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: 63JJZ

Calculation Name: 2YLE-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YLE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NZ56

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 176
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1815839.980669
FMO2-HF: Nuclear repulsion 1745536.168484
FMO2-HF: Total energy -70303.812185
FMO2-MP2: Total energy -70504.294698


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:33:ACE )


Summations of interaction energy for fragment #1(A:33:ACE )
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.
-0.6220.9281.373-1.742-1.18-0.008
Interaction energy analysis for fragmet #1(A:33:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.003
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].
3A35SER 0-0.053-0.0333.8081.8262.439-0.005-0.293-0.3150.001
4A36SER 00.028-0.0347.280-0.023-0.0230.0000.0000.0000.000
5A37ARG 10.8040.89610.0510.8900.8900.0000.0000.0000.000
6A38ASP -1-0.828-0.91713.209-0.248-0.2480.0000.0000.0000.000
7A39ALA 0-0.029-0.02815.3530.0440.0440.0000.0000.0000.000
8A40LEU 00.0400.03510.960-0.081-0.0810.0000.0000.0000.000
9A41SER 0-0.034-0.00915.0110.0850.0850.0000.0000.0000.000
10A42LEU 00.0440.01016.332-0.026-0.0260.0000.0000.0000.000
11A43GLU -1-0.956-0.98716.220-0.308-0.3080.0000.0000.0000.000
12A44GLU -1-0.802-0.89711.605-0.734-0.7340.0000.0000.0000.000
13A45ILE 00.0040.00613.044-0.028-0.0280.0000.0000.0000.000
14A46LEU 0-0.0010.00215.1160.0120.0120.0000.0000.0000.000
15A47ARG 10.9260.97011.2840.4740.4740.0000.0000.0000.000
16A48LEU 0-0.059-0.0288.193-0.007-0.0070.0000.0000.0000.000
17A49TYR 0-0.086-0.08911.8280.0460.0460.0000.0000.0000.000
18A50ASN 0-0.058-0.01714.4410.0320.0320.0000.0000.0000.000
19A51GLN 00.0070.00716.1620.0470.0470.0000.0000.0000.000
20A52PRO 00.0050.01419.386-0.024-0.0240.0000.0000.0000.000
21A53ILE 0-0.0100.00920.713-0.002-0.0020.0000.0000.0000.000
22A54ASN 00.0160.00122.6110.0180.0180.0000.0000.0000.000
23A55GLU -1-0.758-0.90925.380-0.077-0.0770.0000.0000.0000.000
24A56GLU -1-0.793-0.85827.165-0.082-0.0820.0000.0000.0000.000
25A57GLN 00.0510.01520.731-0.003-0.0030.0000.0000.0000.000
26A58ALA 00.0280.02625.292-0.008-0.0080.0000.0000.0000.000
27A59TRP 00.0440.01127.4930.0000.0000.0000.0000.0000.000
28A60ALA 0-0.014-0.01226.1170.0020.0020.0000.0000.0000.000
29A61VAL 00.0250.01323.572-0.002-0.0020.0000.0000.0000.000
30A62CYS 0-0.0120.01026.4300.0020.0020.0000.0000.0000.000
31A63TYR 00.010-0.00329.9520.0060.0060.0000.0000.0000.000
32A64GLN 0-0.025-0.03426.5960.0130.0130.0000.0000.0000.000
33A65CYS 0-0.0190.00927.1440.0000.0000.0000.0000.0000.000
34A66CYS 00.0080.00228.7310.0070.0070.0000.0000.0000.000
35A67GLY 0-0.005-0.00731.9570.0060.0060.0000.0000.0000.000
36A68SER 0-0.027-0.03327.8960.0070.0070.0000.0000.0000.000
37A69LEU 0-0.0040.00230.3910.0050.0050.0000.0000.0000.000
38A70ARG 10.9420.97032.7510.0820.0820.0000.0000.0000.000
39A71ALA 0-0.052-0.03033.4850.0060.0060.0000.0000.0000.000
40A72ALA 00.0420.02032.1670.0040.0040.0000.0000.0000.000
41A73ALA 00.0230.01634.2820.0040.0040.0000.0000.0000.000
42A74ARG 10.8890.94337.5100.0670.0670.0000.0000.0000.000
43A75ARG 10.8980.95836.2470.0750.0750.0000.0000.0000.000
44A76ARG 10.9090.95038.0760.0570.0570.0000.0000.0000.000
45A77GLN 00.0290.02632.172-0.004-0.0040.0000.0000.0000.000
46A78PRO 0-0.025-0.00334.3290.0020.0020.0000.0000.0000.000
47A79ARG 10.8260.90334.2630.0660.0660.0000.0000.0000.000
48A80HIS 0-0.029-0.03228.0320.0120.0120.0000.0000.0000.000
49A81ARG 10.8420.89131.9420.0790.0790.0000.0000.0000.000
50A82VAL 0-0.0050.00426.328-0.007-0.0070.0000.0000.0000.000
51A83ARG 10.9250.94926.6270.1120.1120.0000.0000.0000.000
52A84SER 00.0450.01922.1560.0010.0010.0000.0000.0000.000
53A85ALA 00.1090.04120.709-0.001-0.0010.0000.0000.0000.000
54A86ALA 00.0380.03118.720-0.015-0.0150.0000.0000.0000.000
55A87GLN 0-0.007-0.00219.728-0.006-0.0060.0000.0000.0000.000
56A88ILE 0-0.0010.01221.9440.0120.0120.0000.0000.0000.000
57A89ARG 10.9280.96919.4450.2310.2310.0000.0000.0000.000
58A90VAL 00.0580.02718.4440.0350.0350.0000.0000.0000.000
59A91TRP 0-0.038-0.03718.110-0.047-0.0470.0000.0000.0000.000
60A92ARG 10.9140.95413.4880.3170.3170.0000.0000.0000.000
61A93ASP -1-0.919-0.96218.952-0.144-0.1440.0000.0000.0000.000
62A94GLY 00.0290.00221.7430.0190.0190.0000.0000.0000.000
63A95ALA 0-0.0190.01523.3520.0100.0100.0000.0000.0000.000
64A96VAL 00.0540.01622.867-0.019-0.0190.0000.0000.0000.000
65A97THR 0-0.0290.00123.7060.0130.0130.0000.0000.0000.000
66A98LEU 00.0350.02624.157-0.013-0.0130.0000.0000.0000.000
67A99ALA 0-0.042-0.02422.3360.0080.0080.0000.0000.0000.000
68A100PRO 00.012-0.01224.4670.0100.0100.0000.0000.0000.000
69A101ALA 00.0020.01326.178-0.009-0.0090.0000.0000.0000.000
70A102NME 0-0.0090.00624.5050.0050.0050.0000.0000.0000.000
71A113ACE 00.0540.01949.8340.0000.0000.0000.0000.0000.000
72A114LYS 10.9640.97246.1130.0440.0440.0000.0000.0000.000
73A115LEU 00.0200.01339.9680.0020.0020.0000.0000.0000.000
74A116GLY 0-0.0100.01142.883-0.003-0.0030.0000.0000.0000.000
75A117TYR 00.0500.02244.375-0.001-0.0010.0000.0000.0000.000
76A118SER 0-0.011-0.01940.2990.0000.0000.0000.0000.0000.000
77A119GLN 00.0400.01540.345-0.001-0.0010.0000.0000.0000.000
78A120CYS 0-0.0130.01736.420-0.004-0.0040.0000.0000.0000.000
79A121MET 00.0100.01539.0400.0000.0000.0000.0000.0000.000
80A122GLU -1-0.879-0.96237.938-0.073-0.0730.0000.0000.0000.000
81A123THR 00.0350.01437.462-0.004-0.0040.0000.0000.0000.000
82A124GLU -1-0.711-0.82537.140-0.072-0.0720.0000.0000.0000.000
83A125VAL 0-0.061-0.02832.311-0.004-0.0040.0000.0000.0000.000
84A126ILE 0-0.002-0.00133.053-0.006-0.0060.0000.0000.0000.000
85A127GLU -1-0.815-0.86833.920-0.077-0.0770.0000.0000.0000.000
86A128SER 0-0.085-0.04831.062-0.006-0.0060.0000.0000.0000.000
87A129LEU 0-0.024-0.02927.953-0.008-0.0080.0000.0000.0000.000
88A130GLY 00.0530.02029.449-0.006-0.0060.0000.0000.0000.000
89A131ILE 00.0450.02329.620-0.003-0.0030.0000.0000.0000.000
90A132ILE 0-0.067-0.03324.555-0.006-0.0060.0000.0000.0000.000
91A133ILE 0-0.019-0.02125.817-0.011-0.0110.0000.0000.0000.000
92A134TYR 00.0650.03227.104-0.005-0.0050.0000.0000.0000.000
93A135LYS 10.9430.96625.2020.1110.1110.0000.0000.0000.000
94A136ALA 0-0.019-0.00522.849-0.005-0.0050.0000.0000.0000.000
95A137LEU 0-0.055-0.03123.492-0.004-0.0040.0000.0000.0000.000
96A138ASP -1-0.860-0.93426.238-0.087-0.0870.0000.0000.0000.000
97A139TYR 0-0.032-0.01117.345-0.006-0.0060.0000.0000.0000.000
98A140GLY 0-0.023-0.01522.0190.0010.0010.0000.0000.0000.000
99A141LEU 0-0.048-0.00422.7670.0100.0100.0000.0000.0000.000
100A142LYS 10.8900.92526.4360.0500.0500.0000.0000.0000.000
101A143GLU -1-0.905-0.96028.760-0.063-0.0630.0000.0000.0000.000
102A144ASN 0-0.087-0.04231.380-0.001-0.0010.0000.0000.0000.000
103A145GLU -1-0.926-0.94728.699-0.056-0.0560.0000.0000.0000.000
104A146GLU -1-0.875-0.93032.104-0.062-0.0620.0000.0000.0000.000
105A147ARG 10.8220.90225.8180.0990.0990.0000.0000.0000.000
106A148GLU -1-0.938-0.96331.819-0.044-0.0440.0000.0000.0000.000
107A149LEU 0-0.039-0.01530.741-0.003-0.0030.0000.0000.0000.000
108A150SER 0-0.015-0.00734.3150.0050.0050.0000.0000.0000.000
109A151PRO 00.0730.01436.499-0.002-0.0020.0000.0000.0000.000
110A152PRO 0-0.044-0.02637.951-0.001-0.0010.0000.0000.0000.000
111A153LEU 00.0120.00930.718-0.002-0.0020.0000.0000.0000.000
112A154GLU -1-0.885-0.93935.337-0.060-0.0600.0000.0000.0000.000
113A155GLN 0-0.005-0.00536.6780.0010.0010.0000.0000.0000.000
114A156LEU 0-0.047-0.03033.7770.0000.0000.0000.0000.0000.000
115A157ILE 00.005-0.01431.333-0.002-0.0020.0000.0000.0000.000
116A158ASP -1-0.783-0.85935.324-0.058-0.0580.0000.0000.0000.000
117A159HIS 0-0.052-0.03338.4680.0020.0020.0000.0000.0000.000
118A160MET 0-0.138-0.07632.303-0.001-0.0010.0000.0000.0000.000
119A161ALA 0-0.013-0.01334.819-0.002-0.0020.0000.0000.0000.000
120A162ASN 0-0.125-0.06436.5930.0030.0030.0000.0000.0000.000
121A163THR 0-0.010-0.03737.2800.0000.0000.0000.0000.0000.000
122A164VAL 0-0.0230.01740.4010.0030.0030.0000.0000.0000.000
123A165GLU -1-0.897-0.94643.233-0.045-0.0450.0000.0000.0000.000
124A166NME 0-0.103-0.06146.1610.0010.0010.0000.0000.0000.000
125A185ACE 0-0.012-0.01750.7910.0000.0000.0000.0000.0000.000
126A186GLU -1-0.773-0.88545.525-0.040-0.0400.0000.0000.0000.000
127A187LYS 10.8220.89446.1050.0360.0360.0000.0000.0000.000
128A188ARG 10.8670.94747.2180.0340.0340.0000.0000.0000.000
129A189LYS 11.0711.03446.2200.0380.0380.0000.0000.0000.000
130A190ILE 0-0.0070.02241.4800.0020.0020.0000.0000.0000.000
131A191SER 0-0.030-0.02646.0470.0010.0010.0000.0000.0000.000
132A192ALA 00.0200.01944.800-0.002-0.0020.0000.0000.0000.000
133A193ILE 00.0250.01638.7280.0010.0010.0000.0000.0000.000
134A194ARG 10.9260.95342.5330.0470.0470.0000.0000.0000.000
135A195SER 0-0.040-0.01640.797-0.001-0.0010.0000.0000.0000.000
136A196TYR 00.1140.03734.9080.0000.0000.0000.0000.0000.000
137A197ARG 10.9110.95537.4410.0540.0540.0000.0000.0000.000
138A198ASP -1-0.837-0.91639.755-0.056-0.0560.0000.0000.0000.000
139A199VAL 00.0760.04034.4140.0010.0010.0000.0000.0000.000
140A200MET 0-0.078-0.03133.9390.0010.0010.0000.0000.0000.000
141A201LYS 10.8960.93936.5880.0550.0550.0000.0000.0000.000
142A202LEU 00.0610.03938.2710.0020.0020.0000.0000.0000.000
143A203CYS 0-0.0180.00833.646-0.001-0.0010.0000.0000.0000.000
144A204ALA 0-0.0240.00135.6570.0000.0000.0000.0000.0000.000
145A205ALA 00.0320.02737.4170.0020.0020.0000.0000.0000.000
146A206HIS 10.7890.90332.5910.0730.0730.0000.0000.0000.000
147A207LEU 0-0.031-0.01133.5890.0000.0000.0000.0000.0000.000
148A208PRO 00.0050.00037.5820.0020.0020.0000.0000.0000.000
149A209THR 00.0160.01939.4820.0040.0040.0000.0000.0000.000
150A210GLU -1-0.888-0.94639.007-0.053-0.0530.0000.0000.0000.000
151A211SER 0-0.053-0.04038.630-0.003-0.0030.0000.0000.0000.000
152A212ASP -1-0.874-0.93635.587-0.055-0.0550.0000.0000.0000.000
153A213ALA 0-0.049-0.02734.368-0.005-0.0050.0000.0000.0000.000
154A214PRO 0-0.078-0.04132.734-0.006-0.0060.0000.0000.0000.000
155A215ASN 00.0530.01731.285-0.008-0.0080.0000.0000.0000.000
156A216HIS 0-0.034-0.02529.920-0.005-0.0050.0000.0000.0000.000
157A217TYR 00.006-0.04028.687-0.008-0.0080.0000.0000.0000.000
158A218GLN 0-0.044-0.01426.335-0.004-0.0040.0000.0000.0000.000
159A219ALA 0-0.011-0.01425.089-0.013-0.0130.0000.0000.0000.000
160A220VAL 0-0.0020.00724.295-0.009-0.0090.0000.0000.0000.000
161A221CYS 0-0.030-0.01222.217-0.013-0.0130.0000.0000.0000.000
162A222ARG 10.9530.97420.5480.1000.1000.0000.0000.0000.000
163A223ALA 0-0.033-0.00319.513-0.016-0.0160.0000.0000.0000.000
164A224LEU 00.0390.03118.036-0.011-0.0110.0000.0000.0000.000
165A225PHE 0-0.0270.00714.414-0.038-0.0380.0000.0000.0000.000
166A226ALA 0-0.041-0.03214.640-0.049-0.0490.0000.0000.0000.000
167A227GLU -1-0.803-0.84813.918-0.204-0.2040.0000.0000.0000.000
168A228THR 00.007-0.01712.564-0.043-0.0430.0000.0000.0000.000
169A229MET 0-0.0910.0149.472-0.152-0.1520.0000.0000.0000.000
170A230GLU -1-0.948-0.9708.910-0.393-0.3930.0000.0000.0000.000
171A231LEU 00.0410.0077.658-0.048-0.0480.0000.0000.0000.000
172A232HIS 0-0.036-0.0276.409-0.340-0.3400.0000.0000.0000.000
173A233THR 0-0.122-0.0675.063-0.994-1.1090.000-0.0190.1340.000
174A234PHE 0-0.051-0.0403.308-1.163-0.6540.071-0.374-0.205-0.003
175A235LEU 0-0.0100.0214.1950.5980.8150.001-0.032-0.1860.000
176A236THR -1-0.982-0.9732.356-0.3090.0171.306-1.024-0.608-0.006