# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 20:49:05 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: N,N'-bis(pyridin-3-ylmethyl)pyrimidine-4,6-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccnc1)c2cc(ncn2)C(=O)NCc3cccnc3
#
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
 PB5  PB5  N,N'-bis(pyridin-3-ylmethyl)pyrimidine-4,6-dicarboxamide  ligand  42  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PB5
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
 PB5  C1    C  CR6   0   0.167  -1.1474  -0.7197   0.0168
 PB5  C2    C  CR16  0  -0.288   0.0242  -1.4555  -0.0403
 PB5  C3    C  CR6   0   0.166   1.1914  -0.7268  -0.1950
 PB5  N6    N  N     0  -0.420  -1.1533   0.6030  -0.0755
 PB5  C9    C  C     0   0.557   2.5184  -1.4398  -0.2574
 PB5  C11   C  CH2   0  -0.325   4.9323  -1.1275  -0.4684
 PB5  C12   C  CR6   0  -0.034   5.8974  -0.0299  -0.1280
 PB5  C15   C  C     0   0.558  -2.4678  -1.4245   0.1946
 PB5  C21   C  CR16  0  -0.087  -6.5258   0.6133   1.2187
 PB5  C24   C  CR16  0  -0.319  -7.0597   1.4378  -1.3033
 PB5  C30   C  CR16  0  -0.167   6.0268   0.4433   1.1737
 PB5  C31   C  CR16  0  -0.319   6.9223   1.4665   1.4322
 PB5  C32   C  CR16  0  -0.064   7.6593   1.9831   0.3749
 PB5  C34   C  CR16  0  -0.089   6.6838   0.5627  -1.1079
 PB5  N4    N  N     0  -0.421   1.1883   0.5957  -0.2892
 PB5  C5    C  CR16  0   0.074   0.0153   1.2029  -0.2264
 PB5  N10   N  NH1   0  -0.642   3.5717  -0.6349  -0.3940
 PB5  N16   N  NH1   0  -0.643  -3.5256  -0.6165   0.2471
 PB5  C17   C  CH2   0  -0.321  -4.8747  -1.1150   0.4311
 PB5  C18   C  CR6   0  -0.043  -5.8666  -0.0197   0.1720
 PB5  N22   N  N     0  -0.401  -7.4034   1.5958   1.0551
 PB5  C23   C  CR16  0  -0.064  -7.6606   1.9965  -0.1835
 PB5  C25   C  CR16  0  -0.166  -6.1479   0.4124  -1.1198
 PB5  N33   N  N     0  -0.401   7.5471   1.5435  -0.8718
 PB5  O41   O  O     0  -0.474  -2.5166  -2.6418   0.2794
 PB5  O42   O  O     0  -0.473   2.5732  -2.6570  -0.1774
 PB5  H2    H  HCR6  0   0.292   0.0280  -2.5323   0.0337
 PB5  H111  H  HCH2  0   0.271   5.0448  -1.9556   0.2332
 PB5  H112  H  HCH2  0   0.267   5.1451  -1.5203  -1.4662
 PB5  H21   H  HCR6  0   0.264  -6.3327   0.3027   2.2413
 PB5  H24   H  HCR6  0   0.275  -7.3054   1.7988  -2.2923
 PB5  H30   H  HCR6  0   0.275   5.4357   0.0145   1.9741
 PB5  H31   H  HCR6  0   0.275   7.0526   1.8586   2.4313
 PB5  H32   H  HCR6  0   0.267   8.3696   2.7845   0.5446
 PB5  H34   H  HCR6  0   0.263   6.6109   0.2202  -2.1358
 PB5  H5    H  HCR6  0   0.282   0.0116   2.2830  -0.3040
 PB5  H10   H  HNH1  0   0.415   3.4013   0.3558  -0.4911
 PB5  H16   H  HNH1  0   0.415  -3.3681   0.3796   0.1941
 PB5  H171  H  HCH2  0   0.269  -5.0473  -1.9453  -0.2564
 PB5  H172  H  HCH2  0   0.266  -5.0007  -1.5050   1.4445
 PB5  H23   H  HCR6  0   0.267  -8.3798   2.8001  -0.2936
 PB5  H25   H  HCR6  0   0.276  -5.6629  -0.0510  -1.9706

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
 PB5  C1   C2    aromatic  1.385  0.020  1.385
 PB5  C1   N6    aromatic  1.326  0.020  1.326
 PB5  C1   C15   single    1.507  0.020  1.507
 PB5  C2   C3    aromatic  1.385  0.020  1.385
 PB5  C2   H2    single    0.930  0.020  1.080
 PB5  C3   C9    single    1.508  0.020  1.508
 PB5  C3   N4    aromatic  1.326  0.020  1.326
 PB5  N6   C5    aromatic  1.322  0.020  1.322
 PB5  C9   N10   single    1.333  0.020  1.333
 PB5  C9   O42   double    1.221  0.020  1.221
 PB5  C11  C12   single    1.501  0.020  1.501
 PB5  C11  N10   single    1.449  0.020  1.449
 PB5  C11  H111  single    0.970  0.020  1.090
 PB5  C11  H112  single    0.970  0.020  1.090
 PB5  C12  C30   aromatic  1.391  0.020  1.391
 PB5  C12  C34   aromatic  1.389  0.020  1.389
 PB5  C15  N16   single    1.332  0.020  1.332
 PB5  C15  O41   double    1.221  0.020  1.221
 PB5  C21  C18   aromatic  1.390  0.020  1.390
 PB5  C21  N22   aromatic  1.327  0.020  1.327
 PB5  C21  H21   single    0.930  0.020  1.080
 PB5  C24  C23   aromatic  1.388  0.020  1.388
 PB5  C24  C25   aromatic  1.384  0.020  1.384
 PB5  C24  H24   single    0.930  0.020  1.080
 PB5  C30  C31   aromatic  1.384  0.020  1.384
 PB5  C30  H30   single    0.930  0.020  1.080
 PB5  C31  C32   aromatic  1.389  0.020  1.389
 PB5  C31  H31   single    0.930  0.020  1.080
 PB5  C32  N33   aromatic  1.327  0.020  1.327
 PB5  C32  H32   single    0.930  0.020  1.080
 PB5  C34  N33   aromatic  1.328  0.020  1.328
 PB5  C34  H34   single    0.930  0.020  1.080
 PB5  N4   C5    aromatic  1.322  0.020  1.322
 PB5  C5   H5    single    0.930  0.020  1.080
 PB5  N10  H10   single    0.860  0.020  1.020
 PB5  N16  C17   single    1.450  0.020  1.450
 PB5  N16  H16   single    0.860  0.020  1.020
 PB5  C17  C18   single    1.500  0.020  1.500
 PB5  C17  H171  single    0.970  0.020  1.090
 PB5  C17  H172  single    0.970  0.020  1.090
 PB5  C18  C25   aromatic  1.391  0.020  1.391
 PB5  N22  C23   aromatic  1.327  0.020  1.327
 PB5  C23  H23   single    0.930  0.020  1.080
 PB5  C25  H25   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
 PB5  C15   C1   N6    118.09  3.000
 PB5  C15   C1   C2    119.84  3.000
 PB5  N6    C1   C2    122.07  3.000
 PB5  H2    C2   C3    121.98  3.000
 PB5  H2    C2   C1    122.02  3.000
 PB5  C3    C2   C1    115.99  3.000
 PB5  N4    C3   C9    118.09  3.000
 PB5  N4    C3   C2    122.06  3.000
 PB5  C9    C3   C2    119.85  3.000
 PB5  C5    N6   C1    117.17  3.000
 PB5  O42   C9   N10   124.98  3.000
 PB5  O42   C9   C3    120.54  3.000
 PB5  N10   C9   C3    114.48  3.000
 PB5  H112  C11  H111  107.10  3.000
 PB5  H112  C11  N10   110.60  3.000
 PB5  H111  C11  N10   108.77  3.000
 PB5  H112  C11  C12   110.15  3.000
 PB5  H111  C11  C12   110.06  3.000
 PB5  N10   C11  C12   110.10  3.000
 PB5  C34   C12  C30   117.54  3.000
 PB5  C34   C12  C11   121.07  3.000
 PB5  C30   C12  C11   121.39  3.000
 PB5  O41   C15  N16   124.76  3.000
 PB5  O41   C15  C1    120.62  3.000
 PB5  N16   C15  C1    114.63  3.000
 PB5  H21   C21  N22   116.44  3.000
 PB5  H21   C21  C18   119.65  3.000
 PB5  N22   C21  C18   123.91  3.000
 PB5  H24   C24  C25   121.22  3.000
 PB5  H24   C24  C23   120.34  3.000
 PB5  C25   C24  C23   118.44  3.000
 PB5  H30   C30  C31   120.50  3.000
 PB5  H30   C30  C12   120.39  3.000
 PB5  C31   C30  C12   119.11  3.000
 PB5  H31   C31  C32   120.32  3.000
 PB5  H31   C31  C30   121.24  3.000
 PB5  C32   C31  C30   118.44  3.000
 PB5  H32   C32  N33   116.58  3.000
 PB5  H32   C32  C31   120.23  3.000
 PB5  N33   C32  C31   123.19  3.000
 PB5  H34   C34  N33   116.41  3.000
 PB5  H34   C34  C12   119.69  3.000
 PB5  N33   C34  C12   123.90  3.000
 PB5  C5    N4   C3    117.18  3.000
 PB5  H5    C5   N4    117.23  3.000
 PB5  H5    C5   N6    117.24  3.000
 PB5  N4    C5   N6    125.53  3.000
 PB5  H10   N10  C11   119.14  3.000
 PB5  H10   N10  C9    117.97  3.000
 PB5  C11   N10  C9    122.83  3.000
 PB5  H16   N16  C17   119.40  3.000
 PB5  H16   N16  C15   118.18  3.000
 PB5  C17   N16  C15   122.36  3.000
 PB5  H172  C17  H171  107.11  3.000
 PB5  H172  C17  C18   110.15  3.000
 PB5  H171  C17  C18   110.00  3.000
 PB5  H172  C17  N16   110.34  3.000
 PB5  H171  C17  N16   109.18  3.000
 PB5  C18   C17  N16   110.01  3.000
 PB5  C25   C18  C17   121.40  3.000
 PB5  C25   C18  C21   117.52  3.000
 PB5  C17   C18  C21   121.07  3.000
 PB5  C23   N22  C21   117.82  3.000
 PB5  H23   C23  N22   116.57  3.000
 PB5  H23   C23  C24   120.23  3.000
 PB5  N22   C23  C24   123.20  3.000
 PB5  H25   C25  C18   120.39  3.000
 PB5  H25   C25  C24   120.50  3.000
 PB5  C18   C25  C24   119.11  3.000
 PB5  C34   N33  C32   117.83  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
 PB5  CONST_01  N4   C3   C2   C1      0.00   0.0  0
 PB5  CONST_02  N4   C5   N6   C1      0.00   0.0  0
 PB5  CONST_03  C5   N6   C1   C2      0.00   0.0  0
 PB5  CONST_04  C5   N4   C3   C2      0.00   0.0  0
 PB5  CONST_05  N6   C1   C2   C3      0.00   0.0  0
 PB5  CONST_06  N6   C5   N4   C3      0.00   0.0  0
 PB5  CONST_07  C32  C31  C30  C12     0.00   0.0  0
 PB5  CONST_08  C32  N33  C34  C12     0.00   0.0  0
 PB5  CONST_09  C24  C25  C18  C21     0.00   0.0  0
 PB5  CONST_10  C24  C23  N22  C21     0.00   0.0  0
 PB5  CONST_11  N33  C34  C12  C30     0.00   0.0  0
 PB5  CONST_12  N33  C32  C31  C30     0.00   0.0  0
 PB5  CONST_13  C34  C12  C30  C31     0.00   0.0  0
 PB5  CONST_14  C34  N33  C32  C31     0.00   0.0  0
 PB5  CONST_15  C23  N22  C21  C18     0.00   0.0  0
 PB5  CONST_16  C23  C24  C25  C18     0.00   0.0  0
 PB5  CONST_17  C25  C18  C21  N22     0.00   0.0  0
 PB5  CONST_18  C25  C24  C23  N22     0.00   0.0  0
 PB5  CONST_19  C9   C3   C2   C1    180.00   0.0  0
 PB5  CONST_20  C15  C1   C2   C3    180.00   0.0  0
 PB5  CONST_21  C5   N4   C3   C9    180.00   0.0  0
 PB5  CONST_22  C31  C30  C12  C11   180.00   0.0  0
 PB5  CONST_23  N33  C34  C12  C11   180.00   0.0  0
 PB5  CONST_24  C5   N6   C1   C15   180.00   0.0  0
 PB5  CONST_25  C17  C18  C25  C24   180.00   0.0  0
 PB5  CONST_26  N22  C21  C18  C17   180.00   0.0  0
 PB5  CONST_27  H5   C5   N6   C1    180.00   0.0  0
 PB5  CONST_28  H2   C2   C1   N6    180.00   0.0  0
 PB5  CONST_29  H31  C31  C30  C12   180.00   0.0  0
 PB5  CONST_30  H25  C25  C18  C21   180.00   0.0  0
 PB5  CONST_31  H23  C23  N22  C21   180.00   0.0  0
 PB5  CONST_32  H34  C34  C12  C30   180.00   0.0  0
 PB5  CONST_33  H32  C32  C31  C30   180.00   0.0  0
 PB5  CONST_34  H30  C30  C31  C32   180.00   0.0  0
 PB5  CONST_35  H24  C24  C25  C18   180.00   0.0  0
 PB5  CONST_36  H21  C21  N22  C23   180.00   0.0  0
 PB5  CONST_37  C17  N16  C15  C1    180.00   0.0  0
 PB5  CONST_38  C11  N10  C9   C3    180.00   0.0  0
 PB5  CONST_39  H16  N16  C15  C1      0.00   0.0  0
 PB5  CONST_40  H10  N10  C9   C3      0.00   0.0  0
 PB5  CONST_41  O42  C9   N10  C11     0.00   0.0  0
 PB5  CONST_42  O41  C15  N16  C17     0.00   0.0  0
 PB5  Var_01    N16  C15  C1   C2    179.46  30.0  2
 PB5  Var_02    N10  C9   C3   C2   -179.35  30.0  2
 PB5  Var_03    N16  C17  C18  C21  -104.67  30.0  3
 PB5  Var_04    N10  C11  C12  C30    71.43  30.0  2
 PB5  Var_05    C12  C11  N10  C9   -159.78  30.0  1
 PB5  Var_06    C18  C17  N16  C15  -168.54  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
 PB5  plan-1  C1   0.020
 PB5  plan-1  C2   0.020
 PB5  plan-1  C3   0.020
 PB5  plan-1  N6   0.020
 PB5  plan-1  C9   0.020
 PB5  plan-1  C15  0.020
 PB5  plan-1  N4   0.020
 PB5  plan-1  C5   0.020
 PB5  plan-1  H2   0.020
 PB5  plan-1  H5   0.020
 PB5  plan-2  C11  0.020
 PB5  plan-2  C12  0.020
 PB5  plan-2  C30  0.020
 PB5  plan-2  C31  0.020
 PB5  plan-2  C32  0.020
 PB5  plan-2  C34  0.020
 PB5  plan-2  N33  0.020
 PB5  plan-2  H30  0.020
 PB5  plan-2  H31  0.020
 PB5  plan-2  H32  0.020
 PB5  plan-2  H34  0.020
 PB5  plan-3  C21  0.020
 PB5  plan-3  C24  0.020
 PB5  plan-3  C17  0.020
 PB5  plan-3  C18  0.020
 PB5  plan-3  N22  0.020
 PB5  plan-3  C23  0.020
 PB5  plan-3  C25  0.020
 PB5  plan-3  H21  0.020
 PB5  plan-3  H24  0.020
 PB5  plan-3  H23  0.020
 PB5  plan-3  H25  0.020
 PB5  plan-4  C3   0.020
 PB5  plan-4  C9   0.020
 PB5  plan-4  C11  0.020
 PB5  plan-4  N10  0.020
 PB5  plan-4  O42  0.020
 PB5  plan-4  H10  0.020
 PB5  plan-5  C1   0.020
 PB5  plan-5  C15  0.020
 PB5  plan-5  N16  0.020
 PB5  plan-5  C17  0.020
 PB5  plan-5  O41  0.020
 PB5  plan-5  H16  0.020

