# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:47:42 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: [4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H]2C[C@H](N)[C@@H](O)[C@H](O)[C@H]2O)c1O
#
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
 9YM  9YM  '[4-({[(1R,2S,3S,4R,5S)-5-amino-2,3,4-trihydroxycyclohexyl]amino}methyl)-5-hydroxy-6-methylpyridin-3-yl]methyl dihydrogen phosphate'  ligand  50  26  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9YM
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
 9YM  O2P  O  OH1   0  -0.730  -4.4119  -2.8381  -0.7209
 9YM  P    P  P     0   1.459  -3.1224  -2.5684   0.1756
 9YM  O3P  O  OH1   0  -0.742  -3.5678  -2.6404   1.7092
 9YM  O1P  O  O     0  -0.704  -1.9380  -3.4192  -0.0353
 9YM  O4P  O  O2    0  -0.595  -2.9670  -1.0221  -0.1888
 9YM  C5A  C  CH2   0  -0.222  -1.8379  -0.2969   0.2966
 9YM  C5   C  CR6   0  -0.072  -2.0413   1.1705   0.0504
 9YM  C4   C  CR6   0   0.070  -1.0051   2.0669   0.3515
 9YM  C4A  C  CH2   0  -0.382   0.3167   1.5480   0.8599
 9YM  C3   C  CR6   0   0.252  -1.2332   3.4184   0.1195
 9YM  O3   O  OH1   0  -0.623  -0.3295   4.3912   0.3483
 9YM  C2   C  CR6   0   0.137  -2.4713   3.8421  -0.3931
 9YM  C2A  C  CH3   0  -0.721  -2.7297   5.2947  -0.6503
 9YM  N1   N  N     0  -0.408  -3.4298   2.9763  -0.6634
 9YM  C6   C  CR16  0  -0.141  -3.2265   1.6784  -0.4485
 9YM  OD4  O  OH1   0  -0.679   5.9766  -1.7747   0.3487
 9YM  CD4  C  CH1   0   0.039   4.8969  -0.9934  -0.1182
 9YM  CD5  C  CH1   0  -0.016   3.6531  -1.8510  -0.3306
 9YM  OD5  O  OH1   0  -0.683   3.8747  -2.8520  -1.3079
 9YM  CD6  C  CH1   0   0.069   2.4670  -1.0148  -0.8021
 9YM  OD6  O  OH1   0  -0.659   1.3244  -1.8142  -0.9691
 9YM  CD3  C  CH1   0  -0.116   4.6250   0.1076   0.9073
 9YM  ND3  N  NH2   0  -0.789   5.7511   0.9938   1.1490
 9YM  CD2  C  CH2   0  -0.459   3.4135   0.9241   0.4707
 9YM  CD1  C  CH1   0  -0.099   2.1650   0.0761   0.2204
 9YM  ND1  N  NH1   0  -0.580   1.0117   0.8484  -0.2009
 9YM  H1   H  HOH1  0   0.504  -4.6887  -3.7639  -0.7436
 9YM  H2   H  HOH1  0   0.496  -4.3679  -2.1484   1.9376
 9YM  H3   H  HCH2  0   0.247  -1.7112  -0.4672   1.3724
 9YM  H4   H  HCH2  0   0.289  -0.9269  -0.6391  -0.1989
 9YM  H5   H  HCH2  0   0.215   0.9095   2.3444   1.3341
 9YM  H6   H  HCH2  0   0.265   0.1313   0.8359   1.6690
 9YM  H8   H  HCH3  0   0.247  -2.0497   5.6974  -1.4036
 9YM  H9   H  HCH3  0   0.247  -3.7486   5.4300  -1.0067
 9YM  H10  H  HCH3  0   0.246  -2.5986   5.8976   0.2498
 9YM  H11  H  HCR6  0   0.255  -4.0551   1.0252  -0.6893
 9YM  H13  H  HCH1  0   0.199   5.1571  -0.5103  -1.0744
 9YM  H14  H  HCH1  0   0.212   3.3814  -2.3127   0.6309
 9YM  H15  H  HOH1  0   0.458   4.2686  -3.6199  -0.8848
 9YM  H16  H  HCH1  0   0.191   2.7453  -0.5286  -1.7542
 9YM  H17  H  HOH1  0   0.442   1.5848  -2.5878  -1.4815
 9YM  H18  H  HCH1  0   0.224   4.3841  -0.3772   1.8623
 9YM  H19  H  HNH2  0   0.344   6.5602   0.4462   1.4145
 9YM  H20  H  HNH2  0   0.335   6.0072   1.4549   0.2823
 9YM  H22  H  HCH2  0   0.251   3.2065   1.6782   1.2331
 9YM  H23  H  HCH2  0   0.220   3.6620   1.4691  -0.4492
 9YM  H24  H  HCH1  0   0.231   1.8853  -0.4221   1.1574
 9YM  H25  H  HNH1  0   0.347   1.2640   1.4936  -0.9406
 9YM  H27  H  HOH1  0   0.475   0.4748   4.0450   0.7501
 9YM  H12  H  HOH1  0   0.452   6.3529  -2.2561  -0.3934

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
 9YM  O3   C3   single    1.347  0.020  1.347
 9YM  C2A  C2   single    1.498  0.020  1.498
 9YM  C3   C2   aromatic  1.405  0.020  1.405
 9YM  C3   C4   aromatic  1.390  0.020  1.390
 9YM  C2   N1   aromatic  1.320  0.020  1.320
 9YM  ND3  CD3  single    1.453  0.020  1.453
 9YM  CD2  CD3  single    1.525  0.020  1.525
 9YM  CD2  CD1  single    1.530  0.020  1.530
 9YM  CD3  CD4  single    1.529  0.020  1.529
 9YM  CD1  ND1  single    1.451  0.020  1.451
 9YM  CD1  CD6  single    1.525  0.020  1.525
 9YM  ND1  C4A  single    1.448  0.020  1.448
 9YM  C4A  C4   single    1.508  0.020  1.508
 9YM  C4   C5   aromatic  1.403  0.020  1.403
 9YM  N1   C6   aromatic  1.331  0.020  1.331
 9YM  OD6  CD6  single    1.405  0.020  1.405
 9YM  CD6  CD5  single    1.526  0.020  1.526
 9YM  CD5  CD4  single    1.526  0.020  1.526
 9YM  CD5  OD5  single    1.416  0.020  1.416
 9YM  CD4  OD4  single    1.412  0.020  1.412
 9YM  C5   C6   aromatic  1.383  0.020  1.383
 9YM  C5   C5A  single    1.502  0.020  1.502
 9YM  O1P  P    double    1.473  0.020  1.473
 9YM  O4P  C5A  single    1.427  0.020  1.427
 9YM  O4P  P    single    1.596  0.020  1.596
 9YM  P    O3P  single    1.599  0.020  1.599
 9YM  P    O2P  single    1.593  0.020  1.593
 9YM  O2P  H1   single    0.850  0.020  0.980
 9YM  O3P  H2   single    0.850  0.020  0.980
 9YM  C5A  H3   single    0.970  0.020  1.090
 9YM  C5A  H4   single    0.970  0.020  1.090
 9YM  C4A  H5   single    0.970  0.020  1.090
 9YM  C4A  H6   single    0.970  0.020  1.090
 9YM  C2A  H8   single    0.970  0.020  1.090
 9YM  C2A  H9   single    0.970  0.020  1.090
 9YM  C2A  H10  single    0.970  0.020  1.090
 9YM  C6   H11  single    0.930  0.020  1.080
 9YM  OD4  H12  single    0.850  0.020  0.980
 9YM  CD4  H13  single    0.970  0.020  1.090
 9YM  CD5  H14  single    0.970  0.020  1.090
 9YM  OD5  H15  single    0.850  0.020  0.980
 9YM  CD6  H16  single    0.970  0.020  1.090
 9YM  OD6  H17  single    0.850  0.020  0.980
 9YM  CD3  H18  single    0.970  0.020  1.090
 9YM  ND3  H19  single    0.890  0.020  1.040
 9YM  ND3  H20  single    0.890  0.020  1.040
 9YM  CD2  H22  single    0.970  0.020  1.090
 9YM  CD2  H23  single    0.970  0.020  1.090
 9YM  CD1  H24  single    0.970  0.020  1.090
 9YM  ND1  H25  single    0.890  0.020  1.040
 9YM  O3   H27  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
 9YM  H1   O2P  P    114.02  3.000
 9YM  O4P  P    O1P  116.64  3.000
 9YM  O4P  P    O3P  106.85  3.000
 9YM  O1P  P    O3P  109.59  3.000
 9YM  O3P  P    O2P  107.86  3.000
 9YM  O4P  P    O2P   96.56  3.000
 9YM  O1P  P    O2P  118.17  3.000
 9YM  H2   O3P  P    115.75  3.000
 9YM  C5A  O4P  P    119.45  3.000
 9YM  H4   C5A  H3   107.46  3.000
 9YM  H4   C5A  C5   110.17  3.000
 9YM  H3   C5A  C5   109.17  3.000
 9YM  H4   C5A  O4P  110.27  3.000
 9YM  H3   C5A  O4P  110.26  3.000
 9YM  C5   C5A  O4P  109.49  3.000
 9YM  C6   C5   C4   118.42  3.000
 9YM  C6   C5   C5A  122.29  3.000
 9YM  C4   C5   C5A  119.29  3.000
 9YM  C3   C4   C4A  122.31  3.000
 9YM  C4A  C4   C5   119.99  3.000
 9YM  C3   C4   C5   117.66  3.000
 9YM  H6   C4A  H5   104.11  3.000
 9YM  H6   C4A  ND1  107.98  3.000
 9YM  H5   C4A  ND1  114.00  3.000
 9YM  H6   C4A  C4   108.95  3.000
 9YM  H5   C4A  C4   111.62  3.000
 9YM  ND1  C4A  C4   109.87  3.000
 9YM  C2   C3   O3   115.79  3.000
 9YM  C2   C3   C4   119.90  3.000
 9YM  O3   C3   C4   124.31  3.000
 9YM  H27  O3   C3   111.80  3.000
 9YM  N1   C2   C2A  118.42  3.000
 9YM  N1   C2   C3   121.12  3.000
 9YM  C2A  C2   C3   120.47  3.000
 9YM  H10  C2A  H9   108.30  3.000
 9YM  H10  C2A  H8   106.89  3.000
 9YM  H9   C2A  H8   108.14  3.000
 9YM  H10  C2A  C2   111.93  3.000
 9YM  H9   C2A  C2   109.79  3.000
 9YM  H8   C2A  C2   111.64  3.000
 9YM  C6   N1   C2   119.72  3.000
 9YM  H11  C6   N1   115.82  3.000
 9YM  H11  C6   C5   121.00  3.000
 9YM  N1   C6   C5   123.18  3.000
 9YM  H12  OD4  CD4  108.73  3.000
 9YM  H13  CD4  CD3  107.95  3.000
 9YM  H13  CD4  CD5  108.54  3.000
 9YM  CD3  CD4  CD5  110.68  3.000
 9YM  H13  CD4  OD4  110.42  3.000
 9YM  CD5  CD4  OD4  111.00  3.000
 9YM  CD3  CD4  OD4  108.22  3.000
 9YM  H14  CD5  CD6  107.93  3.000
 9YM  H14  CD5  OD5  110.18  3.000
 9YM  CD6  CD5  OD5  107.20  3.000
 9YM  H14  CD5  CD4  108.39  3.000
 9YM  OD5  CD5  CD4  111.46  3.000
 9YM  CD6  CD5  CD4  111.63  3.000
 9YM  H15  OD5  CD5  108.97  3.000
 9YM  H16  CD6  CD1  108.24  3.000
 9YM  H16  CD6  OD6  110.67  3.000
 9YM  CD1  CD6  OD6  109.01  3.000
 9YM  H16  CD6  CD5  108.16  3.000
 9YM  OD6  CD6  CD5  110.93  3.000
 9YM  CD1  CD6  CD5  109.80  3.000
 9YM  H17  OD6  CD6  107.47  3.000
 9YM  H18  CD3  CD2  108.14  3.000
 9YM  H18  CD3  ND3  107.13  3.000
 9YM  CD2  CD3  ND3  109.68  3.000
 9YM  H18  CD3  CD4  107.73  3.000
 9YM  CD2  CD3  CD4  109.57  3.000
 9YM  ND3  CD3  CD4  114.38  3.000
 9YM  H20  ND3  H19  105.55  3.000
 9YM  H20  ND3  CD3  109.30  3.000
 9YM  H19  ND3  CD3  109.46  3.000
 9YM  H23  CD2  H22  106.56  3.000
 9YM  H23  CD2  CD1  108.83  3.000
 9YM  H22  CD2  CD1  110.01  3.000
 9YM  H23  CD2  CD3  109.03  3.000
 9YM  H22  CD2  CD3  108.69  3.000
 9YM  CD1  CD2  CD3  113.48  3.000
 9YM  H24  CD1  ND1  106.68  3.000
 9YM  H24  CD1  CD2  108.66  3.000
 9YM  ND1  CD1  CD2  113.66  3.000
 9YM  H24  CD1  CD6  107.35  3.000
 9YM  ND1  CD1  CD6  110.09  3.000
 9YM  CD2  CD1  CD6  110.15  3.000
 9YM  H25  ND1  CD1  110.67  3.000
 9YM  H25  ND1  C4A  110.27  3.000
 9YM  CD1  ND1  C4A  115.21  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
 9YM  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 9YM  CONST_02  C2   N1   C6   C5      0.00   0.0  0
 9YM  CONST_03  N1   C2   C3   C4      0.00   0.0  0
 9YM  CONST_04  N1   C6   C5   C4      0.00   0.0  0
 9YM  CONST_05  C6   N1   C2   C3      0.00   0.0  0
 9YM  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 9YM  CONST_07  C3   C4   C5   C5A   180.00   0.0  0
 9YM  CONST_08  N1   C6   C5   C5A   180.00   0.0  0
 9YM  CONST_09  O3   C3   C4   C5    180.00   0.0  0
 9YM  CONST_10  C2A  C2   C3   C4    180.00   0.0  0
 9YM  CONST_11  C2   C3   C4   C4A   180.00   0.0  0
 9YM  CONST_12  C6   C5   C4   C4A   180.00   0.0  0
 9YM  CONST_13  N1   C2   C3   O3    180.00   0.0  0
 9YM  CONST_14  C6   N1   C2   C2A   180.00   0.0  0
 9YM  CONST_15  H11  C6   C5   C4    180.00   0.0  0
 9YM  Var_01    C4   C5   C5A  O4P  -174.91  30.0  1
 9YM  Var_02    ND1  C4A  C4   C5     69.80  30.0  2
 9YM  Var_03    CD1  ND1  C4A  C4   -168.26  30.0  1
 9YM  Var_04    H8   C2A  C2   C3     62.27  30.0  2
 9YM  Var_05    C5   C5A  O4P  P    -169.36  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
 9YM  chir_01  CD4  CD3  CD5  OD4  positiv
 9YM  chir_02  CD5  OD5  CD4  CD6  negativ
 9YM  chir_03  CD6  OD6  CD5  CD1  positiv
 9YM  chir_04  CD3  ND3  CD2  CD4  negativ
 9YM  chir_05  CD1  ND1  CD6  CD2  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
 9YM  plan-1  C5A  0.020
 9YM  plan-1  C5   0.020
 9YM  plan-1  C4   0.020
 9YM  plan-1  C4A  0.020
 9YM  plan-1  C3   0.020
 9YM  plan-1  O3   0.020
 9YM  plan-1  C2   0.020
 9YM  plan-1  C2A  0.020
 9YM  plan-1  N1   0.020
 9YM  plan-1  C6   0.020
 9YM  plan-1  H11  0.020

