# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 20:46:22 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: N,N'-bis(3-methylbenzyl)pyrimidine-4,6-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(CNC(=O)c2cc(ncn2)C(=O)NCc3cccc(C)c3)c1
#
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
 PB3  PB3  N,N'-bis(3-methylbenzyl)pyrimidine-4,6-dicarboxamide  ligand  50  28  .  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_PB3
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
 PB3  C1    C  CR6   0   0.168  -0.9111  -0.1169  -1.1742
 PB3  C2    C  CR16  0  -0.290  -1.6398   0.0043  -0.0032
 PB3  C3    C  CR6   0   0.168  -0.9025   0.0962   1.1651
 PB3  N6    N  N     0  -0.420   0.4147  -0.1409  -1.1784
 PB3  C7    C  CH3   0  -0.723   1.7094  -2.1329   7.9798
 PB3  C8    C  CH3   0  -0.723   1.7850   2.1566  -7.8152
 PB3  C9    C  C     0   0.554  -1.6105   0.2348   2.4884
 PB3  C11   C  CH2   0  -0.322  -1.3185   0.4294   4.9000
 PB3  C12   C  CR6   0   0.067  -0.1806   0.4122   5.8811
 PB3  C15   C  C     0   0.554  -1.6291  -0.2320  -2.4945
 PB3  C21   C  CR16  0  -0.334   0.2479   0.7736  -6.3835
 PB3  C24   C  CR16  0  -0.227   1.4748  -1.5740  -7.1708
 PB3  C30   C  CR16  0  -0.305   0.5007   1.5864   6.1895
 PB3  C31   C  CR16  0  -0.227   1.5745   1.5529   7.0662
 PB3  C32   C  CR16  0  -0.312   1.9724   0.3517   7.6389
 PB3  C34   C  CR16  0  -0.335   0.2299  -0.7837   6.4588
 PB3  N4    N  N     0  -0.420   0.4233   0.0689   1.1644
 PB3  C5    C  CR16  0   0.073   1.0236  -0.0472  -0.0082
 PB3  N10   N  NH1   0  -0.640  -0.8074   0.2880   3.5482
 PB3  N16   N  NH1   0  -0.640  -0.8323  -0.3332  -3.5557
 PB3  C17   C  CH2   0  -0.322  -1.3510  -0.4729  -4.9048
 PB3  C18   C  CR6   0   0.067  -0.2187  -0.4411  -5.8923
 PB3  C4    C  CR6   0   0.115   1.3199   0.8372  -7.2707
 PB3  C23   C  CR16  0  -0.310   1.9292  -0.3552  -7.6552
 PB3  C25   C  CR16  0  -0.307   0.4026  -1.6201  -6.2914
 PB3  C6    C  CR6   0   0.115   1.3042  -0.8341   7.3454
 PB3  O41   O  O     0  -0.477  -2.8504  -0.2289  -2.5394
 PB3  O42   O  O     0  -0.477  -2.8304   0.2905   2.5374
 PB3  H2    H  HCR6  0   0.291  -2.7190   0.0250  -0.0010
 PB3  H71   H  HCH3  0   0.249   1.0412  -2.3908   8.8040
 PB3  H72   H  HCH3  0   0.245   1.6705  -2.9558   7.2663
 PB3  H73   H  HCH3  0   0.244   2.7199  -2.0836   8.3835
 PB3  H81   H  HCH3  0   0.250   1.1786   2.4617  -8.6705
 PB3  H82   H  HCH3  0   0.245   1.7086   2.9467  -7.0687
 PB3  H83   H  HCH3  0   0.244   2.8198   2.1085  -8.1522
 PB3  H111  H  HCH2  0   0.262  -2.0178  -0.3826   5.1119
 PB3  H112  H  HCH2  0   0.262  -1.8797   1.3635   4.9828
 PB3  H21   H  HCR6  0   0.246  -0.2375   1.6925  -6.0705
 PB3  H24   H  HCR6  0   0.256   1.9602  -2.4913  -7.4785
 PB3  H30   H  HCR6  0   0.253   0.1902   2.5245   5.7450
 PB3  H31   H  HCR6  0   0.255   2.1052   2.4656   7.3051
 PB3  H32   H  HCR6  0   0.250   2.8116   0.3383   8.3241
 PB3  H34   H  HCR6  0   0.246  -0.3006  -1.6987   6.2150
 PB3  H5    H  HCR6  0   0.281   2.1064  -0.0675  -0.0106
 PB3  H10   H  HNH1  0   0.414   0.1896   0.2361   3.3974
 PB3  H16   H  HNH1  0   0.414   0.1662  -0.3430  -3.4063
 PB3  H171  H  HCH2  0   0.262  -2.0568   0.3357  -5.1060
 PB3  H172  H  HCH2  0   0.262  -1.9061  -1.4105  -4.9912
 PB3  H23   H  HCR6  0   0.250   2.7666  -0.3308  -8.3426
 PB3  H25   H  HCR6  0   0.253   0.0482  -2.5725  -5.9155

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
 PB3  C1   C2    aromatic  1.385  0.020  1.385
 PB3  C1   N6    aromatic  1.326  0.020  1.326
 PB3  C1   C15   single    1.507  0.020  1.507
 PB3  C2   C3    aromatic  1.385  0.020  1.385
 PB3  C2   H2    single    0.930  0.020  1.080
 PB3  C3   C9    single    1.507  0.020  1.507
 PB3  C3   N4    aromatic  1.326  0.020  1.326
 PB3  N6   C5    aromatic  1.322  0.020  1.322
 PB3  C7   C6    single    1.501  0.020  1.501
 PB3  C7   H71   single    0.970  0.020  1.090
 PB3  C7   H72   single    0.970  0.020  1.090
 PB3  C7   H73   single    0.970  0.020  1.090
 PB3  C8   C4    single    1.501  0.020  1.501
 PB3  C8   H81   single    0.970  0.020  1.090
 PB3  C8   H82   single    0.970  0.020  1.090
 PB3  C8   H83   single    0.970  0.020  1.090
 PB3  C9   N10   single    1.331  0.020  1.331
 PB3  C9   O42   double    1.222  0.020  1.222
 PB3  C11  C12   single    1.503  0.020  1.503
 PB3  C11  N10   single    1.452  0.020  1.452
 PB3  C11  H111  single    0.970  0.020  1.090
 PB3  C11  H112  single    0.970  0.020  1.090
 PB3  C12  C30   aromatic  1.392  0.020  1.392
 PB3  C12  C34   aromatic  1.390  0.020  1.390
 PB3  C15  N16   single    1.331  0.020  1.331
 PB3  C15  O41   double    1.222  0.020  1.222
 PB3  C21  C18   aromatic  1.391  0.020  1.391
 PB3  C21  C4    aromatic  1.393  0.020  1.393
 PB3  C21  H21   single    0.930  0.020  1.080
 PB3  C24  C23   aromatic  1.388  0.020  1.388
 PB3  C24  C25   aromatic  1.387  0.020  1.387
 PB3  C24  H24   single    0.930  0.020  1.080
 PB3  C30  C31   aromatic  1.387  0.020  1.387
 PB3  C30  H30   single    0.930  0.020  1.080
 PB3  C31  C32   aromatic  1.389  0.020  1.389
 PB3  C31  H31   single    0.930  0.020  1.080
 PB3  C32  C6    aromatic  1.392  0.020  1.392
 PB3  C32  H32   single    0.930  0.020  1.080
 PB3  C34  C6    aromatic  1.394  0.020  1.394
 PB3  C34  H34   single    0.930  0.020  1.080
 PB3  N4   C5    aromatic  1.322  0.020  1.322
 PB3  C5   H5    single    0.930  0.020  1.080
 PB3  N10  H10   single    0.860  0.020  1.020
 PB3  N16  C17   single    1.452  0.020  1.452
 PB3  N16  H16   single    0.860  0.020  1.020
 PB3  C17  C18   single    1.503  0.020  1.503
 PB3  C17  H171  single    0.970  0.020  1.090
 PB3  C17  H172  single    0.970  0.020  1.090
 PB3  C18  C25   aromatic  1.391  0.020  1.391
 PB3  C4   C23   aromatic  1.393  0.020  1.393
 PB3  C23  H23   single    0.930  0.020  1.080
 PB3  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
 PB3  C15   C1   N6    118.18  3.000
 PB3  C15   C1   C2    119.79  3.000
 PB3  N6    C1   C2    122.04  3.000
 PB3  H2    C2   C3    121.97  3.000
 PB3  H2    C2   C1    121.98  3.000
 PB3  C3    C2   C1    116.05  3.000
 PB3  N4    C3   C9    118.17  3.000
 PB3  N4    C3   C2    122.04  3.000
 PB3  C9    C3   C2    119.79  3.000
 PB3  C5    N6   C1    117.15  3.000
 PB3  H73   C7   H72   108.05  3.000
 PB3  H73   C7   H71   107.38  3.000
 PB3  H72   C7   H71   107.10  3.000
 PB3  H73   C7   C6    111.59  3.000
 PB3  H72   C7   C6    111.53  3.000
 PB3  H71   C7   C6    110.99  3.000
 PB3  H83   C8   H82   108.10  3.000
 PB3  H83   C8   H81   107.31  3.000
 PB3  H82   C8   H81   107.16  3.000
 PB3  H83   C8   C4    111.57  3.000
 PB3  H82   C8   C4    111.54  3.000
 PB3  H81   C8   C4    110.95  3.000
 PB3  O42   C9   N10   124.65  3.000
 PB3  O42   C9   C3    120.55  3.000
 PB3  N10   C9   C3    114.79  3.000
 PB3  H112  C11  H111  106.97  3.000
 PB3  H112  C11  N10   109.54  3.000
 PB3  H111  C11  N10   109.49  3.000
 PB3  H112  C11  C12   110.44  3.000
 PB3  H111  C11  C12   110.47  3.000
 PB3  N10   C11  C12   109.89  3.000
 PB3  C34   C12  C30   119.28  3.000
 PB3  C34   C12  C11   120.32  3.000
 PB3  C30   C12  C11   120.37  3.000
 PB3  O41   C15  N16   124.69  3.000
 PB3  O41   C15  C1    120.54  3.000
 PB3  N16   C15  C1    114.77  3.000
 PB3  H21   C21  C4    119.29  3.000
 PB3  H21   C21  C18   119.18  3.000
 PB3  C4    C21  C18   121.53  3.000
 PB3  H24   C24  C25   119.90  3.000
 PB3  H24   C24  C23   119.88  3.000
 PB3  C25   C24  C23   120.22  3.000
 PB3  H30   C30  C31   120.14  3.000
 PB3  H30   C30  C12   119.95  3.000
 PB3  C31   C30  C12   119.91  3.000
 PB3  H31   C31  C32   119.85  3.000
 PB3  H31   C31  C30   119.92  3.000
 PB3  C32   C31  C30   120.23  3.000
 PB3  H32   C32  C6    119.63  3.000
 PB3  H32   C32  C31   119.56  3.000
 PB3  C6    C32  C31   120.81  3.000
 PB3  H34   C34  C6    119.28  3.000
 PB3  H34   C34  C12   119.18  3.000
 PB3  C6    C34  C12   121.54  3.000
 PB3  C5    N4   C3    117.14  3.000
 PB3  H5    C5   N4    117.22  3.000
 PB3  H5    C5   N6    117.20  3.000
 PB3  N4    C5   N6    125.58  3.000
 PB3  H10   N10  C11   119.44  3.000
 PB3  H10   N10  C9    118.35  3.000
 PB3  C11   N10  C9    122.20  3.000
 PB3  H16   N16  C17   119.32  3.000
 PB3  H16   N16  C15   118.35  3.000
 PB3  C17   N16  C15   122.29  3.000
 PB3  H172  C17  H171  107.00  3.000
 PB3  H172  C17  C18   110.42  3.000
 PB3  H171  C17  C18   110.50  3.000
 PB3  H172  C17  N16   109.71  3.000
 PB3  H171  C17  N16   109.32  3.000
 PB3  C18   C17  N16   109.84  3.000
 PB3  C25   C18  C17   120.47  3.000
 PB3  C25   C18  C21   119.27  3.000
 PB3  C17   C18  C21   120.22  3.000
 PB3  C23   C4   C21   118.25  3.000
 PB3  C23   C4   C8    121.10  3.000
 PB3  C21   C4   C8    120.64  3.000
 PB3  H23   C23  C4    119.59  3.000
 PB3  H23   C23  C24   119.61  3.000
 PB3  C4    C23  C24   120.80  3.000
 PB3  H25   C25  C18   119.95  3.000
 PB3  H25   C25  C24   120.12  3.000
 PB3  C18   C25  C24   119.92  3.000
 PB3  C34   C6   C32   118.24  3.000
 PB3  C34   C6   C7    120.54  3.000
 PB3  C32   C6   C7    121.21  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
 PB3  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 PB3  CONST_02  N4   C5   N6   C1     0.00   0.0  0
 PB3  CONST_03  C5   N6   C1   C2     0.00   0.0  0
 PB3  CONST_04  C5   N4   C3   C2     0.00   0.0  0
 PB3  CONST_05  N6   C1   C2   C3     0.00   0.0  0
 PB3  CONST_06  N6   C5   N4   C3     0.00   0.0  0
 PB3  CONST_07  C32  C31  C30  C12    0.00   0.0  0
 PB3  CONST_08  C32  C6   C34  C12    0.00   0.0  0
 PB3  CONST_09  C24  C25  C18  C21    0.00   0.0  0
 PB3  CONST_10  C24  C23  C4   C21    0.00   0.0  0
 PB3  CONST_11  C6   C34  C12  C30    0.00   0.0  0
 PB3  CONST_12  C6   C32  C31  C30    0.00   0.0  0
 PB3  CONST_13  C34  C12  C30  C31    0.00   0.0  0
 PB3  CONST_14  C34  C6   C32  C31    0.00   0.0  0
 PB3  CONST_15  C23  C4   C21  C18    0.00   0.0  0
 PB3  CONST_16  C23  C24  C25  C18    0.00   0.0  0
 PB3  CONST_17  C25  C18  C21  C4     0.00   0.0  0
 PB3  CONST_18  C25  C24  C23  C4     0.00   0.0  0
 PB3  CONST_19  C9   C3   C2   C1   180.00   0.0  0
 PB3  CONST_20  C15  C1   C2   C3   180.00   0.0  0
 PB3  CONST_21  C31  C32  C6   C7   180.00   0.0  0
 PB3  CONST_22  C12  C34  C6   C7   180.00   0.0  0
 PB3  CONST_23  C18  C21  C4   C8   180.00   0.0  0
 PB3  CONST_24  C24  C23  C4   C8   180.00   0.0  0
 PB3  CONST_25  C5   N4   C3   C9   180.00   0.0  0
 PB3  CONST_26  C31  C30  C12  C11  180.00   0.0  0
 PB3  CONST_27  C6   C34  C12  C11  180.00   0.0  0
 PB3  CONST_28  C5   N6   C1   C15  180.00   0.0  0
 PB3  CONST_29  C17  C18  C25  C24  180.00   0.0  0
 PB3  CONST_30  C4   C21  C18  C17  180.00   0.0  0
 PB3  CONST_31  H5   C5   N6   C1   180.00   0.0  0
 PB3  CONST_32  H2   C2   C1   N6   180.00   0.0  0
 PB3  CONST_33  H31  C31  C30  C12  180.00   0.0  0
 PB3  CONST_34  H25  C25  C18  C21  180.00   0.0  0
 PB3  CONST_35  H23  C23  C4   C21  180.00   0.0  0
 PB3  CONST_36  H34  C34  C12  C30  180.00   0.0  0
 PB3  CONST_37  H32  C32  C31  C30  180.00   0.0  0
 PB3  CONST_38  H30  C30  C31  C32  180.00   0.0  0
 PB3  CONST_39  H24  C24  C25  C18  180.00   0.0  0
 PB3  CONST_40  H21  C21  C4   C23  180.00   0.0  0
 PB3  CONST_41  C17  N16  C15  C1   180.00   0.0  0
 PB3  CONST_42  C11  N10  C9   C3   180.00   0.0  0
 PB3  CONST_43  H16  N16  C15  C1     0.00   0.0  0
 PB3  CONST_44  H10  N10  C9   C3     0.00   0.0  0
 PB3  CONST_45  O42  C9   N10  C11    0.00   0.0  0
 PB3  CONST_46  O41  C15  N16  C17    0.00   0.0  0
 PB3  Var_01    N16  C15  C1   C2   179.50  30.0  2
 PB3  Var_02    N10  C9   C3   C2   178.72  30.0  2
 PB3  Var_03    N16  C17  C18  C21  -86.72  30.0  2
 PB3  Var_04    N10  C11  C12  C30   86.05  30.0  2
 PB3  Var_05    H81  C8   C4   C21  -83.00  30.0  2
 PB3  Var_06    H71  C7   C6   C32  100.84  30.0  2
 PB3  Var_07    C12  C11  N10  C9   178.08  30.0  2
 PB3  Var_08    C18  C17  N16  C15  175.03  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
 PB3  plan-1  C1   0.020
 PB3  plan-1  C2   0.020
 PB3  plan-1  C3   0.020
 PB3  plan-1  N6   0.020
 PB3  plan-1  C9   0.020
 PB3  plan-1  C15  0.020
 PB3  plan-1  N4   0.020
 PB3  plan-1  C5   0.020
 PB3  plan-1  H2   0.020
 PB3  plan-1  H5   0.020
 PB3  plan-2  C7   0.020
 PB3  plan-2  C11  0.020
 PB3  plan-2  C12  0.020
 PB3  plan-2  C30  0.020
 PB3  plan-2  C31  0.020
 PB3  plan-2  C32  0.020
 PB3  plan-2  C34  0.020
 PB3  plan-2  C6   0.020
 PB3  plan-2  H30  0.020
 PB3  plan-2  H31  0.020
 PB3  plan-2  H32  0.020
 PB3  plan-2  H34  0.020
 PB3  plan-3  C8   0.020
 PB3  plan-3  C21  0.020
 PB3  plan-3  C24  0.020
 PB3  plan-3  C17  0.020
 PB3  plan-3  C18  0.020
 PB3  plan-3  C4   0.020
 PB3  plan-3  C23  0.020
 PB3  plan-3  C25  0.020
 PB3  plan-3  H21  0.020
 PB3  plan-3  H24  0.020
 PB3  plan-3  H23  0.020
 PB3  plan-3  H25  0.020
 PB3  plan-4  C3   0.020
 PB3  plan-4  C9   0.020
 PB3  plan-4  C11  0.020
 PB3  plan-4  N10  0.020
 PB3  plan-4  O42  0.020
 PB3  plan-4  H10  0.020
 PB3  plan-5  C1   0.020
 PB3  plan-5  C15  0.020
 PB3  plan-5  N16  0.020
 PB3  plan-5  C17  0.020
 PB3  plan-5  O41  0.020
 PB3  plan-5  H16  0.020

