# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 15:17:27 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1nccnc1C(=O)NC2Cc3ccccc3C2)C4CCCCC4
#
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
 91Y  91Y  3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxamide  ligand  51  27  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_91Y
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
 91Y  N3   N  NH1   0  -0.759  -2.4176  -0.7280   0.2229
 91Y  C4   C  CR6   0   0.519  -1.7808  -1.9314   0.0419
 91Y  C6   C  CR16  0  -0.083  -1.8371  -4.1928  -0.1484
 91Y  C7   C  CR16  0  -0.128  -0.4619  -4.2398  -0.3231
 91Y  N12  N  NH1   0  -0.652   1.7742  -0.9611  -0.3586
 91Y  C13  C  CR15  0  -0.069   2.7723   0.0792  -0.3486
 91Y  C15  C  CR56  0   0.087   5.0910   0.5218  -0.5445
 91Y  C17  C  CR16  0  -0.260   7.1940   1.6285  -0.2645
 91Y  C20  C  CR56  0   0.089   4.7030   0.9365   0.7283
 91Y  C21  C  CH2   0  -0.488   3.3271   0.4277   1.0478
 91Y  C22  C  CR16  0  -0.424  -4.0305   1.0492   0.3039
 91Y  C24  C  C     0  -0.439  -5.7193   2.8406   0.8188
 91Y  C26  C  C     0  -0.432  -3.9553   3.2553  -0.9202
 91Y  O1   O  O     0  -0.429  -4.6330  -1.2652   0.0252
 91Y  C2   C  C     0   0.574  -3.7616  -0.4388   0.1779
 91Y  N5   N  N     0  -0.377  -2.4828  -3.0552   0.0330
 91Y  N8   N  N     0  -0.377   0.2432  -3.1236  -0.3034
 91Y  C9   C  CR6   0  -0.007  -0.3757  -1.9705  -0.1241
 91Y  O11  O  O     0  -0.506   0.0166   0.3746   0.1161
 91Y  C14  C  CH2   0  -0.508   4.0057  -0.2953  -1.1845
 91Y  C16  C  CR16  0  -0.320   6.3362   0.8626  -1.0480
 91Y  C18  C  CR16  0  -0.259   6.8061   2.0448   1.0047
 91Y  C19  C  CR16  0  -0.326   5.5562   1.6997   1.5093
 91Y  C23  C  C     0  -0.411  -5.4708   1.3388   0.7158
 91Y  C25  C  C     0  -0.429  -5.3862   3.5522  -0.4877
 91Y  C27  C  C     0  -0.423  -3.6970   1.7560  -1.0222
 91Y  H1   H  HNH1  0   0.440  -1.7693   0.0536   0.3029
 91Y  H2   H  HCR6  0   0.285  -2.4275  -5.1010  -0.1515
 91Y  H3   H  HCR6  0   0.284   0.0620  -5.1739  -0.4762
 91Y  H4   H  HNH1  0   0.410   2.0663  -1.9211  -0.4780
 91Y  H5   H  HCR5  0   0.273   2.3290   0.9817  -0.7743
 91Y  H6   H  HCR6  0   0.252   8.1675   1.9080  -0.6467
 91Y  H7   H  HCH2  0   0.260   2.7020   1.1490   1.5750
 91Y  H8   H  HCH2  0   0.254   3.3813  -0.4720   1.6698
 91Y  H9   H  HCR6  0   0.259  -3.3597   1.4515   1.0743
 91Y  H10  H  H     0   0.232  -6.7608   3.0211   1.0946
 91Y  H11  H  H     0   0.213  -5.1081   3.2577   1.6265
 91Y  H12  H  H     0   0.234  -3.7377   3.7295  -1.8799
 91Y  H13  H  H     0   0.215  -3.2589   3.6877  -0.1937
 91Y  H14  H  HCH2  0   0.256   4.2284  -1.3647  -1.0897
 91Y  H15  H  HCH2  0   0.266   3.8686  -0.0883  -2.2465
 91Y  H16  H  HCR6  0   0.248   6.6377   0.5436  -2.0384
 91Y  H17  H  HCR6  0   0.253   7.4792   2.6473   1.6010
 91Y  H18  H  HCR6  0   0.248   5.2566   2.0303   2.4965
 91Y  H19  H  H     0   0.220  -6.1536   0.9103  -0.0234
 91Y  H20  H  H     0   0.236  -5.6961   0.8556   1.6696
 91Y  H21  H  H     0   0.211  -6.0785   3.2205  -1.2692
 91Y  H22  H  H     0   0.230  -5.5319   4.6297  -0.3799
 91Y  H23  H  H     0   0.237  -2.6556   1.5826  -1.3047
 91Y  H24  H  H     0   0.229  -4.3127   1.3269  -1.8198
 91Y  C10  C  C     0   0.591   0.4853  -0.7425  -0.1082

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
 91Y  C25  C24  single    1.525  0.020  1.525
 91Y  C25  C26  single    1.524  0.020  1.524
 91Y  C24  C23  single    1.526  0.020  1.526
 91Y  C26  C27  single    1.525  0.020  1.525
 91Y  C23  C22  single    1.526  0.020  1.526
 91Y  O1   C2   double    1.211  0.020  1.211
 91Y  C27  C22  single    1.539  0.020  1.539
 91Y  C22  C2   single    1.517  0.020  1.517
 91Y  C2   N3   single    1.375  0.020  1.375
 91Y  N5   C6   aromatic  1.321  0.020  1.321
 91Y  N5   C4   aromatic  1.325  0.020  1.325
 91Y  C6   C7   aromatic  1.387  0.020  1.387
 91Y  N3   C4   single    1.374  0.020  1.374
 91Y  C4   C9   aromatic  1.415  0.020  1.415
 91Y  C7   N8   aromatic  1.320  0.020  1.320
 91Y  C9   N8   aromatic  1.321  0.020  1.321
 91Y  C9   C10  single    1.500  0.020  1.500
 91Y  C10  O11  double    1.232  0.020  1.232
 91Y  C10  N12  single    1.331  0.020  1.331
 91Y  N12  C13  single    1.442  0.020  1.442
 91Y  C13  C14  single    1.536  0.020  1.536
 91Y  C13  C21  single    1.542  0.020  1.542
 91Y  C14  C15  single    1.502  0.020  1.502
 91Y  C21  C20  single    1.501  0.020  1.501
 91Y  C15  C20  aromatic  1.394  0.020  1.394
 91Y  C15  C16  aromatic  1.386  0.020  1.386
 91Y  C20  C19  aromatic  1.386  0.020  1.386
 91Y  C16  C17  aromatic  1.392  0.020  1.392
 91Y  C19  C18  aromatic  1.391  0.020  1.391
 91Y  C17  C18  aromatic  1.391  0.020  1.391
 91Y  N3   H1   single    0.860  0.020  1.020
 91Y  C6   H2   single    0.930  0.020  1.080
 91Y  C7   H3   single    0.930  0.020  1.080
 91Y  N12  H4   single    0.860  0.020  1.020
 91Y  C13  H5   single    0.970  0.020  1.090
 91Y  C17  H6   single    0.930  0.020  1.080
 91Y  C21  H7   single    0.970  0.020  1.090
 91Y  C21  H8   single    0.970  0.020  1.090
 91Y  C22  H9   single    0.970  0.020  1.090
 91Y  C24  H10  single    0.970  0.020  1.090
 91Y  C24  H11  single    0.970  0.020  1.090
 91Y  C26  H12  single    0.970  0.020  1.090
 91Y  C26  H13  single    0.970  0.020  1.090
 91Y  C14  H14  single    0.970  0.020  1.090
 91Y  C14  H15  single    0.970  0.020  1.090
 91Y  C16  H16  single    0.930  0.020  1.080
 91Y  C18  H17  single    0.930  0.020  1.080
 91Y  C19  H18  single    0.930  0.020  1.080
 91Y  C23  H19  single    0.970  0.020  1.090
 91Y  C23  H20  single    0.970  0.020  1.090
 91Y  C25  H21  single    0.970  0.020  1.090
 91Y  C25  H22  single    0.970  0.020  1.090
 91Y  C27  H23  single    0.970  0.020  1.090
 91Y  C27  H24  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
 91Y  H1   N3   C2   117.59  3.000
 91Y  H1   N3   C4   112.80  3.000
 91Y  C2   N3   C4   129.27  3.000
 91Y  C9   C4   N5   120.12  3.000
 91Y  C9   C4   N3   120.00  3.000
 91Y  N5   C4   N3   119.88  3.000
 91Y  H2   C6   N5   117.13  3.000
 91Y  H2   C6   C7   120.77  3.000
 91Y  N5   C6   C7   122.09  3.000
 91Y  H3   C7   N8   118.26  3.000
 91Y  H3   C7   C6   121.81  3.000
 91Y  N8   C7   C6   119.93  3.000
 91Y  H4   N12  C13  119.09  3.000
 91Y  H4   N12  C10  117.27  3.000
 91Y  C13  N12  C10  123.40  3.000
 91Y  H5   C13  C14  108.38  3.000
 91Y  H5   C13  C21  108.20  3.000
 91Y  C14  C13  C21  105.00  3.000
 91Y  H5   C13  N12  108.22  3.000
 91Y  C21  C13  N12  114.73  3.000
 91Y  C14  C13  N12  112.09  3.000
 91Y  C16  C15  C14  128.93  3.000
 91Y  C16  C15  C20  120.58  3.000
 91Y  C14  C15  C20  110.48  3.000
 91Y  H6   C17  C18  119.72  3.000
 91Y  H6   C17  C16  119.84  3.000
 91Y  C18  C17  C16  120.44  3.000
 91Y  C19  C20  C21  129.12  3.000
 91Y  C19  C20  C15  120.48  3.000
 91Y  C21  C20  C15  110.40  3.000
 91Y  H8   C21  H7   107.29  3.000
 91Y  H8   C21  C20  110.73  3.000
 91Y  H7   C21  C20  113.83  3.000
 91Y  H8   C21  C13  110.27  3.000
 91Y  H7   C21  C13  112.39  3.000
 91Y  C20  C21  C13  102.33  3.000
 91Y  H9   C22  C27  107.69  3.000
 91Y  H9   C22  C23  108.53  3.000
 91Y  C27  C22  C23  110.49  3.000
 91Y  H9   C22  C2   108.01  3.000
 91Y  C27  C22  C2   109.90  3.000
 91Y  C23  C22  C2   112.08  3.000
 91Y  H11  C24  H10  106.43  3.000
 91Y  H11  C24  C25  109.41  3.000
 91Y  H10  C24  C25  110.34  3.000
 91Y  H11  C24  C23  109.49  3.000
 91Y  H10  C24  C23  109.57  3.000
 91Y  C25  C24  C23  111.47  3.000
 91Y  H13  C26  H12  106.53  3.000
 91Y  H13  C26  C27  108.95  3.000
 91Y  H12  C26  C27  109.53  3.000
 91Y  H13  C26  C25  109.38  3.000
 91Y  H12  C26  C25  110.60  3.000
 91Y  C27  C26  C25  111.70  3.000
 91Y  O1   C2   C22  123.53  3.000
 91Y  C22  C2   N3   112.12  3.000
 91Y  O1   C2   N3   124.33  3.000
 91Y  C6   N5   C4   118.19  3.000
 91Y  C9   N8   C7   119.32  3.000
 91Y  N8   C9   C10  116.56  3.000
 91Y  C10  C9   C4   123.09  3.000
 91Y  N8   C9   C4   120.34  3.000
 91Y  H15  C14  H14  107.15  3.000
 91Y  H15  C14  C15  113.74  3.000
 91Y  H14  C14  C15  110.31  3.000
 91Y  H15  C14  C13  112.49  3.000
 91Y  H14  C14  C13  110.72  3.000
 91Y  C15  C14  C13  102.45  3.000
 91Y  H16  C16  C17  120.35  3.000
 91Y  H16  C16  C15  120.66  3.000
 91Y  C17  C16  C15  118.99  3.000
 91Y  H17  C18  C19  119.79  3.000
 91Y  H17  C18  C17  119.73  3.000
 91Y  C19  C18  C17  120.48  3.000
 91Y  H18  C19  C18  120.21  3.000
 91Y  H18  C19  C20  120.76  3.000
 91Y  C18  C19  C20  119.03  3.000
 91Y  H20  C23  H19  106.74  3.000
 91Y  H20  C23  C24  110.05  3.000
 91Y  H19  C23  C24  109.25  3.000
 91Y  H20  C23  C22  110.26  3.000
 91Y  H19  C23  C22  109.42  3.000
 91Y  C24  C23  C22  111.02  3.000
 91Y  H22  C25  H21  106.54  3.000
 91Y  H22  C25  C26  110.20  3.000
 91Y  H21  C25  C26  109.38  3.000
 91Y  H22  C25  C24  110.28  3.000
 91Y  H21  C25  C24  109.38  3.000
 91Y  C26  C25  C24  110.94  3.000
 91Y  H24  C27  H23  106.58  3.000
 91Y  H24  C27  C26  109.80  3.000
 91Y  H23  C27  C26  109.56  3.000
 91Y  H24  C27  C22  109.01  3.000
 91Y  H23  C27  C22  110.88  3.000
 91Y  C26  C27  C22  110.92  3.000
 91Y  O11  C10  C9   121.73  3.000
 91Y  O11  C10  N12  123.48  3.000
 91Y  C9   C10  N12  114.80  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
 91Y  CONST_01  C7   C6   N5   C4     0.00   0.0  0
 91Y  CONST_02  C7   N8   C9   C4     0.00   0.0  0
 91Y  CONST_03  C9   C4   N5   C6     0.00   0.0  0
 91Y  CONST_04  C9   N8   C7   C6     0.00   0.0  0
 91Y  CONST_05  C18  C19  C20  C15    0.00   0.0  0
 91Y  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 91Y  CONST_07  C20  C15  C16  C17    0.00   0.0  0
 91Y  CONST_08  C20  C19  C18  C17    0.00   0.0  0
 91Y  CONST_09  N8   C7   C6   N5     0.00   0.0  0
 91Y  CONST_10  N8   C9   C4   N5     0.00   0.0  0
 91Y  CONST_11  C19  C20  C15  C16    0.00   0.0  0
 91Y  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 91Y  CONST_13  C6   N5   C4   N3   180.00   0.0  0
 91Y  CONST_14  N8   C9   C4   N3   180.00   0.0  0
 91Y  CONST_15  C10  C9   N8   C7   180.00   0.0  0
 91Y  CONST_16  N5   C4   C9   C10  180.00   0.0  0
 91Y  CONST_17  H2   C6   N5   C4   180.00   0.0  0
 91Y  CONST_18  H18  C19  C20  C15  180.00   0.0  0
 91Y  CONST_19  H6   C17  C16  C15  180.00   0.0  0
 91Y  CONST_20  H16  C16  C15  C20  180.00   0.0  0
 91Y  CONST_21  H17  C18  C19  C20  180.00   0.0  0
 91Y  CONST_22  H3   C7   C6   N5   180.00   0.0  0
 91Y  CONST_23  C22  C2   N3   C4   180.00   0.0  0
 91Y  CONST_24  N12  C10  C9   C4   180.00   0.0  0
 91Y  CONST_25  C9   C10  N12  C13  180.00   0.0  0
 91Y  CONST_26  N5   C4   N3   C2     0.00   0.0  0
 91Y  CONST_27  C9   C4   N3   C2   180.00   0.0  0
 91Y  CONST_28  H1   N3   C4   N5   180.00   0.0  0
 91Y  CONST_29  O1   C2   N3   C4     0.00   0.0  0
 91Y  CONST_30  O11  C10  N12  C13    0.00   0.0  0
 91Y  CONST_31  H4   N12  C10  C9     0.00   0.0  0
 91Y  Var_01    C20  C15  C14  C13   18.32  30.0  1
 91Y  Var_02    C15  C20  C21  C13  -18.51  30.0  1
 91Y  Var_03    C25  C24  C23  C22   56.43  30.0  1
 91Y  Var_04    C25  C26  C27  C22  -55.59  30.0  1
 91Y  Var_05    C27  C26  C25  C24   55.08  30.0  1
 91Y  Var_06    C23  C24  C25  C26  -55.31  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
 91Y  chir_01  C13  N12  C14  C21  positiv
 91Y  chir_02  C22  C23  C27  C2   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
 91Y  plan-1  C15  0.020
 91Y  plan-1  C17  0.020
 91Y  plan-1  C20  0.020
 91Y  plan-1  C21  0.020
 91Y  plan-1  C14  0.020
 91Y  plan-1  C16  0.020
 91Y  plan-1  C18  0.020
 91Y  plan-1  C19  0.020
 91Y  plan-1  H6   0.020
 91Y  plan-1  H16  0.020
 91Y  plan-1  H17  0.020
 91Y  plan-1  H18  0.020
 91Y  plan-2  N3   0.020
 91Y  plan-2  C4   0.020
 91Y  plan-2  C22  0.020
 91Y  plan-2  O1   0.020
 91Y  plan-2  C2   0.020
 91Y  plan-2  H1   0.020
 91Y  plan-3  N3   0.020
 91Y  plan-3  C4   0.020
 91Y  plan-3  C6   0.020
 91Y  plan-3  C7   0.020
 91Y  plan-3  N12  0.020
 91Y  plan-3  C13  0.020
 91Y  plan-3  N5   0.020
 91Y  plan-3  N8   0.020
 91Y  plan-3  C9   0.020
 91Y  plan-3  O11  0.020
 91Y  plan-3  H2   0.020
 91Y  plan-3  H3   0.020
 91Y  plan-3  H4   0.020
 91Y  plan-3  C10  0.020

