZ  CONST_28  O26  C25  N24  C23   180.00   0.0  0
 6BZ  CONST_29  H5   C10  C9   C14   180.00   0.0  0
 6BZ  CONST_30  H3   C11  C10  C9    180.00   0.0  0
 6BZ  CONST_31  H1   C14  C9   C10   180.00   0.0  0
 6BZ  CONST_32  H10  C19  C18  C17     0.00   0.0  0
 6BZ  CONST_33  C32  N31  C21  N20     0.00   0.0  0
 6BZ  CONST_34  C32  N31  C21  N22   180.00   0.0  0
 6BZ  CONST_35  C27  N24  C25  O26     0.00   0.0  0
 6BZ  CONST_36  H20  N31  C21  N20   180.00   0.0  0
 6BZ  Var_01    C6   N5   C9   C14    67.61  30.0  2
 6BZ  Var_02    C17  C16  C12  C11    64.84  30.0  2
 6BZ  Var_03    C28  C27  N24  C23    88.50  30.0  3
 6BZ  Var_04    H6   C1   C2   C3     61.20  30.0  3
 6BZ  Var_05    C29  C28  C27  N24  -177.21  30.0  1
 6BZ  Var_06    H21  C32  N31  C21   -62.12  30.0  3
 6BZ  Var_07    N30  C29  C28  C27  -178.71  30.0  3
 6BZ  Var_08    H17  N30  C29  C28   179.28  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
 6BZ  plan-1  C6   0.020
 6BZ  plan-1  C7   0.020
 6BZ  plan-1  C9   0.020
 6BZ  plan-1  C3   0.020
 6BZ  plan-1  C2   0.020
 6BZ  plan-1  O4   0.020
 6BZ  plan-1  N5   0.020
 6BZ  plan-1  N8   0.020
 6BZ  plan-1  H2   0.020
 6BZ  plan-1  H4   0.020
 6BZ  plan-1  C1   0.020
 6BZ  plan-2  C14  0.020
 6BZ  plan-2  C11  0.020
 6BZ  plan-2  C9   0.020
 6BZ  plan-2  C10  0.020
 6BZ  plan-2  C12  0.020
 6BZ  plan-2  C13  0.020
 6BZ  plan-2  N5   0.020
 6BZ  plan-2  CL1  0.020
 6BZ  plan-2  C16  0.020
 6BZ  plan-2  H1   0.020
 6BZ  plan-2  H3   0.020
 6BZ  plan-2  H5   0.020
 6BZ  plan-3  C12  0.020
 6BZ  plan-3  C16  0.020
 6BZ  plan-3  C17  0.020
 6BZ  plan-3  C18  0.020
 6BZ  plan-3  C19  0.020
 6BZ  plan-3  N20  0.020
 6BZ  plan-3  C21  0.020
 6BZ  plan-3  N22  0.020
 6BZ  plan-3  C23  0.020
 6BZ  plan-3  N24  0.020
 6BZ  plan-3  C25  0.020
 6BZ  plan-3  O26  0.020
 6BZ  plan-3  C27  0.020
 6BZ  plan-3  N31  0.020
 6BZ  plan-3  H9   0.020
 6BZ  plan-3  H10  0.020
 6BZ  plan-4  C21  0.020
 6BZ  plan-4  N31  0.020
 6BZ  plan-4  C32  0.020
 6BZ  plan-4  H20  0.020

