# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 04:24:32 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  45  26  .  2021-08-08  2021-08-08  
;
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  -0.425   0.0212  19.4290  -4.0569
 CF4  C4    C  CR6   0   0.552   0.1683  20.5282  -3.5705
 CF4  N3    N  NR16  0  -0.717  -0.2361  21.6766  -4.1800
 CF4  C2    C  CR6   0   0.574  -0.0951  22.9769  -3.6881
 CF4  O2    O  O     0  -0.469  -0.5023  23.9022  -4.3630
 CF4  N1    N  N     0  -0.548   0.4911  23.1576  -2.4771
 CF4  C4A   C  CR66  0  -0.037   0.8048  20.7599  -2.2535
 CF4  C10   C  CR66  0   0.573   0.9015  22.1240  -1.7966
 CF4  N5    N  N     0  -0.348   1.2346  19.7416  -1.5918
 CF4  C5A   C  CR66  0   0.181   1.8187  19.9503  -0.3919
 CF4  C6    C  CR16  0  -0.360   2.3017  18.8434   0.3263
 CF4  C7    C  CR6   0   0.076   2.9110  18.9866   1.5462
 CF4  C7M   C  CH3   0  -0.735   3.4185  17.7950   2.2980
 CF4  C8    C  CR6   0   0.095   3.0510  20.2938   2.0809
 CF4  C8M   C  CH3   0  -0.737   3.7228  20.4892   3.4029
 CF4  C9    C  CR16  0  -0.380   2.5797  21.3921   1.3886
 CF4  C9A   C  CR66  0   0.446   1.9522  21.2466   0.1471
 CF4  N10   N  NR6   0  -0.567   1.4593  22.3091  -0.5734
 CF4  C1'   C  CH2   0  -0.345   1.5771  23.6772  -0.0626
 CF4  C2'   C  CH2   0  -0.447   2.9140  24.3048  -0.4300
 CF4  C3'   C  CH2   0  -0.437   2.9920  25.7495   0.0430
 CF4  C4'   C  CH2   0  -0.276   4.3298  26.3809  -0.3248
 CF4  N1'   N  NH1   0  -0.637   4.4426  27.7665   0.0655
 CF4  C5'   C  C     0   0.672   4.7919  28.1395   1.3064
 CF4  O1'   O  OH1   0  -0.625   4.7541  29.4710   1.4471
 CF4  O2'   O  O     0  -0.523   5.1201  27.3830   2.2007
 CF4  H3    H  HNR6  0   0.423  -0.6875  21.5855  -5.0822
 CF4  H6    H  HCR6  0   0.275   2.1744  17.8647  -0.1196
 CF4  H7M1  H  HCH3  0   0.260   3.2539  16.8786   1.7341
 CF4  H7M2  H  HCH3  0   0.251   4.4876  17.8748   2.5026
 CF4  H7M3  H  HCH3  0   0.252   2.9176  17.6867   3.2619
 CF4  H8M1  H  HCH3  0   0.259   4.7576  20.1435   3.3705
 CF4  H8M2  H  HCH3  0   0.263   3.7292  21.5367   3.6967
 CF4  H8M3  H  HCH3  0   0.258   3.2241  19.9191   4.1887
 CF4  H9    H  HCR6  0   0.284   2.7178  22.3685   1.8302
 CF4  H1'1  H  HCH2  0   0.298   0.7601  24.2503  -0.4919
 CF4  H1'2  H  HCH2  0   0.285   1.4220  23.6575   1.0145
 CF4  H2'1  H  HCH2  0   0.243   3.7343  23.7274   0.0060
 CF4  H2'2  H  HCH2  0   0.248   3.0412  24.2621  -1.5149
 CF4  H3'1  H  HCH2  0   0.233   2.1818  26.3298  -0.4078
 CF4  H3'2  H  HCH2  0   0.235   2.8532  25.7973   1.1266
 CF4  H4'1  H  HCH2  0   0.243   5.1475  25.8158   0.1249
 CF4  H4'2  H  HCH2  0   0.252   4.4747  26.3350  -1.4050
 CF4  H1'   H  HNH1  0   0.404   4.1254  28.4700  -0.5818
 CF4  HA    H  HOH1  0   0.481   5.0249  29.7001   2.3453

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    1.362  0.020  1.362
 CF4  C4   C4A   single    1.481  0.020  1.481
 CF4  N3   C2    single    1.397  0.020  1.397
 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    1.465  0.020  1.465
 CF4  C1'  C2'   single    1.522  0.020  1.522
 CF4  C2'  C3'   single    1.522  0.020  1.522
 CF4  C3'  C4'   single    1.524  0.020  1.524
 CF4  C4'  N1'   single    1.444  0.020  1.444
 CF4  N1'  C5'   single    1.342  0.020  1.342
 CF4  C5'  O1'   single    1.339  0.020  1.339
 CF4  C5'  O2'   double    1.217  0.020  1.217
 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    0.860  0.020  1.020
 CF4  O1'  HA    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
 CF4  C4A   C4   N3    113.19  3.000
 CF4  C4A   C4   O4    123.46  3.000
 CF4  N3    C4   O4    123.35  3.000
 CF4  H3    N3   C2    116.25  3.000
 CF4  H3    N3   C4    117.08  3.000
 CF4  C2    N3   C4    126.68  3.000
 CF4  N1    C2   O2    122.60  3.000
 CF4  N1    C2   N3    118.78  3.000
 CF4  O2    C2   N3    118.62  3.000
 CF4  C10   N1   C2    119.74  3.000
 CF4  N5    C4A  C10   124.24  3.000
 CF4  N5    C4A  C4    118.46  3.000
 CF4  C10   C4A  C4    117.30  3.000
 CF4  N10   C10  C4A   116.25  3.000
 CF4  N10   C10  N1    119.45  3.000
 CF4  C4A   C10  N1    124.30  3.000
 CF4  C5A   N5   C4A   118.59  3.000
 CF4  C9A   C5A  C6    119.75  3.000
 CF4  C9A   C5A  N5    121.50  3.000
 CF4  C6    C5A  N5    118.75  3.000
 CF4  H6    C6   C7    120.86  3.000
 CF4  H6    C6   C5A   117.46  3.000
 CF4  C7    C6   C5A   121.68  3.000
 CF4  C8    C7   C7M   120.68  3.000
 CF4  C8    C7   C6    118.38  3.000
 CF4  C7M   C7   C6    120.94  3.000
 CF4  H7M3  C7M  H7M2  106.93  3.000
 CF4  H7M3  C7M  H7M1  107.72  3.000
 CF4  H7M2  C7M  H7M1  107.87  3.000
 CF4  H7M3  C7M  C7    111.51  3.000
 CF4  H7M2  C7M  C7    111.59  3.000
 CF4  H7M1  C7M  C7    111.02  3.000
 CF4  C9    C8   C8M   119.50  3.000
 CF4  C9    C8   C7    120.66  3.000
 CF4  C8M   C8   C7    119.85  3.000
 CF4  H8M3  C8M  H8M2  108.13  3.000
 CF4  H8M3  C8M  H8M1  106.80  3.000
 CF4  H8M2  C8M  H8M1  107.90  3.000
 CF4  H8M3  C8M  C8    111.28  3.000
 CF4  H8M2  C8M  C8    111.54  3.000
 CF4  H8M1  C8M  C8    110.99  3.000
 CF4  H9    C9   C9A   120.94  3.000
 CF4  H9    C9   C8    118.04  3.000
 CF4  C9A   C9   C8    121.02  3.000
 CF4  N10   C9A  C9    123.06  3.000
 CF4  N10   C9A  C5A   118.43  3.000
 CF4  C9    C9A  C5A   118.51  3.000
 CF4  C1'   N10  C9A   120.67  3.000
 CF4  C1'   N10  C10   118.34  3.000
 CF4  C9A   N10  C10   120.94  3.000
 CF4  H1'2  C1'  H1'1  107.06  3.000
 CF4  H1'2  C1'  C2'   111.81  3.000
 CF4  H1'1  C1'  C2'   110.34  3.000
 CF4  H1'2  C1'  N10   108.46  3.000
 CF4  H1'1  C1'  N10   107.12  3.000
 CF4  C2'   C1'  N10   111.81  3.000
 CF4  H2'2  C2'  H2'1  106.72  3.000
 CF4  H2'2  C2'  C3'   109.85  3.000
 CF4  H2'1  C2'  C3'   109.80  3.000
 CF4  H2'2  C2'  C1'   109.01  3.000
 CF4  H2'1  C2'  C1'   110.18  3.000
 CF4  C3'   C2'  C1'   111.19  3.000
 CF4  H3'2  C3'  H3'1  106.93  3.000
 CF4  H3'2  C3'  C4'   109.41  3.000
 CF4  H3'1  C3'  C4'   109.32  3.000
 CF4  H3'2  C3'  C2'   110.05  3.000
 CF4  H3'1  C3'  C2'   109.73  3.000
 CF4  C4'   C3'  C2'   111.29  3.000
 CF4  H4'2  C4'  H4'1  106.67  3.000
 CF4  H4'2  C4'  N1'   107.31  3.000
 CF4  H4'1  C4'  N1'   109.09  3.000
 CF4  H4'2  C4'  C3'   109.76  3.000
 CF4  H4'1  C4'  C3'   110.11  3.000
 CF4  N1'   C4'  C3'   113.63  3.000
 CF4  H1'   N1'  C5'   118.82  3.000
 CF4  H1'   N1'  C4'   118.16  3.000
 CF4  C5'   N1'  C4'   122.48  3.000
 CF4  O2'   C5'  O1'   123.27  3.000
 CF4  O2'   C5'  N1'   125.26  3.000
 CF4  O1'   C5'  N1'   111.47  3.000
 CF4  HA    O1'  C5'   109.01  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  CONST_26  HA    O1'  C5'  N1'   180.00   0.0  0
 CF4  Var_01    C2'   C1'  N10  C10   -91.64  30.0  3
 CF4  Var_02    H7M1  C7M  C7   C6      1.46  30.0  2
 CF4  Var_03    H8M1  C8M  C8   C7     61.40  30.0  2
 CF4  Var_04    C3'   C2'  C1'  N10   176.98  30.0  3
 CF4  Var_05    C4'   C3'  C2'  C1'  -179.95  30.0  3
 CF4  Var_06    N1'   C4'  C3'  C2'   178.24  30.0  3
 CF4  Var_07    C5'   N1'  C4'  C3'    82.96  30.0  3
 CF4  Var_08    O1'   C5'  N1'  C4'  -176.45  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
 CF4  plan-2  HA   0.020

