# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:09:53 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: N-methyladenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
#
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
 6MD  6MD  'N-methyladenosine        '  ligand  35  20  .  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_6MD
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
 6MD  O5'  O  OH1   0  -0.668  -3.5153  -2.5882   0.2907
 6MD  C5'  C  CH2   0  -0.164  -3.6865  -1.4401  -0.5016
 6MD  C4'  C  CH1   0  -0.057  -3.4913  -0.2141   0.3709
 6MD  O4'  O  O2    0  -0.491  -2.2355  -0.2532   1.0560
 6MD  C3'  C  CH1   0  -0.033  -3.4598   1.0779  -0.4436
 6MD  O3'  O  OH1   0  -0.666  -3.7368   2.2109   0.3349
 6MD  C2'  C  CH1   0  -0.015  -1.9798   1.1209  -0.8258
 6MD  O2'  O  OH1   0  -0.652  -1.4567   2.3617  -1.1727
 6MD  C1'  C  CH1   0   0.213  -1.3203   0.6173   0.4624
 6MD  N9   N  NR5   0  -0.536  -0.0782  -0.0908   0.2334
 6MD  C8   C  CR15  0   0.102   0.0734  -1.3919  -0.1612
 6MD  N7   N  N     0  -0.453   1.3174  -1.7383  -0.3227
 6MD  C5   C  CR56  0  -0.006   2.0285  -0.6068  -0.0222
 6MD  C6   C  CR6   0   0.496   3.4088  -0.3203   0.0031
 6MD  N6   N  NH1   0  -0.643   4.3346  -1.2253  -0.3169
 6MD  N1   N  N     0  -0.489   3.7854   0.9109   0.3638
 6MD  C2   C  CR16  0   0.040   2.8529   1.8065   0.6832
 6MD  N3   N  N     0  -0.454   1.5408   1.6608   0.6923
 6MD  C4   C  CR56  0   0.485   1.1795   0.4301   0.3297
 6MD  CZ   C  CH3   0  -0.514   5.7520  -0.9603  -0.2912
 6MD  H1   H  HOH1  0   0.460  -3.6352  -3.3586  -0.2718
 6MD  H2   H  HCH2  0   0.199  -2.9815  -1.4288  -1.3445
 6MD  H3   H  HCH2  0   0.225  -4.6940  -1.3822  -0.9345
 6MD  H4   H  HCH1  0   0.264  -4.2791  -0.1914   1.1304
 6MD  H5   H  HCH1  0   0.253  -4.1130   1.0182  -1.3241
 6MD  H6   H  HOH1  0   0.457  -4.6534   2.1640   0.6251
 6MD  H7   H  HCH1  0   0.243  -1.8158   0.3786  -1.6188
 6MD  H8   H  HOH1  0   0.463  -1.7457   2.5791  -2.0644
 6MD  H9   H  HCH1  0   0.263  -1.0792   1.4583   1.1219
 6MD  H10  H  HCR5  0   0.295  -0.7720  -2.0517  -0.2852
 6MD  H11  H  HNH1  0   0.407   4.0213  -2.1441  -0.5799
 6MD  H12  H  HCR6  0   0.249   3.2265   2.7831   0.9725
 6MD  H13  H  HCH3  0   0.238   6.0244  -0.1534  -0.9723
 6MD  H14  H  HCH3  0   0.238   6.0973  -0.6915   0.7080
 6MD  H15  H  HCH3  0   0.253   6.2706  -1.8623  -0.6028

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
 6MD  C2   N1   aromatic  1.332  0.020  1.332
 6MD  C2   N3   aromatic  1.320  0.020  1.320
 6MD  N1   C6   aromatic  1.337  0.020  1.337
 6MD  N3   C4   aromatic  1.333  0.020  1.333
 6MD  CZ   N6   single    1.442  0.020  1.442
 6MD  C6   N6   single    1.334  0.020  1.334
 6MD  C6   C5   aromatic  1.410  0.020  1.410
 6MD  C4   C5   aromatic  1.386  0.020  1.386
 6MD  C4   N9   aromatic  1.365  0.020  1.365
 6MD  C4'  O4'  single    1.431  0.020  1.431
 6MD  C4'  C5'  single    1.517  0.020  1.517
 6MD  C4'  C3'  single    1.528  0.020  1.528
 6MD  O4'  C1'  single    1.396  0.020  1.396
 6MD  C5   N7   aromatic  1.370  0.020  1.370
 6MD  C5'  O5'  single    1.405  0.020  1.405
 6MD  O3'  C3'  single    1.402  0.020  1.402
 6MD  C1'  N9   single    1.448  0.020  1.448
 6MD  C1'  C2'  single    1.532  0.020  1.532
 6MD  N9   C8   aromatic  1.368  0.020  1.368
 6MD  C3'  C2'  single    1.529  0.020  1.529
 6MD  C2'  O2'  single    1.390  0.020  1.390
 6MD  N7   C8   aromatic  1.301  0.020  1.301
 6MD  O5'  H1   single    0.850  0.020  0.980
 6MD  C5'  H2   single    0.970  0.020  1.090
 6MD  C5'  H3   single    0.970  0.020  1.090
 6MD  C4'  H4   single    0.970  0.020  1.090
 6MD  C3'  H5   single    0.970  0.020  1.090
 6MD  O3'  H6   single    0.850  0.020  0.980
 6MD  C2'  H7   single    0.970  0.020  1.090
 6MD  O2'  H8   single    0.850  0.020  0.980
 6MD  C1'  H9   single    0.970  0.020  1.090
 6MD  C8   H10  single    0.930  0.020  1.080
 6MD  N6   H11  single    0.860  0.020  1.020
 6MD  C2   H12  single    0.930  0.020  1.080
 6MD  CZ   H13  single    0.970  0.020  1.090
 6MD  CZ   H14  single    0.970  0.020  1.090
 6MD  CZ   H15  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
 6MD  H1   O5'  C5'  108.03  3.000
 6MD  H3   C5'  H2   106.60  3.000
 6MD  H3   C5'  C4'  107.59  3.000
 6MD  H2   C5'  C4'  110.50  3.000
 6MD  H3   C5'  O5'  112.15  3.000
 6MD  H2   C5'  O5'  111.26  3.000
 6MD  C4'  C5'  O5'  108.67  3.000
 6MD  H4   C4'  C3'  111.55  3.000
 6MD  H4   C4'  O4'  107.46  3.000
 6MD  C3'  C4'  O4'  105.09  3.000
 6MD  H4   C4'  C5'  108.85  3.000
 6MD  C3'  C4'  C5'  112.29  3.000
 6MD  O4'  C4'  C5'  111.47  3.000
 6MD  C1'  O4'  C4'  110.78  3.000
 6MD  H5   C3'  C2'  112.14  3.000
 6MD  H5   C3'  O3'  111.81  3.000
 6MD  C2'  C3'  O3'  107.89  3.000
 6MD  H5   C3'  C4'  111.68  3.000
 6MD  C2'  C3'  C4'  100.20  3.000
 6MD  O3'  C3'  C4'  112.53  3.000
 6MD  H6   O3'  C3'  108.43  3.000
 6MD  H7   C2'  C1'  108.69  3.000
 6MD  H7   C2'  O2'  111.52  3.000
 6MD  C1'  C2'  O2'  109.94  3.000
 6MD  H7   C2'  C3'  107.81  3.000
 6MD  O2'  C2'  C3'  116.84  3.000
 6MD  C1'  C2'  C3'  101.37  3.000
 6MD  H8   O2'  C2'  108.65  3.000
 6MD  H9   C1'  N9   106.37  3.000
 6MD  H9   C1'  C2'  110.39  3.000
 6MD  N9   C1'  C2'  113.39  3.000
 6MD  H9   C1'  O4'  111.54  3.000
 6MD  C2'  C1'  O4'  106.28  3.000
 6MD  N9   C1'  O4'  108.95  3.000
 6MD  C4   N9   C8   106.34  3.000
 6MD  C8   N9   C1'  127.28  3.000
 6MD  C4   N9   C1'  126.35  3.000
 6MD  H10  C8   N7   124.86  3.000
 6MD  H10  C8   N9   121.85  3.000
 6MD  N7   C8   N9   113.26  3.000
 6MD  C5   N7   C8   104.43  3.000
 6MD  C4   C5   C6   116.31  3.000
 6MD  C4   C5   N7   110.84  3.000
 6MD  C6   C5   N7   132.84  3.000
 6MD  N1   C6   N6   119.61  3.000
 6MD  N6   C6   C5   122.51  3.000
 6MD  N1   C6   C5   117.88  3.000
 6MD  H11  N6   CZ   118.60  3.000
 6MD  H11  N6   C6   117.80  3.000
 6MD  CZ   N6   C6   123.59  3.000
 6MD  C2   N1   C6   119.12  3.000
 6MD  H12  C2   N3   116.09  3.000
 6MD  H12  C2   N1   115.35  3.000
 6MD  N3   C2   N1   128.56  3.000
 6MD  C4   N3   C2   111.68  3.000
 6MD  N3   C4   C5   126.44  3.000
 6MD  C5   C4   N9   105.14  3.000
 6MD  N3   C4   N9   128.42  3.000
 6MD  H15  CZ   H14  108.43  3.000
 6MD  H15  CZ   H13  108.42  3.000
 6MD  H14  CZ   H13  108.10  3.000
 6MD  H15  CZ   N6   108.16  3.000
 6MD  H14  CZ   N6   111.88  3.000
 6MD  H13  CZ   N6   111.74  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
 6MD  CONST_01  C2   N3  C4  N9   180.00   0.0  0
 6MD  CONST_02  C6   C5  C4  N9   180.00   0.0  0
 6MD  CONST_03  N7   C5  C4  N9     0.00   0.0  0
 6MD  CONST_04  C5   N7  C8  N9     0.00   0.0  0
 6MD  CONST_05  N3   C4  N9  C8   180.00   0.0  0
 6MD  CONST_06  C5   C4  N9  C8     0.00   0.0  0
 6MD  CONST_07  C6   C5  N7  C8   180.00   0.0  0
 6MD  CONST_08  C4   C5  N7  C8     0.00   0.0  0
 6MD  CONST_09  N1   C6  C5  N7   180.00   0.0  0
 6MD  CONST_10  N3   C4  C5  N7   180.00   0.0  0
 6MD  CONST_11  C4   N9  C8  N7     0.00   0.0  0
 6MD  CONST_12  C2   N1  C6  C5     0.00   0.0  0
 6MD  CONST_13  C2   N3  C4  C5     0.00   0.0  0
 6MD  CONST_14  N3   C2  N1  C6     0.00   0.0  0
 6MD  CONST_15  N3   C4  C5  C6     0.00   0.0  0
 6MD  CONST_16  C4   N3  C2  N1     0.00   0.0  0
 6MD  CONST_17  C4   C5  C6  N1     0.00   0.0  0
 6MD  CONST_18  N3   C4  N9  C1'    0.00   0.0  0
 6MD  CONST_19  C5   C4  N9  C1'  180.00   0.0  0
 6MD  CONST_20  N7   C8  N9  C1'  180.00   0.0  0
 6MD  CONST_21  N6   C6  C5  N7     0.00   0.0  0
 6MD  CONST_22  C2   N1  C6  N6   180.00   0.0  0
 6MD  CONST_23  C4   C5  C6  N6   180.00   0.0  0
 6MD  CONST_24  H10  C8  N9  C1'    0.00   0.0  0
 6MD  CONST_25  H12  C2  N1  C6   180.00   0.0  0
 6MD  CONST_26  CZ   N6  C6  C5   180.00   0.0  0
 6MD  CONST_27  CZ   N6  C6  N1     0.00   0.0  0
 6MD  CONST_28  H11  N6  C6  C5     0.00   0.0  0
 6MD  Var_01    H13  CZ  N6  C6   -60.26  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
 6MD  chir_01  C4'  O4'  C5'  C3'  positiv
 6MD  chir_02  C3'  O3'  C4'  C2'  positiv
 6MD  chir_03  C2'  O2'  C3'  C1'  positiv
 6MD  chir_04  C1'  O4'  N9   C2'  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
 6MD  plan-1  C1'  0.020
 6MD  plan-1  N9   0.020
 6MD  plan-1  C8   0.020
 6MD  plan-1  N7   0.020
 6MD  plan-1  C5   0.020
 6MD  plan-1  C6   0.020
 6MD  plan-1  N6   0.020
 6MD  plan-1  N1   0.020
 6MD  plan-1  C2   0.020
 6MD  plan-1  N3   0.020
 6MD  plan-1  C4   0.020
 6MD  plan-1  H10  0.020
 6MD  plan-1  H12  0.020
 6MD  plan-2  C6   0.020
 6MD  plan-2  N6   0.020
 6MD  plan-2  CZ   0.020
 6MD  plan-2  H11  0.020

