# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 15:08:36 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3S,4S)-4-(2-{[2,2-difluoro-2-(3-fluorophenyl)ethyl]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)c3cccc(F)c3)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
 3XA  3XA  6-{[(3S,4S)-4-(2-{[2,2-difluoro-2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XA
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
 3XA  O1    O  O2    0  -0.493   1.2081  -2.3174   0.0223
 3XA  C2    C  CH2   0  -0.158   0.3203  -3.3923  -0.1809
 3XA  C3    C  CH2   0  -0.300  -1.0354  -3.0046   0.3640
 3XA  N4    N  NH1   0  -0.613  -1.5865  -1.8792  -0.3681
 3XA  C5    C  CH2   0  -0.361  -2.8733  -1.4664   0.1340
 3XA  C6    C  CT    0   0.775  -3.5714  -0.5120  -0.8156
 3XA  F7    F  F     0  -0.348  -2.7719   0.5775  -1.0357
 3XA  F8    F  F     0  -0.339  -3.7272  -1.0986  -2.0356
 3XA  N1'   N  NH1   0  -0.613   4.6736  -2.9762  -0.2427
 3XA  C11   C  CR6   0  -0.080  -4.9096  -0.0585  -0.2960
 3XA  C12   C  CR16  0  -0.453  -4.9858   1.0670   0.5169
 3XA  C13   C  CR6   0   0.551  -6.2166   1.4314   1.0255
 3XA  F13   F  F     0  -0.312  -6.2900   2.5196   1.8068
 3XA  C14   C  CR16  0  -0.409  -7.3712   0.7221   0.7594
 3XA  C15   C  CR16  0  -0.223  -7.2768  -0.4003  -0.0500
 3XA  C16   C  CR16  0  -0.300  -6.0554  -0.7936  -0.5787
 3XA  N1A   N  N     0  -0.479   4.2140   1.4317   1.1992
 3XA  C2'   C  CH2   0  -0.315   3.3466  -3.5272  -0.0484
 3XA  C2A   C  CR6   0   0.270   3.4528   1.2535   0.1185
 3XA  C3'   C  CH1   0   0.073   2.4319  -2.4479  -0.6523
 3XA  C3A   C  CR16  0  -0.423   3.4860   2.1122  -0.9682
 3XA  C4'   C  CH1   0  -0.293   3.2705  -1.1438  -0.5622
 3XA  C4A   C  CR6   0   0.204   4.3538   3.2075  -0.9443
 3XA  C5'   C  CH2   0  -0.274   4.5536  -1.5837   0.1505
 3XA  C5A   C  CR16  0  -0.447   5.1510   3.3814   0.1701
 3XA  C6A   C  CR6   0   0.442   5.0506   2.4653   1.2294
 3XA  N6A   N  NH2   0  -0.840   5.8522   2.5796   2.3299
 3XA  C7A   C  CH2   0  -0.496   2.5676   0.0378   0.1074
 3XA  C8A   C  CH3   0  -0.727   4.3955   4.1746  -2.0882
 3XA  H2    H  HCH2  0   0.202   0.2366  -3.6257  -1.2515
 3XA  H2A   H  HCH2  0   0.213   0.6675  -4.3019   0.3261
 3XA  H3    H  HCH2  0   0.235  -1.7034  -3.8622   0.2489
 3XA  H3A   H  HCH2  0   0.205  -0.9531  -2.8163   1.4457
 3XA  HN4   H  HNH1  0   0.348  -0.9346  -1.1071  -0.3104
 3XA  H5    H  HCH2  0   0.258  -3.5159  -2.3443   0.2406
 3XA  H5A   H  HCH2  0   0.238  -2.8394  -0.9940   1.1274
 3XA  HN1'  H  HNH1  0   0.350   5.3684  -3.4677   0.3036
 3XA  H12   H  HCR6  0   0.285  -4.1115   1.6563   0.7608
 3XA  H14   H  HCR6  0   0.286  -8.3193   1.0364   1.1752
 3XA  H15   H  HCR6  0   0.275  -8.1671  -0.9732  -0.2711
 3XA  H16   H  HCR6  0   0.269  -6.0095  -1.6742  -1.2046
 3XA  H2'   H  HCH2  0   0.231   3.2434  -4.5003  -0.5333
 3XA  H2'A  H  HCH2  0   0.200   3.0818  -3.6510   1.0145
 3XA  H3'   H  HCH1  0   0.216   2.2374  -2.6797  -1.7082
 3XA  H3AA  H  HCR6  0   0.240   2.8430   1.9339  -1.8216
 3XA  H4'   H  HCH1  0   0.254   3.5297  -0.8455  -1.5818
 3XA  H5'   H  HCH2  0   0.196   4.4403  -1.4496   1.2375
 3XA  H5'A  H  HCH2  0   0.229   5.4268  -1.0074  -0.1597
 3XA  H5AA  H  HCR6  0   0.254   5.8444   4.2116   0.2329
 3XA  HN6A  H  HNH2  0   0.378   5.5545   2.0740   3.1480
 3XA  HN6B  H  HNH2  0   0.387   6.2464   3.4840   2.5271
 3XA  H7A   H  HCH2  0   0.237   2.2997  -0.2146   1.1344
 3XA  H7AA  H  HCH2  0   0.245   1.6428   0.2676  -0.4259
 3XA  H8A   H  HCH3  0   0.254   3.5015   4.8007  -2.0919
 3XA  H8AA  H  HCH3  0   0.246   5.2617   4.8316  -2.0307
 3XA  H8AB  H  HCH3  0   0.248   4.4238   3.6532  -3.0452

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
 3XA  O1   C2    single    1.409  0.020  1.409
 3XA  O1   C3'   single    1.403  0.020  1.403
 3XA  C3   C2    single    1.512  0.020  1.512
 3XA  C2   H2    single    0.970  0.020  1.090
 3XA  C2   H2A   single    0.970  0.020  1.090
 3XA  N4   C3    single    1.451  0.020  1.451
 3XA  C3   H3    single    0.970  0.020  1.090
 3XA  C3   H3A   single    0.970  0.020  1.090
 3XA  C5   N4    single    1.442  0.020  1.442
 3XA  N4   HN4   single    0.890  0.020  1.040
 3XA  C5   C6    single    1.517  0.020  1.517
 3XA  C5   H5    single    0.970  0.020  1.090
 3XA  C5   H5A   single    0.970  0.020  1.090
 3XA  C11  C6    single    1.505  0.020  1.505
 3XA  C6   F7    single    1.369  0.020  1.369
 3XA  C6   F8    single    1.363  0.020  1.363
 3XA  C2'  N1'   single    1.450  0.020  1.450
 3XA  N1'  C5'   single    1.452  0.020  1.452
 3XA  N1'  HN1'  single    0.890  0.020  1.040
 3XA  C16  C11   aromatic  1.390  0.020  1.390
 3XA  C12  C11   aromatic  1.390  0.020  1.390
 3XA  C13  C12   aromatic  1.381  0.020  1.381
 3XA  C12  H12   single    0.930  0.020  1.080
 3XA  C14  C13   aromatic  1.381  0.020  1.381
 3XA  F13  C13   single    1.342  0.020  1.342
 3XA  C14  C15   aromatic  1.387  0.020  1.387
 3XA  C14  H14   single    0.930  0.020  1.080
 3XA  C15  C16   aromatic  1.388  0.020  1.388
 3XA  C15  H15   single    0.930  0.020  1.080
 3XA  C16  H16   single    0.930  0.020  1.080
 3XA  N1A  C2A   aromatic  1.334  0.020  1.334
 3XA  N1A  C6A   aromatic  1.330  0.020  1.330
 3XA  C2'  C3'   single    1.538  0.020  1.538
 3XA  C2'  H2'   single    0.970  0.020  1.090
 3XA  C2'  H2'A  single    0.970  0.020  1.090
 3XA  C7A  C2A   single    1.504  0.020  1.504
 3XA  C2A  C3A   aromatic  1.385  0.020  1.385
 3XA  C3'  C4'   single    1.553  0.020  1.553
 3XA  C3'  H3'   single    0.970  0.020  1.090
 3XA  C3A  C4A   aromatic  1.398  0.020  1.398
 3XA  C3A  H3AA  single    0.930  0.020  1.080
 3XA  C7A  C4'   single    1.529  0.020  1.529
 3XA  C5'  C4'   single    1.532  0.020  1.532
 3XA  C4'  H4'   single    0.970  0.020  1.090
 3XA  C5A  C4A   aromatic  1.381  0.020  1.381
 3XA  C4A  C8A   single    1.499  0.020  1.499
 3XA  C5'  H5'   single    0.970  0.020  1.090
 3XA  C5'  H5'A  single    0.970  0.020  1.090
 3XA  C6A  C5A   aromatic  1.404  0.020  1.404
 3XA  C5A  H5AA  single    0.930  0.020  1.080
 3XA  N6A  C6A   single    1.366  0.020  1.366
 3XA  N6A  HN6A  single    0.890  0.020  1.040
 3XA  N6A  HN6B  single    0.890  0.020  1.040
 3XA  C7A  H7A   single    0.970  0.020  1.090
 3XA  C7A  H7AA  single    0.970  0.020  1.090
 3XA  C8A  H8A   single    0.970  0.020  1.090
 3XA  C8A  H8AA  single    0.970  0.020  1.090
 3XA  C8A  H8AB  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
 3XA  C3'   O1   C2    114.16  3.000
 3XA  H2A   C2   H2    107.34  3.000
 3XA  H2A   C2   C3    109.26  3.000
 3XA  H2    C2   C3    109.71  3.000
 3XA  H2A   C2   O1    111.48  3.000
 3XA  H2    C2   O1    110.52  3.000
 3XA  C3    C2   O1    108.51  3.000
 3XA  H3A   C3   H3    106.45  3.000
 3XA  H3A   C3   N4    113.04  3.000
 3XA  H3    C3   N4    108.86  3.000
 3XA  H3A   C3   C2    109.32  3.000
 3XA  H3    C3   C2    107.99  3.000
 3XA  N4    C3   C2    110.96  3.000
 3XA  HN4   N4   C5    109.67  3.000
 3XA  HN4   N4   C3    108.55  3.000
 3XA  C5    N4   C3    112.66  3.000
 3XA  H5A   C5   H5    105.95  3.000
 3XA  H5A   C5   C6    108.02  3.000
 3XA  H5    C5   C6    107.21  3.000
 3XA  H5A   C5   N4    114.19  3.000
 3XA  H5    C5   N4    109.19  3.000
 3XA  C6    C5   N4    111.90  3.000
 3XA  C11   C6   F8    109.70  3.000
 3XA  F8    C6   F7    105.39  3.000
 3XA  C11   C6   F7    109.56  3.000
 3XA  F8    C6   C5    110.02  3.000
 3XA  F7    C6   C5    109.43  3.000
 3XA  C11   C6   C5    112.49  3.000
 3XA  HN1'  N1'  C5'   112.12  3.000
 3XA  HN1'  N1'  C2'   111.82  3.000
 3XA  C5'   N1'  C2'   104.63  3.000
 3XA  C16   C11  C12   120.11  3.000
 3XA  C12   C11  C6    119.63  3.000
 3XA  C16   C11  C6    120.20  3.000
 3XA  H12   C12  C13   119.57  3.000
 3XA  H12   C12  C11   121.88  3.000
 3XA  C13   C12  C11   118.55  3.000
 3XA  C14   C13  F13   118.89  3.000
 3XA  F13   C13  C12   118.51  3.000
 3XA  C14   C13  C12   122.60  3.000
 3XA  H14   C14  C15   121.26  3.000
 3XA  H14   C14  C13   120.62  3.000
 3XA  C15   C14  C13   118.11  3.000
 3XA  H15   C15  C16   119.77  3.000
 3XA  H15   C15  C14   119.47  3.000
 3XA  C16   C15  C14   120.77  3.000
 3XA  H16   C16  C15   119.26  3.000
 3XA  H16   C16  C11   120.88  3.000
 3XA  C15   C16  C11   119.87  3.000
 3XA  C6A   N1A  C2A   118.76  3.000
 3XA  H2'A  C2'  H2'   107.78  3.000
 3XA  H2'A  C2'  C3'   108.33  3.000
 3XA  H2'   C2'  C3'   113.25  3.000
 3XA  H2'A  C2'  N1'   113.06  3.000
 3XA  H2'   C2'  N1'   111.44  3.000
 3XA  C3'   C2'  N1'   103.00  3.000
 3XA  C7A   C2A  C3A   120.62  3.000
 3XA  C3A   C2A  N1A   122.62  3.000
 3XA  C7A   C2A  N1A   116.74  3.000
 3XA  H3'   C3'  C4'   109.18  3.000
 3XA  H3'   C3'  C2'   109.55  3.000
 3XA  C4'   C3'  C2'   104.20  3.000
 3XA  H3'   C3'  O1    109.11  3.000
 3XA  C4'   C3'  O1    111.40  3.000
 3XA  C2'   C3'  O1    113.26  3.000
 3XA  H3AA  C3A  C4A   120.73  3.000
 3XA  H3AA  C3A  C2A   120.11  3.000
 3XA  C4A   C3A  C2A   119.15  3.000
 3XA  H4'   C4'  C7A   107.85  3.000
 3XA  H4'   C4'  C5'   108.27  3.000
 3XA  C7A   C4'  C5'   113.77  3.000
 3XA  H4'   C4'  C3'   107.63  3.000
 3XA  C5'   C4'  C3'   103.77  3.000
 3XA  C7A   C4'  C3'   115.21  3.000
 3XA  C8A   C4A  C5A   121.24  3.000
 3XA  C8A   C4A  C3A   120.66  3.000
 3XA  C5A   C4A  C3A   118.09  3.000
 3XA  H5'A  C5'  H5'   107.37  3.000
 3XA  H5'A  C5'  C4'   112.72  3.000
 3XA  H5'   C5'  C4'   109.76  3.000
 3XA  H5'A  C5'  N1'   111.31  3.000
 3XA  H5'   C5'  N1'   113.12  3.000
 3XA  C4'   C5'  N1'   102.62  3.000
 3XA  H5AA  C5A  C6A   120.13  3.000
 3XA  H5AA  C5A  C4A   120.84  3.000
 3XA  C6A   C5A  C4A   119.03  3.000
 3XA  N6A   C6A  C5A   120.74  3.000
 3XA  N6A   C6A  N1A   116.89  3.000
 3XA  C5A   C6A  N1A   122.34  3.000
 3XA  HN6B  N6A  HN6A  114.07  3.000
 3XA  HN6B  N6A  C6A   117.58  3.000
 3XA  HN6A  N6A  C6A   116.04  3.000
 3XA  H7AA  C7A  H7A   107.48  3.000
 3XA  H7AA  C7A  C4'   109.75  3.000
 3XA  H7A   C7A  C4'   110.26  3.000
 3XA  H7AA  C7A  C2A   109.39  3.000
 3XA  H7A   C7A  C2A   108.95  3.000
 3XA  C4'   C7A  C2A   110.93  3.000
 3XA  H8AB  C8A  H8AA  108.33  3.000
 3XA  H8AB  C8A  H8A   107.02  3.000
 3XA  H8AA  C8A  H8A   107.80  3.000
 3XA  H8AB  C8A  C4A   111.23  3.000
 3XA  H8AA  C8A  C4A   111.80  3.000
 3XA  H8A   C8A  C4A   110.48  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
 3XA  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 3XA  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 3XA  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 3XA  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 3XA  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 3XA  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 3XA  CONST_07  C4A   C3A  C2A  N1A     0.00   0.0  0
 3XA  CONST_08  C4A   C5A  C6A  N1A     0.00   0.0  0
 3XA  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 3XA  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 3XA  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 3XA  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 3XA  CONST_13  C15   C16  C11  C6    180.00   0.0  0
 3XA  CONST_14  C13   C12  C11  C6    180.00   0.0  0
 3XA  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 3XA  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 3XA  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 3XA  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 3XA  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 3XA  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 3XA  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 3XA  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 3XA  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 3XA  CONST_24  H16   C16  C11  C12   180.00   0.0  0
 3XA  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 3XA  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 3XA  CONST_27  H3AA  C3A  C2A  N1A   180.00   0.0  0
 3XA  CONST_28  H5AA  C5A  C6A  N1A   180.00   0.0  0
 3XA  Var_01    C4'   C5'  N1'  C2'   -46.48  30.0  1
 3XA  Var_02    C5'   N1'  C2'  C3'    44.49  30.0  1
 3XA  Var_03    C4'   C7A  C2A  N1A   -92.40  30.0  1
 3XA  Var_04    C16   C11  C6   C5    -88.67  30.0  2
 3XA  Var_05    H8A   C8A  C4A  C3A    72.85  30.0  2
 3XA  Var_06    C11   C6   C5   N4   -179.28  30.0  3
 3XA  Var_07    H2    C2   O1   C3'   -48.60  30.0  3
 3XA  Var_08    N4    C3   C2   O1     63.65  30.0  1
 3XA  Var_09    C5    N4   C3   C2   -179.20  30.0  2
 3XA  Var_10    C6    C5   N4   C3   -167.21  30.0  1

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
 3XA  chir_01  C3'  O1   C2'  C4'  positiv
 3XA  chir_02  C4'  C3'  C7A  C5'  negativ

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
 3XA  plan-1  C6    0.020
 3XA  plan-1  C11   0.020
 3XA  plan-1  C12   0.020
 3XA  plan-1  C13   0.020
 3XA  plan-1  F13   0.020
 3XA  plan-1  C14   0.020
 3XA  plan-1  C15   0.020
 3XA  plan-1  C16   0.020
 3XA  plan-1  H12   0.020
 3XA  plan-1  H14   0.020
 3XA  plan-1  H15   0.020
 3XA  plan-1  H16   0.020
 3XA  plan-2  N1A   0.020
 3XA  plan-2  C2A   0.020
 3XA  plan-2  C3A   0.020
 3XA  plan-2  C4A   0.020
 3XA  plan-2  C5A   0.020
 3XA  plan-2  C6A   0.020
 3XA  plan-2  N6A   0.020
 3XA  plan-2  C7A   0.020
 3XA  plan-2  C8A   0.020
 3XA  plan-2  H3AA  0.020
 3XA  plan-2  H5AA  0.020
 3XA  plan-3  C6A   0.020
 3XA  plan-3  N6A   0.020
 3XA  plan-3  HN6A  0.020
 3XA  plan-3  HN6B  0.020

