FMODB

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

Last updated: 2026-04-18

All entries: 88827

Number of unique PDB entries: 32070

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FMODB ID: 2RGVR

Calculation Name: 4PDB-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PDB

Chain ID: A

ChEMBL ID:

UniProt ID: Q81VR6

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 129
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1117171.829862
FMO2-HF: Nuclear repulsion 1066798.995359
FMO2-HF: Total energy -50372.834503
FMO2-MP2: Total energy -50521.348633


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:27:THR)


Summations of interaction energy for fragment #1(A:27:THR)
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.
143.739147.0940.028-1.353-2.0290
Interaction energy analysis for fragmet #1(A:27:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.870 / q_NPA : 0.927
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].
3A29PRO00.0650.0323.2824.6467.4490.030-1.257-1.5760.000
4A30ILE00.0140.0275.5543.8613.956-0.001-0.004-0.0900.000
6A32ASP-1-0.876-0.9324.271-45.323-45.0500.000-0.048-0.2240.000
80A106PRO0-0.032-0.0264.4112.7822.966-0.001-0.044-0.1390.000
5A31ALA00.0050.0065.9563.1663.1660.0000.0000.0000.000
7A33MET0-0.026-0.0027.2743.1123.1120.0000.0000.0000.000
8A34LEU00.011-0.00810.7031.7611.7610.0000.0000.0000.000
9A35THR0-0.019-0.0189.3322.1232.1230.0000.0000.0000.000
10A36ARG10.9070.9538.88625.44725.4470.0000.0000.0000.000
11A37ILE00.0270.01613.3091.2751.2750.0000.0000.0000.000
12A38ARG10.8930.94611.61022.74422.7440.0000.0000.0000.000
13A39ASN00.006-0.01013.3381.0981.0980.0000.0000.0000.000
14A40ALA00.0360.01516.8300.8850.8850.0000.0000.0000.000
15A41ASN00.0280.00919.1251.2551.2550.0000.0000.0000.000
16A42MET0-0.044-0.00719.3610.5080.5080.0000.0000.0000.000
17A43VAL0-0.0130.00220.4090.6840.6840.0000.0000.0000.000
18A44ARG10.8970.94623.11311.07011.0700.0000.0000.0000.000
19A45HIS0-0.017-0.00221.3650.1400.1400.0000.0000.0000.000
20A46GLU-1-0.841-0.92223.980-11.276-11.2760.0000.0000.0000.000
21A47LYS10.9290.96522.02511.76011.7600.0000.0000.0000.000
22A48LEU0-0.0270.00015.262-0.328-0.3280.0000.0000.0000.000
23A49GLU-1-0.771-0.87416.155-14.334-14.3340.0000.0000.0000.000
24A50VAL0-0.055-0.02811.252-1.527-1.5270.0000.0000.0000.000
25A51PRO00.0500.0358.5430.8840.8840.0000.0000.0000.000
26A52ALA00.0080.02111.265-1.106-1.1060.0000.0000.0000.000
27A53SER00.016-0.00810.522-0.879-0.8790.0000.0000.0000.000
28A54LYS10.9430.97112.87816.26716.2670.0000.0000.0000.000
29A55ILE00.0860.04611.1360.2550.2550.0000.0000.0000.000
30A56LYS10.8360.9148.24626.54426.5440.0000.0000.0000.000
31A57LYS10.9841.00113.59815.42615.4260.0000.0000.0000.000
32A58GLU-1-0.850-0.93717.184-16.312-16.3120.0000.0000.0000.000
33A59ILE0-0.005-0.00813.4330.4100.4100.0000.0000.0000.000
34A60ALA00.0150.01117.1470.5470.5470.0000.0000.0000.000
35A61GLU-1-0.880-0.96018.775-12.926-12.9260.0000.0000.0000.000
36A62LEU0-0.073-0.01420.4810.6820.6820.0000.0000.0000.000
37A63LEU00.0110.00317.9330.4630.4630.0000.0000.0000.000
38A64LYS10.8660.92822.22411.66011.6600.0000.0000.0000.000
39A65ARG10.8850.94123.66412.62612.6260.0000.0000.0000.000
40A66GLU-1-0.894-0.95924.853-11.126-11.1260.0000.0000.0000.000
41A67GLY0-0.0310.00526.9140.1610.1610.0000.0000.0000.000
42A68PHE00.0530.01222.8160.1200.1200.0000.0000.0000.000
43A69ILE0-0.065-0.02720.569-0.220-0.2200.0000.0000.0000.000
44A70ARG10.9140.96424.07911.02711.0270.0000.0000.0000.000
45A71ASP-1-0.835-0.92424.715-11.014-11.0140.0000.0000.0000.000
46A72VAL0-0.041-0.02218.981-0.651-0.6510.0000.0000.0000.000
47A73GLU-1-0.829-0.88821.424-11.493-11.4930.0000.0000.0000.000
48A74TYR0-0.088-0.05617.249-1.221-1.2210.0000.0000.0000.000
49A75ILE0-0.021-0.01119.4060.6450.6450.0000.0000.0000.000
50A76GLU-1-0.844-0.92419.198-13.918-13.9180.0000.0000.0000.000
51A77ASP-1-0.773-0.89115.872-16.167-16.1670.0000.0000.0000.000
52A78ASN0-0.044-0.03019.5390.1920.1920.0000.0000.0000.000
53A79LYS10.8720.94114.31814.40614.4060.0000.0000.0000.000
54A80GLN0-0.057-0.0399.161-1.171-1.1710.0000.0000.0000.000
55A81GLY00.0710.05514.470-0.097-0.0970.0000.0000.0000.000
56A82ILE0-0.043-0.02513.939-1.604-1.6040.0000.0000.0000.000
57A83LEU0-0.030-0.01314.7240.7450.7450.0000.0000.0000.000
58A84ARG10.7930.88016.45312.33212.3320.0000.0000.0000.000
59A85ILE0-0.017-0.01216.0500.3080.3080.0000.0000.0000.000
60A86PHE00.011-0.00319.942-0.128-0.1280.0000.0000.0000.000
61A87LEU0-0.014-0.00519.769-0.078-0.0780.0000.0000.0000.000
62A88LYS10.8810.92423.75011.09411.0940.0000.0000.0000.000
63A89TYR0-0.040-0.03624.009-0.330-0.3300.0000.0000.0000.000
64A90GLY00.0290.01529.2200.2220.2220.0000.0000.0000.000
65A91ALA0-0.014-0.01232.3840.0280.0280.0000.0000.0000.000
66A92ASN00.0310.01035.2670.0360.0360.0000.0000.0000.000
67A93ASN0-0.020-0.01231.038-0.309-0.3090.0000.0000.0000.000
68A94GLU-1-0.916-0.93529.808-9.932-9.9320.0000.0000.0000.000
69A95ARG10.8290.89823.85912.16512.1650.0000.0000.0000.000
70A96VAL00.0170.01626.6790.0710.0710.0000.0000.0000.000
71A97ILE0-0.0360.00320.059-0.232-0.2320.0000.0000.0000.000
72A98THR00.003-0.01523.5180.1780.1780.0000.0000.0000.000
73A99GLY0-0.065-0.04719.663-0.308-0.3080.0000.0000.0000.000
74A100LEU00.0270.02015.435-0.061-0.0610.0000.0000.0000.000
75A101LYS10.9040.96114.58117.22317.2230.0000.0000.0000.000
76A102ARG10.8190.8878.13232.34832.3480.0000.0000.0000.000
77A103ILE0-0.040-0.01312.2240.4670.4670.0000.0000.0000.000
78A104SER0-0.050-0.03612.322-1.059-1.0590.0000.0000.0000.000
79A105LYS10.9580.9637.03830.11230.1120.0000.0000.0000.000
81A107GLY0-0.016-0.0016.731-1.404-1.4040.0000.0000.0000.000
82A108LEU0-0.006-0.0018.6962.6322.6320.0000.0000.0000.000
83A109ARG10.8860.9508.15028.46728.4670.0000.0000.0000.000
84A110VAL00.0250.01012.9591.1571.1570.0000.0000.0000.000
85A111TYR00.008-0.00415.001-0.488-0.4880.0000.0000.0000.000
86A112ALA00.0170.02119.0390.2960.2960.0000.0000.0000.000
87A113LYS10.9930.99122.51111.08611.0860.0000.0000.0000.000
88A114ALA00.0290.00426.076-0.168-0.1680.0000.0000.0000.000
89A115ASP-1-0.882-0.94828.378-10.513-10.5130.0000.0000.0000.000
90A116GLU-1-0.939-0.95925.448-11.257-11.2570.0000.0000.0000.000
91A117VAL0-0.064-0.01523.492-0.647-0.6470.0000.0000.0000.000
92A118PRO00.0230.00821.1220.4120.4120.0000.0000.0000.000
93A119ARG10.9760.98824.24910.34810.3480.0000.0000.0000.000
94A120VAL0-0.0050.00621.824-0.166-0.1660.0000.0000.0000.000
95A121LEU00.0350.00924.7910.3220.3220.0000.0000.0000.000
96A122ASN0-0.016-0.01927.5790.1260.1260.0000.0000.0000.000
97A123GLY0-0.0120.00328.6390.3480.3480.0000.0000.0000.000
98A124LEU0-0.0100.00329.4770.1310.1310.0000.0000.0000.000
99A125GLY0-0.0120.00524.969-0.143-0.1430.0000.0000.0000.000
100A126ILE00.0020.00421.8320.1880.1880.0000.0000.0000.000
101A127ALA0-0.020-0.02120.605-0.754-0.7540.0000.0000.0000.000
102A128LEU0-0.030-0.00817.3030.3780.3780.0000.0000.0000.000
103A129VAL00.006-0.00818.452-1.005-1.0050.0000.0000.0000.000
104A130SER0-0.015-0.00116.3170.6810.6810.0000.0000.0000.000
105A131THR00.0550.01518.6390.1790.1790.0000.0000.0000.000
106A132SER0-0.010-0.00521.296-0.169-0.1690.0000.0000.0000.000
107A133LYS10.8940.93123.28311.76711.7670.0000.0000.0000.000
108A134GLY00.0590.04720.9480.2520.2520.0000.0000.0000.000
109A135VAL0-0.025-0.01717.005-0.140-0.1400.0000.0000.0000.000
110A136MET0-0.0430.00420.2910.6630.6630.0000.0000.0000.000
111A137THR00.0340.00322.298-0.603-0.6030.0000.0000.0000.000
112A138ASP-1-0.735-0.87423.900-12.051-12.0510.0000.0000.0000.000
113A139LYS10.9220.97125.35410.16110.1610.0000.0000.0000.000
114A140ASP-1-0.782-0.88326.660-11.170-11.1700.0000.0000.0000.000
115A141ALA0-0.016-0.01424.9220.2630.2630.0000.0000.0000.000
116A142ARG10.7510.85726.71111.84711.8470.0000.0000.0000.000
117A143GLN0-0.052-0.02130.0200.2350.2350.0000.0000.0000.000
118A144LEU0-0.024-0.02828.1900.3110.3110.0000.0000.0000.000
119A145GLN0-0.045-0.00631.1610.1360.1360.0000.0000.0000.000
120A146THR0-0.027-0.01525.176-0.005-0.0050.0000.0000.0000.000
121A147GLY00.0300.01324.951-0.068-0.0680.0000.0000.0000.000
122A148GLY0-0.004-0.01921.0110.0810.0810.0000.0000.0000.000
123A149GLU-1-0.852-0.87312.726-24.384-24.3840.0000.0000.0000.000
124A150VAL00.0300.00917.2080.2380.2380.0000.0000.0000.000
125A151VAL0-0.002-0.00413.098-1.528-1.5280.0000.0000.0000.000
126A152ALA0-0.001-0.02113.387-2.070-2.0700.0000.0000.0000.000
127A153TYR00.0020.00515.6951.0771.0770.0000.0000.0000.000
128A154VAL00.001-0.01217.766-1.047-1.0470.0000.0000.0000.000
129A155TRP-1-0.729-0.81918.666-13.094-13.0940.0000.0000.0000.000