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: 98M62

Calculation Name: 2YWI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YWI

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KZG6

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 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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2128739.101726
FMO2-HF: Nuclear repulsion 2053626.251538
FMO2-HF: Total energy -75112.850188
FMO2-MP2: Total energy -75328.162365


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:5:VAL)


Summations of interaction energy for fragment #1(A:5:VAL)
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.
-2.362-0.491-0.032-0.832-1.0070.002
Interaction energy analysis for fragmet #1(A:5:VAL)
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 : -0.029
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].
3A7GLY00.0080.0103.796-1.2320.628-0.031-0.828-1.0020.002
4A8MET00.0140.0075.059-0.625-0.614-0.001-0.004-0.0050.000
5A9PRO0-0.0190.0006.3880.1980.1980.0000.0000.0000.000
6A10ALA0-0.019-0.0048.913-0.008-0.0080.0000.0000.0000.000
7A11VAL0-0.009-0.01412.681-0.027-0.0270.0000.0000.0000.000
8A12GLU-1-0.919-0.97715.024-0.102-0.1020.0000.0000.0000.000
9A13SER0-0.024-0.03818.675-0.010-0.0100.0000.0000.0000.000
10A14ASN0-0.025-0.01420.556-0.006-0.0060.0000.0000.0000.000
11A15MET0-0.100-0.03423.0410.0080.0080.0000.0000.0000.000
12A16PHE00.0570.03326.4730.0070.0070.0000.0000.0000.000
13A17PRO0-0.001-0.01228.8460.0080.0080.0000.0000.0000.000
14A18LEU00.0240.02632.0680.0020.0020.0000.0000.0000.000
15A19GLY0-0.019-0.01834.7960.0010.0010.0000.0000.0000.000
16A20LYS10.8730.95232.1350.1060.1060.0000.0000.0000.000
17A21GLN0-0.032-0.03636.1660.0020.0020.0000.0000.0000.000
18A22ALA00.0290.01934.550-0.006-0.0060.0000.0000.0000.000
19A23PRO0-0.029-0.00931.3320.0030.0030.0000.0000.0000.000
20A24PRO00.0270.02534.4840.0020.0020.0000.0000.0000.000
21A25PHE00.0230.00333.286-0.008-0.0080.0000.0000.0000.000
22A26ALA0-0.013-0.00734.9440.0070.0070.0000.0000.0000.000
23A27LEU0-0.017-0.00330.620-0.005-0.0050.0000.0000.0000.000
24A28THR00.0070.01233.9050.0060.0060.0000.0000.0000.000
25A29ASN00.0540.01833.489-0.009-0.0090.0000.0000.0000.000
26A30VAL0-0.007-0.00530.8700.0040.0040.0000.0000.0000.000
27A31ILE00.0040.01134.2570.0040.0040.0000.0000.0000.000
28A32ASP-1-0.856-0.92036.662-0.052-0.0520.0000.0000.0000.000
29A33GLY0-0.0160.00637.6100.0020.0020.0000.0000.0000.000
30A34ASN0-0.060-0.03338.645-0.001-0.0010.0000.0000.0000.000
31A35VAL0-0.035-0.01937.686-0.004-0.0040.0000.0000.0000.000
32A36VAL00.005-0.00136.9580.0040.0040.0000.0000.0000.000
33A37ARG10.9400.94737.2350.0640.0640.0000.0000.0000.000
34A38LEU0-0.0100.01636.3710.0030.0030.0000.0000.0000.000
35A39GLU-1-0.929-0.99338.540-0.068-0.0680.0000.0000.0000.000
36A40ASP-1-0.882-0.92840.941-0.057-0.0570.0000.0000.0000.000
37A41VAL0-0.032-0.01137.1750.0020.0020.0000.0000.0000.000
38A42LYS10.9300.98940.5730.0530.0530.0000.0000.0000.000
39A43SER00.0210.01342.0480.0030.0030.0000.0000.0000.000
40A44ASP-1-0.866-0.93543.734-0.039-0.0390.0000.0000.0000.000
41A45ALA0-0.060-0.03144.2880.0010.0010.0000.0000.0000.000
42A46ALA0-0.005-0.01039.118-0.001-0.0010.0000.0000.0000.000
43A47THR0-0.004-0.00836.4690.0020.0020.0000.0000.0000.000
44A48VAL0-0.009-0.01332.549-0.003-0.0030.0000.0000.0000.000
45A49ILE0-0.0090.00229.9490.0010.0010.0000.0000.0000.000
46A50MET0-0.029-0.01828.273-0.001-0.0010.0000.0000.0000.000
47A51PHE00.0350.03223.9110.0000.0000.0000.0000.0000.000
48A52ILE0-0.014-0.03623.107-0.002-0.0020.0000.0000.0000.000
49A53CYS0-0.028-0.01519.825-0.013-0.0130.0000.0000.0000.000
50A54ASN00.0310.00822.2460.0220.0220.0000.0000.0000.000
51A55HIS0-0.047-0.01717.5800.0300.0300.0000.0000.0000.000
52A56CYS0-0.0100.03117.100-0.028-0.0280.0000.0000.0000.000
53A57PRO0-0.007-0.00615.5570.0190.0190.0000.0000.0000.000
54A58PHE00.0580.01314.7600.0180.0180.0000.0000.0000.000
55A59VAL00.0260.00519.9130.0090.0090.0000.0000.0000.000
56A60LYS10.8680.93221.5910.0700.0700.0000.0000.0000.000
57A61HIS0-0.056-0.02722.4690.0140.0140.0000.0000.0000.000
58A62VAL00.0200.00124.2420.0060.0060.0000.0000.0000.000
59A63GLN00.0140.00125.8160.0070.0070.0000.0000.0000.000
60A64HIS00.0260.01728.212-0.001-0.0010.0000.0000.0000.000
61A65GLU-1-0.731-0.85030.444-0.024-0.0240.0000.0000.0000.000
62A66LEU0-0.008-0.00227.653-0.001-0.0010.0000.0000.0000.000
63A67VAL00.0380.02731.860-0.001-0.0010.0000.0000.0000.000
64A68ARG10.8150.90434.7510.0190.0190.0000.0000.0000.000
65A69LEU0-0.020-0.01833.2670.0010.0010.0000.0000.0000.000
66A70ALA00.0190.01035.7500.0000.0000.0000.0000.0000.000
67A71ASN00.010-0.00837.473-0.001-0.0010.0000.0000.0000.000
68A72ASP-1-0.837-0.89139.676-0.019-0.0190.0000.0000.0000.000
69A73TYR0-0.100-0.11539.2910.0010.0010.0000.0000.0000.000
70A74MET00.0010.02739.341-0.001-0.0010.0000.0000.0000.000
71A75PRO0-0.052-0.02342.0710.0000.0000.0000.0000.0000.000
72A76LYS10.8180.92242.9040.0260.0260.0000.0000.0000.000
73A77GLY00.0240.02245.1310.0000.0000.0000.0000.0000.000
74A78VAL0-0.051-0.00338.848-0.002-0.0020.0000.0000.0000.000
75A79SER00.0160.00639.3300.0020.0020.0000.0000.0000.000
76A80PHE00.011-0.00834.184-0.002-0.0020.0000.0000.0000.000
77A81VAL00.0220.00432.9450.0010.0010.0000.0000.0000.000
78A82ALA0-0.0130.01829.232-0.004-0.0040.0000.0000.0000.000
79A83ILE0-0.004-0.00827.3350.0020.0020.0000.0000.0000.000
80A84ASN0-0.010-0.02123.337-0.023-0.0230.0000.0000.0000.000
81A85SER00.024-0.03523.0400.0070.0070.0000.0000.0000.000
82A86ASN0-0.040-0.02218.727-0.035-0.0350.0000.0000.0000.000
83A87ASP-1-0.795-0.89118.414-0.268-0.2680.0000.0000.0000.000
84A88ALA0-0.006-0.00719.463-0.017-0.0170.0000.0000.0000.000
85A89GLU-1-0.935-0.96320.468-0.165-0.1650.0000.0000.0000.000
86A90GLN0-0.184-0.09914.467-0.070-0.0700.0000.0000.0000.000
87A91TYR0-0.005-0.00412.058-0.044-0.0440.0000.0000.0000.000
88A92PRO00.1030.05818.3760.0250.0250.0000.0000.0000.000
89A93GLU-1-0.884-0.94418.215-0.171-0.1710.0000.0000.0000.000
90A94ASP-1-0.749-0.85820.371-0.169-0.1690.0000.0000.0000.000
91A95SER00.0020.00423.3740.0050.0050.0000.0000.0000.000
92A96PRO00.0520.00125.8650.0080.0080.0000.0000.0000.000
93A97GLU-1-0.878-0.92429.380-0.059-0.0590.0000.0000.0000.000
94A98ASN00.004-0.01025.0630.0200.0200.0000.0000.0000.000
95A99MET0-0.056-0.00526.7580.0030.0030.0000.0000.0000.000
96A100LYS10.8440.92628.7940.0600.0600.0000.0000.0000.000
97A101LYS10.8500.91229.6480.0650.0650.0000.0000.0000.000
98A102VAL00.0460.03126.5770.0050.0050.0000.0000.0000.000
99A103ALA0-0.035-0.01730.0090.0050.0050.0000.0000.0000.000
100A104GLU-1-0.990-0.99032.523-0.030-0.0300.0000.0000.0000.000
101A105GLU-1-0.971-0.98730.255-0.029-0.0290.0000.0000.0000.000
102A106LEU0-0.086-0.04928.2990.0050.0050.0000.0000.0000.000
103A107GLY00.0070.01532.9920.0020.0020.0000.0000.0000.000
104A108TYR0-0.045-0.02827.6000.0020.0020.0000.0000.0000.000
105A109PRO00.0040.01534.755-0.001-0.0010.0000.0000.0000.000
106A110PHE0-0.032-0.01931.4820.0000.0000.0000.0000.0000.000
107A111PRO00.002-0.00535.390-0.001-0.0010.0000.0000.0000.000
108A112TYR00.005-0.02726.003-0.007-0.0070.0000.0000.0000.000
109A113LEU00.0230.00431.4420.0010.0010.0000.0000.0000.000
110A114TYR00.0210.01127.979-0.004-0.0040.0000.0000.0000.000
111A115ASP-1-0.776-0.87626.639-0.157-0.1570.0000.0000.0000.000
112A116GLU-1-0.823-0.90925.829-0.188-0.1880.0000.0000.0000.000
113A117THR00.0450.02125.358-0.016-0.0160.0000.0000.0000.000
114A118GLN0-0.025-0.02919.954-0.028-0.0280.0000.0000.0000.000
115A119GLU-1-0.973-0.98025.239-0.139-0.1390.0000.0000.0000.000
116A120VAL00.0180.00728.0110.0050.0050.0000.0000.0000.000
117A121ALA00.0160.00723.4930.0030.0030.0000.0000.0000.000
118A122LYS10.8980.95622.4260.2300.2300.0000.0000.0000.000
119A123ALA0-0.034-0.00125.4880.0040.0040.0000.0000.0000.000
120A124TYR0-0.046-0.05327.7120.0100.0100.0000.0000.0000.000
121A125ASP-1-0.898-0.92523.663-0.185-0.1850.0000.0000.0000.000
122A126ALA0-0.0300.01023.585-0.002-0.0020.0000.0000.0000.000
123A127ALA00.026-0.00218.848-0.019-0.0190.0000.0000.0000.000
124A128CYS0-0.122-0.05817.892-0.033-0.0330.0000.0000.0000.000
125A129THR0-0.0060.03618.2790.0240.0240.0000.0000.0000.000
126A130PRO0-0.005-0.03319.352-0.004-0.0040.0000.0000.0000.000
127A131ASP-1-0.667-0.80222.155-0.167-0.1670.0000.0000.0000.000
128A132PHE0-0.045-0.02424.2250.0050.0050.0000.0000.0000.000
129A133TYR0-0.039-0.03626.185-0.002-0.0020.0000.0000.0000.000
130A134ILE00.0070.00630.8450.0040.0040.0000.0000.0000.000
131A135PHE0-0.017-0.01132.216-0.002-0.0020.0000.0000.0000.000
132A136ASP-1-0.746-0.88137.253-0.053-0.0530.0000.0000.0000.000
133A137ARG10.9210.96440.9470.0380.0380.0000.0000.0000.000
134A138ASP-1-0.930-0.95143.314-0.048-0.0480.0000.0000.0000.000
135A139LEU0-0.023-0.02938.858-0.003-0.0030.0000.0000.0000.000
136A140LYS10.8540.92738.5190.0480.0480.0000.0000.0000.000
137A141CYS0-0.069-0.00633.1480.0020.0020.0000.0000.0000.000
138A142VAL00.0390.01435.7920.0010.0010.0000.0000.0000.000
139A143TYR0-0.019-0.04229.9510.0050.0050.0000.0000.0000.000
140A144ARG10.8550.92728.4330.0860.0860.0000.0000.0000.000
141A145GLY00.0230.02026.0900.0020.0020.0000.0000.0000.000
142A146GLN0-0.013-0.02125.566-0.005-0.0050.0000.0000.0000.000
143A147LEU00.0410.04126.5650.0030.0030.0000.0000.0000.000
144A148ASP-1-0.720-0.83227.789-0.023-0.0230.0000.0000.0000.000
145A149ASP-1-0.765-0.87027.216-0.035-0.0350.0000.0000.0000.000
146A150SER0-0.070-0.02526.1990.0040.0040.0000.0000.0000.000
147A151ARG10.8300.88320.9820.0430.0430.0000.0000.0000.000
148A152PRO00.0210.01319.1770.0120.0120.0000.0000.0000.000
149A153ASN0-0.038-0.02318.4130.0020.0020.0000.0000.0000.000
150A154ASN0-0.005-0.01920.5460.0130.0130.0000.0000.0000.000
151A155GLY00.0130.02123.9680.0030.0030.0000.0000.0000.000
152A156ILE0-0.045-0.00826.7770.0000.0000.0000.0000.0000.000
153A157PRO0-0.006-0.01128.523-0.003-0.0030.0000.0000.0000.000
154A158VAL00.0060.01127.858-0.003-0.0030.0000.0000.0000.000
155A159THR00.001-0.01430.4800.0010.0010.0000.0000.0000.000
156A160GLY00.015-0.00931.714-0.001-0.0010.0000.0000.0000.000
157A161GLU-1-0.981-0.99332.744-0.020-0.0200.0000.0000.0000.000
158A162SER0-0.010-0.00531.178-0.001-0.0010.0000.0000.0000.000
159A163ILE00.0400.02630.111-0.001-0.0010.0000.0000.0000.000
160A164ARG10.7400.86034.1190.0260.0260.0000.0000.0000.000
161A165ALA00.0360.02536.8510.0010.0010.0000.0000.0000.000
162A166ALA0-0.027-0.01835.9210.0000.0000.0000.0000.0000.000
163A167LEU00.0160.00236.9800.0000.0000.0000.0000.0000.000
164A168ASP-1-0.826-0.88839.744-0.026-0.0260.0000.0000.0000.000
165A169ALA0-0.059-0.02841.1720.0010.0010.0000.0000.0000.000
166A170LEU0-0.004-0.00838.8510.0000.0000.0000.0000.0000.000
167A171LEU0-0.050-0.02143.1370.0010.0010.0000.0000.0000.000
168A172GLU-1-0.847-0.88745.660-0.022-0.0220.0000.0000.0000.000
169A173GLY0-0.0380.00146.6160.0010.0010.0000.0000.0000.000
170A174ARG10.7380.84243.1020.0270.0270.0000.0000.0000.000
171A175PRO00.004-0.01142.826-0.002-0.0020.0000.0000.0000.000
172A176VAL0-0.0050.00936.5610.0020.0020.0000.0000.0000.000
173A177PRO0-0.008-0.00936.6910.0000.0000.0000.0000.0000.000
174A178GLU-1-0.892-0.95636.496-0.044-0.0440.0000.0000.0000.000
175A179LYS10.8870.94831.2750.0260.0260.0000.0000.0000.000
176A180GLN00.0340.02330.739-0.005-0.0050.0000.0000.0000.000
177A181LYS10.8060.90426.3070.0370.0370.0000.0000.0000.000
178A182PRO00.0950.02922.4290.0040.0040.0000.0000.0000.000
179A183SER0-0.077-0.04022.6670.0180.0180.0000.0000.0000.000
180A184ILE0-0.002-0.01315.949-0.008-0.0080.0000.0000.0000.000
181A185GLY00.0190.00117.1420.0270.0270.0000.0000.0000.000
182A186CYS0-0.024-0.01914.034-0.037-0.0370.0000.0000.0000.000
183A187SER00.0220.01213.1690.0200.0200.0000.0000.0000.000
184A188ILE0-0.0040.01214.957-0.007-0.0070.0000.0000.0000.000
185A189LYS10.8140.90812.3560.4550.4550.0000.0000.0000.000
186A190TRP00.0230.01215.9770.0470.0470.0000.0000.0000.000
187A191LYS10.8320.91616.6700.1670.1670.0000.0000.0000.000
188A192PRO0-0.017-0.01917.005-0.014-0.0140.0000.0000.0000.000
189A193SER0-0.020-0.00918.2470.0270.0270.0000.0000.0000.000
190A194ALA0-0.0050.01020.2550.0090.0090.0000.0000.0000.000