# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 20:20:32 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-{2-(hydroxyamino)-5-[(1S)-1-hydroxyethyl]phenoxy}-N,N-dimethylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)c1ccc(NO)c(Oc2cccc(c2)C(=O)N(C)C)c1
#
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
 6NY  6NY  3-{2-(hydroxyamino)-5-[(1S)-1-hydroxyethyl]phenoxy}-N,N-dimethylbenzamide  ligand  43  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6NY
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
 6NY  O01   O  O     0  -0.490   4.5516   0.9398  -0.5648
 6NY  C02   C  C     0   0.509   3.6665   0.1889  -0.1732
 6NY  N03   N  NT    0  -0.438   3.4323  -0.0445   1.1327
 6NY  C04   C  CH3   0  -0.532   2.6684  -1.1621   1.6546
 6NY  C05   C  CH3   0  -0.526   4.1837   0.6950   2.1265
 6NY  C06   C  CR6   0  -0.043   2.7678  -0.4724  -1.1720
 6NY  C07   C  CR16  0  -0.352   1.3845  -0.3710  -1.0462
 6NY  C08   C  CR6   0   0.352   0.5643  -0.9446  -2.0077
 6NY  O09   O  O2    0  -0.507  -0.7976  -0.9197  -1.9417
 6NY  C10   C  CR6   0   0.278  -1.3993  -0.3294  -0.8522
 6NY  C11   C  CR16  0  -0.357  -1.9496   0.9276  -0.9980
 6NY  C12   C  CR6   0   0.073  -2.6084   1.5495   0.0590
 6NY  C13   C  CH1   0  -0.013  -3.1820   2.9400  -0.1315
 6NY  O14   O  OH1   0  -0.660  -4.1529   3.2611   0.8377
 6NY  C15   C  CH3   0  -0.692  -2.0728   3.9849  -0.1801
 6NY  C16   C  CR16  0  -0.323  -2.6846   0.8661   1.2643
 6NY  C17   C  CR16  0  -0.305  -2.1260  -0.3958   1.4186
 6NY  C18   C  CR6   0   0.232  -1.4743  -1.0254   0.3618
 6NY  N19   N  NH1   0  -0.427  -0.9825  -2.3273   0.4556
 6NY  O20   O  OH1   0  -0.555  -0.6564  -2.7017   1.7516
 6NY  C21   C  CR16  0  -0.325   1.1177  -1.6082  -3.0988
 6NY  C22   C  CR16  0  -0.235   2.4944  -1.6846  -3.2220
 6NY  C23   C  CR16  0  -0.294   3.3274  -1.1123  -2.2692
 6NY  H041  H  HCH3  0   0.257   3.2906  -1.7325   2.3466
 6NY  H042  H  HCH3  0   0.244   1.7833  -0.8218   2.1953
 6NY  H043  H  HCH3  0   0.260   2.3557  -1.8363   0.8642
 6NY  H051  H  HCH3  0   0.255   4.4306   1.6890   1.7654
 6NY  H053  H  HCH3  0   0.248   3.5762   0.7955   3.0245
 6NY  H052  H  HCH3  0   0.241   5.1091   0.1807   2.3968
 6NY  H071  H  HCR6  0   0.291   0.9605   0.1610  -0.2035
 6NY  H111  H  HCR6  0   0.263  -1.8659   1.4198  -1.9613
 6NY  H131  H  HCH1  0   0.240  -3.7087   2.9548  -1.0914
 6NY  H141  H  HOH1  0   0.450  -3.7081   3.5620   1.6371
 6NY  H151  H  HCH3  0   0.239  -1.3719   3.7786  -0.9885
 6NY  H152  H  HCH3  0   0.241  -2.4866   4.9811  -0.3429
 6NY  H153  H  HCH3  0   0.229  -1.5054   3.9926   0.7537
 6NY  H161  H  HCR6  0   0.247  -3.1929   1.3067   2.1119
 6NY  H171  H  HCR6  0   0.264  -2.2062  -0.8949   2.3737
 6NY  H191  H  HNH1  0   0.385  -0.1779  -2.5152  -0.1290
 6NY  H201  H  HOH1  0   0.473  -1.2530  -3.4312   1.9526
 6NY  H211  H  HCR6  0   0.276   0.4710  -2.0585  -3.8411
 6NY  H221  H  HCR6  0   0.268   2.9225  -2.1985  -4.0722
 6NY  H231  H  HCR6  0   0.262   4.4019  -1.1784  -2.3760

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
 6NY  O14  C13   single    1.409  0.020  1.409
 6NY  C13  C15   single    1.525  0.020  1.525
 6NY  C13  C12   single    1.516  0.020  1.516
 6NY  C16  C12   aromatic  1.388  0.020  1.388
 6NY  C16  C17   aromatic  1.389  0.020  1.389
 6NY  C12  C11   aromatic  1.392  0.020  1.392
 6NY  C17  C18   aromatic  1.392  0.020  1.392
 6NY  C11  C10   aromatic  1.380  0.020  1.380
 6NY  C18  C10   aromatic  1.401  0.020  1.401
 6NY  C18  N19   single    1.395  0.020  1.395
 6NY  C10  O09   single    1.378  0.020  1.378
 6NY  N19  O20   single    1.388  0.020  1.388
 6NY  O09  C08   single    1.364  0.020  1.364
 6NY  C21  C08   aromatic  1.392  0.020  1.392
 6NY  C21  C22   aromatic  1.384  0.020  1.384
 6NY  C08  C07   aromatic  1.388  0.020  1.388
 6NY  C22  C23   aromatic  1.389  0.020  1.389
 6NY  C04  N03   single    1.451  0.020  1.451
 6NY  C07  C06   aromatic  1.393  0.020  1.393
 6NY  C23  C06   aromatic  1.388  0.020  1.388
 6NY  C06  C02   single    1.497  0.020  1.497
 6NY  N03  C02   single    1.347  0.020  1.347
 6NY  N03  C05   single    1.449  0.020  1.449
 6NY  C02  O01   double    1.225  0.020  1.225
 6NY  C04  H041  single    0.970  0.020  1.090
 6NY  C04  H042  single    0.970  0.020  1.090
 6NY  C04  H043  single    0.970  0.020  1.090
 6NY  C05  H051  single    0.970  0.020  1.090
 6NY  C05  H053  single    0.970  0.020  1.090
 6NY  C05  H052  single    0.970  0.020  1.090
 6NY  C07  H071  single    0.930  0.020  1.080
 6NY  C11  H111  single    0.930  0.020  1.080
 6NY  C13  H131  single    0.970  0.020  1.090
 6NY  O14  H141  single    0.850  0.020  0.980
 6NY  C15  H151  single    0.970  0.020  1.090
 6NY  C15  H152  single    0.970  0.020  1.090
 6NY  C15  H153  single    0.970  0.020  1.090
 6NY  C16  H161  single    0.930  0.020  1.080
 6NY  C17  H171  single    0.930  0.020  1.080
 6NY  N19  H191  single    0.890  0.020  1.040
 6NY  O20  H201  single    0.850  0.020  0.980
 6NY  C21  H211  single    0.930  0.020  1.080
 6NY  C22  H221  single    0.930  0.020  1.080
 6NY  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
 6NY  C06   C02  N03   117.76  3.000
 6NY  N03   C02  O01   122.80  3.000
 6NY  C06   C02  O01   119.41  3.000
 6NY  C05   N03  C04   114.80  3.000
 6NY  C05   N03  C02   119.10  3.000
 6NY  C04   N03  C02   125.01  3.000
 6NY  H043  C04  H042  108.71  3.000
 6NY  H043  C04  H041  107.55  3.000
 6NY  H042  C04  H041  108.13  3.000
 6NY  H043  C04  N03   111.61  3.000
 6NY  H042  C04  N03   111.40  3.000
 6NY  H041  C04  N03   109.30  3.000
 6NY  H052  C05  H053  108.17  3.000
 6NY  H052  C05  H051  108.69  3.000
 6NY  H053  C05  H051  108.45  3.000
 6NY  H052  C05  N03   111.64  3.000
 6NY  H053  C05  N03   108.87  3.000
 6NY  H051  C05  N03   110.92  3.000
 6NY  C23   C06  C07   120.36  3.000
 6NY  C23   C06  C02   119.27  3.000
 6NY  C07   C06  C02   120.24  3.000
 6NY  H071  C07  C08   120.72  3.000
 6NY  H071  C07  C06   119.66  3.000
 6NY  C08   C07  C06   119.62  3.000
 6NY  C21   C08  O09   116.35  3.000
 6NY  C21   C08  C07   120.34  3.000
 6NY  O09   C08  C07   123.30  3.000
 6NY  C10   O09  C08   118.84  3.000
 6NY  C18   C10  C11   121.51  3.000
 6NY  C18   C10  O09   119.72  3.000
 6NY  C11   C10  O09   118.75  3.000
 6NY  H111  C11  C12   120.52  3.000
 6NY  H111  C11  C10   118.44  3.000
 6NY  C12   C11  C10   121.03  3.000
 6NY  C16   C12  C13   122.69  3.000
 6NY  C16   C12  C11   117.74  3.000
 6NY  C13   C12  C11   119.56  3.000
 6NY  H131  C13  C15   108.22  3.000
 6NY  H131  C13  O14   105.57  3.000
 6NY  C15   C13  O14   111.53  3.000
 6NY  H131  C13  C12   107.73  3.000
 6NY  C15   C13  C12   110.94  3.000
 6NY  O14   C13  C12   112.54  3.000
 6NY  H141  O14  C13   108.90  3.000
 6NY  H153  C15  H152  108.54  3.000
 6NY  H153  C15  H151  107.53  3.000
 6NY  H152  C15  H151  107.83  3.000
 6NY  H153  C15  C13   110.82  3.000
 6NY  H152  C15  C13   110.77  3.000
 6NY  H151  C15  C13   111.22  3.000
 6NY  H161  C16  C17   118.16  3.000
 6NY  H161  C16  C12   120.38  3.000
 6NY  C17   C16  C12   121.46  3.000
 6NY  H171  C17  C18   119.79  3.000
 6NY  H171  C17  C16   119.21  3.000
 6NY  C18   C17  C16   121.00  3.000
 6NY  N19   C18  C17   122.42  3.000
 6NY  N19   C18  C10   120.20  3.000
 6NY  C17   C18  C10   117.26  3.000
 6NY  H191  N19  O20   107.61  3.000
 6NY  H191  N19  C18   114.50  3.000
 6NY  O20   N19  C18   113.42  3.000
 6NY  H201  O20  N19   104.68  3.000
 6NY  H211  C21  C22   120.67  3.000
 6NY  H211  C21  C08   119.89  3.000
 6NY  C22   C21  C08   119.44  3.000
 6NY  H221  C22  C23   119.84  3.000
 6NY  H221  C22  C21   119.32  3.000
 6NY  C23   C22  C21   120.84  3.000
 6NY  H231  C23  C22   120.18  3.000
 6NY  H231  C23  C06   120.44  3.000
 6NY  C22   C23  C06   119.37  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
 6NY  CONST_01  C21   C08  C07  C06     0.00   0.0  0
 6NY  CONST_02  C21   C22  C23  C06     0.00   0.0  0
 6NY  CONST_03  C22   C21  C08  C07     0.00   0.0  0
 6NY  CONST_04  C22   C23  C06  C07     0.00   0.0  0
 6NY  CONST_05  C23   C22  C21  C08     0.00   0.0  0
 6NY  CONST_06  C23   C06  C07  C08     0.00   0.0  0
 6NY  CONST_07  C16   C12  C11  C10     0.00   0.0  0
 6NY  CONST_08  C16   C17  C18  C10     0.00   0.0  0
 6NY  CONST_09  C17   C16  C12  C11     0.00   0.0  0
 6NY  CONST_10  C17   C18  C10  C11     0.00   0.0  0
 6NY  CONST_11  C18   C17  C16  C12     0.00   0.0  0
 6NY  CONST_12  C18   C10  C11  C12     0.00   0.0  0
 6NY  CONST_13  C08   C07  C06  C02   180.00   0.0  0
 6NY  CONST_14  C22   C23  C06  C02   180.00   0.0  0
 6NY  CONST_15  O09   C08  C07  C06   180.00   0.0  0
 6NY  CONST_16  C12   C11  C10  O09   180.00   0.0  0
 6NY  CONST_17  C17   C18  C10  O09   180.00   0.0  0
 6NY  CONST_18  C22   C21  C08  O09   180.00   0.0  0
 6NY  CONST_19  C13   C12  C11  C10   180.00   0.0  0
 6NY  CONST_20  N19   C18  C10  C11   180.00   0.0  0
 6NY  CONST_21  C17   C16  C12  C13   180.00   0.0  0
 6NY  CONST_22  N19   C18  C17  C16   180.00   0.0  0
 6NY  CONST_23  H221  C22  C23  C06   180.00   0.0  0
 6NY  CONST_24  H211  C21  C08  C07   180.00   0.0  0
 6NY  CONST_25  H231  C23  C06  C07   180.00   0.0  0
 6NY  CONST_26  H171  C17  C18  C10   180.00   0.0  0
 6NY  CONST_27  H161  C16  C12  C11   180.00   0.0  0
 6NY  CONST_28  H111  C11  C12  C16   180.00   0.0  0
 6NY  CONST_29  H071  C07  C08  C21   180.00   0.0  0
 6NY  CONST_34  C06   C02  N03  C05   180.00   0.0  0
 6NY  CONST_37  C05   N03  C02  O01     0.00   0.0  0
 6NY  Var_01    C11   C10  O09  C08   103.38  30.0  3
 6NY  Var_02    C21   C08  O09  C10   177.10  30.0  2
 6NY  Var_03    C07   C06  C02  O01  -127.16  30.0  3
 6NY  Var_04    H041  C04  N03  C02   122.60  30.0  3
 6NY  Var_05    H051  C05  N03  C02    31.75  30.0  3

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
 6NY  chir_01  C13  O14  C15  C12  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
 6NY  plan-1  O09   0.020
 6NY  plan-1  C10   0.020
 6NY  plan-1  C11   0.020
 6NY  plan-1  C12   0.020
 6NY  plan-1  C13   0.020
 6NY  plan-1  C16   0.020
 6NY  plan-1  C17   0.020
 6NY  plan-1  C18   0.020
 6NY  plan-1  N19   0.020
 6NY  plan-1  H111  0.020
 6NY  plan-1  H161  0.020
 6NY  plan-1  H171  0.020
 6NY  plan-2  C02   0.020
 6NY  plan-2  C06   0.020
 6NY  plan-2  C07   0.020
 6NY  plan-2  C08   0.020
 6NY  plan-2  O09   0.020
 6NY  plan-2  C21   0.020
 6NY  plan-2  C22   0.020
 6NY  plan-2  C23   0.020
 6NY  plan-2  H071  0.020
 6NY  plan-2  H211  0.020
 6NY  plan-2  H221  0.020
 6NY  plan-2  H231  0.020
 6NY  plan-3  O01   0.020
 6NY  plan-3  C02   0.020
 6NY  plan-3  N03   0.020
 6NY  plan-3  C04   0.020
 6NY  plan-3  C05   0.020
 6NY  plan-3  C06   0.020
 6NY  plan-4  C18   0.020
 6NY  plan-4  N19   0.020
 6NY  plan-4  O20   0.020
 6NY  plan-4  H191  0.020

