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

tag_button

FMODB ID: VYJ41

Calculation Name: 3P2F-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3P2F

Chain ID: A

ChEMBL ID:

UniProt ID: Q4VSJ8

Base Structure: X-ray

Registration Date: 2025-10-05

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2167388.555124
FMO2-HF: Nuclear repulsion 2090164.567493
FMO2-HF: Total energy -77223.987632
FMO2-MP2: Total energy -77443.65094


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.
-261.054-260.8158.626-25.008-33.86-0.237
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 : 0.730 / q_NPA : 0.857
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].
3A3THR0-0.008-0.0182.7250.6383.3260.403-1.055-2.036-0.004
4A4PHE0-0.004-0.0014.4363.2863.401-0.001-0.021-0.0920.000
57A57GLY00.0660.0172.868-1.703-1.9383.425-1.922-1.2690.008
58A58ARG10.7180.8053.09033.25231.716-0.0032.401-0.862-0.003
59A59ASP-1-0.714-0.8572.577-59.859-57.0041.673-2.210-2.318-0.028
60A60ALA0-0.035-0.0083.8982.9482.932-0.001-0.0050.0220.000
65A65CYS0-0.021-0.0023.167-2.420-1.6911.393-0.521-1.6000.004
66A66GLY00.0480.0004.275-1.894-1.5720.011-0.082-0.2520.000
67A67CYS0-0.092-0.0375.1580.7500.808-0.001-0.003-0.0540.000
105A107ALA00.0100.0022.243-0.621-0.5521.203-0.328-0.944-0.001
106A108THR0-0.094-0.0434.1611.8192.0050.001-0.038-0.1500.000
107A109PRO00.0110.0272.1933.6043.7323.882-1.053-2.9570.000
108A110GLU-1-0.805-0.9101.738-123.048-124.58813.335-6.866-4.929-0.074
109A111GLU-1-0.789-0.8911.811-128.236-131.30122.762-11.915-7.781-0.125
110A112GLY00.0030.0105.2386.2246.230-0.001-0.0050.0010.000
118A120TRP0-0.0230.0144.6654.4434.552-0.001-0.007-0.1010.000
119A121SER00.035-0.0102.229-0.082-0.5613.003-0.824-1.7000.000
120A122VAL0-0.054-0.0292.5231.600-0.2173.1050.519-1.807-0.016
121A123ARG10.8410.8955.26828.02028.123-0.001-0.004-0.0980.000
122A124PRO00.0460.0202.5681.7423.2891.039-0.503-2.0820.000
123A125MET0-0.0070.0132.9192.2722.2213.400-0.531-2.8170.002
124A126LEU0-0.032-0.0205.4162.1692.2370.000-0.035-0.0340.000
5A5VAL00.0430.0218.0081.0221.0220.0000.0000.0000.000
6A6HIS0-0.066-0.03710.6661.2581.2580.0000.0000.0000.000
7A7GLU-1-0.769-0.90313.814-15.486-15.4860.0000.0000.0000.000
8A8ALA0-0.036-0.00717.0160.6530.6530.0000.0000.0000.000
9A9GLY00.0090.01919.6460.5120.5120.0000.0000.0000.000
10A10ARG10.8030.85319.95010.34610.3460.0000.0000.0000.000
11A11LEU0-0.0010.01215.281-0.117-0.1170.0000.0000.0000.000
12A12PRO00.0200.00917.4790.5670.5670.0000.0000.0000.000
13A13ALA00.0330.01318.696-0.510-0.5100.0000.0000.0000.000
14A14HIS00.0540.02516.2530.5220.5220.0000.0000.0000.000
15A15ILE00.0590.03113.066-0.540-0.5400.0000.0000.0000.000
16A16ALA0-0.016-0.00714.833-0.532-0.5320.0000.0000.0000.000
17A17ALA0-0.010-0.01416.927-0.154-0.1540.0000.0000.0000.000
18A18GLU-1-0.763-0.85511.180-22.497-22.4970.0000.0000.0000.000
19A19LEU00.0590.03611.069-0.702-0.7020.0000.0000.0000.000
20A20GLY00.011-0.03013.246-0.013-0.0130.0000.0000.0000.000
21A21SER0-0.123-0.08115.8890.4780.4780.0000.0000.0000.000
22A22TYR00.0830.0136.898-0.258-0.2580.0000.0000.0000.000
23A23ARG10.8490.86212.32815.81115.8110.0000.0000.0000.000
24A24TYR00.0020.00213.5100.4860.4860.0000.0000.0000.000
25A25ARG10.8980.95312.29821.17721.1770.0000.0000.0000.000
26A26VAL00.0560.0299.6390.4800.4800.0000.0000.0000.000
27A27PHE00.003-0.00511.1880.7290.7290.0000.0000.0000.000
28A28VAL0-0.021-0.00615.5630.8550.8550.0000.0000.0000.000
29A29GLU0-0.044-0.03117.329-0.197-0.1970.0000.0000.0000.000
30A30GLN0-0.016-0.01517.308-0.348-0.3480.0000.0000.0000.000
31A31LEU00.0140.03711.9240.2110.2110.0000.0000.0000.000
32A32GLY00.0170.00615.712-0.036-0.0360.0000.0000.0000.000
33A33TRP0-0.012-0.01417.176-0.154-0.1540.0000.0000.0000.000
34A34GLN00.0000.00119.314-0.252-0.2520.0000.0000.0000.000
35A35LEU0-0.052-0.01718.9280.4060.4060.0000.0000.0000.000
36A36PRO00.0540.03215.851-0.563-0.5630.0000.0000.0000.000
37A37SER00.0200.00714.475-1.047-1.0470.0000.0000.0000.000
38A38GLU0-0.0010.01315.9590.3230.3230.0000.0000.0000.000
39A39ASP00.0950.02215.834-0.673-0.6730.0000.0000.0000.000
40A40GLU0-0.1420.01411.5050.2650.2650.0000.0000.0000.000
41A41LYS10.8590.89416.67813.85413.8540.0000.0000.0000.000
42A42MET00.0110.05718.2870.5270.5270.0000.0000.0000.000
43A43GLU0-0.033-0.04718.5910.1870.1870.0000.0000.0000.000
44A44ARG10.9030.96219.09412.71312.7130.0000.0000.0000.000
45A45ASP-1-0.751-0.83520.272-12.348-12.3480.0000.0000.0000.000
46A46GLN00.0560.01822.466-0.296-0.2960.0000.0000.0000.000
47A47TYR0-0.070-0.06620.7960.1090.1090.0000.0000.0000.000
48A48ASP-1-0.778-0.80518.033-14.616-14.6160.0000.0000.0000.000
49A49ARG10.7880.85720.60211.65211.6520.0000.0000.0000.000
50A50ASP-1-0.770-0.85621.332-11.433-11.4330.0000.0000.0000.000
51A51ASP-1-0.835-0.89122.297-11.584-11.5840.0000.0000.0000.000
52A52THR0-0.067-0.02917.0780.0300.0300.0000.0000.0000.000
53A53VAL00.0260.03314.497-0.226-0.2260.0000.0000.0000.000
54A54TYR0-0.029-0.06311.9990.2030.2030.0000.0000.0000.000
55A55VAL00.0070.0106.610-0.139-0.1390.0000.0000.0000.000
56A56LEU0-0.038-0.0227.0920.7160.7160.0000.0000.0000.000
61A61ASN0-0.065-0.0336.1696.1616.1610.0000.0000.0000.000
62A62GLY0-0.0030.0147.0693.2773.2770.0000.0000.0000.000
63A63GLU-1-0.947-0.9717.716-21.675-21.6750.0000.0000.0000.000
64A64ILE0-0.089-0.0436.137-4.074-4.0740.0000.0000.0000.000
68A68ALA00.0360.0198.0300.0000.0000.0000.0000.0000.000
69A69ARG10.7770.86810.09913.73113.7310.0000.0000.0000.000
70A70LEU00.0180.01212.4700.1050.1050.0000.0000.0000.000
71A71LEU0-0.038-0.01315.8930.4010.4010.0000.0000.0000.000
72A72PRO00.0410.03919.7460.0080.0080.0000.0000.0000.000
73A73THR00.026-0.00522.7170.4410.4410.0000.0000.0000.000
74A74THR0-0.021-0.01125.0120.3260.3260.0000.0000.0000.000
75A75ARG10.8790.94225.01210.16410.1640.0000.0000.0000.000
76A76PRO00.0540.03225.927-0.187-0.1870.0000.0000.0000.000
77A77TYR0-0.016-0.02922.002-0.461-0.4610.0000.0000.0000.000
78A78LEU00.0250.00718.9540.2840.2840.0000.0000.0000.000
79A79LEU0-0.033-0.03621.7290.2840.2840.0000.0000.0000.000
80A80GLN00.0000.00423.3620.2090.2090.0000.0000.0000.000
81A81GLU-1-0.841-0.89426.400-9.372-9.3720.0000.0000.0000.000
82A82VAL0-0.052-0.01524.6320.2260.2260.0000.0000.0000.000
83A83PHE0-0.061-0.03422.0870.0130.0130.0000.0000.0000.000
84A84PRO00.0770.04626.091-0.098-0.0980.0000.0000.0000.000
85A85HIS0-0.009-0.01027.2440.0800.0800.0000.0000.0000.000
86A86LEU0-0.046-0.02023.245-0.015-0.0150.0000.0000.0000.000
87A87LEU0-0.049-0.02225.083-0.328-0.3280.0000.0000.0000.000
88A88ALA0-0.030-0.01828.2670.2330.2330.0000.0000.0000.000
89A89ASP-1-0.942-0.95930.461-8.465-8.4650.0000.0000.0000.000
90A90GLU-1-0.887-0.95430.978-8.603-8.6030.0000.0000.0000.000
91A93ALA0-0.033-0.01728.013-0.265-0.2650.0000.0000.0000.000
92A94PRO0-0.028-0.00426.0000.1160.1160.0000.0000.0000.000
93A95ARG10.9290.96427.4388.8228.8220.0000.0000.0000.000
94A96SER0-0.007-0.00827.3430.2550.2550.0000.0000.0000.000
95A97ALA00.0240.00725.927-0.302-0.3020.0000.0000.0000.000
96A98HIS00.0050.01224.535-0.286-0.2860.0000.0000.0000.000
97A99VAL0-0.0030.00822.916-0.342-0.3420.0000.0000.0000.000
98A100TRP00.0530.03118.6200.0630.0630.0000.0000.0000.000
99A101GLU-1-0.760-0.87818.125-12.824-12.8240.0000.0000.0000.000
100A102LEU0-0.0050.00811.623-0.539-0.5390.0000.0000.0000.000
101A103SER0-0.032-0.04115.1000.1910.1910.0000.0000.0000.000
102A104ARG10.8170.89513.39913.33813.3380.0000.0000.0000.000
103A105PHE00.0360.0266.942-0.535-0.5350.0000.0000.0000.000
104A106ALA0-0.019-0.0197.5240.9110.9110.0000.0000.0000.000
111A113ALA0-0.067-0.0307.7664.1114.1110.0000.0000.0000.000
112A114ASP-1-0.854-0.9176.369-41.183-41.1830.0000.0000.0000.000
113A115ALA0-0.008-0.0038.3990.7080.7080.0000.0000.0000.000
114A116GLY00.0080.0166.937-0.962-0.9620.0000.0000.0000.000
115A117SER0-0.011-0.0177.5395.0185.0180.0000.0000.0000.000
116A118LEU0-0.005-0.0188.201-1.411-1.4110.0000.0000.0000.000
117A119ALA0-0.014-0.0298.1470.0690.0690.0000.0000.0000.000
125A127ALA00.0560.0387.9121.9141.9140.0000.0000.0000.000
126A128ALA00.0200.0026.9431.8371.8370.0000.0000.0000.000
127A129ALA0-0.022-0.0218.9151.7701.7700.0000.0000.0000.000
128A130VAL00.003-0.00211.0961.4491.4490.0000.0000.0000.000
129A131GLU-1-0.878-0.91110.833-20.552-20.5520.0000.0000.0000.000
130A132CYS0-0.0350.00012.8571.2271.2270.0000.0000.0000.000
131A133ALA00.022-0.00214.5131.0601.0600.0000.0000.0000.000
132A134ALA00.0280.01816.9620.8360.8360.0000.0000.0000.000
133A135ARG10.8520.90913.61618.99618.9960.0000.0000.0000.000
134A136ARG10.8010.90118.53014.18214.1820.0000.0000.0000.000
135A137GLY0-0.0030.00520.9520.5280.5280.0000.0000.0000.000
136A138ALA0-0.078-0.03119.5210.4770.4770.0000.0000.0000.000
137A139ARG10.9820.97221.22010.41010.4100.0000.0000.0000.000
138A140GLN0-0.054-0.03620.8360.2880.2880.0000.0000.0000.000
139A141LEU00.0020.01714.619-0.032-0.0320.0000.0000.0000.000
140A142ILE00.012-0.00218.7340.3120.3120.0000.0000.0000.000
141A143GLY00.0680.03417.321-0.274-0.2740.0000.0000.0000.000
142A144VAL0-0.0100.01018.4040.1750.1750.0000.0000.0000.000
143A145THR0-0.030-0.01214.555-0.901-0.9010.0000.0000.0000.000
144A146PHE00.0470.01814.7670.5500.5500.0000.0000.0000.000
145A147CYS00.006-0.01515.960-0.431-0.4310.0000.0000.0000.000
146A148SER0-0.054-0.02814.3320.1100.1100.0000.0000.0000.000
147A149MET00.0430.0348.441-0.948-0.9480.0000.0000.0000.000
148A150GLU-1-0.730-0.82712.918-13.073-13.0730.0000.0000.0000.000
149A151ARG10.9300.95715.90214.00514.0050.0000.0000.0000.000
150A152MET0-0.034-0.0049.763-0.674-0.6740.0000.0000.0000.000
151A153PHE00.0550.0199.992-0.675-0.6750.0000.0000.0000.000
152A154ARG10.9460.96613.22013.21413.2140.0000.0000.0000.000
153A155ARG10.8930.95712.69317.94217.9420.0000.0000.0000.000
154A156ILE0-0.014-0.0088.428-0.331-0.3310.0000.0000.0000.000
155A157GLY00.0290.03412.5990.0280.0280.0000.0000.0000.000
156A158VAL00.0050.01213.0960.6130.6130.0000.0000.0000.000
157A159HIS0-0.027-0.01015.9470.6600.6600.0000.0000.0000.000
158A160ALA0-0.045-0.02816.6230.2470.2470.0000.0000.0000.000
159A161HIS10.8170.89618.72811.94311.9430.0000.0000.0000.000
160A162ARG10.8010.85921.81511.39511.3950.0000.0000.0000.000
161A163ALA00.0300.01223.5620.1920.1920.0000.0000.0000.000
162A164GLY00.0600.03925.5170.3440.3440.0000.0000.0000.000
163A165ALA0-0.019-0.00426.341-0.248-0.2480.0000.0000.0000.000
164A166PRO0-0.053-0.02924.050-0.203-0.2030.0000.0000.0000.000
165A167VAL00.0430.01824.6600.3830.3830.0000.0000.0000.000
166A168SER0-0.034-0.02324.325-0.529-0.5290.0000.0000.0000.000
167A169ILE00.0350.01423.4070.3650.3650.0000.0000.0000.000
168A170ASP-1-0.881-0.93223.758-10.475-10.4750.0000.0000.0000.000
169A171GLY00.002-0.00324.703-0.209-0.2090.0000.0000.0000.000
170A172ARG10.8420.91918.52511.74811.7480.0000.0000.0000.000
171A173MET00.0000.01719.2840.3070.3070.0000.0000.0000.000
172A174VAL0-0.016-0.01219.106-0.756-0.7560.0000.0000.0000.000
173A175VAL00.012-0.00420.1140.5420.5420.0000.0000.0000.000
174A176ALA00.0420.05020.271-0.549-0.5490.0000.0000.0000.000
175A177CYS0-0.078-0.05118.0990.2350.2350.0000.0000.0000.000
176A178TRP00.0670.02619.565-0.149-0.1490.0000.0000.0000.000
177A179ILE0-0.011-0.01014.260-0.351-0.3510.0000.0000.0000.000
178A180ASP-1-0.781-0.85218.510-11.640-11.6400.0000.0000.0000.000
179A181ILE0-0.059-0.03117.501-0.735-0.7350.0000.0000.0000.000
180A182ASP-1-0.751-0.86519.662-12.676-12.6760.0000.0000.0000.000
181A183ALA00.0860.02819.757-0.717-0.7170.0000.0000.0000.000
182A184GLN0-0.097-0.03319.0580.0600.0600.0000.0000.0000.000
183A185THR0-0.045-0.05115.187-1.008-1.0080.0000.0000.0000.000
184A186LEU0-0.0090.00115.137-1.373-1.3730.0000.0000.0000.000
185A187ALA00.0180.01715.539-1.141-1.1410.0000.0000.0000.000
186A188ALA0-0.031-0.01114.242-0.857-0.8570.0000.0000.0000.000
187A189LEU0-0.088-0.0579.770-1.852-1.8520.0000.0000.0000.000
188A190ASP-1-0.855-0.89111.349-26.279-26.2790.0000.0000.0000.000
189A191LEU0-0.053-0.02011.631-0.190-0.1900.0000.0000.0000.000
190A192ASP-1-0.829-0.92314.904-13.877-13.8770.0000.0000.0000.000
191A193PRO00.002-0.00518.1990.2650.2650.0000.0000.0000.000
192A194ALA0-0.040-0.02021.1120.6430.6430.0000.0000.0000.000
193A195LEU0-0.087-0.04816.7310.2750.2750.0000.0000.0000.000
194A196CYS-1-0.901-0.94420.925-12.769-12.7690.0000.0000.0000.000