Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YV6G2

Calculation Name: 2PJU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PJU

Chain ID: A

ChEMBL ID:

UniProt ID: P77743

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1888440.983278
FMO2-HF: Nuclear repulsion 1817647.692197
FMO2-HF: Total energy -70793.291081
FMO2-MP2: Total energy -71002.184392


3D Structure
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:11:LYS)


Summations of interaction energy for fragment #1(A:11:LYS)
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.
-162.406-159.96131.979-13.979-20.444-0.178
Interaction energy analysis for fragmet #1(A:11:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.866 / q_NPA : 0.942
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].
3A13VAL0-0.031-0.0143.275-11.082-8.7540.061-1.243-1.1460.001
4A14ILE00.0250.0136.0084.9734.9730.0000.0000.0000.000
5A15TRP00.0300.0088.5180.7110.7110.0000.0000.0000.000
6A16THR00.002-0.00310.8721.0711.0710.0000.0000.0000.000
7A17VAL0-0.024-0.01213.6660.5280.5280.0000.0000.0000.000
8A18SER0-0.034-0.01616.9160.5280.5280.0000.0000.0000.000
9A19VAL00.020-0.00619.3540.0060.0060.0000.0000.0000.000
10A20THR00.0710.02721.858-0.144-0.1440.0000.0000.0000.000
11A21ARG10.9140.95221.40410.62610.6260.0000.0000.0000.000
12A22LEU0-0.029-0.00319.041-0.336-0.3360.0000.0000.0000.000
13A23PHE0-0.017-0.00516.160-1.114-1.1140.0000.0000.0000.000
14A24GLU-1-0.847-0.90316.475-15.919-15.9190.0000.0000.0000.000
15A25LEU00.0040.01316.776-0.806-0.8060.0000.0000.0000.000
16A26PHE0-0.035-0.04813.901-0.829-0.8290.0000.0000.0000.000
17A27ARG10.7630.83612.39215.74215.7420.0000.0000.0000.000
18A28ASP-1-0.845-0.89212.074-19.968-19.9680.0000.0000.0000.000
19A29ILE0-0.038-0.02012.394-0.290-0.2900.0000.0000.0000.000
20A30SER0-0.031-0.0188.218-0.345-0.3450.0000.0000.0000.000
21A31LEU00.0300.0167.561-4.496-4.4960.0000.0000.0000.000
22A32GLU-1-0.836-0.8688.858-22.342-22.3420.0000.0000.0000.000
23A33PHE0-0.033-0.0326.7990.7890.7890.0000.0000.0000.000
24A34ASP-1-0.784-0.8873.625-57.209-56.7670.000-0.170-0.271-0.001
25A35HIS0-0.038-0.0141.897-44.708-45.1038.089-4.046-3.648-0.052
26A36LEU0-0.033-0.0152.232-8.897-7.7074.037-2.137-3.090-0.034
27A37ALA0-0.006-0.0182.541-0.0891.7782.285-1.043-3.109-0.013
28A38ASN0-0.039-0.0141.833-56.427-60.15617.499-5.047-8.723-0.079
29A39ILE00.0620.0363.64811.97112.2950.009-0.075-0.258-0.001
30A40THR0-0.060-0.0336.5451.7941.7940.0000.0000.0000.000
31A41PRO00.0310.0369.9931.7181.7180.0000.0000.0000.000
32A42ILE0-0.008-0.01612.9080.8500.8500.0000.0000.0000.000
33A43GLN00.0120.00916.3210.7660.7660.0000.0000.0000.000
34A44LEU0-0.041-0.02019.5120.8940.8940.0000.0000.0000.000
35A45GLY00.0510.00521.521-0.384-0.3840.0000.0000.0000.000
36A46PHE00.013-0.00623.8670.2600.2600.0000.0000.0000.000
37A47GLU-1-0.896-0.94025.023-10.854-10.8540.0000.0000.0000.000
38A48LYS10.9730.99725.44710.84510.8450.0000.0000.0000.000
39A49ALA00.0340.02820.997-0.410-0.4100.0000.0000.0000.000
40A50VAL00.0150.00221.210-0.560-0.5600.0000.0000.0000.000
41A51THR0-0.038-0.03222.307-0.152-0.1520.0000.0000.0000.000
42A52TYR0-0.002-0.00416.377-0.369-0.3690.0000.0000.0000.000
43A53ILE00.0310.01116.635-0.508-0.5080.0000.0000.0000.000
44A54ARG10.8880.93617.94412.24412.2440.0000.0000.0000.000
45A55LYS10.9470.96819.97512.63112.6310.0000.0000.0000.000
46A56LYS10.8430.92911.65225.25625.2560.0000.0000.0000.000
47A57LEU00.003-0.01114.235-0.477-0.4770.0000.0000.0000.000
48A58ALA0-0.070-0.02316.1680.0330.0330.0000.0000.0000.000
49A59ASN0-0.080-0.03416.2120.9000.9000.0000.0000.0000.000
50A60GLU-1-0.838-0.89811.142-26.236-26.2360.0000.0000.0000.000
51A61ARG10.7860.8543.90236.99037.408-0.001-0.218-0.1990.001
52A62CYS0-0.013-0.0149.959-2.200-2.2000.0000.0000.0000.000
53A63ASP-1-0.759-0.8296.502-31.414-31.4140.0000.0000.0000.000
54A64ALA00.0230.0059.9262.0462.0460.0000.0000.0000.000
55A65ILE0-0.009-0.01111.166-1.284-1.2840.0000.0000.0000.000
56A66ILE00.0030.02611.5350.9210.9210.0000.0000.0000.000
57A67ALA00.0230.01715.1480.0930.0930.0000.0000.0000.000
58A68ALA00.0450.02318.7780.1510.1510.0000.0000.0000.000
59A69GLY00.0260.02321.8830.3330.3330.0000.0000.0000.000
60A70SER00.0470.01225.502-0.324-0.3240.0000.0000.0000.000
61A71ASN00.0510.03121.9560.3380.3380.0000.0000.0000.000
62A72GLY00.0650.01221.689-0.246-0.2460.0000.0000.0000.000
63A73ALA0-0.005-0.00322.497-0.159-0.1590.0000.0000.0000.000
64A74TYR00.0020.01225.2700.0830.0830.0000.0000.0000.000
65A75LEU00.0130.00019.9190.1210.1210.0000.0000.0000.000
66A76LYS10.9020.94319.72614.79414.7940.0000.0000.0000.000
67A77SER0-0.031-0.02122.2020.2680.2680.0000.0000.0000.000
68A78ARG10.8510.93123.87111.69111.6910.0000.0000.0000.000
69A79LEU0-0.016-0.00118.537-0.013-0.0130.0000.0000.0000.000
70A80SER00.0350.02019.899-0.008-0.0080.0000.0000.0000.000
71A81VAL00.0220.02213.668-0.060-0.0600.0000.0000.0000.000
72A82PRO00.0350.00514.1020.7220.7220.0000.0000.0000.000
73A83VAL0-0.0220.01114.819-1.104-1.1040.0000.0000.0000.000
74A84ILE00.0230.02113.8991.3841.3840.0000.0000.0000.000
75A85LEU0-0.068-0.03017.003-0.027-0.0270.0000.0000.0000.000
76A86ILE00.0510.01816.9950.6070.6070.0000.0000.0000.000
77A87LYS10.9500.95921.04612.26212.2620.0000.0000.0000.000
78A88PRO00.0440.03624.609-0.174-0.1740.0000.0000.0000.000
79A89SER00.0290.01526.1630.4390.4390.0000.0000.0000.000
80A90GLY00.0430.01328.4380.0000.0000.0000.0000.0000.000
81A91TYR00.0450.01727.4420.1670.1670.0000.0000.0000.000
82A92ASP-1-0.780-0.84624.344-13.386-13.3860.0000.0000.0000.000
83A93VAL00.0360.01927.187-0.008-0.0080.0000.0000.0000.000
84A94LEU00.0130.00729.7560.1230.1230.0000.0000.0000.000
85A95GLN0-0.0150.00026.0730.0400.0400.0000.0000.0000.000
86A96PHE00.000-0.00324.3020.0030.0030.0000.0000.0000.000
87A97LEU00.0330.00928.3770.1160.1160.0000.0000.0000.000
88A98ALA0-0.029-0.01631.8620.2400.2400.0000.0000.0000.000
89A99LYS10.8810.93626.63511.75011.7500.0000.0000.0000.000
90A100ALA00.0050.01730.3010.0540.0540.0000.0000.0000.000
91A101GLY00.0020.00631.7290.2480.2480.0000.0000.0000.000
92A102LYS10.8280.89234.2108.7918.7910.0000.0000.0000.000
93A103LEU0-0.027-0.00535.1170.1470.1470.0000.0000.0000.000
94A104THR00.0330.01336.7360.1740.1740.0000.0000.0000.000
95A105SER0-0.064-0.01938.5100.2190.2190.0000.0000.0000.000
96A106SER00.0190.00640.5450.0260.0260.0000.0000.0000.000
97A107ILE0-0.0200.00635.664-0.117-0.1170.0000.0000.0000.000
98A108GLY00.0840.04938.0400.1850.1850.0000.0000.0000.000
99A109VAL0-0.072-0.04533.647-0.338-0.3380.0000.0000.0000.000
100A110VAL00.0370.02734.6180.2220.2220.0000.0000.0000.000
101A111THR0-0.047-0.05331.417-0.378-0.3780.0000.0000.0000.000
102A112TYR0-0.030-0.01231.7390.1580.1580.0000.0000.0000.000
103A113GLN00.0000.00033.568-0.348-0.3480.0000.0000.0000.000
104A114GLU-1-0.938-0.95533.952-8.993-8.9930.0000.0000.0000.000
105A115THR00.0130.02635.730-0.148-0.1480.0000.0000.0000.000
106A116ILE00.0270.00630.588-0.011-0.0110.0000.0000.0000.000
107A117PRO00.0670.02734.4500.1160.1160.0000.0000.0000.000
108A118ALA00.004-0.00533.5240.1800.1800.0000.0000.0000.000
109A119LEU0-0.0050.00533.4730.0330.0330.0000.0000.0000.000
110A120VAL00.0460.03436.1130.2280.2280.0000.0000.0000.000
111A121ALA0-0.016-0.01138.5910.2290.2290.0000.0000.0000.000
112A122PHE00.0360.02136.9670.1660.1660.0000.0000.0000.000
113A123GLN00.005-0.01339.3490.0140.0140.0000.0000.0000.000
114A124LYS10.9030.94141.3857.4187.4180.0000.0000.0000.000
115A125THR0-0.053-0.02041.9360.1860.1860.0000.0000.0000.000
116A126PHE0-0.030-0.02439.7840.1080.1080.0000.0000.0000.000
117A127ASN0-0.048-0.00743.7680.0590.0590.0000.0000.0000.000
118A128LEU00.0220.02038.8780.0530.0530.0000.0000.0000.000
119A129ARG10.8750.93641.9437.5297.5290.0000.0000.0000.000
120A130LEU00.0120.01036.190-0.149-0.1490.0000.0000.0000.000
121A131ASP-1-0.767-0.85239.914-7.458-7.4580.0000.0000.0000.000
122A132GLN0-0.062-0.05037.246-0.363-0.3630.0000.0000.0000.000
123A133ARG10.7810.83938.4617.5697.5690.0000.0000.0000.000
124A134SER0-0.063-0.04637.218-0.205-0.2050.0000.0000.0000.000
125A135TYR00.0050.01232.1800.0290.0290.0000.0000.0000.000
126A136ILE0-0.068-0.04136.602-0.268-0.2680.0000.0000.0000.000
127A137THR0-0.062-0.06836.735-0.194-0.1940.0000.0000.0000.000
128A138GLU-1-0.802-0.90436.444-8.805-8.8050.0000.0000.0000.000
129A139GLU-1-0.923-0.94538.141-7.193-7.1930.0000.0000.0000.000
130A140ASP-1-0.702-0.82540.090-8.067-8.0670.0000.0000.0000.000
131A141ALA0-0.019-0.01236.8220.0050.0050.0000.0000.0000.000
132A142ARG10.8000.86737.5048.4108.4100.0000.0000.0000.000
133A143GLY00.0120.01340.7780.1110.1110.0000.0000.0000.000
134A144GLN0-0.014-0.02440.3740.0800.0800.0000.0000.0000.000
135A145ILE0-0.019-0.00736.4210.0110.0110.0000.0000.0000.000
136A146ASN00.0100.00040.5680.0100.0100.0000.0000.0000.000
137A147GLU-1-0.859-0.90144.164-6.853-6.8530.0000.0000.0000.000
138A148LEU0-0.039-0.01339.0640.0460.0460.0000.0000.0000.000
139A149LYS10.8630.92341.9097.6907.6900.0000.0000.0000.000
140A150ALA0-0.042-0.01743.9520.1080.1080.0000.0000.0000.000
141A151ASN0-0.055-0.02044.6720.0600.0600.0000.0000.0000.000
142A152GLY00.0060.01546.0900.0610.0610.0000.0000.0000.000
143A153THR0-0.080-0.04439.675-0.135-0.1350.0000.0000.0000.000
144A154GLU-1-0.816-0.89739.080-7.913-7.9130.0000.0000.0000.000
145A155ALA0-0.036-0.02234.890-0.180-0.1800.0000.0000.0000.000
146A156VAL00.0180.00634.8030.1710.1710.0000.0000.0000.000
147A157VAL0-0.021-0.00930.303-0.338-0.3380.0000.0000.0000.000
148A158GLY00.0650.01230.3540.3020.3020.0000.0000.0000.000
149A159ALA0-0.013-0.00727.443-0.471-0.4710.0000.0000.0000.000
150A160GLY00.0230.00826.9790.2230.2230.0000.0000.0000.000
151A161LEU00.0990.06627.8190.1500.1500.0000.0000.0000.000
152A162ILE0-0.0100.01231.3750.2280.2280.0000.0000.0000.000
153A163THR0-0.070-0.04029.0090.0520.0520.0000.0000.0000.000
154A164ASP-1-0.807-0.90529.450-10.972-10.9720.0000.0000.0000.000
155A165LEU00.0260.00532.1580.2390.2390.0000.0000.0000.000
156A166ALA0-0.026-0.00734.0460.2590.2590.0000.0000.0000.000
157A167GLU-1-0.831-0.91731.758-9.604-9.6040.0000.0000.0000.000
158A168GLU-1-0.896-0.93035.131-8.498-8.4980.0000.0000.0000.000
159A169ALA0-0.0140.00837.6810.2660.2660.0000.0000.0000.000
160A170GLY00.0140.00938.6520.2270.2270.0000.0000.0000.000
161A171MET0-0.121-0.05837.6790.2480.2480.0000.0000.0000.000
162A172THR00.0010.00732.267-0.136-0.1360.0000.0000.0000.000
163A173GLY00.0560.01631.7070.0720.0720.0000.0000.0000.000
164A174ILE0-0.078-0.03629.230-0.477-0.4770.0000.0000.0000.000
165A175PHE00.014-0.00921.7040.0480.0480.0000.0000.0000.000
166A176ILE0-0.038-0.02326.160-0.208-0.2080.0000.0000.0000.000
167A177TYR0-0.050-0.02021.466-0.036-0.0360.0000.0000.0000.000
168A178SER00.025-0.01722.430-0.516-0.5160.0000.0000.0000.000
169A179ALA00.0570.00918.611-0.582-0.5820.0000.0000.0000.000
170A180ALA0-0.039-0.00617.899-0.979-0.9790.0000.0000.0000.000
171A181THR0-0.008-0.02918.848-0.797-0.7970.0000.0000.0000.000
172A182VAL0-0.009-0.00214.660-0.476-0.4760.0000.0000.0000.000
173A183ARG10.8350.88214.07518.23818.2380.0000.0000.0000.000
174A184GLN0-0.065-0.03514.354-0.886-0.8860.0000.0000.0000.000
175A185ALA00.0260.01315.296-0.734-0.7340.0000.0000.0000.000
176A186PHE00.011-0.0139.203-0.941-0.9410.0000.0000.0000.000
177A187SER0-0.008-0.00510.671-2.189-2.1890.0000.0000.0000.000
178A188ASP-1-0.842-0.91212.419-18.078-18.0780.0000.0000.0000.000
179A189ALA0-0.035-0.01610.4250.3560.3560.0000.0000.0000.000
180A190LEU0-0.0020.0125.827-0.820-0.8200.0000.0000.0000.000
181A191ASP-1-0.800-0.8749.268-20.539-20.5390.0000.0000.0000.000
182A192MET0-0.043-0.00911.7471.1971.1970.0000.0000.0000.000
183A193THR0-0.024-0.0427.0950.3270.3270.0000.0000.0000.000
184A194ARG10.7800.8609.46422.57922.5790.0000.0000.0000.000
185A195MET0-0.064-0.02910.1751.1091.1090.0000.0000.0000.000
186A196SER0-0.070-0.01011.3831.5031.5030.0000.0000.0000.000