# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:00:35 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(c1)C(=O)N[C@@H](C(=O)NO)c2ccc(cc2)n3cccn3
#
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
 R5X  R5X  3-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide  ligand  43  26  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R5X
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
 R5X  C10  C  CR15  0  -0.508  -6.9533   1.8990  -0.0916
 R5X  C21  C  CR16  0  -0.352   4.8288   0.2631   0.0828
 R5X  C22  C  CR6   0   0.332   5.8122   1.2337   0.2948
 R5X  C24  C  CR16  0  -0.235   4.2004   2.9229  -0.3339
 R5X  C01  C  CR16  0  -0.283  -2.7170   0.6031   0.9715
 R5X  C02  C  CR16  0  -0.277  -1.4549   0.0741   0.7662
 R5X  C03  C  CR6   0   0.087  -1.1327  -0.5623  -0.4301
 R5X  C04  C  CR16  0  -0.303  -2.1105  -0.6753  -1.4100
 R5X  C05  C  CR16  0  -0.303  -3.3842  -0.1672  -1.2095
 R5X  C06  C  CR6   0   0.376  -3.6858   0.4842  -0.0200
 R5X  N07  N  NR5   0  -0.400  -4.9665   1.0287   0.1838
 R5X  N08  N  N     0  -0.279  -5.4262   1.2286   1.4216
 R5X  C09  C  CR15  0  -0.034  -6.6240   1.7515   1.2688
 R5X  C11  C  CR15  0   0.039  -5.8562   1.4225  -0.7593
 R5X  C12  C  CH1   0  -0.242   0.2390  -1.1459  -0.6619
 R5X  N13  N  NH1   0  -0.664   1.2609  -0.1617  -0.4138
 R5X  C14  C  C     0   0.536   0.4249  -2.3486   0.2740
 R5X  O15  O  O     0  -0.458   0.6654  -2.2227   1.4558
 R5X  N16  N  NH1   0  -0.371   0.1804  -3.5203  -0.3387
 R5X  O17  O  OH1   0  -0.541   0.3935  -4.6815   0.3422
 R5X  C18  C  C     0   0.555   2.5617  -0.4824  -0.5284
 R5X  C19  C  CR6   0  -0.022   3.5465   0.6188  -0.3170
 R5X  O20  O  O     0  -0.485   2.9110  -1.6255  -0.7918
 R5X  C23  C  CR16  0  -0.320   5.4747   2.5764   0.0794
 R5X  C25  C  CR16  0  -0.336   3.2240   1.9568  -0.5345
 R5X  H1   H  HCR5  0   0.271  -7.8552   2.3023  -0.5194
 R5X  H2   H  HCR6  0   0.259   5.0705  -0.7813   0.2389
 R5X  H3   H  HCR6  0   0.261   3.9642   3.9651  -0.5046
 R5X  H4   H  HCR6  0   0.279  -2.9481   1.1077   1.8987
 R5X  H5   H  HCR6  0   0.270  -0.7184   0.1680   1.5538
 R5X  H6   H  HCR6  0   0.267  -1.8846  -1.1724  -2.3453
 R5X  H7   H  HCR6  0   0.283  -4.1315  -0.2942  -1.9812
 R5X  H8   H  HCR5  0   0.269  -7.2197   2.0032   2.1328
 R5X  H9   H  HCR5  0   0.301  -5.6433   1.3599  -1.8132
 R5X  H10  H  HCH1  0   0.297   0.2977  -1.4792  -1.7029
 R5X  H11  H  HNH1  0   0.419   0.9808   0.7645  -0.1353
 R5X  H12  H  HNH1  0   0.416   0.2407  -3.6120  -1.3434
 R5X  H13  H  HOH1  0   0.480  -0.4806  -5.0053   0.5947
 R5X  H14  H  HCR6  0   0.263   6.2199   3.3478   0.2334
 R5X  H15  H  HCR6  0   0.252   2.2448   2.2575  -0.8826
 R5X  H16  H  HNH2  0   0.382   7.1866  -0.0148   1.1167
 R5X  H17  H  HNH2  0   0.382   7.6485   1.5901   1.0861
 R5X  N26  N  NH2   0  -0.861   7.0909   0.8731   0.6511

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
 R5X  N26  C22  single    1.376  0.020  1.376
 R5X  O17  N16  single    1.363  0.020  1.363
 R5X  C22  C21  aromatic  1.398  0.020  1.398
 R5X  C22  C23  aromatic  1.401  0.020  1.401
 R5X  C21  C19  aromatic  1.390  0.020  1.390
 R5X  O15  C14  double    1.213  0.020  1.213
 R5X  N16  C14  single    1.345  0.020  1.345
 R5X  C23  C24  aromatic  1.384  0.020  1.384
 R5X  C14  C12  single    1.535  0.020  1.535
 R5X  C19  C18  single    1.492  0.020  1.492
 R5X  C19  C25  aromatic  1.393  0.020  1.393
 R5X  N13  C18  single    1.345  0.020  1.345
 R5X  N13  C12  single    1.440  0.020  1.440
 R5X  C18  O20  double    1.224  0.020  1.224
 R5X  C12  C03  single    1.509  0.020  1.509
 R5X  C24  C25  aromatic  1.388  0.020  1.388
 R5X  C03  C04  aromatic  1.389  0.020  1.389
 R5X  C03  C02  aromatic  1.393  0.020  1.393
 R5X  C04  C05  aromatic  1.386  0.020  1.386
 R5X  C02  C01  aromatic  1.384  0.020  1.384
 R5X  C05  C06  aromatic  1.389  0.020  1.389
 R5X  C01  C06  aromatic  1.391  0.020  1.391
 R5X  C06  N07  single    1.407  0.020  1.407
 R5X  N07  N08  aromatic  1.335  0.020  1.335
 R5X  N07  C11  aromatic  1.355  0.020  1.355
 R5X  N08  C09  aromatic  1.316  0.020  1.316
 R5X  C11  C10  aromatic  1.370  0.020  1.370
 R5X  C09  C10  aromatic  1.407  0.020  1.407
 R5X  C10  H1   single    0.930  0.020  1.080
 R5X  C21  H2   single    0.930  0.020  1.080
 R5X  C24  H3   single    0.930  0.020  1.080
 R5X  C01  H4   single    0.930  0.020  1.080
 R5X  C02  H5   single    0.930  0.020  1.080
 R5X  C04  H6   single    0.930  0.020  1.080
 R5X  C05  H7   single    0.930  0.020  1.080
 R5X  C09  H8   single    0.930  0.020  1.080
 R5X  C11  H9   single    0.930  0.020  1.080
 R5X  C12  H10  single    0.970  0.020  1.090
 R5X  N13  H11  single    0.860  0.020  1.020
 R5X  N16  H12  single    0.890  0.020  1.040
 R5X  O17  H13  single    0.850  0.020  0.980
 R5X  C23  H14  single    0.930  0.020  1.080
 R5X  C25  H15  single    0.930  0.020  1.080
 R5X  N26  H16  single    0.890  0.020  1.040
 R5X  N26  H17  single    0.890  0.020  1.040

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
 R5X  H1   C10  C11  127.42  3.000
 R5X  H1   C10  C09  128.26  3.000
 R5X  C11  C10  C09  104.32  3.000
 R5X  H2   C21  C19  119.62  3.000
 R5X  H2   C21  C22  119.38  3.000
 R5X  C19  C21  C22  121.00  3.000
 R5X  N26  C22  C23  120.99  3.000
 R5X  C23  C22  C21  118.21  3.000
 R5X  N26  C22  C21  120.74  3.000
 R5X  H3   C24  C25  119.60  3.000
 R5X  H3   C24  C23  119.29  3.000
 R5X  C25  C24  C23  121.11  3.000
 R5X  H4   C01  C06  120.16  3.000
 R5X  H4   C01  C02  120.06  3.000
 R5X  C06  C01  C02  119.78  3.000
 R5X  H5   C02  C03  120.48  3.000
 R5X  H5   C02  C01  118.65  3.000
 R5X  C03  C02  C01  120.87  3.000
 R5X  C12  C03  C04  120.02  3.000
 R5X  C04  C03  C02  118.70  3.000
 R5X  C12  C03  C02  121.27  3.000
 R5X  H6   C04  C05  119.00  3.000
 R5X  H6   C04  C03  119.99  3.000
 R5X  C05  C04  C03  121.01  3.000
 R5X  H7   C05  C06  121.05  3.000
 R5X  H7   C05  C04  119.25  3.000
 R5X  C06  C05  C04  119.69  3.000
 R5X  N07  C06  C05  120.22  3.000
 R5X  N07  C06  C01  119.84  3.000
 R5X  C05  C06  C01  119.94  3.000
 R5X  C11  N07  N08  112.06  3.000
 R5X  C11  N07  C06  127.55  3.000
 R5X  N08  N07  C06  120.38  3.000
 R5X  C09  N08  N07  105.38  3.000
 R5X  H8   C09  N08  120.14  3.000
 R5X  H8   C09  C10  128.33  3.000
 R5X  N08  C09  C10  111.52  3.000
 R5X  H9   C11  N07  122.30  3.000
 R5X  H9   C11  C10  130.96  3.000
 R5X  N07  C11  C10  106.72  3.000
 R5X  H10  C12  C14  109.56  3.000
 R5X  H10  C12  N13  109.50  3.000
 R5X  C14  C12  N13  110.15  3.000
 R5X  H10  C12  C03  108.22  3.000
 R5X  N13  C12  C03  110.75  3.000
 R5X  C14  C12  C03  108.63  3.000
 R5X  H11  N13  C18  120.80  3.000
 R5X  H11  N13  C12  118.61  3.000
 R5X  C18  N13  C12  120.58  3.000
 R5X  N16  C14  O15  124.80  3.000
 R5X  N16  C14  C12  112.51  3.000
 R5X  O15  C14  C12  122.46  3.000
 R5X  H12  N16  O17  114.21  3.000
 R5X  H12  N16  C14  121.41  3.000
 R5X  O17  N16  C14  119.10  3.000
 R5X  H13  O17  N16  105.94  3.000
 R5X  O20  C18  C19  122.10  3.000
 R5X  O20  C18  N13  121.14  3.000
 R5X  C19  C18  N13  116.77  3.000
 R5X  C25  C19  C18  122.26  3.000
 R5X  C25  C19  C21  120.29  3.000
 R5X  C18  C19  C21  117.44  3.000
 R5X  H14  C23  C24  119.84  3.000
 R5X  H14  C23  C22  119.65  3.000
 R5X  C24  C23  C22  120.51  3.000
 R5X  H15  C25  C19  121.78  3.000
 R5X  H15  C25  C24  119.32  3.000
 R5X  C19  C25  C24  118.88  3.000
 R5X  H17  N26  H16  112.04  3.000
 R5X  H17  N26  C22  116.10  3.000
 R5X  H16  N26  C22  116.05  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
 R5X  CONST_01  C06  N07  C11  C10  180.00   0.0  0
 R5X  CONST_02  N08  N07  C11  C10    0.00   0.0  0
 R5X  CONST_03  N07  N08  C09  C10    0.00   0.0  0
 R5X  CONST_04  C24  C23  C22  C21    0.00   0.0  0
 R5X  CONST_05  C24  C25  C19  C21    0.00   0.0  0
 R5X  CONST_06  C25  C19  C21  C22    0.00   0.0  0
 R5X  CONST_07  C25  C24  C23  C22    0.00   0.0  0
 R5X  CONST_08  C04  C03  C02  C01    0.00   0.0  0
 R5X  CONST_09  C04  C05  C06  C01    0.00   0.0  0
 R5X  CONST_12  C05  C04  C03  C02    0.00   0.0  0
 R5X  CONST_13  C05  C06  C01  C02    0.00   0.0  0
 R5X  CONST_14  N07  C06  C01  C02  180.00   0.0  0
 R5X  CONST_15  C06  C05  C04  C03    0.00   0.0  0
 R5X  CONST_16  C06  C01  C02  C03    0.00   0.0  0
 R5X  CONST_17  N07  C06  C05  C04  180.00   0.0  0
 R5X  CONST_20  C09  N08  N07  C06  180.00   0.0  0
 R5X  CONST_21  C09  C10  C11  N07    0.00   0.0  0
 R5X  CONST_22  C11  C10  C09  N08    0.00   0.0  0
 R5X  CONST_23  C11  N07  N08  C09    0.00   0.0  0
 R5X  CONST_24  C23  C22  C21  C19    0.00   0.0  0
 R5X  CONST_25  C23  C24  C25  C19    0.00   0.0  0
 R5X  CONST_26  C18  C19  C21  C22  180.00   0.0  0
 R5X  CONST_27  N26  C22  C23  C24  180.00   0.0  0
 R5X  CONST_28  C18  C19  C25  C24  180.00   0.0  0
 R5X  CONST_29  C12  C03  C02  C01  180.00   0.0  0
 R5X  CONST_30  C12  C03  C04  C05  180.00   0.0  0
 R5X  CONST_31  N26  C22  C21  C19  180.00   0.0  0
 R5X  CONST_32  H14  C23  C22  C21  180.00   0.0  0
 R5X  CONST_33  H15  C25  C19  C21  180.00   0.0  0
 R5X  CONST_34  H3   C24  C23  C22  180.00   0.0  0
 R5X  CONST_35  H7   C05  C06  C01  180.00   0.0  0
 R5X  CONST_36  H6   C04  C03  C02  180.00   0.0  0
 R5X  CONST_37  H4   C01  C02  C03  180.00   0.0  0
 R5X  CONST_38  H5   C02  C03  C04  180.00   0.0  0
 R5X  CONST_39  H9   C11  N07  C06    0.00   0.0  0
 R5X  CONST_40  H8   C09  N08  N07  180.00   0.0  0
 R5X  CONST_41  H1   C10  C11  N07  180.00   0.0  0
 R5X  CONST_42  H2   C21  C22  C23  180.00   0.0  0
 R5X  CONST_45  C19  C18  N13  C12  180.00   0.0  0
 R5X  CONST_46  H11  N13  C18  C19    0.00   0.0  0
 R5X  CONST_47  O17  N16  C14  C12  180.00   0.0  0
 R5X  CONST_48  O20  C18  N13  C12    0.00   0.0  0
 R5X  CONST_49  O17  N16  C14  O15    0.00   0.0  0
 R5X  Var_01    N13  C18  C19  C21  155.63  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
 R5X  chir_01  C12  C14  N13  C03  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
 R5X  plan-1  C10  0.020
 R5X  plan-1  C06  0.020
 R5X  plan-1  N07  0.020
 R5X  plan-1  N08  0.020
 R5X  plan-1  C09  0.020
 R5X  plan-1  C11  0.020
 R5X  plan-1  H1   0.020
 R5X  plan-1  H8   0.020
 R5X  plan-1  H9   0.020
 R5X  plan-2  C21  0.020
 R5X  plan-2  C22  0.020
 R5X  plan-2  C24  0.020
 R5X  plan-2  C18  0.020
 R5X  plan-2  C19  0.020
 R5X  plan-2  C23  0.020
 R5X  plan-2  C25  0.020
 R5X  plan-2  H2   0.020
 R5X  plan-2  H3   0.020
 R5X  plan-2  H14  0.020
 R5X  plan-2  H15  0.020
 R5X  plan-2  N26  0.020
 R5X  plan-3  C01  0.020
 R5X  plan-3  C02  0.020
 R5X  plan-3  C03  0.020
 R5X  plan-3  C04  0.020
 R5X  plan-3  C05  0.020
 R5X  plan-3  C06  0.020
 R5X  plan-3  N07  0.020
 R5X  plan-3  C12  0.020
 R5X  plan-3  H4   0.020
 R5X  plan-3  H5   0.020
 R5X  plan-3  H6   0.020
 R5X  plan-3  H7   0.020
 R5X  plan-4  C12  0.020
 R5X  plan-4  C14  0.020
 R5X  plan-4  O15  0.020
 R5X  plan-4  N16  0.020
 R5X  plan-4  O17  0.020
 R5X  plan-4  H12  0.020
 R5X  plan-5  C12  0.020
 R5X  plan-5  N13  0.020
 R5X  plan-5  C18  0.020
 R5X  plan-5  C19  0.020
 R5X  plan-5  O20  0.020
 R5X  plan-5  H11  0.020
 R5X  plan-6  C22  0.020
 R5X  plan-6  H16  0.020
 R5X  plan-6  H17  0.020
 R5X  plan-6  N26  0.020

