# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 15:23:14 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[2-(2-chlorophenyl)-2,2-difluoroethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCNCC(F)(F)c3ccccc3Cl)c1
#
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
 8BX  8BX  6-{[(3R,4R)-4-(2-{[2-(2-chlorophenyl)-2,2-difluoroethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8BX
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
 8BX  N01   N   N     0  -0.484  -5.2745   0.7053  -1.1217
 8BX  C02   C   CR6   0   0.436  -6.3065   1.5337  -1.0139
 8BX  N02   N   NH2   0  -0.839  -7.3623   1.3235  -1.8569
 8BX  C03   C   CR16  0  -0.448  -6.3498   2.5596  -0.0534
 8BX  C04   C   CR6   0   0.204  -5.2845   2.7140   0.8094
 8BX  C05   C   CR16  0  -0.428  -4.2025   1.8346   0.6850
 8BX  C06   C   CR6   0   0.277  -4.2421   0.8513  -0.2870
 8BX  C07   C   CH3   0  -0.728  -5.2774   3.7843   1.8576
 8BX  C08   C   CH2   0  -0.492  -3.1186  -0.1335  -0.4485
 8BX  O09   O   O2    0  -0.489  -1.2812  -2.1120  -0.6857
 8BX  N1'   N   NH1   0  -0.612  -3.5620  -2.9325   1.8984
 8BX  C10   C   CH2   0  -0.161  -0.3326  -3.0861  -1.0522
 8BX  C11   C   CH2   0  -0.298   0.8619  -2.3867  -1.6596
 8BX  N12   N   NH1   0  -0.616   1.5264  -1.5504  -0.6774
 8BX  C13   C   CH2   0  -0.381   2.6372  -0.8183  -1.2353
 8BX  C14   C   CT    0   0.771   3.4486  -0.1609  -0.1328
 8BX  F15   F   F     0  -0.358   2.6093   0.6421   0.5967
 8BX  F16   F   F     0  -0.348   3.8803  -1.1217   0.7354
 8BX  C2'   C   CH2   0  -0.270  -3.8400  -1.5532   1.5418
 8BX  C21   C   CR6   0   0.033   4.6367   0.6600  -0.5742
 8BX  C22   C   CR6   0  -0.067   5.4487   1.3264   0.3473
 8BX  CL22  CL  CL    0  -0.117   5.1403   1.2545   2.0512
 8BX  C23   C   CR16  0  -0.199   6.5415   2.0734  -0.0629
 8BX  C24   C   CR16  0  -0.263   6.8480   2.1654  -1.4120
 8BX  C25   C   CR16  0  -0.225   6.0609   1.5101  -2.3438
 8BX  C26   C   CR16  0  -0.333   4.9687   0.7675  -1.9212
 8BX  C3'   C   CH1   0  -0.297  -3.5333  -1.5197   0.0414
 8BX  C4'   C   CH1   0   0.080  -2.4671  -2.6327  -0.1460
 8BX  C5'   C   CH2   0  -0.317  -2.2923  -3.2267   1.2622
 8BX  HN02  H   HNH2  0   0.378  -7.1606   0.7792  -2.6799
 8BX  HN0A  H   HNH2  0   0.386  -7.9784   2.1011  -2.0275
 8BX  H03   H   HCR6  0   0.254  -7.2098   3.2163   0.0003
 8BX  H05   H   HCR6  0   0.241  -3.3441   1.9204   1.3400
 8BX  H07   H   HCH3  0   0.252  -5.2646   3.3451   2.8564
 8BX  H07A  H   HCH3  0   0.250  -4.3868   4.4081   1.7733
 8BX  H07B  H   HCH3  0   0.246  -6.1519   4.4285   1.7848
 8BX  H08   H   HCH2  0   0.246  -2.8379  -0.1772  -1.5030
 8BX  H08A  H   HCH2  0   0.239  -2.2442   0.2135   0.1053
 8BX  HN1'  H   HNH1  0   0.351  -3.5191  -3.0663   2.8999
 8BX  H10   H   HCH2  0   0.205  -0.0060  -3.6735  -0.1841
 8BX  H10A  H   HCH2  0   0.209  -0.7582  -3.7884  -1.7819
 8BX  H11   H   HCH2  0   0.234   1.5604  -3.1535  -2.0048
 8BX  H11A  H   HCH2  0   0.203   0.5406  -1.8295  -2.5535
 8BX  HN12  H   HNH1  0   0.349   0.8501  -0.9000  -0.2980
 8BX  H13   H   HCH2  0   0.258   3.2879  -1.5149  -1.7696
 8BX  H13A  H   HCH2  0   0.235   2.3349  -0.0487  -1.9599
 8BX  H2'   H   HCH2  0   0.231  -4.8724  -1.2824   1.7683
 8BX  H2'A  H   HCH2  0   0.195  -3.1884  -0.8355   2.0673
 8BX  H23   H   HCR6  0   0.286   7.1522   2.5814   0.6709
 8BX  H24   H   HCR6  0   0.275   7.7035   2.7481  -1.7260
 8BX  H25   H   HCR6  0   0.272   6.2917   1.5721  -3.3983
 8BX  H26   H   HCR6  0   0.276   4.3700   0.2663  -2.6686
 8BX  H3'   H   HCH1  0   0.252  -4.4319  -1.8144  -0.5060
 8BX  H4'   H   HCH1  0   0.213  -2.8641  -3.4021  -0.8223
 8BX  H5'   H   HCH2  0   0.200  -1.4380  -2.7247   1.7453
 8BX  H5'A  H   HCH2  0   0.232  -2.0904  -4.2995   1.2593

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
 8BX  C02  N01   aromatic  1.328  0.020  1.328
 8BX  C06  N01   aromatic  1.336  0.020  1.336
 8BX  C03  C02   aromatic  1.406  0.020  1.406
 8BX  C02  N02   single    1.367  0.020  1.367
 8BX  N02  HN02  single    0.890  0.020  1.040
 8BX  N02  HN0A  single    0.890  0.020  1.040
 8BX  C04  C03   aromatic  1.380  0.020  1.380
 8BX  C03  H03   single    0.930  0.020  1.080
 8BX  C07  C04   single    1.498  0.020  1.498
 8BX  C04  C05   aromatic  1.400  0.020  1.400
 8BX  C05  C06   aromatic  1.383  0.020  1.383
 8BX  C05  H05   single    0.930  0.020  1.080
 8BX  C06  C08   single    1.503  0.020  1.503
 8BX  C07  H07   single    0.970  0.020  1.090
 8BX  C07  H07A  single    0.970  0.020  1.090
 8BX  C07  H07B  single    0.970  0.020  1.090
 8BX  C3'  C08   single    1.528  0.020  1.528
 8BX  C08  H08   single    0.970  0.020  1.090
 8BX  C08  H08A  single    0.970  0.020  1.090
 8BX  C4'  O09   single    1.403  0.020  1.403
 8BX  O09  C10   single    1.408  0.020  1.408
 8BX  N1'  C2'   single    1.451  0.020  1.451
 8BX  N1'  C5'   single    1.450  0.020  1.450
 8BX  N1'  HN1'  single    0.890  0.020  1.040
 8BX  C10  C11   single    1.512  0.020  1.512
 8BX  C10  H10   single    0.970  0.020  1.090
 8BX  C10  H10A  single    0.970  0.020  1.090
 8BX  N12  C11   single    1.451  0.020  1.451
 8BX  C11  H11   single    0.970  0.020  1.090
 8BX  C11  H11A  single    0.970  0.020  1.090
 8BX  N12  C13   single    1.443  0.020  1.443
 8BX  N12  HN12  single    0.890  0.020  1.040
 8BX  C13  C14   single    1.519  0.020  1.519
 8BX  C13  H13   single    0.970  0.020  1.090
 8BX  C13  H13A  single    0.970  0.020  1.090
 8BX  F16  C14   single    1.365  0.020  1.365
 8BX  C14  C21   single    1.510  0.020  1.510
 8BX  C14  F15   single    1.372  0.020  1.372
 8BX  C2'  C3'   single    1.532  0.020  1.532
 8BX  C2'  H2'   single    0.970  0.020  1.090
 8BX  C2'  H2'A  single    0.970  0.020  1.090
 8BX  C26  C21   aromatic  1.391  0.020  1.391
 8BX  C21  C22   aromatic  1.397  0.020  1.397
 8BX  C22  C23   aromatic  1.386  0.020  1.386
 8BX  C22  CL22  single    1.733  0.020  1.733
 8BX  C24  C23   aromatic  1.386  0.020  1.386
 8BX  C23  H23   single    0.930  0.020  1.080
 8BX  C25  C24   aromatic  1.385  0.020  1.385
 8BX  C24  H24   single    0.930  0.020  1.080
 8BX  C26  C25   aromatic  1.387  0.020  1.387
 8BX  C25  H25   single    0.930  0.020  1.080
 8BX  C26  H26   single    0.930  0.020  1.080
 8BX  C3'  C4'   single    1.553  0.020  1.553
 8BX  C3'  H3'   single    0.970  0.020  1.090
 8BX  C5'  C4'   single    1.538  0.020  1.538
 8BX  C4'  H4'   single    0.970  0.020  1.090
 8BX  C5'  H5'   single    0.970  0.020  1.090
 8BX  C5'  H5'A  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
 8BX  C06   N01  C02   118.81  3.000
 8BX  C03   C02  N02   120.64  3.000
 8BX  N02   C02  N01   117.01  3.000
 8BX  C03   C02  N01   122.32  3.000
 8BX  HN0A  N02  HN02  113.68  3.000
 8BX  HN0A  N02  C02   117.28  3.000
 8BX  HN02  N02  C02   115.61  3.000
 8BX  H03   C03  C04   120.94  3.000
 8BX  H03   C03  C02   120.03  3.000
 8BX  C04   C03  C02   119.02  3.000
 8BX  C07   C04  C05   120.49  3.000
 8BX  C05   C04  C03   118.10  3.000
 8BX  C07   C04  C03   121.41  3.000
 8BX  H05   C05  C06   120.26  3.000
 8BX  H05   C05  C04   120.60  3.000
 8BX  C06   C05  C04   119.14  3.000
 8BX  C08   C06  C05   121.33  3.000
 8BX  C08   C06  N01   116.05  3.000
 8BX  C05   C06  N01   122.62  3.000
 8BX  H07B  C07  H07A  108.21  3.000
 8BX  H07B  C07  H07   107.99  3.000
 8BX  H07A  C07  H07   106.94  3.000
 8BX  H07B  C07  C04   111.85  3.000
 8BX  H07A  C07  C04   111.00  3.000
 8BX  H07   C07  C04   110.67  3.000
 8BX  H08A  C08  H08   107.26  3.000
 8BX  H08A  C08  C3'   110.07  3.000
 8BX  H08   C08  C3'   110.06  3.000
 8BX  H08A  C08  C06   109.64  3.000
 8BX  H08   C08  C06   108.80  3.000
 8BX  C3'   C08  C06   110.93  3.000
 8BX  C4'   O09  C10   114.38  3.000
 8BX  HN1'  N1'  C5'   111.74  3.000
 8BX  HN1'  N1'  C2'   112.16  3.000
 8BX  C5'   N1'  C2'   104.64  3.000
 8BX  H10A  C10  H10   107.36  3.000
 8BX  H10A  C10  C11   109.57  3.000
 8BX  H10   C10  C11   109.28  3.000
 8BX  H10A  C10  O09   110.74  3.000
 8BX  H10   C10  O09   111.39  3.000
 8BX  C11   C10  O09   108.48  3.000
 8BX  H11A  C11  H11   106.56  3.000
 8BX  H11A  C11  N12   113.05  3.000
 8BX  H11   C11  N12   108.99  3.000
 8BX  H11A  C11  C10   109.25  3.000
 8BX  H11   C11  C10   107.90  3.000
 8BX  N12   C11  C10   110.89  3.000
 8BX  HN12  N12  C13   109.47  3.000
 8BX  HN12  N12  C11   108.55  3.000
 8BX  C13   N12  C11   112.54  3.000
 8BX  H13A  C13  H13   106.72  3.000
 8BX  H13A  C13  C14   108.81  3.000
 8BX  H13   C13  C14   108.22  3.000
 8BX  H13A  C13  N12   113.48  3.000
 8BX  H13   C13  N12   108.91  3.000
 8BX  C14   C13  N12   110.51  3.000
 8BX  C21   C14  F16   108.65  3.000
 8BX  C21   C14  F15   108.58  3.000
 8BX  F16   C14  F15   105.50  3.000
 8BX  F15   C14  C13   108.22  3.000
 8BX  C21   C14  C13   116.33  3.000
 8BX  F16   C14  C13   109.03  3.000
 8BX  H2'A  C2'  H2'   107.38  3.000
 8BX  H2'A  C2'  C3'   109.53  3.000
 8BX  H2'   C2'  C3'   112.79  3.000
 8BX  H2'A  C2'  N1'   112.85  3.000
 8BX  H2'   C2'  N1'   111.47  3.000
 8BX  C3'   C2'  N1'   102.89  3.000
 8BX  C26   C21  C22   117.57  3.000
 8BX  C22   C21  C14   121.58  3.000
 8BX  C26   C21  C14   120.85  3.000
 8BX  C23   C22  CL22  116.99  3.000
 8BX  CL22  C22  C21   121.68  3.000
 8BX  C23   C22  C21   121.34  3.000
 8BX  H23   C23  C24   120.28  3.000
 8BX  H23   C23  C22   119.84  3.000
 8BX  C24   C23  C22   119.88  3.000
 8BX  H24   C24  C25   120.61  3.000
 8BX  H24   C24  C23   119.54  3.000
 8BX  C25   C24  C23   119.85  3.000
 8BX  H25   C25  C26   119.74  3.000
 8BX  H25   C25  C24   120.52  3.000
 8BX  C26   C25  C24   119.74  3.000
 8BX  H26   C26  C25   118.29  3.000
 8BX  H26   C26  C21   120.09  3.000
 8BX  C25   C26  C21   121.62  3.000
 8BX  H3'   C3'  C4'   108.12  3.000
 8BX  H3'   C3'  C2'   108.67  3.000
 8BX  C4'   C3'  C2'   103.88  3.000
 8BX  H3'   C3'  C08   107.90  3.000
 8BX  C4'   C3'  C08   115.18  3.000
 8BX  C2'   C3'  C08   112.85  3.000
 8BX  H4'   C4'  C5'   109.52  3.000
 8BX  H4'   C4'  C3'   109.15  3.000
 8BX  C5'   C4'  C3'   104.14  3.000
 8BX  H4'   C4'  O09   109.18  3.000
 8BX  C5'   C4'  O09   113.54  3.000
 8BX  C3'   C4'  O09   111.15  3.000
 8BX  H5'A  C5'  H5'   107.78  3.000
 8BX  H5'A  C5'  C4'   113.46  3.000
 8BX  H5'   C5'  C4'   108.26  3.000
 8BX  H5'A  C5'  N1'   111.25  3.000
 8BX  H5'   C5'  N1'   113.19  3.000
 8BX  C4'   C5'  N1'   102.93  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
 8BX  CONST_01  C04  C03  C02  N01      0.00   0.0  0
 8BX  CONST_02  C04  C05  C06  N01      0.00   0.0  0
 8BX  CONST_03  C05  C06  N01  C02      0.00   0.0  0
 8BX  CONST_04  C05  C04  C03  C02      0.00   0.0  0
 8BX  CONST_05  C06  N01  C02  C03      0.00   0.0  0
 8BX  CONST_06  C06  C05  C04  C03      0.00   0.0  0
 8BX  CONST_07  C24  C25  C26  C21      0.00   0.0  0
 8BX  CONST_08  C24  C23  C22  C21      0.00   0.0  0
 8BX  CONST_09  C25  C26  C21  C22      0.00   0.0  0
 8BX  CONST_10  C25  C24  C23  C22      0.00   0.0  0
 8BX  CONST_11  C26  C21  C22  C23      0.00   0.0  0
 8BX  CONST_12  C26  C25  C24  C23      0.00   0.0  0
 8BX  CONST_13  C08  C06  N01  C02    180.00   0.0  0
 8BX  CONST_14  C07  C04  C03  C02    180.00   0.0  0
 8BX  CONST_15  C06  N01  C02  N02    180.00   0.0  0
 8BX  CONST_16  C04  C03  C02  N02    180.00   0.0  0
 8BX  CONST_17  C08  C06  C05  C04    180.00   0.0  0
 8BX  CONST_18  C07  C04  C05  C06    180.00   0.0  0
 8BX  CONST_19  C25  C26  C21  C14    180.00   0.0  0
 8BX  CONST_20  C23  C22  C21  C14    180.00   0.0  0
 8BX  CONST_21  C26  C21  C22  CL22   180.00   0.0  0
 8BX  CONST_22  C24  C23  C22  CL22   180.00   0.0  0
 8BX  CONST_23  H03  C03  C02  N01    180.00   0.0  0
 8BX  CONST_24  H05  C05  C06  N01    180.00   0.0  0
 8BX  CONST_25  H25  C25  C26  C21    180.00   0.0  0
 8BX  CONST_26  H23  C23  C22  C21    180.00   0.0  0
 8BX  CONST_27  H26  C26  C21  C22    180.00   0.0  0
 8BX  CONST_28  H24  C24  C23  C22    180.00   0.0  0
 8BX  Var_01    C4'  C5'  N1'  C2'    -44.72  30.0  1
 8BX  Var_02    C5'  N1'  C2'  C3'     45.86  30.0  1
 8BX  Var_03    C3'  C08  C06  N01    -71.55  30.0  2
 8BX  Var_04    C26  C21  C14  C13     -1.47  30.0  2
 8BX  Var_05    H07  C07  C04  C03    116.20  30.0  2
 8BX  Var_06    C21  C14  C13  N12   -179.12  30.0  3
 8BX  Var_07    H10  C10  O09  C4'    -61.71  30.0  3
 8BX  Var_08    N12  C11  C10  O09     64.66  30.0  3
 8BX  Var_09    C13  N12  C11  C10   -177.37  30.0  1
 8BX  Var_10    C14  C13  N12  C11   -169.76  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8BX  chir_01  C3'  C08  C2'  C4'  positiv
 8BX  chir_02  C4'  O09  C3'  C5'  positiv

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
 8BX  plan-1  N01   0.020
 8BX  plan-1  C02   0.020
 8BX  plan-1  N02   0.020
 8BX  plan-1  C03   0.020
 8BX  plan-1  C04   0.020
 8BX  plan-1  C05   0.020
 8BX  plan-1  C06   0.020
 8BX  plan-1  C07   0.020
 8BX  plan-1  C08   0.020
 8BX  plan-1  H03   0.020
 8BX  plan-1  H05   0.020
 8BX  plan-2  C14   0.020
 8BX  plan-2  C21   0.020
 8BX  plan-2  C22   0.020
 8BX  plan-2  CL22  0.020
 8BX  plan-2  C23   0.020
 8BX  plan-2  C24   0.020
 8BX  plan-2  C25   0.020
 8BX  plan-2  C26   0.020
 8BX  plan-2  H23   0.020
 8BX  plan-2  H24   0.020
 8BX  plan-2  H25   0.020
 8BX  plan-2  H26   0.020
 8BX  plan-3  C02   0.020
 8BX  plan-3  N02   0.020
 8BX  plan-3  HN02  0.020
 8BX  plan-3  HN0A  0.020

