# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:42:23 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1c2cc(C)c(C)cc2N=C3C(=O)NC(=O)N=C13
#
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
 LFN  LFN  7,8,10-trimethylbenzo[g]pteridine-2,4(3H,10H)-dione  ligand  31  19  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LFN
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
 LFN  N1    N  N     0  -0.549  -2.4213   1.3526  -0.0046
 LFN  C2    C  CR6   0   0.577  -3.6088   0.6960  -0.0004
 LFN  C10   C  CR66  0   0.579  -1.3057   0.6778   0.0014
 LFN  O2    O  OC    0  -0.470  -4.6776   1.2751  -0.0079
 LFN  N3    N  NR16  0  -0.716  -3.6053  -0.7012   0.0136
 LFN  C4    C  CR6   0   0.553  -2.5111  -1.5107   0.0216
 LFN  O4    O  OC    0  -0.425  -2.5771  -2.7199   0.0326
 LFN  C4A   C  CR66  0  -0.046  -1.2318  -0.7642   0.0147
 LFN  N5    N  N     0  -0.347  -0.1335  -1.4375   0.0187
 LFN  C5A   C  CR66  0   0.186   1.0370  -0.7632   0.0092
 LFN  C6    C  CR16  0  -0.357   2.2407  -1.4872   0.0104
 LFN  C9A   C  CR66  0   0.440   1.0707   0.6449  -0.0028
 LFN  C7    C  CR6   0   0.076   3.4591  -0.8569  -0.0010
 LFN  C7M   C  CH3   0  -0.736   4.7323  -1.6448  -0.0003
 LFN  C8    C  CR6   0   0.099   3.4868   0.5619  -0.0137
 LFN  C8M   C  CH3   0  -0.736   4.7982   1.2805  -0.0295
 LFN  C9    C  CR16  0  -0.388   2.3111   1.2881  -0.0135
 LFN  N10   N  NR6   0  -0.560  -0.1187   1.3342  -0.0046
 LFN  C1'   C  CH3   0  -0.572  -0.0939   2.7929  -0.0150
 LFN  H3    H  HNR6  0   0.422  -4.5125  -1.1516   0.0142
 LFN  H6    H  HCR6  0   0.275   2.1752  -2.5682   0.0200
 LFN  H7M1  H  HCH3  0   0.252   5.3455  -1.4168   0.8735
 LFN  H7M2  H  HCH3  0   0.260   4.5298  -2.7142   0.0068
 LFN  H7M3  H  HCH3  0   0.252   5.3400  -1.4267  -0.8803
 LFN  H8M1  H  HCH3  0   0.258   5.4011   1.0203   0.8424
 LFN  H8M2  H  HCH3  0   0.259   5.3840   1.0099  -0.9100
 LFN  H8M3  H  HCH3  0   0.262   4.6623   2.3601  -0.0345
 LFN  H9    H  HCR6  0   0.294   2.3737   2.3665  -0.0229
 LFN  H1'1  H  HCH3  0   0.278   0.4155   3.1466  -0.9093
 LFN  H1'2  H  HCH3  0   0.305  -1.1110   3.1614  -0.0107
 LFN  H1'3  H  HCH3  0   0.278   0.4270   3.1578   0.8678

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
 LFN  N1   C2    aromatic  1.357  0.020  1.357
 LFN  N1   C10   aromatic  1.304  0.020  1.304
 LFN  C2   O2    double    1.216  0.020  1.216
 LFN  C2   N3    aromatic  1.397  0.020  1.397
 LFN  C10  C4A   aromatic  1.444  0.020  1.444
 LFN  C10  N10   aromatic  1.356  0.020  1.356
 LFN  N3   C4    aromatic  1.361  0.020  1.361
 LFN  N3   H3    single    0.860  0.020  1.020
 LFN  C4   O4    double    1.211  0.020  1.211
 LFN  C4   C4A   aromatic  1.481  0.020  1.481
 LFN  C4A  N5    aromatic  1.288  0.020  1.288
 LFN  N5   C5A   aromatic  1.351  0.020  1.351
 LFN  C5A  C6    aromatic  1.405  0.020  1.405
 LFN  C5A  C9A   aromatic  1.409  0.020  1.409
 LFN  C6   C7    aromatic  1.372  0.020  1.372
 LFN  C6   H6    single    0.930  0.020  1.080
 LFN  C9A  C9    aromatic  1.397  0.020  1.397
 LFN  C9A  N10   aromatic  1.375  0.020  1.375
 LFN  C7   C7M   single    1.497  0.020  1.497
 LFN  C7   C8    aromatic  1.419  0.020  1.419
 LFN  C7M  H7M1  single    0.970  0.020  1.090
 LFN  C7M  H7M2  single    0.970  0.020  1.090
 LFN  C7M  H7M3  single    0.970  0.020  1.090
 LFN  C8   C8M   single    1.495  0.020  1.495
 LFN  C8   C9    aromatic  1.382  0.020  1.382
 LFN  C8M  H8M1  single    0.970  0.020  1.090
 LFN  C8M  H8M2  single    0.970  0.020  1.090
 LFN  C8M  H8M3  single    0.970  0.020  1.090
 LFN  C9   H9    single    0.930  0.020  1.080
 LFN  N10  C1'   single    1.459  0.020  1.459
 LFN  C1'  H1'1  single    0.970  0.020  1.090
 LFN  C1'  H1'2  single    0.970  0.020  1.090
 LFN  C1'  H1'3  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
 LFN  C10   N1   C2    119.89  3.000
 LFN  N3    C2   O2    118.59  3.000
 LFN  N3    C2   N1    118.80  3.000
 LFN  O2    C2   N1    122.61  3.000
 LFN  N10   C10  C4A   116.01  3.000
 LFN  N10   C10  N1    119.89  3.000
 LFN  C4A   C10  N1    124.10  3.000
 LFN  H3    N3   C4    117.10  3.000
 LFN  H3    N3   C2    116.26  3.000
 LFN  C4    N3   C2    126.64  3.000
 LFN  C4A   C4   O4    123.39  3.000
 LFN  C4A   C4   N3    113.24  3.000
 LFN  O4    C4   N3    123.38  3.000
 LFN  N5    C4A  C4    118.23  3.000
 LFN  N5    C4A  C10   124.44  3.000
 LFN  C4    C4A  C10   117.33  3.000
 LFN  C5A   N5   C4A   118.54  3.000
 LFN  C9A   C5A  C6    119.65  3.000
 LFN  C9A   C5A  N5    121.32  3.000
 LFN  C6    C5A  N5    119.03  3.000
 LFN  H6    C6   C7    120.83  3.000
 LFN  H6    C6   C5A   117.56  3.000
 LFN  C7    C6   C5A   121.62  3.000
 LFN  N10   C9A  C9    122.50  3.000
 LFN  N10   C9A  C5A   118.72  3.000
 LFN  C9    C9A  C5A   118.78  3.000
 LFN  C8    C7   C7M   120.63  3.000
 LFN  C8    C7   C6    118.48  3.000
 LFN  C7M   C7   C6    120.89  3.000
 LFN  H7M3  C7M  H7M2  107.76  3.000
 LFN  H7M3  C7M  H7M1  106.91  3.000
 LFN  H7M2  C7M  H7M1  107.73  3.000
 LFN  H7M3  C7M  C7    111.59  3.000
 LFN  H7M2  C7M  C7    111.03  3.000
 LFN  H7M1  C7M  C7    111.60  3.000
 LFN  C9    C8   C8M   119.58  3.000
 LFN  C9    C8   C7    120.58  3.000
 LFN  C8M   C8   C7    119.84  3.000
 LFN  H8M3  C8M  H8M2  108.02  3.000
 LFN  H8M3  C8M  H8M1  108.01  3.000
 LFN  H8M2  C8M  H8M1  106.79  3.000
 LFN  H8M3  C8M  C8    111.54  3.000
 LFN  H8M2  C8M  C8    111.10  3.000
 LFN  H8M1  C8M  C8    111.18  3.000
 LFN  H9    C9   C8    118.38  3.000
 LFN  H9    C9   C9A   120.73  3.000
 LFN  C8    C9   C9A   120.89  3.000
 LFN  C1'   N10  C9A   119.12  3.000
 LFN  C1'   N10  C10   119.92  3.000
 LFN  C9A   N10  C10   120.97  3.000
 LFN  H1'3  C1'  H1'2  109.43  3.000
 LFN  H1'3  C1'  H1'1  109.50  3.000
 LFN  H1'2  C1'  H1'1  109.43  3.000
 LFN  H1'3  C1'  N10   109.74  3.000
 LFN  H1'2  C1'  N10   108.94  3.000
 LFN  H1'1  C1'  N10   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
 LFN  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 LFN  CONST_02  C4    C4A  C10  N1      0.00   0.0  0
 LFN  CONST_03  N5    C4A  C10  N1    180.00   0.0  0
 LFN  CONST_04  C9A   N10  C10  N1    180.00   0.0  0
 LFN  CONST_05  C4A   C10  N1   C2      0.00   0.0  0
 LFN  CONST_06  N10   C10  N1   C2    180.00   0.0  0
 LFN  CONST_07  C4A   C4   N3   C2      0.00   0.0  0
 LFN  CONST_08  N3    C2   N1   C10     0.00   0.0  0
 LFN  CONST_09  N3    C4   C4A  C10     0.00   0.0  0
 LFN  CONST_10  C5A   N5   C4A  C10     0.00   0.0  0
 LFN  CONST_11  C5A   C9A  N10  C10     0.00   0.0  0
 LFN  CONST_12  C9    C9A  N10  C10   180.00   0.0  0
 LFN  CONST_13  N5    C4A  C4   N3    180.00   0.0  0
 LFN  CONST_14  N10   C10  C4A  C4    180.00   0.0  0
 LFN  CONST_15  C5A   N5   C4A  C4    180.00   0.0  0
 LFN  CONST_16  C9A   N10  C10  C4A     0.00   0.0  0
 LFN  CONST_17  C6    C5A  N5   C4A   180.00   0.0  0
 LFN  CONST_18  C9A   C5A  N5   C4A     0.00   0.0  0
 LFN  CONST_19  N10   C10  C4A  N5      0.00   0.0  0
 LFN  CONST_20  C7    C6   C5A  N5    180.00   0.0  0
 LFN  CONST_21  C9    C9A  C5A  N5    180.00   0.0  0
 LFN  CONST_22  N10   C9A  C5A  N5      0.00   0.0  0
 LFN  CONST_23  C8    C7   C6   C5A     0.00   0.0  0
 LFN  CONST_24  C8    C9   C9A  C5A     0.00   0.0  0
 LFN  CONST_25  C9    C9A  C5A  C6      0.00   0.0  0
 LFN  CONST_26  N10   C9A  C5A  C6    180.00   0.0  0
 LFN  CONST_27  C9    C8   C7   C6      0.00   0.0  0
 LFN  CONST_28  C7    C6   C5A  C9A     0.00   0.0  0
 LFN  CONST_29  C7    C8   C9   C9A     0.00   0.0  0
 LFN  CONST_30  N10   C9A  C9   C8    180.00   0.0  0
 LFN  CONST_31  C1'   N10  C10  N1      0.00   0.0  0
 LFN  CONST_32  O4    C4   N3   C2    180.00   0.0  0
 LFN  CONST_33  O2    C2   N1   C10   180.00   0.0  0
 LFN  CONST_34  O4    C4   C4A  C10   180.00   0.0  0
 LFN  CONST_35  C4    N3   C2   O2    180.00   0.0  0
 LFN  CONST_36  N5    C4A  C4   O4      0.00   0.0  0
 LFN  CONST_37  C1'   N10  C10  C4A   180.00   0.0  0
 LFN  CONST_38  C7M   C7   C6   C5A   180.00   0.0  0
 LFN  CONST_39  C1'   N10  C9A  C5A   180.00   0.0  0
 LFN  CONST_40  C8M   C8   C7   C6    180.00   0.0  0
 LFN  CONST_41  C8M   C8   C9   C9A   180.00   0.0  0
 LFN  CONST_42  C9    C8   C7   C7M   180.00   0.0  0
 LFN  CONST_43  C1'   N10  C9A  C9      0.00   0.0  0
 LFN  CONST_44  H3    N3   C2   N1    180.00   0.0  0
 LFN  CONST_45  H6    C6   C5A  N5      0.00   0.0  0
 LFN  CONST_46  H9    C9   C9A  C5A   180.00   0.0  0
 LFN  Var_01    H1'1  C1'  N10  C10  -119.50  30.0  2
 LFN  Var_02    H7M1  C7M  C7   C6   -120.03  30.0  2
 LFN  Var_03    H8M1  C8M  C8   C7    -59.17  30.0  2

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
 LFN  plan-1  N1   0.020
 LFN  plan-1  C2   0.020
 LFN  plan-1  C10  0.020
 LFN  plan-1  O2   0.020
 LFN  plan-1  N3   0.020
 LFN  plan-1  C4   0.020
 LFN  plan-1  O4   0.020
 LFN  plan-1  C4A  0.020
 LFN  plan-1  N5   0.020
 LFN  plan-1  C5A  0.020
 LFN  plan-1  C6   0.020
 LFN  plan-1  C9A  0.020
 LFN  plan-1  C7   0.020
 LFN  plan-1  C7M  0.020
 LFN  plan-1  C8   0.020
 LFN  plan-1  C8M  0.020
 LFN  plan-1  C9   0.020
 LFN  plan-1  N10  0.020
 LFN  plan-1  C1'  0.020
 LFN  plan-1  H3   0.020
 LFN  plan-1  H6   0.020
 LFN  plan-1  H9   0.020

