# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:16:52 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-{5-[(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)methoxy]-2-methylpentan-2-yl}benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CCCOCN1C=CC(=O)NC1=O)N[S](=O)(=O)c2ccccc2
#
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
 MSJ  MSJ  N-{5-[(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)methoxy]-2-methylpentan-2-yl}benzenesulfonamide  ligand  49  26  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MSJ
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
 MSJ  O1    O  O     0  -0.463   5.7407  -3.4020   0.9807
 MSJ  C2    C  CR6   0   0.567   5.4344  -2.2298   0.8692
 MSJ  N3    N  NR16  0  -0.731   5.4743  -1.6064  -0.3697
 MSJ  C4    C  CR6   0   0.740   5.1600  -0.3080  -0.6713
 MSJ  N5    N  NR6   0  -0.544   4.7592   0.4545   0.4094
 MSJ  C6    C  CR16  0   0.086   4.6948  -0.0821   1.6633
 MSJ  C7    C  CR16  0  -0.504   5.0091  -1.3585   1.9375
 MSJ  O8    O  O     0  -0.474   5.2339   0.1367  -1.7962
 MSJ  C9    C  CH2   0  -0.055   4.3559   1.8356   0.1606
 MSJ  C10   C  CT    0   0.148  -1.8266   1.5492  -0.3752
 MSJ  O10   O  O2    0  -0.468   3.1290   1.9304  -0.4708
 MSJ  C11   C  CH2   0  -0.139   2.0138   1.6135   0.3427
 MSJ  C12   C  CH2   0  -0.482   0.7529   1.7828  -0.4813
 MSJ  S12   S  S     0   1.381  -4.3333   0.6463   0.4625
 MSJ  C13   C  CH2   0  -0.467  -0.4748   1.4388   0.3519
 MSJ  O13   O  OS    0  -0.652  -4.9733   1.4215  -0.5892
 MSJ  C14   C  CR6   0  -0.169  -4.2520  -1.0392  -0.0969
 MSJ  C15   C  CR16  0  -0.241  -3.5835  -1.9680   0.6919
 MSJ  C16   C  CR16  0  -0.244  -3.5197  -3.2866   0.2734
 MSJ  C17   C  CR16  0  -0.241  -4.1273  -3.6709  -0.9169
 MSJ  N17   N  NC1   0  -0.782  -2.8110   1.1785   0.6686
 MSJ  C18   C  CR16  0  -0.243  -4.7994  -2.7358  -1.6903
 MSJ  O19   O  OS    0  -0.667  -4.9173   0.6193   1.7960
 MSJ  C20   C  CR16  0  -0.243  -4.8663  -1.4098  -1.2827
 MSJ  C25   C  CH3   0  -0.637  -2.0914   2.9851  -0.8230
 MSJ  C26   C  CH3   0  -0.682  -1.8689   0.5946  -1.5656
 MSJ  HN3   H  HNR6  0   0.426   5.7665  -2.1737  -1.1564
 MSJ  H6    H  HCR6  0   0.326   4.3751   0.5963   2.4425
 MSJ  H7    H  HCR6  0   0.294   4.9468  -1.7364   2.9461
 MSJ  H9    H  HCH2  0   0.248   4.3673   2.3457   1.1293
 MSJ  H9A   H  HCH2  0   0.274   5.0938   2.3053  -0.4852
 MSJ  H11   H  HCH2  0   0.214   2.0738   0.5802   0.7083
 MSJ  H11A  H  HCH2  0   0.214   1.9900   2.2696   1.2234
 MSJ  H12   H  HCH2  0   0.241   0.6960   2.8103  -0.8479
 MSJ  H12A  H  HCH2  0   0.241   0.8162   1.1291  -1.3536
 MSJ  H13   H  HCH2  0   0.246  -0.5043   2.0949   1.2294
 MSJ  H13A  H  HCH2  0   0.244  -0.3722   0.4143   0.7270
 MSJ  H15   H  HCR6  0   0.281  -3.1042  -1.6744   1.6173
 MSJ  H16   H  HCR6  0   0.273  -2.9951  -4.0153   0.8764
 MSJ  H17   H  HCR6  0   0.271  -4.0746  -4.7020  -1.2406
 MSJ  HN17  H  HNC1  0   0.423  -2.4380   0.9583   1.5830
 MSJ  H18   H  HCR6  0   0.271  -5.2728  -3.0340  -2.6159
 MSJ  H20   H  HCR6  0   0.281  -5.3860  -0.6824  -1.8905
 MSJ  H25   H  HCH3  0   0.228  -1.3876   3.2915  -1.5968
 MSJ  H25A  H  HCH3  0   0.244  -3.0939   3.0870  -1.2350
 MSJ  H25B  H  HCH3  0   0.231  -1.9958   3.6745   0.0169
 MSJ  H26   H  HCH3  0   0.241  -1.6665  -0.4326  -1.2603
 MSJ  H26A  H  HCH3  0   0.243  -2.8284   0.6207  -2.0815
 MSJ  H26B  H  HCH3  0   0.251  -1.1171   0.8788  -2.3006

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
 MSJ  O1   C2    double    1.217  0.020  1.217
 MSJ  C2   N3    single    1.388  0.020  1.388
 MSJ  C2   C7    single    1.443  0.020  1.443
 MSJ  N3   C4    single    1.370  0.020  1.370
 MSJ  C4   N5    single    1.382  0.020  1.382
 MSJ  C4   O8    double    1.212  0.020  1.212
 MSJ  N5   C6    single    1.365  0.020  1.365
 MSJ  N5   C9    single    1.460  0.020  1.460
 MSJ  C6   C7    double    1.343  0.020  1.343
 MSJ  C9   O10   single    1.383  0.020  1.383
 MSJ  C10  C13   single    1.539  0.020  1.539
 MSJ  C10  N17   single    1.482  0.020  1.482
 MSJ  C10  C25   single    1.527  0.020  1.527
 MSJ  C10  C26   single    1.526  0.020  1.526
 MSJ  O10  C11   single    1.416  0.020  1.416
 MSJ  C11  C12   single    1.516  0.020  1.516
 MSJ  C12  C13   single    1.523  0.020  1.523
 MSJ  S12  O13   double    1.455  0.020  1.455
 MSJ  S12  C14   single    1.778  0.020  1.778
 MSJ  S12  N17   single    1.626  0.020  1.626
 MSJ  S12  O19   double    1.456  0.020  1.456
 MSJ  C14  C15   aromatic  1.390  0.020  1.390
 MSJ  C14  C20   aromatic  1.386  0.020  1.386
 MSJ  C15  C16   aromatic  1.385  0.020  1.385
 MSJ  C16  C17   aromatic  1.391  0.020  1.391
 MSJ  C17  C18   aromatic  1.387  0.020  1.387
 MSJ  C18  C20   aromatic  1.389  0.020  1.389
 MSJ  N3   HN3   single    0.860  0.020  1.020
 MSJ  C6   H6    single    0.930  0.020  1.080
 MSJ  C7   H7    single    0.930  0.020  1.080
 MSJ  C9   H9    single    0.970  0.020  1.090
 MSJ  C9   H9A   single    0.970  0.020  1.090
 MSJ  C11  H11   single    0.970  0.020  1.090
 MSJ  C11  H11A  single    0.970  0.020  1.090
 MSJ  C12  H12   single    0.970  0.020  1.090
 MSJ  C12  H12A  single    0.970  0.020  1.090
 MSJ  C13  H13   single    0.970  0.020  1.090
 MSJ  C13  H13A  single    0.970  0.020  1.090
 MSJ  C15  H15   single    0.930  0.020  1.080
 MSJ  C16  H16   single    0.930  0.020  1.080
 MSJ  C17  H17   single    0.930  0.020  1.080
 MSJ  N17  HN17  single    0.890  0.020  1.040
 MSJ  C18  H18   single    0.930  0.020  1.080
 MSJ  C20  H20   single    0.930  0.020  1.080
 MSJ  C25  H25   single    0.970  0.020  1.090
 MSJ  C25  H25A  single    0.970  0.020  1.090
 MSJ  C25  H25B  single    0.970  0.020  1.090
 MSJ  C26  H26   single    0.970  0.020  1.090
 MSJ  C26  H26A  single    0.970  0.020  1.090
 MSJ  C26  H26B  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
 MSJ  C7    C2   N3    113.48  3.000
 MSJ  C7    C2   O1    126.03  3.000
 MSJ  N3    C2   O1    120.49  3.000
 MSJ  HN3   N3   C4    115.22  3.000
 MSJ  HN3   N3   C2    116.76  3.000
 MSJ  C4    N3   C2    128.02  3.000
 MSJ  O8    C4   N5    122.76  3.000
 MSJ  O8    C4   N3    122.57  3.000
 MSJ  N5    C4   N3    114.67  3.000
 MSJ  C9    N5   C6    121.01  3.000
 MSJ  C9    N5   C4    117.95  3.000
 MSJ  C6    N5   C4    121.00  3.000
 MSJ  H6    C6   C7    121.21  3.000
 MSJ  H6    C6   N5    115.42  3.000
 MSJ  C7    C6   N5    123.37  3.000
 MSJ  H7    C7   C6    120.69  3.000
 MSJ  H7    C7   C2    119.85  3.000
 MSJ  C6    C7   C2    119.46  3.000
 MSJ  H9A   C9   H9    108.49  3.000
 MSJ  H9A   C9   O10   107.53  3.000
 MSJ  H9    C9   O10   112.41  3.000
 MSJ  H9A   C9   N5    108.81  3.000
 MSJ  H9    C9   N5    106.69  3.000
 MSJ  O10   C9   N5    112.81  3.000
 MSJ  C26   C10  C25   110.77  3.000
 MSJ  C26   C10  N17   111.99  3.000
 MSJ  C25   C10  N17   109.06  3.000
 MSJ  C26   C10  C13   110.36  3.000
 MSJ  C25   C10  C13   111.00  3.000
 MSJ  N17   C10  C13   103.46  3.000
 MSJ  C11   O10  C9    114.89  3.000
 MSJ  H11A  C11  H11   107.24  3.000
 MSJ  H11A  C11  C12   110.55  3.000
 MSJ  H11   C11  C12   109.37  3.000
 MSJ  H11A  C11  O10   110.12  3.000
 MSJ  H11   C11  O10   111.03  3.000
 MSJ  C12   C11  O10   108.53  3.000
 MSJ  H12A  C12  H12   107.34  3.000
 MSJ  H12A  C12  C13   110.39  3.000
 MSJ  H12   C12  C13   110.74  3.000
 MSJ  H12A  C12  C11   108.62  3.000
 MSJ  H12   C12  C11   109.32  3.000
 MSJ  C13   C12  C11   110.36  3.000
 MSJ  O19   S12  N17   105.40  3.000
 MSJ  O19   S12  C14   106.80  3.000
 MSJ  N17   S12  C14   107.91  3.000
 MSJ  O19   S12  O13   119.70  3.000
 MSJ  N17   S12  O13   109.22  3.000
 MSJ  C14   S12  O13   107.33  3.000
 MSJ  H13A  C13  H13   106.74  3.000
 MSJ  H13A  C13  C12   108.84  3.000
 MSJ  H13   C13  C12   108.93  3.000
 MSJ  H13A  C13  C10   108.12  3.000
 MSJ  H13   C13  C10   108.16  3.000
 MSJ  C12   C13  C10   115.68  3.000
 MSJ  C20   C14  C15   121.34  3.000
 MSJ  C20   C14  S12   120.17  3.000
 MSJ  C15   C14  S12   118.48  3.000
 MSJ  H15   C15  C16   119.74  3.000
 MSJ  H15   C15  C14   121.12  3.000
 MSJ  C16   C15  C14   119.14  3.000
 MSJ  H16   C16  C17   120.20  3.000
 MSJ  H16   C16  C15   119.69  3.000
 MSJ  C17   C16  C15   120.11  3.000
 MSJ  H17   C17  C18   119.94  3.000
 MSJ  H17   C17  C16   119.88  3.000
 MSJ  C18   C17  C16   120.18  3.000
 MSJ  HN17  N17  S12   112.86  3.000
 MSJ  HN17  N17  C10   116.50  3.000
 MSJ  S12   N17  C10   127.92  3.000
 MSJ  H18   C18  C20   119.55  3.000
 MSJ  H18   C18  C17   120.23  3.000
 MSJ  C20   C18  C17   120.22  3.000
 MSJ  H20   C20  C18   120.04  3.000
 MSJ  H20   C20  C14   120.94  3.000
 MSJ  C18   C20  C14   119.02  3.000
 MSJ  H25B  C25  H25A  108.24  3.000
 MSJ  H25B  C25  H25   108.20  3.000
 MSJ  H25A  C25  H25   107.43  3.000
 MSJ  H25B  C25  C10   110.69  3.000
 MSJ  H25A  C25  C10   111.02  3.000
 MSJ  H25   C25  C10   111.13  3.000
 MSJ  H26B  C26  H26A  106.38  3.000
 MSJ  H26B  C26  H26   107.85  3.000
 MSJ  H26A  C26  H26   108.57  3.000
 MSJ  H26B  C26  C10   110.12  3.000
 MSJ  H26A  C26  C10   112.25  3.000
 MSJ  H26   C26  C10   111.45  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
 MSJ  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 MSJ  CONST_02  C17  C18  C20  C14     0.00   0.0  0
 MSJ  CONST_03  C18  C20  C14  C15     0.00   0.0  0
 MSJ  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 MSJ  CONST_05  C20  C14  C15  C16     0.00   0.0  0
 MSJ  CONST_06  C20  C18  C17  C16     0.00   0.0  0
 MSJ  CONST_07  N5   C4   N3   C2      0.00   0.0  0
 MSJ  CONST_08  C6   N5   C4   N3      0.00   0.0  0
 MSJ  CONST_09  C7   C2   N3   C4      0.00   0.0  0
 MSJ  CONST_10  C16  C15  C14  S12   180.00   0.0  0
 MSJ  CONST_11  C18  C20  C14  S12   180.00   0.0  0
 MSJ  CONST_12  C4   N3   C2   O1    180.00   0.0  0
 MSJ  CONST_13  O8   C4   N3   C2    180.00   0.0  0
 MSJ  CONST_14  C9   N5   C4   N3    180.00   0.0  0
 MSJ  CONST_15  O8   C4   N5   C6    180.00   0.0  0
 MSJ  CONST_16  H16  C16  C15  C14   180.00   0.0  0
 MSJ  CONST_17  H18  C18  C20  C14   180.00   0.0  0
 MSJ  CONST_18  H20  C20  C14  C15   180.00   0.0  0
 MSJ  CONST_19  H17  C17  C16  C15   180.00   0.0  0
 MSJ  CONST_20  H15  C15  C16  C17   180.00   0.0  0
 MSJ  CONST_21  HN3  N3   C4   N5    180.00   0.0  0
 MSJ  CONST_22  C9   N5   C4   O8      0.00   0.0  0
 MSJ  Var_01    O10  C9   N5   C4     72.59  30.0  3
 MSJ  Var_02    C15  C14  S12  O13   175.02  30.0  2
 MSJ  Var_03    C14  S12  N17  C10    74.25  30.0  1
 MSJ  Var_04    C12  C11  O10  C9    179.20  30.0  3
 MSJ  Var_05    C11  C12  C13  C10  -179.12  30.0  1
 MSJ  Var_06    C13  C12  C11  O10   179.46  30.0  3
 MSJ  Var_07    N17  C10  C13  C12  -179.36  30.0  1
 MSJ  Var_08    C13  C10  N17  S12  -158.93  30.0  1
 MSJ  Var_09    H25  C25  C10  C13    66.96  30.0  3
 MSJ  Var_10    H26  C26  C10  C13    55.83  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
 MSJ  plan-1  O1   0.020
 MSJ  plan-1  C2   0.020
 MSJ  plan-1  N3   0.020
 MSJ  plan-1  C4   0.020
 MSJ  plan-1  N5   0.020
 MSJ  plan-1  C6   0.020
 MSJ  plan-1  C7   0.020
 MSJ  plan-1  O8   0.020
 MSJ  plan-1  C9   0.020
 MSJ  plan-1  HN3  0.020
 MSJ  plan-1  H6   0.020
 MSJ  plan-1  H7   0.020
 MSJ  plan-2  S12  0.020
 MSJ  plan-2  C14  0.020
 MSJ  plan-2  C15  0.020
 MSJ  plan-2  C16  0.020
 MSJ  plan-2  C17  0.020
 MSJ  plan-2  C18  0.020
 MSJ  plan-2  C20  0.020
 MSJ  plan-2  H15  0.020
 MSJ  plan-2  H16  0.020
 MSJ  plan-2  H17  0.020
 MSJ  plan-2  H18  0.020
 MSJ  plan-2  H20  0.020

