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: 5JZ6Z

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 OptHSide
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 -1884342.960195
FMO2-HF: Nuclear repulsion 1813549.957684
FMO2-HF: Total energy -70793.002511
FMO2-MP2: Total energy -71001.90836


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.
-155.566-152.78429.715-13.476-19.025-0.172
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 : 0.850 / q_NPA : 0.930
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].
3A13VAL0-0.044-0.0203.472-10.212-8.2030.025-1.002-1.0320.003
4A14ILE00.0220.0076.0135.2835.2830.0000.0000.0000.000
5A15TRP00.0190.0038.4050.3360.3360.0000.0000.0000.000
6A16THR00.0190.02011.0301.6511.6510.0000.0000.0000.000
7A17VAL0-0.006-0.00913.5960.5570.5570.0000.0000.0000.000
8A18SER0-0.038-0.01716.9540.4820.4820.0000.0000.0000.000
9A19VAL00.0360.00119.275-0.136-0.1360.0000.0000.0000.000
10A20THR00.0520.01521.719-0.170-0.1700.0000.0000.0000.000
11A21ARG10.9490.96421.44610.80610.8060.0000.0000.0000.000
12A22LEU0-0.0170.00118.845-0.361-0.3610.0000.0000.0000.000
13A23PHE0-0.023-0.00716.312-1.130-1.1300.0000.0000.0000.000
14A24GLU-1-0.849-0.91116.444-15.931-15.9310.0000.0000.0000.000
15A25LEU0-0.0030.00616.841-0.768-0.7680.0000.0000.0000.000
16A26PHE0-0.029-0.04713.757-0.899-0.8990.0000.0000.0000.000
17A27ARG10.7850.88212.31616.02916.0290.0000.0000.0000.000
18A28ASP-1-0.862-0.91612.019-19.851-19.8510.0000.0000.0000.000
19A29ILE0-0.018-0.01812.374-0.807-0.8070.0000.0000.0000.000
20A30SER00.0310.0088.185-0.586-0.5860.0000.0000.0000.000
21A31LEU0-0.0070.0077.388-4.773-4.7730.0000.0000.0000.000
22A32GLU-1-0.836-0.8678.541-23.200-23.2000.0000.0000.0000.000
23A33PHE0-0.037-0.0386.7720.5020.5020.0000.0000.0000.000
24A34ASP-1-0.801-0.8873.525-58.206-57.6340.001-0.238-0.335-0.001
25A35HIS0-0.058-0.0221.815-47.662-49.79710.655-4.573-3.947-0.058
26A36LEU0-0.042-0.0312.534-4.018-1.9801.747-1.527-2.259-0.025
27A37ALA0-0.003-0.0162.4000.9112.8212.758-1.449-3.219-0.016
28A38ASN0-0.040-0.0061.777-51.465-53.74014.512-4.489-7.749-0.074
29A39ILE00.0600.0293.48911.74212.0900.017-0.080-0.286-0.001
30A40THR0-0.054-0.0226.6511.5331.5330.0000.0000.0000.000
31A41PRO00.0200.0229.6621.3301.3300.0000.0000.0000.000
32A42ILE0-0.010-0.01312.8591.0901.0900.0000.0000.0000.000
33A43GLN00.0030.00016.1660.7090.7090.0000.0000.0000.000
34A44LEU0-0.053-0.02919.3050.9340.9340.0000.0000.0000.000
35A45GLY00.0490.01021.695-0.341-0.3410.0000.0000.0000.000
36A46PHE00.006-0.00823.9140.2960.2960.0000.0000.0000.000
37A47GLU-1-0.881-0.94025.075-10.871-10.8710.0000.0000.0000.000
38A48LYS10.9740.99225.35810.92510.9250.0000.0000.0000.000
39A49ALA00.0290.02520.983-0.402-0.4020.0000.0000.0000.000
40A50VAL00.0090.00421.217-0.553-0.5530.0000.0000.0000.000
41A51THR0-0.027-0.02522.256-0.175-0.1750.0000.0000.0000.000
42A52TYR00.0070.00116.229-0.348-0.3480.0000.0000.0000.000
43A53ILE00.0330.01116.665-0.552-0.5520.0000.0000.0000.000
44A54ARG10.8940.94017.96412.23912.2390.0000.0000.0000.000
45A55LYS10.9260.95920.00112.62312.6230.0000.0000.0000.000
46A56LYS10.8380.92811.71724.96124.9610.0000.0000.0000.000
47A57LEU0-0.026-0.02513.887-0.626-0.6260.0000.0000.0000.000
48A58ALA0-0.049-0.00616.1930.2000.2000.0000.0000.0000.000
49A59ASN0-0.057-0.02515.9960.7510.7510.0000.0000.0000.000
50A60GLU-1-0.847-0.90010.965-25.967-25.9670.0000.0000.0000.000
51A61ARG10.8300.8943.43837.79238.1070.000-0.118-0.1980.000
52A62CYS0-0.019-0.0219.607-2.187-2.1870.0000.0000.0000.000
53A63ASP-1-0.777-0.8476.301-31.934-31.9340.0000.0000.0000.000
54A64ALA00.0130.0029.6752.1252.1250.0000.0000.0000.000
55A65ILE00.002-0.00311.171-1.434-1.4340.0000.0000.0000.000
56A66ILE00.0020.02511.3360.8080.8080.0000.0000.0000.000
57A67ALA00.0230.01115.0250.1420.1420.0000.0000.0000.000
58A68ALA00.0550.03618.6550.1340.1340.0000.0000.0000.000
59A69GLY00.0150.01921.8490.2660.2660.0000.0000.0000.000
60A70SER00.0660.01925.351-0.315-0.3150.0000.0000.0000.000
61A71ASN00.0450.02321.5590.3610.3610.0000.0000.0000.000
62A72GLY00.0630.01021.624-0.198-0.1980.0000.0000.0000.000
63A73ALA0-0.007-0.00622.378-0.144-0.1440.0000.0000.0000.000
64A74TYR0-0.013-0.00525.1030.1030.1030.0000.0000.0000.000
65A75LEU00.013-0.00819.8220.1090.1090.0000.0000.0000.000
66A76LYS10.9150.95119.60614.76714.7670.0000.0000.0000.000
67A77SER0-0.034-0.01322.1560.1740.1740.0000.0000.0000.000
68A78ARG10.8830.95223.94111.61311.6130.0000.0000.0000.000
69A79LEU0-0.0360.00218.6380.0650.0650.0000.0000.0000.000
70A80SER00.0300.01520.0550.0670.0670.0000.0000.0000.000
71A81VAL00.0080.01313.770-0.119-0.1190.0000.0000.0000.000
72A82PRO00.0380.02113.9670.8510.8510.0000.0000.0000.000
73A83VAL0-0.0140.00315.036-1.004-1.0040.0000.0000.0000.000
74A84ILE00.0210.01313.8371.2831.2830.0000.0000.0000.000
75A85LEU0-0.063-0.02516.757-0.094-0.0940.0000.0000.0000.000
76A86ILE00.0570.01116.9500.4660.4660.0000.0000.0000.000
77A87LYS10.9450.95520.83312.40612.4060.0000.0000.0000.000
78A88PRO00.0340.02824.556-0.061-0.0610.0000.0000.0000.000
79A89SER00.0420.03226.0310.5530.5530.0000.0000.0000.000
80A90GLY00.0600.00928.302-0.054-0.0540.0000.0000.0000.000
81A91TYR00.0420.02327.4250.1870.1870.0000.0000.0000.000
82A92ASP-1-0.808-0.88524.347-13.386-13.3860.0000.0000.0000.000
83A93VAL00.0370.02327.185-0.010-0.0100.0000.0000.0000.000
84A94LEU0-0.002-0.00129.5880.1070.1070.0000.0000.0000.000
85A95GLN0-0.058-0.01826.293-0.011-0.0110.0000.0000.0000.000
86A96PHE00.0210.00023.883-0.012-0.0120.0000.0000.0000.000
87A97LEU00.0280.00928.3850.1360.1360.0000.0000.0000.000
88A98ALA0-0.023-0.02332.1150.1810.1810.0000.0000.0000.000
89A99LYS10.9110.96326.87611.79211.7920.0000.0000.0000.000
90A100ALA0-0.0080.01330.3900.0910.0910.0000.0000.0000.000
91A101GLY00.0100.00631.8720.2540.2540.0000.0000.0000.000
92A102LYS10.8320.89334.4008.7488.7480.0000.0000.0000.000
93A103LEU0-0.022-0.00535.2660.1280.1280.0000.0000.0000.000
94A104THR00.0350.01336.9470.1650.1650.0000.0000.0000.000
95A105SER0-0.084-0.02838.8660.2320.2320.0000.0000.0000.000
96A106SER00.0280.00940.8700.0290.0290.0000.0000.0000.000
97A107ILE0-0.0240.00135.597-0.146-0.1460.0000.0000.0000.000
98A108GLY00.0720.04537.6750.2120.2120.0000.0000.0000.000
99A109VAL0-0.075-0.04133.521-0.341-0.3410.0000.0000.0000.000
100A110VAL00.0490.02934.6980.2260.2260.0000.0000.0000.000
101A111THR0-0.057-0.06431.755-0.332-0.3320.0000.0000.0000.000
102A112TYR0-0.047-0.01931.9240.1610.1610.0000.0000.0000.000
103A113GLN0-0.018-0.01233.883-0.372-0.3720.0000.0000.0000.000
104A114GLU-1-0.938-0.96334.165-8.908-8.9080.0000.0000.0000.000
105A115THR00.0210.03635.353-0.275-0.2750.0000.0000.0000.000
106A116ILE00.0370.01330.842-0.125-0.1250.0000.0000.0000.000
107A117PRO00.0640.02534.3390.1280.1280.0000.0000.0000.000
108A118ALA0-0.001-0.00333.1610.1630.1630.0000.0000.0000.000
109A119LEU00.0370.01733.3340.0490.0490.0000.0000.0000.000
110A120VAL00.0060.01136.0550.2480.2480.0000.0000.0000.000
111A121ALA0-0.015-0.01438.4690.2300.2300.0000.0000.0000.000
112A122PHE00.0360.01436.7460.1740.1740.0000.0000.0000.000
113A123GLN00.018-0.00339.2030.0000.0000.0000.0000.0000.000
114A124LYS10.8990.94241.3297.4207.4200.0000.0000.0000.000
115A125THR0-0.046-0.01742.0640.1880.1880.0000.0000.0000.000
116A126PHE0-0.038-0.03239.6710.1230.1230.0000.0000.0000.000
117A127ASN0-0.0340.00643.5430.0310.0310.0000.0000.0000.000
118A128LEU00.0250.02838.9380.0480.0480.0000.0000.0000.000
119A129ARG10.8820.94242.1697.4627.4620.0000.0000.0000.000
120A130LEU0-0.005-0.00136.424-0.184-0.1840.0000.0000.0000.000
121A131ASP-1-0.802-0.87640.136-7.438-7.4380.0000.0000.0000.000
122A132GLN0-0.070-0.05037.582-0.324-0.3240.0000.0000.0000.000
123A133ARG10.8130.87138.5327.5937.5930.0000.0000.0000.000
124A134SER0-0.032-0.01237.534-0.206-0.2060.0000.0000.0000.000
125A135TYR0-0.0030.00132.4960.0460.0460.0000.0000.0000.000
126A136ILE0-0.029-0.01936.938-0.283-0.2830.0000.0000.0000.000
127A137THR0-0.058-0.06336.558-0.289-0.2890.0000.0000.0000.000
128A138GLU-1-0.814-0.90736.514-8.778-8.7780.0000.0000.0000.000
129A139GLU-1-0.914-0.95938.031-7.218-7.2180.0000.0000.0000.000
130A140ASP-1-0.751-0.83739.857-7.860-7.8600.0000.0000.0000.000
131A141ALA0-0.018-0.02036.7800.0540.0540.0000.0000.0000.000
132A142ARG10.8460.90537.6688.4008.4000.0000.0000.0000.000
133A143GLY00.0370.03240.7940.0890.0890.0000.0000.0000.000
134A144GLN0-0.013-0.02140.1390.0640.0640.0000.0000.0000.000
135A145ILE0-0.004-0.00436.5010.0270.0270.0000.0000.0000.000
136A146ASN0-0.015-0.01040.6250.0150.0150.0000.0000.0000.000
137A147GLU-1-0.869-0.91744.134-6.896-6.8960.0000.0000.0000.000
138A148LEU0-0.039-0.02039.2540.0470.0470.0000.0000.0000.000
139A149LYS10.8840.93242.2077.6447.6440.0000.0000.0000.000
140A150ALA0-0.048-0.02643.9140.1050.1050.0000.0000.0000.000
141A151ASN0-0.040-0.00945.0930.0620.0620.0000.0000.0000.000
142A152GLY00.0030.01045.9980.0310.0310.0000.0000.0000.000
143A153THR0-0.081-0.03539.704-0.131-0.1310.0000.0000.0000.000
144A154GLU-1-0.783-0.88839.410-7.913-7.9130.0000.0000.0000.000
145A155ALA0-0.018-0.00134.886-0.189-0.1890.0000.0000.0000.000
146A156VAL00.0270.00934.8800.1490.1490.0000.0000.0000.000
147A157VAL0-0.030-0.01130.096-0.333-0.3330.0000.0000.0000.000
148A158GLY00.0700.01430.3540.2920.2920.0000.0000.0000.000
149A159ALA0-0.0010.00527.228-0.428-0.4280.0000.0000.0000.000
150A160GLY0-0.0060.00227.3220.1810.1810.0000.0000.0000.000
151A161LEU00.0860.04727.9490.1030.1030.0000.0000.0000.000
152A162ILE0-0.0070.00831.5550.2070.2070.0000.0000.0000.000
153A163THR0-0.043-0.03128.7410.0620.0620.0000.0000.0000.000
154A164ASP-1-0.815-0.89029.708-10.872-10.8720.0000.0000.0000.000
155A165LEU00.0250.00932.2190.2420.2420.0000.0000.0000.000
156A166ALA0-0.015-0.00934.2580.2640.2640.0000.0000.0000.000
157A167GLU-1-0.844-0.92431.731-9.663-9.6630.0000.0000.0000.000
158A168GLU-1-0.954-0.96835.166-8.604-8.6040.0000.0000.0000.000
159A169ALA0-0.0320.00137.6150.2720.2720.0000.0000.0000.000
160A170GLY00.0010.00138.7690.2660.2660.0000.0000.0000.000
161A171MET0-0.133-0.04437.8570.1750.1750.0000.0000.0000.000
162A172THR00.002-0.00232.705-0.127-0.1270.0000.0000.0000.000
163A173GLY00.0290.01531.8820.1200.1200.0000.0000.0000.000
164A174ILE0-0.074-0.03928.928-0.344-0.3440.0000.0000.0000.000
165A175PHE00.010-0.01821.8090.0390.0390.0000.0000.0000.000
166A176ILE0-0.042-0.03526.329-0.164-0.1640.0000.0000.0000.000
167A177TYR0-0.061-0.02321.381-0.075-0.0750.0000.0000.0000.000
168A178SER00.0430.00722.359-0.385-0.3850.0000.0000.0000.000
169A179ALA00.0570.00818.396-0.567-0.5670.0000.0000.0000.000
170A180ALA0-0.016-0.00117.694-0.993-0.9930.0000.0000.0000.000
171A181THR0-0.002-0.02018.797-0.723-0.7230.0000.0000.0000.000
172A182VAL0-0.015-0.00514.529-0.441-0.4410.0000.0000.0000.000
173A183ARG10.8190.86713.99518.34718.3470.0000.0000.0000.000
174A184GLN0-0.053-0.03714.012-1.058-1.0580.0000.0000.0000.000
175A185ALA00.0170.01515.339-0.382-0.3820.0000.0000.0000.000
176A186PHE00.010-0.0099.330-0.894-0.8940.0000.0000.0000.000
177A187SER0-0.015-0.01310.464-1.905-1.9050.0000.0000.0000.000
178A188ASP-1-0.826-0.89712.303-17.876-17.8760.0000.0000.0000.000
179A189ALA0-0.049-0.02310.2190.3290.3290.0000.0000.0000.000
180A190LEU0-0.0170.0075.656-0.753-0.7530.0000.0000.0000.000
181A191ASP-1-0.799-0.8898.937-20.561-20.5610.0000.0000.0000.000
182A192MET0-0.059-0.02011.3941.1001.1000.0000.0000.0000.000
183A193THR0-0.035-0.0516.8990.2630.2630.0000.0000.0000.000
184A194ARG10.8060.8939.04822.61822.6180.0000.0000.0000.000
185A195MET0-0.081-0.0379.7281.1591.1590.0000.0000.0000.000
186A196SER0-0.0480.00411.2161.5101.5100.0000.0000.0000.000