# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:23:14 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: ~{N}-[(4-methylphenyl)methyl]-1~{H}-pyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CNC(=O)c2[nH]ccc2)cc1
#
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
 DKR  DKR  ~{N}-[(4-methylphenyl)methyl]-1~{H}-pyrrole-2-carboxamide  ligand  30  16  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DKR
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
 DKR  C10   C  CR6   0   0.080  19.0651  25.0477  83.4529
 DKR  C13   C  CR6   0   0.083  20.4799  25.4873  81.0507
 DKR  C15   C  CR16  0  -0.288  18.4577  25.6730  82.3682
 DKR  C02   C  CR15  0  -0.044  19.5889  19.4676  86.9114
 DKR  C03   C  CR15  0  -0.348  20.1433  20.3400  87.8246
 DKR  C04   C  CR15  0  -0.366  19.8568  21.6444  87.3756
 DKR  C05   C  CR5   0   0.228  19.1359  21.5262  86.2025
 DKR  C06   C  C     0   0.492  18.5589  22.5075  85.2780
 DKR  C09   C  CH2   0  -0.335  18.2939  24.8709  84.7404
 DKR  C11   C  CR16  0  -0.277  20.3872  24.6412  83.3207
 DKR  C12   C  CR16  0  -0.288  21.0801  24.8550  82.1364
 DKR  C14   C  CR16  0  -0.287  19.1535  25.8914  81.1883
 DKR  C16   C  CH3   0  -0.722  21.2413  25.7435  79.7823
 DKR  N01   N  NR15  0  -0.607  18.9885  20.1955  85.9479
 DKR  N07   N  NH1   0  -0.662  18.7683  23.8017  85.5809
 DKR  O08   O  O     0  -0.498  17.9206  22.1532  84.2924
 DKR  H151  H  HCR6  0   0.244  17.4231  25.9891  82.4418
 DKR  H031  H  HCR5  0   0.254  20.6899  20.0656  88.7126
 DKR  H041  H  HCR5  0   0.255  20.1456  22.5628  87.8638
 DKR  H091  H  HCH2  0   0.274  18.3566  25.7865  85.3304
 DKR  H092  H  HCH2  0   0.255  17.2357  24.7249  84.5145
 DKR  H111  H  HCR6  0   0.239  20.8862  24.1419  84.1422
 DKR  H121  H  HCR6  0   0.244  22.1079  24.5197  82.0563
 DKR  H141  H  HCR6  0   0.244  18.6528  26.3767  80.3584
 DKR  H161  H  HCH3  0   0.246  21.7050  26.7324  79.7963
 DKR  H163  H  HCH3  0   0.242  22.0386  25.0147  79.6400
 DKR  H162  H  HCH3  0   0.242  20.5903  25.7065  78.9089
 DKR  H1    H  HNR5  0   0.412  18.5049  19.8219  85.1466
 DKR  H071  H  HNH1  0   0.408  19.3200  24.0426  86.3867
 DKR  H021  H  HCR5  0   0.278  19.5797  18.3905  86.8872

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
 DKR  C16  C13   single    1.501  0.020  1.501
 DKR  C13  C14   aromatic  1.393  0.020  1.393
 DKR  C13  C12   aromatic  1.392  0.020  1.392
 DKR  C14  C15   aromatic  1.387  0.020  1.387
 DKR  C12  C11   aromatic  1.389  0.020  1.389
 DKR  C15  C10   aromatic  1.392  0.020  1.392
 DKR  C11  C10   aromatic  1.390  0.020  1.390
 DKR  C10  C09   single    1.511  0.020  1.511
 DKR  O08  C06   double    1.226  0.020  1.226
 DKR  C09  N07   single    1.440  0.020  1.440
 DKR  C06  N07   single    1.346  0.020  1.346
 DKR  C06  C05   single    1.466  0.020  1.466
 DKR  N01  C05   aromatic  1.363  0.020  1.363
 DKR  N01  C02   aromatic  1.349  0.020  1.349
 DKR  C05  C04   aromatic  1.382  0.020  1.382
 DKR  C02  C03   aromatic  1.379  0.020  1.379
 DKR  C04  C03   aromatic  1.409  0.020  1.409
 DKR  C15  H151  single    0.930  0.020  1.080
 DKR  C02  H021  single    0.930  0.020  1.080
 DKR  C03  H031  single    0.930  0.020  1.080
 DKR  C04  H041  single    0.930  0.020  1.080
 DKR  C09  H091  single    0.970  0.020  1.090
 DKR  C09  H092  single    0.970  0.020  1.090
 DKR  C11  H111  single    0.930  0.020  1.080
 DKR  C12  H121  single    0.930  0.020  1.080
 DKR  C14  H141  single    0.930  0.020  1.080
 DKR  C16  H161  single    0.970  0.020  1.090
 DKR  C16  H163  single    0.970  0.020  1.090
 DKR  C16  H162  single    0.970  0.020  1.090
 DKR  N01  H1    single    0.860  0.020  1.020
 DKR  N07  H071  single    0.860  0.020  1.020

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
 DKR  C11   C10  C09   122.17  3.000
 DKR  C09   C10  C15   119.60  3.000
 DKR  C11   C10  C15   118.20  3.000
 DKR  C16   C13  C14   121.11  3.000
 DKR  C14   C13  C12   117.71  3.000
 DKR  C16   C13  C12   121.17  3.000
 DKR  H151  C15  C14   119.37  3.000
 DKR  H151  C15  C10   119.64  3.000
 DKR  C14   C15  C10   120.99  3.000
 DKR  H021  C02  N01   121.32  3.000
 DKR  H021  C02  C03   130.59  3.000
 DKR  N01   C02  C03   108.09  3.000
 DKR  H031  C03  C04   126.95  3.000
 DKR  H031  C03  C02   126.02  3.000
 DKR  C04   C03  C02   107.03  3.000
 DKR  H041  C04  C05   126.60  3.000
 DKR  H041  C04  C03   126.09  3.000
 DKR  C05   C04  C03   107.31  3.000
 DKR  N01   C05  C06   119.54  3.000
 DKR  N01   C05  C04   107.36  3.000
 DKR  C06   C05  C04   133.10  3.000
 DKR  O08   C06  N07   122.66  3.000
 DKR  N07   C06  C05   116.13  3.000
 DKR  O08   C06  C05   121.21  3.000
 DKR  H092  C09  H091  106.24  3.000
 DKR  H092  C09  N07   109.92  3.000
 DKR  H091  C09  N07   106.76  3.000
 DKR  H092  C09  C10   109.51  3.000
 DKR  H091  C09  C10   109.47  3.000
 DKR  N07   C09  C10   114.58  3.000
 DKR  H111  C11  C12   119.20  3.000
 DKR  H111  C11  C10   120.07  3.000
 DKR  C12   C11  C10   120.72  3.000
 DKR  H121  C12  C11   119.24  3.000
 DKR  H121  C12  C13   119.44  3.000
 DKR  C11   C12  C13   121.32  3.000
 DKR  H141  C14  C15   119.35  3.000
 DKR  H141  C14  C13   119.60  3.000
 DKR  C15   C14  C13   121.05  3.000
 DKR  H162  C16  H163  108.04  3.000
 DKR  H162  C16  H161  107.13  3.000
 DKR  H163  C16  H161  107.26  3.000
 DKR  H162  C16  C13   111.60  3.000
 DKR  H163  C16  C13   111.55  3.000
 DKR  H161  C16  C13   111.04  3.000
 DKR  H1    N01  C05   124.22  3.000
 DKR  H1    N01  C02   125.57  3.000
 DKR  C05   N01  C02   110.21  3.000
 DKR  H071  N07  C09   118.06  3.000
 DKR  H071  N07  C06   119.74  3.000
 DKR  C09   N07  C06   122.09  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
 DKR  CONST_01  C13   C14  C15  C10     0.00   0.0  0
 DKR  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 DKR  CONST_03  C12   C13  C14  C15     0.00   0.0  0
 DKR  CONST_04  C12   C11  C10  C15     0.00   0.0  0
 DKR  CONST_05  C04   C05  N01  C02     0.00   0.0  0
 DKR  CONST_06  C05   C04  C03  C02     0.00   0.0  0
 DKR  CONST_07  C05   N01  C02  C03     0.00   0.0  0
 DKR  CONST_08  N01   C05  C04  C03     0.00   0.0  0
 DKR  CONST_09  N01   C02  C03  C04     0.00   0.0  0
 DKR  CONST_10  C14   C13  C12  C11     0.00   0.0  0
 DKR  CONST_11  C14   C15  C10  C11     0.00   0.0  0
 DKR  CONST_12  C16   C13  C14  C15   180.00   0.0  0
 DKR  CONST_13  C06   C05  N01  C02   180.00   0.0  0
 DKR  CONST_14  C06   C05  C04  C03   180.00   0.0  0
 DKR  CONST_15  C14   C15  C10  C09   180.00   0.0  0
 DKR  CONST_16  C12   C11  C10  C09   180.00   0.0  0
 DKR  CONST_17  C16   C13  C12  C11   180.00   0.0  0
 DKR  CONST_18  H141  C14  C15  C10   180.00   0.0  0
 DKR  CONST_19  H121  C12  C11  C10   180.00   0.0  0
 DKR  CONST_20  H151  C15  C14  C13   180.00   0.0  0
 DKR  CONST_21  H111  C11  C12  C13   180.00   0.0  0
 DKR  CONST_22  H041  C04  C03  C02   180.00   0.0  0
 DKR  CONST_23  H1    N01  C02  C03   180.00   0.0  0
 DKR  CONST_24  H021  C02  C03  C04   180.00   0.0  0
 DKR  CONST_25  H031  C03  C04  C05   180.00   0.0  0
 DKR  CONST_26  C09   N07  C06  C05   180.00   0.0  0
 DKR  CONST_27  H071  N07  C06  C05     0.00   0.0  0
 DKR  CONST_28  O08   C06  N07  C09     0.00   0.0  0
 DKR  Var_01    N07   C09  C10  C15   156.79  30.0  2
 DKR  Var_02    O08   C06  C05  C04  -178.38  30.0  3
 DKR  Var_03    H161  C16  C13  C12   -92.32  30.0  2
 DKR  Var_04    C06   N07  C09  C10   -73.34  30.0  3

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
 DKR  plan-1  C02   0.020
 DKR  plan-1  C03   0.020
 DKR  plan-1  C04   0.020
 DKR  plan-1  C05   0.020
 DKR  plan-1  C06   0.020
 DKR  plan-1  N01   0.020
 DKR  plan-1  H031  0.020
 DKR  plan-1  H041  0.020
 DKR  plan-1  H1    0.020
 DKR  plan-1  H021  0.020
 DKR  plan-2  C10   0.020
 DKR  plan-2  C13   0.020
 DKR  plan-2  C15   0.020
 DKR  plan-2  C09   0.020
 DKR  plan-2  C11   0.020
 DKR  plan-2  C12   0.020
 DKR  plan-2  C14   0.020
 DKR  plan-2  C16   0.020
 DKR  plan-2  H151  0.020
 DKR  plan-2  H111  0.020
 DKR  plan-2  H121  0.020
 DKR  plan-2  H141  0.020
 DKR  plan-3  C05   0.020
 DKR  plan-3  C06   0.020
 DKR  plan-3  C09   0.020
 DKR  plan-3  N07   0.020
 DKR  plan-3  O08   0.020
 DKR  plan-3  H071  0.020

