# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:23:57 2021
#   Inital geometry file: a 87 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2N=[N+]=[NH-]
#
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
 P6D  P6D  'None                     '  ligand  32  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P6D
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
 P6D  C02  C  CH1    0  -0.014  -11.7283  22.6938  24.0421
 P6D  C03  C  CH1    0  -0.016  -11.5102  22.8824  22.5414
 P6D  C04  C  CH2    0  -0.172  -12.8012  23.0226  21.7512
 P6D  C11  C  CH1    0   0.219  -10.5520  24.6950  23.6425
 P6D  C12  C  CH1    0  -0.201  -11.6757  24.1422  24.5274
 P6D  C17  C  CR16   0   0.107  -11.6247  26.7200  22.8595
 P6D  C18  C  CR16   0  -0.475  -11.6931  28.0524  22.6942
 P6D  C19  C  CR6    0   0.519  -10.5977  28.8138  23.2118
 P6D  C21  C  CR6    0   0.597   -9.5073  26.9107  23.9799
 P6D  N13  N  N      0  -0.245  -11.3680  24.2234  25.9319
 P6D  N14  N  N      1   0.097  -11.7056  25.2845  26.4778
 P6D  N15  N  N     -1  -0.414  -11.9216  25.5383  27.6685
 P6D  N16  N  NR6    0  -0.560  -10.5753  26.1322  23.4892
 P6D  N20  N  N      0  -0.541   -9.5722  28.2465  23.8149
 P6D  N23  N  NH2    0  -0.805  -10.6021  30.1376  23.0813
 P6D  O01  O  OH1    0  -0.667  -10.6625  21.9392  24.5567
 P6D  O05  O  OH1    0  -0.667  -13.4372  21.7688  21.7568
 P6D  O10  O  O2     0  -0.496  -10.7482  24.0827  22.3947
 P6D  O22  O  O      0  -0.512   -8.5679  26.3612  24.5375
 P6D  H1   H  HCH1   0   0.263  -12.6977  22.2320  24.2595
 P6D  H2   H  HCH1   0   0.261  -10.9362  22.0433  22.1352
 P6D  H3   H  HCH2   0   0.197  -13.4338  23.8026  22.1987
 P6D  H4   H  HCH2   0   0.225  -12.5555  23.3544  20.7349
 P6D  H5   H  HCH1   0   0.275   -9.5818  24.4391  24.0691
 P6D  H6   H  HCH1   0   0.286  -12.6248  24.6356  24.2886
 P6D  H7   H  HCR6   0   0.313  -12.4039  26.0709  22.4854
 P6D  H8   H  HCR6   0   0.292  -12.5298  28.5129  22.1917
 P6D  H10  H  H      0   0.394  -11.8338  26.5425  27.8149
 P6D  H11  H  HNH2   0   0.405   -9.8412  30.6858  23.4455
 P6D  H12  H  HNH2   0   0.416  -11.3680  30.6216  22.6464
 P6D  H13  H  HOH1   0   0.456  -10.7177  21.9535  25.5189
 P6D  H14  H  HOH1   0   0.463  -14.2607  21.8451  21.2669

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
 P6D  C04  C03  single  1.520  0.020  1.520
 P6D  C04  O05  single  1.406  0.020  1.406
 P6D  O10  C03  single  1.429  0.020  1.429
 P6D  O10  C11  single  1.404  0.020  1.404
 P6D  C03  C02  single  1.528  0.020  1.528
 P6D  O22  C21  double  1.223  0.020  1.223
 P6D  C11  N16  single  1.446  0.020  1.446
 P6D  C11  C12  single  1.533  0.020  1.533
 P6D  C21  N20  single  1.348  0.020  1.348
 P6D  C21  N16  single  1.410  0.020  1.410
 P6D  N20  C19  double  1.318  0.020  1.318
 P6D  N16  C17  single  1.358  0.020  1.358
 P6D  C19  N23  single  1.330  0.020  1.330
 P6D  C19  C18  single  1.431  0.020  1.431
 P6D  C17  C18  double  1.344  0.020  1.344
 P6D  C02  C12  single  1.528  0.020  1.528
 P6D  C02  O01  single  1.404  0.020  1.404
 P6D  C12  N13  single  1.440  0.020  1.440
 P6D  N13  N14  double  1.240  0.020  1.240
 P6D  N14  N15  double  1.236  0.020  1.236
 P6D  C02  H1   single  0.970  0.020  1.090
 P6D  C03  H2   single  0.970  0.020  1.090
 P6D  C04  H3   single  0.970  0.020  1.090
 P6D  C04  H4   single  0.970  0.020  1.090
 P6D  C11  H5   single  0.970  0.020  1.090
 P6D  C12  H6   single  0.970  0.020  1.090
 P6D  C17  H7   single  0.930  0.020  1.080
 P6D  C18  H8   single  0.930  0.020  1.080
 P6D  N15  H10  single  0.890  0.020  1.040
 P6D  N23  H11  single  0.860  0.020  1.020
 P6D  N23  H12  single  0.860  0.020  1.020
 P6D  O01  H13  single  0.850  0.020  0.980
 P6D  O05  H14  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
 P6D  H1   C02  O01  111.87  3.000
 P6D  H1   C02  C12  111.52  3.000
 P6D  O01  C02  C12  111.53  3.000
 P6D  H1   C02  C03  111.91  3.000
 P6D  O01  C02  C03  108.55  3.000
 P6D  C12  C02  C03  100.95  3.000
 P6D  H2   C03  O10  109.03  3.000
 P6D  H2   C03  C04  108.85  3.000
 P6D  O10  C03  C04  108.78  3.000
 P6D  H2   C03  C02  110.15  3.000
 P6D  O10  C03  C02  106.29  3.000
 P6D  C04  C03  C02  113.62  3.000
 P6D  H4   C04  H3   106.94  3.000
 P6D  H4   C04  O05  112.01  3.000
 P6D  H3   C04  O05  111.76  3.000
 P6D  H4   C04  C03  108.62  3.000
 P6D  H3   C04  C03  110.03  3.000
 P6D  O05  C04  C03  107.45  3.000
 P6D  H5   C11  O10  111.71  3.000
 P6D  H5   C11  N16  106.81  3.000
 P6D  O10  C11  N16  109.70  3.000
 P6D  H5   C11  C12  109.98  3.000
 P6D  N16  C11  C12  114.06  3.000
 P6D  O10  C11  C12  104.67  3.000
 P6D  H6   C12  N13  111.85  3.000
 P6D  H6   C12  C11  110.28  3.000
 P6D  N13  C12  C11  112.69  3.000
 P6D  H6   C12  C02  109.13  3.000
 P6D  N13  C12  C02  111.75  3.000
 P6D  C11  C12  C02  100.58  3.000
 P6D  H7   C17  N16  117.24  3.000
 P6D  H7   C17  C18  121.06  3.000
 P6D  N16  C17  C18  121.70  3.000
 P6D  H8   C18  C19  122.33  3.000
 P6D  H8   C18  C17  121.31  3.000
 P6D  C19  C18  C17  116.35  3.000
 P6D  N23  C19  N20  118.41  3.000
 P6D  N23  C19  C18  119.44  3.000
 P6D  N20  C19  C18  122.15  3.000
 P6D  O22  C21  N20  122.57  3.000
 P6D  N20  C21  N16  117.93  3.000
 P6D  O22  C21  N16  119.50  3.000
 P6D  N14  N13  C12  114.80  3.000
 P6D  N15  N14  N13  130.33  3.000
 P6D  H10  N15  N14  109.01  3.000
 P6D  C21  N16  C17  120.52  3.000
 P6D  C17  N16  C11  119.48  3.000
 P6D  C21  N16  C11  120.00  3.000
 P6D  C21  N20  C19  121.35  3.000
 P6D  H12  N23  H11  118.08  3.000
 P6D  H12  N23  C19  121.62  3.000
 P6D  H11  N23  C19  120.28  3.000
 P6D  H13  O01  C02  108.33  3.000
 P6D  H14  O05  C04  108.34  3.000
 P6D  C11  O10  C03  110.46  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
 P6D  CONST_01  N20  C21  N16  C11  180.00  0.0  0
 P6D  CONST_02  N20  C21  N16  C17    0.00  0.0  0
 P6D  CONST_03  C21  N20  C19  C18    0.00  0.0  0
 P6D  CONST_04  N16  C21  N20  C19    0.00  0.0  0
 P6D  CONST_05  O22  C21  N16  C11    0.00  0.0  0
 P6D  CONST_06  O22  C21  N16  C17  180.00  0.0  0
 P6D  CONST_07  O22  C21  N20  C19  180.00  0.0  0
 P6D  CONST_08  N23  C19  N20  C21  180.00  0.0  0
 P6D  CONST_09  H11  N23  C19  C18  180.00  0.0  0
 P6D  CONST_10  H12  N23  C19  C18    0.00  0.0  0

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
 P6D  chir_01  C02  C03  C12  O01  positiv
 P6D  chir_02  C03  O10  C02  C04  negativ
 P6D  chir_03  C11  O10  N16  C12  negativ
 P6D  chir_04  C12  N13  C11  C02  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
 P6D  plan-1  C11  0.020
 P6D  plan-1  C17  0.020
 P6D  plan-1  C18  0.020
 P6D  plan-1  C19  0.020
 P6D  plan-1  C21  0.020
 P6D  plan-1  N16  0.020
 P6D  plan-1  N20  0.020
 P6D  plan-1  N23  0.020
 P6D  plan-1  O22  0.020
 P6D  plan-1  H7   0.020
 P6D  plan-1  H8   0.020
 P6D  plan-1  H11  0.020
 P6D  plan-1  H12  0.020
 P6D  plan-2  C02  0.020
 P6D  plan-2  C11  0.020
 P6D  plan-2  C12  0.020
 P6D  plan-2  N13  0.020
 P6D  plan-2  N14  0.020
 P6D  plan-2  N15  0.020
 P6D  plan-2  H6   0.020
 P6D  plan-2  H10  0.020

