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: YV822

Calculation Name: 4JZ5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JZ5

Chain ID: A

ChEMBL ID:

UniProt ID: B6D7J9

Base Structure: X-ray

Registration Date: 2023-09-23

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2498661.822977
FMO2-HF: Nuclear repulsion 2417113.18058
FMO2-HF: Total energy -81548.642397
FMO2-MP2: Total energy -81785.881341


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:-3:GLY)


Summations of interaction energy for fragment #1(A:-3:GLY)
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.
-1.4291.06-0.023-1.357-1.1080.004
Interaction energy analysis for fragmet #1(A:-3:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.016
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].
3A-1HIS00.0450.0223.766-0.4621.926-0.023-1.322-1.0420.004
4A0MET0-0.034-0.0016.7540.6820.6820.0000.0000.0000.000
5A1MET0-0.048-0.0236.249-0.166-0.1660.0000.0000.0000.000
6A2VAL00.0210.0125.469-0.117-0.1170.0000.0000.0000.000
7A3LEU00.0440.0377.9660.1390.1390.0000.0000.0000.000
8A4VAL0-0.009-0.00411.687-0.023-0.0230.0000.0000.0000.000
9A5LEU0-0.0040.00414.2380.0040.0040.0000.0000.0000.000
10A6ASP-1-0.788-0.88317.8980.0530.0530.0000.0000.0000.000
11A7ILE00.0160.00821.137-0.015-0.0150.0000.0000.0000.000
12A8SER00.0290.00324.3280.0150.0150.0000.0000.0000.000
13A9LYS10.9120.96228.0020.0050.0050.0000.0000.0000.000
14A10TRP0-0.040-0.03729.159-0.006-0.0060.0000.0000.0000.000
15A11GLN00.0160.01525.0750.0010.0010.0000.0000.0000.000
16A12PRO00.0030.00328.428-0.003-0.0030.0000.0000.0000.000
17A13THR0-0.016-0.01129.4500.0000.0000.0000.0000.0000.000
18A14VAL00.0340.02323.579-0.004-0.0040.0000.0000.0000.000
19A15ASN0-0.0080.00124.5610.0050.0050.0000.0000.0000.000
20A16TYR00.041-0.03122.709-0.022-0.0220.0000.0000.0000.000
21A17SER0-0.021-0.00221.144-0.019-0.0190.0000.0000.0000.000
22A18GLY0-0.010-0.01120.346-0.034-0.0340.0000.0000.0000.000
23A19LEU0-0.021-0.02017.974-0.019-0.0190.0000.0000.0000.000
24A20LYS10.8480.91816.1000.2650.2650.0000.0000.0000.000
25A21GLU-1-0.977-0.96114.134-0.666-0.6660.0000.0000.0000.000
26A22ASP-1-0.863-0.93311.914-0.833-0.8330.0000.0000.0000.000
27A23VAL0-0.095-0.04511.6240.0140.0140.0000.0000.0000.000
28A24GLY0-0.001-0.00111.094-0.028-0.0280.0000.0000.0000.000
29A25PHE0-0.012-0.02912.0100.0700.0700.0000.0000.0000.000
30A26VAL00.0100.00615.085-0.019-0.0190.0000.0000.0000.000
31A27VAL0-0.0100.00918.4820.0190.0190.0000.0000.0000.000
32A28ILE0-0.003-0.00321.018-0.015-0.0150.0000.0000.0000.000
33A29ARG10.8580.93424.5970.0020.0020.0000.0000.0000.000
34A30SER00.004-0.01027.709-0.007-0.0070.0000.0000.0000.000
35A31SER00.005-0.00830.185-0.004-0.0040.0000.0000.0000.000
36A32ASN0-0.0100.01832.3830.0050.0050.0000.0000.0000.000
37A33GLY00.0530.02334.993-0.003-0.0030.0000.0000.0000.000
38A34THR00.028-0.01736.854-0.001-0.0010.0000.0000.0000.000
39A35GLN0-0.0450.01039.235-0.001-0.0010.0000.0000.0000.000
40A36LYS10.8410.89835.936-0.006-0.0060.0000.0000.0000.000
41A37TYR00.0320.00434.3230.0050.0050.0000.0000.0000.000
42A38ASP-1-0.763-0.87431.239-0.012-0.0120.0000.0000.0000.000
43A39GLU-1-0.763-0.88733.414-0.009-0.0090.0000.0000.0000.000
44A40ARG10.8470.92730.4460.0410.0410.0000.0000.0000.000
45A41LEU00.0190.02729.000-0.005-0.0050.0000.0000.0000.000
46A42GLU-1-0.878-0.95029.554-0.015-0.0150.0000.0000.0000.000
47A43GLN0-0.083-0.03429.5130.0000.0000.0000.0000.0000.000
48A44HIS00.0370.03825.840-0.018-0.0180.0000.0000.0000.000
49A45ALA00.0220.01925.879-0.009-0.0090.0000.0000.0000.000
50A46LYS10.9850.99226.3860.0370.0370.0000.0000.0000.000
51A47GLY0-0.037-0.01626.659-0.010-0.0100.0000.0000.0000.000
52A48LEU0-0.018-0.03020.651-0.022-0.0220.0000.0000.0000.000
53A49ASP-1-0.870-0.93522.322-0.070-0.0700.0000.0000.0000.000
54A50LYS10.9060.97324.0750.1150.1150.0000.0000.0000.000
55A51VAL0-0.057-0.03120.573-0.012-0.0120.0000.0000.0000.000
56A52GLY00.0600.03319.973-0.036-0.0360.0000.0000.0000.000
57A53MET0-0.128-0.04715.901-0.014-0.0140.0000.0000.0000.000
58A54PRO00.0000.00814.8220.0290.0290.0000.0000.0000.000
59A55PHE00.028-0.01017.940-0.007-0.0070.0000.0000.0000.000
60A56GLY00.0670.03820.0410.0220.0220.0000.0000.0000.000
61A57LEU0-0.045-0.01521.905-0.020-0.0200.0000.0000.0000.000
62A58TYR00.0820.02124.0450.0200.0200.0000.0000.0000.000
63A59HIS10.7400.86726.139-0.070-0.0700.0000.0000.0000.000
64A60TYR0-0.051-0.04729.6750.0090.0090.0000.0000.0000.000
65A61ALA0-0.029-0.02331.345-0.005-0.0050.0000.0000.0000.000
66A62LEU0-0.073-0.04533.727-0.003-0.0030.0000.0000.0000.000
67A63PHE0-0.0070.01633.998-0.001-0.0010.0000.0000.0000.000
68A64GLU-1-0.906-0.98239.0110.0400.0400.0000.0000.0000.000
69A65GLY00.0150.01841.1950.0010.0010.0000.0000.0000.000
70A66GLY00.0110.00242.140-0.003-0.0030.0000.0000.0000.000
71A67GLN00.026-0.00942.2820.0050.0050.0000.0000.0000.000
72A68ASP-1-0.792-0.88341.6970.0450.0450.0000.0000.0000.000
73A69THR0-0.023-0.02236.922-0.001-0.0010.0000.0000.0000.000
74A70ILE00.0070.01137.5100.0030.0030.0000.0000.0000.000
75A71ASN00.0150.00638.5050.0010.0010.0000.0000.0000.000
76A72GLU-1-0.712-0.85735.8360.0510.0510.0000.0000.0000.000
77A73ALA0-0.0050.00134.0210.0000.0000.0000.0000.0000.000
78A74ASN00.0390.00234.3020.0040.0040.0000.0000.0000.000
79A75MET0-0.0450.01335.410-0.005-0.0050.0000.0000.0000.000
80A76LEU0-0.0080.00628.105-0.005-0.0050.0000.0000.0000.000
81A77VAL00.0290.01131.468-0.002-0.0020.0000.0000.0000.000
82A78SER0-0.032-0.02433.197-0.005-0.0050.0000.0000.0000.000
83A79ALA0-0.023-0.01331.207-0.006-0.0060.0000.0000.0000.000
84A80TYR00.0320.01426.464-0.009-0.0090.0000.0000.0000.000
85A81LYS10.9720.97930.345-0.049-0.0490.0000.0000.0000.000
86A82LYS10.9140.97033.343-0.015-0.0150.0000.0000.0000.000
87A83CYS0-0.040-0.01628.324-0.008-0.0080.0000.0000.0000.000
88A84ARG10.8600.90428.685-0.041-0.0410.0000.0000.0000.000
89A85GLN0-0.069-0.01930.840-0.001-0.0010.0000.0000.0000.000
90A86LEU0-0.112-0.06431.353-0.006-0.0060.0000.0000.0000.000
91A87GLY00.0090.01430.336-0.008-0.0080.0000.0000.0000.000
92A88ALA00.0150.02526.206-0.002-0.0020.0000.0000.0000.000
93A89GLU-1-0.792-0.88623.8850.0410.0410.0000.0000.0000.000
94A90PRO0-0.069-0.02223.0060.0040.0040.0000.0000.0000.000
95A91THR00.013-0.01918.735-0.003-0.0030.0000.0000.0000.000
96A92PHE0-0.064-0.03418.6560.0410.0410.0000.0000.0000.000
97A93LEU0-0.030-0.00121.774-0.029-0.0290.0000.0000.0000.000
98A94PHE00.0210.01218.9550.0200.0200.0000.0000.0000.000
99A95LEU0-0.0070.00625.042-0.019-0.0190.0000.0000.0000.000
100A96ASH0-0.103-0.09026.8260.0090.0090.0000.0000.0000.000
101A97TYR00.043-0.00627.947-0.010-0.0100.0000.0000.0000.000
102A98GLU-1-0.808-0.88028.8220.0680.0680.0000.0000.0000.000
103A99GLU-1-0.865-0.90331.3370.0350.0350.0000.0000.0000.000
104A100VAL0-0.021-0.01735.1450.0040.0040.0000.0000.0000.000
105A101LYS10.9350.97137.953-0.042-0.0420.0000.0000.0000.000
106A102LEU0-0.055-0.01238.684-0.002-0.0020.0000.0000.0000.000
107A103LYS10.9520.97841.919-0.039-0.0390.0000.0000.0000.000
108A104SER0-0.030-0.01144.606-0.001-0.0010.0000.0000.0000.000
109A105GLY00.0560.03242.8640.0010.0010.0000.0000.0000.000
110A106ASN00.0120.00138.0050.0040.0040.0000.0000.0000.000
111A107VAL00.0590.01933.8580.0010.0010.0000.0000.0000.000
112A108VAL00.0230.02432.8600.0020.0020.0000.0000.0000.000
113A109ASN00.0320.00634.4310.0090.0090.0000.0000.0000.000
114A110GLU-1-0.821-0.89836.7160.0760.0760.0000.0000.0000.000
115A111CYS0-0.021-0.01031.334-0.001-0.0010.0000.0000.0000.000
116A112GLN0-0.033-0.01230.4990.0080.0080.0000.0000.0000.000
117A113ARG10.8460.91733.415-0.074-0.0740.0000.0000.0000.000
118A114PHE0-0.0050.00330.145-0.002-0.0020.0000.0000.0000.000
119A115ILE00.023-0.00627.891-0.001-0.0010.0000.0000.0000.000
120A116ASP-1-0.864-0.92530.9780.1330.1330.0000.0000.0000.000
121A117HIS0-0.046-0.02633.0420.0010.0010.0000.0000.0000.000
122A118VAL00.006-0.00629.465-0.004-0.0040.0000.0000.0000.000
123A119LYS10.8540.92126.138-0.189-0.1890.0000.0000.0000.000
124A120GLY0-0.0100.00230.3040.0000.0000.0000.0000.0000.000
125A121GLN0-0.067-0.02733.669-0.010-0.0100.0000.0000.0000.000
126A122THR0-0.052-0.03429.487-0.003-0.0030.0000.0000.0000.000
127A123GLY00.0090.01829.228-0.002-0.0020.0000.0000.0000.000
128A124VAL0-0.043-0.00824.1010.0150.0150.0000.0000.0000.000
129A125LYS10.9190.95620.145-0.290-0.2900.0000.0000.0000.000
130A126VAL00.018-0.00423.971-0.016-0.0160.0000.0000.0000.000
131A127GLY00.0050.01222.3570.0180.0180.0000.0000.0000.000
132A128LEU0-0.032-0.01823.191-0.027-0.0270.0000.0000.0000.000
133A129TYR0-0.025-0.03322.1370.0220.0220.0000.0000.0000.000
134A130ALA00.0260.01824.390-0.014-0.0140.0000.0000.0000.000
135A131GLY00.0420.02924.5490.0120.0120.0000.0000.0000.000
136A132ASP-1-0.756-0.85724.2750.1630.1630.0000.0000.0000.000
137A133SER0-0.016-0.01325.7420.0050.0050.0000.0000.0000.000
138A134PHE00.0560.03329.4620.0000.0000.0000.0000.0000.000
139A135TRP00.019-0.01823.680-0.002-0.0020.0000.0000.0000.000
140A136LYS10.8800.93627.695-0.139-0.1390.0000.0000.0000.000
141A137THR0-0.038-0.01930.125-0.003-0.0030.0000.0000.0000.000
142A138HIS10.8550.93232.390-0.098-0.0980.0000.0000.0000.000
143A139ASP-1-0.863-0.92332.2640.1210.1210.0000.0000.0000.000
144A140LEU00.021-0.00828.2460.0040.0040.0000.0000.0000.000
145A141ASP-1-0.837-0.89226.3000.2250.2250.0000.0000.0000.000
146A142LYS10.8570.93028.255-0.119-0.1190.0000.0000.0000.000
147A143VAL0-0.043-0.00428.732-0.005-0.0050.0000.0000.0000.000
148A144LYS10.9150.95927.783-0.151-0.1510.0000.0000.0000.000
149A145HIS00.0400.00422.685-0.011-0.0110.0000.0000.0000.000
150A146ASP-1-0.817-0.90021.6880.2580.2580.0000.0000.0000.000
151A147LEU0-0.051-0.03916.0740.0410.0410.0000.0000.0000.000
152A148ARG10.8050.89319.429-0.331-0.3310.0000.0000.0000.000
153A149TRP0-0.026-0.00718.6620.0440.0440.0000.0000.0000.000
154A150VAL00.0160.00519.412-0.026-0.0260.0000.0000.0000.000
155A151ALA00.0330.02719.9730.0060.0060.0000.0000.0000.000
156A152ARG10.8480.90921.365-0.108-0.1080.0000.0000.0000.000
157A153TYR00.0670.00921.1560.0010.0010.0000.0000.0000.000
158A154GLY0-0.033-0.00123.082-0.011-0.0110.0000.0000.0000.000
159A155VAL0-0.028-0.02623.831-0.003-0.0030.0000.0000.0000.000
160A156ASP-1-0.773-0.84423.736-0.016-0.0160.0000.0000.0000.000
161A157ASN00.013-0.00222.123-0.004-0.0040.0000.0000.0000.000
162A158GLY00.0360.01921.315-0.018-0.0180.0000.0000.0000.000
163A159LYS10.8920.93716.5230.2320.2320.0000.0000.0000.000
164A160PRO00.0040.00614.0130.0220.0220.0000.0000.0000.000
165A161SER00.0670.04417.167-0.011-0.0110.0000.0000.0000.000
166A162THR0-0.048-0.03819.1790.0190.0190.0000.0000.0000.000
167A163LYS10.9921.00113.679-0.368-0.3680.0000.0000.0000.000
168A164PRO0-0.031-0.01818.400-0.019-0.0190.0000.0000.0000.000
169A165SER0-0.072-0.06221.2570.0120.0120.0000.0000.0000.000
170A166ILE00.0040.01222.5000.0020.0020.0000.0000.0000.000
171A167PRO00.0380.00819.3610.0110.0110.0000.0000.0000.000
172A168TYR0-0.026-0.01112.833-0.053-0.0530.0000.0000.0000.000
173A169ASP-1-0.797-0.88515.0570.5440.5440.0000.0000.0000.000
174A170LEU0-0.059-0.03613.7550.0730.0730.0000.0000.0000.000
175A171TRP0-0.055-0.02714.203-0.024-0.0240.0000.0000.0000.000
176A172GLN00.0640.05916.136-0.014-0.0140.0000.0000.0000.000
177A173TYR00.004-0.01714.069-0.006-0.0060.0000.0000.0000.000
178A174THR0-0.074-0.04618.860-0.021-0.0210.0000.0000.0000.000
179A175SER00.0350.00421.382-0.001-0.0010.0000.0000.0000.000
180A176LYS10.8540.92523.4180.0200.0200.0000.0000.0000.000
181A177GLY00.0260.01720.793-0.015-0.0150.0000.0000.0000.000
182A178ARG10.9520.96720.8190.2060.2060.0000.0000.0000.000
183A179ILE00.0480.01518.093-0.030-0.0300.0000.0000.0000.000
184A180LYS10.9860.98720.9230.2550.2550.0000.0000.0000.000
185A181ALA0-0.024-0.00321.6170.0160.0160.0000.0000.0000.000
186A182ILE00.0090.00222.1750.0180.0180.0000.0000.0000.000
187A183ALA0-0.0020.00725.165-0.003-0.0030.0000.0000.0000.000
188A184SER0-0.021-0.01127.7350.0000.0000.0000.0000.0000.000
189A185PRO00.0060.01225.638-0.009-0.0090.0000.0000.0000.000
190A186VAL0-0.021-0.01120.8040.0060.0060.0000.0000.0000.000
191A187ASP-1-0.787-0.87621.370-0.003-0.0030.0000.0000.0000.000
192A188MET0-0.116-0.04915.662-0.017-0.0170.0000.0000.0000.000
193A189ASN00.003-0.01715.5020.0580.0580.0000.0000.0000.000
194A190THR0-0.036-0.02610.0070.0070.0070.0000.0000.0000.000
195A191CYS00.0130.0009.756-0.040-0.0400.0000.0000.0000.000
196A192SER00.0340.0337.3290.0230.0230.0000.0000.0000.000
197A193SER00.0600.0024.113-0.0890.0120.000-0.035-0.0660.000
198A194ASP-1-0.907-0.9426.4320.8530.8530.0000.0000.0000.000
199A195ILE00.0290.0149.685-0.281-0.2810.0000.0000.0000.000
200A196LEU0-0.022-0.0068.103-0.183-0.1830.0000.0000.0000.000
201A197ASN0-0.030-0.02310.015-0.168-0.1680.0000.0000.0000.000
202A198LYS10.9670.99411.672-0.573-0.5730.0000.0000.0000.000
203A199LEU0-0.035-0.01413.315-0.081-0.0810.0000.0000.0000.000
204A200LYS10.9130.95810.472-0.049-0.0490.0000.0000.0000.000
205A201GLY00.0380.03515.748-0.038-0.0380.0000.0000.0000.000
206A202SER0-0.082-0.02615.161-0.009-0.0090.0000.0000.0000.000