# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:34:25 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-{(S)-(2-chlorophenyl)[(4,4-difluorocyclohexyl)methoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccnc2cc([nH]c12)[C@@H](OCC3CCC(F)(F)CC3)c4ccccc4Cl
#
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
 DKV  DKV  '2-{(S)-(2-chlorophenyl)[(4,4-difluorocyclohexyl)methoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid'  ligand  50  30  .  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_DKV
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
 DKV  C10  C   CR5    0   0.373  -1.4422   0.2124   0.7540
 DKV  C13  C   CR16   0  -0.323  -0.2977   2.0411  -1.7559
 DKV  C15  C   CR16   0  -0.274  -1.3050   4.1381  -2.3499
 DKV  C17  C   CR6    0  -0.102  -1.3129   3.3863  -0.0758
 DKV  C21  C   CH1    0  -0.292   3.1850   0.1473  -0.0746
 DKV  C22  C   CH2    0  -0.449   4.4999   0.9248  -0.1351
 DKV  C24  C   CT     0   0.757   5.7670  -1.1723   0.3735
 DKV  C28  C   CH2    0  -0.437   3.3134  -1.0464   0.8723
 DKV  C02  C   C      0   0.421  -3.1503  -2.8859  -1.9260
 DKV  C03  C   CR6    0  -0.062  -3.5619  -2.3809  -0.5534
 DKV  C04  C   CR16   0  -0.397  -4.6533  -2.8778   0.1419
 DKV  C05  C   CR16   0  -0.116  -4.9853  -2.3794   1.4077
 DKV  C07  C   CR56   0   0.166  -3.2615  -0.9273   1.3911
 DKV  C08  C   CR56   0   0.263  -2.8630  -1.3739   0.1077
 DKV  C11  C   CH1    0  -0.087  -0.2875   1.1510   0.6095
 DKV  C12  C   CR6    0   0.156  -0.6292   2.2232  -0.4152
 DKV  C14  C   CR16   0  -0.227  -0.6274   2.9838  -2.7163
 DKV  C16  C   CR16   0  -0.198  -1.6502   4.3420  -1.0236
 DKV  C23  C   CH2    0  -0.556   5.6650   0.0261  -0.5390
 DKV  C27  C   CH2    0  -0.559   4.4787  -1.9525   0.4817
 DKV  C29  C   CR15   0  -0.441  -2.3356   0.0870   1.7819
 DKV  F25  F   F      0  -0.359   6.1521  -0.7552   1.6278
 DKV  F26  F   F      0  -0.357   6.7799  -1.9975  -0.0482
 DKV  N06  N   N      0  -0.433  -4.3178  -1.4263   2.0378
 DKV  N09  N   NR15   0  -0.710  -1.7654  -0.6570  -0.2493
 DKV  O01  O   O      0  -0.592  -2.1348  -2.3486  -2.4189
 DKV  O19  O   O2     0  -0.486   0.8276   0.3925   0.2285
 DKV  O30  O   OC    -1  -0.576  -3.8493  -3.7774  -2.4319
 DKV  H1   H   HCR6   0   0.269   0.2410   1.1502  -2.0537
 DKV  H2   H   HCR6   0   0.269  -1.5661   4.8818  -3.0908
 DKV  H3   H   HCH2   0   0.212   2.2121   1.4419   1.3511
 DKV  H4   H   HCH2   0   0.221   2.0621   1.9607  -0.3338
 DKV  H5   H   HCH1   0   0.233   2.9704  -0.2284  -1.0838
 DKV  H6   H   HCH2   0   0.250   4.4209   1.7434  -0.8535
 DKV  H7   H   HCH2   0   0.231   4.7038   1.3836   0.8374
 DKV  H8   H   HCH2   0   0.225   3.4494  -0.6821   1.8959
 DKV  H9   H   HCH2   0   0.252   2.3958  -1.6358   0.8727
 DKV  H10  H   HCR6   0   0.252  -5.2597  -3.6603  -0.2940
 DKV  H11  H   HCR6   0   0.244  -5.8443  -2.7896   1.9281
 DKV  H12  H   HCH1   0   0.257  -0.1147   1.6271   1.5834
 DKV  H13  H   HCR6   0   0.265  -0.3540   2.8156  -3.7493
 DKV  H14  H   HCR6   0   0.280  -2.1788   5.2373  -0.7256
 DKV  H15  H   HCH2   0   0.251   5.5120  -0.3368  -1.5588
 DKV  H16  H   HCH2   0   0.266   6.6059   0.5815  -0.5313
 DKV  H17  H   HCH2   0   0.249   4.2768  -2.4093  -0.4908
 DKV  H18  H   HCH2   0   0.265   4.5959  -2.7652   1.2024
 DKV  H19  H   HCR5   0   0.252  -2.3315   0.6545   2.6987
 DKV  H20  H   HNR5   0   0.401  -1.2790  -0.8204  -1.1176
 DKV  C20  C   CH2    0  -0.125   2.0589   1.0816   0.3236
 DKV  CL1  CL  CL     0  -0.124  -1.7796   3.6807   1.5721

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
 DKV  F26  C24  single    1.373  0.020  1.373
 DKV  C24  F25  single    1.377  0.020  1.377
 DKV  C24  C23  single    1.510  0.020  1.510
 DKV  C24  C27  single    1.510  0.020  1.510
 DKV  C23  C22  single    1.526  0.020  1.526
 DKV  C27  C28  single    1.527  0.020  1.527
 DKV  C22  C21  single    1.529  0.020  1.529
 DKV  C28  C21  single    1.529  0.020  1.529
 DKV  C21  C20  single    1.516  0.020  1.516
 DKV  C20  O19  single    1.414  0.020  1.414
 DKV  O19  C11  single    1.401  0.020  1.401
 DKV  C29  C07  aromatic  1.428  0.020  1.428
 DKV  C29  C10  aromatic  1.368  0.020  1.368
 DKV  C13  C14  aromatic  1.386  0.020  1.386
 DKV  C13  C12  aromatic  1.393  0.020  1.393
 DKV  N06  C07  aromatic  1.335  0.020  1.335
 DKV  N06  C05  aromatic  1.323  0.020  1.323
 DKV  C11  C10  single    1.495  0.020  1.495
 DKV  C11  C12  single    1.522  0.020  1.522
 DKV  C14  C15  aromatic  1.388  0.020  1.388
 DKV  C07  C08  aromatic  1.416  0.020  1.416
 DKV  C10  N09  aromatic  1.366  0.020  1.366
 DKV  C12  C17  aromatic  1.391  0.020  1.391
 DKV  C05  C04  aromatic  1.400  0.020  1.400
 DKV  C15  C16  aromatic  1.386  0.020  1.386
 DKV  C08  N09  aromatic  1.359  0.020  1.359
 DKV  C08  C03  aromatic  1.393  0.020  1.393
 DKV  C17  C16  aromatic  1.388  0.020  1.388
 DKV  C17  CL1  single    1.738  0.020  1.738
 DKV  C04  C03  aromatic  1.386  0.020  1.386
 DKV  C03  C02  single    1.519  0.020  1.519
 DKV  C02  O01  deloc     1.250  0.020  1.250
 DKV  C02  O30  deloc     1.241  0.020  1.241
 DKV  C13  H1   single    0.930  0.020  1.080
 DKV  C15  H2   single    0.930  0.020  1.080
 DKV  C20  H3   single    0.970  0.020  1.090
 DKV  C20  H4   single    0.970  0.020  1.090
 DKV  C21  H5   single    0.970  0.020  1.090
 DKV  C22  H6   single    0.970  0.020  1.090
 DKV  C22  H7   single    0.970  0.020  1.090
 DKV  C28  H8   single    0.970  0.020  1.090
 DKV  C28  H9   single    0.970  0.020  1.090
 DKV  C04  H10  single    0.930  0.020  1.080
 DKV  C05  H11  single    0.930  0.020  1.080
 DKV  C11  H12  single    0.970  0.020  1.090
 DKV  C14  H13  single    0.930  0.020  1.080
 DKV  C16  H14  single    0.930  0.020  1.080
 DKV  C23  H15  single    0.970  0.020  1.090
 DKV  C23  H16  single    0.970  0.020  1.090
 DKV  C27  H17  single    0.970  0.020  1.090
 DKV  C27  H18  single    0.970  0.020  1.090
 DKV  C29  H19  single    0.930  0.020  1.080
 DKV  N09  H20  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
 DKV  N09  C10  C29  109.82  3.000
 DKV  N09  C10  C11  120.74  3.000
 DKV  C29  C10  C11  129.40  3.000
 DKV  H1   C13  C14  119.18  3.000
 DKV  H1   C13  C12  119.39  3.000
 DKV  C14  C13  C12  121.43  3.000
 DKV  H2   C15  C16  119.62  3.000
 DKV  H2   C15  C14  120.59  3.000
 DKV  C16  C15  C14  119.79  3.000
 DKV  CL1  C17  C16  117.76  3.000
 DKV  CL1  C17  C12  120.33  3.000
 DKV  C16  C17  C12  121.91  3.000
 DKV  H5   C21  C28  108.57  3.000
 DKV  H5   C21  C22  107.80  3.000
 DKV  C28  C21  C22  110.44  3.000
 DKV  H5   C21  C20  107.88  3.000
 DKV  C28  C21  C20  112.38  3.000
 DKV  C22  C21  C20  109.62  3.000
 DKV  H7   C22  H6   106.48  3.000
 DKV  H7   C22  C23  109.87  3.000
 DKV  H6   C22  C23  108.82  3.000
 DKV  H7   C22  C21  109.77  3.000
 DKV  H6   C22  C21  110.18  3.000
 DKV  C23  C22  C21  111.58  3.000
 DKV  F26  C24  F25  104.81  3.000
 DKV  F25  C24  C27  109.26  3.000
 DKV  F26  C24  C27  109.94  3.000
 DKV  C27  C24  C23  113.31  3.000
 DKV  F25  C24  C23  109.21  3.000
 DKV  F26  C24  C23  109.96  3.000
 DKV  H9   C28  H8   106.50  3.000
 DKV  H9   C28  C27  108.75  3.000
 DKV  H8   C28  C27  109.99  3.000
 DKV  H9   C28  C21  110.58  3.000
 DKV  H8   C28  C21  109.25  3.000
 DKV  C27  C28  C21  111.65  3.000
 DKV  O30  C02  O01  127.28  3.000
 DKV  O30  C02  C03  117.04  3.000
 DKV  O01  C02  C03  115.68  3.000
 DKV  C08  C03  C04  114.60  3.000
 DKV  C04  C03  C02  123.18  3.000
 DKV  C08  C03  C02  122.23  3.000
 DKV  H10  C04  C05  119.26  3.000
 DKV  H10  C04  C03  119.91  3.000
 DKV  C05  C04  C03  120.83  3.000
 DKV  H11  C05  N06  116.32  3.000
 DKV  H11  C05  C04  119.13  3.000
 DKV  N06  C05  C04  124.56  3.000
 DKV  N06  C07  C29  130.23  3.000
 DKV  N06  C07  C08  122.94  3.000
 DKV  C29  C07  C08  106.83  3.000
 DKV  N09  C08  C07  107.40  3.000
 DKV  N09  C08  C03  131.46  3.000
 DKV  C07  C08  C03  121.13  3.000
 DKV  H12  C11  O19  110.53  3.000
 DKV  H12  C11  C12  109.10  3.000
 DKV  O19  C11  C12  112.14  3.000
 DKV  H12  C11  C10  107.94  3.000
 DKV  C12  C11  C10  109.51  3.000
 DKV  O19  C11  C10  107.52  3.000
 DKV  C11  C12  C17  122.35  3.000
 DKV  C17  C12  C13  117.46  3.000
 DKV  C11  C12  C13  120.16  3.000
 DKV  H13  C14  C15  120.32  3.000
 DKV  H13  C14  C13  119.74  3.000
 DKV  C15  C14  C13  119.94  3.000
 DKV  H14  C16  C17  120.05  3.000
 DKV  H14  C16  C15  120.48  3.000
 DKV  C17  C16  C15  119.47  3.000
 DKV  H16  C23  H15  107.21  3.000
 DKV  H16  C23  C24  109.94  3.000
 DKV  H15  C23  C24  108.04  3.000
 DKV  H16  C23  C22  110.88  3.000
 DKV  H15  C23  C22  109.61  3.000
 DKV  C24  C23  C22  111.04  3.000
 DKV  H18  C27  H17  107.20  3.000
 DKV  H18  C27  C28  110.77  3.000
 DKV  H17  C27  C28  109.55  3.000
 DKV  H18  C27  C24  109.88  3.000
 DKV  H17  C27  C24  108.04  3.000
 DKV  C28  C27  C24  111.28  3.000
 DKV  H19  C29  C07  127.52  3.000
 DKV  H19  C29  C10  126.04  3.000
 DKV  C07  C29  C10  106.45  3.000
 DKV  C07  N06  C05  115.95  3.000
 DKV  H20  N09  C08  122.03  3.000
 DKV  H20  N09  C10  128.40  3.000
 DKV  C08  N09  C10  109.50  3.000
 DKV  C11  O19  C20  114.25  3.000
 DKV  H4   C20  H3   107.26  3.000
 DKV  H4   C20  O19  110.64  3.000
 DKV  H3   C20  O19  110.11  3.000
 DKV  H4   C20  C21  109.51  3.000
 DKV  H3   C20  C21  110.11  3.000
 DKV  O19  C20  C21  109.19  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
 DKV  CONST_01  N06  C07  C29  C10   180.00   0.0  0
 DKV  CONST_02  C08  C07  C29  C10     0.00   0.0  0
 DKV  CONST_03  C07  C08  N09  C10     0.00   0.0  0
 DKV  CONST_04  C03  C08  N09  C10   180.00   0.0  0
 DKV  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 DKV  CONST_06  C16  C17  C12  C13     0.00   0.0  0
 DKV  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 DKV  CONST_08  C12  C17  C16  C15     0.00   0.0  0
 DKV  CONST_09  C14  C13  C12  C17     0.00   0.0  0
 DKV  CONST_10  C14  C15  C16  C17     0.00   0.0  0
 DKV  CONST_11  C29  C07  C08  C03   180.00   0.0  0
 DKV  CONST_12  N06  C07  C08  C03     0.00   0.0  0
 DKV  CONST_13  N06  C05  C04  C03     0.00   0.0  0
 DKV  CONST_14  C07  N06  C05  C04     0.00   0.0  0
 DKV  CONST_15  C07  C08  C03  C04     0.00   0.0  0
 DKV  CONST_16  N09  C08  C03  C04   180.00   0.0  0
 DKV  CONST_17  C29  C07  N06  C05   180.00   0.0  0
 DKV  CONST_18  C08  C07  N06  C05     0.00   0.0  0
 DKV  CONST_19  C08  C03  C04  C05     0.00   0.0  0
 DKV  CONST_20  N09  C10  C29  C07     0.00   0.0  0
 DKV  CONST_21  C29  C10  N09  C08     0.00   0.0  0
 DKV  CONST_22  N09  C08  C07  C29     0.00   0.0  0
 DKV  CONST_23  N09  C08  C07  N06   180.00   0.0  0
 DKV  CONST_24  CL1  C17  C12  C13   180.00   0.0  0
 DKV  CONST_25  CL1  C17  C16  C15   180.00   0.0  0
 DKV  CONST_26  C07  C08  C03  C02   180.00   0.0  0
 DKV  CONST_27  N09  C08  C03  C02     0.00   0.0  0
 DKV  CONST_28  C05  C04  C03  C02   180.00   0.0  0
 DKV  CONST_29  C11  C10  C29  C07   180.00   0.0  0
 DKV  CONST_30  C11  C10  N09  C08   180.00   0.0  0
 DKV  CONST_31  C14  C13  C12  C11   180.00   0.0  0
 DKV  CONST_32  C16  C17  C12  C11   180.00   0.0  0
 DKV  CONST_33  H2   C15  C14  C13   180.00   0.0  0
 DKV  CONST_34  H1   C13  C14  C15   180.00   0.0  0
 DKV  CONST_35  H20  N09  C08  C03     0.00   0.0  0
 DKV  CONST_36  H11  C05  C04  C03   180.00   0.0  0
 DKV  CONST_37  H19  C29  C07  C08   180.00   0.0  0
 DKV  CONST_38  H10  C04  C03  C08   180.00   0.0  0
 DKV  CONST_39  H13  C14  C13  C12   180.00   0.0  0
 DKV  CONST_40  H14  C16  C17  C12   180.00   0.0  0
 DKV  Var_01    C24  C23  C22  C21   -54.70  30.0  1
 DKV  Var_02    C24  C27  C28  C21    53.93  30.0  1
 DKV  Var_03    C27  C24  C23  C22    53.63  30.0  1
 DKV  Var_04    C23  C24  C27  C28   -53.28  30.0  1
 DKV  Var_05    O01  C02  C03  C04  -179.26  30.0  2
 DKV  Var_06    H3   C20  O19  C11    57.36  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
 DKV  chir_01  C21  C22  C28  C20  negativ
 DKV  chir_02  C11  O19  C10  C12  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
 DKV  plan-1  C13  0.020
 DKV  plan-1  C15  0.020
 DKV  plan-1  C17  0.020
 DKV  plan-1  C11  0.020
 DKV  plan-1  C12  0.020
 DKV  plan-1  C14  0.020
 DKV  plan-1  C16  0.020
 DKV  plan-1  H1   0.020
 DKV  plan-1  H2   0.020
 DKV  plan-1  H13  0.020
 DKV  plan-1  H14  0.020
 DKV  plan-1  CL1  0.020
 DKV  plan-2  C10  0.020
 DKV  plan-2  C02  0.020
 DKV  plan-2  C03  0.020
 DKV  plan-2  C04  0.020
 DKV  plan-2  C05  0.020
 DKV  plan-2  C07  0.020
 DKV  plan-2  C08  0.020
 DKV  plan-2  C11  0.020
 DKV  plan-2  C29  0.020
 DKV  plan-2  N06  0.020
 DKV  plan-2  N09  0.020
 DKV  plan-2  H10  0.020
 DKV  plan-2  H11  0.020
 DKV  plan-2  H19  0.020
 DKV  plan-2  H20  0.020
 DKV  plan-3  C02  0.020
 DKV  plan-3  C03  0.020
 DKV  plan-3  O01  0.020
 DKV  plan-3  O30  0.020

