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: 6YL7Z

Calculation Name: 2CW5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CW5

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLF5

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2633103.949689
FMO2-HF: Nuclear repulsion 2547841.096126
FMO2-HF: Total energy -85262.853563
FMO2-MP2: Total energy -85518.652253


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.
-10.51-3.2948.967-4.738-11.446-0.039
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 : 0.027 / q_NPA : 0.020
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].
3A3PRO0-0.021-0.0023.8730.1742.2350.003-0.855-1.2090.001
4A4VAL00.0330.0105.909-0.337-0.3370.0000.0000.0000.000
5A5TYR00.0170.0078.7860.0230.0230.0000.0000.0000.000
6A6PHE00.008-0.00712.422-0.057-0.0570.0000.0000.0000.000
7A7LEU00.0090.00514.776-0.006-0.0060.0000.0000.0000.000
8A8SER0-0.022-0.00318.527-0.008-0.0080.0000.0000.0000.000
9A9ASP-1-0.760-0.87821.4430.0420.0420.0000.0000.0000.000
10A10PHE0-0.005-0.00121.714-0.006-0.0060.0000.0000.0000.000
11A11GLY00.0530.03924.327-0.005-0.0050.0000.0000.0000.000
12A12LEU0-0.047-0.05720.3360.0000.0000.0000.0000.0000.000
13A13GLU-1-0.962-0.97422.7440.0280.0280.0000.0000.0000.000
14A14ASP-1-0.862-0.90423.948-0.002-0.0020.0000.0000.0000.000
15A15PRO00.0380.00322.3960.0060.0060.0000.0000.0000.000
16A16TYR0-0.011-0.01019.0220.0010.0010.0000.0000.0000.000
17A17VAL0-0.014-0.01518.2250.0040.0040.0000.0000.0000.000
18A18ALA00.0130.00217.0020.0170.0170.0000.0000.0000.000
19A19VAL00.0100.00416.331-0.008-0.0080.0000.0000.0000.000
20A20VAL0-0.0140.00113.722-0.021-0.0210.0000.0000.0000.000
21A21LYS10.8510.90012.365-0.168-0.1680.0000.0000.0000.000
22A22ALA00.0000.00711.5520.0010.0010.0000.0000.0000.000
23A23VAL00.0150.00211.501-0.056-0.0560.0000.0000.0000.000
24A24LEU0-0.032-0.0238.454-0.111-0.1110.0000.0000.0000.000
25A25ALA0-0.018-0.0056.888-0.041-0.0410.0000.0000.0000.000
26A26GLU-1-0.845-0.8678.601-0.563-0.5630.0000.0000.0000.000
27A27ARG10.7520.8414.3430.6830.799-0.001-0.013-0.1020.000
28A28ALA0-0.0670.0035.8870.1240.1240.0000.0000.0000.000
29A29PRO0-0.018-0.0342.327-0.3700.2150.683-0.289-0.9800.001
30A30GLY00.0640.0152.624-3.228-2.0930.777-0.674-1.239-0.007
31A31PRO0-0.016-0.0043.0200.8722.4222.726-1.258-3.018-0.002
32A32ALA0-0.0020.0083.789-0.525-2.0830.0471.816-0.305-0.001
33A33VAL00.002-0.0076.842-0.027-0.0270.0000.0000.0000.000
34A34VAL0-0.021-0.0079.646-0.125-0.1250.0000.0000.0000.000
35A35ASP-1-0.767-0.85712.7130.1670.1670.0000.0000.0000.000
36A36LEU0-0.035-0.01515.747-0.005-0.0050.0000.0000.0000.000
37A37ALA00.022-0.00717.917-0.014-0.0140.0000.0000.0000.000
38A38HIS10.7930.87117.023-0.130-0.1300.0000.0000.0000.000
39A39ALA00.0210.01922.281-0.010-0.0100.0000.0000.0000.000
40A40LEU0-0.0100.01423.120-0.003-0.0030.0000.0000.0000.000
41A41PRO00.0270.00026.726-0.004-0.0040.0000.0000.0000.000
42A42PRO00.0360.01029.1990.0010.0010.0000.0000.0000.000
43A43GLN0-0.079-0.06128.725-0.006-0.0060.0000.0000.0000.000
44A44ASP-1-0.830-0.89629.7140.0440.0440.0000.0000.0000.000
45A45LEU00.000-0.01826.3780.0060.0060.0000.0000.0000.000
46A46ARG10.7830.88627.444-0.035-0.0350.0000.0000.0000.000
47A47ARG10.7920.88826.284-0.074-0.0740.0000.0000.0000.000
48A48ALA0-0.011-0.00524.0110.0080.0080.0000.0000.0000.000
49A49ALA00.0290.01623.7530.0100.0100.0000.0000.0000.000
50A50TYR00.003-0.01224.3020.0090.0090.0000.0000.0000.000
51A51ALA00.0050.01022.7520.0070.0070.0000.0000.0000.000
52A52LEU0-0.062-0.03018.3760.0150.0150.0000.0000.0000.000
53A53PHE0-0.034-0.01820.4780.0120.0120.0000.0000.0000.000
54A54GLU-1-0.836-0.92022.6100.1050.1050.0000.0000.0000.000
55A55ALA00.002-0.00317.8860.0080.0080.0000.0000.0000.000
56A56LEU0-0.0010.00415.9190.0170.0170.0000.0000.0000.000
57A57PRO0-0.012-0.00516.9470.0200.0200.0000.0000.0000.000
58A58TYR0-0.046-0.01817.2860.0080.0080.0000.0000.0000.000
59A59LEU0-0.046-0.00212.7130.0250.0250.0000.0000.0000.000
60A60PRO00.000-0.0039.015-0.001-0.0010.0000.0000.0000.000
61A61GLU-1-0.787-0.88311.0550.2850.2850.0000.0000.0000.000
62A62GLY0-0.006-0.0128.0320.1170.1170.0000.0000.0000.000
63A63ALA0-0.067-0.0257.468-0.144-0.1440.0000.0000.0000.000
64A64VAL00.0250.0137.051-0.061-0.0610.0000.0000.0000.000
65A65VAL0-0.017-0.0209.6300.0920.0920.0000.0000.0000.000
66A66LEU0-0.0080.00912.775-0.044-0.0440.0000.0000.0000.000
67A67ALA00.002-0.00914.4460.0200.0200.0000.0000.0000.000
68A68VAL0-0.032-0.03018.051-0.019-0.0190.0000.0000.0000.000
69A69VAL00.0310.03220.6980.0010.0010.0000.0000.0000.000
70A70ASP-1-0.778-0.87424.124-0.008-0.0080.0000.0000.0000.000
71A71PRO00.0650.03226.023-0.004-0.0040.0000.0000.0000.000
72A72GLY0-0.0340.01128.733-0.002-0.0020.0000.0000.0000.000
73A73VAL00.0070.00628.597-0.005-0.0050.0000.0000.0000.000
74A74GLY0-0.016-0.00229.5290.0000.0000.0000.0000.0000.000
75A75THR0-0.051-0.03530.5810.0010.0010.0000.0000.0000.000
76A76ALA0-0.011-0.00830.185-0.003-0.0030.0000.0000.0000.000
77A77ARG10.8490.88524.8000.0250.0250.0000.0000.0000.000
78A78ARG10.8280.90223.8500.0080.0080.0000.0000.0000.000
79A79ALA00.0070.02120.4480.0100.0100.0000.0000.0000.000
80A80VAL00.002-0.01119.044-0.010-0.0100.0000.0000.0000.000
81A81ALA00.0330.01913.6010.0070.0070.0000.0000.0000.000
82A82ALA0-0.011-0.00915.058-0.002-0.0020.0000.0000.0000.000
83A83LEU00.010-0.00210.6500.0030.0030.0000.0000.0000.000
84A84GLY00.0500.01513.2750.0000.0000.0000.0000.0000.000
85A85ARG10.7520.87312.798-0.221-0.2210.0000.0000.0000.000
86A86TRP0-0.029-0.02211.3880.0400.0400.0000.0000.0000.000
87A87THR0-0.0040.0059.463-0.051-0.0510.0000.0000.0000.000
88A88TYR0-0.030-0.03111.5440.0330.0330.0000.0000.0000.000
89A89VAL00.0210.01712.214-0.032-0.0320.0000.0000.0000.000
90A90GLY00.0520.01115.2080.0260.0260.0000.0000.0000.000
91A91PRO0-0.041-0.01418.717-0.014-0.0140.0000.0000.0000.000
92A92ASP-1-0.778-0.85922.3940.0100.0100.0000.0000.0000.000
93A93ASN0-0.011-0.02923.9280.0020.0020.0000.0000.0000.000
94A94GLY00.0550.03625.2850.0020.0020.0000.0000.0000.000
95A95LEU0-0.0050.02821.3280.0070.0070.0000.0000.0000.000
96A96PHE00.0290.00517.4810.0090.0090.0000.0000.0000.000
97A97THR0-0.010-0.02121.8960.0040.0040.0000.0000.0000.000
98A98LEU00.0220.00224.7720.0020.0020.0000.0000.0000.000
99A99ALA00.0300.02119.1870.0050.0050.0000.0000.0000.000
100A100TRP0-0.005-0.01917.9050.0030.0030.0000.0000.0000.000
101A101LEU0-0.041-0.00321.610-0.002-0.0020.0000.0000.0000.000
102A102LEU0-0.044-0.01121.1290.0020.0020.0000.0000.0000.000
103A103ASP-1-0.794-0.88115.9710.1550.1550.0000.0000.0000.000
104A104PRO00.0150.01319.133-0.008-0.0080.0000.0000.0000.000
105A105PRO0-0.031-0.00917.7170.0060.0060.0000.0000.0000.000
106A106ARG10.8690.93515.770-0.156-0.1560.0000.0000.0000.000
107A107ARG10.7160.81414.3880.0310.0310.0000.0000.0000.000
108A108ALA00.0100.00816.9350.0050.0050.0000.0000.0000.000
109A109PHE00.0340.01714.851-0.006-0.0060.0000.0000.0000.000
110A110LEU0-0.029-0.01018.1830.0100.0100.0000.0000.0000.000
111A111LEU0-0.027-0.02715.406-0.013-0.0130.0000.0000.0000.000
112A112GLU-1-0.900-0.96119.175-0.088-0.0880.0000.0000.0000.000
113A113PRO0-0.055-0.01820.514-0.013-0.0130.0000.0000.0000.000
114A114PRO00.0090.00719.9280.0030.0030.0000.0000.0000.000
115A134GLY00.0330.01324.5260.0040.0040.0000.0000.0000.000
116A135ARG10.9010.91621.3140.0030.0030.0000.0000.0000.000
117A136ASP-1-0.937-0.95719.339-0.076-0.0760.0000.0000.0000.000
118A137VAL00.0690.03018.103-0.019-0.0190.0000.0000.0000.000
119A138PHE0-0.034-0.01616.406-0.014-0.0140.0000.0000.0000.000
120A139ALA00.0240.01413.2810.0030.0030.0000.0000.0000.000
121A140PRO00.0410.01211.838-0.002-0.0020.0000.0000.0000.000
122A141ALA00.0500.03511.581-0.069-0.0690.0000.0000.0000.000
123A142ALA00.000-0.00410.370-0.048-0.0480.0000.0000.0000.000
124A143ALA00.0090.0027.4450.0690.0690.0000.0000.0000.000
125A144HIS0-0.025-0.0256.827-0.227-0.2270.0000.0000.0000.000
126A145LEU00.018-0.0057.117-0.226-0.2260.0000.0000.0000.000
127A146ALA0-0.029-0.0024.557-0.771-0.5100.002-0.075-0.1880.000
128A147LEU0-0.043-0.0362.333-3.891-1.6954.684-3.024-3.856-0.029
129A148GLY0-0.042-0.0093.405-2.249-1.4670.045-0.344-0.482-0.002
130A149LEU0-0.038-0.0064.0240.5240.6120.001-0.022-0.0670.000
131A150PRO00.0230.0027.6600.1080.1080.0000.0000.0000.000
132A151PRO00.0320.04010.037-0.024-0.0240.0000.0000.0000.000
133A152GLU-1-0.775-0.90112.000-0.116-0.1160.0000.0000.0000.000
134A153GLY0-0.068-0.02513.6500.0140.0140.0000.0000.0000.000
135A154LEU0-0.064-0.02611.858-0.002-0.0020.0000.0000.0000.000
136A155GLY00.0630.03115.4540.0160.0160.0000.0000.0000.000
137A156PRO0-0.0300.00418.5780.0010.0010.0000.0000.0000.000
138A157GLU-1-0.792-0.85818.689-0.028-0.0280.0000.0000.0000.000
139A158VAL0-0.076-0.04520.2620.0050.0050.0000.0000.0000.000
140A159PRO00.0210.00121.8050.0050.0050.0000.0000.0000.000
141A160VAL00.0690.03820.135-0.003-0.0030.0000.0000.0000.000
142A161GLU-1-0.862-0.93822.8490.0370.0370.0000.0000.0000.000
143A162THR0-0.090-0.04125.105-0.002-0.0020.0000.0000.0000.000
144A163LEU0-0.062-0.01020.389-0.003-0.0030.0000.0000.0000.000
145A164ALA00.0300.01624.8490.0050.0050.0000.0000.0000.000
146A165ARG10.8300.89825.323-0.030-0.0300.0000.0000.0000.000
147A166LEU0-0.010-0.00528.062-0.004-0.0040.0000.0000.0000.000
148A167PRO0-0.0250.00230.3340.0020.0020.0000.0000.0000.000
149A168LEU0-0.012-0.02129.7140.0010.0010.0000.0000.0000.000
150A169ALA00.0170.00031.4820.0010.0010.0000.0000.0000.000
151A170LEU0-0.0300.00528.173-0.001-0.0010.0000.0000.0000.000
152A171THR00.0290.00532.3820.0000.0000.0000.0000.0000.000
153A172GLU-1-0.778-0.85734.8570.0650.0650.0000.0000.0000.000
154A173GLY0-0.0230.02137.509-0.001-0.0010.0000.0000.0000.000
155A174PRO0-0.063-0.04740.416-0.001-0.0010.0000.0000.0000.000
156A175GLU-1-0.863-0.94142.4140.0320.0320.0000.0000.0000.000
157A176GLY00.0270.00238.9880.0020.0020.0000.0000.0000.000
158A177GLU-1-0.852-0.91236.6990.0360.0360.0000.0000.0000.000
159A178VAL0-0.0100.00037.1520.0040.0040.0000.0000.0000.000
160A179LEU00.0150.00629.756-0.003-0.0030.0000.0000.0000.000
161A180THR00.0310.00129.988-0.001-0.0010.0000.0000.0000.000
162A181PHE00.0250.02332.936-0.001-0.0010.0000.0000.0000.000
163A182ASP-1-0.781-0.89730.4950.0680.0680.0000.0000.0000.000
164A183ARG10.8830.93829.472-0.080-0.0800.0000.0000.0000.000
165A184PHE0-0.020-0.01332.408-0.002-0.0020.0000.0000.0000.000
166A185GLY00.0290.02635.395-0.003-0.0030.0000.0000.0000.000
167A186ASN0-0.037-0.02134.261-0.005-0.0050.0000.0000.0000.000
168A187ALA00.007-0.01335.2850.0010.0010.0000.0000.0000.000
169A188ILE0-0.0180.00830.8140.0010.0010.0000.0000.0000.000
170A189THR0-0.025-0.02534.117-0.004-0.0040.0000.0000.0000.000
171A190THR00.0280.01233.2510.0040.0040.0000.0000.0000.000
172A191LEU00.0010.01334.4780.0010.0010.0000.0000.0000.000
173A192LEU00.0500.02730.7020.0030.0030.0000.0000.0000.000
174A193ARG10.7610.84632.928-0.067-0.0670.0000.0000.0000.000
175A194ALA00.0630.02037.475-0.003-0.0030.0000.0000.0000.000
176A195PRO0-0.030-0.00639.1990.0010.0010.0000.0000.0000.000
177A196VAL00.0550.01540.744-0.002-0.0020.0000.0000.0000.000
178A197GLY0-0.058-0.01543.311-0.001-0.0010.0000.0000.0000.000
179A198GLY0-0.0060.00645.536-0.002-0.0020.0000.0000.0000.000
180A199PHE0-0.024-0.04246.729-0.001-0.0010.0000.0000.0000.000
181A200VAL00.0270.01642.1550.0000.0000.0000.0000.0000.000
182A201GLU-1-0.928-0.95945.4160.0280.0280.0000.0000.0000.000
183A202VAL00.0470.01242.9790.0010.0010.0000.0000.0000.000
184A203GLY00.0300.01445.949-0.001-0.0010.0000.0000.0000.000
185A204GLY0-0.027-0.00448.298-0.001-0.0010.0000.0000.0000.000
186A205ARG10.9230.97049.153-0.027-0.0270.0000.0000.0000.000
187A206ARG10.9270.96948.767-0.029-0.0290.0000.0000.0000.000
188A207VAL00.0100.01243.919-0.001-0.0010.0000.0000.0000.000
189A208PRO0-0.023-0.00146.2760.0010.0010.0000.0000.0000.000
190A209VAL00.0270.02441.1610.0010.0010.0000.0000.0000.000
191A210ARG10.8530.91742.028-0.043-0.0430.0000.0000.0000.000
192A211ARG10.9680.97739.238-0.055-0.0550.0000.0000.0000.000
193A212THR00.0040.00037.6770.0030.0030.0000.0000.0000.000
194A213PHE00.0400.02235.335-0.003-0.0030.0000.0000.0000.000
195A214GLY00.0420.01740.287-0.002-0.0020.0000.0000.0000.000
196A215GLU-1-0.911-0.95842.2590.0480.0480.0000.0000.0000.000
197A216VAL0-0.027-0.01844.401-0.002-0.0020.0000.0000.0000.000
198A217PRO00.0260.01046.4230.0010.0010.0000.0000.0000.000
199A218GLU-1-0.831-0.91346.3280.0350.0350.0000.0000.0000.000
200A219GLY00.0090.00045.993-0.002-0.0020.0000.0000.0000.000
201A220ALA0-0.048-0.01747.262-0.001-0.0010.0000.0000.0000.000
202A221PRO00.001-0.01544.8170.0020.0020.0000.0000.0000.000
203A222VAL0-0.055-0.02041.331-0.001-0.0010.0000.0000.0000.000
204A223ALA00.0320.01740.3200.0010.0010.0000.0000.0000.000
205A224TYR0-0.057-0.04634.119-0.003-0.0030.0000.0000.0000.000
206A225LEU0-0.008-0.00533.0600.0000.0000.0000.0000.0000.000
207A226GLY00.0350.01932.0350.0010.0010.0000.0000.0000.000
208A227SER0-0.013-0.01427.1900.0000.0000.0000.0000.0000.000
209A228ALA0-0.0010.00326.3770.0080.0080.0000.0000.0000.000
210A229GLY0-0.013-0.00127.4550.0000.0000.0000.0000.0000.000
211A230LEU0-0.0120.00229.676-0.003-0.0030.0000.0000.0000.000
212A231LEU0-0.039-0.01032.4440.0000.0000.0000.0000.0000.000
213A232GLU-1-0.824-0.89531.5300.0720.0720.0000.0000.0000.000
214A233VAL0-0.023-0.02336.272-0.002-0.0020.0000.0000.0000.000
215A234ALA00.0290.01438.1720.0000.0000.0000.0000.0000.000
216A235VAL00.0200.01740.120-0.002-0.0020.0000.0000.0000.000
217A236ASN0-0.017-0.00141.8150.0030.0030.0000.0000.0000.000
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