# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 08:45:31 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 5-[(3,4-dimethoxyphenyl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cc2cnc(N)nc2N)cc1OC
#
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
 KUP  KUP  5-[(3,4-dimethoxyphenyl)methyl]pyrimidine-2,4-diamine  ligand  35  19  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KUP
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
 KUP  N12  N  NH2   0  -0.823   5.3773   1.8270  -0.6976
 KUP  C17  C  CR6   0   0.326  -2.6741  -0.5785   0.6064
 KUP  C01  C  CH3   0  -0.435  -4.3792   1.5641  -1.7829
 KUP  O02  O  O2    0  -0.465  -4.1197   0.7444  -0.6626
 KUP  C03  C  CR6   0   0.294  -2.8665   0.2774  -0.4971
 KUP  C04  C  CR16  0  -0.370  -1.7886   0.5751  -1.3135
 KUP  C05  C  CR16  0  -0.295  -0.5292   0.0365  -1.0543
 KUP  C06  C  CR6   0   0.085  -0.3301  -0.8095   0.0208
 KUP  C08  C  CR6   0  -0.067   2.1904  -0.5534   0.0291
 KUP  C09  C  CR16  0  -0.079   3.1171  -0.8161  -0.9511
 KUP  N10  N  N     0  -0.486   4.1854  -0.0649  -1.2132
 KUP  C11  C  CR6   0   0.530   4.3252   1.0118  -0.4410
 KUP  N13  N  N     0  -0.506   3.5034   1.3853   0.5397
 KUP  C14  C  CR6   0   0.459   2.4436   0.6202   0.7793
 KUP  N15  N  NH2   0  -0.823   1.6359   0.9877   1.7947
 KUP  C16  C  CR16  0  -0.449  -1.4162  -1.1059   0.8507
 KUP  C19  C  CH3   0  -0.438  -3.6430  -1.6883   2.4597
 KUP  H1   H  HNH2  0   0.387   6.1263   1.4581  -1.2580
 KUP  H2   H  HNH2  0   0.387   5.6421   2.4891   0.0112
 KUP  H3   H  HCH3  0   0.226  -3.8073   2.4957  -1.7511
 KUP  H4   H  HCH3  0   0.227  -4.1620   1.0510  -2.7239
 KUP  H5   H  HCH3  0   0.258  -5.4392   1.8048  -1.7519
 KUP  H6   H  HCR6  0   0.279  -1.9068   1.2322  -2.1646
 KUP  H7   H  HCR6  0   0.246   0.2950   0.2905  -1.7094
 KUP  H8   H  HCH2  0   0.257   1.0360  -1.8087   1.3253
 KUP  H9   H  HCH2  0   0.273   1.1176  -2.3398  -0.3306
 KUP  H10  H  HCR6  0   0.253   2.9926  -1.6998  -1.5721
 KUP  H11  H  HNH2  0   0.391   1.7632   1.9063   2.1859
 KUP  H12  H  HNH2  0   0.403   0.7032   0.6163   1.8517
 KUP  H13  H  HCR6  0   0.278  -1.2565  -1.7684   1.6924
 KUP  H14  H  HCH3  0   0.260  -4.6315  -1.7647   2.9062
 KUP  H15  H  HCH3  0   0.228  -3.3145  -2.6868   2.1592
 KUP  H16  H  HCH3  0   0.227  -2.9479  -1.3018   3.2099
 KUP  C07  C  CH2   0  -0.574   1.0165  -1.4457   0.2924
 KUP  O18  O  O2    0  -0.465  -3.7677  -0.8176   1.3545

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
 KUP  N15  C14  single    1.348  0.020  1.348
 KUP  C14  N13  aromatic  1.329  0.020  1.329
 KUP  C14  C08  aromatic  1.416  0.020  1.416
 KUP  N13  C11  aromatic  1.333  0.020  1.333
 KUP  C07  C08  single    1.498  0.020  1.498
 KUP  C07  C06  single    1.514  0.020  1.514
 KUP  C08  C09  aromatic  1.374  0.020  1.374
 KUP  C11  N12  single    1.355  0.020  1.355
 KUP  C11  N10  aromatic  1.332  0.020  1.332
 KUP  C06  C16  aromatic  1.399  0.020  1.399
 KUP  C06  C05  aromatic  1.382  0.020  1.382
 KUP  C09  N10  aromatic  1.332  0.020  1.332
 KUP  C16  C17  aromatic  1.386  0.020  1.386
 KUP  C05  C04  aromatic  1.394  0.020  1.394
 KUP  C19  O18  single    1.412  0.020  1.412
 KUP  C17  O18  single    1.346  0.020  1.346
 KUP  C17  C03  aromatic  1.410  0.020  1.410
 KUP  C04  C03  aromatic  1.385  0.020  1.385
 KUP  C03  O02  single    1.348  0.020  1.348
 KUP  O02  C01  single    1.412  0.020  1.412
 KUP  N12  H1   single    0.890  0.020  1.040
 KUP  N12  H2   single    0.890  0.020  1.040
 KUP  C01  H3   single    0.970  0.020  1.090
 KUP  C01  H4   single    0.970  0.020  1.090
 KUP  C01  H5   single    0.970  0.020  1.090
 KUP  C04  H6   single    0.930  0.020  1.080
 KUP  C05  H7   single    0.930  0.020  1.080
 KUP  C07  H8   single    0.970  0.020  1.090
 KUP  C07  H9   single    0.970  0.020  1.090
 KUP  C09  H10  single    0.930  0.020  1.080
 KUP  N15  H11  single    0.890  0.020  1.040
 KUP  N15  H12  single    0.890  0.020  1.040
 KUP  C16  H13  single    0.930  0.020  1.080
 KUP  C19  H14  single    0.970  0.020  1.090
 KUP  C19  H15  single    0.970  0.020  1.090
 KUP  C19  H16  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
 KUP  H2   N12  H1   116.00  3.000
 KUP  H2   N12  C11  117.84  3.000
 KUP  H1   N12  C11  117.58  3.000
 KUP  O18  C17  C16  124.88  3.000
 KUP  O18  C17  C03  115.58  3.000
 KUP  C16  C17  C03  119.54  3.000
 KUP  H5   C01  H4   108.79  3.000
 KUP  H5   C01  H3   108.69  3.000
 KUP  H4   C01  H3   108.71  3.000
 KUP  H5   C01  O02  106.56  3.000
 KUP  H4   C01  O02  111.95  3.000
 KUP  H3   C01  O02  112.04  3.000
 KUP  C03  O02  C01  118.00  3.000
 KUP  C04  C03  O02  125.24  3.000
 KUP  O02  C03  C17  115.69  3.000
 KUP  C04  C03  C17  119.07  3.000
 KUP  H6   C04  C05  118.67  3.000
 KUP  H6   C04  C03  120.63  3.000
 KUP  C05  C04  C03  120.70  3.000
 KUP  H7   C05  C06  120.29  3.000
 KUP  H7   C05  C04  118.97  3.000
 KUP  C06  C05  C04  120.74  3.000
 KUP  C16  C06  C07  119.68  3.000
 KUP  C16  C06  C05  118.64  3.000
 KUP  C07  C06  C05  121.65  3.000
 KUP  C14  C08  C09  114.57  3.000
 KUP  C09  C08  C07  122.68  3.000
 KUP  C14  C08  C07  122.74  3.000
 KUP  H10  C09  N10  115.96  3.000
 KUP  H10  C09  C08  119.05  3.000
 KUP  N10  C09  C08  124.99  3.000
 KUP  C11  N10  C09  115.21  3.000
 KUP  N13  C11  N10  126.03  3.000
 KUP  N10  C11  N12  117.24  3.000
 KUP  N13  C11  N12  116.70  3.000
 KUP  C14  N13  C11  117.58  3.000
 KUP  N15  C14  N13  117.16  3.000
 KUP  N13  C14  C08  121.63  3.000
 KUP  N15  C14  C08  121.19  3.000
 KUP  H12  N15  H11  115.62  3.000
 KUP  H12  N15  C14  119.84  3.000
 KUP  H11  N15  C14  117.76  3.000
 KUP  H13  C16  C06  118.44  3.000
 KUP  H13  C16  C17  120.25  3.000
 KUP  C06  C16  C17  121.31  3.000
 KUP  H16  C19  H15  108.68  3.000
 KUP  H16  C19  H14  108.73  3.000
 KUP  H15  C19  H14  108.78  3.000
 KUP  H16  C19  O18  112.03  3.000
 KUP  H15  C19  O18  111.99  3.000
 KUP  H14  C19  O18  106.52  3.000
 KUP  H9   C07  H8   105.34  3.000
 KUP  H9   C07  C08  108.31  3.000
 KUP  H8   C07  C08  110.45  3.000
 KUP  H9   C07  C06  108.87  3.000
 KUP  H8   C07  C06  108.93  3.000
 KUP  C08  C07  C06  114.53  3.000
 KUP  C19  O18  C17  118.19  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
 KUP  CONST_01  C05  C06  C16  C17     0.00   0.0  0
 KUP  CONST_02  C05  C04  C03  C17     0.00   0.0  0
 KUP  CONST_03  C06  C16  C17  C03     0.00   0.0  0
 KUP  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 KUP  CONST_05  C16  C06  C05  C04     0.00   0.0  0
 KUP  CONST_06  C16  C17  C03  C04     0.00   0.0  0
 KUP  CONST_07  C11  N13  C14  C08     0.00   0.0  0
 KUP  CONST_08  C11  N10  C09  C08     0.00   0.0  0
 KUP  CONST_09  N13  C14  C08  C09     0.00   0.0  0
 KUP  CONST_10  N13  C11  N10  C09     0.00   0.0  0
 KUP  CONST_11  C14  N13  C11  N10     0.00   0.0  0
 KUP  CONST_12  C14  C08  C09  N10     0.00   0.0  0
 KUP  CONST_13  C14  N13  C11  N12   180.00   0.0  0
 KUP  CONST_14  C09  N10  C11  N12   180.00   0.0  0
 KUP  CONST_15  C07  C06  C16  C17   180.00   0.0  0
 KUP  CONST_16  C16  C17  C03  O02   180.00   0.0  0
 KUP  CONST_17  C05  C04  C03  O02   180.00   0.0  0
 KUP  CONST_18  C07  C06  C05  C04   180.00   0.0  0
 KUP  CONST_19  O18  C17  C03  C04   180.00   0.0  0
 KUP  CONST_20  O18  C17  C16  C06   180.00   0.0  0
 KUP  CONST_21  N13  C14  C08  C07   180.00   0.0  0
 KUP  CONST_22  N10  C09  C08  C07   180.00   0.0  0
 KUP  CONST_23  N15  C14  C08  C09   180.00   0.0  0
 KUP  CONST_24  N15  C14  N13  C11   180.00   0.0  0
 KUP  CONST_25  H6   C04  C03  C17   180.00   0.0  0
 KUP  CONST_26  H13  C16  C17  C03   180.00   0.0  0
 KUP  CONST_27  H7   C05  C04  C03   180.00   0.0  0
 KUP  CONST_28  H10  C09  N10  C11   180.00   0.0  0
 KUP  CONST_29  H11  N15  C14  C08   180.00   0.0  0
 KUP  Var_01    C08  C07  C06  C05    38.47  30.0  2
 KUP  Var_02    C14  C08  C07  C06    65.38  30.0  2
 KUP  Var_03    C04  C03  O02  C01     2.51  30.0  2
 KUP  Var_04    H14  C19  O18  C17  -178.57  30.0  3
 KUP  Var_05    H3   C01  O02  C03   -63.05  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
 KUP  plan-1  C17  0.020
 KUP  plan-1  O02  0.020
 KUP  plan-1  C03  0.020
 KUP  plan-1  C04  0.020
 KUP  plan-1  C05  0.020
 KUP  plan-1  C06  0.020
 KUP  plan-1  C16  0.020
 KUP  plan-1  H6   0.020
 KUP  plan-1  H7   0.020
 KUP  plan-1  H13  0.020
 KUP  plan-1  C07  0.020
 KUP  plan-1  O18  0.020
 KUP  plan-2  N12  0.020
 KUP  plan-2  C08  0.020
 KUP  plan-2  C09  0.020
 KUP  plan-2  N10  0.020
 KUP  plan-2  C11  0.020
 KUP  plan-2  N13  0.020
 KUP  plan-2  C14  0.020
 KUP  plan-2  N15  0.020
 KUP  plan-2  H10  0.020
 KUP  plan-2  C07  0.020
 KUP  plan-3  N12  0.020
 KUP  plan-3  C11  0.020
 KUP  plan-3  H1   0.020
 KUP  plan-3  H2   0.020
 KUP  plan-4  C14  0.020
 KUP  plan-4  N15  0.020
 KUP  plan-4  H11  0.020
 KUP  plan-4  H12  0.020

