# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 06:45:33 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [3-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)propyl]carbamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2N=C3C(=O)NC(=O)N=C3N(CCCNC(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
 C3F  C3F  '[3-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)propyl]carbamic acid'  ligand  41  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C3F
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
 C3F  O4    O  O      0  -0.425  -4.2017   2.5819   0.7881
 C3F  C4    C  C      0   0.552  -3.0455   2.5069   0.4359
 C3F  N3    N  NH1    0  -0.717  -2.2501   3.5945   0.2394
 C3F  C2    C  C      0   0.573  -0.9126   3.5890  -0.1661
 C3F  O2    O  O      0  -0.468  -0.3387   4.6529  -0.2940
 C3F  N1    N  N      0  -0.547  -0.3055   2.3977  -0.4001
 C3F  C4A   C  CR6    0  -0.037  -2.3522   1.2239   0.1783
 C3F  C10   C  CR6    0   0.571  -0.9754   1.2903  -0.2455
 C3F  N5    N  N      0  -0.348  -3.0086   0.1276   0.3428
 C3F  C5A   C  CR66   0   0.182  -2.3717  -1.0444   0.1299
 C3F  C6    C  CR16   0  -0.359  -3.0759  -2.2442   0.3287
 C3F  C7    C  CR6    0   0.074  -2.4799  -3.4663   0.1517
 C3F  C7M   C  CH3    0  -0.736  -3.2441  -4.7365   0.3661
 C3F  C8    C  CR6    0   0.095  -1.1126  -3.5020  -0.2282
 C3F  C8M   C  CH3    0  -0.737  -0.4226  -4.8167  -0.4068
 C3F  C9    C  CR16   0  -0.380  -0.4095  -2.3319  -0.4377
 C3F  C9A   C  CR66   0   0.445  -1.0228  -1.0853  -0.2793
 C3F  N10   N  NR6    0  -0.566  -0.3705   0.1040  -0.5038
 C3F  C1'   C  CH2    0  -0.346   1.0041   0.1140  -1.0098
 C3F  C2'   C  CH2    0  -0.473   2.0364   0.0462   0.1047
 C3F  C3'   C  CH2    0  -0.228   3.4464   0.0499  -0.4711
 C3F  C5'   C  C      0   0.502   5.7939  -0.1078   0.3118
 C3F  N1'   N  NH1    0  -0.666   4.4201   0.0167   0.5896
 C3F  O2'   O  OC    -1  -0.660   6.5677   0.1923   1.2469
 C3F  O1'   O  O      0  -0.647   6.1080  -0.5295  -0.8210
 C3F  H3    H  HNH1   0   0.422  -2.6636   4.5040   0.4048
 C3F  H6    H  HCR6   0   0.274  -4.1139  -2.1704   0.6285
 C3F  H7M1  H  HCH3   0   0.251  -3.2104  -5.3769  -0.5166
 C3F  H7M2  H  HCH3   0   0.253  -2.8297  -5.3154   1.1937
 C3F  H7M3  H  HCH3   0   0.260  -4.2891  -4.5331   0.5926
 C3F  H8M1  H  HCH3   0   0.260  -0.8782  -5.3891  -1.2175
 C3F  H8M2  H  HCH3   0   0.263   0.6322  -4.6867  -0.6395
 C3F  H8M3  H  HCH3   0   0.258  -0.4994  -5.4303   0.4922
 C3F  H9    H  HCR6   0   0.284   0.6336  -2.4060  -0.7111
 C3F  H1'1  H  HCH2   0   0.283   1.1106  -0.7148  -1.7077
 C3F  H1'2  H  HCH2   0   0.297   1.1277   1.0284  -1.5840
 C3F  H2'1  H  HCH2   0   0.246   1.9012   0.9045   0.7684
 C3F  H2'2  H  HCH2   0   0.241   1.8932  -0.8522   0.7112
 C3F  H3'1  H  HCH2   0   0.216   3.5766  -0.8276  -1.1074
 C3F  H3'2  H  HCH2   0   0.194   3.5588   0.9246  -1.1300
 C3F  H1'   H  HNH1   0   0.344   4.2147   0.6331   1.3614

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
 C3F  O4   C4    double    1.211  0.020  1.211
 C3F  C4   N3    single    1.362  0.020  1.362
 C3F  C4   C4A   single    1.481  0.020  1.481
 C3F  N3   C2    single    1.398  0.020  1.398
 C3F  C2   O2    double    1.216  0.020  1.216
 C3F  C2   N1    single    1.357  0.020  1.357
 C3F  N1   C10   double    1.304  0.020  1.304
 C3F  C4A  C10   single    1.442  0.020  1.442
 C3F  C4A  N5    double    1.288  0.020  1.288
 C3F  C10  N10   single    1.356  0.020  1.356
 C3F  N5   C5A   single    1.351  0.020  1.351
 C3F  C5A  C6    aromatic  1.405  0.020  1.405
 C3F  C5A  C9A   aromatic  1.410  0.020  1.410
 C3F  C6   C7    aromatic  1.371  0.020  1.371
 C3F  C7   C7M   single    1.498  0.020  1.498
 C3F  C7   C8    aromatic  1.420  0.020  1.420
 C3F  C8   C8M   single    1.495  0.020  1.495
 C3F  C8   C9    aromatic  1.381  0.020  1.381
 C3F  C9   C9A   aromatic  1.398  0.020  1.398
 C3F  C9A  N10   single    1.375  0.020  1.375
 C3F  N10  C1'   single    1.465  0.020  1.465
 C3F  C1'  C2'   single    1.521  0.020  1.521
 C3F  C2'  C3'   single    1.523  0.020  1.523
 C3F  C3'  N1'   single    1.440  0.020  1.440
 C3F  C5'  O1'   deloc     1.249  0.020  1.249
 C3F  C5'  O2'   deloc     1.250  0.020  1.250
 C3F  C5'  N1'   single    1.407  0.020  1.407
 C3F  N3   H3    single    0.860  0.020  1.020
 C3F  C6   H6    single    0.930  0.020  1.080
 C3F  C7M  H7M1  single    0.970  0.020  1.090
 C3F  C7M  H7M2  single    0.970  0.020  1.090
 C3F  C7M  H7M3  single    0.970  0.020  1.090
 C3F  C8M  H8M1  single    0.970  0.020  1.090
 C3F  C8M  H8M2  single    0.970  0.020  1.090
 C3F  C8M  H8M3  single    0.970  0.020  1.090
 C3F  C9   H9    single    0.930  0.020  1.080
 C3F  C1'  H1'1  single    0.970  0.020  1.090
 C3F  C1'  H1'2  single    0.970  0.020  1.090
 C3F  C2'  H2'1  single    0.970  0.020  1.090
 C3F  C2'  H2'2  single    0.970  0.020  1.090
 C3F  C3'  H3'1  single    0.970  0.020  1.090
 C3F  C3'  H3'2  single    0.970  0.020  1.090
 C3F  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
 C3F  C4A   C4   N3    113.17  3.000
 C3F  C4A   C4   O4    123.45  3.000
 C3F  N3    C4   O4    123.38  3.000
 C3F  H3    N3   C2    116.21  3.000
 C3F  H3    N3   C4    117.09  3.000
 C3F  C2    N3   C4    126.70  3.000
 C3F  N1    C2   O2    122.60  3.000
 C3F  N1    C2   N3    118.79  3.000
 C3F  O2    C2   N3    118.61  3.000
 C3F  C10   N1   C2    119.69  3.000
 C3F  N5    C4A  C10   124.27  3.000
 C3F  N5    C4A  C4    118.46  3.000
 C3F  C10   C4A  C4    117.27  3.000
 C3F  N10   C10  C4A   116.20  3.000
 C3F  N10   C10  N1    119.42  3.000
 C3F  C4A   C10  N1    124.37  3.000
 C3F  C5A   N5   C4A   118.56  3.000
 C3F  C9A   C5A  C6    119.71  3.000
 C3F  C9A   C5A  N5    121.46  3.000
 C3F  C6    C5A  N5    118.83  3.000
 C3F  H6    C6   C7    120.87  3.000
 C3F  H6    C6   C5A   117.47  3.000
 C3F  C7    C6   C5A   121.66  3.000
 C3F  C8    C7   C7M   120.56  3.000
 C3F  C8    C7   C6    118.40  3.000
 C3F  C7M   C7   C6    121.03  3.000
 C3F  H7M3  C7M  H7M2  107.80  3.000
 C3F  H7M3  C7M  H7M1  107.92  3.000
 C3F  H7M2  C7M  H7M1  106.88  3.000
 C3F  H7M3  C7M  C7    111.17  3.000
 C3F  H7M2  C7M  C7    111.38  3.000
 C3F  H7M1  C7M  C7    111.48  3.000
 C3F  C9    C8   C8M   119.46  3.000
 C3F  C9    C8   C7    120.64  3.000
 C3F  C8M   C8   C7    119.90  3.000
 C3F  H8M3  C8M  H8M2  108.16  3.000
 C3F  H8M3  C8M  H8M1  106.71  3.000
 C3F  H8M2  C8M  H8M1  107.96  3.000
 C3F  H8M3  C8M  C8    111.31  3.000
 C3F  H8M2  C8M  C8    111.59  3.000
 C3F  H8M1  C8M  C8    110.91  3.000
 C3F  H9    C9   C9A   120.86  3.000
 C3F  H9    C9   C8    118.14  3.000
 C3F  C9A   C9   C8    120.99  3.000
 C3F  N10   C9A  C9    122.99  3.000
 C3F  N10   C9A  C5A   118.44  3.000
 C3F  C9    C9A  C5A   118.57  3.000
 C3F  C1'   N10  C9A   120.50  3.000
 C3F  C1'   N10  C10   118.58  3.000
 C3F  C9A   N10  C10   120.92  3.000
 C3F  H1'2  C1'  H1'1  106.90  3.000
 C3F  H1'2  C1'  C2'   110.34  3.000
 C3F  H1'1  C1'  C2'   111.69  3.000
 C3F  H1'2  C1'  N10   107.15  3.000
 C3F  H1'1  C1'  N10   107.94  3.000
 C3F  C2'   C1'  N10   112.56  3.000
 C3F  H2'2  C2'  H2'1  106.98  3.000
 C3F  H2'2  C2'  C3'   109.45  3.000
 C3F  H2'1  C2'  C3'   110.00  3.000
 C3F  H2'2  C2'  C1'   110.75  3.000
 C3F  H2'1  C2'  C1'   109.02  3.000
 C3F  C3'   C2'  C1'   110.57  3.000
 C3F  H3'2  C3'  H3'1  106.12  3.000
 C3F  H3'2  C3'  N1'   112.97  3.000
 C3F  H3'1  C3'  N1'   109.28  3.000
 C3F  H3'2  C3'  C2'   108.83  3.000
 C3F  H3'1  C3'  C2'   109.19  3.000
 C3F  N1'   C3'  C2'   110.33  3.000
 C3F  O1'   C5'  O2'   127.14  3.000
 C3F  O2'   C5'  N1'   115.81  3.000
 C3F  O1'   C5'  N1'   117.03  3.000
 C3F  H1'   N1'  C5'   113.82  3.000
 C3F  H1'   N1'  C3'   114.31  3.000
 C3F  C5'   N1'  C3'   121.11  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
 C3F  CONST_01  C8    C7   C6   C5A    0.00   0.0  0
 C3F  CONST_02  C8    C9   C9A  C5A    0.00   0.0  0
 C3F  CONST_03  C9    C9A  C5A  C6     0.00   0.0  0
 C3F  CONST_04  C9    C8   C7   C6     0.00   0.0  0
 C3F  CONST_05  C9A   C5A  C6   C7     0.00   0.0  0
 C3F  CONST_06  C9A   C9   C8   C7     0.00   0.0  0
 C3F  CONST_07  N1    C2   N3   C4     0.00   0.0  0
 C3F  CONST_08  C10   N1   C2   N3     0.00   0.0  0
 C3F  CONST_09  C4A   C4   N3   C2     0.00   0.0  0
 C3F  CONST_10  C4A   C10  N1   C2     0.00   0.0  0
 C3F  CONST_11  N10   C10  N1   C2   180.00   0.0  0
 C3F  CONST_12  C9A   N10  C10  N1   180.00   0.0  0
 C3F  CONST_13  C9A   N10  C10  C4A    0.00   0.0  0
 C3F  CONST_14  C7M   C7   C6   C5A  180.00   0.0  0
 C3F  CONST_15  C8M   C8   C7   C6   180.00   0.0  0
 C3F  CONST_16  C9    C8   C7   C7M  180.00   0.0  0
 C3F  CONST_17  C9A   C9   C8   C8M  180.00   0.0  0
 C3F  CONST_18  C2    N3   C4   O4   180.00   0.0  0
 C3F  CONST_19  O2    C2   N3   C4   180.00   0.0  0
 C3F  CONST_20  C10   N1   C2   O2   180.00   0.0  0
 C3F  CONST_21  C1'   N10  C10  N1     0.00   0.0  0
 C3F  CONST_22  C1'   N10  C10  C4A  180.00   0.0  0
 C3F  CONST_23  H6    C6   C5A  N5     0.00   0.0  0
 C3F  CONST_24  H9    C9   C9A  C5A  180.00   0.0  0
 C3F  CONST_25  H3    N3   C2   N1   180.00   0.0  0
 C3F  Var_01    C2'   C1'  N10  C10   91.32  30.0  3
 C3F  Var_02    H7M1  C7M  C7   C6   124.55  30.0  2
 C3F  Var_03    H8M1  C8M  C8   C7    62.98  30.0  2
 C3F  Var_04    C3'   C2'  C1'  N10  179.63  30.0  3
 C3F  Var_05    N1'   C3'  C2'  C1'  178.68  30.0  3
 C3F  Var_06    C5'   N1'  C3'  C2'  174.23  30.0  3
 C3F  Var_07    O1'   C5'  N1'  C3'  -18.07  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
 C3F  plan-1  O4   0.020
 C3F  plan-1  C4   0.020
 C3F  plan-1  N3   0.020
 C3F  plan-1  C2   0.020
 C3F  plan-1  O2   0.020
 C3F  plan-1  N1   0.020
 C3F  plan-1  C4A  0.020
 C3F  plan-1  C10  0.020
 C3F  plan-1  N5   0.020
 C3F  plan-1  C5A  0.020
 C3F  plan-1  C6   0.020
 C3F  plan-1  C7   0.020
 C3F  plan-1  C7M  0.020
 C3F  plan-1  C8   0.020
 C3F  plan-1  C8M  0.020
 C3F  plan-1  C9   0.020
 C3F  plan-1  C9A  0.020
 C3F  plan-1  N10  0.020
 C3F  plan-1  C1'  0.020
 C3F  plan-1  H3   0.020
 C3F  plan-1  H6   0.020
 C3F  plan-1  H9   0.020
 C3F  plan-2  C5'  0.020
 C3F  plan-2  N1'  0.020
 C3F  plan-2  O2'  0.020
 C3F  plan-2  O1'  0.020

