# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 23:39:50 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-bromo-N~4~-[3-(3-methoxypropyl)-1H-pyrazol-5-yl]-N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCc1cc([nH]n1)Nc2nc(NCc3onc(C)c3)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
 0S8  0S8  5-bromo-N~4~-[3-(3-methoxypropyl)-1H-pyrazol-5-yl]-N~2~-[(3-methyl-1,2-oxazol-5-yl)methyl]pyrimidine-2,4-diamine  ligand  46  26  .  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_0S8
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
 0S8  C1   C   CH3   0  -0.396   6.4421   6.8082   0.2224
 0S8  O2   O   O2    0  -0.488   5.2102   6.3781  -0.2944
 0S8  C3   C   CH2   0  -0.119   4.7576   5.1882   0.3034
 0S8  C4   C   CH2   0  -0.466   3.4317   4.7885  -0.3128
 0S8  C5   C   CH2   0  -0.507   2.9200   3.4881   0.2928
 0S8  C6   C   CR5   0   0.277   1.5951   3.0418  -0.2368
 0S8  C7   C   CR15  0  -0.522   0.9492   1.8162   0.0371
 0S8  C8   C   CR5   0   0.630  -0.2385   1.8950  -0.6613
 0S8  N9   N   NH1   0  -0.774  -1.3331   1.0679  -0.8169
 0S8  C10  C   CR6   0   0.615  -1.4840  -0.1805  -0.3125
 0S8  N11  N   N     0  -0.513  -0.4810  -0.7176   0.3556
 0S8  C12  C   CR6   0   0.633  -0.6352  -1.9455   0.8559
 0S8  N13  N   NH1   0  -0.652   0.4165  -2.4326   1.5450
 0S8  C14  C   CH2   0  -0.403   0.4924  -3.7692   2.0708
 0S8  C15  C   CR5   0   0.449   1.1145  -4.7339   1.1173
 0S8  C16  C   CR15  0  -0.516   2.2027  -5.5317   1.2010
 0S8  C17  C   CR5   0   0.261   2.2442  -6.1855  -0.0604
 0S8  C18  C   CH3   0  -0.733   3.2384  -7.1799  -0.5421
 0S8  N19  N   N     0  -0.182   1.2584  -5.7925  -0.8143
 0S8  O20  O   O     0  -0.339   0.5461  -4.8867  -0.0810
 0S8  N21  N   N     0  -0.478  -1.7281  -2.6987   0.7489
 0S8  C22  C   CR16  0   0.004  -2.7361  -2.1593   0.0783
 0S8  C23  C   CR6   0  -0.324  -2.6846  -0.9057  -0.4872
 0S8  BR1  BR  BR    0  -0.023  -4.1618  -0.2226  -1.4275
 0S8  N25  N   NR15  0  -0.520  -0.2351   3.0915  -1.2816
 0S8  N27  N   N     0  -0.307   0.8714   3.7997  -1.0334
 0S8  H1   H   HCH3  0   0.202   7.2321   6.0604   0.0807
 0S8  H2   H   HCH3  0   0.232   6.7322   7.7169  -0.3045
 0S8  H3   H   HCH3  0   0.202   6.3846   7.0342   1.2942
 0S8  H4   H   HCH2  0   0.192   5.4953   4.3828   0.1660
 0S8  H5   H   HCH2  0   0.192   4.6407   5.3216   1.3896
 0S8  H6   H   HCH2  0   0.229   2.7011   5.5858  -0.1572
 0S8  H7   H   HCH2  0   0.228   3.5510   4.6725  -1.3931
 0S8  H8   H   HCH2  0   0.244   3.6519   2.6908   0.1302
 0S8  H9   H   HCH2  0   0.244   2.8442   3.5947   1.3801
 0S8  H10  H   HCR5  0   0.267   1.3025   1.0077   0.6482
 0S8  H11  H   HNH1  0   0.421  -2.1042   1.4543  -1.3409
 0S8  H12  H   HNH1  0   0.402   1.2667  -1.8941   1.5122
 0S8  H13  H   HCH2  0   0.294   1.0928  -3.7571   2.9796
 0S8  H14  H   HCH2  0   0.287  -0.5068  -4.1043   2.3479
 0S8  H15  H   HCR5  0   0.278   2.8835  -5.6425   2.0280
 0S8  H16  H   HCH3  0   0.259   3.2874  -8.0321   0.1351
 0S8  H17  H   HCH3  0   0.257   2.9846  -7.5410  -1.5365
 0S8  H18  H   HCH3  0   0.260   4.2338  -6.7368  -0.5799
 0S8  H19  H   HCR6  0   0.285  -3.6328  -2.7631  -0.0137
 0S8  H20  H   HNR5  0   0.417  -0.9459   3.4708  -1.8865

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
 0S8  BR1  C23  single    1.880  0.020  1.880
 0S8  C22  C23  aromatic  1.376  0.020  1.376
 0S8  C22  N21  aromatic  1.325  0.020  1.325
 0S8  C23  C10  aromatic  1.413  0.020  1.413
 0S8  N21  C12  aromatic  1.332  0.020  1.332
 0S8  C10  N9   single    1.355  0.020  1.355
 0S8  C10  N11  aromatic  1.319  0.020  1.319
 0S8  N9   C8   single    1.381  0.020  1.381
 0S8  C12  N11  aromatic  1.335  0.020  1.335
 0S8  C12  N13  single    1.348  0.020  1.348
 0S8  C8   N25  aromatic  1.348  0.020  1.348
 0S8  C8   C7   aromatic  1.380  0.020  1.380
 0S8  N13  C14  single    1.438  0.020  1.438
 0S8  N25  N27  aromatic  1.337  0.020  1.337
 0S8  C7   C6   aromatic  1.412  0.020  1.412
 0S8  C14  C15  single    1.492  0.020  1.492
 0S8  N27  C6   aromatic  1.316  0.020  1.316
 0S8  C6   C5   single    1.495  0.020  1.495
 0S8  C15  C16  aromatic  1.352  0.020  1.352
 0S8  C15  O20  aromatic  1.335  0.020  1.335
 0S8  C16  C17  aromatic  1.421  0.020  1.421
 0S8  C5   C4   single    1.523  0.020  1.523
 0S8  O20  N19  aromatic  1.366  0.020  1.366
 0S8  C17  N19  aromatic  1.302  0.020  1.302
 0S8  C17  C18  single    1.486  0.020  1.486
 0S8  C4   C3   single    1.516  0.020  1.516
 0S8  C3   O2   single    1.406  0.020  1.406
 0S8  O2   C1   single    1.403  0.020  1.403
 0S8  C1   H1   single    0.970  0.020  1.090
 0S8  C1   H2   single    0.970  0.020  1.090
 0S8  C1   H3   single    0.970  0.020  1.090
 0S8  C3   H4   single    0.970  0.020  1.090
 0S8  C3   H5   single    0.970  0.020  1.090
 0S8  C4   H6   single    0.970  0.020  1.090
 0S8  C4   H7   single    0.970  0.020  1.090
 0S8  C5   H8   single    0.970  0.020  1.090
 0S8  C5   H9   single    0.970  0.020  1.090
 0S8  C7   H10  single    0.930  0.020  1.080
 0S8  N9   H11  single    0.860  0.020  1.020
 0S8  N13  H12  single    0.860  0.020  1.020
 0S8  C14  H13  single    0.970  0.020  1.090
 0S8  C14  H14  single    0.970  0.020  1.090
 0S8  C16  H15  single    0.930  0.020  1.080
 0S8  C18  H16  single    0.970  0.020  1.090
 0S8  C18  H17  single    0.970  0.020  1.090
 0S8  C18  H18  single    0.970  0.020  1.090
 0S8  C22  H19  single    0.930  0.020  1.080
 0S8  N25  H20  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
 0S8  H3   C1   H2   108.34  3.000
 0S8  H3   C1   H1   107.72  3.000
 0S8  H2   C1   H1   108.31  3.000
 0S8  H3   C1   O2   112.14  3.000
 0S8  H2   C1   O2   108.13  3.000
 0S8  H1   C1   O2   112.06  3.000
 0S8  C3   O2   C1   112.66  3.000
 0S8  H5   C3   H4   106.44  3.000
 0S8  H5   C3   C4   109.89  3.000
 0S8  H4   C3   C4   110.04  3.000
 0S8  H5   C3   O2   110.55  3.000
 0S8  H4   C3   O2   110.50  3.000
 0S8  C4   C3   O2   109.38  3.000
 0S8  H7   C4   H6   106.94  3.000
 0S8  H7   C4   C5   109.82  3.000
 0S8  H6   C4   C5   109.99  3.000
 0S8  H7   C4   C3   109.53  3.000
 0S8  H6   C4   C3   109.55  3.000
 0S8  C5   C4   C3   110.94  3.000
 0S8  H9   C5   H8   105.35  3.000
 0S8  H9   C5   C6   108.63  3.000
 0S8  H8   C5   C6   108.82  3.000
 0S8  H9   C5   C4   109.57  3.000
 0S8  H8   C5   C4   109.77  3.000
 0S8  C6   C5   C4   114.31  3.000
 0S8  N27  C6   C7   111.44  3.000
 0S8  N27  C6   C5   121.99  3.000
 0S8  C7   C6   C5   126.56  3.000
 0S8  H10  C7   C8   127.91  3.000
 0S8  H10  C7   C6   127.85  3.000
 0S8  C8   C7   C6   104.24  3.000
 0S8  N25  C8   N9   118.81  3.000
 0S8  N25  C8   C7   106.34  3.000
 0S8  N9   C8   C7   134.84  3.000
 0S8  H11  N9   C10  117.45  3.000
 0S8  H11  N9   C8   115.78  3.000
 0S8  C10  N9   C8   126.75  3.000
 0S8  C23  C10  N11  119.96  3.000
 0S8  N11  C10  N9   118.61  3.000
 0S8  C23  C10  N9   121.42  3.000
 0S8  C12  N11  C10  118.45  3.000
 0S8  N21  C12  N13  118.48  3.000
 0S8  N13  C12  N11  115.71  3.000
 0S8  N21  C12  N11  125.80  3.000
 0S8  H12  N13  C14  117.67  3.000
 0S8  H12  N13  C12  116.66  3.000
 0S8  C14  N13  C12  124.31  3.000
 0S8  H14  C14  H13  107.26  3.000
 0S8  H14  C14  C15  110.24  3.000
 0S8  H13  C14  C15  108.09  3.000
 0S8  H14  C14  N13  109.29  3.000
 0S8  H13  C14  N13  108.89  3.000
 0S8  C15  C14  N13  112.91  3.000
 0S8  O20  C15  C16  109.31  3.000
 0S8  O20  C15  C14  118.03  3.000
 0S8  C16  C15  C14  132.65  3.000
 0S8  H15  C16  C17  128.01  3.000
 0S8  H15  C16  C15  128.10  3.000
 0S8  C17  C16  C15  103.89  3.000
 0S8  N19  C17  C18  121.39  3.000
 0S8  C18  C17  C16  127.94  3.000
 0S8  N19  C17  C16  110.67  3.000
 0S8  H18  C18  H17  108.43  3.000
 0S8  H18  C18  H16  107.36  3.000
 0S8  H17  C18  H16  108.60  3.000
 0S8  H18  C18  C17  110.49  3.000
 0S8  H17  C18  C17  111.24  3.000
 0S8  H16  C18  C17  110.61  3.000
 0S8  O20  N19  C17  106.51  3.000
 0S8  N19  O20  C15  109.62  3.000
 0S8  C22  N21  C12  115.76  3.000
 0S8  H19  C22  C23  120.20  3.000
 0S8  H19  C22  N21  116.42  3.000
 0S8  C23  C22  N21  123.38  3.000
 0S8  BR1  C23  C22  120.48  3.000
 0S8  C22  C23  C10  116.64  3.000
 0S8  BR1  C23  C10  122.88  3.000
 0S8  H20  N25  N27  119.72  3.000
 0S8  H20  N25  C8   127.51  3.000
 0S8  N27  N25  C8   112.77  3.000
 0S8  N25  N27  C6   105.21  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
 0S8  CONST_01  N25  C8   C7   C6      0.00   0.0  0
 0S8  CONST_02  C8   N25  N27  C6      0.00   0.0  0
 0S8  CONST_03  N27  N25  C8   C7      0.00   0.0  0
 0S8  CONST_04  N25  N27  C6   C7      0.00   0.0  0
 0S8  CONST_05  N27  C6   C7   C8      0.00   0.0  0
 0S8  CONST_06  N21  C22  C23  C10     0.00   0.0  0
 0S8  CONST_07  N21  C12  N11  C10     0.00   0.0  0
 0S8  CONST_08  C22  C23  C10  N11     0.00   0.0  0
 0S8  CONST_09  C22  N21  C12  N11     0.00   0.0  0
 0S8  CONST_10  C23  C22  N21  C12     0.00   0.0  0
 0S8  CONST_11  C23  C10  N11  C12     0.00   0.0  0
 0S8  CONST_12  N19  C17  C16  C15     0.00   0.0  0
 0S8  CONST_13  C17  N19  O20  C15     0.00   0.0  0
 0S8  CONST_14  N19  O20  C15  C16     0.00   0.0  0
 0S8  CONST_15  O20  N19  C17  C16     0.00   0.0  0
 0S8  CONST_16  O20  C15  C16  C17     0.00   0.0  0
 0S8  CONST_17  C8   C7   C6   C5    180.00   0.0  0
 0S8  CONST_18  N25  N27  C6   C5    180.00   0.0  0
 0S8  CONST_19  N9   C8   C7   C6    180.00   0.0  0
 0S8  CONST_20  C22  C23  C10  N9    180.00   0.0  0
 0S8  CONST_21  C12  N11  C10  N9    180.00   0.0  0
 0S8  CONST_22  N27  N25  C8   N9    180.00   0.0  0
 0S8  CONST_23  N13  C12  N11  C10   180.00   0.0  0
 0S8  CONST_24  BR1  C23  C10  N11   180.00   0.0  0
 0S8  CONST_25  C22  N21  C12  N13   180.00   0.0  0
 0S8  CONST_26  C17  C16  C15  C14   180.00   0.0  0
 0S8  CONST_27  N19  O20  C15  C14   180.00   0.0  0
 0S8  CONST_28  C18  C17  C16  C15   180.00   0.0  0
 0S8  CONST_29  O20  N19  C17  C18   180.00   0.0  0
 0S8  CONST_30  BR1  C23  C22  N21   180.00   0.0  0
 0S8  CONST_31  H20  N25  N27  C6    180.00   0.0  0
 0S8  CONST_32  H19  C22  C23  C10   180.00   0.0  0
 0S8  CONST_33  H15  C16  C17  N19   180.00   0.0  0
 0S8  CONST_34  H10  C7   C8   N25   180.00   0.0  0
 0S8  CONST_35  C14  N13  C12  N11   180.00   0.0  0
 0S8  CONST_36  N21  C12  N13  C14     0.00   0.0  0
 0S8  CONST_37  H12  N13  C12  N11     0.00   0.0  0
 0S8  Var_01    C10  N9   C8   C7     -3.73  30.0  1
 0S8  Var_02    C23  C10  N9   C8    176.84  30.0  3
 0S8  Var_03    C7   C6   C5   C4    173.00  30.0  1
 0S8  Var_04    C15  C14  N13  C12    90.96  30.0  3
 0S8  Var_05    C16  C15  C14  N13   121.08  30.0  2
 0S8  Var_06    H16  C18  C17  C16    56.56  30.0  2
 0S8  Var_07    C6   C5   C4   C3    178.47  30.0  1
 0S8  Var_08    C4   C3   O2   C1   -179.67  30.0  1
 0S8  Var_09    C5   C4   C3   O2    179.00  30.0  1
 0S8  Var_10    H1   C1   O2   C3     59.44  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
 0S8  plan-1  C5   0.020
 0S8  plan-1  C6   0.020
 0S8  plan-1  C7   0.020
 0S8  plan-1  C8   0.020
 0S8  plan-1  N9   0.020
 0S8  plan-1  N25  0.020
 0S8  plan-1  N27  0.020
 0S8  plan-1  H10  0.020
 0S8  plan-1  H20  0.020
 0S8  plan-2  C14  0.020
 0S8  plan-2  C15  0.020
 0S8  plan-2  C16  0.020
 0S8  plan-2  C17  0.020
 0S8  plan-2  C18  0.020
 0S8  plan-2  N19  0.020
 0S8  plan-2  O20  0.020
 0S8  plan-2  H15  0.020
 0S8  plan-3  N9   0.020
 0S8  plan-3  C10  0.020
 0S8  plan-3  N11  0.020
 0S8  plan-3  C12  0.020
 0S8  plan-3  N13  0.020
 0S8  plan-3  N21  0.020
 0S8  plan-3  C22  0.020
 0S8  plan-3  C23  0.020
 0S8  plan-3  BR1  0.020
 0S8  plan-3  H19  0.020
 0S8  plan-4  C12  0.020
 0S8  plan-4  N13  0.020
 0S8  plan-4  C14  0.020
 0S8  plan-4  H12  0.020

