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: 2R5NR

Calculation Name: 4TLF-C-Xray547

Preferred Name:

Target Type:

Ligand Name: fe (ii) ion

Ligand 3-letter code: FE2

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4TLF

Chain ID: C

ChEMBL ID:

UniProt ID: Q9I0N5

Base Structure: X-ray

Registration Date: 2025-10-04

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 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2235356.336876
FMO2-HF: Nuclear repulsion 2159061.22903
FMO2-HF: Total energy -76295.107845
FMO2-MP2: Total energy -76522.526778


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:4:ILE)


Summations of interaction energy for fragment #1(A:4:ILE)
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.
-142.641-143.74117.066-7.935-8.032-0.083
Interaction energy analysis for fragmet #1(A:4:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.768 / q_NPA : 0.877
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].
3A6ARG10.9420.9493.68544.17345.949-0.009-0.621-1.1450.000
194A197LYS10.8040.8813.51728.17928.4530.009-0.043-0.2410.000
195A198GLU-1-0.901-0.9631.937-123.578-126.89917.055-7.204-6.530-0.083
196A199ASN-1-0.914-0.9323.887-31.401-31.2300.011-0.067-0.1160.000
4A7LEU0-0.019-0.0345.6247.3817.3810.0000.0000.0000.000
5A8ASP-1-0.860-0.8997.731-31.500-31.5000.0000.0000.0000.000
6A9ARG10.8880.9339.31831.79731.7970.0000.0000.0000.000
7A10LEU00.0070.00911.1062.2092.2090.0000.0000.0000.000
8A11ARG10.8760.9277.70130.83430.8340.0000.0000.0000.000
9A12GLN0-0.050-0.02113.6000.9960.9960.0000.0000.0000.000
10A13PHE00.0510.02315.6041.3671.3670.0000.0000.0000.000
11A14ILE0-0.053-0.02814.9351.2471.2470.0000.0000.0000.000
12A15GLY00.0250.01217.9070.9670.9670.0000.0000.0000.000
13A16GLU-1-0.836-0.90419.529-15.274-15.2740.0000.0000.0000.000
14A17LEU00.0070.00321.2140.8490.8490.0000.0000.0000.000
15A18ALA0-0.037-0.02222.3330.7000.7000.0000.0000.0000.000
16A19THR00.005-0.00823.5050.6430.6430.0000.0000.0000.000
17A20LEU0-0.0310.00025.6040.5520.5520.0000.0000.0000.000
18A21LEU0-0.006-0.01025.7720.6050.6050.0000.0000.0000.000
19A22ASP-1-0.876-0.91727.276-10.772-10.7720.0000.0000.0000.000
20A23SER0-0.106-0.06630.0920.4750.4750.0000.0000.0000.000
21A24ARG10.8630.93832.2679.2819.2810.0000.0000.0000.000
22A25PRO00.0310.03730.9560.3120.3120.0000.0000.0000.000
23A26ASP-1-0.800-0.89234.251-8.682-8.6820.0000.0000.0000.000
24A27GLU-1-0.765-0.86733.793-9.238-9.2380.0000.0000.0000.000
25A28SER0-0.045-0.01333.612-0.230-0.2300.0000.0000.0000.000
26A29THR00.010-0.00533.149-0.233-0.2330.0000.0000.0000.000
27A30LEU0-0.013-0.00128.245-0.311-0.3110.0000.0000.0000.000
28A31LEU0-0.008-0.00729.077-0.451-0.4510.0000.0000.0000.000
29A32ALA0-0.015-0.01029.004-0.381-0.3810.0000.0000.0000.000
30A33GLN0-0.001-0.00628.337-0.397-0.3970.0000.0000.0000.000
31A34ALA00.0220.00224.972-0.467-0.4670.0000.0000.0000.000
32A35HIS0-0.048-0.01724.053-0.742-0.7420.0000.0000.0000.000
33A36PRO00.0380.01423.673-0.558-0.5580.0000.0000.0000.000
34A37LEU00.0020.01121.034-0.670-0.6700.0000.0000.0000.000
35A38LEU0-0.040-0.02518.737-0.949-0.9490.0000.0000.0000.000
36A39ALA00.016-0.00319.129-0.759-0.7590.0000.0000.0000.000
37A40GLU-1-0.872-0.92715.125-20.792-20.7920.0000.0000.0000.000
38A41LEU0-0.048-0.01413.476-1.286-1.2860.0000.0000.0000.000
39A42VAL0-0.078-0.04914.408-1.539-1.5390.0000.0000.0000.000
40A43HIS00.0260.03015.721-0.624-0.6240.0000.0000.0000.000
41A44GLN0-0.047-0.04510.908-1.165-1.1650.0000.0000.0000.000
42A45ASP-1-0.808-0.86910.121-26.953-26.9530.0000.0000.0000.000
43A46ASP-1-0.801-0.8836.136-37.262-37.2620.0000.0000.0000.000
44A47TRP00.0200.0035.773-9.445-9.4450.0000.0000.0000.000
45A48LEU00.0170.0167.0390.6290.6290.0000.0000.0000.000
46A49PRO0-0.012-0.0196.248-1.547-1.5470.0000.0000.0000.000
47A50GLU-1-0.839-0.9376.416-21.657-21.6570.0000.0000.0000.000
48A51ASP-1-0.917-0.9458.322-19.655-19.6550.0000.0000.0000.000
49A52CYS0-0.089-0.04010.4411.7361.7360.0000.0000.0000.000
50A53ALA00.0460.02010.5640.5960.5960.0000.0000.0000.000
51A54ARG10.9220.9639.20021.78721.7870.0000.0000.0000.000
52A55PRO00.0060.01714.2460.5340.5340.0000.0000.0000.000
53A56ASP-1-0.826-0.92218.012-12.188-12.1880.0000.0000.0000.000
54A57PRO0-0.028-0.01620.7720.2230.2230.0000.0000.0000.000
55A58GLN0-0.0270.00124.1290.4750.4750.0000.0000.0000.000
56A59ARG10.8240.90224.44310.53010.5300.0000.0000.0000.000
57A60TYR00.0630.05222.222-0.099-0.0990.0000.0000.0000.000
58A61GLN0-0.0360.00418.5670.1980.1980.0000.0000.0000.000
59A62GLN0-0.017-0.01920.060-0.118-0.1180.0000.0000.0000.000
60A63TYR00.021-0.00915.3300.4000.4000.0000.0000.0000.000
61A64LEU0-0.055-0.02016.877-0.491-0.4910.0000.0000.0000.000
62A65LEU00.005-0.00812.243-0.665-0.6650.0000.0000.0000.000
63A66HIS00.0280.01015.243-0.948-0.9480.0000.0000.0000.000
64A67VAL0-0.004-0.01217.8400.6240.6240.0000.0000.0000.000
65A68ASP-1-0.784-0.85821.620-11.889-11.8890.0000.0000.0000.000
66A69SER00.0390.00723.6160.2160.2160.0000.0000.0000.000
67A70ARG10.8860.94925.40410.01010.0100.0000.0000.0000.000
68A71GLN0-0.025-0.02526.5100.3180.3180.0000.0000.0000.000
69A72ARG10.7630.84626.10311.31611.3160.0000.0000.0000.000
70A73PHE00.0170.00620.2840.0900.0900.0000.0000.0000.000
71A74SER0-0.047-0.02721.965-0.180-0.1800.0000.0000.0000.000
72A75VAL00.0340.01616.8510.1920.1920.0000.0000.0000.000
73A76VAL0-0.005-0.01317.977-0.303-0.3030.0000.0000.0000.000
74A77SER00.0120.01114.3250.1550.1550.0000.0000.0000.000
75A78PHE0-0.033-0.02716.7180.6700.6700.0000.0000.0000.000
76A79VAL00.0040.01615.254-0.309-0.3090.0000.0000.0000.000
77A80TRP0-0.026-0.03518.3521.0821.0820.0000.0000.0000.000
78A81GLY00.0940.02720.177-0.505-0.5050.0000.0000.0000.000
79A82PRO0-0.030-0.00720.9210.2820.2820.0000.0000.0000.000
80A83GLY00.0170.00523.7010.3390.3390.0000.0000.0000.000
81A84GLN0-0.055-0.00823.0310.0180.0180.0000.0000.0000.000
82A85ILE00.0360.01226.353-0.157-0.1570.0000.0000.0000.000
83A86THR0-0.025-0.00227.334-0.036-0.0360.0000.0000.0000.000
84A87PRO00.0410.02529.6230.2380.2380.0000.0000.0000.000
85A88VAL00.0600.05132.464-0.311-0.3110.0000.0000.0000.000
86A89HIS10.7890.88629.58010.01410.0140.0000.0000.0000.000
87A90ASP-1-0.736-0.83133.849-8.650-8.6500.0000.0000.0000.000
88A91HIS10.7590.84328.9389.6859.6850.0000.0000.0000.000
89A92ARG10.7840.86032.1137.9947.9940.0000.0000.0000.000
90A93VAL0-0.0110.00929.5810.1390.1390.0000.0000.0000.000
91A94TRP00.0570.03225.7540.0040.0040.0000.0000.0000.000
92A95GLY0-0.006-0.02427.257-0.233-0.2330.0000.0000.0000.000
93A96LEU0-0.0260.00024.5840.3430.3430.0000.0000.0000.000
94A97ILE0-0.033-0.02322.545-0.343-0.3430.0000.0000.0000.000
95A98GLY00.0850.04920.3690.4350.4350.0000.0000.0000.000
96A99MET0-0.0600.00219.255-0.326-0.3260.0000.0000.0000.000
97A100LEU0-0.0060.00911.603-0.162-0.1620.0000.0000.0000.000
98A101ARG10.8360.8798.99824.06124.0610.0000.0000.0000.000
99A102GLY00.0070.00615.9600.6650.6650.0000.0000.0000.000
100A103ALA00.029-0.00219.222-0.029-0.0290.0000.0000.0000.000
101A104GLU-1-0.776-0.84222.360-13.042-13.0420.0000.0000.0000.000
102A105TYR0-0.011-0.00824.7200.2100.2100.0000.0000.0000.000
103A106SER0-0.025-0.01828.3910.0880.0880.0000.0000.0000.000
104A107GLN0-0.014-0.03130.1090.1590.1590.0000.0000.0000.000
105A108PRO00.019-0.00133.861-0.006-0.0060.0000.0000.0000.000
106A109TYR00.011-0.00335.7490.2690.2690.0000.0000.0000.000
107A110ALA0-0.013-0.00538.844-0.085-0.0850.0000.0000.0000.000
108A111PHE00.0150.00640.7020.0230.0230.0000.0000.0000.000
109A112ASP-1-0.746-0.86544.812-6.398-6.3980.0000.0000.0000.000
110A113ALA0-0.014-0.02048.459-0.044-0.0440.0000.0000.0000.000
111A114GLY0-0.049-0.00950.2320.1240.1240.0000.0000.0000.000
112A115GLY00.0210.00446.708-0.020-0.0200.0000.0000.0000.000
113A116ARG10.8860.96744.9936.1476.1470.0000.0000.0000.000
114A117PRO0-0.0380.00140.4550.0550.0550.0000.0000.0000.000
115A118HIS10.8250.88542.6246.9226.9220.0000.0000.0000.000
116A119PRO00.0380.01839.448-0.080-0.0800.0000.0000.0000.000
117A120SER0-0.010-0.00539.7890.1210.1210.0000.0000.0000.000
118A121GLY00.0270.01239.7020.0750.0750.0000.0000.0000.000
119A122ALA0-0.0090.00837.624-0.032-0.0320.0000.0000.0000.000
120A123ARG10.9170.97332.1479.1839.1830.0000.0000.0000.000
121A124ARG10.9360.97030.9069.6219.6210.0000.0000.0000.000
122A125ARG10.7720.85425.58911.59211.5920.0000.0000.0000.000
123A126LEU0-0.0130.01923.0330.1490.1490.0000.0000.0000.000
124A127GLU-1-0.763-0.88722.971-12.820-12.8200.0000.0000.0000.000
125A128PRO0-0.059-0.03917.699-0.136-0.1360.0000.0000.0000.000
126A129GLY00.0400.03118.9550.1910.1910.0000.0000.0000.000
127A130GLU-1-0.905-0.93219.836-11.662-11.6620.0000.0000.0000.000
128A131VAL00.013-0.02021.974-0.464-0.4640.0000.0000.0000.000
129A132GLU-1-0.867-0.91324.398-10.156-10.1560.0000.0000.0000.000
130A133ALA00.009-0.01126.745-0.358-0.3580.0000.0000.0000.000
131A134LEU0-0.060-0.01929.0800.2980.2980.0000.0000.0000.000
132A135SER00.038-0.01831.463-0.131-0.1310.0000.0000.0000.000
133A136PRO0-0.060-0.02833.9590.1630.1630.0000.0000.0000.000
134A137ARG10.8350.90235.8738.8448.8440.0000.0000.0000.000
135A138ILE0-0.012-0.00333.0660.1900.1900.0000.0000.0000.000
136A139GLY00.0170.02036.8490.0500.0500.0000.0000.0000.000
137A140ASP-1-0.719-0.84833.630-9.510-9.5100.0000.0000.0000.000
138A141VAL0-0.013-0.00834.032-0.242-0.2420.0000.0000.0000.000
139A142HIS00.0410.01828.233-0.048-0.0480.0000.0000.0000.000
140A143GLN0-0.047-0.01831.8680.1690.1690.0000.0000.0000.000
141A144VAL0-0.0020.00925.5580.0260.0260.0000.0000.0000.000
142A145SER00.009-0.00627.2110.2370.2370.0000.0000.0000.000
143A146ASN00.0230.01721.921-0.231-0.2310.0000.0000.0000.000
144A147ALA0-0.043-0.02224.5170.4680.4680.0000.0000.0000.000
145A148PHE0-0.013-0.00922.5270.2640.2640.0000.0000.0000.000
146A149SER00.014-0.00525.062-0.159-0.1590.0000.0000.0000.000
147A150ASP-1-0.797-0.86023.746-12.380-12.3800.0000.0000.0000.000
148A151ARG10.8250.88118.99213.05113.0510.0000.0000.0000.000
149A152THR0-0.008-0.00815.8910.8080.8080.0000.0000.0000.000
150A153SER0-0.016-0.01917.863-0.566-0.5660.0000.0000.0000.000
151A154ILE0-0.041-0.01313.1620.1990.1990.0000.0000.0000.000
152A155SER00.026-0.01717.170-0.280-0.2800.0000.0000.0000.000
153A156ILE0-0.0100.00813.9650.0310.0310.0000.0000.0000.000
154A157HIS10.8000.88618.00514.06914.0690.0000.0000.0000.000
155A158VAL00.0290.01720.228-0.485-0.4850.0000.0000.0000.000
156A159TYR00.0180.01922.5910.4580.4580.0000.0000.0000.000
157A160GLY00.0470.02025.724-0.252-0.2520.0000.0000.0000.000
158A161ALA0-0.009-0.00927.2480.4210.4210.0000.0000.0000.000
159A162ASN00.0410.05225.470-0.784-0.7840.0000.0000.0000.000
160A163ILE00.0140.00624.2230.3880.3880.0000.0000.0000.000
161A164GLY00.0230.02125.6350.3010.3010.0000.0000.0000.000
162A165ALA0-0.031-0.02926.6770.3060.3060.0000.0000.0000.000
163A166VAL0-0.047-0.01029.6430.3800.3800.0000.0000.0000.000
164A167ARG10.9350.96431.7098.0748.0740.0000.0000.0000.000
165A168ARG10.8450.92528.08210.29410.2940.0000.0000.0000.000
166A169ALA00.0120.01035.5990.1460.1460.0000.0000.0000.000
167A170VAL0-0.064-0.03533.378-0.302-0.3020.0000.0000.0000.000
168A171PHE00.029-0.00836.0580.1910.1910.0000.0000.0000.000
169A172SER0-0.043-0.03338.005-0.186-0.1860.0000.0000.0000.000
170A173ALA0-0.001-0.00240.488-0.057-0.0570.0000.0000.0000.000
171A174GLU-1-0.850-0.90641.530-6.979-6.9790.0000.0000.0000.000
172A175GLY0-0.057-0.02342.4650.1150.1150.0000.0000.0000.000
173A176GLU-1-0.927-0.97943.517-6.603-6.6030.0000.0000.0000.000
174A177GLU-1-0.881-0.93940.676-7.678-7.6780.0000.0000.0000.000
175A178LYS10.9620.97837.7947.9817.9810.0000.0000.0000.000
176A179PRO0-0.003-0.00938.272-0.213-0.2130.0000.0000.0000.000
177A180PHE0-0.044-0.01729.408-0.135-0.1350.0000.0000.0000.000
178A181ILE00.0140.00431.2910.0490.0490.0000.0000.0000.000
179A182SER0-0.019-0.00326.3130.1000.1000.0000.0000.0000.000
180A183GLY00.0030.01126.563-0.153-0.1530.0000.0000.0000.000
181A184TYR0-0.008-0.03720.917-0.206-0.2060.0000.0000.0000.000
182A185SER0-0.003-0.01419.0650.3910.3910.0000.0000.0000.000
183A186ASN0-0.038-0.00815.9980.5430.5430.0000.0000.0000.000
184A187SER0-0.012-0.00518.731-0.053-0.0530.0000.0000.0000.000
185A188ARG10.9500.96316.26714.71614.7160.0000.0000.0000.000
186A189LEU00.0420.03115.434-0.297-0.2970.0000.0000.0000.000
187A190PRO00.0260.0229.979-0.202-0.2020.0000.0000.0000.000
188A191ASN00.022-0.00411.0930.2800.2800.0000.0000.0000.000
189A192ILE00.0160.0099.033-1.969-1.9690.0000.0000.0000.000
190A193TRP00.0310.0129.989-1.257-1.2570.0000.0000.0000.000
191A194ASP-1-0.852-0.9059.518-23.673-23.6730.0000.0000.0000.000
192A195LEU00.020-0.0088.167-2.499-2.4990.0000.0000.0000.000
193A196SER0-0.069-0.0178.661-0.843-0.8430.0000.0000.0000.000