Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5JN7Z

Calculation Name: 1YZF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YZF

Chain ID: A

ChEMBL ID:

UniProt ID: Q839J6

Base Structure: X-ray

Registration Date: 2023-09-22

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2187602.771621
FMO2-HF: Nuclear repulsion 2112800.090672
FMO2-HF: Total energy -74802.680948
FMO2-MP2: Total energy -75022.766266


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: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.
-11.812-7.05410.431-3.655-11.532-0.045
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 : 0 / q_Mulliken : -0.056 / q_NPA : -0.025
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].
3A3LYS10.8390.9043.058-1.9440.7440.133-1.351-1.471-0.005
4A4ILE0-0.008-0.0025.5360.3600.3600.0000.0000.0000.000
5A5VAL00.004-0.0088.2170.1880.1880.0000.0000.0000.000
6A6LEU0-0.001-0.00411.304-0.006-0.0060.0000.0000.0000.000
7A7PHE00.002-0.00214.0740.0110.0110.0000.0000.0000.000
8A8GLY00.0660.01617.2410.0000.0000.0000.0000.0000.000
9A9ASP-1-0.868-0.93720.457-0.003-0.0030.0000.0000.0000.000
10A10SER00.035-0.00822.2530.0040.0040.0000.0000.0000.000
11A11ILE00.0090.02921.8370.0040.0040.0000.0000.0000.000
12A12THR00.0100.02117.0860.0070.0070.0000.0000.0000.000
13A13ALA00.0100.01918.3720.0140.0140.0000.0000.0000.000
14A14GLY00.0450.03519.6500.0090.0090.0000.0000.0000.000
15A15TYR0-0.052-0.04620.6740.0100.0100.0000.0000.0000.000
16A16LEU0-0.0210.00322.700-0.004-0.0040.0000.0000.0000.000
17A17ASP-1-0.890-0.95126.3050.0080.0080.0000.0000.0000.000
18A18GLU-1-0.972-0.96624.0400.0100.0100.0000.0000.0000.000
19A19ALA00.015-0.00624.6450.0030.0030.0000.0000.0000.000
20A20VAL0-0.018-0.02219.6440.0010.0010.0000.0000.0000.000
21A21SER00.001-0.00119.4770.0010.0010.0000.0000.0000.000
22A22PRO0-0.0060.00814.8590.0070.0070.0000.0000.0000.000
23A23VAL00.0100.01014.5890.0360.0360.0000.0000.0000.000
24A24LEU00.0640.03815.2050.0150.0150.0000.0000.0000.000
25A25VAL00.012-0.0069.7710.0160.0160.0000.0000.0000.000
26A26ASP-1-0.908-0.96111.0480.3070.3070.0000.0000.0000.000
27A27LEU0-0.059-0.02112.3750.0050.0050.0000.0000.0000.000
28A28VAL00.0430.0199.930-0.007-0.0070.0000.0000.0000.000
29A29LYS10.9150.9606.504-1.132-1.1320.0000.0000.0000.000
30A30ARG10.9410.9819.396-0.139-0.1390.0000.0000.0000.000
31A31ASP-1-0.861-0.93812.2120.0450.0450.0000.0000.0000.000
32A32ILE0-0.030-0.0267.638-0.034-0.0340.0000.0000.0000.000
33A33ALA0-0.019-0.0119.454-0.040-0.0400.0000.0000.0000.000
34A34ALA0-0.018-0.00610.674-0.044-0.0440.0000.0000.0000.000
35A35MET0-0.103-0.03112.607-0.016-0.0160.0000.0000.0000.000
36A36GLY0-0.0120.00212.5960.0010.0010.0000.0000.0000.000
37A37LEU0-0.030-0.0119.3740.0060.0060.0000.0000.0000.000
38A38GLU-1-0.882-0.9374.8290.5760.685-0.001-0.004-0.1040.000
39A39GLU-1-0.944-0.9752.878-6.668-3.9761.688-1.392-2.988-0.011
40A40VAL0-0.003-0.0111.982-2.567-2.4546.070-2.623-3.559-0.022
41A41ALA0-0.007-0.0062.5682.9832.2432.5041.519-3.282-0.007
42A42VAL0-0.009-0.0054.019-1.206-1.3100.0370.196-0.1280.000
43A43ILE0-0.010-0.0067.5520.1630.1630.0000.0000.0000.000
44A44ASN0-0.001-0.01610.509-0.091-0.0910.0000.0000.0000.000
45A45ALA00.0170.02314.084-0.008-0.0080.0000.0000.0000.000
46A46GLY00.0310.00216.306-0.015-0.0150.0000.0000.0000.000
47A47MET0-0.030-0.00519.2040.0030.0030.0000.0000.0000.000
48A48PRO00.014-0.01722.639-0.001-0.0010.0000.0000.0000.000
49A49GLY0-0.0040.00425.548-0.003-0.0030.0000.0000.0000.000
50A50ASP-1-0.732-0.85224.219-0.021-0.0210.0000.0000.0000.000
51A51THR0-0.071-0.03326.9670.0010.0010.0000.0000.0000.000
52A52THR00.022-0.04525.735-0.002-0.0020.0000.0000.0000.000
53A53GLU-1-0.946-0.96126.691-0.021-0.0210.0000.0000.0000.000
54A54ASP-1-0.884-0.94327.093-0.019-0.0190.0000.0000.0000.000
55A55GLY00.0560.02023.363-0.003-0.0030.0000.0000.0000.000
56A56LEU0-0.024-0.02222.829-0.008-0.0080.0000.0000.0000.000
57A57LYS10.8700.94824.2750.0200.0200.0000.0000.0000.000
58A58ARG10.7290.84919.2420.0210.0210.0000.0000.0000.000
59A59LEU00.0140.03819.178-0.008-0.0080.0000.0000.0000.000
60A60ASN00.0410.00618.194-0.023-0.0230.0000.0000.0000.000
61A61LYS10.9250.95017.6980.0450.0450.0000.0000.0000.000
62A62GLU-1-0.875-0.94616.133-0.045-0.0450.0000.0000.0000.000
63A63VAL00.0180.03014.174-0.005-0.0050.0000.0000.0000.000
64A64LEU00.0040.00213.336-0.061-0.0610.0000.0000.0000.000
65A65ILE0-0.048-0.02113.676-0.047-0.0470.0000.0000.0000.000
66A66GLU-1-0.866-0.9199.514-0.195-0.1950.0000.0000.0000.000
67A67LYS10.8480.9208.8590.0780.0780.0000.0000.0000.000
68A68PRO00.0060.0208.516-0.223-0.2230.0000.0000.0000.000
69A69ASP-1-0.870-0.9366.186-1.494-1.4940.0000.0000.0000.000
70A70GLU-1-0.907-0.9899.575-0.018-0.0180.0000.0000.0000.000
71A71VAL0-0.0120.00110.962-0.044-0.0440.0000.0000.0000.000
72A72VAL0-0.0070.00113.0180.0210.0210.0000.0000.0000.000
73A73ILE0-0.011-0.00815.4860.0090.0090.0000.0000.0000.000
74A74PHE0-0.030-0.02818.9540.0060.0060.0000.0000.0000.000
75A75PHE00.0520.03520.9140.0040.0040.0000.0000.0000.000
76A76GLY00.042-0.00424.4590.0010.0010.0000.0000.0000.000
77A77ALA00.0060.01127.3050.0010.0010.0000.0000.0000.000
78A78ASN0-0.059-0.03727.6380.0020.0020.0000.0000.0000.000
79A79ASP-1-0.738-0.85428.774-0.014-0.0140.0000.0000.0000.000
80A80ALA00.013-0.00331.6770.0000.0000.0000.0000.0000.000
81A81SER0-0.058-0.01633.7880.0000.0000.0000.0000.0000.000
82A82LEU0-0.011-0.02935.762-0.001-0.0010.0000.0000.0000.000
83A83ASP-1-0.885-0.92437.671-0.004-0.0040.0000.0000.0000.000
84A84ARG10.7570.87830.9130.0080.0080.0000.0000.0000.000
85A85ASN00.0130.00235.4440.0010.0010.0000.0000.0000.000
86A86ILE00.0280.03731.958-0.001-0.0010.0000.0000.0000.000
87A87THR00.0440.02635.1480.0010.0010.0000.0000.0000.000
88A88VAL00.0550.01535.098-0.001-0.0010.0000.0000.0000.000
89A89ALA0-0.019-0.01834.389-0.001-0.0010.0000.0000.0000.000
90A90THR00.0700.03732.798-0.001-0.0010.0000.0000.0000.000
91A91PHE00.0370.02627.475-0.002-0.0020.0000.0000.0000.000
92A92ARG10.8510.91429.6250.0060.0060.0000.0000.0000.000
93A93GLU-1-0.947-0.97229.951-0.018-0.0180.0000.0000.0000.000
94A94ASN00.0350.00927.925-0.004-0.0040.0000.0000.0000.000
95A95LEU0-0.013-0.00524.444-0.005-0.0050.0000.0000.0000.000
96A96GLU-1-0.829-0.89925.148-0.024-0.0240.0000.0000.0000.000
97A97THR0-0.011-0.01226.105-0.003-0.0030.0000.0000.0000.000
98A98MET0-0.045-0.02121.873-0.006-0.0060.0000.0000.0000.000
99A99ILE0-0.015-0.00821.443-0.011-0.0110.0000.0000.0000.000
100A100HIS0-0.126-0.05121.757-0.002-0.0020.0000.0000.0000.000
101A101GLU-1-0.894-0.94521.573-0.056-0.0560.0000.0000.0000.000
102A102ILE0-0.068-0.02516.061-0.017-0.0170.0000.0000.0000.000
103A103GLY00.0390.01517.167-0.019-0.0190.0000.0000.0000.000
104A104SER00.0280.00018.297-0.011-0.0110.0000.0000.0000.000
105A105GLU-1-0.892-0.94216.004-0.071-0.0710.0000.0000.0000.000
106A106LYS10.8160.90312.9190.1590.1590.0000.0000.0000.000
107A107VAL0-0.0280.00314.538-0.026-0.0260.0000.0000.0000.000
108A108ILE00.0160.02513.7680.0160.0160.0000.0000.0000.000
109A109LEU0-0.024-0.00317.568-0.003-0.0030.0000.0000.0000.000
110A110ILE0-0.011-0.00218.0470.0060.0060.0000.0000.0000.000
111A111THR0-0.067-0.02121.925-0.001-0.0010.0000.0000.0000.000
112A112PRO00.0560.01325.0350.0010.0010.0000.0000.0000.000
113A113PRO00.0030.01826.1700.0010.0010.0000.0000.0000.000
114A114TYR0-0.022-0.02827.877-0.001-0.0010.0000.0000.0000.000
115A115ALA00.0310.01630.6140.0010.0010.0000.0000.0000.000
116A116ASP-1-0.769-0.86433.1450.0030.0030.0000.0000.0000.000
117A117SER0-0.050-0.04436.5470.0000.0000.0000.0000.0000.000
118A118GLY0-0.0250.00638.9690.0000.0000.0000.0000.0000.000
119A119ARG10.8090.88135.689-0.005-0.0050.0000.0000.0000.000
120A120ARG10.7980.89835.124-0.001-0.0010.0000.0000.0000.000
121A121PRO00.0280.02038.4340.0000.0000.0000.0000.0000.000
122A122GLU-1-0.782-0.87436.945-0.001-0.0010.0000.0000.0000.000
123A123ARG10.8370.91231.6190.0010.0010.0000.0000.0000.000
124A124PRO00.0480.03937.2440.0010.0010.0000.0000.0000.000
125A125GLN00.0750.05035.5790.0000.0000.0000.0000.0000.000
126A126THR0-0.053-0.03437.3190.0000.0000.0000.0000.0000.000
127A127ARG10.8910.93935.7920.0060.0060.0000.0000.0000.000
128A128ILE00.0420.02531.794-0.001-0.0010.0000.0000.0000.000
129A129LYS10.9290.96333.062-0.002-0.0020.0000.0000.0000.000
130A130GLU-1-0.944-0.96934.556-0.004-0.0040.0000.0000.0000.000
131A131LEU0-0.016-0.00230.850-0.001-0.0010.0000.0000.0000.000
132A132VAL0-0.012-0.00229.740-0.001-0.0010.0000.0000.0000.000
133A133LYS10.9250.98130.2100.0010.0010.0000.0000.0000.000
134A134VAL0-0.032-0.00930.1080.0000.0000.0000.0000.0000.000
135A135ALA00.0430.02026.321-0.001-0.0010.0000.0000.0000.000
136A136GLN0-0.066-0.05127.144-0.002-0.0020.0000.0000.0000.000
137A137GLU-1-0.856-0.93028.710-0.004-0.0040.0000.0000.0000.000
138A138VAL0-0.0020.00525.9980.0000.0000.0000.0000.0000.000
139A139GLY00.026-0.00424.755-0.002-0.0020.0000.0000.0000.000
140A140ALA0-0.005-0.00725.5880.0000.0000.0000.0000.0000.000
141A141ALA0-0.024-0.00228.1490.0020.0020.0000.0000.0000.000
142A142HIS10.7670.85224.2390.0210.0210.0000.0000.0000.000
143A143ASN0-0.073-0.02524.1880.0010.0010.0000.0000.0000.000
144A144LEU0-0.0150.01720.4210.0020.0020.0000.0000.0000.000
145A145PRO0-0.020-0.01317.7670.0050.0050.0000.0000.0000.000
146A146VAL00.0160.01120.672-0.006-0.0060.0000.0000.0000.000
147A147ILE00.0020.00817.7070.0050.0050.0000.0000.0000.000
148A148ASP-1-0.829-0.93122.3030.0010.0010.0000.0000.0000.000
149A149LEU00.0450.01423.1590.0020.0020.0000.0000.0000.000
150A150TYR0-0.006-0.03725.4920.0020.0020.0000.0000.0000.000
151A151LYS10.9400.98629.040-0.008-0.0080.0000.0000.0000.000
152A152ALA0-0.047-0.02826.2170.0010.0010.0000.0000.0000.000
153A153MET00.0130.02127.1890.0000.0000.0000.0000.0000.000
154A154THR0-0.029-0.02729.5360.0000.0000.0000.0000.0000.000
155A155VAL0-0.088-0.02931.0580.0000.0000.0000.0000.0000.000
156A156TYR0-0.026-0.00630.7930.0000.0000.0000.0000.0000.000
157A157PRO00.005-0.00532.934-0.001-0.0010.0000.0000.0000.000
158A158GLY00.0090.01134.576-0.001-0.0010.0000.0000.0000.000
159A159THR00.006-0.01532.1270.0010.0010.0000.0000.0000.000
160A160ASP-1-0.882-0.95332.2250.0060.0060.0000.0000.0000.000
161A161GLU-1-0.918-0.94732.1420.0090.0090.0000.0000.0000.000
162A162PHE0-0.066-0.02027.5680.0010.0010.0000.0000.0000.000
163A163LEU0-0.066-0.02228.2720.0010.0010.0000.0000.0000.000
164A164GLN00.0350.02129.1290.0010.0010.0000.0000.0000.000
165A165ALA00.0340.00031.819-0.001-0.0010.0000.0000.0000.000
166A166ASP-1-0.774-0.86232.5900.0050.0050.0000.0000.0000.000
167A167GLY0-0.0130.00034.317-0.001-0.0010.0000.0000.0000.000
168A168LEU0-0.046-0.03430.329-0.001-0.0010.0000.0000.0000.000
169A169HIS0-0.042-0.03927.1190.0010.0010.0000.0000.0000.000
170A170PHE00.0190.00523.666-0.001-0.0010.0000.0000.0000.000
171A171SER00.036-0.00226.5590.0030.0030.0000.0000.0000.000
172A172GLN0-0.040-0.04024.0820.0000.0000.0000.0000.0000.000
173A173VAL00.0310.01824.0680.0040.0040.0000.0000.0000.000
174A174GLY00.0310.02124.9340.0010.0010.0000.0000.0000.000
175A175TYR0-0.057-0.05219.8650.0000.0000.0000.0000.0000.000
176A176GLU-1-0.893-0.93320.1780.0360.0360.0000.0000.0000.000
177A177LEU0-0.036-0.00720.6390.0020.0020.0000.0000.0000.000
178A178LEU0-0.016-0.01318.785-0.001-0.0010.0000.0000.0000.000
179A179GLY00.029-0.00116.573-0.002-0.0020.0000.0000.0000.000
180A180ALA00.0400.02216.2500.0000.0000.0000.0000.0000.000
181A181LEU0-0.080-0.04918.112-0.004-0.0040.0000.0000.0000.000
182A182ILE00.0280.01513.294-0.007-0.0070.0000.0000.0000.000
183A183VAL00.0170.00712.504-0.016-0.0160.0000.0000.0000.000
184A184ARG10.8690.93214.126-0.027-0.0270.0000.0000.0000.000
185A185GLU-1-0.902-0.95615.709-0.001-0.0010.0000.0000.0000.000
186A186ILE00.0320.0068.910-0.001-0.0010.0000.0000.0000.000
187A187LYS10.9230.97111.377-0.048-0.0480.0000.0000.0000.000
188A188GLY0-0.039-0.01112.6010.0150.0150.0000.0000.0000.000
189A189ARG10.8470.94110.8330.1180.1180.0000.0000.0000.000
190A190LEU0-0.071-0.0196.700-0.014-0.0140.0000.0000.0000.000
191A191LYS10.8710.9236.372-1.054-1.0540.0000.0000.0000.000
192A192PRO00.016-0.0019.695-0.038-0.0380.0000.0000.0000.000
193A193LYS10.9380.9866.5610.4910.4910.0000.0000.0000.000
194A194GLN0-0.035-0.02110.1490.0290.0290.0000.0000.0000.000
195A195ALA00.0100.00711.863-0.066-0.0660.0000.0000.0000.000