FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 9R5K2

Calculation Name: 6IOC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: iron/sulfur cluster | uracil

Ligand 3-letter code: SF4 | URA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6IOC

Chain ID: A

ChEMBL ID:

UniProt ID: I7F541

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2304158.940308
FMO2-HF: Nuclear repulsion 2225157.536859
FMO2-HF: Total energy -79001.403449
FMO2-MP2: Total energy -79231.244206


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)


Summations of interaction energy for fragment #1(A:-2:GLY)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-64.352-61.2695.701-4.894-3.889-0.065
Interaction energy analysis for fragmet #1(A:-2:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.820 / q_NPA : 0.903
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A0HIS00.0150.0273.0648.98710.5460.081-0.594-1.046-0.003
4A1MET00.000-0.0201.956-37.602-36.2055.621-4.296-2.722-0.062
5A2ALA00.0420.0334.705-0.237-0.110-0.001-0.004-0.1210.000
6A3GLY0-0.013-0.0096.3474.4444.4440.0000.0000.0000.000
7A4ALA00.019-0.0169.3941.0331.0330.0000.0000.0000.000
8A5GLN00.0050.0089.7293.1863.1860.0000.0000.0000.000
9A6ASP-1-0.919-0.9599.363-30.797-30.7970.0000.0000.0000.000
10A7PHE0-0.018-0.02812.2421.5001.5000.0000.0000.0000.000
11A8VAL00.0000.01214.9201.3931.3930.0000.0000.0000.000
12A9PRO0-0.0020.00916.892-0.358-0.3580.0000.0000.0000.000
13A10HIS0-0.030-0.02415.5100.7450.7450.0000.0000.0000.000
14A11THR0-0.033-0.03820.4810.7100.7100.0000.0000.0000.000
15A12ALA00.0490.02322.899-0.458-0.4580.0000.0000.0000.000
16A13ASP-1-0.867-0.91725.473-10.508-10.5080.0000.0000.0000.000
17A14LEU00.0460.00725.897-0.462-0.4620.0000.0000.0000.000
18A15ALA0-0.0180.00026.822-0.217-0.2170.0000.0000.0000.000
19A16GLU-1-0.892-0.92225.090-12.287-12.2870.0000.0000.0000.000
20A17LEU0-0.021-0.01120.653-0.614-0.6140.0000.0000.0000.000
21A18ALA0-0.002-0.00122.525-0.532-0.5320.0000.0000.0000.000
22A19ALA0-0.006-0.00624.618-0.158-0.1580.0000.0000.0000.000
23A20ALA0-0.015-0.00720.255-0.206-0.2060.0000.0000.0000.000
24A21ALA0-0.002-0.01319.870-0.797-0.7970.0000.0000.0000.000
25A22GLY0-0.043-0.02220.912-0.285-0.2850.0000.0000.0000.000
26A23GLU-1-0.941-0.96020.519-14.096-14.0960.0000.0000.0000.000
27A24CYS0-0.131-0.00815.693-1.518-1.5180.0000.0000.0000.000
28A25ARG10.9370.95515.74118.27418.2740.0000.0000.0000.000
29A26GLY00.0360.01212.201-0.870-0.8700.0000.0000.0000.000
30A27CYS0-0.052-0.02911.660-1.709-1.7090.0000.0000.0000.000
31A28GLY0-0.012-0.02313.9931.0531.0530.0000.0000.0000.000
32A29LEU00.025-0.00716.9330.8730.8730.0000.0000.0000.000
33A30TYR00.0380.03116.6741.0641.0640.0000.0000.0000.000
34A31ARG10.9020.97217.19517.66817.6680.0000.0000.0000.000
35A32ASP-1-0.908-0.94922.913-12.389-12.3890.0000.0000.0000.000
36A33ALA0-0.068-0.03824.1190.6510.6510.0000.0000.0000.000
37A34THR0-0.061-0.04625.8290.0950.0950.0000.0000.0000.000
38A35GLN0-0.038-0.02926.3020.0410.0410.0000.0000.0000.000
39A36ALA0-0.0210.00822.552-0.174-0.1740.0000.0000.0000.000
40A37VAL0-0.055-0.02424.1880.4760.4760.0000.0000.0000.000
41A38PHE00.0320.00321.127-0.617-0.6170.0000.0000.0000.000
42A39GLY00.016-0.00125.4890.3120.3120.0000.0000.0000.000
43A40ALA0-0.054-0.01827.3080.1630.1630.0000.0000.0000.000
44A41GLY00.0750.03731.102-0.026-0.0260.0000.0000.0000.000
45A42GLY0-0.004-0.00332.268-0.130-0.1300.0000.0000.0000.000
46A43ARG10.8810.90728.77310.93610.9360.0000.0000.0000.000
47A44SER0-0.0120.00731.533-0.106-0.1060.0000.0000.0000.000
48A45ALA0-0.0290.01131.9550.2350.2350.0000.0000.0000.000
49A46ARG10.8240.88631.9378.6878.6870.0000.0000.0000.000
50A47ILE00.0090.01331.447-0.136-0.1360.0000.0000.0000.000
51A48MET0-0.0160.00624.861-0.202-0.2020.0000.0000.0000.000
52A49MET0-0.026-0.00628.4290.0960.0960.0000.0000.0000.000
53A50ILE00.0210.01822.064-0.246-0.2460.0000.0000.0000.000
54A51GLY00.0270.01325.5780.1860.1860.0000.0000.0000.000
55A52GLU-1-0.862-0.91822.463-13.860-13.8600.0000.0000.0000.000
56A53GLN0-0.053-0.04922.289-0.821-0.8210.0000.0000.0000.000
57A54PRO00.0280.02623.8650.5500.5500.0000.0000.0000.000
58A55GLY00.0310.01227.063-0.129-0.1290.0000.0000.0000.000
59A56ASP-1-0.818-0.89930.105-9.353-9.3530.0000.0000.0000.000
60A57LYS10.8560.90332.3238.7788.7780.0000.0000.0000.000
61A58GLU-1-0.740-0.85129.600-9.864-9.8640.0000.0000.0000.000
62A59ASP-1-0.747-0.84228.077-11.294-11.2940.0000.0000.0000.000
63A60LEU0-0.052-0.02529.8130.0130.0130.0000.0000.0000.000
64A61ALA0-0.017-0.00633.2330.1280.1280.0000.0000.0000.000
65A62GLY00.0400.03329.7300.0880.0880.0000.0000.0000.000
66A63LEU00.0030.00529.836-0.209-0.2090.0000.0000.0000.000
67A64PRO00.0240.00328.0580.1050.1050.0000.0000.0000.000
68A65PHE0-0.010-0.01328.4570.3470.3470.0000.0000.0000.000
69A66VAL00.0300.02332.6470.3120.3120.0000.0000.0000.000
70A67GLY0-0.015-0.00634.3790.2910.2910.0000.0000.0000.000
71A68PRO0-0.070-0.06535.8230.0700.0700.0000.0000.0000.000
72A69ALA00.0350.01332.9610.1460.1460.0000.0000.0000.000
73A70GLY00.0640.04334.944-0.029-0.0290.0000.0000.0000.000
74A71ARG10.9570.98335.7757.7007.7000.0000.0000.0000.000
75A72LEU0-0.073-0.03637.1020.2280.2280.0000.0000.0000.000
76A73LEU00.0370.02032.6570.0400.0400.0000.0000.0000.000
77A74ASP-1-0.799-0.88636.296-8.399-8.3990.0000.0000.0000.000
78A75ARG10.9320.96439.3227.5267.5260.0000.0000.0000.000
79A76ALA00.0020.00537.3890.1420.1420.0000.0000.0000.000
80A77LEU00.011-0.00135.4830.0160.0160.0000.0000.0000.000
81A78GLU-1-0.952-0.96839.411-6.936-6.9360.0000.0000.0000.000
82A79ALA0-0.020-0.01442.5310.1200.1200.0000.0000.0000.000
83A80ALA0-0.015-0.01639.8420.0830.0830.0000.0000.0000.000
84A81ASP-1-0.872-0.90241.757-7.012-7.0120.0000.0000.0000.000
85A82ILE0-0.051-0.03137.083-0.053-0.0530.0000.0000.0000.000
86A83ASP-1-0.865-0.93740.594-7.878-7.8780.0000.0000.0000.000
87A84ARG10.8050.86834.1278.8178.8170.0000.0000.0000.000
88A85ASP-1-0.932-0.96936.153-8.630-8.6300.0000.0000.0000.000
89A86ALA0-0.054-0.01637.240-0.095-0.0950.0000.0000.0000.000
90A87LEU0-0.040-0.01532.905-0.190-0.1900.0000.0000.0000.000
91A88TYR0-0.013-0.03525.1100.0210.0210.0000.0000.0000.000
92A89VAL0-0.0060.00229.290-0.289-0.2890.0000.0000.0000.000
93A90THR00.013-0.03523.931-0.101-0.1010.0000.0000.0000.000
94A91ASN0-0.052-0.01823.4360.4180.4180.0000.0000.0000.000
95A92ALA00.0300.02119.047-0.464-0.4640.0000.0000.0000.000
96A93VAL0-0.064-0.05417.862-1.032-1.0320.0000.0000.0000.000
97A94LYS10.8580.90019.34515.68215.6820.0000.0000.0000.000
98A95HIS00.0310.03119.0321.0081.0080.0000.0000.0000.000
99A96PHE0-0.029-0.01522.110-0.082-0.0820.0000.0000.0000.000
100A97LYS10.8310.91218.86916.14216.1420.0000.0000.0000.000
101A98PHE0-0.051-0.02523.7430.6490.6490.0000.0000.0000.000
102A99THR00.0190.00226.120-0.274-0.2740.0000.0000.0000.000
103A100ARG10.9430.94727.64011.80711.8070.0000.0000.0000.000
104A101ALA0-0.0020.00830.5590.3030.3030.0000.0000.0000.000
105A102ALA0-0.0160.00132.2510.1920.1920.0000.0000.0000.000
106A103GLY00.0340.02135.635-0.090-0.0900.0000.0000.0000.000
107A104GLY00.041-0.00235.732-0.008-0.0080.0000.0000.0000.000
108A105LYS10.9320.97234.0639.2029.2020.0000.0000.0000.000
109A106ARG10.9520.98232.6808.6978.6970.0000.0000.0000.000
110A107ARG10.7940.87730.56610.43410.4340.0000.0000.0000.000
111A108ILE0-0.0190.00231.3500.0970.0970.0000.0000.0000.000
112A109GLN00.0610.03427.302-0.364-0.3640.0000.0000.0000.000
113A110LYS10.8170.90024.85511.52011.5200.0000.0000.0000.000
114A111THR00.0720.04421.821-0.127-0.1270.0000.0000.0000.000
115A112PRO00.0340.03218.624-0.437-0.4370.0000.0000.0000.000
116A113SER0-0.021-0.00215.191-0.427-0.4270.0000.0000.0000.000
117A114ARG10.9070.93612.67120.81820.8180.0000.0000.0000.000
118A115THR00.025-0.0079.861-1.214-1.2140.0000.0000.0000.000
119A116GLU-1-0.774-0.86411.326-19.335-19.3350.0000.0000.0000.000
120A117VAL00.0100.00314.0690.0340.0340.0000.0000.0000.000
121A118VAL0-0.034-0.0198.6980.2590.2590.0000.0000.0000.000
122A119ALA0-0.0050.00210.026-0.811-0.8110.0000.0000.0000.000
123A120CYS0-0.0220.01210.9400.4820.4820.0000.0000.0000.000
124A121ARG10.9010.95912.75321.87121.8710.0000.0000.0000.000
125A122PRO0-0.016-0.00911.5291.0691.0690.0000.0000.0000.000
126A123TRP00.0530.00514.3090.9260.9260.0000.0000.0000.000
127A124LEU00.0110.01617.5730.7560.7560.0000.0000.0000.000
128A125ILE0-0.0100.00414.9210.6110.6110.0000.0000.0000.000
129A126ALA00.0510.03418.1010.7430.7430.0000.0000.0000.000
130A127GLU-1-0.696-0.80419.909-13.363-13.3630.0000.0000.0000.000
131A128MET0-0.016-0.01619.7650.6880.6880.0000.0000.0000.000
132A129THR0-0.017-0.02020.5660.3870.3870.0000.0000.0000.000
133A130SER0-0.069-0.04023.2710.5390.5390.0000.0000.0000.000
134A131VAL0-0.037-0.03325.7700.4850.4850.0000.0000.0000.000
135A132GLU-1-0.966-0.95326.717-10.735-10.7350.0000.0000.0000.000
136A133PRO0-0.063-0.01726.3390.3180.3180.0000.0000.0000.000
137A134ASP-1-0.737-0.85728.727-9.613-9.6130.0000.0000.0000.000
138A135VAL0-0.010-0.00229.578-0.168-0.1680.0000.0000.0000.000
139A136VAL0-0.014-0.01324.263-0.085-0.0850.0000.0000.0000.000
140A137VAL00.0260.01627.516-0.023-0.0230.0000.0000.0000.000
141A138LEU0-0.026-0.01422.863-0.324-0.3240.0000.0000.0000.000
142A139LEU00.0200.00526.3290.2860.2860.0000.0000.0000.000
143A140GLY0-0.006-0.01427.016-0.192-0.1920.0000.0000.0000.000
144A141ALA0-0.033-0.02824.294-0.416-0.4160.0000.0000.0000.000
145A142THR0-0.072-0.07119.719-0.637-0.6370.0000.0000.0000.000
146A143ALA00.0360.02420.270-0.855-0.8550.0000.0000.0000.000
147A144ALA00.0520.02721.568-0.356-0.3560.0000.0000.0000.000
148A145LYS10.9390.97318.59714.83214.8320.0000.0000.0000.000
149A146ALA0-0.060-0.00816.761-1.239-1.2390.0000.0000.0000.000
150A147LEU0-0.001-0.00316.452-1.259-1.2590.0000.0000.0000.000
151A148LEU00.0660.05118.760-0.090-0.0900.0000.0000.0000.000
152A149GLY00.0670.05816.6960.1180.1180.0000.0000.0000.000
153A150ASN0-0.107-0.09015.1280.6070.6070.0000.0000.0000.000
154A151ASP-1-0.887-0.95117.253-15.834-15.8340.0000.0000.0000.000
155A152PHE00.0220.02620.3130.9070.9070.0000.0000.0000.000
156A153ARG10.8570.92922.42511.66011.6600.0000.0000.0000.000
157A154VAL00.1090.03925.8330.2730.2730.0000.0000.0000.000
158A155THR0-0.025-0.02927.9690.1610.1610.0000.0000.0000.000
159A156GLN0-0.074-0.03928.1150.0510.0510.0000.0000.0000.000
160A157HIS10.8500.91927.28611.09411.0940.0000.0000.0000.000
161A158ARG10.7990.89230.5748.7568.7560.0000.0000.0000.000
162A159GLY00.0580.03131.9510.2790.2790.0000.0000.0000.000
163A160GLU-1-0.886-0.92230.530-10.158-10.1580.0000.0000.0000.000
164A161VAL00.006-0.00130.556-0.260-0.2600.0000.0000.0000.000
165A162LEU0-0.066-0.03025.950-0.026-0.0260.0000.0000.0000.000
166A163HIS00.0290.00725.4240.4460.4460.0000.0000.0000.000
167A164VAL0-0.057-0.04120.064-0.163-0.1630.0000.0000.0000.000
168A165ASP-1-0.869-0.92719.097-14.782-14.7820.0000.0000.0000.000
169A166ASP-1-0.971-0.98814.958-20.127-20.1270.0000.0000.0000.000
170A167VAL0-0.013-0.01316.361-1.170-1.1700.0000.0000.0000.000
171A168PRO0-0.040-0.01418.3830.2940.2940.0000.0000.0000.000
172A169GLY00.021-0.01220.9600.3250.3250.0000.0000.0000.000
173A170ASP-1-0.913-0.92523.357-12.046-12.0460.0000.0000.0000.000
174A171PRO00.0300.02723.6530.4330.4330.0000.0000.0000.000
175A172ALA00.0580.03225.996-0.292-0.2920.0000.0000.0000.000
176A173LEU0-0.048-0.03322.260-0.088-0.0880.0000.0000.0000.000
177A174VAL00.0470.02926.7980.2040.2040.0000.0000.0000.000
178A175ALA0-0.038-0.01126.443-0.213-0.2130.0000.0000.0000.000
179A176THR00.015-0.03328.1420.4530.4530.0000.0000.0000.000
180A177VAL0-0.048-0.02629.386-0.429-0.4290.0000.0000.0000.000
181A178HIS00.0810.04627.1570.2940.2940.0000.0000.0000.000
182A179PRO00.0870.03530.6740.2140.2140.0000.0000.0000.000
183A180SER0-0.003-0.03630.8970.3320.3320.0000.0000.0000.000
184A181SER0-0.080-0.03931.3810.1020.1020.0000.0000.0000.000
185A182LEU00.0380.03633.7480.2080.2080.0000.0000.0000.000
186A183LEU0-0.0480.00335.1180.3200.3200.0000.0000.0000.000
187A184ARG10.8520.90637.6788.1058.1050.0000.0000.0000.000
188A185GLY00.0440.02337.666-0.263-0.2630.0000.0000.0000.000
189A186PRO00.0380.01739.1950.1790.1790.0000.0000.0000.000
190A187LYS10.8360.90541.9546.8506.8500.0000.0000.0000.000
191A188GLU-1-0.864-0.93643.832-6.846-6.8460.0000.0000.0000.000
192A189GLU-1-0.859-0.93139.202-7.713-7.7130.0000.0000.0000.000
193A190ARG10.7790.88738.4357.6387.6380.0000.0000.0000.000
194A191GLU-1-0.777-0.86640.125-7.428-7.4280.0000.0000.0000.000
195A192SER0-0.033-0.01240.898-0.046-0.0460.0000.0000.0000.000
196A193ALA0-0.005-0.00536.338-0.107-0.1070.0000.0000.0000.000
197A194PHE0-0.042-0.02337.375-0.211-0.2110.0000.0000.0000.000
198A195ALA00.0180.01039.481-0.040-0.0400.0000.0000.0000.000
199A196GLY00.0280.01237.899-0.032-0.0320.0000.0000.0000.000
200A197LEU0-0.037-0.02133.514-0.165-0.1650.0000.0000.0000.000
201A198VAL00.011-0.00136.410-0.109-0.1090.0000.0000.0000.000
202A199ASP-1-0.908-0.94638.752-7.810-7.8100.0000.0000.0000.000
203A200ASP-1-0.765-0.83633.607-9.379-9.3790.0000.0000.0000.000
204A201LEU0-0.030-0.01534.168-0.191-0.1910.0000.0000.0000.000
205A202ARG10.8040.88636.2867.3517.3510.0000.0000.0000.000
206A203VAL0-0.021-0.00534.9990.0580.0580.0000.0000.0000.000
207A204ALA0-0.016-0.02333.102-0.062-0.0620.0000.0000.0000.000
208A205ALA0-0.027-0.01034.687-0.082-0.0820.0000.0000.0000.000
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