# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 02:58:00 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 5-bromo-N~4~-(3-methyl-1H-pyrazol-5-yl)-N~2~-[2-(pyridin-3-yl)ethyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc([nH]n1)Nc2nc(NCCc3cccnc3)ncc2Br
#
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
 0S7  0S7  5-bromo-N~4~-(3-methyl-1H-pyrazol-5-yl)-N~2~-[2-(pyridin-3-yl)ethyl]pyrimidine-2,4-diamine  ligand  39  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_0S7
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
 0S7  C1   C   CH3   0  -0.734  -2.6599   5.4458  -0.0066
 0S7  C2   C   CR5   0   0.252  -3.0785   4.0159  -0.0028
 0S7  C3   C   CR15  0  -0.520  -2.2384   2.8820   0.0088
 0S7  C4   C   CR5   0   0.632  -3.1112   1.8126  -0.0048
 0S7  N5   N   NH1   0  -0.773  -2.9642   0.4408   0.0012
 0S7  C6   C   CR6   0   0.611  -1.7982  -0.2514   0.0044
 0S7  N7   N   N     0  -0.513  -0.6636   0.4191   0.0004
 0S7  C8   C   CR6   0   0.626   0.4835  -0.2695   0.0058
 0S7  N9   N   NH1   0  -0.666   1.6128   0.4526  -0.0012
 0S7  C10  C   CH2   0  -0.225   2.9366  -0.1238   0.0142
 0S7  C11  C   CH2   0  -0.565   3.9864   0.9825   0.0046
 0S7  C12  C   CR6   0   0.026   5.3700   0.4044   0.0353
 0S7  C13  C   CR16  0  -0.189   6.0094   0.0893   1.2290
 0S7  C14  C   CR16  0  -0.318   7.2722  -0.4807   1.1946
 0S7  C15  C   CR16  0  -0.073   7.8557  -0.7224  -0.0400
 0S7  N16  N   N     0  -0.401   7.2620  -0.4280  -1.1908
 0S7  C17  C   CR16  0  -0.098   6.0542   0.1193  -1.1430
 0S7  N18  N   N     0  -0.484   0.5937  -1.6000   0.0170
 0S7  C19  C   CR16  0   0.004  -0.5494  -2.2715   0.0198
 0S7  C20  C   CR6   0  -0.326  -1.7849  -1.6657   0.0131
 0S7  BR1  BR  BR    0  -0.027  -3.3544  -2.7020   0.0177
 0S7  N22  N   NR15  0  -0.524  -4.3530   2.3358  -0.0220
 0S7  N24  N   N     0  -0.302  -4.3508   3.6737  -0.0207
 0S7  H1   H   HCH3  0   0.245  -2.1580   5.7093  -0.9389
 0S7  H2   H   HCH3  0   0.244  -3.5208   6.1026   0.1073
 0S7  H3   H   HCH3  0   0.244  -1.9620   5.6559   0.8045
 0S7  H4   H   HCR5  0   0.270  -1.1657   2.8551   0.0244
 0S7  H5   H   HNH1  0   0.420  -3.8206  -0.0924   0.0023
 0S7  H6   H   HNH1  0   0.401   1.5126   1.4545  -0.0061
 0S7  H7   H   HCH2  0   0.238   3.0679  -0.7515   0.9005
 0S7  H8   H   HCH2  0   0.239   3.0786  -0.7740  -0.8539
 0S7  H9   H   HCH2  0   0.263   3.8597   1.5985  -0.8896
 0S7  H10  H   HCH2  0   0.265   3.8379   1.6368   0.8675
 0S7  H11  H   HCR6  0   0.268   5.5272   0.2931   2.1776
 0S7  H12  H   HCR6  0   0.271   7.7973  -0.7317   2.1061
 0S7  H13  H   HCR6  0   0.263   8.8419  -1.1691  -0.1018
 0S7  H14  H   HCR6  0   0.257   5.5947   0.3547  -2.0987
 0S7  H15  H   HCR6  0   0.283  -0.4733  -3.3540   0.0278
 0S7  H16  H   HNR5  0   0.418  -5.2287   1.8372  -0.0408

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
 0S7  BR1  C20  single    1.881  0.020  1.881
 0S7  C19  C20  aromatic  1.376  0.020  1.376
 0S7  C19  N18  aromatic  1.326  0.020  1.326
 0S7  C20  C6   aromatic  1.414  0.020  1.414
 0S7  N18  C8   aromatic  1.335  0.020  1.335
 0S7  C6   N5   single    1.356  0.020  1.356
 0S7  C6   N7   aromatic  1.318  0.020  1.318
 0S7  N5   C4   single    1.380  0.020  1.380
 0S7  C8   N7   aromatic  1.338  0.020  1.338
 0S7  C8   N9   single    1.340  0.020  1.340
 0S7  N9   C10  single    1.444  0.020  1.444
 0S7  C4   N22  aromatic  1.348  0.020  1.348
 0S7  C4   C3   aromatic  1.380  0.020  1.380
 0S7  N22  N24  aromatic  1.338  0.020  1.338
 0S7  C3   C2   aromatic  1.411  0.020  1.411
 0S7  C10  C11  single    1.525  0.020  1.525
 0S7  N24  C2   aromatic  1.318  0.020  1.318
 0S7  C2   C1   single    1.490  0.020  1.490
 0S7  C11  C12  single    1.500  0.020  1.500
 0S7  C12  C17  aromatic  1.392  0.020  1.392
 0S7  C12  C13  aromatic  1.390  0.020  1.390
 0S7  C17  N16  aromatic  1.327  0.020  1.327
 0S7  C13  C14  aromatic  1.386  0.020  1.386
 0S7  N16  C15  aromatic  1.328  0.020  1.328
 0S7  C14  C15  aromatic  1.387  0.020  1.387
 0S7  C1   H1   single    0.970  0.020  1.090
 0S7  C1   H2   single    0.970  0.020  1.090
 0S7  C1   H3   single    0.970  0.020  1.090
 0S7  C3   H4   single    0.930  0.020  1.080
 0S7  N5   H5   single    0.860  0.020  1.020
 0S7  N9   H6   single    0.860  0.020  1.020
 0S7  C10  H7   single    0.970  0.020  1.090
 0S7  C10  H8   single    0.970  0.020  1.090
 0S7  C11  H9   single    0.970  0.020  1.090
 0S7  C11  H10  single    0.970  0.020  1.090
 0S7  C13  H11  single    0.930  0.020  1.080
 0S7  C14  H12  single    0.930  0.020  1.080
 0S7  C15  H13  single    0.930  0.020  1.080
 0S7  C17  H14  single    0.930  0.020  1.080
 0S7  C19  H15  single    0.930  0.020  1.080
 0S7  N22  H16  single    0.860  0.020  1.020

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
 0S7  H3   C1   H2   108.18  3.000
 0S7  H3   C1   H1   107.13  3.000
 0S7  H2   C1   H1   107.90  3.000
 0S7  H3   C1   C2   111.28  3.000
 0S7  H2   C1   C2   110.89  3.000
 0S7  H1   C1   C2   111.29  3.000
 0S7  N24  C2   C3   111.49  3.000
 0S7  N24  C2   C1   121.37  3.000
 0S7  C3   C2   C1   127.15  3.000
 0S7  H4   C3   C4   127.79  3.000
 0S7  H4   C3   C2   127.97  3.000
 0S7  C4   C3   C2   104.24  3.000
 0S7  N22  C4   N5   118.96  3.000
 0S7  N22  C4   C3   106.37  3.000
 0S7  N5   C4   C3   134.66  3.000
 0S7  H5   N5   C6   117.40  3.000
 0S7  H5   N5   C4   115.79  3.000
 0S7  C6   N5   C4   126.81  3.000
 0S7  C20  C6   N7   120.04  3.000
 0S7  N7   C6   N5   118.72  3.000
 0S7  C20  C6   N5   121.24  3.000
 0S7  C8   N7   C6   118.44  3.000
 0S7  N18  C8   N9   117.86  3.000
 0S7  N9   C8   N7   116.43  3.000
 0S7  N18  C8   N7   125.71  3.000
 0S7  H6   N9   C10  119.24  3.000
 0S7  H6   N9   C8   116.89  3.000
 0S7  C10  N9   C8   123.87  3.000
 0S7  H8   C10  H7   106.64  3.000
 0S7  H8   C10  C11  109.69  3.000
 0S7  H7   C10  C11  109.80  3.000
 0S7  H8   C10  N9   110.35  3.000
 0S7  H7   C10  N9   110.34  3.000
 0S7  C11  C10  N9   109.96  3.000
 0S7  H10  C11  H9   107.02  3.000
 0S7  H10  C11  C12  109.87  3.000
 0S7  H9   C11  C12  109.93  3.000
 0S7  H10  C11  C10  109.62  3.000
 0S7  H9   C11  C10  109.51  3.000
 0S7  C12  C11  C10  110.81  3.000
 0S7  C17  C12  C13  117.02  3.000
 0S7  C13  C12  C11  121.95  3.000
 0S7  C17  C12  C11  121.00  3.000
 0S7  H11  C13  C14  120.30  3.000
 0S7  H11  C13  C12  120.29  3.000
 0S7  C14  C13  C12  119.40  3.000
 0S7  H12  C14  C15  120.37  3.000
 0S7  H12  C14  C13  121.14  3.000
 0S7  C15  C14  C13  118.50  3.000
 0S7  H13  C15  N16  116.65  3.000
 0S7  H13  C15  C14  120.34  3.000
 0S7  N16  C15  C14  123.01  3.000
 0S7  C17  N16  C15  117.85  3.000
 0S7  H14  C17  N16  116.28  3.000
 0S7  H14  C17  C12  119.50  3.000
 0S7  N16  C17  C12  124.22  3.000
 0S7  C19  N18  C8   115.70  3.000
 0S7  H15  C19  C20  120.14  3.000
 0S7  H15  C19  N18  116.41  3.000
 0S7  C20  C19  N18  123.45  3.000
 0S7  BR1  C20  C19  120.44  3.000
 0S7  C19  C20  C6   116.66  3.000
 0S7  BR1  C20  C6   122.89  3.000
 0S7  H16  N22  N24  119.75  3.000
 0S7  H16  N22  C4   127.50  3.000
 0S7  N24  N22  C4   112.75  3.000
 0S7  N22  N24  C2   105.14  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
 0S7  CONST_01  N22  C4   C3   C2      0.00   0.0  0
 0S7  CONST_02  C4   N22  N24  C2      0.00   0.0  0
 0S7  CONST_03  N24  N22  C4   C3      0.00   0.0  0
 0S7  CONST_04  N22  N24  C2   C3      0.00   0.0  0
 0S7  CONST_05  N24  C2   C3   C4      0.00   0.0  0
 0S7  CONST_06  N18  C19  C20  C6      0.00   0.0  0
 0S7  CONST_07  N18  C8   N7   C6      0.00   0.0  0
 0S7  CONST_08  C19  C20  C6   N7      0.00   0.0  0
 0S7  CONST_09  C19  N18  C8   N7      0.00   0.0  0
 0S7  CONST_10  C20  C19  N18  C8      0.00   0.0  0
 0S7  CONST_11  C20  C6   N7   C8      0.00   0.0  0
 0S7  CONST_12  C15  N16  C17  C12     0.00   0.0  0
 0S7  CONST_13  C15  C14  C13  C12     0.00   0.0  0
 0S7  CONST_14  N16  C17  C12  C13     0.00   0.0  0
 0S7  CONST_15  N16  C15  C14  C13     0.00   0.0  0
 0S7  CONST_16  C17  C12  C13  C14     0.00   0.0  0
 0S7  CONST_17  C17  N16  C15  C14     0.00   0.0  0
 0S7  CONST_18  C4   C3   C2   C1    180.00   0.0  0
 0S7  CONST_19  N22  N24  C2   C1    180.00   0.0  0
 0S7  CONST_20  N5   C4   C3   C2    180.00   0.0  0
 0S7  CONST_21  C19  C20  C6   N5    180.00   0.0  0
 0S7  CONST_22  C8   N7   C6   N5    180.00   0.0  0
 0S7  CONST_23  N24  N22  C4   N5    180.00   0.0  0
 0S7  CONST_24  N9   C8   N7   C6    180.00   0.0  0
 0S7  CONST_25  BR1  C20  C6   N7    180.00   0.0  0
 0S7  CONST_26  C19  N18  C8   N9    180.00   0.0  0
 0S7  CONST_27  N16  C17  C12  C11   180.00   0.0  0
 0S7  CONST_28  C14  C13  C12  C11   180.00   0.0  0
 0S7  CONST_29  BR1  C20  C19  N18   180.00   0.0  0
 0S7  CONST_30  H16  N22  N24  C2    180.00   0.0  0
 0S7  CONST_31  H15  C19  C20  C6    180.00   0.0  0
 0S7  CONST_32  H12  C14  C13  C12   180.00   0.0  0
 0S7  CONST_33  H14  C17  C12  C13   180.00   0.0  0
 0S7  CONST_34  H13  C15  C14  C13   180.00   0.0  0
 0S7  CONST_35  H11  C13  C14  C15   180.00   0.0  0
 0S7  CONST_36  H4   C3   C4   N22   180.00   0.0  0
 0S7  CONST_37  C10  N9   C8   N7    180.00   0.0  0
 0S7  CONST_38  N18  C8   N9   C10     0.00   0.0  0
 0S7  CONST_39  H6   N9   C8   N7      0.00   0.0  0
 0S7  Var_01    C6   N5   C4   C3     -1.05  30.0  2
 0S7  Var_02    C20  C6   N5   C4    179.88  30.0  2
 0S7  Var_03    C17  C12  C11  C10    90.87  30.0  2
 0S7  Var_04    H1   C1   C2   C3     66.85  30.0  2
 0S7  Var_05    C11  C10  N9   C8   -179.83  30.0  3
 0S7  Var_06    C12  C11  C10  N9    179.39  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
 0S7  plan-1  C1   0.020
 0S7  plan-1  C2   0.020
 0S7  plan-1  C3   0.020
 0S7  plan-1  C4   0.020
 0S7  plan-1  N5   0.020
 0S7  plan-1  N22  0.020
 0S7  plan-1  N24  0.020
 0S7  plan-1  H4   0.020
 0S7  plan-1  H16  0.020
 0S7  plan-2  C11  0.020
 0S7  plan-2  C12  0.020
 0S7  plan-2  C13  0.020
 0S7  plan-2  C14  0.020
 0S7  plan-2  C15  0.020
 0S7  plan-2  N16  0.020
 0S7  plan-2  C17  0.020
 0S7  plan-2  H11  0.020
 0S7  plan-2  H12  0.020
 0S7  plan-2  H13  0.020
 0S7  plan-2  H14  0.020
 0S7  plan-3  N5   0.020
 0S7  plan-3  C6   0.020
 0S7  plan-3  N7   0.020
 0S7  plan-3  C8   0.020
 0S7  plan-3  N9   0.020
 0S7  plan-3  N18  0.020
 0S7  plan-3  C19  0.020
 0S7  plan-3  C20  0.020
 0S7  plan-3  BR1  0.020
 0S7  plan-3  H15  0.020
 0S7  plan-4  C8   0.020
 0S7  plan-4  N9   0.020
 0S7  plan-4  C10  0.020
 0S7  plan-4  H6   0.020

