# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 21:11:47 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: ~{N}-[(3~{R},5~{S})-5-(hydroxymethyl)-1-methyl-pyrrolidin-3-yl]-2-(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C[C@@H](C[C@H]1CO)NC(=O)Cc2ccc3OCC(=O)Nc3c2
#
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
 YAJ  YAJ  "~{N}-[(3~{R},5~{S})-5-(hydroxymethyl)-1-methyl-pyrrolidin-3-yl]-2-(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)ethanamide"
  ligand  44  23  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YAJ
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
 YAJ  C10   C  CR16  0  -0.299  24.3506  -2.6069  6.4212
 YAJ  C13   C  CR6   0   0.332  27.0814  -3.0329  6.5735
 YAJ  C20   C  CH2   0  -0.490  21.7212   2.5570  8.6780
 YAJ  C21   C  CH1   0  -0.061  21.3750   3.3796  7.4323
 YAJ  C22   C  CH2   0  -0.181  20.4033   4.5166  7.6810
 YAJ  C03   C  CH2   0  -0.268  23.5047   2.6140  7.0473
 YAJ  C04   C  CH1   0  -0.061  23.1582   2.0567  8.4342
 YAJ  C06   C  C     0   0.551  24.4252  -0.0375  8.6021
 YAJ  C08   C  CH2   0  -0.661  24.3182  -1.5520  8.7035
 YAJ  C09   C  CR6   0   0.121  25.0393  -2.2208  7.5661
 YAJ  C11   C  CR16  0  -0.342  25.0166  -3.1919  5.3519
 YAJ  C12   C  CR6   0   0.320  26.3795  -3.4113  5.4300
 YAJ  C14   C  CR16  0  -0.372  26.4130  -2.4338  7.6298
 YAJ  C16   C  C     0   0.478  29.1765  -3.6071  5.5238
 YAJ  C18   C  CH2   0  -0.310  28.3724  -3.6122  4.2380
 YAJ  N02   N  NT    0  -0.425  22.6794   3.7969  6.9410
 YAJ  N05   N  NH1   0  -0.645  23.2573   0.6165  8.5254
 YAJ  N15   N  NH1   0  -0.718  28.4468  -3.3132  6.6241
 YAJ  O07   O  O     0  -0.488  25.5107   0.5252  8.6014
 YAJ  O17   O  O     0  -0.447  30.3746  -3.8039  5.5423
 YAJ  O19   O  O2    0  -0.472  27.0358  -4.0361  4.4211
 YAJ  O23   O  OH1   0  -0.663  20.9435   5.4334  8.6026
 YAJ  H101  H  HCR6  0   0.254  23.2814  -2.4481  6.3561
 YAJ  H201  H  HCH2  0   0.253  21.6777   3.1665  9.5795
 YAJ  H202  H  HCH2  0   0.246  21.0116   1.7387  8.8113
 YAJ  H211  H  HCH1  0   0.204  20.8827   2.7156  6.6963
 YAJ  H222  H  HCH2  0   0.204  20.1582   5.0031  6.7274
 YAJ  H221  H  HCH2  0   0.204  19.4678   4.0716  8.0454
 YAJ  H013  H  HCH3  0   0.235  23.6976   4.6161  5.3204
 YAJ  H011  H  HCH3  0   0.191  22.2607   3.6896  4.8570
 YAJ  H012  H  HCH3  0   0.237  22.0999   5.2932  5.5931
 YAJ  H031  H  HCH2  0   0.192  23.2568   1.8607  6.2780
 YAJ  H032  H  HCH2  0   0.239  24.5633   2.8577  6.9402
 YAJ  H041  H  HCH1  0   0.259  23.8325   2.4901  9.1745
 YAJ  H081  H  HCH2  0   0.273  23.2774  -1.8777  8.7275
 YAJ  H082  H  HCH2  0   0.287  24.7662  -1.8442  9.6563
 YAJ  H111  H  HCR6  0   0.268  24.4761  -3.4957  4.4644
 YAJ  H141  H  HCR6  0   0.266  26.9686  -2.1489  8.5155
 YAJ  H182  H  HCH2  0   0.281  28.8338  -4.2970  3.5296
 YAJ  H181  H  HCH2  0   0.266  28.4083  -2.6020  3.8081
 YAJ  H051  H  HNH1  0   0.400  22.4063   0.0792  8.4799
 YAJ  H151  H  HNH1  0   0.414  28.9322  -3.2159  7.5061
 YAJ  H231  H  HOH1  0   0.453  20.2664   6.0843  8.8071
 YAJ  C01   C  CH3   0  -0.526  22.6776   4.3690  5.6174

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
 YAJ  C18  O19   single    1.414  0.020  1.414
 YAJ  C18  C16   single    1.516  0.020  1.516
 YAJ  O19  C12   single    1.356  0.020  1.356
 YAJ  O17  C16   double    1.214  0.020  1.214
 YAJ  C16  N15   single    1.353  0.020  1.353
 YAJ  C12  C11   aromatic  1.383  0.020  1.383
 YAJ  C12  C13   aromatic  1.394  0.020  1.394
 YAJ  C11  C10   aromatic  1.389  0.020  1.389
 YAJ  C01  N02   single    1.442  0.020  1.442
 YAJ  N15  C13   single    1.395  0.020  1.395
 YAJ  C13  C14   aromatic  1.386  0.020  1.386
 YAJ  C10  C09   aromatic  1.391  0.020  1.391
 YAJ  N02  C21   single    1.455  0.020  1.455
 YAJ  N02  C03   single    1.446  0.020  1.446
 YAJ  C14  C09   aromatic  1.392  0.020  1.392
 YAJ  C22  C21   single    1.516  0.020  1.516
 YAJ  C22  O23   single    1.408  0.020  1.408
 YAJ  C21  C20   single    1.532  0.020  1.532
 YAJ  C09  C08   single    1.504  0.020  1.504
 YAJ  C03  C04   single    1.534  0.020  1.534
 YAJ  N05  C06   single    1.341  0.020  1.341
 YAJ  N05  C04   single    1.447  0.020  1.447
 YAJ  C08  C06   single    1.522  0.020  1.522
 YAJ  C06  O07   double    1.223  0.020  1.223
 YAJ  C04  C20   single    1.541  0.020  1.541
 YAJ  C10  H101  single    0.930  0.020  1.080
 YAJ  C20  H201  single    0.970  0.020  1.090
 YAJ  C20  H202  single    0.970  0.020  1.090
 YAJ  C21  H211  single    0.970  0.020  1.090
 YAJ  C22  H222  single    0.970  0.020  1.090
 YAJ  C22  H221  single    0.970  0.020  1.090
 YAJ  C01  H013  single    0.970  0.020  1.090
 YAJ  C01  H011  single    0.970  0.020  1.090
 YAJ  C01  H012  single    0.970  0.020  1.090
 YAJ  C03  H031  single    0.970  0.020  1.090
 YAJ  C03  H032  single    0.970  0.020  1.090
 YAJ  C04  H041  single    0.970  0.020  1.090
 YAJ  C08  H081  single    0.970  0.020  1.090
 YAJ  C08  H082  single    0.970  0.020  1.090
 YAJ  C11  H111  single    0.930  0.020  1.080
 YAJ  C14  H141  single    0.930  0.020  1.080
 YAJ  C18  H182  single    0.970  0.020  1.090
 YAJ  C18  H181  single    0.970  0.020  1.090
 YAJ  N05  H051  single    0.860  0.020  1.020
 YAJ  N15  H151  single    0.860  0.020  1.020
 YAJ  O23  H231  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
 YAJ  H101  C10  C11   119.27  3.000
 YAJ  H101  C10  C09   119.85  3.000
 YAJ  C11   C10  C09   120.88  3.000
 YAJ  N15   C13  C14   122.09  3.000
 YAJ  C14   C13  C12   119.97  3.000
 YAJ  N15   C13  C12   117.91  3.000
 YAJ  H202  C20  H201  107.01  3.000
 YAJ  H202  C20  C04   112.48  3.000
 YAJ  H201  C20  C04   110.48  3.000
 YAJ  H202  C20  C21   110.79  3.000
 YAJ  H201  C20  C21   111.31  3.000
 YAJ  C04   C20  C21   104.85  3.000
 YAJ  H211  C21  N02   110.26  3.000
 YAJ  H211  C21  C22   105.89  3.000
 YAJ  N02   C21  C22   114.51  3.000
 YAJ  H211  C21  C20   108.60  3.000
 YAJ  C22   C21  C20   114.46  3.000
 YAJ  N02   C21  C20   103.06  3.000
 YAJ  H221  C22  H222  106.11  3.000
 YAJ  H221  C22  O23   111.94  3.000
 YAJ  H222  C22  O23   111.44  3.000
 YAJ  H221  C22  C21   107.25  3.000
 YAJ  H222  C22  C21   109.44  3.000
 YAJ  O23   C22  C21   110.48  3.000
 YAJ  H032  C03  H031  107.54  3.000
 YAJ  H032  C03  N02   111.32  3.000
 YAJ  H031  C03  N02   112.24  3.000
 YAJ  H032  C03  C04   112.87  3.000
 YAJ  H031  C03  C04   109.33  3.000
 YAJ  N02   C03  C04   103.57  3.000
 YAJ  H041  C04  N05   108.08  3.000
 YAJ  H041  C04  C03   109.24  3.000
 YAJ  N05   C04  C03   113.78  3.000
 YAJ  H041  C04  C20   109.88  3.000
 YAJ  N05   C04  C20   112.15  3.000
 YAJ  C03   C04  C20   103.63  3.000
 YAJ  O07   C06  N05   123.29  3.000
 YAJ  O07   C06  C08   121.36  3.000
 YAJ  N05   C06  C08   115.35  3.000
 YAJ  H082  C08  H081  106.99  3.000
 YAJ  H082  C08  C09   110.12  3.000
 YAJ  H081  C08  C09   109.96  3.000
 YAJ  H082  C08  C06   107.19  3.000
 YAJ  H081  C08  C06   111.45  3.000
 YAJ  C09   C08  C06   111.01  3.000
 YAJ  C14   C09  C08   120.45  3.000
 YAJ  C08   C09  C10   120.58  3.000
 YAJ  C14   C09  C10   118.95  3.000
 YAJ  H111  C11  C12   119.59  3.000
 YAJ  H111  C11  C10   120.66  3.000
 YAJ  C12   C11  C10   119.74  3.000
 YAJ  O19   C12  C11   120.54  3.000
 YAJ  C11   C12  C13   119.97  3.000
 YAJ  O19   C12  C13   119.44  3.000
 YAJ  H141  C14  C09   120.22  3.000
 YAJ  H141  C14  C13   119.29  3.000
 YAJ  C09   C14  C13   120.48  3.000
 YAJ  O17   C16  N15   123.72  3.000
 YAJ  N15   C16  C18   113.85  3.000
 YAJ  O17   C16  C18   122.38  3.000
 YAJ  H181  C18  H182  108.07  3.000
 YAJ  H181  C18  O19   110.93  3.000
 YAJ  H182  C18  O19   107.25  3.000
 YAJ  H181  C18  C16   108.15  3.000
 YAJ  H182  C18  C16   109.22  3.000
 YAJ  O19   C18  C16   113.11  3.000
 YAJ  C03   N02  C01   113.12  3.000
 YAJ  C03   N02  C21   104.60  3.000
 YAJ  C01   N02  C21   115.00  3.000
 YAJ  H051  N05  C06   118.57  3.000
 YAJ  H051  N05  C04   118.06  3.000
 YAJ  C06   N05  C04   123.29  3.000
 YAJ  H151  N15  C16   118.13  3.000
 YAJ  H151  N15  C13   118.82  3.000
 YAJ  C16   N15  C13   122.83  3.000
 YAJ  C18   O19  C12   114.56  3.000
 YAJ  H231  O23  C22   108.06  3.000
 YAJ  H012  C01  H011  107.87  3.000
 YAJ  H012  C01  H013  107.30  3.000
 YAJ  H011  C01  H013  107.80  3.000
 YAJ  H012  C01  N02   110.94  3.000
 YAJ  H011  C01  N02   112.92  3.000
 YAJ  H013  C01  N02   109.80  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
 YAJ  CONST_01  C13   C12  C11  C10     0.00   0.0  0
 YAJ  CONST_02  C13   C14  C09  C10     0.00   0.0  0
 YAJ  CONST_03  C12   C11  C10  C09     0.00   0.0  0
 YAJ  CONST_04  C12   C13  C14  C09     0.00   0.0  0
 YAJ  CONST_05  C14   C13  C12  C11     0.00   0.0  0
 YAJ  CONST_06  C14   C09  C10  C11     0.00   0.0  0
 YAJ  CONST_07  C18   C16  N15  C13     0.00   0.0  0
 YAJ  CONST_08  C08   C09  C14  C13   180.00   0.0  0
 YAJ  CONST_09  C11   C10  C09  C08   180.00   0.0  0
 YAJ  CONST_10  O17   C16  N15  C13   180.00   0.0  0
 YAJ  CONST_11  H141  C14  C09  C10   180.00   0.0  0
 YAJ  CONST_12  H111  C11  C12  C13   180.00   0.0  0
 YAJ  CONST_13  H111  C11  C10  C09   180.00   0.0  0
 YAJ  CONST_14  H101  C10  C11  C12   180.00   0.0  0
 YAJ  CONST_15  H141  C14  C13  C12   180.00   0.0  0
 YAJ  CONST_16  H101  C10  C09  C14   180.00   0.0  0
 YAJ  CONST_17  H141  C14  C13  N15     0.00   0.0  0
 YAJ  CONST_18  H111  C11  C12  O19     0.00   0.0  0
 YAJ  CONST_19  H151  N15  C16  C18   180.00   0.0  0
 YAJ  CONST_20  H151  N15  C16  O17     0.00   0.0  0
 YAJ  CONST_21  C08   C06  N05  C04   180.00   0.0  0
 YAJ  CONST_22  O07   C06  N05  C04     0.00   0.0  0
 YAJ  CONST_23  H051  N05  C06  C08     0.00   0.0  0
 YAJ  CONST_24  H051  N05  C06  O07   180.00   0.0  0
 YAJ  Var_01    C18   O19  C12  C13   -34.16  30.0  1
 YAJ  Var_02    C04   C03  N02  C21   -44.49  30.0  1
 YAJ  Var_03    C18   O19  C12  C11   148.18  30.0  1
 YAJ  Var_04    C16   C18  O19  C12    49.91  30.0  1
 YAJ  Var_05    C16   N15  C13  C12    17.41  30.0  1
 YAJ  Var_06    C16   N15  C13  C14  -164.47  30.0  1
 YAJ  Var_07    O19   C18  C16  N15   -32.59  30.0  1
 YAJ  Var_08    C04   C03  N02  C01  -170.38  30.0  1
 YAJ  Var_09    O19   C18  C16  O17   149.88  30.0  1
 YAJ  Var_10    H031  C03  N02  C21    73.32  30.0  1
 YAJ  Var_11    H032  C03  N02  C21  -166.06  30.0  1
 YAJ  Var_12    H182  C18  O19  C12   170.39  30.0  1
 YAJ  Var_13    H181  C18  O19  C12   -71.81  30.0  1
 YAJ  Var_14    H151  N15  C13  C12  -168.03  30.0  1
 YAJ  Var_15    H151  N15  C13  C14    10.08  30.0  1
 YAJ  Var_16    H182  C18  C16  N15  -151.94  30.0  1
 YAJ  Var_17    H181  C18  C16  N15    90.68  30.0  1
 YAJ  Var_18    C06   C08  C09  C10   -95.27  30.0  2
 YAJ  Var_19    C14   C09  C08  C06    83.17  30.0  3
 YAJ  Var_20    H081  C08  C09  C10    28.53  30.0  2
 YAJ  Var_21    H082  C08  C09  C10   146.18  30.0  2
 YAJ  Var_22    H013  C01  N02  C21  -177.89  30.0  3
 YAJ  Var_23    H011  C01  N02  C21   -57.57  30.0  3
 YAJ  Var_24    H012  C01  N02  C21    63.67  30.0  3
 YAJ  Var_25    H031  C03  N02  C01   -52.56  30.0  1
 YAJ  Var_26    H032  C03  N02  C01    68.06  30.0  1
 YAJ  Var_27    H013  C01  N02  C03   -57.79  30.0  3
 YAJ  Var_28    H011  C01  N02  C03    62.54  30.0  3
 YAJ  Var_29    H012  C01  N02  C03  -176.22  30.0  3
 YAJ  Var_30    H081  C08  C09  C14  -153.03  30.0  2
 YAJ  Var_31    H082  C08  C09  C14   -35.38  30.0  2
 YAJ  Var_32    H182  C18  C16  O17    30.53  30.0  1
 YAJ  Var_33    H181  C18  C16  O17   -86.86  30.0  1
 YAJ  Var_34    N05   C06  C08  C09   121.27  30.0  3
 YAJ  Var_35    O07   C06  C08  C09   -59.21  30.0  3
 YAJ  Var_36    H081  C08  C06  N05    -1.67  30.0  1
 YAJ  Var_37    H082  C08  C06  N05  -118.42  30.0  1
 YAJ  Var_38    H081  C08  C06  O07   177.85  30.0  1
 YAJ  Var_39    H082  C08  C06  O07    61.10  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
 YAJ  chir_01  C21  N02  C22  C20  positiv
 YAJ  chir_02  C04  N05  C03  C20  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
 YAJ  plan-1  C04   0.020
 YAJ  plan-1  C06   0.020
 YAJ  plan-1  C08   0.020
 YAJ  plan-1  N05   0.020
 YAJ  plan-1  O07   0.020
 YAJ  plan-1  H051  0.020
 YAJ  plan-2  C10   0.020
 YAJ  plan-2  C13   0.020
 YAJ  plan-2  C08   0.020
 YAJ  plan-2  C09   0.020
 YAJ  plan-2  C11   0.020
 YAJ  plan-2  C12   0.020
 YAJ  plan-2  C14   0.020
 YAJ  plan-2  N15   0.020
 YAJ  plan-2  O19   0.020
 YAJ  plan-2  H101  0.020
 YAJ  plan-2  H111  0.020
 YAJ  plan-2  H141  0.020
 YAJ  plan-3  C13   0.020
 YAJ  plan-3  C16   0.020
 YAJ  plan-3  C18   0.020
 YAJ  plan-3  N15   0.020
 YAJ  plan-3  O17   0.020
 YAJ  plan-3  H151  0.020

