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: Z73QN

Calculation Name: 2DRV-B-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DRV

Chain ID: B

ChEMBL ID:

UniProt ID: O58796

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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2252943.300727
FMO2-HF: Nuclear repulsion 2172406.74316
FMO2-HF: Total energy -80536.557566
FMO2-MP2: Total energy -80770.162882


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
108.389111.4472.436-1.957-3.538-0.017
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.878 / q_NPA : 0.932
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].
3A3LEU00.0050.0042.381-3.674-0.9552.438-1.851-3.306-0.017
4A4TYR00.0620.0144.7962.3432.501-0.001-0.015-0.1420.000
140A140ASN00.034-0.0013.9654.4214.602-0.001-0.091-0.0900.000
5A5MET00.0520.0287.9250.5180.5180.0000.0000.0000.000
6A6ARG10.9260.9677.32030.84830.8480.0000.0000.0000.000
7A7PHE0-0.046-0.00910.1210.8920.8920.0000.0000.0000.000
8A8THR0-0.024-0.02712.7351.3431.3430.0000.0000.0000.000
9A9GLU-1-0.908-0.94810.622-23.879-23.8790.0000.0000.0000.000
10A10ASN0-0.044-0.03311.7102.1822.1820.0000.0000.0000.000
11A11PHE00.0080.01915.3690.6810.6810.0000.0000.0000.000
12A12GLU-1-0.803-0.89918.081-13.081-13.0810.0000.0000.0000.000
13A13ARG10.8790.92516.90617.75417.7540.0000.0000.0000.000
14A14ALA00.0180.00216.4360.3730.3730.0000.0000.0000.000
15A15LYS10.8350.92818.48212.96912.9690.0000.0000.0000.000
16A16LYS10.8710.93022.05013.77513.7750.0000.0000.0000.000
17A17GLU-1-0.860-0.92117.899-17.115-17.1150.0000.0000.0000.000
18A18ALA0-0.037-0.00821.1940.3480.3480.0000.0000.0000.000
19A19LEU00.0020.00122.7810.5320.5320.0000.0000.0000.000
20A20MET00.0120.01123.7280.5290.5290.0000.0000.0000.000
21A21SER0-0.032-0.02723.2070.2890.2890.0000.0000.0000.000
22A22LEU0-0.033-0.01425.7660.3480.3480.0000.0000.0000.000
23A23GLU-1-0.927-0.96428.115-9.651-9.6510.0000.0000.0000.000
24A24ILE0-0.052-0.02828.1180.4370.4370.0000.0000.0000.000
25A25ALA00.0560.03528.7140.3030.3030.0000.0000.0000.000
26A26LEU0-0.052-0.03530.7980.3770.3770.0000.0000.0000.000
27A27ARG10.9080.95032.5379.8789.8780.0000.0000.0000.000
28A28LYS10.8200.91030.86210.48110.4810.0000.0000.0000.000
29A29GLY0-0.0010.01735.5360.1450.1450.0000.0000.0000.000
30A30GLU-1-0.850-0.92230.925-10.306-10.3060.0000.0000.0000.000
31A31VAL0-0.068-0.03130.071-0.355-0.3550.0000.0000.0000.000
32A32ASP-1-0.757-0.86532.210-9.538-9.5380.0000.0000.0000.000
33A33GLU-1-0.725-0.85734.128-8.468-8.4680.0000.0000.0000.000
34A34ASP-1-0.861-0.94236.244-8.583-8.5830.0000.0000.0000.000
35A35ILE00.001-0.00330.3190.0010.0010.0000.0000.0000.000
36A36ILE0-0.0050.01733.114-0.271-0.2710.0000.0000.0000.000
37A37PRO0-0.017-0.00634.166-0.184-0.1840.0000.0000.0000.000
38A38LEU00.0560.03231.061-0.208-0.2080.0000.0000.0000.000
39A39LEU00.004-0.00327.769-0.326-0.3260.0000.0000.0000.000
40A40LYS10.9580.98729.8298.6618.6610.0000.0000.0000.000
41A41LYS10.9370.98031.8849.2979.2970.0000.0000.0000.000
42A42ILE00.0040.00926.238-0.129-0.1290.0000.0000.0000.000
43A43ASN0-0.025-0.04226.410-0.698-0.6980.0000.0000.0000.000
44A44SER0-0.074-0.04028.4100.0010.0010.0000.0000.0000.000
45A45ILE00.0210.02627.8510.1780.1780.0000.0000.0000.000
46A46GLU-1-0.899-0.95025.597-12.154-12.1540.0000.0000.0000.000
47A47ASN0-0.017-0.03522.796-0.513-0.5130.0000.0000.0000.000
48A48TYR0-0.023-0.04322.393-0.728-0.7280.0000.0000.0000.000
49A49PHE00.0190.02017.7790.1320.1320.0000.0000.0000.000
50A50THR00.0010.02022.704-0.298-0.2980.0000.0000.0000.000
51A51THR0-0.042-0.03819.150-0.434-0.4340.0000.0000.0000.000
52A52SER00.0300.01022.1360.5500.5500.0000.0000.0000.000
53A53SER0-0.023-0.01723.504-0.382-0.3820.0000.0000.0000.000
54A54CYS0-0.065-0.01526.3050.3060.3060.0000.0000.0000.000
55A55SER0-0.010-0.04129.504-0.026-0.0260.0000.0000.0000.000
56A56GLY00.0290.02231.7650.2540.2540.0000.0000.0000.000
57A57ARG10.8960.93529.31510.29710.2970.0000.0000.0000.000
58A58ILE00.0700.04735.141-0.126-0.1260.0000.0000.0000.000
59A59SER0-0.085-0.06535.404-0.259-0.2590.0000.0000.0000.000
60A60VAL00.0580.05137.6950.0260.0260.0000.0000.0000.000
61A61MET0-0.039-0.01732.890-0.018-0.0180.0000.0000.0000.000
62A62GLU-1-0.674-0.81337.812-7.593-7.5930.0000.0000.0000.000
63A63MET00.0010.00933.132-0.340-0.3400.0000.0000.0000.000
64A64PRO00.0050.01433.5350.1880.1880.0000.0000.0000.000
65A65HIS00.0610.02433.215-0.013-0.0130.0000.0000.0000.000
66A66PHE0-0.0170.00132.568-0.361-0.3610.0000.0000.0000.000
67A67GLY0-0.001-0.00129.680-0.178-0.1780.0000.0000.0000.000
68A68ASP-1-0.878-0.92728.243-11.463-11.4630.0000.0000.0000.000
69A69LYS10.9290.93524.77912.31312.3130.0000.0000.0000.000
70A70VAL0-0.040-0.00624.708-0.048-0.0480.0000.0000.0000.000
71A71ASN0-0.051-0.03227.6800.3080.3080.0000.0000.0000.000
72A72ALA0-0.0030.00331.0220.3730.3730.0000.0000.0000.000
73A73LYS10.8790.94032.9297.7437.7430.0000.0000.0000.000
74A74TRP0-0.053-0.04030.2300.0560.0560.0000.0000.0000.000
75A75LEU0-0.0290.00037.1150.0820.0820.0000.0000.0000.000
76A76GLY00.0220.00240.1060.2420.2420.0000.0000.0000.000
77A77LYS10.9010.95131.6269.4759.4750.0000.0000.0000.000
78A78TRP00.0360.02837.948-0.063-0.0630.0000.0000.0000.000
79A79HIS0-0.049-0.03335.455-0.073-0.0730.0000.0000.0000.000
80A80ARG10.8500.90537.1927.7917.7910.0000.0000.0000.000
81A81GLU-1-0.890-0.95540.709-7.241-7.2410.0000.0000.0000.000
82A82VAL0-0.029-0.01542.2710.0140.0140.0000.0000.0000.000
83A83SER0-0.004-0.03045.0470.1420.1420.0000.0000.0000.000
84A84LEU00.043-0.00147.798-0.112-0.1120.0000.0000.0000.000
85A85TYR0-0.011-0.01149.662-0.040-0.0400.0000.0000.0000.000
86A86GLU-1-0.784-0.86945.599-7.042-7.0420.0000.0000.0000.000
87A87VAL0-0.011-0.00844.187-0.144-0.1440.0000.0000.0000.000
88A88LEU00.0290.01946.208-0.088-0.0880.0000.0000.0000.000
89A89GLU-1-0.861-0.91848.177-6.249-6.2490.0000.0000.0000.000
90A90ALA0-0.073-0.03743.033-0.076-0.0760.0000.0000.0000.000
91A91ILE00.0400.01544.846-0.087-0.0870.0000.0000.0000.000
92A92LYS10.9721.00046.2496.1216.1210.0000.0000.0000.000
93A93LYS10.8240.91444.0417.2777.2770.0000.0000.0000.000
94A94HIS0-0.055-0.01442.193-0.017-0.0170.0000.0000.0000.000
95A95ARG10.7860.87343.5766.8846.8840.0000.0000.0000.000
96A96SER00.0260.02240.9610.0680.0680.0000.0000.0000.000
97A97GLY00.0170.01738.943-0.143-0.1430.0000.0000.0000.000
98A98GLN00.024-0.00437.212-0.046-0.0460.0000.0000.0000.000
99A99LEU0-0.015-0.00238.733-0.219-0.2190.0000.0000.0000.000
100A100TRP00.012-0.01637.0090.0540.0540.0000.0000.0000.000
101A101PHE00.0490.01938.937-0.063-0.0630.0000.0000.0000.000
102A102LEU0-0.088-0.04333.182-0.174-0.1740.0000.0000.0000.000
103A103VAL00.0230.02036.1650.0120.0120.0000.0000.0000.000
104A104ARG10.7490.84230.1859.4809.4800.0000.0000.0000.000
105A105SER00.0890.02829.6810.1520.1520.0000.0000.0000.000
106A106PRO0-0.057-0.00330.260-0.230-0.2300.0000.0000.0000.000
107A107ILE0-0.032-0.00623.805-0.227-0.2270.0000.0000.0000.000
108A108LEU00.0330.02125.3760.0930.0930.0000.0000.0000.000
109A109HIS0-0.051-0.02119.903-0.670-0.6700.0000.0000.0000.000
110A110VAL00.0300.01621.3460.1840.1840.0000.0000.0000.000
111A111GLY0-0.0080.00818.484-0.809-0.8090.0000.0000.0000.000
112A112ALA0-0.002-0.00818.3470.9780.9780.0000.0000.0000.000
113A113LYS10.9520.99817.77714.20114.2010.0000.0000.0000.000
114A114THR0-0.001-0.03416.674-1.063-1.0630.0000.0000.0000.000
115A115LEU00.029-0.00714.779-0.001-0.0010.0000.0000.0000.000
116A116GLU-1-0.885-0.93417.266-12.517-12.5170.0000.0000.0000.000
117A117ASP-1-0.763-0.84920.733-13.811-13.8110.0000.0000.0000.000
118A118ALA00.0010.01018.7750.5280.5280.0000.0000.0000.000
119A119VAL00.0140.00520.0130.4510.4510.0000.0000.0000.000
120A120LYS10.9500.98322.49812.12812.1280.0000.0000.0000.000
121A121LEU00.0310.02323.4260.5030.5030.0000.0000.0000.000
122A122VAL0-0.024-0.01021.7040.3970.3970.0000.0000.0000.000
123A123ASN00.0190.00025.0180.3390.3390.0000.0000.0000.000
124A124LEU00.0320.03527.8930.4460.4460.0000.0000.0000.000
125A125ALA00.0450.03327.3340.4730.4730.0000.0000.0000.000
126A126VAL0-0.022-0.01327.5400.4310.4310.0000.0000.0000.000
127A127SER0-0.078-0.04630.2380.4400.4400.0000.0000.0000.000
128A128CYS0-0.048-0.02332.4680.4220.4220.0000.0000.0000.000
129A129GLY00.0340.01333.1420.2660.2660.0000.0000.0000.000
130A130PHE0-0.037-0.01928.7860.0450.0450.0000.0000.0000.000
131A131LYS10.9610.98228.7039.4609.4600.0000.0000.0000.000
132A132TYR0-0.032-0.00225.825-0.090-0.0900.0000.0000.0000.000
133A133SER0-0.004-0.01924.476-0.533-0.5330.0000.0000.0000.000
134A134ASN0-0.069-0.03119.726-0.626-0.6260.0000.0000.0000.000
135A135ILE00.0460.01315.398-0.030-0.0300.0000.0000.0000.000
136A136LYS10.8760.95216.00316.20316.2030.0000.0000.0000.000
137A137SER0-0.026-0.02111.454-1.217-1.2170.0000.0000.0000.000
138A138ILE00.0560.02610.1831.2781.2780.0000.0000.0000.000
139A139SER0-0.026-0.0217.609-3.220-3.2200.0000.0000.0000.000
141A141LYS10.9590.9838.17631.26331.2630.0000.0000.0000.000
142A142LYS11.0091.00011.48823.26723.2670.0000.0000.0000.000
143A143LEU00.0270.04512.268-2.173-2.1730.0000.0000.0000.000
144A144ILE0-0.045-0.02514.4161.1481.1480.0000.0000.0000.000
145A145VAL00.0450.02216.731-0.506-0.5060.0000.0000.0000.000
146A146GLU-1-0.829-0.89819.717-14.568-14.5680.0000.0000.0000.000
147A147ILE00.0300.01221.4870.2130.2130.0000.0000.0000.000
148A148ARG10.9040.95023.69612.68512.6850.0000.0000.0000.000
149A149SER00.008-0.02027.1420.0380.0380.0000.0000.0000.000
150A150THR0-0.030-0.02429.839-0.222-0.2220.0000.0000.0000.000
151A151GLU-1-0.754-0.83331.828-8.992-8.9920.0000.0000.0000.000
152A152ARG10.8320.88629.3879.7499.7490.0000.0000.0000.000
153A153MET00.0160.03134.8140.2160.2160.0000.0000.0000.000
154A154ASP-1-0.770-0.86034.006-9.711-9.7110.0000.0000.0000.000
155A155VAL00.0380.01537.1920.0850.0850.0000.0000.0000.000
156A156LEU00.0070.02340.089-0.059-0.0590.0000.0000.0000.000
157A157LEU0-0.003-0.02341.5520.1660.1660.0000.0000.0000.000
158A158GLY00.0660.03043.6040.2200.2200.0000.0000.0000.000
159A159GLU-1-0.877-0.92841.605-7.840-7.8400.0000.0000.0000.000
160A160ASN0-0.051-0.02343.3940.0580.0580.0000.0000.0000.000
161A161GLY0-0.009-0.00945.0930.1360.1360.0000.0000.0000.000
162A162GLU-1-0.940-0.95547.433-6.190-6.1900.0000.0000.0000.000
163A163ILE0-0.061-0.04947.178-0.190-0.1900.0000.0000.0000.000
164A164PHE00.0070.00044.6390.0930.0930.0000.0000.0000.000
165A165VAL0-0.049-0.01546.8330.0580.0580.0000.0000.0000.000
166A166GLY00.0550.03149.9930.0730.0730.0000.0000.0000.000
167A167GLU-1-0.912-0.97151.842-5.923-5.9230.0000.0000.0000.000
168A168GLU-1-0.896-0.94852.539-5.705-5.7050.0000.0000.0000.000
169A169TYR0-0.016-0.01045.327-0.095-0.0950.0000.0000.0000.000
170A170LEU00.0230.00446.446-0.156-0.1560.0000.0000.0000.000
171A171ASN00.0150.00348.075-0.159-0.1590.0000.0000.0000.000
172A172LYS10.8580.91449.0006.0856.0850.0000.0000.0000.000
173A173ILE0-0.021-0.00543.134-0.145-0.1450.0000.0000.0000.000
174A174VAL0-0.004-0.01344.281-0.195-0.1950.0000.0000.0000.000
175A175GLU-1-0.856-0.90045.507-6.433-6.4330.0000.0000.0000.000
176A176ILE00.0440.01242.006-0.132-0.1320.0000.0000.0000.000
177A177ALA0-0.034-0.02240.987-0.220-0.2200.0000.0000.0000.000
178A178ASN00.0320.01341.025-0.370-0.3700.0000.0000.0000.000
179A179ASP-1-0.822-0.90642.841-7.068-7.0680.0000.0000.0000.000
180A180GLN0-0.091-0.06637.987-0.240-0.2400.0000.0000.0000.000
181A181MET0-0.0110.01736.556-0.277-0.2770.0000.0000.0000.000
182A182ARG10.9120.95739.2056.7576.7570.0000.0000.0000.000
183A183ARG10.8990.94138.2648.0208.0200.0000.0000.0000.000
184A184PHE0-0.020-0.01534.376-0.267-0.2670.0000.0000.0000.000
185A185LYS10.8120.91036.0828.5338.5330.0000.0000.0000.000
186A186GLU-1-0.938-0.96038.438-7.783-7.7830.0000.0000.0000.000
187A187LYS10.8080.89234.1529.1199.1190.0000.0000.0000.000
188A188LEU0-0.024-0.01231.846-0.247-0.2470.0000.0000.0000.000
189A189LYS11.0111.00634.7917.9047.9040.0000.0000.0000.000
190A190ARG10.9090.97036.7448.5528.5520.0000.0000.0000.000
191A191LEU00.0220.00529.334-0.027-0.0270.0000.0000.0000.000
192A192GLU-1-0.901-0.95433.827-8.859-8.8590.0000.0000.0000.000
193A193SER0-0.081-0.05335.1160.0540.0540.0000.0000.0000.000
194A194LYS10.9650.96834.1388.6388.6380.0000.0000.0000.000
195A195ILE0-0.033-0.00829.493-0.142-0.1420.0000.0000.0000.000
196A196ASN0-0.079-0.05532.173-0.243-0.2430.0000.0000.0000.000
197A197ALA00.0050.01633.3030.1120.1120.0000.0000.0000.000
198A198LEU-1-0.969-0.96727.442-10.905-10.9050.0000.0000.0000.000