# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 21:47:48 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: N-{3-[(2R)-6-amino-2,4-dimethyl-3-oxo-2,3,4,5-tetrahydropyrazin-2-yl]phenyl}-5-chloropyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC(=N[C@@](C)(C1=O)c2cccc(NC(=O)c3ccc(Cl)cn3)c2)N
#
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
 18P  18P  N-{3-[(2R)-6-amino-2,4-dimethyl-3-oxo-2,3,4,5-tetrahydropyrazin-2-yl]phenyl}-5-chloropyridine-2-carboxamide  ligand  44  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_18P
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
 18P  C     C   CR16  0  -0.020   4.1248  -1.6598   0.2410
 18P  N     N   N     0  -0.440   3.1272  -0.7988   0.1829
 18P  O     O   O     0  -0.455   2.3324   2.6181   0.5805
 18P  CL    CL  CL    0  -0.094   6.6801  -2.4243   0.6200
 18P  N01   N   NT    0  -0.456  -4.7853  -0.6181   0.8392
 18P  C02   C   CH2   0  -0.374  -3.6906  -1.5184   1.1176
 18P  C03   C   C     0   0.419  -3.1610  -2.1019  -0.1631
 18P  N03   N   N     0  -0.421  -3.1459  -1.4530  -1.2617
 18P  C04   C   CT    0  -0.148  -3.6247  -0.0863  -1.2298
 18P  N04   N   NH1   0  -0.763   1.0348   0.8170   0.0326
 18P  C05   C   CH3   0  -0.627  -4.0041   0.3009  -2.6593
 18P  C06   C   C     0   0.595  -4.8434   0.0727  -0.3086
 18P  C07   C   CR6   0   0.156  -2.5473   0.8849  -0.7291
 18P  C08   C   CR16  0  -0.308  -2.8650   2.2226  -0.4871
 18P  C09   C   CR16  0  -0.231  -1.8824   3.1006  -0.0647
 18P  C10   C   CR16  0  -0.332  -0.5697   2.6884   0.1242
 18P  C11   C   CR6   0   0.423  -0.2433   1.3571  -0.1234
 18P  C12   C   CR16  0  -0.444  -1.2377   0.4708  -0.5499
 18P  C13   C   C     0   0.540   2.1907   1.4281   0.3585
 18P  C14   C   CR6   0   0.130   3.3577   0.4850   0.4333
 18P  C15   C   CR16  0  -0.298   4.6162   0.9697   0.7568
 18P  C16   C   CR16  0  -0.090   5.6731   0.0767   0.8215
 18P  C17   C   CR6   0  -0.109   5.4177  -1.2574   0.5586
 18P  H     H   HCR6  0   0.297   3.9029  -2.6994   0.0321
 18P  H01   H   HCH3  0   0.252  -5.5250  -0.9278   2.7532
 18P  H01A  H   HCH3  0   0.250  -6.0676   0.5710   2.0052
 18P  H01B  H   HCH3  0   0.246  -6.7621  -0.9731   1.4926
 18P  H02   H   HCH2  0   0.283  -2.8703  -1.0121   1.6419
 18P  H02A  H   HCH2  0   0.286  -4.0462  -2.3110   1.7762
 18P  HN02  H   HNH2  0   0.404  -2.5761  -3.8058   0.8122
 18P  HN0A  H   HNH2  0   0.392  -2.1379  -3.7245  -0.8368
 18P  HN04  H   HNH1  0   0.422   1.1206  -0.1806  -0.1212
 18P  H05   H   HCH3  0   0.234  -4.7977  -0.3451  -3.0358
 18P  H05A  H   HCH3  0   0.231  -4.3358   1.3342  -2.7340
 18P  H05B  H   HCH3  0   0.233  -3.1322   0.1780  -3.3014
 18P  H08   H   HCR6  0   0.253  -3.8768   2.5812  -0.6248
 18P  H09   H   HCR6  0   0.258  -2.1374   4.1347   0.1281
 18P  H10   H   HCR6  0   0.278   0.1713   3.3962   0.4571
 18P  H12   H   HCR6  0   0.273  -0.9676  -0.5580  -0.7525
 18P  H15   H   HCR6  0   0.290   4.7747   2.0196   0.9553
 18P  H16   H   HCR6  0   0.304   6.6690   0.4153   1.0713
 18P  C01   C   CH3   0  -0.521  -5.8459  -0.4780   1.8178
 18P  O01   O   O     0  -0.499  -5.7942   0.7895  -0.5914
 18P  N02   N   NH2   0  -0.818  -2.7007  -3.3668  -0.0830

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
 18P  C    N     aromatic  1.319  0.020  1.319
 18P  C    C17   aromatic  1.391  0.020  1.391
 18P  N    C14   aromatic  1.328  0.020  1.328
 18P  O    C13   double    1.219  0.020  1.219
 18P  CL   C17   single    1.720  0.020  1.720
 18P  C01  N01   single    1.450  0.020  1.450
 18P  N01  C02   single    1.444  0.020  1.444
 18P  N01  C06   single    1.341  0.020  1.341
 18P  O01  C06   double    1.224  0.020  1.224
 18P  C02  C03   single    1.504  0.020  1.504
 18P  N02  C03   single    1.348  0.020  1.348
 18P  C03  N03   double    1.276  0.020  1.276
 18P  N03  C04   single    1.449  0.020  1.449
 18P  C04  C05   single    1.529  0.020  1.529
 18P  C04  C06   single    1.536  0.020  1.536
 18P  C04  C07   single    1.534  0.020  1.534
 18P  N04  C11   single    1.396  0.020  1.396
 18P  N04  C13   single    1.347  0.020  1.347
 18P  C07  C08   aromatic  1.396  0.020  1.396
 18P  C07  C12   aromatic  1.385  0.020  1.385
 18P  C08  C09   aromatic  1.384  0.020  1.384
 18P  C09  C10   aromatic  1.389  0.020  1.389
 18P  C10  C11   aromatic  1.393  0.020  1.393
 18P  C11  C12   aromatic  1.399  0.020  1.399
 18P  C13  C14   single    1.502  0.020  1.502
 18P  C14  C15   aromatic  1.387  0.020  1.387
 18P  C15  C16   aromatic  1.385  0.020  1.385
 18P  C16  C17   aromatic  1.384  0.020  1.384
 18P  C    H     single    0.930  0.020  1.080
 18P  C01  H01   single    0.970  0.020  1.090
 18P  C01  H01A  single    0.970  0.020  1.090
 18P  C01  H01B  single    0.970  0.020  1.090
 18P  C02  H02   single    0.970  0.020  1.090
 18P  C02  H02A  single    0.970  0.020  1.090
 18P  N02  HN02  single    0.890  0.020  1.040
 18P  N02  HN0A  single    0.890  0.020  1.040
 18P  N04  HN04  single    0.860  0.020  1.020
 18P  C05  H05   single    0.970  0.020  1.090
 18P  C05  H05A  single    0.970  0.020  1.090
 18P  C05  H05B  single    0.970  0.020  1.090
 18P  C08  H08   single    0.930  0.020  1.080
 18P  C09  H09   single    0.930  0.020  1.080
 18P  C10  H10   single    0.930  0.020  1.080
 18P  C12  H12   single    0.930  0.020  1.080
 18P  C15  H15   single    0.930  0.020  1.080
 18P  C16  H16   single    0.930  0.020  1.080

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
 18P  H     C    C17   120.80  3.000
 18P  H     C    N     117.58  3.000
 18P  C17   C    N     121.62  3.000
 18P  C14   N    C     119.43  3.000
 18P  C06   N01  C02   121.26  3.000
 18P  C06   N01  C01   119.75  3.000
 18P  C02   N01  C01   118.98  3.000
 18P  H02A  C02  H02   106.90  3.000
 18P  H02A  C02  C03   110.32  3.000
 18P  H02   C02  C03   108.83  3.000
 18P  H02A  C02  N01   108.80  3.000
 18P  H02   C02  N01   111.79  3.000
 18P  C03   C02  N01   110.16  3.000
 18P  N03   C03  N02   121.61  3.000
 18P  N03   C03  C02   122.69  3.000
 18P  N02   C03  C02   115.70  3.000
 18P  C04   N03  C03   117.19  3.000
 18P  C07   C04  C06   107.21  3.000
 18P  C07   C04  C05   108.60  3.000
 18P  C06   C04  C05   109.74  3.000
 18P  C07   C04  N03   111.86  3.000
 18P  C06   C04  N03   111.91  3.000
 18P  C05   C04  N03   107.48  3.000
 18P  HN04  N04  C13   114.24  3.000
 18P  HN04  N04  C11   116.20  3.000
 18P  C13   N04  C11   129.56  3.000
 18P  H05B  C05  H05A  108.10  3.000
 18P  H05B  C05  H05   108.18  3.000
 18P  H05A  C05  H05   108.49  3.000
 18P  H05B  C05  C04   108.90  3.000
 18P  H05A  C05  C04   112.36  3.000
 18P  H05   C05  C04   110.70  3.000
 18P  C04   C06  O01   122.58  3.000
 18P  C04   C06  N01   115.19  3.000
 18P  O01   C06  N01   122.22  3.000
 18P  C12   C07  C08   118.63  3.000
 18P  C12   C07  C04   121.12  3.000
 18P  C08   C07  C04   120.22  3.000
 18P  H08   C08  C09   119.51  3.000
 18P  H08   C08  C07   120.54  3.000
 18P  C09   C08  C07   119.95  3.000
 18P  H09   C09  C10   118.82  3.000
 18P  H09   C09  C08   119.55  3.000
 18P  C10   C09  C08   121.63  3.000
 18P  H10   C10  C11   121.44  3.000
 18P  H10   C10  C09   119.81  3.000
 18P  C11   C10  C09   118.75  3.000
 18P  C12   C11  C10   119.56  3.000
 18P  C12   C11  N04   116.09  3.000
 18P  C10   C11  N04   124.35  3.000
 18P  H12   C12  C11   118.80  3.000
 18P  H12   C12  C07   119.72  3.000
 18P  C11   C12  C07   121.48  3.000
 18P  C14   C13  N04   113.19  3.000
 18P  C14   C13  O     120.90  3.000
 18P  N04   C13  O     125.91  3.000
 18P  C15   C14  C13   119.81  3.000
 18P  C15   C14  N     122.64  3.000
 18P  C13   C14  N     117.55  3.000
 18P  H15   C15  C16   120.41  3.000
 18P  H15   C15  C14   121.04  3.000
 18P  C16   C15  C14   118.55  3.000
 18P  H16   C16  C17   121.06  3.000
 18P  H16   C16  C15   120.78  3.000
 18P  C17   C16  C15   118.16  3.000
 18P  C16   C17  CL    120.79  3.000
 18P  C16   C17  C     119.60  3.000
 18P  CL    C17  C     119.61  3.000
 18P  H01B  C01  H01A  108.52  3.000
 18P  H01B  C01  H01   108.47  3.000
 18P  H01A  C01  H01   108.11  3.000
 18P  H01B  C01  N01   111.67  3.000
 18P  H01A  C01  N01   111.00  3.000
 18P  H01   C01  N01   108.97  3.000
 18P  HN0A  N02  HN02  116.27  3.000
 18P  HN0A  N02  C03   118.67  3.000
 18P  HN02  N02  C03   120.34  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
 18P  CONST_01  C15   C14  N    C      0.00   0.0  0
 18P  CONST_02  C15   C16  C17  C      0.00   0.0  0
 18P  CONST_03  C16   C17  C    N      0.00   0.0  0
 18P  CONST_04  C16   C15  C14  N      0.00   0.0  0
 18P  CONST_05  C10   C09  C08  C07    0.00   0.0  0
 18P  CONST_06  C10   C11  C12  C07    0.00   0.0  0
 18P  CONST_07  C11   C12  C07  C08    0.00   0.0  0
 18P  CONST_08  C11   C10  C09  C08    0.00   0.0  0
 18P  CONST_09  C12   C07  C08  C09    0.00   0.0  0
 18P  CONST_10  C12   C11  C10  C09    0.00   0.0  0
 18P  CONST_11  C17   C    N    C14    0.00   0.0  0
 18P  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 18P  CONST_13  C09   C08  C07  C04  180.00   0.0  0
 18P  CONST_14  C11   C12  C07  C04  180.00   0.0  0
 18P  CONST_15  C04   C06  N01  C02    0.00   0.0  0
 18P  CONST_16  C04   N03  C03  C02    0.00   0.0  0
 18P  CONST_17  C13   C14  N    C    180.00   0.0  0
 18P  CONST_18  CL    C17  C    N    180.00   0.0  0
 18P  CONST_19  C15   C16  C17  CL   180.00   0.0  0
 18P  CONST_20  C09   C10  C11  N04  180.00   0.0  0
 18P  CONST_21  C07   C12  C11  N04  180.00   0.0  0
 18P  CONST_22  C16   C15  C14  C13  180.00   0.0  0
 18P  CONST_23  C04   C06  N01  C01  180.00   0.0  0
 18P  CONST_24  C02   N01  C06  O01  180.00   0.0  0
 18P  CONST_25  C04   N03  C03  N02  180.00   0.0  0
 18P  CONST_26  H16   C16  C17  C    180.00   0.0  0
 18P  CONST_27  H15   C15  C14  N    180.00   0.0  0
 18P  CONST_28  H08   C08  C07  C04    0.00   0.0  0
 18P  CONST_29  H12   C12  C07  C04    0.00   0.0  0
 18P  CONST_30  H09   C09  C08  C07  180.00   0.0  0
 18P  CONST_31  H10   C10  C09  C08  180.00   0.0  0
 18P  CONST_32  H     C    N    C14  180.00   0.0  0
 18P  CONST_33  C14   C13  N04  C11  180.00   0.0  0
 18P  CONST_34  C13   N04  C11  C10    0.00   0.0  0
 18P  CONST_35  C13   N04  C11  C12  180.00   0.0  0
 18P  CONST_36  O01   C06  N01  C01    0.00   0.0  0
 18P  CONST_37  HN04  N04  C11  C10  180.00   0.0  0
 18P  CONST_38  HN02  N02  C03  C02    0.00   0.0  0
 18P  CONST_39  HN0A  N02  C03  C02  180.00   0.0  0
 18P  CONST_40  C11   N04  C13  O      0.00   0.0  0
 18P  Var_01    N03   C03  C02  N01   33.34  30.0  1
 18P  Var_02    C06   N01  C02  C03  -30.33  30.0  1
 18P  Var_03    O     C13  C14  N    179.79  30.0  2
 18P  Var_04    H01   C01  N01  C02   13.21  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
 18P  chir_01  C04  N03  C06  C07  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
 18P  plan-1  C     0.020
 18P  plan-1  N     0.020
 18P  plan-1  CL    0.020
 18P  plan-1  C13   0.020
 18P  plan-1  C14   0.020
 18P  plan-1  C15   0.020
 18P  plan-1  C16   0.020
 18P  plan-1  C17   0.020
 18P  plan-1  H     0.020
 18P  plan-1  H15   0.020
 18P  plan-1  H16   0.020
 18P  plan-2  C04   0.020
 18P  plan-2  N04   0.020
 18P  plan-2  C07   0.020
 18P  plan-2  C08   0.020
 18P  plan-2  C09   0.020
 18P  plan-2  C10   0.020
 18P  plan-2  C11   0.020
 18P  plan-2  C12   0.020
 18P  plan-2  H08   0.020
 18P  plan-2  H09   0.020
 18P  plan-2  H10   0.020
 18P  plan-2  H12   0.020
 18P  plan-3  O     0.020
 18P  plan-3  N04   0.020
 18P  plan-3  C11   0.020
 18P  plan-3  C13   0.020
 18P  plan-3  C14   0.020
 18P  plan-3  HN04  0.020
 18P  plan-4  C02   0.020
 18P  plan-4  C03   0.020
 18P  plan-4  N03   0.020
 18P  plan-4  C04   0.020
 18P  plan-4  HN02  0.020
 18P  plan-4  HN0A  0.020
 18P  plan-4  N02   0.020
 18P  plan-5  N01   0.020
 18P  plan-5  C02   0.020
 18P  plan-5  C04   0.020
 18P  plan-5  C06   0.020
 18P  plan-5  C01   0.020
 18P  plan-5  O01   0.020

