# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 16:26:56 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-[[1,3-dicyclohexyl-4-oxidanyl-2,6-bis(oxidanylidene)pyrimidin-5-yl]carbonylamino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)C1=C(O)N(C2CCCCC2)C(=O)N(C3CCCCC3)C1=O
#
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
 A0W  A0W  '2-[[1,3-dicyclohexyl-4-oxidanyl-2,6-bis(oxidanylidene)pyrimidin-5-yl]carbonylamino]ethanoic acid'  ligand  54  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A0W
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
 A0W  O01   O  O      0  -0.481   2.0358  -2.2149   0.0422
 A0W  C02   C  CR6    0   0.776   1.3154  -1.2370   0.0154
 A0W  N03   N  NR6    0  -0.638   1.8566   0.0419   0.0005
 A0W  C04   C  CH1    0  -0.077   3.3339   0.1490   0.0123
 A0W  C05   C  CH2    0  -0.432   3.9098   0.7830  -1.2518
 A0W  C06   C  CH2    0  -0.441   5.4325   0.6598  -1.2290
 A0W  C07   C  CH2    0  -0.432   6.0220   1.2764   0.0357
 A0W  C08   C  CH2    0  -0.441   5.4104   0.6619   1.2908
 A0W  C09   C  CH2    0  -0.432   3.8873   0.7829   1.2865
 A0W  C10   C  CR6    0   0.683   1.0793   1.1751  -0.0169
 A0W  O11   O  OH1    0  -0.562   1.6303   2.2935  -0.0213
 A0W  C12   C  CR6    0  -0.493  -0.3310   1.0219  -0.0288
 A0W  C13   C  C      0   0.680  -1.1321   2.2133  -0.0466
 A0W  N14   N  NH1    0  -0.643  -2.4392   2.2052  -0.0592
 A0W  C15   C  CH2    0  -0.425  -3.2798   3.3802  -0.0779
 A0W  C16   C  C      0   0.405  -4.7681   2.9708  -0.0843
 A0W  O17   O  O      0  -0.591  -5.0181   1.7518  -0.0814
 A0W  O18   O  OC    -1  -0.605  -5.5712   3.9177  -0.0923
 A0W  O19   O  O      0  -0.601  -0.5515   3.3793  -0.0510
 A0W  C20   C  CR6    0   0.636  -0.9297  -0.2734  -0.0216
 A0W  N21   N  NR6    0  -0.637  -0.0601  -1.3589  -0.0022
 A0W  C22   C  CH1    0  -0.079  -0.6119  -2.7331   0.0083
 A0W  C23   C  CH2    0  -0.430  -1.3867  -3.0821  -1.2621
 A0W  C24   C  CH2    0  -0.441  -1.7611  -4.5626  -1.2353
 A0W  C25   C  CH2    0  -0.429  -2.5500  -4.9143   0.0224
 A0W  C26   C  CH2    0  -0.441  -1.7727  -4.5371   1.2799
 A0W  C27   C  CH2    0  -0.430  -1.3961  -3.0570   1.2796
 A0W  O28   O  O      0  -0.499  -2.1414  -0.4667  -0.0306
 A0W  H041  H  HCH1   0   0.265   3.6712  -0.8850   0.0149
 A0W  H052  H  HCH2   0   0.235   3.5026   0.2807  -2.1331
 A0W  H051  H  HCH2   0   0.234   3.6376   1.8361  -1.3249
 A0W  H061  H  HCH2   0   0.214   5.7159  -0.3969  -1.2869
 A0W  H062  H  HCH2   0   0.233   5.8511   1.1406  -2.1158
 A0W  H072  H  HCH2   0   0.230   7.1073   1.1521   0.0454
 A0W  H071  H  HCH2   0   0.212   5.8324   2.3552   0.0330
 A0W  H081  H  HCH2   0   0.214   5.6935  -0.3945   1.3555
 A0W  H082  H  HCH2   0   0.233   5.8129   1.1444   2.1842
 A0W  H092  H  HCH2   0   0.233   3.6114   1.8356   1.3555
 A0W  H091  H  HCH2   0   0.236   3.4654   0.2794   2.1601
 A0W  H111  H  HOH1   0   0.496   0.4527   3.1991  -0.0403
 A0W  H141  H  HNH1   0   0.424  -2.9162   1.3065  -0.0568
 A0W  H151  H  HCH2   0   0.257  -3.0870   4.0106   0.7943
 A0W  H152  H  HCH2   0   0.257  -3.0746   3.9909  -0.9613
 A0W  H221  H  HCH1   0   0.264   0.2637  -3.3785   0.0166
 A0W  H232  H  HCH2   0   0.234  -2.2919  -2.4809  -1.3432
 A0W  H231  H  HCH2   0   0.233  -0.7691  -2.8655  -2.1377
 A0W  H241  H  HCH2   0   0.232  -2.3356  -4.8132  -2.1297
 A0W  H242  H  HCH2   0   0.212  -0.8502  -5.1701  -1.2687
 A0W  H251  H  HCH2   0   0.212  -3.5079  -4.3837   0.0125
 A0W  H252  H  HCH2   0   0.229  -2.7852  -5.9814   0.0323
 A0W  H262  H  HCH2   0   0.232  -2.3562  -4.7680   2.1739
 A0W  H261  H  HCH2   0   0.212  -0.8629  -5.1447   1.3346
 A0W  H272  H  HCH2   0   0.233  -0.7851  -2.8234   2.1553
 A0W  H271  H  HCH2   0   0.233  -2.3006  -2.4521   1.3416

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
 A0W  O17  C16   deloc   1.244  0.020  1.244
 A0W  C16  C15   single  1.544  0.020  1.544
 A0W  C16  O18   deloc   1.242  0.020  1.242
 A0W  C15  N14   single  1.445  0.020  1.445
 A0W  O19  C13   double  1.303  0.020  1.303
 A0W  N14  C13   single  1.307  0.020  1.307
 A0W  C13  C12   single  1.436  0.020  1.436
 A0W  O11  C10   single  1.247  0.020  1.247
 A0W  C12  C10   double  1.419  0.020  1.419
 A0W  C12  C20   single  1.427  0.020  1.427
 A0W  O28  C20   double  1.227  0.020  1.227
 A0W  C10  N03   single  1.374  0.020  1.374
 A0W  C20  N21   single  1.391  0.020  1.391
 A0W  N03  C04   single  1.481  0.020  1.481
 A0W  N03  C02   single  1.389  0.020  1.389
 A0W  C05  C04   single  1.527  0.020  1.527
 A0W  C05  C06   single  1.528  0.020  1.528
 A0W  N21  C02   single  1.381  0.020  1.381
 A0W  N21  C22   single  1.481  0.020  1.481
 A0W  C09  C04   single  1.527  0.020  1.527
 A0W  C09  C08   single  1.528  0.020  1.528
 A0W  C02  O01   double  1.215  0.020  1.215
 A0W  C06  C07   single  1.525  0.020  1.525
 A0W  C07  C08   single  1.525  0.020  1.525
 A0W  C22  C23   single  1.529  0.020  1.529
 A0W  C22  C27   single  1.528  0.020  1.528
 A0W  C23  C24   single  1.527  0.020  1.527
 A0W  C27  C26   single  1.527  0.020  1.527
 A0W  C24  C25   single  1.526  0.020  1.526
 A0W  C26  C25   single  1.526  0.020  1.526
 A0W  C04  H041  single  0.970  0.020  1.090
 A0W  C05  H052  single  0.970  0.020  1.090
 A0W  C05  H051  single  0.970  0.020  1.090
 A0W  C06  H061  single  0.970  0.020  1.090
 A0W  C06  H062  single  0.970  0.020  1.090
 A0W  C07  H072  single  0.970  0.020  1.090
 A0W  C07  H071  single  0.970  0.020  1.090
 A0W  C08  H081  single  0.970  0.020  1.090
 A0W  C08  H082  single  0.970  0.020  1.090
 A0W  C09  H092  single  0.970  0.020  1.090
 A0W  C09  H091  single  0.970  0.020  1.090
 A0W  O11  H111  single  0.850  0.020  0.980
 A0W  N14  H141  single  0.860  0.020  1.020
 A0W  C15  H151  single  0.970  0.020  1.090
 A0W  C15  H152  single  0.970  0.020  1.090
 A0W  C22  H221  single  0.970  0.020  1.090
 A0W  C23  H232  single  0.970  0.020  1.090
 A0W  C23  H231  single  0.970  0.020  1.090
 A0W  C24  H241  single  0.970  0.020  1.090
 A0W  C24  H242  single  0.970  0.020  1.090
 A0W  C25  H251  single  0.970  0.020  1.090
 A0W  C25  H252  single  0.970  0.020  1.090
 A0W  C26  H262  single  0.970  0.020  1.090
 A0W  C26  H261  single  0.970  0.020  1.090
 A0W  C27  H272  single  0.970  0.020  1.090
 A0W  C27  H271  single  0.970  0.020  1.090

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
 A0W  N21   C02  N03   117.99  3.000
 A0W  N21   C02  O01   121.32  3.000
 A0W  N03   C02  O01   120.69  3.000
 A0W  C10   N03  C04   120.31  3.000
 A0W  C04   N03  C02   117.07  3.000
 A0W  C10   N03  C02   122.62  3.000
 A0W  H041  C04  C09   106.28  3.000
 A0W  H041  C04  C05   106.24  3.000
 A0W  C09   C04  C05   112.44  3.000
 A0W  H041  C04  N03   103.92  3.000
 A0W  C09   C04  N03   113.46  3.000
 A0W  C05   C04  N03   113.55  3.000
 A0W  H051  C05  H052  107.27  3.000
 A0W  H051  C05  C06   109.13  3.000
 A0W  H052  C05  C06   110.26  3.000
 A0W  H051  C05  C04   111.25  3.000
 A0W  H052  C05  C04   109.65  3.000
 A0W  C06   C05  C04   109.27  3.000
 A0W  H062  C06  H061  106.41  3.000
 A0W  H062  C06  C07   110.31  3.000
 A0W  H061  C06  C07   109.49  3.000
 A0W  H062  C06  C05   109.53  3.000
 A0W  H061  C06  C05   109.56  3.000
 A0W  C07   C06  C05   111.40  3.000
 A0W  H071  C07  H072  106.50  3.000
 A0W  H071  C07  C08   109.23  3.000
 A0W  H072  C07  C08   110.19  3.000
 A0W  H071  C07  C06   109.22  3.000
 A0W  H072  C07  C06   110.20  3.000
 A0W  C08   C07  C06   111.37  3.000
 A0W  H082  C08  H081  106.41  3.000
 A0W  H082  C08  C09   109.56  3.000
 A0W  H081  C08  C09   109.52  3.000
 A0W  H082  C08  C07   110.32  3.000
 A0W  H081  C08  C07   109.47  3.000
 A0W  C09   C08  C07   111.43  3.000
 A0W  H091  C09  H092  107.24  3.000
 A0W  H091  C09  C08   110.24  3.000
 A0W  H092  C09  C08   109.18  3.000
 A0W  H091  C09  C04   109.62  3.000
 A0W  H092  C09  C04   111.22  3.000
 A0W  C08   C09  C04   109.32  3.000
 A0W  C12   C10  O11   122.42  3.000
 A0W  C12   C10  N03   118.25  3.000
 A0W  O11   C10  N03   119.33  3.000
 A0W  H111  O11  C10   101.34  3.000
 A0W  C20   C12  C13   121.28  3.000
 A0W  C20   C12  C10   121.00  3.000
 A0W  C13   C12  C10   117.72  3.000
 A0W  O19   C13  N14   116.83  3.000
 A0W  N14   C13  C12   123.56  3.000
 A0W  O19   C13  C12   119.61  3.000
 A0W  H141  N14  C15   116.46  3.000
 A0W  H141  N14  C13   118.31  3.000
 A0W  C15   N14  C13   125.22  3.000
 A0W  H152  C15  H151  106.82  3.000
 A0W  H152  C15  C16   109.01  3.000
 A0W  H151  C15  C16   109.04  3.000
 A0W  H152  C15  N14   110.83  3.000
 A0W  H151  C15  N14   110.86  3.000
 A0W  C16   C15  N14   110.20  3.000
 A0W  O18   C16  O17   128.11  3.000
 A0W  O18   C16  C15   114.92  3.000
 A0W  O17   C16  C15   116.97  3.000
 A0W  O28   C20  N21   119.63  3.000
 A0W  N21   C20  C12   116.50  3.000
 A0W  O28   C20  C12   123.87  3.000
 A0W  C22   N21  C20   119.43  3.000
 A0W  C22   N21  C02   116.93  3.000
 A0W  C20   N21  C02   123.64  3.000
 A0W  H221  C22  C27   106.32  3.000
 A0W  H221  C22  C23   106.20  3.000
 A0W  C27   C22  C23   112.51  3.000
 A0W  H221  C22  N21   104.52  3.000
 A0W  C27   C22  N21   113.19  3.000
 A0W  C23   C22  N21   113.26  3.000
 A0W  H231  C23  H232  107.48  3.000
 A0W  H231  C23  C24   110.16  3.000
 A0W  H232  C23  C24   109.42  3.000
 A0W  H231  C23  C22   109.51  3.000
 A0W  H232  C23  C22   110.92  3.000
 A0W  C24   C23  C22   109.33  3.000
 A0W  H242  C24  H241  106.56  3.000
 A0W  H242  C24  C25   109.10  3.000
 A0W  H241  C24  C25   110.50  3.000
 A0W  H242  C24  C23   109.47  3.000
 A0W  H241  C24  C23   109.69  3.000
 A0W  C25   C24  C23   111.39  3.000
 A0W  H252  C25  H251  106.56  3.000
 A0W  H252  C25  C26   110.10  3.000
 A0W  H251  C25  C26   109.47  3.000
 A0W  H252  C25  C24   110.11  3.000
 A0W  H251  C25  C24   109.45  3.000
 A0W  C26   C25  C24   111.04  3.000
 A0W  H261  C26  H262  106.60  3.000
 A0W  H261  C26  C27   109.44  3.000
 A0W  H262  C26  C27   109.68  3.000
 A0W  H261  C26  C25   109.09  3.000
 A0W  H262  C26  C25   110.49  3.000
 A0W  C27   C26  C25   111.41  3.000
 A0W  H271  C27  H272  107.44  3.000
 A0W  H271  C27  C26   109.47  3.000
 A0W  H272  C27  C26   110.16  3.000
 A0W  H271  C27  C22   110.83  3.000
 A0W  H272  C27  C22   109.53  3.000
 A0W  C26   C27  C22   109.39  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
 A0W  CONST_01  C12   C20  N21  C02     0.00   0.0  0
 A0W  CONST_02  C20   N21  C02  N03     0.00   0.0  0
 A0W  CONST_03  C22   N21  C02  N03   180.00   0.0  0
 A0W  CONST_04  N21   C02  N03  C04   180.00   0.0  0
 A0W  CONST_05  N21   C02  N03  C10     0.00   0.0  0
 A0W  CONST_06  C22   N21  C20  C12   180.00   0.0  0
 A0W  CONST_07  C10   N03  C02  O01   180.00   0.0  0
 A0W  CONST_08  C04   N03  C02  O01     0.00   0.0  0
 A0W  CONST_09  C20   N21  C02  O01   180.00   0.0  0
 A0W  CONST_10  C22   N21  C02  O01     0.00   0.0  0
 A0W  CONST_11  O28   C20  N21  C02   180.00   0.0  0
 A0W  CONST_12  O28   C20  N21  C22     0.00   0.0  0
 A0W  CONST_13  C15   N14  C13  C12   180.00   0.0  0
 A0W  CONST_14  H141  N14  C13  C12     0.00   0.0  0
 A0W  CONST_15  O19   C13  N14  C15     0.00   0.0  0
 A0W  Var_01    C07   C06  C05  C04   -55.86  30.0  1
 A0W  Var_02    C07   C08  C09  C04    55.71  30.0  1
 A0W  Var_03    C08   C07  C06  C05    55.76  30.0  1
 A0W  Var_04    C09   C08  C07  C06   -55.68  30.0  1
 A0W  Var_05    C25   C24  C23  C22    56.02  30.0  1
 A0W  Var_06    C25   C26  C27  C22   -55.85  30.0  1
 A0W  Var_07    C26   C25  C24  C23   -56.40  30.0  1
 A0W  Var_08    C27   C26  C25  C24    56.30  30.0  1
 A0W  Var_09    O19   C13  C12  C10    -0.01  30.0  2
 A0W  Var_10    C16   C15  N14  C13  -179.83  30.0  1
 A0W  Var_11    O17   C16  C15  N14    -0.43  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
 A0W  chir_01  C04  N03  C05  C09  negativ
 A0W  chir_02  C22  N21  C23  C27  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
 A0W  plan-1  O01   0.020
 A0W  plan-1  C02   0.020
 A0W  plan-1  N03   0.020
 A0W  plan-1  C04   0.020
 A0W  plan-1  C10   0.020
 A0W  plan-1  O11   0.020
 A0W  plan-1  C12   0.020
 A0W  plan-1  C13   0.020
 A0W  plan-1  C20   0.020
 A0W  plan-1  N21   0.020
 A0W  plan-1  C22   0.020
 A0W  plan-1  O28   0.020
 A0W  plan-2  C12   0.020
 A0W  plan-2  C13   0.020
 A0W  plan-2  N14   0.020
 A0W  plan-2  C15   0.020
 A0W  plan-2  O19   0.020
 A0W  plan-2  H141  0.020
 A0W  plan-3  C15   0.020
 A0W  plan-3  C16   0.020
 A0W  plan-3  O17   0.020
 A0W  plan-3  O18   0.020

