# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 22:15:26 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2R)-2-cyano-3-[3-(1H-pyrrolo[2,3-b]pyridin-3-ylcarbonyl)phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@H](Cc1cccc(c1)C(=O)c2c[nH]c3ncccc23)C#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
 1LC  1LC  (2R)-2-cyano-3-[3-(1H-pyrrolo[2,3-b]pyridin-3-ylcarbonyl)phenyl]propanamide  ligand  38  24  .  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_1LC
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
 1LC  O01   O  O     0  -0.416  -1.3145  -0.8285   1.8352
 1LC  C02   C  C     0   0.320  -1.2838  -0.0136   0.9258
 1LC  C03   C  CR6   0  -0.006  -0.0581   0.8090   0.7107
 1LC  C04   C  CR16  0  -0.336   1.1863   0.2126   0.9118
 1LC  C05   C  CR6   0   0.133   2.3603   0.9366   0.7588
 1LC  C06   C  CH2   0  -0.513   3.6999   0.2744   0.9184
 1LC  C07   C  CH1   0  -0.493   4.3005  -0.1164  -0.4407
 1LC  C08   C  CSP   0   0.147   3.4324  -1.0573  -1.1371
 1LC  N09   N  NS    0  -0.252   2.7447  -1.8091  -1.6710
 1LC  C10   C  C     0   0.574   5.7191  -0.7080  -0.3129
 1LC  N11   N  NH2   0  -0.799   6.2699  -1.0772  -1.4722
 1LC  O12   O  O     0  -0.456   6.2633  -0.8038   0.7692
 1LC  C13   C  CR16  0  -0.302   2.2773   2.2886   0.4281
 1LC  C14   C  CR16  0  -0.224   1.0458   2.8983   0.2527
 1LC  C15   C  CR16  0  -0.310  -0.1230   2.1610   0.3849
 1LC  C16   C  CR5   0  -0.206  -2.4141   0.1550   0.0324
 1LC  C17   C  CR15  0   0.013  -2.4317   0.7890  -1.1943
 1LC  N18   N  NR15  0  -0.657  -3.6519   0.6795  -1.7543
 1LC  C19   C  CR56  0   0.469  -4.4794  -0.0278  -0.9216
 1LC  N20   N  N     0  -0.419  -5.7459  -0.3092  -1.1627
 1LC  C21   C  CR16  0  -0.084  -6.3520  -1.0098  -0.2141
 1LC  C22   C  CR16  0  -0.335  -5.7275  -1.4328   0.9628
 1LC  C23   C  CR16  0  -0.236  -4.3971  -1.1254   1.1939
 1LC  C24   C  CR56  0   0.029  -3.7321  -0.3890   0.2168
 1LC  H041  H  HCR6  0   0.259   1.2387  -0.8358   1.1805
 1LC  H062  H  HCH2  0   0.288   4.4000   0.9555   1.4025
 1LC  H061  H  HCH2  0   0.281   3.6198  -0.6104   1.5506
 1LC  H071  H  HCH1  0   0.361   4.3695   0.7773  -1.0723
 1LC  H112  H  HNH2  0   0.414   7.1998  -1.4655  -1.4896
 1LC  H111  H  HNH2  0   0.418   5.8145  -0.9380  -2.3588
 1LC  H131  H  HCR6  0   0.261   3.1847   2.8709   0.3172
 1LC  H141  H  HCR6  0   0.265   0.9928   3.9532   0.0184
 1LC  H151  H  HCR6  0   0.275  -1.0791   2.6533   0.2643
 1LC  H171  H  HCR5  0   0.317  -1.6367   1.2940  -1.7186
 1LC  H181  H  HNR5  0   0.424  -3.9129   1.0500  -2.6551
 1LC  H211  H  HCR6  0   0.262  -7.3929  -1.2556  -0.3886
 1LC  H1    H  HCR6  0   0.270  -6.2938  -2.0035   1.6855
 1LC  H231  H  HCR6  0   0.265  -3.9010  -1.4510   2.0969

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
 1LC  C21  N20   aromatic  1.326  0.020  1.326
 1LC  C21  C22   aromatic  1.398  0.020  1.398
 1LC  N20  C19   aromatic  1.320  0.020  1.320
 1LC  C22  C23   aromatic  1.385  0.020  1.385
 1LC  C19  N18   aromatic  1.371  0.020  1.371
 1LC  C19  C24   aromatic  1.409  0.020  1.409
 1LC  C23  C24   aromatic  1.393  0.020  1.393
 1LC  N18  C17   aromatic  1.347  0.020  1.347
 1LC  C24  C16   aromatic  1.438  0.020  1.438
 1LC  C17  C16   aromatic  1.381  0.020  1.381
 1LC  C16  C02   single    1.451  0.020  1.451
 1LC  N11  C10   single    1.336  0.020  1.336
 1LC  C02  O01   double    1.221  0.020  1.221
 1LC  C02  C03   single    1.492  0.020  1.492
 1LC  C04  C03   aromatic  1.395  0.020  1.395
 1LC  C04  C05   aromatic  1.388  0.020  1.388
 1LC  C03  C15   aromatic  1.392  0.020  1.392
 1LC  C10  O12   double    1.215  0.020  1.215
 1LC  C10  C07   single    1.542  0.020  1.542
 1LC  C06  C05   single    1.503  0.020  1.503
 1LC  C06  C07   single    1.536  0.020  1.536
 1LC  C05  C13   aromatic  1.394  0.020  1.394
 1LC  C07  C08   single    1.457  0.020  1.457
 1LC  C15  C14   aromatic  1.388  0.020  1.388
 1LC  C13  C14   aromatic  1.385  0.020  1.385
 1LC  C08  N09   triple    1.150  0.020  1.150
 1LC  C04  H041  single    0.930  0.020  1.080
 1LC  C06  H062  single    0.970  0.020  1.090
 1LC  C06  H061  single    0.970  0.020  1.090
 1LC  C07  H071  single    0.970  0.020  1.090
 1LC  N11  H112  single    0.860  0.020  1.020
 1LC  N11  H111  single    0.860  0.020  1.020
 1LC  C13  H131  single    0.930  0.020  1.080
 1LC  C14  H141  single    0.930  0.020  1.080
 1LC  C15  H151  single    0.930  0.020  1.080
 1LC  C17  H171  single    0.930  0.020  1.080
 1LC  N18  H181  single    0.860  0.020  1.020
 1LC  C21  H211  single    0.930  0.020  1.080
 1LC  C22  H1    single    0.930  0.020  1.080
 1LC  C23  H231  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
 1LC  C16   C02  C03   119.16  3.000
 1LC  C03   C02  O01   119.73  3.000
 1LC  C16   C02  O01   121.10  3.000
 1LC  C15   C03  C04   119.38  3.000
 1LC  C15   C03  C02   122.08  3.000
 1LC  C04   C03  C02   118.46  3.000
 1LC  H041  C04  C05   119.42  3.000
 1LC  H041  C04  C03   119.52  3.000
 1LC  C05   C04  C03   121.05  3.000
 1LC  C13   C05  C06   120.36  3.000
 1LC  C13   C05  C04   118.80  3.000
 1LC  C06   C05  C04   120.83  3.000
 1LC  H061  C06  H062  107.26  3.000
 1LC  H061  C06  C07   109.58  3.000
 1LC  H062  C06  C07   107.50  3.000
 1LC  H061  C06  C05   110.71  3.000
 1LC  H062  C06  C05   110.14  3.000
 1LC  C07   C06  C05   111.50  3.000
 1LC  H071  C07  C10   107.61  3.000
 1LC  H071  C07  C08   106.76  3.000
 1LC  C10   C07  C08   109.87  3.000
 1LC  H071  C07  C06   109.08  3.000
 1LC  C08   C07  C06   110.74  3.000
 1LC  C10   C07  C06   112.57  3.000
 1LC  N09   C08  C07   180.00  3.000
 1LC  O12   C10  N11   124.51  3.000
 1LC  O12   C10  C07   121.07  3.000
 1LC  N11   C10  C07   114.42  3.000
 1LC  H111  N11  H112  117.11  3.000
 1LC  H111  N11  C10   122.67  3.000
 1LC  H112  N11  C10   120.13  3.000
 1LC  H131  C13  C14   119.66  3.000
 1LC  H131  C13  C05   119.69  3.000
 1LC  C14   C13  C05   120.64  3.000
 1LC  H141  C14  C15   119.82  3.000
 1LC  H141  C14  C13   120.00  3.000
 1LC  C15   C14  C13   120.17  3.000
 1LC  H151  C15  C14   119.45  3.000
 1LC  H151  C15  C03   120.59  3.000
 1LC  C14   C15  C03   119.92  3.000
 1LC  C24   C16  C17   106.02  3.000
 1LC  C17   C16  C02   127.62  3.000
 1LC  C24   C16  C02   126.25  3.000
 1LC  H171  C17  N18   120.26  3.000
 1LC  H171  C17  C16   129.63  3.000
 1LC  N18   C17  C16   110.09  3.000
 1LC  H181  N18  C19   125.18  3.000
 1LC  H181  N18  C17   125.17  3.000
 1LC  C19   N18  C17   109.65  3.000
 1LC  C24   C19  N20   127.02  3.000
 1LC  C24   C19  N18   107.64  3.000
 1LC  N20   C19  N18   125.34  3.000
 1LC  C21   N20  C19   114.88  3.000
 1LC  H211  C21  C22   119.74  3.000
 1LC  H211  C21  N20   116.34  3.000
 1LC  C22   C21  N20   123.92  3.000
 1LC  H1    C22  C23   120.59  3.000
 1LC  H1    C22  C21   119.24  3.000
 1LC  C23   C22  C21   120.17  3.000
 1LC  H231  C23  C24   121.77  3.000
 1LC  H231  C23  C22   120.91  3.000
 1LC  C24   C23  C22   117.32  3.000
 1LC  C23   C24  C19   116.70  3.000
 1LC  C23   C24  C16   136.70  3.000
 1LC  C19   C24  C16   106.60  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
 1LC  CONST_01  C13   C05  C04  C03     0.00   0.0  0
 1LC  CONST_02  C13   C14  C15  C03     0.00   0.0  0
 1LC  CONST_03  C14   C15  C03  C04     0.00   0.0  0
 1LC  CONST_04  C14   C13  C05  C04     0.00   0.0  0
 1LC  CONST_05  C15   C03  C04  C05     0.00   0.0  0
 1LC  CONST_06  C15   C14  C13  C05     0.00   0.0  0
 1LC  CONST_07  N20   C19  C24  C16   180.00   0.0  0
 1LC  CONST_08  N18   C19  C24  C16     0.00   0.0  0
 1LC  CONST_09  C22   C23  C24  C16   180.00   0.0  0
 1LC  CONST_10  C19   N18  C17  C16     0.00   0.0  0
 1LC  CONST_11  N20   C19  N18  C17   180.00   0.0  0
 1LC  CONST_12  C24   C19  N18  C17     0.00   0.0  0
 1LC  CONST_13  C19   C24  C16  C17     0.00   0.0  0
 1LC  CONST_14  C23   C24  C16  C17   180.00   0.0  0
 1LC  CONST_15  C21   N20  C19  N18   180.00   0.0  0
 1LC  CONST_16  C23   C24  C19  N18   180.00   0.0  0
 1LC  CONST_17  C24   C16  C17  N18     0.00   0.0  0
 1LC  CONST_18  C22   C21  N20  C19     0.00   0.0  0
 1LC  CONST_19  C22   C23  C24  C19     0.00   0.0  0
 1LC  CONST_20  C23   C22  C21  N20     0.00   0.0  0
 1LC  CONST_21  C23   C24  C19  N20     0.00   0.0  0
 1LC  CONST_22  C24   C19  N20  C21     0.00   0.0  0
 1LC  CONST_23  C24   C23  C22  C21     0.00   0.0  0
 1LC  CONST_24  C19   C24  C16  C02   180.00   0.0  0
 1LC  CONST_25  C23   C24  C16  C02     0.00   0.0  0
 1LC  CONST_26  N18   C17  C16  C02   180.00   0.0  0
 1LC  CONST_27  C05   C04  C03  C02   180.00   0.0  0
 1LC  CONST_28  C14   C15  C03  C02   180.00   0.0  0
 1LC  CONST_29  C06   C05  C04  C03   180.00   0.0  0
 1LC  CONST_30  C14   C13  C05  C06   180.00   0.0  0
 1LC  CONST_31  H141  C14  C15  C03   180.00   0.0  0
 1LC  CONST_32  H151  C15  C03  C04   180.00   0.0  0
 1LC  CONST_33  H131  C13  C05  C04   180.00   0.0  0
 1LC  CONST_34  H041  C04  C05  C13   180.00   0.0  0
 1LC  CONST_35  H231  C23  C24  C16     0.00   0.0  0
 1LC  CONST_36  H181  N18  C17  C16   180.00   0.0  0
 1LC  CONST_37  H211  C21  N20  C19   180.00   0.0  0
 1LC  CONST_38  H171  C17  N18  C19   180.00   0.0  0
 1LC  CONST_39  H1    C22  C21  N20   180.00   0.0  0
 1LC  CONST_40  H112  N11  C10  C07   180.00   0.0  0
 1LC  CONST_41  H111  N11  C10  C07     0.00   0.0  0
 1LC  Var_01    C24   C16  C02  C03  -169.41  30.0  2
 1LC  Var_02    C16   C02  C03  C04  -141.60  30.0  2
 1LC  Var_03    C07   C06  C05  C04    97.74  30.0  2

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
 1LC  chir_01  C07  C10  C06  C08  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
 1LC  plan-1  C02   0.020
 1LC  plan-1  C03   0.020
 1LC  plan-1  C04   0.020
 1LC  plan-1  C05   0.020
 1LC  plan-1  C06   0.020
 1LC  plan-1  C13   0.020
 1LC  plan-1  C14   0.020
 1LC  plan-1  C15   0.020
 1LC  plan-1  H041  0.020
 1LC  plan-1  H131  0.020
 1LC  plan-1  H141  0.020
 1LC  plan-1  H151  0.020
 1LC  plan-2  C02   0.020
 1LC  plan-2  C16   0.020
 1LC  plan-2  C17   0.020
 1LC  plan-2  N18   0.020
 1LC  plan-2  C19   0.020
 1LC  plan-2  N20   0.020
 1LC  plan-2  C21   0.020
 1LC  plan-2  C22   0.020
 1LC  plan-2  C23   0.020
 1LC  plan-2  C24   0.020
 1LC  plan-2  H171  0.020
 1LC  plan-2  H181  0.020
 1LC  plan-2  H211  0.020
 1LC  plan-2  H1    0.020
 1LC  plan-2  H231  0.020
 1LC  plan-3  C07   0.020
 1LC  plan-3  C10   0.020
 1LC  plan-3  N11   0.020
 1LC  plan-3  O12   0.020
 1LC  plan-3  H112  0.020
 1LC  plan-3  H111  0.020
 1LC  plan-4  O01   0.020
 1LC  plan-4  C02   0.020
 1LC  plan-4  C03   0.020
 1LC  plan-4  C16   0.020

