# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:26:10 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cc(OC)ccc2OC
#
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
 N22  N22  5-[3-(2,5-dimethoxyphenyl)prop-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine  ligand  43  23  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N22
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
 N22  C8    C  CH3   0  -0.665  -2.8326   0.0253   3.0445
 N22  C7    C  CH2   0  -0.522  -3.4052   1.0683   2.0838
 N22  C5    C  CR6   0   0.273  -3.4830   0.5308   0.6868
 N22  N4    N  N     0  -0.500  -4.6338  -0.0159   0.3131
 N22  C3    C  CR6   0   0.533  -4.6816  -0.5355  -0.9184
 N22  N8    N  NH2   0  -0.819  -5.8403  -1.1191  -1.2838
 N22  N2    N  N     0  -0.504  -3.6906  -0.5559  -1.8080
 N22  C1    C  CR6   0   0.461  -2.5383  -0.0084  -1.4391
 N22  N7    N  NH2   0  -0.839  -1.5264  -0.0240  -2.3140
 N22  C6    C  CR6   0  -0.318  -2.3735   0.5724  -0.1524
 N22  C9    C  CSP   0   0.127  -1.1265   1.1389   0.2073
 N22  C10   C  CSP   0   0.047  -0.0217   1.5794   0.4134
 N22  C11   C  CH2   0  -0.671   1.3314   2.0672   0.6529
 N22  C13   C  CR6   0   0.036   2.3694   1.0128   0.3494
 N22  C18   C  CR16  0  -0.387   3.1155   0.4542   1.3687
 N22  C17   C  CR6   0   0.375   4.0800  -0.5247   1.1151
 N22  O2    O  O2    0  -0.478   4.7483  -0.9973   2.1905
 N22  C4    C  CH3   0  -0.435   5.7338  -1.9855   1.9790
 N22  C16   C  CR16  0  -0.382   4.2865  -0.9393  -0.1911
 N22  C15   C  CR16  0  -0.363   3.5367  -0.3832  -1.2274
 N22  C14   C  CR6   0   0.340   2.5812   0.5867  -0.9708
 N22  O10   O  O2    0  -0.480   1.8111   1.1713  -1.9182
 N22  C2    C  CH3   0  -0.450   2.0500   0.8423  -3.2722
 N22  H8    H  HCH3  0   0.238  -2.7865   0.4242   4.0578
 N22  H8A   H  HCH3  0   0.229  -3.4532  -0.8708   3.0649
 N22  H8B   H  HCH3  0   0.231  -1.8236  -0.2678   2.7535
 N22  H7    H  HCH2  0   0.249  -4.4066   1.3559   2.4061
 N22  H7A   H  HCH2  0   0.243  -2.7806   1.9633   2.1043
 N22  HN8   H  HNH2  0   0.393  -6.6605  -0.9445  -0.7297
 N22  HN8A  H  HNH2  0   0.393  -5.9836  -1.3491  -2.2517
 N22  HN7   H  HNH2  0   0.398  -1.6621  -0.4035  -3.2347
 N22  HN7A  H  HNH2  0   0.411  -0.6516   0.4237  -2.0989
 N22  H11   H  HCH2  0   0.286   1.5125   2.9652   0.0549
 N22  H11A  H  HCH2  0   0.287   1.4217   2.3740   1.6970
 N22  H18   H  HCR6  0   0.261   2.9533   0.7817   2.3892
 N22  H4    H  HCH3  0   0.258   6.1487  -2.2253   2.9550
 N22  H4A   H  HCH3  0   0.225   5.3153  -2.8966   1.5423
 N22  H4B   H  HCH3  0   0.225   6.5411  -1.6284   1.3332
 N22  H16   H  HCR6  0   0.280   5.0223  -1.6931  -0.4365
 N22  H15   H  HCR6  0   0.283   3.7230  -0.7332  -2.2335
 N22  H2    H  HCH3  0   0.238   3.0761   1.0712  -3.5723
 N22  H2A   H  HCH3  0   0.230   1.8504  -0.2128  -3.4777
 N22  H2B   H  HCH3  0   0.262   1.3685   1.4497  -3.8630

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
 N22  C8   C7    single    1.529  0.020  1.529
 N22  C7   C5    single    1.499  0.020  1.499
 N22  C5   N4    aromatic  1.328  0.020  1.328
 N22  C5   C6    aromatic  1.392  0.020  1.392
 N22  N4   C3    aromatic  1.338  0.020  1.338
 N22  C3   N8    single    1.348  0.020  1.348
 N22  C3   N2    aromatic  1.332  0.020  1.332
 N22  N2   C1    aromatic  1.328  0.020  1.328
 N22  C1   N7    single    1.338  0.020  1.338
 N22  C1   C6    aromatic  1.421  0.020  1.421
 N22  C6   C9    single    1.416  0.020  1.416
 N22  C9   C10   triple    1.207  0.020  1.207
 N22  C10  C11   single    1.458  0.020  1.458
 N22  C11  C13   single    1.510  0.020  1.510
 N22  C13  C18   aromatic  1.381  0.020  1.381
 N22  C13  C14   aromatic  1.403  0.020  1.403
 N22  C18  C17   aromatic  1.397  0.020  1.397
 N22  C17  O2    single    1.351  0.020  1.351
 N22  C17  C16   aromatic  1.386  0.020  1.386
 N22  O2   C4    single    1.412  0.020  1.412
 N22  C16  C15   aromatic  1.395  0.020  1.395
 N22  C15  C14   aromatic  1.385  0.020  1.385
 N22  C14  O10   single    1.354  0.020  1.354
 N22  O10  C2    single    1.414  0.020  1.414
 N22  C8   H8    single    0.970  0.020  1.090
 N22  C8   H8A   single    0.970  0.020  1.090
 N22  C8   H8B   single    0.970  0.020  1.090
 N22  C7   H7    single    0.970  0.020  1.090
 N22  C7   H7A   single    0.970  0.020  1.090
 N22  N8   HN8   single    0.890  0.020  1.040
 N22  N8   HN8A  single    0.890  0.020  1.040
 N22  N7   HN7   single    0.860  0.020  1.020
 N22  N7   HN7A  single    0.860  0.020  1.020
 N22  C11  H11   single    0.970  0.020  1.090
 N22  C11  H11A  single    0.970  0.020  1.090
 N22  C18  H18   single    0.930  0.020  1.080
 N22  C4   H4    single    0.970  0.020  1.090
 N22  C4   H4A   single    0.970  0.020  1.090
 N22  C4   H4B   single    0.970  0.020  1.090
 N22  C16  H16   single    0.930  0.020  1.080
 N22  C15  H15   single    0.930  0.020  1.080
 N22  C2   H2    single    0.970  0.020  1.090
 N22  C2   H2A   single    0.970  0.020  1.090
 N22  C2   H2B   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
 N22  H8B   C8   H8A  108.11  3.000
 N22  H8B   C8   H8   107.90  3.000
 N22  H8A   C8   H8   107.91  3.000
 N22  H8B   C8   C7   111.23  3.000
 N22  H8A   C8   C7   111.05  3.000
 N22  H8    C8   C7   110.51  3.000
 N22  H7A   C7   H7   107.68  3.000
 N22  H7A   C7   C5   109.95  3.000
 N22  H7    C7   C5   108.81  3.000
 N22  H7A   C7   C8   109.46  3.000
 N22  H7    C7   C8   109.75  3.000
 N22  C5    C7   C8   111.12  3.000
 N22  C6    C5   N4   122.24  3.000
 N22  C6    C5   C7   120.66  3.000
 N22  N4    C5   C7   117.06  3.000
 N22  C3    N4   C5   116.75  3.000
 N22  N2    C3   N8   116.87  3.000
 N22  N2    C3   N4   126.47  3.000
 N22  N8    C3   N4   116.65  3.000
 N22  HN8A  N8   HN8  117.02  3.000
 N22  HN8A  N8   C3   118.86  3.000
 N22  HN8   N8   C3   118.48  3.000
 N22  C1    N2   C3   116.99  3.000
 N22  C6    C1   N7   120.61  3.000
 N22  C6    C1   N2   121.37  3.000
 N22  N7    C1   N2   118.02  3.000
 N22  HN7A  N7   HN7  118.77  3.000
 N22  HN7A  N7   C1   120.84  3.000
 N22  HN7   N7   C1   120.10  3.000
 N22  C9    C6   C1   119.71  3.000
 N22  C9    C6   C5   124.11  3.000
 N22  C1    C6   C5   116.19  3.000
 N22  C10   C9   C6   180.00  3.000
 N22  C11   C10  C9   180.00  3.000
 N22  H11A  C11  H11  106.16  3.000
 N22  H11A  C11  C13  109.35  3.000
 N22  H11   C11  C13  110.45  3.000
 N22  H11A  C11  C10  109.14  3.000
 N22  H11   C11  C10  109.78  3.000
 N22  C13   C11  C10  111.79  3.000
 N22  C14   C13  C18  119.33  3.000
 N22  C14   C13  C11  120.31  3.000
 N22  C18   C13  C11  120.35  3.000
 N22  H18   C18  C17  119.06  3.000
 N22  H18   C18  C13  119.45  3.000
 N22  C17   C18  C13  121.48  3.000
 N22  C16   C17  O2   124.86  3.000
 N22  C16   C17  C18  118.91  3.000
 N22  O2    C17  C18  116.22  3.000
 N22  C4    O2   C17  118.09  3.000
 N22  H4B   C4   H4A  108.58  3.000
 N22  H4B   C4   H4   108.69  3.000
 N22  H4A   C4   H4   108.71  3.000
 N22  H4B   C4   O2   112.04  3.000
 N22  H4A   C4   O2   112.07  3.000
 N22  H4    C4   O2   106.64  3.000
 N22  H16   C16  C15  118.36  3.000
 N22  H16   C16  C17  121.58  3.000
 N22  C15   C16  C17  120.06  3.000
 N22  H15   C15  C14  121.17  3.000
 N22  H15   C15  C16  118.01  3.000
 N22  C14   C15  C16  120.82  3.000
 N22  O10   C14  C15  124.41  3.000
 N22  O10   C14  C13  116.19  3.000
 N22  C15   C14  C13  119.40  3.000
 N22  C2    O10  C14  118.27  3.000
 N22  H2B   C2   H2A  108.82  3.000
 N22  H2B   C2   H2   108.79  3.000
 N22  H2A   C2   H2   108.77  3.000
 N22  H2B   C2   O10  106.53  3.000
 N22  H2A   C2   O10  111.94  3.000
 N22  H2    C2   O10  111.89  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
 N22  CONST_01  N2    C3   N4   C5      0.00   0.0  0
 N22  CONST_02  N2    C1   C6   C5      0.00   0.0  0
 N22  CONST_03  C1    C6   C5   N4      0.00   0.0  0
 N22  CONST_04  C1    N2   C3   N4      0.00   0.0  0
 N22  CONST_05  C6    C5   N4   C3      0.00   0.0  0
 N22  CONST_06  C6    C1   N2   C3      0.00   0.0  0
 N22  CONST_07  C16   C17  C18  C13     0.00   0.0  0
 N22  CONST_08  C16   C15  C14  C13     0.00   0.0  0
 N22  CONST_09  C15   C14  C13  C18     0.00   0.0  0
 N22  CONST_10  C15   C16  C17  C18     0.00   0.0  0
 N22  CONST_11  C14   C13  C18  C17     0.00   0.0  0
 N22  CONST_12  C14   C15  C16  C17     0.00   0.0  0
 N22  CONST_13  C3    N4   C5   C7    180.00   0.0  0
 N22  CONST_14  C1    C6   C5   C7    180.00   0.0  0
 N22  CONST_15  N8    C3   N4   C5    180.00   0.0  0
 N22  CONST_16  N7    C1   C6   C5    180.00   0.0  0
 N22  CONST_17  C9    C6   C5   N4    180.00   0.0  0
 N22  CONST_18  N7    C1   N2   C3    180.00   0.0  0
 N22  CONST_19  C1    N2   C3   N8    180.00   0.0  0
 N22  CONST_20  C9    C6   C1   N2    180.00   0.0  0
 N22  CONST_21  C17   C18  C13  C11   180.00   0.0  0
 N22  CONST_22  C15   C14  C13  C11   180.00   0.0  0
 N22  CONST_23  O2    C17  C18  C13   180.00   0.0  0
 N22  CONST_24  O10   C14  C13  C18   180.00   0.0  0
 N22  CONST_25  C15   C16  C17  O2    180.00   0.0  0
 N22  CONST_26  O10   C14  C15  C16   180.00   0.0  0
 N22  CONST_27  H15   C15  C14  C13   180.00   0.0  0
 N22  CONST_28  H16   C16  C17  C18   180.00   0.0  0
 N22  CONST_29  H18   C18  C17  C16   180.00   0.0  0
 N22  CONST_30  HN8   N8   C3   N4      0.00   0.0  0
 N22  CONST_31  HN8A  N8   C3   N4    180.00   0.0  0
 N22  CONST_32  HN7   N7   C1   N2      0.00   0.0  0
 N22  CONST_33  HN7A  N7   C1   N2    180.00   0.0  0
 N22  Var_01    N4    C5   C7   C8     93.90  30.0  2
 N22  Var_02    C18   C13  C11  C10  -111.96  30.0  2
 N22  Var_03    C16   C17  O2   C4      0.11  30.0  3
 N22  Var_04    C13   C11  C10  C9      5.13  30.0  3
 N22  Var_05    H8    C8   C7   C5   -179.64  30.0  3
 N22  Var_06    H4    C4   O2   C17   179.86  30.0  3
 N22  Var_07    H2    C2   O10  C14   -58.42  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
 N22  plan-1  C7    0.020
 N22  plan-1  C5    0.020
 N22  plan-1  N4    0.020
 N22  plan-1  C3    0.020
 N22  plan-1  N8    0.020
 N22  plan-1  N2    0.020
 N22  plan-1  C1    0.020
 N22  plan-1  N7    0.020
 N22  plan-1  C6    0.020
 N22  plan-1  C9    0.020
 N22  plan-1  C10   0.020
 N22  plan-2  C11   0.020
 N22  plan-2  C13   0.020
 N22  plan-2  C18   0.020
 N22  plan-2  C17   0.020
 N22  plan-2  O2    0.020
 N22  plan-2  C16   0.020
 N22  plan-2  C15   0.020
 N22  plan-2  C14   0.020
 N22  plan-2  O10   0.020
 N22  plan-2  H18   0.020
 N22  plan-2  H16   0.020
 N22  plan-2  H15   0.020
 N22  plan-3  C3    0.020
 N22  plan-3  N8    0.020
 N22  plan-3  HN8   0.020
 N22  plan-3  HN8A  0.020
 N22  plan-4  C1    0.020
 N22  plan-4  N7    0.020
 N22  plan-4  HN7   0.020
 N22  plan-4  HN7A  0.020

