FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

tag_button

FMODB ID: 4JRZN

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:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
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
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1882838.233803
FMO2-HF: Nuclear repulsion 1812046.063132
FMO2-HF: Total energy -70792.170671
FMO2-MP2: Total energy -71001.079189


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.
-146.011-134.43814.843-11.032-15.381-0.149
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 : 0.817 / q_NPA : 0.908
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].
3A13VAL0-0.068-0.0213.425-9.884-8.4160.033-0.658-0.8420.000
4A14ILE00.0440.0225.9975.0745.0740.0000.0000.0000.000
5A15TRP00.016-0.0048.3610.1370.1370.0000.0000.0000.000
6A16THR00.0220.02111.4011.5821.5820.0000.0000.0000.000
7A17VAL0-0.008-0.01013.8620.4820.4820.0000.0000.0000.000
8A18SER0-0.035-0.01217.4930.5520.5520.0000.0000.0000.000
9A19VAL00.0400.00519.790-0.154-0.1540.0000.0000.0000.000
10A20THR00.0370.00622.171-0.070-0.0700.0000.0000.0000.000
11A21ARG10.9790.99721.83310.88810.8880.0000.0000.0000.000
12A22LEU0-0.029-0.00619.361-0.364-0.3640.0000.0000.0000.000
13A23PHE0-0.016-0.00516.349-1.125-1.1250.0000.0000.0000.000
14A24GLU-1-0.943-0.98116.831-15.264-15.2640.0000.0000.0000.000
15A25LEU00.0160.01717.169-0.801-0.8010.0000.0000.0000.000
16A26PHE0-0.015-0.03914.208-0.968-0.9680.0000.0000.0000.000
17A27ARG10.9480.98512.66216.51516.5150.0000.0000.0000.000
18A28ASP-1-0.903-0.95012.292-19.827-19.8270.0000.0000.0000.000
19A29ILE0-0.027-0.02612.716-0.842-0.8420.0000.0000.0000.000
20A30SER0-0.052-0.0238.849-2.252-2.2520.0000.0000.0000.000
21A31LEU00.0420.0227.718-4.300-4.3000.0000.0000.0000.000
22A32GLU-1-0.858-0.9018.618-23.366-23.3660.0000.0000.0000.000
23A33PHE0-0.040-0.0377.0010.4450.4450.0000.0000.0000.000
24A34ASP-1-0.793-0.8843.845-55.383-54.888-0.001-0.208-0.286-0.001
25A35HIS0-0.071-0.0281.843-47.877-47.5497.568-4.278-3.618-0.059
26A36LEU0-0.045-0.0372.618-5.183-2.7791.112-1.554-1.961-0.024
27A37ALA0-0.006-0.0082.367-0.1732.2811.673-1.446-2.680-0.015
28A38ASN0-0.052-0.0212.122-40.457-36.4864.452-2.801-5.622-0.050
29A39ILE00.0590.0323.97711.06611.3240.004-0.054-0.2080.000
30A40THR0-0.069-0.0337.1771.3601.3600.0000.0000.0000.000
31A41PRO00.0250.0239.9701.4251.4250.0000.0000.0000.000
32A42ILE0-0.022-0.01813.2820.9460.9460.0000.0000.0000.000
33A43GLN0-0.014-0.00516.4951.0281.0280.0000.0000.0000.000
34A44LEU0-0.042-0.02319.6950.8840.8840.0000.0000.0000.000
35A45GLY00.0450.01122.146-0.325-0.3250.0000.0000.0000.000
36A46PHE00.015-0.00824.2170.2770.2770.0000.0000.0000.000
37A47GLU-1-0.859-0.93325.028-10.720-10.7200.0000.0000.0000.000
38A48LYS10.9600.99625.53110.75310.7530.0000.0000.0000.000
39A49ALA00.0260.02421.091-0.403-0.4030.0000.0000.0000.000
40A50VAL00.0110.00621.205-0.535-0.5350.0000.0000.0000.000
41A51THR0-0.027-0.03622.242-0.155-0.1550.0000.0000.0000.000
42A52TYR00.0070.00416.539-0.376-0.3760.0000.0000.0000.000
43A53ILE00.0260.01016.801-0.565-0.5650.0000.0000.0000.000
44A54ARG10.9070.94317.94811.97311.9730.0000.0000.0000.000
45A55LYS10.9220.95819.97112.38512.3850.0000.0000.0000.000
46A56LYS10.9140.98211.99324.44224.4420.0000.0000.0000.000
47A57LEU0-0.021-0.02913.954-0.629-0.6290.0000.0000.0000.000
48A58ALA0-0.064-0.00616.1620.2270.2270.0000.0000.0000.000
49A59ASN0-0.041-0.01915.9740.7260.7260.0000.0000.0000.000
50A60GLU-1-0.935-0.95810.903-24.454-24.4540.0000.0000.0000.000
51A61ARG10.9560.9803.41732.89533.0900.002-0.033-0.1640.000
52A62CYS0-0.044-0.0379.560-2.181-2.1810.0000.0000.0000.000
53A63ASP-1-0.832-0.8926.395-28.327-28.3270.0000.0000.0000.000
54A64ALA00.001-0.0109.6751.9941.9940.0000.0000.0000.000
55A65ILE00.0070.00211.127-1.459-1.4590.0000.0000.0000.000
56A66ILE00.0000.02111.3620.7700.7700.0000.0000.0000.000
57A67ALA00.0140.00714.9890.0980.0980.0000.0000.0000.000
58A68ALA00.0540.03818.6190.1270.1270.0000.0000.0000.000
59A69GLY00.0120.01721.8690.2520.2520.0000.0000.0000.000
60A70SER00.0680.02025.315-0.294-0.2940.0000.0000.0000.000
61A71ASN00.0490.02621.6380.3790.3790.0000.0000.0000.000
62A72GLY00.0590.00921.586-0.183-0.1830.0000.0000.0000.000
63A73ALA0-0.003-0.00322.339-0.129-0.1290.0000.0000.0000.000
64A74TYR0-0.018-0.01125.0650.0970.0970.0000.0000.0000.000
65A75LEU00.000-0.01719.6060.0980.0980.0000.0000.0000.000
66A76LYS10.9400.97719.76514.22114.2210.0000.0000.0000.000
67A77SER0-0.046-0.01322.1150.1890.1890.0000.0000.0000.000
68A78ARG10.9070.96123.90911.25511.2550.0000.0000.0000.000
69A79LEU0-0.0350.00318.4500.0500.0500.0000.0000.0000.000
70A80SER00.0210.00920.0820.0640.0640.0000.0000.0000.000
71A81VAL00.0160.01613.764-0.071-0.0710.0000.0000.0000.000
72A82PRO00.0400.02013.8140.8020.8020.0000.0000.0000.000
73A83VAL0-0.0180.00114.996-0.982-0.9820.0000.0000.0000.000
74A84ILE00.0140.00513.1961.1511.1510.0000.0000.0000.000
75A85LEU0-0.067-0.03116.726-0.105-0.1050.0000.0000.0000.000
76A86ILE00.0600.01417.1840.4150.4150.0000.0000.0000.000
77A87LYS10.9300.94420.80712.31412.3140.0000.0000.0000.000
78A88PRO00.0320.03324.532-0.078-0.0780.0000.0000.0000.000
79A89SER00.0500.03226.1570.5100.5100.0000.0000.0000.000
80A90GLY00.0480.00528.341-0.059-0.0590.0000.0000.0000.000
81A91TYR00.0740.03327.7430.1640.1640.0000.0000.0000.000
82A92ASP-1-0.822-0.87724.908-13.011-13.0110.0000.0000.0000.000
83A93VAL00.0400.02727.373-0.005-0.0050.0000.0000.0000.000
84A94LEU0-0.004-0.00329.9470.1050.1050.0000.0000.0000.000
85A95GLN0-0.109-0.06326.842-0.101-0.1010.0000.0000.0000.000
86A96PHE00.0410.00523.916-0.056-0.0560.0000.0000.0000.000
87A97LEU00.0180.00628.8040.1240.1240.0000.0000.0000.000
88A98ALA0-0.022-0.02132.5300.1700.1700.0000.0000.0000.000
89A99LYS10.9140.96527.14911.64111.6410.0000.0000.0000.000
90A100ALA0-0.0070.01130.7580.0770.0770.0000.0000.0000.000
91A101GLY00.0070.00432.1980.2480.2480.0000.0000.0000.000
92A102LYS10.8490.91934.7268.6878.6870.0000.0000.0000.000
93A103LEU0-0.034-0.01535.3840.1290.1290.0000.0000.0000.000
94A104THR00.0220.00637.3610.1790.1790.0000.0000.0000.000
95A105SER0-0.085-0.04139.3610.1990.1990.0000.0000.0000.000
96A106SER0-0.011-0.00241.2670.0010.0010.0000.0000.0000.000
97A107ILE0-0.0040.00436.064-0.153-0.1530.0000.0000.0000.000
98A108GLY00.0670.04238.1240.2100.2100.0000.0000.0000.000
99A109VAL0-0.078-0.04233.930-0.337-0.3370.0000.0000.0000.000
100A110VAL00.0460.03035.2100.2260.2260.0000.0000.0000.000
101A111THR0-0.063-0.06932.038-0.318-0.3180.0000.0000.0000.000
102A112TYR0-0.042-0.01631.6630.1490.1490.0000.0000.0000.000
103A113GLN0-0.016-0.01033.931-0.328-0.3280.0000.0000.0000.000
104A114GLU-1-0.934-0.96234.356-8.723-8.7230.0000.0000.0000.000
105A115THR00.0100.03435.369-0.275-0.2750.0000.0000.0000.000
106A116ILE00.0450.01431.194-0.130-0.1300.0000.0000.0000.000
107A117PRO00.0580.02634.1000.1380.1380.0000.0000.0000.000
108A118ALA00.009-0.00133.1470.1580.1580.0000.0000.0000.000
109A119LEU00.0290.02033.1420.0390.0390.0000.0000.0000.000
110A120VAL00.0010.01136.1910.2430.2430.0000.0000.0000.000
111A121ALA0-0.025-0.02038.4950.2250.2250.0000.0000.0000.000
112A122PHE00.0350.00937.1960.1690.1690.0000.0000.0000.000
113A123GLN00.0340.01039.348-0.003-0.0030.0000.0000.0000.000
114A124LYS10.8930.93941.5067.3487.3480.0000.0000.0000.000
115A125THR0-0.042-0.01242.1590.1900.1900.0000.0000.0000.000
116A126PHE0-0.036-0.02840.1800.1170.1170.0000.0000.0000.000
117A127ASN0-0.0300.00743.714-0.002-0.0020.0000.0000.0000.000
118A128LEU00.0190.02239.4340.0370.0370.0000.0000.0000.000
119A129ARG10.9350.97642.6207.3807.3800.0000.0000.0000.000
120A130LEU0-0.015-0.00437.262-0.180-0.1800.0000.0000.0000.000
121A131ASP-1-0.807-0.89040.598-7.356-7.3560.0000.0000.0000.000
122A132GLN0-0.067-0.05037.751-0.286-0.2860.0000.0000.0000.000
123A133ARG10.8250.90038.9307.5557.5550.0000.0000.0000.000
124A134SER0-0.034-0.01337.831-0.216-0.2160.0000.0000.0000.000
125A135TYR00.0180.00833.0520.0390.0390.0000.0000.0000.000
126A136ILE0-0.026-0.01137.221-0.280-0.2800.0000.0000.0000.000
127A137THR0-0.019-0.01336.928-0.271-0.2710.0000.0000.0000.000
128A138GLU-1-0.857-0.94736.807-8.705-8.7050.0000.0000.0000.000
129A139GLU-1-0.939-0.97438.537-7.112-7.1120.0000.0000.0000.000
130A140ASP-1-0.771-0.88140.331-7.688-7.6880.0000.0000.0000.000
131A141ALA0-0.024-0.02637.2960.0520.0520.0000.0000.0000.000
132A142ARG10.8980.94638.5578.2458.2450.0000.0000.0000.000
133A143GLY00.0420.03541.2720.0830.0830.0000.0000.0000.000
134A144GLN00.0310.00440.5750.0530.0530.0000.0000.0000.000
135A145ILE0-0.004-0.00237.0090.0230.0230.0000.0000.0000.000
136A146ASN0-0.018-0.01741.095-0.018-0.0180.0000.0000.0000.000
137A147GLU-1-0.918-0.95344.590-6.838-6.8380.0000.0000.0000.000
138A148LEU0-0.039-0.01939.7080.0470.0470.0000.0000.0000.000
139A149LYS10.8790.92642.8647.5497.5490.0000.0000.0000.000
140A150ALA0-0.046-0.03044.3400.1020.1020.0000.0000.0000.000
141A151ASN0-0.033-0.01145.7300.0360.0360.0000.0000.0000.000
142A152GLY00.0110.01346.4090.0320.0320.0000.0000.0000.000
143A153THR0-0.085-0.02940.148-0.119-0.1190.0000.0000.0000.000
144A154GLU-1-0.777-0.90239.838-7.795-7.7950.0000.0000.0000.000
145A155ALA0-0.030-0.00835.271-0.191-0.1910.0000.0000.0000.000
146A156VAL00.0280.01035.2060.1540.1540.0000.0000.0000.000
147A157VAL0-0.026-0.00830.559-0.322-0.3220.0000.0000.0000.000
148A158GLY00.0610.00730.8380.2950.2950.0000.0000.0000.000
149A159ALA00.0000.00327.678-0.425-0.4250.0000.0000.0000.000
150A160GLY00.012-0.00627.8080.1680.1680.0000.0000.0000.000
151A161LEU00.0830.04628.4220.1060.1060.0000.0000.0000.000
152A162ILE0-0.0010.01132.0270.1990.1990.0000.0000.0000.000
153A163THR0-0.068-0.03129.1780.0450.0450.0000.0000.0000.000
154A164ASP-1-0.792-0.89130.095-10.754-10.7540.0000.0000.0000.000
155A165LEU00.0160.00032.6190.2510.2510.0000.0000.0000.000
156A166ALA0-0.016-0.00634.6790.2620.2620.0000.0000.0000.000
157A167GLU-1-0.850-0.93332.109-9.619-9.6190.0000.0000.0000.000
158A168GLU-1-0.978-0.97535.522-8.674-8.6740.0000.0000.0000.000
159A169ALA0-0.037-0.00137.9650.2710.2710.0000.0000.0000.000
160A170GLY0-0.0090.00139.1150.2710.2710.0000.0000.0000.000
161A171MET0-0.119-0.03838.4230.1650.1650.0000.0000.0000.000
162A172THR0-0.015-0.00933.093-0.183-0.1830.0000.0000.0000.000
163A173GLY00.0370.02332.2750.1380.1380.0000.0000.0000.000
164A174ILE0-0.063-0.03329.345-0.333-0.3330.0000.0000.0000.000
165A175PHE00.010-0.01522.1700.0520.0520.0000.0000.0000.000
166A176ILE0-0.042-0.03226.694-0.151-0.1510.0000.0000.0000.000
167A177TYR0-0.049-0.01921.868-0.017-0.0170.0000.0000.0000.000
168A178SER00.049-0.00122.824-0.461-0.4610.0000.0000.0000.000
169A179ALA00.0400.00318.714-0.529-0.5290.0000.0000.0000.000
170A180ALA0-0.011-0.00118.148-0.952-0.9520.0000.0000.0000.000
171A181THR0-0.019-0.00618.979-0.624-0.6240.0000.0000.0000.000
172A182VAL00.0200.00515.037-0.407-0.4070.0000.0000.0000.000
173A183ARG10.8360.89914.30117.99217.9920.0000.0000.0000.000
174A184GLN0-0.034-0.01914.199-0.869-0.8690.0000.0000.0000.000
175A185ALA00.0120.01015.322-0.306-0.3060.0000.0000.0000.000
176A186PHE00.006-0.0119.255-0.620-0.6200.0000.0000.0000.000
177A187SER0-0.010-0.00610.453-1.837-1.8370.0000.0000.0000.000
178A188ASP-1-0.830-0.90612.300-17.348-17.3480.0000.0000.0000.000
179A189ALA0-0.061-0.03110.1590.3800.3800.0000.0000.0000.000
180A190LEU0-0.019-0.0065.741-0.647-0.6470.0000.0000.0000.000
181A191ASP-1-0.893-0.9528.922-19.846-19.8460.0000.0000.0000.000
182A192MET0-0.064-0.02411.5900.9920.9920.0000.0000.0000.000
183A193THR0-0.019-0.0286.2870.4330.4330.0000.0000.0000.000
184A194ARG10.8960.9508.94322.11322.1130.0000.0000.0000.000
185A195MET0-0.086-0.0379.7271.0621.0620.0000.0000.0000.000
186A196SER0-0.0510.00111.3021.3641.3640.0000.0000.0000.000