# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 10:17:42 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: ~{N}-[4-[2-bromanyl-6-(2-hydroxyethylamino)pyridin-4-yl]sulfanylphenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccc(Sc2cc(Br)nc(NCCO)c2)cc1
#
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
 H40  H40  "~{N}-[4-[2-bromanyl-6-(2-hydroxyethylamino)pyridin-4-yl]sulfanylphenyl]propanamide"
  ligand  41  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H40
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
 H40  C1   C   CR6   0   0.514  -5.7904  -7.9812  3.7426
 H40  C2   C   CR16  0  -0.412  -5.6402  -6.6750  3.2517
 H40  C3   C   CR6   0  -0.004  -4.3616  -6.1564  3.1279
 H40  C11  C   CR16  0  -0.342  -0.5867  -3.2382  3.6231
 H40  C12  C   CR16  0  -0.197  -1.9348  -3.5360  3.6155
 H40  C13  C   CR6   0   0.384   0.2343  -3.5860  2.5440
 H40  C17  C   CH2   0  -0.157  -8.6289  -7.0725  4.9612
 H40  C20  C   C     0   0.549   2.6008  -3.4668  1.7661
 H40  C21  C   CH2   0  -0.585   3.9193  -2.8797  2.2248
 H40  C23  C   CH3   0  -0.656   5.0822  -3.2083  1.3077
 H40  C4   C   CR16  0  -0.306  -3.2539  -6.9229  3.4950
 H40  C5   C   CR6   0   0.090  -3.5424  -8.1876  3.9686
 H40  N6   N   N     0  -0.461  -4.7277  -8.7192  4.0992
 H40  S7   S   S2    0   0.104  -4.2338  -4.5211  2.4888
 H40  C8   C   CR6   0  -0.215  -2.4997  -4.1905  2.5253
 H40  C9   C   CR16  0  -0.194  -1.6914  -4.5316  1.4482
 H40  C10  C   CR16  0  -0.311  -0.3358  -4.2433  1.4492
 H40  N14  N   NH1   0  -0.646  -6.9908  -8.5893  3.8623
 H40  BR1  BR  BR    0  -0.056  -2.0885  -9.2981  4.4952
 H40  O18  O   OH1   0  -0.665  -8.7065  -7.9096  6.0907
 H40  O22  O   O     0  -0.453   2.4709  -4.0748  0.7225
 H40  H1   H   HCR6  0   0.283  -6.4990  -6.0806  2.9709
 H40  H2   H   HCR6  0   0.277  -0.1614  -2.7274  4.4789
 H40  H3   H   HCR6  0   0.276  -2.5479  -3.2583  4.4628
 H40  H4   H   HCH2  0   0.249  -8.2947  -7.3039  2.8585
 H40  H5   H   HCH2  0   0.268  -9.0240  -8.6955  3.6133
 H40  H6   H   HCH2  0   0.203  -7.8798  -6.2815  5.0938
 H40  H7   H   HCH2  0   0.204  -9.5837  -6.5739  4.7490
 H40  H8   H   HCH2  0   0.270   4.1221  -3.2296  3.2411
 H40  H9   H   HCH2  0   0.274   3.7954  -1.7955  2.3086
 H40  H10  H   HCH3  0   0.236   5.9951  -2.7566  1.6937
 H40  H11  H   HCH3  0   0.230   5.2489  -4.2825  1.2368
 H40  H12  H   HCH3  0   0.230   4.9239  -2.8247  0.3007
 H40  H13  H   HCR6  0   0.286  -2.2427  -6.5542  3.4178
 H40  H14  H   HCR6  0   0.276  -2.1198  -5.0344  0.5906
 H40  H15  H   HCR6  0   0.287   0.2606  -4.5268  0.5986
 H40  H16  H   HNH1  0   0.389  -6.9732  -9.4756  4.3408
 H40  H17  H   HOH1  0   0.454  -8.8451  -7.3593  6.8664
 H40  H18  H   HNH1  0   0.421   1.8242  -2.7316  3.4792
 H40  N19  N   NH1   0  -0.745   1.5767  -3.2366  2.6403
 H40  C16  C   CH2   0  -0.349  -8.2665  -7.9240  3.7565

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
 H40  O22  C20  double    1.215  0.020  1.215
 H40  C9   C10  aromatic  1.386  0.020  1.386
 H40  C9   C8   aromatic  1.389  0.020  1.389
 H40  C10  C13  aromatic  1.398  0.020  1.398
 H40  C23  C21  single    1.517  0.020  1.517
 H40  S7   C8   single    1.766  0.020  1.766
 H40  S7   C3   single    1.760  0.020  1.760
 H40  C20  C21  single    1.514  0.020  1.514
 H40  C20  N19  single    1.366  0.020  1.366
 H40  C8   C12  aromatic  1.391  0.020  1.391
 H40  C13  N19  single    1.390  0.020  1.390
 H40  C13  C11  aromatic  1.400  0.020  1.400
 H40  C3   C2   aromatic  1.385  0.020  1.385
 H40  C3   C4   aromatic  1.396  0.020  1.396
 H40  C2   C1   aromatic  1.403  0.020  1.403
 H40  C12  C11  aromatic  1.381  0.020  1.381
 H40  C4   C5   aromatic  1.381  0.020  1.381
 H40  C1   N14  single    1.351  0.020  1.351
 H40  C1   N6   aromatic  1.342  0.020  1.342
 H40  C16  N14  single    1.443  0.020  1.443
 H40  C16  C17  single    1.519  0.020  1.519
 H40  C5   N6   aromatic  1.306  0.020  1.306
 H40  C5   BR1  single    1.904  0.020  1.904
 H40  C17  O18  single    1.408  0.020  1.408
 H40  C2   H1   single    0.930  0.020  1.080
 H40  C11  H2   single    0.930  0.020  1.080
 H40  C12  H3   single    0.930  0.020  1.080
 H40  C16  H4   single    0.970  0.020  1.090
 H40  C16  H5   single    0.970  0.020  1.090
 H40  C17  H6   single    0.970  0.020  1.090
 H40  C17  H7   single    0.970  0.020  1.090
 H40  C21  H8   single    0.970  0.020  1.090
 H40  C21  H9   single    0.970  0.020  1.090
 H40  C23  H10  single    0.970  0.020  1.090
 H40  C23  H11  single    0.970  0.020  1.090
 H40  C23  H12  single    0.970  0.020  1.090
 H40  C4   H13  single    0.930  0.020  1.080
 H40  C9   H14  single    0.930  0.020  1.080
 H40  C10  H15  single    0.930  0.020  1.080
 H40  N14  H16  single    0.890  0.020  1.040
 H40  O18  H17  single    0.850  0.020  0.980
 H40  N19  H18  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
 H40  N14  C1   N6   115.63  3.000
 H40  N6   C1   C2   121.33  3.000
 H40  N14  C1   C2   123.03  3.000
 H40  H1   C2   C3   120.26  3.000
 H40  H1   C2   C1   121.16  3.000
 H40  C3   C2   C1   118.59  3.000
 H40  S7   C3   C4   123.22  3.000
 H40  C4   C3   C2   120.21  3.000
 H40  S7   C3   C2   116.57  3.000
 H40  H2   C11  C13  119.72  3.000
 H40  H2   C11  C12  119.29  3.000
 H40  C13  C11  C12  120.99  3.000
 H40  H3   C12  C8   120.27  3.000
 H40  H3   C12  C11  119.58  3.000
 H40  C8   C12  C11  120.15  3.000
 H40  N19  C13  C10  124.47  3.000
 H40  N19  C13  C11  116.77  3.000
 H40  C10  C13  C11  118.76  3.000
 H40  H7   C17  H6   106.84  3.000
 H40  H7   C17  O18  112.16  3.000
 H40  H6   C17  O18  111.67  3.000
 H40  H7   C17  C16  107.98  3.000
 H40  H6   C17  C16  109.70  3.000
 H40  O18  C17  C16  108.43  3.000
 H40  O22  C20  N19  123.64  3.000
 H40  N19  C20  C21  113.17  3.000
 H40  O22  C20  C21  123.19  3.000
 H40  H9   C21  H8   105.48  3.000
 H40  H9   C21  C23  110.34  3.000
 H40  H8   C21  C23  110.50  3.000
 H40  H9   C21  C20  107.98  3.000
 H40  H8   C21  C20  108.59  3.000
 H40  C23  C21  C20  113.59  3.000
 H40  H12  C23  H11  108.02  3.000
 H40  H12  C23  H10  107.66  3.000
 H40  H11  C23  H10  107.69  3.000
 H40  H12  C23  C21  111.79  3.000
 H40  H11  C23  C21  111.73  3.000
 H40  H10  C23  C21  109.78  3.000
 H40  H13  C4   C5   122.22  3.000
 H40  H13  C4   C3   122.49  3.000
 H40  C5   C4   C3   115.29  3.000
 H40  BR1  C5   N6   115.35  3.000
 H40  BR1  C5   C4   118.01  3.000
 H40  N6   C5   C4   126.64  3.000
 H40  C5   N6   C1   117.93  3.000
 H40  C8   S7   C3   103.75  3.000
 H40  C9   C8   S7   120.62  3.000
 H40  S7   C8   C12  120.20  3.000
 H40  C9   C8   C12  119.13  3.000
 H40  H14  C9   C10  118.96  3.000
 H40  H14  C9   C8   119.87  3.000
 H40  C10  C9   C8   121.16  3.000
 H40  H15  C10  C9   119.10  3.000
 H40  H15  C10  C13  121.09  3.000
 H40  C9   C10  C13  119.81  3.000
 H40  H16  N14  C16  117.14  3.000
 H40  H16  N14  C1   115.00  3.000
 H40  C16  N14  C1   124.86  3.000
 H40  H17  O18  C17  108.36  3.000
 H40  H18  N19  C20  115.60  3.000
 H40  H18  N19  C13  114.82  3.000
 H40  C20  N19  C13  129.57  3.000
 H40  H5   C16  H4   106.01  3.000
 H40  H5   C16  N14  107.31  3.000
 H40  H4   C16  N14  110.19  3.000
 H40  H5   C16  C17  109.57  3.000
 H40  H4   C16  C17  109.14  3.000
 H40  N14  C16  C17  114.28  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
 H40  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 H40  CONST_02  C4   C5   N6   C1      0.00   0.0  0
 H40  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 H40  CONST_04  C5   N6   C1   C2      0.00   0.0  0
 H40  CONST_05  N6   C1   C2   C3      0.00   0.0  0
 H40  CONST_06  N6   C5   C4   C3      0.00   0.0  0
 H40  CONST_07  C9   C10  C13  C11     0.00   0.0  0
 H40  CONST_08  C9   C8   C12  C11     0.00   0.0  0
 H40  CONST_09  C10  C9   C8   C12     0.00   0.0  0
 H40  CONST_10  C10  C13  C11  C12     0.00   0.0  0
 H40  CONST_11  C8   C9   C10  C13     0.00   0.0  0
 H40  CONST_12  C8   C12  C11  C13     0.00   0.0  0
 H40  CONST_13  S7   C3   C2   C1    180.00   0.0  0
 H40  CONST_14  BR1  C5   N6   C1    180.00   0.0  0
 H40  CONST_15  N14  C1   C2   C3    180.00   0.0  0
 H40  CONST_16  BR1  C5   C4   C3    180.00   0.0  0
 H40  CONST_17  S7   C8   C12  C11   180.00   0.0  0
 H40  CONST_18  N19  C13  C11  C12   180.00   0.0  0
 H40  CONST_19  S7   C3   C4   C5    180.00   0.0  0
 H40  CONST_20  N14  C1   N6   C5    180.00   0.0  0
 H40  CONST_21  C10  C9   C8   S7    180.00   0.0  0
 H40  CONST_22  N19  C13  C10  C9    180.00   0.0  0
 H40  CONST_23  H13  C4   C3   C2    180.00   0.0  0
 H40  CONST_24  H15  C10  C13  C11   180.00   0.0  0
 H40  CONST_25  H14  C9   C8   C12   180.00   0.0  0
 H40  CONST_26  H14  C9   C10  C13   180.00   0.0  0
 H40  CONST_27  H3   C12  C11  C13   180.00   0.0  0
 H40  CONST_28  H1   C2   C3   C4    180.00   0.0  0
 H40  CONST_29  H1   C2   C1   N6    180.00   0.0  0
 H40  CONST_30  H13  C4   C5   N6    180.00   0.0  0
 H40  CONST_31  H15  C10  C9   C8    180.00   0.0  0
 H40  CONST_32  H2   C11  C12  C8    180.00   0.0  0
 H40  CONST_33  H3   C12  C8   C9    180.00   0.0  0
 H40  CONST_34  H2   C11  C13  C10   180.00   0.0  0
 H40  CONST_35  C16  N14  C1   C2      0.00   0.0  0
 H40  CONST_36  C20  N19  C13  C11   180.00   0.0  0
 H40  CONST_37  N6   C1   N14  C16   180.00   0.0  0
 H40  CONST_38  C10  C13  N19  C20     0.00   0.0  0
 H40  CONST_39  H16  N14  C1   C2    180.00   0.0  0
 H40  CONST_40  H18  N19  C13  C11     0.00   0.0  0
 H40  CONST_41  H16  N14  C1   N6      0.00   0.0  0
 H40  CONST_42  H18  N19  C13  C10   180.00   0.0  0
 H40  CONST_43  O22  C20  N19  C13     0.00   0.0  0
 H40  CONST_44  C21  C20  N19  C13   180.00   0.0  0
 H40  CONST_45  H18  N19  C20  C21     0.00   0.0  0
 H40  CONST_46  H18  N19  C20  O22   180.00   0.0  0
 H40  Var_01    C8   S7   C3   C2    178.23  30.0  2
 H40  Var_02    C9   C8   S7   C3     88.26  30.0  2
 H40  Var_03    C12  C8   S7   C3    -94.26  30.0  2
 H40  Var_04    C8   S7   C3   C4     -2.08  30.0  2
 H40  Var_05    C17  C16  N14  C1    -74.08  30.0  2
 H40  Var_06    H4   C16  N14  C1     49.23  30.0  2
 H40  Var_07    H5   C16  N14  C1    164.22  30.0  2
 H40  Var_08    O22  C20  C21  C23    -4.16  30.0  2
 H40  Var_09    N19  C20  C21  C23   176.15  30.0  2
 H40  Var_10    O18  C17  C16  N14   -61.37  30.0  3
 H40  Var_11    H16  N14  C16  C17    85.27  30.0  3
 H40  Var_12    H10  C23  C21  C20   179.93  30.0  3
 H40  Var_13    H11  C23  C21  C20   -60.67  30.0  3
 H40  Var_14    H12  C23  C21  C20    60.53  30.0  3
 H40  Var_15    H6   C17  C16  N14    60.81  30.0  3
 H40  Var_16    H7   C17  C16  N14   176.89  30.0  3
 H40  Var_17    H4   C16  C17  O18   174.75  30.0  1
 H40  Var_18    H5   C16  C17  O18    59.08  30.0  1
 H40  Var_19    H8   C21  C20  N19    52.77  30.0  3
 H40  Var_20    H9   C21  C20  N19   -61.13  30.0  3
 H40  Var_21    H8   C21  C20  O22  -127.54  30.0  3
 H40  Var_22    H9   C21  C20  O22   118.56  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
 H40  plan-1  C1   0.020
 H40  plan-1  C2   0.020
 H40  plan-1  C3   0.020
 H40  plan-1  C4   0.020
 H40  plan-1  C5   0.020
 H40  plan-1  N6   0.020
 H40  plan-1  S7   0.020
 H40  plan-1  N14  0.020
 H40  plan-1  BR1  0.020
 H40  plan-1  H1   0.020
 H40  plan-1  H13  0.020
 H40  plan-2  C11  0.020
 H40  plan-2  C12  0.020
 H40  plan-2  C13  0.020
 H40  plan-2  S7   0.020
 H40  plan-2  C8   0.020
 H40  plan-2  C9   0.020
 H40  plan-2  C10  0.020
 H40  plan-2  H2   0.020
 H40  plan-2  H3   0.020
 H40  plan-2  H14  0.020
 H40  plan-2  H15  0.020
 H40  plan-2  N19  0.020
 H40  plan-3  C13  0.020
 H40  plan-3  C20  0.020
 H40  plan-3  C21  0.020
 H40  plan-3  O22  0.020
 H40  plan-3  H18  0.020
 H40  plan-3  N19  0.020
 H40  plan-4  C1   0.020
 H40  plan-4  N14  0.020
 H40  plan-4  H16  0.020
 H40  plan-4  C16  0.020

