# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 15:13:59 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (2S)-1-[2-({[(2R,3S,6R)-6-amino-2-methylpiperidin-3-yl]methyl}amino)ethyl]-6-chloro-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-1,2-dihydropyrazin-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N[C@@H](N)CC[C@H]1CNCCN2[C@@H](O)C(=NC=C2Cl)NCC(F)(F)c3ccccn3
#
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
 C1D  C1D  (2S)-1-[2-({[(2R,3S,6R)-6-amino-2-methylpiperidin-3-yl]methyl}amino)ethyl]-6-chloro-3-[(2,2-difluoro-2-pyridin-2-ylethyl)amino]-1,2-dihydropyrazin-2-ol  ligand  61  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C1D
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
 C1D  C1    C   CR16  0  -0.077    6.8173  -5.8381  -5.6488
 C1D  N2    N   N     0  -0.415    5.6588  -5.8382  -5.0062
 C1D  C3    C   CR6   0   0.081    5.6767  -5.9020  -3.6807
 C1D  C4    C   CR16  0  -0.330    6.8444  -5.9521  -2.9349
 C1D  C5    C   CR16  0  -0.143    8.0531  -5.9517  -3.6176
 C1D  C6    C   CR16  0  -0.315    8.0440  -5.8957  -5.0009
 C1D  C11   C   CT    0   0.775    4.3134  -5.8661  -3.0353
 C1D  C12   C   CH2   0  -0.394    3.6387  -4.5096  -3.1774
 C1D  F13   F   F     0  -0.349    3.5227  -6.8226  -3.6049
 C1D  F14   F   F     0  -0.330    4.4096  -6.2058  -1.7224
 C1D  N15   N   NH1   0  -0.665    2.3483  -4.4550  -2.5599
 C1D  C18   C   C     0   0.476    2.1445  -4.0094  -1.3010
 C1D  C19   C   CH1   0   0.057    0.7062  -4.0033  -0.8183
 C1D  N20   N   NT    0  -0.465    0.5314  -2.8093  -0.0511
 C1D  C21   C   C     0   0.193    1.5270  -2.5543   0.8606
 C1D  C22   C   C1    0  -0.182    2.7749  -3.0053   0.6438
 C1D  N23   N   N     0  -0.452    3.1112  -3.6185  -0.5472
 C1D  C24   C   CH2   0  -0.345   -0.7381  -2.1153  -0.0843
 C1D  C25   C   CH2   0  -0.252   -1.8357  -2.7889   0.7357
 C1D  N28   N   NH1   0  -0.602   -3.0119  -1.9467   0.7466
 C1D  C29   C   CH2   0  -0.244   -4.1364  -2.5508   1.4380
 C1D  C30   C   CH1   0  -0.256   -5.3214  -1.5929   1.5213
 C1D  C33   C   CH2   0  -0.422   -5.7409  -1.1086   0.1335
 C1D  C34   C   CH2   0  -0.436   -6.9551  -0.1953   0.2036
 C1D  C2    C   CH3   0  -0.683   -6.2227  -2.6498   3.6622
 C1D  C35   C   CH1   0   0.099   -8.0916  -0.8765   0.9450
 C1D  C37   C   CH1   0  -0.045   -6.5241  -2.2262   2.2317
 C1D  O42   O   OH1   0  -0.641    0.3997  -5.1953  -0.1396
 C1D  N6    N   NH2   0  -0.815   -9.2077   0.0380   1.1017
 C1D  CL43  CL  CL    0  -0.113    1.1283  -1.6748   2.2981
 C1D  N29   N   NH1   0  -0.611   -7.6196  -1.2632   2.2625
 C1D  H1    H   HCR6  0   0.272    6.7710  -5.7889  -6.7305
 C1D  H4    H   HCR6  0   0.279    6.8264  -5.9901  -1.8554
 C1D  H5    H   HCR6  0   0.282    8.9859  -5.9942  -3.0715
 C1D  H6    H   HCR6  0   0.278    8.9620  -5.8926  -5.5717
 C1D  H121  H   HCH2  0   0.288    3.5466  -4.2894  -4.2420
 C1D  H122  H   HCH2  0   0.277    4.2814  -3.7463  -2.7379
 C1D  H15   H   HNH1  0   0.407    1.5635  -4.8174  -3.0741
 C1D  H119  H   HCH1  0   0.276    0.0130  -3.9585  -1.6602
 C1D  H22   H   H     0   0.258    3.5584  -2.8707   1.3760
 C1D  H241  H   HCH2  0   0.251   -0.5861  -1.0917   0.2620
 C1D  H242  H   HCH2  0   0.264   -1.0558  -2.0428  -1.1268
 C1D  H251  H   HCH2  0   0.226   -2.0964  -3.7461   0.2756
 C1D  H252  H   HCH2  0   0.195   -1.4577  -3.0214   1.7429
 C1D  H28   H   HNH1  0   0.338   -2.7830  -1.0734   1.2099
 C1D  H291  H   HCH2  0   0.211   -4.4353  -3.4516   0.8890
 C1D  H292  H   HCH2  0   0.205   -3.8528  -2.8836   2.4472
 C1D  H330  H   HCH1  0   0.209   -5.0166  -0.7214   2.1194
 C1D  H33   H   HCH2  0   0.204   -5.9764  -1.9808  -0.4889
 C1D  H331  H   HCH2  0   0.235   -4.9101  -0.5996  -0.3552
 C1D  H34   H   HCH2  0   0.211   -6.7038   0.7312   0.7293
 C1D  H341  H   HCH2  0   0.226   -7.2848   0.0804  -0.8022
 C1D  H2C1  H   HCH3  0   0.231   -7.1305  -2.9964   4.1607
 C1D  H2C2  H   HCH3  0   0.231   -5.5066  -3.4688   3.7040
 C1D  H2C3  H   HCH3  0   0.221   -5.8208  -1.8147   4.2394
 C1D  H335  H   HCH1  0   0.161   -8.3763  -1.7750   0.3597
 C1D  H337  H   HCH1  0   0.183   -6.8030  -3.1295   1.6574
 C1D  H42   H   HOH1  0   0.455    1.0379  -5.3322   0.5704
 C1D  H6N1  H   HNH2  0   0.343  -10.0072  -0.4609   1.4759
 C1D  H6N2  H   HNH2  0   0.343   -9.4991   0.3519   0.1836
 C1D  HN1   H   HNH1  0   0.339   -8.3906  -1.6807   2.7733

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
 C1D  C1   N2    aromatic  1.325  0.020  1.325
 C1D  C1   C6    aromatic  1.388  0.020  1.388
 C1D  C1   H1    single    0.930  0.020  1.080
 C1D  N2   C3    aromatic  1.327  0.020  1.327
 C1D  C3   C4    aromatic  1.386  0.020  1.386
 C1D  C3   C11   single    1.509  0.020  1.509
 C1D  C4   C5    aromatic  1.388  0.020  1.388
 C1D  C4   H4    single    0.930  0.020  1.080
 C1D  C5   C6    aromatic  1.384  0.020  1.384
 C1D  C5   H5    single    0.930  0.020  1.080
 C1D  C6   H6    single    0.930  0.020  1.080
 C1D  C11  C12   single    1.522  0.020  1.522
 C1D  C11  F13   single    1.365  0.020  1.365
 C1D  C11  F14   single    1.359  0.020  1.359
 C1D  C12  N15   single    1.432  0.020  1.432
 C1D  C12  H121  single    0.970  0.020  1.090
 C1D  C12  H122  single    0.970  0.020  1.090
 C1D  N15  C18   single    1.351  0.020  1.351
 C1D  N15  H15   single    0.860  0.020  1.020
 C1D  C18  C19   single    1.517  0.020  1.517
 C1D  C18  N23   double    1.287  0.020  1.287
 C1D  C19  N20   single    1.430  0.020  1.430
 C1D  C19  O42   single    1.406  0.020  1.406
 C1D  C19  H119  single    0.970  0.020  1.090
 C1D  N20  C21   single    1.374  0.020  1.374
 C1D  N20  C24   single    1.447  0.020  1.447
 C1D  C21  C22   double    1.345  0.020  1.345
 C1D  C21  CL43  single    1.732  0.020  1.732
 C1D  C22  N23   single    1.381  0.020  1.381
 C1D  C22  H22   single    0.930  0.020  1.080
 C1D  C24  C25   single    1.527  0.020  1.527
 C1D  C24  H241  single    0.970  0.020  1.090
 C1D  C24  H242  single    0.970  0.020  1.090
 C1D  C25  N28   single    1.447  0.020  1.447
 C1D  C25  H251  single    0.970  0.020  1.090
 C1D  C25  H252  single    0.970  0.020  1.090
 C1D  N28  C29   single    1.452  0.020  1.452
 C1D  N28  H28   single    0.890  0.020  1.040
 C1D  C29  C30   single    1.526  0.020  1.526
 C1D  C29  H291  single    0.970  0.020  1.090
 C1D  C29  H292  single    0.970  0.020  1.090
 C1D  C30  C33   single    1.529  0.020  1.529
 C1D  C30  C37   single    1.534  0.020  1.534
 C1D  C30  H330  single    0.970  0.020  1.090
 C1D  C33  C34   single    1.521  0.020  1.521
 C1D  C33  H33   single    0.970  0.020  1.090
 C1D  C33  H331  single    0.970  0.020  1.090
 C1D  C34  C35   single    1.518  0.020  1.518
 C1D  C34  H34   single    0.970  0.020  1.090
 C1D  C34  H341  single    0.970  0.020  1.090
 C1D  C2   C37   single    1.522  0.020  1.522
 C1D  C2   H2C1  single    0.970  0.020  1.090
 C1D  C2   H2C2  single    0.970  0.020  1.090
 C1D  C2   H2C3  single    0.970  0.020  1.090
 C1D  C35  N6    single    1.451  0.020  1.451
 C1D  C35  N29   single    1.452  0.020  1.452
 C1D  C35  H335  single    0.970  0.020  1.090
 C1D  C37  N29   single    1.459  0.020  1.459
 C1D  C37  H337  single    0.970  0.020  1.090
 C1D  O42  H42   single    0.850  0.020  0.980
 C1D  N6   H6N1  single    0.890  0.020  1.040
 C1D  N6   H6N2  single    0.890  0.020  1.040
 C1D  HN1  N29   single    0.890  0.020  1.040

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
 C1D  H1    C1   C6    120.36  3.000
 C1D  H1    C1   N2    116.53  3.000
 C1D  C6    C1   N2    123.11  3.000
 C1D  C3    N2   C1    118.20  3.000
 C1D  C11   C3   C4    122.12  3.000
 C1D  C11   C3   N2    114.45  3.000
 C1D  C4    C3   N2    123.39  3.000
 C1D  H4    C4   C5    120.39  3.000
 C1D  H4    C4   C3    121.65  3.000
 C1D  C5    C4   C3    117.95  3.000
 C1D  H5    C5   C6    120.78  3.000
 C1D  H5    C5   C4    120.17  3.000
 C1D  C6    C5   C4    119.06  3.000
 C1D  H6    C6   C5    121.47  3.000
 C1D  H6    C6   C1    120.25  3.000
 C1D  C5    C6   C1    118.28  3.000
 C1D  F14   C11  F13   105.59  3.000
 C1D  F14   C11  C12   110.14  3.000
 C1D  F13   C11  C12   109.19  3.000
 C1D  F14   C11  C3    110.07  3.000
 C1D  F13   C11  C3    109.15  3.000
 C1D  C12   C11  C3    112.45  3.000
 C1D  H122  C12  H121  107.56  3.000
 C1D  H122  C12  N15   109.31  3.000
 C1D  H121  C12  N15   109.70  3.000
 C1D  H122  C12  C11   108.97  3.000
 C1D  H121  C12  C11   107.97  3.000
 C1D  N15   C12  C11   113.17  3.000
 C1D  H15   N15  C18   118.53  3.000
 C1D  H15   N15  C12   117.97  3.000
 C1D  C18   N15  C12   123.40  3.000
 C1D  N23   C18  C19   121.64  3.000
 C1D  N23   C18  N15   122.20  3.000
 C1D  C19   C18  N15   116.16  3.000
 C1D  H119  C19  O42   105.59  3.000
 C1D  H119  C19  N20   107.58  3.000
 C1D  O42   C19  N20   114.99  3.000
 C1D  H119  C19  C18   110.91  3.000
 C1D  O42   C19  C18   110.91  3.000
 C1D  N20   C19  C18   106.86  3.000
 C1D  C24   N20  C21   124.19  3.000
 C1D  C24   N20  C19   119.69  3.000
 C1D  C21   N20  C19   114.99  3.000
 C1D  CL43  C21  C22   121.19  3.000
 C1D  CL43  C21  N20   118.58  3.000
 C1D  C22   C21  N20   120.22  3.000
 C1D  H22   C22  N23   117.58  3.000
 C1D  H22   C22  C21   121.45  3.000
 C1D  N23   C22  C21   120.93  3.000
 C1D  C22   N23  C18   117.20  3.000
 C1D  H242  C24  H241  106.33  3.000
 C1D  H242  C24  C25   109.44  3.000
 C1D  H241  C24  C25   110.09  3.000
 C1D  H242  C24  N20   107.99  3.000
 C1D  H241  C24  N20   108.68  3.000
 C1D  C25   C24  N20   114.00  3.000
 C1D  H252  C25  H251  106.38  3.000
 C1D  H252  C25  N28   113.29  3.000
 C1D  H251  C25  N28   108.60  3.000
 C1D  H252  C25  C24   109.74  3.000
 C1D  H251  C25  C24   109.36  3.000
 C1D  N28   C25  C24   109.37  3.000
 C1D  H28   N28  C29   108.39  3.000
 C1D  H28   N28  C25   108.73  3.000
 C1D  C29   N28  C25   113.02  3.000
 C1D  H292  C29  H291  106.33  3.000
 C1D  H292  C29  C30   109.88  3.000
 C1D  H291  C29  C30   109.35  3.000
 C1D  H292  C29  N28   111.29  3.000
 C1D  H291  C29  N28   108.34  3.000
 C1D  C30   C29  N28   111.49  3.000
 C1D  H330  C30  C37   107.01  3.000
 C1D  H330  C30  C33   108.58  3.000
 C1D  C37   C30  C33   109.64  3.000
 C1D  H330  C30  C29   108.17  3.000
 C1D  C37   C30  C29   112.03  3.000
 C1D  C33   C30  C29   111.25  3.000
 C1D  H331  C33  H33   106.29  3.000
 C1D  H331  C33  C34   110.41  3.000
 C1D  H33   C33  C34   109.40  3.000
 C1D  H331  C33  C30   110.23  3.000
 C1D  H33   C33  C30   108.79  3.000
 C1D  C34   C33  C30   111.56  3.000
 C1D  H341  C34  H34   107.31  3.000
 C1D  H341  C34  C35   109.66  3.000
 C1D  H34   C34  C35   108.49  3.000
 C1D  H341  C34  C33   110.46  3.000
 C1D  H34   C34  C33   110.31  3.000
 C1D  C35   C34  C33   110.53  3.000
 C1D  H2C3  C2   H2C2  108.24  3.000
 C1D  H2C3  C2   H2C1  107.91  3.000
 C1D  H2C2  C2   H2C1  106.89  3.000
 C1D  H2C3  C2   C37   110.91  3.000
 C1D  H2C2  C2   C37   112.06  3.000
 C1D  H2C1  C2   C37   110.65  3.000
 C1D  H335  C35  N29   110.27  3.000
 C1D  H335  C35  N6    111.71  3.000
 C1D  N29   C35  N6    108.65  3.000
 C1D  H335  C35  C34   107.33  3.000
 C1D  N29   C35  C34   108.62  3.000
 C1D  N6    C35  C34   110.22  3.000
 C1D  H337  C37  N29   111.14  3.000
 C1D  H337  C37  C2    108.10  3.000
 C1D  N29   C37  C2    108.21  3.000
 C1D  H337  C37  C30   107.12  3.000
 C1D  N29   C37  C30   109.03  3.000
 C1D  C2    C37  C30   113.27  3.000
 C1D  H42   O42  C19   109.36  3.000
 C1D  H6N2  N6   H6N1  105.08  3.000
 C1D  H6N2  N6   C35   108.58  3.000
 C1D  H6N1  N6   C35   109.64  3.000
 C1D  HN1   N29  C37   108.03  3.000
 C1D  HN1   N29  C35   108.62  3.000
 C1D  C37   N29  C35   113.62  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
 C1D  CONST_01  C4   C3   N2   C1      0.00   0.0  0
 C1D  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 C1D  CONST_03  C5   C6   C1   N2      0.00   0.0  0
 C1D  CONST_04  C5   C4   C3   N2      0.00   0.0  0
 C1D  CONST_05  C6   C1   N2   C3      0.00   0.0  0
 C1D  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 C1D  CONST_07  C22  N23  C18  C19     0.00   0.0  0
 C1D  CONST_08  C11  C3   N2   C1    180.00   0.0  0
 C1D  CONST_09  C11  C3   C4   C5    180.00   0.0  0
 C1D  CONST_10  C22  N23  C18  N15   180.00   0.0  0
 C1D  CONST_11  H5   C5   C6   C1    180.00   0.0  0
 C1D  CONST_12  H6   C6   C1   N2    180.00   0.0  0
 C1D  CONST_13  H4   C4   C3   N2    180.00   0.0  0
 C1D  CONST_14  H1   C1   N2   C3    180.00   0.0  0
 C1D  CONST_15  C19  C18  N15  C12   180.00   0.0  0
 C1D  CONST_16  N23  C18  N15  C12     0.00   0.0  0
 C1D  CONST_17  H15  N15  C18  C19     0.00   0.0  0
 C1D  Var_01    C21  C22  N23  C18   -15.28  30.0  1
 C1D  Var_02    C22  C21  N20  C19    27.82  30.0  1
 C1D  Var_03    N23  C22  C21  N20     6.17  30.0  1
 C1D  Var_04    C35  C34  C33  C30   -54.24  30.0  1
 C1D  Var_05    C12  C11  C3   N2    -69.09  30.0  2
 C1D  Var_06    C25  C24  N20  C19    75.86  30.0  3
 C1D  Var_07    N15  C12  C11  C3   -179.49  30.0  3
 C1D  Var_08    C18  N15  C12  C11    94.28  30.0  3
 C1D  Var_09    N28  C25  C24  N20   174.12  30.0  3
 C1D  Var_10    C30  C29  N28  C25   175.66  30.0  3
 C1D  Var_11    C29  N28  C25  C24   176.43  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
 C1D  chir_01  C19  C18  N20  O42  positiv
 C1D  chir_02  C30  C29  C33  C37  negativ
 C1D  chir_03  C35  N29  N6   C34  negativ
 C1D  chir_04  C37  N29  C30  C2   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
 C1D  plan-1  C1   0.020
 C1D  plan-1  N2   0.020
 C1D  plan-1  C3   0.020
 C1D  plan-1  C4   0.020
 C1D  plan-1  C5   0.020
 C1D  plan-1  C6   0.020
 C1D  plan-1  C11  0.020
 C1D  plan-1  H1   0.020
 C1D  plan-1  H4   0.020
 C1D  plan-1  H5   0.020
 C1D  plan-1  H6   0.020
 C1D  plan-2  C12  0.020
 C1D  plan-2  N15  0.020
 C1D  plan-2  C18  0.020
 C1D  plan-2  C19  0.020
 C1D  plan-2  C22  0.020
 C1D  plan-2  N23  0.020
 C1D  plan-2  H15  0.020
 C1D  plan-3  C19  0.020
 C1D  plan-3  N20  0.020
 C1D  plan-3  C21  0.020
 C1D  plan-3  C24  0.020

