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: 4J98N

Calculation Name: 2YWJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YWJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q59055

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptAll
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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2055915.408587
FMO2-HF: Nuclear repulsion 1984145.127753
FMO2-HF: Total energy -71770.280834
FMO2-MP2: Total energy -71979.267638


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.
-15.71-6.86614.065-7.221-15.688-0.043
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 : -0.029 / q_NPA : 0.004
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].
3A3ILE0-0.020-0.0102.6821.0443.0261.839-1.175-2.6460.003
4A4GLY00.0460.0145.607-0.489-0.4890.0000.0000.0000.000
5A5VAL0-0.003-0.0139.4310.2660.2660.0000.0000.0000.000
6A6LEU0-0.030-0.01412.079-0.081-0.0810.0000.0000.0000.000
7A7ALA00.0710.03615.5960.0160.0160.0000.0000.0000.000
8A8ILE0-0.0090.00418.070-0.023-0.0230.0000.0000.0000.000
9A9GLN0-0.107-0.06621.003-0.010-0.0100.0000.0000.0000.000
10A10GLY00.0250.02021.6810.0140.0140.0000.0000.0000.000
11A11ASP-1-0.882-0.92719.557-0.167-0.1670.0000.0000.0000.000
12A12VAL00.036-0.00314.8190.0300.0300.0000.0000.0000.000
13A13GLU-1-0.757-0.85914.668-0.250-0.2500.0000.0000.0000.000
14A14GLU-1-0.944-0.95715.197-0.087-0.0870.0000.0000.0000.000
15A15HIS00.0370.00412.444-0.034-0.0340.0000.0000.0000.000
16A16GLU-1-0.894-0.96110.428-0.526-0.5260.0000.0000.0000.000
17A17GLU-1-0.861-0.90710.363-0.473-0.4730.0000.0000.0000.000
18A18ALA00.0120.00611.604-0.004-0.0040.0000.0000.0000.000
19A19ILE0-0.041-0.0275.3010.1520.1520.0000.0000.0000.000
20A20LYS10.9070.9456.9780.4270.4270.0000.0000.0000.000
21A21LYS10.8600.9199.0750.2000.2000.0000.0000.0000.000
22A22ALA0-0.053-0.0116.7980.1040.1040.0000.0000.0000.000
23A23GLY0-0.042-0.0156.7580.2600.2600.0000.0000.0000.000
24A24TYR0-0.053-0.0352.414-2.084-0.3093.638-1.189-4.224-0.011
25A25GLU-1-0.873-0.9363.863-2.445-1.7110.000-0.208-0.5260.000
26A26ALA0-0.011-0.0095.1870.0840.098-0.001-0.0130.0000.000
27A27LYS10.8930.9557.9500.7560.7560.0000.0000.0000.000
28A28LYS10.8160.87610.6520.4490.4490.0000.0000.0000.000
29A29VAL0-0.0260.00212.212-0.004-0.0040.0000.0000.0000.000
30A30LYS10.8410.91614.9200.2300.2300.0000.0000.0000.000
31A31ARG10.8400.89518.3540.1730.1730.0000.0000.0000.000
32A32VAL00.0140.01317.818-0.013-0.0130.0000.0000.0000.000
33A33GLU-1-0.850-0.94717.525-0.177-0.1770.0000.0000.0000.000
34A34ASP-1-0.808-0.89814.230-0.405-0.4050.0000.0000.0000.000
35A35LEU0-0.048-0.02412.504-0.063-0.0630.0000.0000.0000.000
36A36GLU-1-0.921-0.94612.036-0.537-0.5370.0000.0000.0000.000
37A37GLY0-0.002-0.0078.684-0.047-0.0470.0000.0000.0000.000
38A38ILE0-0.077-0.0356.116-0.448-0.4480.0000.0000.0000.000
39A39ASP-1-0.822-0.9062.438-7.951-4.8554.946-3.716-4.327-0.036
40A40ALA0-0.035-0.0294.8850.0140.215-0.001-0.028-0.1720.000
41A41LEU0-0.031-0.0076.539-0.504-0.5040.0000.0000.0000.000
42A42ILE00.0230.0228.4460.1420.1420.0000.0000.0000.000
43A43ILE0-0.037-0.02911.637-0.146-0.1460.0000.0000.0000.000
44A44PRO00.0910.06814.6350.0220.0220.0000.0000.0000.000
45A45GLY00.029-0.00717.246-0.026-0.0260.0000.0000.0000.000
46A46GLY00.0060.00020.9590.0130.0130.0000.0000.0000.000
47A47GLU-1-0.760-0.86324.5220.0480.0480.0000.0000.0000.000
48A48SER00.0320.03624.344-0.003-0.0030.0000.0000.0000.000
49A49THR0-0.058-0.06025.380-0.005-0.0050.0000.0000.0000.000
50A50ALA0-0.015-0.01627.098-0.006-0.0060.0000.0000.0000.000
51A51ILE00.0570.03520.874-0.011-0.0110.0000.0000.0000.000
52A52GLY00.0890.03523.757-0.005-0.0050.0000.0000.0000.000
53A53LYS10.9090.94524.907-0.021-0.0210.0000.0000.0000.000
54A54LEU0-0.027-0.00724.317-0.008-0.0080.0000.0000.0000.000
55A55MET00.0280.00918.730-0.011-0.0110.0000.0000.0000.000
56A56LYS10.8410.92522.916-0.012-0.0120.0000.0000.0000.000
57A57LYS10.8770.95025.8840.0440.0440.0000.0000.0000.000
58A58TYR00.007-0.00623.732-0.007-0.0070.0000.0000.0000.000
59A59GLY00.0460.02623.088-0.014-0.0140.0000.0000.0000.000
60A60LEU00.0300.00217.6500.0080.0080.0000.0000.0000.000
61A61LEU0-0.037-0.01019.5020.0210.0210.0000.0000.0000.000
62A62GLU-1-0.775-0.89421.0780.0250.0250.0000.0000.0000.000
63A63LYS10.9170.98316.7890.1370.1370.0000.0000.0000.000
64A64ILE00.0260.01115.2680.0030.0030.0000.0000.0000.000
65A65LYS10.8030.89416.870-0.058-0.0580.0000.0000.0000.000
66A66ASN0-0.102-0.04319.0890.0080.0080.0000.0000.0000.000
67A67SER0-0.029-0.01713.666-0.007-0.0070.0000.0000.0000.000
68A68ASN00.016-0.00612.1710.0610.0610.0000.0000.0000.000
69A69LEU00.0340.0238.6140.0410.0410.0000.0000.0000.000
70A70PRO00.0110.0076.150-0.096-0.0960.0000.0000.0000.000
71A71ILE0-0.056-0.0299.3200.0330.0330.0000.0000.0000.000
72A72LEU00.0290.03110.750-0.042-0.0420.0000.0000.0000.000
73A73GLY0-0.014-0.01912.318-0.089-0.0890.0000.0000.0000.000
74A74THR0-0.021-0.02214.9960.0160.0160.0000.0000.0000.000
75A75CYS00.0330.02417.593-0.043-0.0430.0000.0000.0000.000
76A76ALA0-0.055-0.02021.4260.0040.0040.0000.0000.0000.000
77A77GLY00.0470.01818.032-0.005-0.0050.0000.0000.0000.000
78A78MET0-0.0220.01319.0060.0090.0090.0000.0000.0000.000
79A79VAL0-0.047-0.02820.486-0.007-0.0070.0000.0000.0000.000
80A80LEU0-0.019-0.01220.354-0.007-0.0070.0000.0000.0000.000
81A81LEU00.0430.02015.478-0.016-0.0160.0000.0000.0000.000
82A82SER0-0.075-0.02019.773-0.003-0.0030.0000.0000.0000.000
83A83LYS10.8790.93022.078-0.180-0.1800.0000.0000.0000.000
84A84GLY00.0130.00025.909-0.013-0.0130.0000.0000.0000.000
85A85THR0-0.015-0.02427.0340.0070.0070.0000.0000.0000.000
86A86GLY00.0020.00829.665-0.003-0.0030.0000.0000.0000.000
87A87ILE0-0.042-0.01831.669-0.007-0.0070.0000.0000.0000.000
88A88ASN0-0.0050.00132.0800.0060.0060.0000.0000.0000.000
89A89GLN00.0210.01626.874-0.006-0.0060.0000.0000.0000.000
90A90ILE0-0.0040.00825.1100.0030.0030.0000.0000.0000.000
91A91LEU0-0.0070.00524.1430.0020.0020.0000.0000.0000.000
92A92LEU00.0380.00517.538-0.016-0.0160.0000.0000.0000.000
93A93GLU-1-0.920-0.94121.6630.0760.0760.0000.0000.0000.000
94A94LEU00.0080.01516.441-0.002-0.0020.0000.0000.0000.000
95A95MET0-0.0060.00617.2940.0050.0050.0000.0000.0000.000
96A96ASP-1-0.815-0.88020.1510.1520.1520.0000.0000.0000.000
97A97ILE0-0.008-0.01021.211-0.005-0.0050.0000.0000.0000.000
98A98THR0-0.025-0.00724.694-0.015-0.0150.0000.0000.0000.000
99A99VAL00.015-0.00123.7670.0040.0040.0000.0000.0000.000
100A100LYS10.9060.95727.155-0.103-0.1030.0000.0000.0000.000
101A101ARG10.8760.90128.114-0.063-0.0630.0000.0000.0000.000
102A102ASN0-0.057-0.02929.158-0.011-0.0110.0000.0000.0000.000
103A103ALA00.0240.02829.936-0.007-0.0070.0000.0000.0000.000
104A104TYR0-0.006-0.01927.7770.0010.0010.0000.0000.0000.000
105A105GLY0-0.0150.00232.584-0.006-0.0060.0000.0000.0000.000
106A106ARG10.8280.87933.332-0.044-0.0440.0000.0000.0000.000
107A107GLN00.0110.00635.589-0.005-0.0050.0000.0000.0000.000
108A108VAL00.0270.02433.416-0.002-0.0020.0000.0000.0000.000
109A109ASP-1-0.924-0.94532.2270.0270.0270.0000.0000.0000.000
110A110SER0-0.082-0.08027.6390.0020.0020.0000.0000.0000.000
111A111PHE0-0.028-0.00427.965-0.004-0.0040.0000.0000.0000.000
112A112GLU-1-0.829-0.89026.2430.0570.0570.0000.0000.0000.000
113A113LYS10.8190.89925.783-0.110-0.1100.0000.0000.0000.000
114A114GLU-1-0.879-0.93724.0310.1250.1250.0000.0000.0000.000
115A115ILE0-0.069-0.03822.072-0.006-0.0060.0000.0000.0000.000
116A116GLU-1-0.818-0.90021.8650.1790.1790.0000.0000.0000.000
117A117PHE0-0.027-0.02015.8840.0030.0030.0000.0000.0000.000
118A118LYS10.8910.92419.513-0.308-0.3080.0000.0000.0000.000
119A119ASP-1-0.913-0.96218.0800.3320.3320.0000.0000.0000.000
120A120LEU0-0.056-0.01414.4110.0350.0350.0000.0000.0000.000
121A121GLY00.0110.01717.815-0.025-0.0250.0000.0000.0000.000
122A122LYS10.8310.90220.063-0.115-0.1150.0000.0000.0000.000
123A123VAL0-0.028-0.01116.6910.0070.0070.0000.0000.0000.000
124A124TYR0-0.016-0.04519.927-0.001-0.0010.0000.0000.0000.000
125A125GLY0-0.0060.00620.4210.0070.0070.0000.0000.0000.000
126A126VAL00.0690.03721.529-0.009-0.0090.0000.0000.0000.000
127A127PHE00.004-0.00922.6920.0160.0160.0000.0000.0000.000
128A128ILE00.0390.02224.510-0.013-0.0130.0000.0000.0000.000
129A129ARG10.9520.97026.007-0.029-0.0290.0000.0000.0000.000
130A130ALA00.0600.05125.6460.0010.0010.0000.0000.0000.000
131A131PRO0-0.070-0.02024.121-0.010-0.0100.0000.0000.0000.000
132A132VAL00.0120.02025.5270.0090.0090.0000.0000.0000.000
133A133VAL00.0310.00623.345-0.009-0.0090.0000.0000.0000.000
134A134ASP-1-0.932-0.94726.2500.0890.0890.0000.0000.0000.000
135A135LYS10.8600.91928.532-0.106-0.1060.0000.0000.0000.000
136A136ILE00.0310.01024.9030.0080.0080.0000.0000.0000.000
137A137LEU0-0.066-0.04025.753-0.013-0.0130.0000.0000.0000.000
138A138SER00.009-0.01522.729-0.014-0.0140.0000.0000.0000.000
139A139ASP-1-0.897-0.95024.5410.1560.1560.0000.0000.0000.000
140A140ASP-1-0.881-0.90519.1730.2590.2590.0000.0000.0000.000
141A141VAL0-0.073-0.03419.5920.0390.0390.0000.0000.0000.000
142A142GLU-1-0.835-0.90017.7700.3500.3500.0000.0000.0000.000
143A143VAL0-0.046-0.04320.2280.0190.0190.0000.0000.0000.000
144A144ILE00.0030.02016.119-0.015-0.0150.0000.0000.0000.000
145A145ALA00.0400.02720.079-0.005-0.0050.0000.0000.0000.000
146A146ARG10.9050.93722.338-0.171-0.1710.0000.0000.0000.000
147A147ASP-1-0.763-0.84426.0060.1110.1110.0000.0000.0000.000
148A148GLY00.0260.01428.477-0.008-0.0080.0000.0000.0000.000
149A149ASP-1-0.831-0.90730.9040.1050.1050.0000.0000.0000.000
150A150LYS10.8140.90328.589-0.090-0.0900.0000.0000.0000.000
151A151ILE00.0200.00724.2040.0080.0080.0000.0000.0000.000
152A152VAL00.0330.01323.0080.0000.0000.0000.0000.0000.000
153A153GLY00.0100.00220.0780.0120.0120.0000.0000.0000.000
154A154VAL0-0.027-0.02019.191-0.019-0.0190.0000.0000.0000.000
155A155LYS10.9000.94012.377-0.616-0.6160.0000.0000.0000.000
156A156GLN00.016-0.00815.723-0.046-0.0460.0000.0000.0000.000
157A157GLY00.0520.03014.3780.0190.0190.0000.0000.0000.000
158A158LYS10.9070.9719.783-0.291-0.2910.0000.0000.0000.000
159A159TYR00.0280.00510.9390.1380.1380.0000.0000.0000.000
160A160MET00.0090.01412.321-0.012-0.0120.0000.0000.0000.000
161A161ALA0-0.0050.00614.544-0.012-0.0120.0000.0000.0000.000
162A162LEU0-0.0030.00515.440-0.017-0.0170.0000.0000.0000.000
163A163SER0-0.010-0.04919.087-0.013-0.0130.0000.0000.0000.000
164A164PHE0-0.032-0.02018.338-0.022-0.0220.0000.0000.0000.000
165A165HIS0-0.033-0.03118.6720.0240.0240.0000.0000.0000.000
166A166PRO0-0.007-0.00514.671-0.020-0.0200.0000.0000.0000.000
167A167GLU-1-0.764-0.86815.1230.1500.1500.0000.0000.0000.000
168A168LEU0-0.022-0.00516.169-0.030-0.0300.0000.0000.0000.000
169A169SER0-0.005-0.00518.464-0.003-0.0030.0000.0000.0000.000
170A170GLU-1-0.884-0.94417.6210.0290.0290.0000.0000.0000.000
171A171ASP-1-0.767-0.87617.0420.1480.1480.0000.0000.0000.000
172A172GLY0-0.0040.00814.8180.0490.0490.0000.0000.0000.000
173A173TYR0-0.017-0.02011.0030.0860.0860.0000.0000.0000.000
174A174LYS10.8360.92010.671-0.067-0.0670.0000.0000.0000.000
175A175VAL0-0.0080.00411.8930.1090.1090.0000.0000.0000.000
176A176TYR0-0.027-0.0468.2590.1400.1400.0000.0000.0000.000
177A177LYS10.9040.9687.1200.0390.0390.0000.0000.0000.000
178A178TYR0-0.022-0.0207.8940.3480.3480.0000.0000.0000.000
179A179PHE00.0490.0067.3150.1320.1320.0000.0000.0000.000
180A180VAL00.0320.0112.685-0.457-0.4511.907-0.321-1.5920.002
181A181GLU-1-0.874-0.9395.8481.1031.1030.0000.0000.0000.000
182A182ASN0-0.039-0.0157.504-0.364-0.3640.0000.0000.0000.000
183A183CYS0-0.138-0.0488.434-0.346-0.3460.0000.0000.0000.000
184A184VAL0-0.0090.0052.391-1.043-0.5771.724-0.492-1.698-0.001
185A185LYS10.8220.9103.441-2.893-2.3230.013-0.079-0.5030.000