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: 2R4ZR

Calculation Name: 3VPR-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3VPR

Chain ID: B

ChEMBL ID:

UniProt ID: Q53WD9

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 187
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2013777.195138
FMO2-HF: Nuclear repulsion 1939546.117725
FMO2-HF: Total energy -74231.077413
FMO2-MP2: Total energy -74449.485147


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:3:THR)


Summations of interaction energy for fragment #1(A:3: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.
-13.078-10.120.223-1.18-2.003-0.007
Interaction energy analysis for fragmet #1(A:3:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.874 / q_NPA : 0.920
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].
3A5ARG10.8350.8723.55321.34622.5560.000-0.587-0.624-0.001
5A7ARG10.9740.9813.23646.68847.4120.023-0.203-0.545-0.001
6A8ILE0-0.026-0.0032.487-0.6500.3090.201-0.387-0.773-0.005
33A35LEU0-0.051-0.0284.389-1.857-1.792-0.001-0.003-0.0610.000
4A6ASP-1-0.850-0.9266.010-34.006-34.0060.0000.0000.0000.000
7A9LEU0-0.021-0.0065.6265.2795.2790.0000.0000.0000.000
8A10GLU-1-0.876-0.9328.205-26.600-26.6000.0000.0000.0000.000
9A11GLU-1-0.858-0.9237.059-27.615-27.6150.0000.0000.0000.000
10A12ALA0-0.019-0.0059.3632.8332.8330.0000.0000.0000.000
11A13ALA00.0060.00511.3622.2802.2800.0000.0000.0000.000
12A14LYS10.8010.90510.32728.36328.3630.0000.0000.0000.000
13A15LEU00.0700.03513.3301.6061.6060.0000.0000.0000.000
14A16PHE0-0.026-0.03614.1981.3051.3050.0000.0000.0000.000
15A17THR0-0.042-0.03317.0521.4671.4670.0000.0000.0000.000
16A18GLU-1-0.981-0.98416.340-17.855-17.8550.0000.0000.0000.000
17A19LYS10.8010.89018.52816.19016.1900.0000.0000.0000.000
18A20GLY00.0350.03120.4440.7070.7070.0000.0000.0000.000
19A21TYR0-0.033-0.03517.268-0.220-0.2200.0000.0000.0000.000
20A22GLU-1-0.921-0.96719.999-13.682-13.6820.0000.0000.0000.000
21A23ALA0-0.0020.00522.232-0.094-0.0940.0000.0000.0000.000
22A24THR0-0.0040.01015.747-0.417-0.4170.0000.0000.0000.000
23A25SER0-0.033-0.05118.411-0.018-0.0180.0000.0000.0000.000
24A26VAL00.024-0.01914.260-0.840-0.8400.0000.0000.0000.000
25A27GLN00.006-0.00414.162-2.095-2.0950.0000.0000.0000.000
26A28ASP-1-0.757-0.83714.640-17.269-17.2690.0000.0000.0000.000
27A29LEU00.0340.02111.447-1.118-1.1180.0000.0000.0000.000
28A30ALA0-0.046-0.01910.247-2.434-2.4340.0000.0000.0000.000
29A31GLN0-0.021-0.01810.082-1.847-1.8470.0000.0000.0000.000
30A32ALA00.0130.01411.287-0.779-0.7790.0000.0000.0000.000
31A33LEU0-0.037-0.0166.185-1.810-1.8100.0000.0000.0000.000
32A34GLY0-0.0020.0185.842-7.147-7.1470.0000.0000.0000.000
34A36SER00.0410.0198.3742.9372.9370.0000.0000.0000.000
35A37LYS10.9650.96211.09815.89415.8940.0000.0000.0000.000
36A38ALA0-0.0230.01013.5100.0170.0170.0000.0000.0000.000
37A39ALA00.0430.0238.5790.0990.0990.0000.0000.0000.000
38A40LEU00.0250.0148.758-1.160-1.1600.0000.0000.0000.000
39A41TYR00.011-0.01410.2990.6250.6250.0000.0000.0000.000
40A42HIS0-0.038-0.03111.9160.8250.8250.0000.0000.0000.000
41A43HIS0-0.0020.0207.236-1.435-1.4350.0000.0000.0000.000
42A44PHE00.0400.0156.651-0.762-0.7620.0000.0000.0000.000
43A45GLY00.0240.04312.1061.4801.4800.0000.0000.0000.000
44A46SER0-0.058-0.05215.1971.1441.1440.0000.0000.0000.000
45A47LYS10.8850.93314.89314.36314.3630.0000.0000.0000.000
46A48GLU-1-0.801-0.86016.455-15.493-15.4930.0000.0000.0000.000
47A49GLU-1-0.836-0.91813.832-19.367-19.3670.0000.0000.0000.000
48A50ILE0-0.011-0.01011.064-0.506-0.5060.0000.0000.0000.000
49A51LEU00.0140.02213.275-0.382-0.3820.0000.0000.0000.000
50A52TYR00.0040.01116.4680.7330.7330.0000.0000.0000.000
51A53GLU-1-0.761-0.86611.701-26.370-26.3700.0000.0000.0000.000
52A54ILE0-0.0080.00612.4790.0830.0830.0000.0000.0000.000
53A55SER0-0.018-0.03714.7560.9960.9960.0000.0000.0000.000
54A56LEU0-0.054-0.02516.8520.8900.8900.0000.0000.0000.000
55A57LEU00.0190.00611.4530.7240.7240.0000.0000.0000.000
56A58ALA0-0.0050.01116.1070.6470.6470.0000.0000.0000.000
57A59LEU0-0.009-0.01918.5960.8010.8010.0000.0000.0000.000
58A60LYS10.9350.96918.22317.51117.5110.0000.0000.0000.000
59A61GLY00.0250.02519.3360.4590.4590.0000.0000.0000.000
60A62LEU0-0.0040.00620.1890.5340.5340.0000.0000.0000.000
61A63VAL00.0020.00023.2130.5650.5650.0000.0000.0000.000
62A64ALA00.0030.00222.3650.4810.4810.0000.0000.0000.000
63A65ALA0-0.045-0.02223.4800.3860.3860.0000.0000.0000.000
64A66GLY00.0110.00125.2430.4190.4190.0000.0000.0000.000
65A67GLU-1-0.878-0.93827.877-10.702-10.7020.0000.0000.0000.000
66A68LYS10.9110.96324.51112.75912.7590.0000.0000.0000.000
67A69ALA0-0.044-0.02428.9220.1800.1800.0000.0000.0000.000
68A70LEU0-0.0020.00032.1060.3640.3640.0000.0000.0000.000
69A71GLU-1-0.904-0.96132.726-9.012-9.0120.0000.0000.0000.000
70A72VAL0-0.084-0.02534.0560.2060.2060.0000.0000.0000.000
71A73ALA00.0600.02836.6970.1490.1490.0000.0000.0000.000
72A74ASP-1-0.823-0.92440.427-7.374-7.3740.0000.0000.0000.000
73A75PRO00.0430.02939.961-0.230-0.2300.0000.0000.0000.000
74A76LYS10.9650.99039.7386.9856.9850.0000.0000.0000.000
75A77GLU-1-0.774-0.85436.312-8.909-8.9090.0000.0000.0000.000
76A78ALA0-0.015-0.00335.656-0.306-0.3060.0000.0000.0000.000
77A79LEU00.0140.00634.757-0.328-0.3280.0000.0000.0000.000
78A80ARG10.7590.83934.4598.7668.7660.0000.0000.0000.000
79A81ARG10.9200.95729.8819.7539.7530.0000.0000.0000.000
80A82PHE00.0250.02230.484-0.436-0.4360.0000.0000.0000.000
81A83MET0-0.048-0.01230.002-0.282-0.2820.0000.0000.0000.000
82A84GLU-1-0.782-0.88630.148-9.830-9.8300.0000.0000.0000.000
83A85ALA0-0.0120.00026.482-0.430-0.4300.0000.0000.0000.000
84A86HIS00.0200.02425.361-0.510-0.5100.0000.0000.0000.000
85A87ALA00.017-0.00225.324-0.464-0.4640.0000.0000.0000.000
86A88ARG10.8250.91523.22812.15412.1540.0000.0000.0000.000
87A89TYR00.0010.01017.596-0.670-0.6700.0000.0000.0000.000
88A90PHE0-0.018-0.01720.523-0.793-0.7930.0000.0000.0000.000
89A91GLU-1-0.789-0.88521.441-12.780-12.7800.0000.0000.0000.000
90A92GLU-1-0.938-0.98418.390-15.474-15.4740.0000.0000.0000.000
91A93ASN0-0.049-0.02615.868-2.193-2.1930.0000.0000.0000.000
92A94TYR00.0140.02517.490-0.336-0.3360.0000.0000.0000.000
93A95PRO00.0490.01015.0370.4740.4740.0000.0000.0000.000
94A96PHE00.0080.01411.180-0.027-0.0270.0000.0000.0000.000
95A97PHE0-0.008-0.00316.7550.6090.6090.0000.0000.0000.000
96A98VAL00.0130.00820.1520.6470.6470.0000.0000.0000.000
97A99THR0-0.012-0.01516.2790.2620.2620.0000.0000.0000.000
98A100MET0-0.0040.01319.1670.5850.5850.0000.0000.0000.000
99A101LEU0-0.078-0.03920.8820.6570.6570.0000.0000.0000.000
100A102GLN0-0.012-0.00621.4370.7300.7300.0000.0000.0000.000
101A103GLY00.0640.04021.6310.1800.1800.0000.0000.0000.000
102A104ILE0-0.044-0.02422.6790.1960.1960.0000.0000.0000.000
103A105LYS10.9220.94125.08510.35210.3520.0000.0000.0000.000
104A106SER00.0150.01022.8070.5100.5100.0000.0000.0000.000
105A107LEU0-0.0220.01820.187-0.244-0.2440.0000.0000.0000.000
106A108SER00.0190.00722.7010.9730.9730.0000.0000.0000.000
107A109PRO00.000-0.02024.6210.0260.0260.0000.0000.0000.000
108A110GLU-1-0.899-0.94424.232-12.502-12.5020.0000.0000.0000.000
109A111ASN00.0250.00720.3370.2310.2310.0000.0000.0000.000
110A112ARG10.8740.93923.56111.18711.1870.0000.0000.0000.000
111A113LEU00.0260.01226.2820.1500.1500.0000.0000.0000.000
112A114LYS10.9380.97222.86513.26113.2610.0000.0000.0000.000
113A115THR0-0.018-0.02623.184-0.246-0.2460.0000.0000.0000.000
114A116ILE0-0.048-0.01624.9940.0630.0630.0000.0000.0000.000
115A117ALA00.0330.01827.9640.0970.0970.0000.0000.0000.000
116A118LEU0-0.021-0.01022.4220.0790.0790.0000.0000.0000.000
117A119ARG10.9090.94324.41512.25512.2550.0000.0000.0000.000
118A120ASP-1-0.859-0.92828.475-9.659-9.6590.0000.0000.0000.000
119A121ARG10.8890.95528.46410.37610.3760.0000.0000.0000.000
120A122HIS00.022-0.00527.6750.1600.1600.0000.0000.0000.000
121A123GLU-1-0.775-0.86029.818-8.708-8.7080.0000.0000.0000.000
122A124GLU-1-0.891-0.95433.278-8.307-8.3070.0000.0000.0000.000
123A125ASN0-0.050-0.03029.8700.4760.4760.0000.0000.0000.000
124A126LEU0-0.0040.01633.4390.2180.2180.0000.0000.0000.000
125A127ARG10.8300.88735.0038.8308.8300.0000.0000.0000.000
126A128ALA0-0.035-0.01136.5910.2740.2740.0000.0000.0000.000
127A129ILE0-0.0060.00334.0100.2160.2160.0000.0000.0000.000
128A130LEU0-0.025-0.01538.3720.2270.2270.0000.0000.0000.000
129A131ARG10.9420.97739.3728.1348.1340.0000.0000.0000.000
130A132ARG10.8790.95338.4208.2358.2350.0000.0000.0000.000
131A133GLY00.010-0.02042.6760.1420.1420.0000.0000.0000.000
132A134VAL0-0.035-0.00544.1650.1440.1440.0000.0000.0000.000
133A135GLU-1-0.912-0.95845.300-6.991-6.9910.0000.0000.0000.000
134A136GLN0-0.052-0.03444.4680.0060.0060.0000.0000.0000.000
135A137GLY00.0120.00748.4790.0560.0560.0000.0000.0000.000
136A138VAL0-0.091-0.03744.7780.0480.0480.0000.0000.0000.000
137A139PHE0-0.071-0.03241.002-0.078-0.0780.0000.0000.0000.000
138A140ARG11.0020.99947.0576.5216.5210.0000.0000.0000.000
139A141GLU-1-0.908-0.95648.325-6.301-6.3010.0000.0000.0000.000
140A142VAL0-0.049-0.03345.3500.0750.0750.0000.0000.0000.000
141A143ASP-1-0.817-0.89944.597-7.240-7.2400.0000.0000.0000.000
142A144VAL00.0430.01141.249-0.142-0.1420.0000.0000.0000.000
143A145ALA0-0.0200.00140.335-0.252-0.2520.0000.0000.0000.000
144A146LEU0-0.018-0.02139.976-0.241-0.2410.0000.0000.0000.000
145A147ALA00.0130.01341.010-0.128-0.1280.0000.0000.0000.000
146A148GLY00.0510.01337.567-0.165-0.1650.0000.0000.0000.000
147A149ARG10.8200.88536.0728.5368.5360.0000.0000.0000.000
148A150ALA00.0230.02636.803-0.194-0.1940.0000.0000.0000.000
149A151VAL00.0330.01634.335-0.158-0.1580.0000.0000.0000.000
150A152LEU00.015-0.00730.716-0.301-0.3010.0000.0000.0000.000
151A153SER0-0.090-0.05232.393-0.281-0.2810.0000.0000.0000.000
152A154MET0-0.039-0.01633.839-0.142-0.1420.0000.0000.0000.000
153A155LEU00.0160.01029.929-0.174-0.1740.0000.0000.0000.000
154A156ASN0-0.010-0.01628.323-0.681-0.6810.0000.0000.0000.000
155A157TRP00.003-0.00329.167-0.355-0.3550.0000.0000.0000.000
156A158MET0-0.0130.01828.5710.0100.0100.0000.0000.0000.000
157A159ILE00.001-0.00124.808-0.140-0.1400.0000.0000.0000.000
158A160ARG10.8670.93327.11310.23110.2310.0000.0000.0000.000
159A161TRP0-0.027-0.00529.7830.1300.1300.0000.0000.0000.000
160A162PHE0-0.0230.00924.9500.1070.1070.0000.0000.0000.000
161A163ARG10.9560.96326.60511.13011.1300.0000.0000.0000.000
162A164PRO00.0200.00521.9280.2080.2080.0000.0000.0000.000
163A165ASP-1-0.923-0.95224.095-12.078-12.0780.0000.0000.0000.000
164A166GLY0-0.0030.01325.7650.4710.4710.0000.0000.0000.000
165A167PRO0-0.010-0.01928.795-0.163-0.1630.0000.0000.0000.000
166A168MET0-0.025-0.00231.1010.0620.0620.0000.0000.0000.000
167A169ARG10.8340.89925.79911.36011.3600.0000.0000.0000.000
168A170ALA00.003-0.01326.3800.4320.4320.0000.0000.0000.000
169A171GLU-1-0.781-0.87627.829-10.669-10.6690.0000.0000.0000.000
170A172GLU-1-0.871-0.93329.497-9.531-9.5310.0000.0000.0000.000
171A173VAL0-0.0060.00231.5890.3390.3390.0000.0000.0000.000
172A174ALA00.0070.00231.1050.2740.2740.0000.0000.0000.000
173A175ARG10.8290.89431.9849.8429.8420.0000.0000.0000.000
174A176ALA0-0.0050.00135.3440.2750.2750.0000.0000.0000.000
175A177TYR00.004-0.02133.2680.1380.1380.0000.0000.0000.000
176A178HIS0-0.031-0.01636.3920.1850.1850.0000.0000.0000.000
177A179ASP-1-0.858-0.91738.183-7.220-7.2200.0000.0000.0000.000
178A180LEU00.0110.00840.6580.1720.1720.0000.0000.0000.000
179A181ILE0-0.061-0.03738.9160.1610.1610.0000.0000.0000.000
180A182LEU0-0.071-0.02741.9470.1150.1150.0000.0000.0000.000
181A183ARG10.8660.91443.2047.3367.3360.0000.0000.0000.000
182A184GLY00.0090.02645.4230.1640.1640.0000.0000.0000.000
183A185LEU0-0.033-0.04045.895-0.055-0.0550.0000.0000.0000.000
184A186GLU-1-0.957-0.95648.825-5.873-5.8730.0000.0000.0000.000
185A187ARG10.9530.95751.6715.7205.7200.0000.0000.0000.000
186A188GLY0-0.040-0.01254.3040.1080.1080.0000.0000.0000.000
187A189SER-1-0.953-0.96552.198-6.106-6.1060.0000.0000.0000.000