# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 10:39:21 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: [4-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)butyl]carbamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CCCCNC(O)=O)c2cc1C
#
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
 CF4  CF4  '[4-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)butyl]carbamic acid'  ligand  44  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CF4
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
 CF4  O4    O  O      0  -0.426  -0.0162  19.4397  -3.9985
 CF4  C4    C  CR6    0   0.551   0.1449  20.5396  -3.5179
 CF4  N3    N  NR16   0  -0.717  -0.2540  21.6890  -4.1290
 CF4  C2    C  CR6    0   0.573  -0.0977  22.9901  -3.6432
 CF4  O2    O  O      0  -0.469  -0.5041  23.9159  -4.3182
 CF4  N1    N  N      0  -0.548   0.5007  23.1704  -2.4386
 CF4  C4A   C  CR66   0  -0.038   0.7943  20.7710  -2.2073
 CF4  C10   C  CR66   0   0.572   0.9091  22.1360  -1.7576
 CF4  N5    N  N      0  -0.348   1.2199  19.7513  -1.5449
 CF4  C5A   C  CR66   0   0.181   1.8185  19.9598  -0.3523
 CF4  C6    C  CR16   0  -0.360   2.2975  18.8513   0.3663
 CF4  C7    C  CR6    0   0.076   2.9238  18.9944   1.5774
 CF4  C7M   C  CH3    0  -0.735   3.4300  17.8020   2.3289
 CF4  C8    C  CR6    0   0.095   3.0860  20.3030   2.1026
 CF4  C8M   C  CH3    0  -0.737   3.7800  20.4978   3.4132
 CF4  C9    C  CR16   0  -0.380   2.6173  21.4026   1.4108
 CF4  C9A   C  CR66   0   0.445   1.9725  21.2575   0.1779
 CF4  N10   N  NR6    0  -0.566   1.4823  22.3215  -0.5417
 CF4  C1'   C  CH2    0  -0.344   1.6243  23.6923  -0.0416
 CF4  C2'   C  CH2    0  -0.443   2.9609  24.3040  -0.4358
 CF4  C3'   C  CH2    0  -0.438   3.0659  25.7535   0.0180
 CF4  C4'   C  CH2    0  -0.258   4.3924  26.3866  -0.3986
 CF4  N1'   N  NH1    0  -0.657   4.5447  27.7688  -0.0285
 CF4  C5'   C  C      0   0.499   4.7739  28.1559   1.3030
 CF4  O1'   O  OC    -1  -0.663   4.5702  29.3624   1.5643
 CF4  O2'   O  O      0  -0.648   5.1907  27.2789   2.0896
 CF4  H3    H  HNR6   0   0.422  -0.7126  21.5985  -5.0276
 CF4  H6    H  HCR6   0   0.274   2.1540  17.8717  -0.0727
 CF4  H7M1  H  HCH3   0   0.259   3.2251  16.8815   1.7853
 CF4  H7M2  H  HCH3   0   0.251   4.5076  17.8603   2.4933
 CF4  H7M3  H  HCH3   0   0.251   2.9625  17.7198   3.3118
 CF4  H8M1  H  HCH3   0   0.259   4.8118  20.1447   3.3642
 CF4  H8M2  H  HCH3   0   0.263   3.7985  21.5461   3.7037
 CF4  H8M3  H  HCH3   0   0.258   3.2909  19.9333   4.2088
 CF4  H9    H  HCR6   0   0.284   2.7713  22.3799   1.8450
 CF4  H1'1  H  HCH2   0   0.295   0.8064  24.2712  -0.4612
 CF4  H1'2  H  HCH2   0   0.282   1.4864  23.6805   1.0380
 CF4  H2'1  H  HCH2   0   0.236   3.7828  23.7222  -0.0079
 CF4  H2'2  H  HCH2   0   0.241   3.0695  24.2467  -1.5224
 CF4  H3'1  H  HCH2   0   0.215   2.2392  26.3304  -0.4096
 CF4  H3'2  H  HCH2   0   0.225   2.9686  25.8159   1.1053
 CF4  H4'1  H  HCH2   0   0.212   5.2160  25.8148   0.0317
 CF4  H4'2  H  HCH2   0   0.212   4.4967  26.3077  -1.4851
 CF4  H1'   H  HNH1   0   0.342   3.9780  28.4132  -0.5571

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
 CF4  O4   C4    double    1.211  0.020  1.211
 CF4  C4   N3    single    1.361  0.020  1.361
 CF4  C4   C4A   single    1.481  0.020  1.481
 CF4  N3   C2    single    1.398  0.020  1.398
 CF4  C2   O2    double    1.216  0.020  1.216
 CF4  C2   N1    single    1.357  0.020  1.357
 CF4  N1   C10   double    1.304  0.020  1.304
 CF4  C4A  C10   single    1.442  0.020  1.442
 CF4  C4A  N5    double    1.288  0.020  1.288
 CF4  C10  N10   single    1.357  0.020  1.357
 CF4  N5   C5A   single    1.351  0.020  1.351
 CF4  C5A  C6    aromatic  1.405  0.020  1.405
 CF4  C5A  C9A   aromatic  1.410  0.020  1.410
 CF4  C6   C7    aromatic  1.371  0.020  1.371
 CF4  C7   C7M   single    1.498  0.020  1.498
 CF4  C7   C8    aromatic  1.419  0.020  1.419
 CF4  C8   C8M   single    1.496  0.020  1.496
 CF4  C8   C9    aromatic  1.381  0.020  1.381
 CF4  C9   C9A   aromatic  1.399  0.020  1.399
 CF4  C9A  N10   single    1.375  0.020  1.375
 CF4  N10  C1'   single    1.466  0.020  1.466
 CF4  C1'  C2'   single    1.522  0.020  1.522
 CF4  C2'  C3'   single    1.522  0.020  1.522
 CF4  C3'  C4'   single    1.528  0.020  1.528
 CF4  C4'  N1'   single    1.439  0.020  1.439
 CF4  N1'  C5'   single    1.406  0.020  1.406
 CF4  C5'  O1'   deloc     1.251  0.020  1.251
 CF4  C5'  O2'   deloc     1.250  0.020  1.250
 CF4  N3   H3    single    0.860  0.020  1.020
 CF4  C6   H6    single    0.930  0.020  1.080
 CF4  C7M  H7M1  single    0.970  0.020  1.090
 CF4  C7M  H7M2  single    0.970  0.020  1.090
 CF4  C7M  H7M3  single    0.970  0.020  1.090
 CF4  C8M  H8M1  single    0.970  0.020  1.090
 CF4  C8M  H8M2  single    0.970  0.020  1.090
 CF4  C8M  H8M3  single    0.970  0.020  1.090
 CF4  C9   H9    single    0.930  0.020  1.080
 CF4  C1'  H1'1  single    0.970  0.020  1.090
 CF4  C1'  H1'2  single    0.970  0.020  1.090
 CF4  C2'  H2'1  single    0.970  0.020  1.090
 CF4  C2'  H2'2  single    0.970  0.020  1.090
 CF4  C3'  H3'1  single    0.970  0.020  1.090
 CF4  C3'  H3'2  single    0.970  0.020  1.090
 CF4  C4'  H4'1  single    0.970  0.020  1.090
 CF4  C4'  H4'2  single    0.970  0.020  1.090
 CF4  N1'  H1'   single    0.890  0.020  1.040

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
 CF4  C4A   C4   N3    113.19  3.000
 CF4  C4A   C4   O4    123.47  3.000
 CF4  N3    C4   O4    123.34  3.000
 CF4  H3    N3   C2    116.25  3.000
 CF4  H3    N3   C4    117.09  3.000
 CF4  C2    N3   C4    126.67  3.000
 CF4  N1    C2   O2    122.62  3.000
 CF4  N1    C2   N3    118.79  3.000
 CF4  O2    C2   N3    118.59  3.000
 CF4  C10   N1   C2    119.75  3.000
 CF4  N5    C4A  C10   124.25  3.000
 CF4  N5    C4A  C4    118.44  3.000
 CF4  C10   C4A  C4    117.32  3.000
 CF4  N10   C10  C4A   116.27  3.000
 CF4  N10   C10  N1    119.45  3.000
 CF4  C4A   C10  N1    124.28  3.000
 CF4  C5A   N5   C4A   118.57  3.000
 CF4  C9A   C5A  C6    119.76  3.000
 CF4  C9A   C5A  N5    121.50  3.000
 CF4  C6    C5A  N5    118.74  3.000
 CF4  H6    C6   C7    120.87  3.000
 CF4  H6    C6   C5A   117.45  3.000
 CF4  C7    C6   C5A   121.68  3.000
 CF4  C8    C7   C7M   120.65  3.000
 CF4  C8    C7   C6    118.38  3.000
 CF4  C7M   C7   C6    120.97  3.000
 CF4  H7M3  C7M  H7M2  106.93  3.000
 CF4  H7M3  C7M  H7M1  107.78  3.000
 CF4  H7M2  C7M  H7M1  107.83  3.000
 CF4  H7M3  C7M  C7    111.53  3.000
 CF4  H7M2  C7M  C7    111.52  3.000
 CF4  H7M1  C7M  C7    111.04  3.000
 CF4  C9    C8   C8M   119.51  3.000
 CF4  C9    C8   C7    120.66  3.000
 CF4  C8M   C8   C7    119.82  3.000
 CF4  H8M3  C8M  H8M2  108.14  3.000
 CF4  H8M3  C8M  H8M1  106.79  3.000
 CF4  H8M2  C8M  H8M1  107.91  3.000
 CF4  H8M3  C8M  C8    111.31  3.000
 CF4  H8M2  C8M  C8    111.56  3.000
 CF4  H8M1  C8M  C8    110.93  3.000
 CF4  H9    C9   C9A   120.91  3.000
 CF4  H9    C9   C8    118.07  3.000
 CF4  C9A   C9   C8    121.02  3.000
 CF4  N10   C9A  C9    123.05  3.000
 CF4  N10   C9A  C5A   118.45  3.000
 CF4  C9    C9A  C5A   118.50  3.000
 CF4  C1'   N10  C9A   120.70  3.000
 CF4  C1'   N10  C10   118.32  3.000
 CF4  C9A   N10  C10   120.92  3.000
 CF4  H1'2  C1'  H1'1  107.07  3.000
 CF4  H1'2  C1'  C2'   111.87  3.000
 CF4  H1'1  C1'  C2'   110.30  3.000
 CF4  H1'2  C1'  N10   108.42  3.000
 CF4  H1'1  C1'  N10   107.07  3.000
 CF4  C2'   C1'  N10   111.87  3.000
 CF4  H2'2  C2'  H2'1  106.63  3.000
 CF4  H2'2  C2'  C3'   109.83  3.000
 CF4  H2'1  C2'  C3'   109.75  3.000
 CF4  H2'2  C2'  C1'   108.87  3.000
 CF4  H2'1  C2'  C1'   110.16  3.000
 CF4  C3'   C2'  C1'   111.47  3.000
 CF4  H3'2  C3'  H3'1  106.92  3.000
 CF4  H3'2  C3'  C4'   108.95  3.000
 CF4  H3'1  C3'  C4'   109.31  3.000
 CF4  H3'2  C3'  C2'   110.16  3.000
 CF4  H3'1  C3'  C2'   109.46  3.000
 CF4  C4'   C3'  C2'   111.91  3.000
 CF4  H4'2  C4'  H4'1  106.37  3.000
 CF4  H4'2  C4'  N1'   108.33  3.000
 CF4  H4'1  C4'  N1'   108.79  3.000
 CF4  H4'2  C4'  C3'   108.88  3.000
 CF4  H4'1  C4'  C3'   109.31  3.000
 CF4  N1'   C4'  C3'   114.82  3.000
 CF4  H1'   N1'  C5'   114.35  3.000
 CF4  H1'   N1'  C4'   114.82  3.000
 CF4  C5'   N1'  C4'   121.70  3.000
 CF4  O2'   C5'  O1'   126.84  3.000
 CF4  O2'   C5'  N1'   117.22  3.000
 CF4  O1'   C5'  N1'   115.91  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
 CF4  CONST_01  C8    C7   C6   C5A     0.00   0.0  0
 CF4  CONST_02  C8    C9   C9A  C5A     0.00   0.0  0
 CF4  CONST_03  C9    C9A  C5A  C6      0.00   0.0  0
 CF4  CONST_04  C9    C8   C7   C6      0.00   0.0  0
 CF4  CONST_05  C9A   C5A  C6   C7      0.00   0.0  0
 CF4  CONST_06  C9A   C9   C8   C7      0.00   0.0  0
 CF4  CONST_07  N1    C2   N3   C4      0.00   0.0  0
 CF4  CONST_08  C10   N1   C2   N3      0.00   0.0  0
 CF4  CONST_09  C4A   C4   N3   C2      0.00   0.0  0
 CF4  CONST_10  C4A   C10  N1   C2      0.00   0.0  0
 CF4  CONST_11  N10   C10  N1   C2    180.00   0.0  0
 CF4  CONST_12  C9A   N10  C10  N1    180.00   0.0  0
 CF4  CONST_13  C9A   N10  C10  C4A     0.00   0.0  0
 CF4  CONST_14  C7M   C7   C6   C5A   180.00   0.0  0
 CF4  CONST_15  C8M   C8   C7   C6    180.00   0.0  0
 CF4  CONST_16  C9    C8   C7   C7M   180.00   0.0  0
 CF4  CONST_17  C9A   C9   C8   C8M   180.00   0.0  0
 CF4  CONST_18  C2    N3   C4   O4    180.00   0.0  0
 CF4  CONST_19  O2    C2   N3   C4    180.00   0.0  0
 CF4  CONST_20  C10   N1   C2   O2    180.00   0.0  0
 CF4  CONST_21  C1'   N10  C10  N1      0.00   0.0  0
 CF4  CONST_22  C1'   N10  C10  C4A   180.00   0.0  0
 CF4  CONST_23  H6    C6   C5A  N5      0.00   0.0  0
 CF4  CONST_24  H9    C9   C9A  C5A   180.00   0.0  0
 CF4  CONST_25  H3    N3   C2   N1    180.00   0.0  0
 CF4  Var_01    C2'   C1'  N10  C10   -91.20  30.0  3
 CF4  Var_02    H7M1  C7M  C7   C6     -0.12  30.0  2
 CF4  Var_03    H8M1  C8M  C8   C7     61.68  30.0  2
 CF4  Var_04    C3'   C2'  C1'  N10   176.69  30.0  3
 CF4  Var_05    C4'   C3'  C2'  C1'  -178.79  30.0  3
 CF4  Var_06    N1'   C4'  C3'  C2'   178.58  30.0  3
 CF4  Var_07    C5'   N1'  C4'  C3'    73.19  30.0  3
 CF4  Var_08    O1'   C5'  N1'  C4'  -163.33  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
 CF4  plan-1  O4   0.020
 CF4  plan-1  C4   0.020
 CF4  plan-1  N3   0.020
 CF4  plan-1  C2   0.020
 CF4  plan-1  O2   0.020
 CF4  plan-1  N1   0.020
 CF4  plan-1  C4A  0.020
 CF4  plan-1  C10  0.020
 CF4  plan-1  N5   0.020
 CF4  plan-1  C5A  0.020
 CF4  plan-1  C6   0.020
 CF4  plan-1  C7   0.020
 CF4  plan-1  C7M  0.020
 CF4  plan-1  C8   0.020
 CF4  plan-1  C8M  0.020
 CF4  plan-1  C9   0.020
 CF4  plan-1  C9A  0.020
 CF4  plan-1  N10  0.020
 CF4  plan-1  C1'  0.020
 CF4  plan-1  H3   0.020
 CF4  plan-1  H6   0.020
 CF4  plan-1  H9   0.020
 CF4  plan-2  N1'  0.020
 CF4  plan-2  C5'  0.020
 CF4  plan-2  O1'  0.020
 CF4  plan-2  O2'  0.020

