# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 04:31:15 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-[4-(hydroxymethyl)-1~{H}-pyrazolo[4,3-c]pyridin-6-yl]-3-[(1~{S})-1-phenylethyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)Nc1cc2[nH]ncc2c(CO)n1)c3ccccc3
#
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
 08G  08G  "1-[4-(hydroxymethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-3-[(1S)-1-phenylethyl]urea"  ligand  40  23  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_08G
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
 08G  C12  C  CR15  0  -0.144  40.9692   -8.0724  24.2853
 08G  C13  C  CR56  0  -0.177  40.1512   -8.1313  23.1247
 08G  C14  C  CR6   0   0.169  39.4767   -9.1093  22.3798
 08G  C15  C  CH2   0  -0.201  39.5543  -10.5491  22.8011
 08G  C19  C  CR16  0  -0.295  37.2677  -10.0005  17.1616
 08G  C20  C  CR16  0  -0.240  38.2190  -10.8673  16.6385
 08G  C21  C  CR16  0  -0.264  39.2714  -10.3683  15.8841
 08G  C22  C  CR16  0  -0.238  39.3653   -9.0005  15.6571
 08G  C01  C  CH3   0  -0.665  35.2407   -7.3994  16.4222
 08G  C02  C  CH1   0  -0.176  36.2871   -7.7044  17.4892
 08G  C04  C  C     0   0.707  37.6233   -6.2486  19.0541
 08G  C07  C  CR6   0   0.472  38.7113   -7.4902  20.9125
 08G  C08  C  CR16  0  -0.436  39.3278   -6.4367  21.5585
 08G  C09  C  CR56  0   0.550  40.0608   -6.8030  22.6904
 08G  C18  C  CR6   0   0.104  37.3565   -8.6302  16.9406
 08G  C23  C  CR16  0  -0.292  38.4148   -8.1370  16.1823
 08G  N03  N  NH1   0  -0.661  36.8220   -6.4492  17.9787
 08G  N06  N  NH1   0  -0.750  37.9319   -7.3785  19.7686
 08G  N10  N  NR15  0  -0.553  40.7876   -6.0818  23.5651
 08G  N11  N  N     0  -0.225  41.3352   -6.8417  24.5265
 08G  N17  N  N     0  -0.492  38.7896   -8.7793  21.3161
 08G  O05  O  O     0  -0.512  38.0259   -5.1342  19.3571
 08G  O16  O  OH1   0  -0.654  38.7489  -11.3502  21.9872
 08G  H1   H  HCR5  0   0.269  41.2900   -8.8767  24.9300
 08G  H2   H  HCH2  0   0.225  39.2639  -10.6054  23.8599
 08G  H3   H  HCH2  0   0.227  40.6118  -10.8487  22.7640
 08G  H5   H  HCR6  0   0.255  38.1397  -11.9304  16.8262
 08G  H6   H  HCR6  0   0.254  40.0172  -11.0395  15.4782
 08G  H7   H  HCR6  0   0.254  40.1843   -8.6042  15.0703
 08G  H8   H  HCH3  0   0.248  34.4388   -6.7837  16.8306
 08G  H9   H  HCH3  0   0.237  35.6877   -6.8728  15.5772
 08G  H10  H  HCH3  0   0.252  34.8047   -8.3246  16.0500
 08G  H11  H  HCH1  0   0.264  35.7715   -8.2183  18.3094
 08G  H12  H  HCR6  0   0.294  39.2528   -5.4170  21.2218
 08G  H13  H  HCR6  0   0.250  38.5034   -7.0718  16.0046
 08G  H14  H  HNH1  0   0.402  36.6279   -5.6166  17.4444
 08G  H15  H  HNH1  0   0.416  37.5925   -8.2747  19.4528
 08G  H16  H  HNR5  0   0.417  40.9449   -5.0867  23.5658
 08G  H17  H  HOH1  0   0.459  38.8427  -12.2587  22.2874
 08G  H4   H  HCR6  0   0.253  36.4498  -10.3957  17.7538

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
 08G  C22  C21  aromatic  1.390  0.020  1.390
 08G  C22  C23  aromatic  1.387  0.020  1.387
 08G  C21  C20  aromatic  1.388  0.020  1.388
 08G  C23  C18  aromatic  1.392  0.020  1.392
 08G  C20  C19  aromatic  1.389  0.020  1.389
 08G  C18  C19  aromatic  1.391  0.020  1.391
 08G  C18  C02  single    1.517  0.020  1.517
 08G  N03  C02  single    1.450  0.020  1.450
 08G  N03  C04  single    1.356  0.020  1.356
 08G  C02  C01  single    1.525  0.020  1.525
 08G  C04  O05  double    1.223  0.020  1.223
 08G  C04  N06  single    1.372  0.020  1.372
 08G  N06  C07  single    1.389  0.020  1.389
 08G  C07  N17  aromatic  1.353  0.020  1.353
 08G  C07  C08  aromatic  1.381  0.020  1.381
 08G  N17  C14  aromatic  1.309  0.020  1.309
 08G  C08  C09  aromatic  1.397  0.020  1.397
 08G  O16  C15  single    1.397  0.020  1.397
 08G  C14  C15  single    1.502  0.020  1.502
 08G  C14  C13  aromatic  1.402  0.020  1.402
 08G  C09  C13  aromatic  1.400  0.020  1.400
 08G  C09  N10  aromatic  1.347  0.020  1.347
 08G  C13  C12  aromatic  1.421  0.020  1.421
 08G  N10  N11  aromatic  1.342  0.020  1.342
 08G  C12  N11  aromatic  1.306  0.020  1.306
 08G  C12  H1   single    0.930  0.020  1.080
 08G  C15  H2   single    0.970  0.020  1.090
 08G  C15  H3   single    0.970  0.020  1.090
 08G  C19  H4   single    0.930  0.020  1.080
 08G  C20  H5   single    0.930  0.020  1.080
 08G  C21  H6   single    0.930  0.020  1.080
 08G  C22  H7   single    0.930  0.020  1.080
 08G  C01  H8   single    0.970  0.020  1.090
 08G  C01  H9   single    0.970  0.020  1.090
 08G  C01  H10  single    0.970  0.020  1.090
 08G  C02  H11  single    0.970  0.020  1.090
 08G  C08  H12  single    0.930  0.020  1.080
 08G  C23  H13  single    0.930  0.020  1.080
 08G  N03  H14  single    0.860  0.020  1.020
 08G  N06  H15  single    0.860  0.020  1.020
 08G  N10  H16  single    0.860  0.020  1.020
 08G  O16  H17  single    0.850  0.020  0.980

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
 08G  H1   C12  N11  120.55  3.000
 08G  H1   C12  C13  128.90  3.000
 08G  N11  C12  C13  110.55  3.000
 08G  C09  C13  C14  117.76  3.000
 08G  C09  C13  C12  104.55  3.000
 08G  C14  C13  C12  137.70  3.000
 08G  N17  C14  C15  119.79  3.000
 08G  C15  C14  C13  119.65  3.000
 08G  N17  C14  C13  120.56  3.000
 08G  H3   C15  H2   105.81  3.000
 08G  H3   C15  O16  112.23  3.000
 08G  H2   C15  O16  112.30  3.000
 08G  H3   C15  C14  107.54  3.000
 08G  H2   C15  C14  107.79  3.000
 08G  O16  C15  C14  110.87  3.000
 08G  H4   C19  C18  119.60  3.000
 08G  H4   C19  C20  119.65  3.000
 08G  C18  C19  C20  120.74  3.000
 08G  H5   C20  C21  120.20  3.000
 08G  H5   C20  C19  119.82  3.000
 08G  C21  C20  C19  119.98  3.000
 08G  H6   C21  C22  120.17  3.000
 08G  H6   C21  C20  120.23  3.000
 08G  C22  C21  C20  119.60  3.000
 08G  H7   C22  C23  119.71  3.000
 08G  H7   C22  C21  120.00  3.000
 08G  C23  C22  C21  120.29  3.000
 08G  H10  C01  H9   108.03  3.000
 08G  H10  C01  H8   108.26  3.000
 08G  H9   C01  H8   108.59  3.000
 08G  H10  C01  C02  110.13  3.000
 08G  H9   C01  C02  110.92  3.000
 08G  H8   C01  C02  110.82  3.000
 08G  H11  C02  N03  109.07  3.000
 08G  H11  C02  C18  108.41  3.000
 08G  N03  C02  C18  112.98  3.000
 08G  H11  C02  C01  107.12  3.000
 08G  N03  C02  C01  108.44  3.000
 08G  C18  C02  C01  110.65  3.000
 08G  O05  C04  N06  123.19  3.000
 08G  N06  C04  N03  115.09  3.000
 08G  O05  C04  N03  121.72  3.000
 08G  N17  C07  N06  110.78  3.000
 08G  N17  C07  C08  124.15  3.000
 08G  N06  C07  C08  125.07  3.000
 08G  H12  C08  C09  122.56  3.000
 08G  H12  C08  C07  123.04  3.000
 08G  C09  C08  C07  114.40  3.000
 08G  N10  C09  C08  131.98  3.000
 08G  N10  C09  C13  105.76  3.000
 08G  C08  C09  C13  122.25  3.000
 08G  C23  C18  C02  121.10  3.000
 08G  C02  C18  C19  119.92  3.000
 08G  C23  C18  C19  118.95  3.000
 08G  H13  C23  C18  119.99  3.000
 08G  H13  C23  C22  119.58  3.000
 08G  C18  C23  C22  120.43  3.000
 08G  H14  N03  C04  114.32  3.000
 08G  H14  N03  C02  117.72  3.000
 08G  C04  N03  C02  127.88  3.000
 08G  H15  N06  C07  112.03  3.000
 08G  H15  N06  C04  119.53  3.000
 08G  C07  N06  C04  128.42  3.000
 08G  H16  N10  N11  119.67  3.000
 08G  H16  N10  C09  127.85  3.000
 08G  N11  N10  C09  112.47  3.000
 08G  N10  N11  C12  106.66  3.000
 08G  C07  N17  C14  120.87  3.000
 08G  H17  O16  C15  107.68  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
 08G  CONST_01  N17  C14  C13  C12   180.00   0.0  0
 08G  CONST_02  C08  C09  C13  C12   180.00   0.0  0
 08G  CONST_03  N10  C09  C13  C12     0.00   0.0  0
 08G  CONST_04  C09  N10  N11  C12     0.00   0.0  0
 08G  CONST_05  C07  N17  C14  C13     0.00   0.0  0
 08G  CONST_06  C07  C08  C09  C13     0.00   0.0  0
 08G  CONST_07  N11  N10  C09  C13     0.00   0.0  0
 08G  CONST_08  N10  N11  C12  C13     0.00   0.0  0
 08G  CONST_09  C08  C07  N17  C14     0.00   0.0  0
 08G  CONST_10  C08  C09  C13  C14     0.00   0.0  0
 08G  CONST_11  N10  C09  C13  C14   180.00   0.0  0
 08G  CONST_12  N11  C12  C13  C14   180.00   0.0  0
 08G  CONST_13  C22  C21  C20  C19     0.00   0.0  0
 08G  CONST_14  C22  C23  C18  C19     0.00   0.0  0
 08G  CONST_15  C23  C22  C21  C20     0.00   0.0  0
 08G  CONST_16  C23  C18  C19  C20     0.00   0.0  0
 08G  CONST_17  C18  C23  C22  C21     0.00   0.0  0
 08G  CONST_18  C18  C19  C20  C21     0.00   0.0  0
 08G  CONST_19  N10  C09  C08  C07   180.00   0.0  0
 08G  CONST_20  N11  N10  C09  C08   180.00   0.0  0
 08G  CONST_21  N17  C07  C08  C09     0.00   0.0  0
 08G  CONST_22  N17  C14  C13  C09     0.00   0.0  0
 08G  CONST_23  N11  C12  C13  C09     0.00   0.0  0
 08G  CONST_24  C15  C14  C13  C12     0.00   0.0  0
 08G  CONST_25  N06  C07  N17  C14   180.00   0.0  0
 08G  CONST_26  C07  N17  C14  C15   180.00   0.0  0
 08G  CONST_27  C09  C13  C14  C15   180.00   0.0  0
 08G  CONST_28  C02  C18  C19  C20   180.00   0.0  0
 08G  CONST_29  C02  C18  C23  C22   180.00   0.0  0
 08G  CONST_30  N06  C07  C08  C09   180.00   0.0  0
 08G  CONST_31  H16  N10  N11  C12   180.00   0.0  0
 08G  CONST_32  H12  C08  C09  C13   180.00   0.0  0
 08G  CONST_33  H16  N10  C09  C13   180.00   0.0  0
 08G  CONST_34  H1   C12  C13  C14     0.00   0.0  0
 08G  CONST_35  H6   C21  C20  C19   180.00   0.0  0
 08G  CONST_36  H13  C23  C18  C19   180.00   0.0  0
 08G  CONST_37  H7   C22  C21  C20   180.00   0.0  0
 08G  CONST_38  H13  C23  C22  C21   180.00   0.0  0
 08G  CONST_39  H4   C19  C20  C21   180.00   0.0  0
 08G  CONST_40  H5   C20  C21  C22   180.00   0.0  0
 08G  CONST_41  H16  N10  C09  C08     0.00   0.0  0
 08G  CONST_42  H1   C12  C13  C09   180.00   0.0  0
 08G  CONST_43  H7   C22  C23  C18   180.00   0.0  0
 08G  CONST_44  H5   C20  C19  C18   180.00   0.0  0
 08G  CONST_45  H6   C21  C22  C23   180.00   0.0  0
 08G  CONST_46  H4   C19  C18  C23   180.00   0.0  0
 08G  CONST_47  H12  C08  C09  N10     0.00   0.0  0
 08G  CONST_48  H1   C12  N11  N10   180.00   0.0  0
 08G  CONST_49  H12  C08  C07  N17   180.00   0.0  0
 08G  CONST_50  N17  C07  N06  C04   180.00   0.0  0
 08G  CONST_51  C08  C07  N06  C04     0.00   0.0  0
 08G  CONST_52  H15  N06  C07  C08   180.00   0.0  0
 08G  CONST_53  H15  N06  C07  N17     0.00   0.0  0
 08G  CONST_54  O05  C04  N06  C07     0.00   0.0  0
 08G  CONST_55  N03  C04  N06  C07   180.00   0.0  0
 08G  CONST_56  O05  C04  N03  C02   180.00   0.0  0
 08G  CONST_57  N06  C04  N03  C02     0.00   0.0  0
 08G  CONST_58  H14  N03  C04  O05     0.00   0.0  0
 08G  CONST_59  H15  N06  C04  O05   180.00   0.0  0
 08G  CONST_60  H15  N06  C04  N03     0.00   0.0  0
 08G  CONST_61  H14  N03  C04  N06   180.00   0.0  0
 08G  Var_01    O16  C15  C14  C13   176.11  30.0  2
 08G  Var_02    O16  C15  C14  N17    -4.41  30.0  2
 08G  Var_03    H2   C15  C14  C13    52.83  30.0  2
 08G  Var_04    H3   C15  C14  C13   -60.85  30.0  2
 08G  Var_05    H2   C15  C14  N17  -127.70  30.0  2
 08G  Var_06    H3   C15  C14  N17   118.63  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
 08G  chir_01  C02  C18  N03  C01  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
 08G  plan-1  C19  0.020
 08G  plan-1  C20  0.020
 08G  plan-1  C21  0.020
 08G  plan-1  C22  0.020
 08G  plan-1  C02  0.020
 08G  plan-1  C18  0.020
 08G  plan-1  C23  0.020
 08G  plan-1  H5   0.020
 08G  plan-1  H6   0.020
 08G  plan-1  H7   0.020
 08G  plan-1  H13  0.020
 08G  plan-1  H4   0.020
 08G  plan-2  C12  0.020
 08G  plan-2  C13  0.020
 08G  plan-2  C14  0.020
 08G  plan-2  C15  0.020
 08G  plan-2  C07  0.020
 08G  plan-2  C08  0.020
 08G  plan-2  C09  0.020
 08G  plan-2  N06  0.020
 08G  plan-2  N10  0.020
 08G  plan-2  N11  0.020
 08G  plan-2  N17  0.020
 08G  plan-2  H1   0.020
 08G  plan-2  H12  0.020
 08G  plan-2  H16  0.020
 08G  plan-3  C02  0.020
 08G  plan-3  C04  0.020
 08G  plan-3  C07  0.020
 08G  plan-3  N03  0.020
 08G  plan-3  N06  0.020
 08G  plan-3  O05  0.020
 08G  plan-3  H14  0.020
 08G  plan-3  H15  0.020

