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: QVYJY

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2051065.669174
FMO2-HF: Nuclear repulsion 1979296.468672
FMO2-HF: Total energy -71769.200502
FMO2-MP2: Total energy -71978.131947


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.
-6.5783.26812.452-6.322-15.978-0.037
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 : -0.054 / q_NPA : -0.026
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].
3A3ILE0-0.023-0.0112.3010.5452.3341.974-0.945-2.819-0.001
4A4GLY00.0490.0164.7630.0350.074-0.001-0.008-0.0300.000
5A5VAL00.004-0.0018.4950.1310.1310.0000.0000.0000.000
6A6LEU0-0.036-0.01811.2590.0180.0180.0000.0000.0000.000
7A7ALA00.0490.01814.628-0.012-0.0120.0000.0000.0000.000
8A8ILE0-0.0280.00117.4590.0010.0010.0000.0000.0000.000
9A9GLN0-0.094-0.07820.2890.0110.0110.0000.0000.0000.000
10A10GLY00.0060.01020.8770.0000.0000.0000.0000.0000.000
11A11ASP-1-0.935-0.94919.757-0.146-0.1460.0000.0000.0000.000
12A12VAL0-0.001-0.02014.4140.0160.0160.0000.0000.0000.000
13A13GLU-1-0.835-0.92014.682-0.303-0.3030.0000.0000.0000.000
14A14GLU-1-0.941-0.96315.426-0.269-0.2690.0000.0000.0000.000
15A15HIS00.018-0.00312.353-0.072-0.0720.0000.0000.0000.000
16A16GLU-1-0.915-0.98010.649-0.610-0.6100.0000.0000.0000.000
17A17GLU-1-0.912-0.95310.672-0.740-0.7400.0000.0000.0000.000
18A18ALA0-0.004-0.00611.930-0.066-0.0660.0000.0000.0000.000
19A19ILE0-0.040-0.0275.596-0.014-0.0140.0000.0000.0000.000
20A20LYS10.9730.9937.2000.4380.4380.0000.0000.0000.000
21A21LYS10.9110.9658.7720.4080.4080.0000.0000.0000.000
22A22ALA0-0.089-0.0396.8870.1000.1000.0000.0000.0000.000
23A23GLY0-0.035-0.0076.3850.0840.0840.0000.0000.0000.000
24A24TYR0-0.047-0.0332.296-2.859-0.7453.025-1.269-3.869-0.011
25A25GLU-1-0.897-0.9453.592-0.0560.8160.002-0.216-0.6580.000
26A26ALA0-0.026-0.0095.101-0.530-0.549-0.001-0.0130.0320.000
27A27LYS10.9510.9837.7260.2320.2320.0000.0000.0000.000
28A28LYS10.9711.0039.8220.2890.2890.0000.0000.0000.000
29A29VAL00.0010.00111.5460.0590.0590.0000.0000.0000.000
30A30LYS10.8720.93314.2640.0970.0970.0000.0000.0000.000
31A31ARG10.8550.90317.8610.0320.0320.0000.0000.0000.000
32A32VAL00.0290.00817.4910.0020.0020.0000.0000.0000.000
33A33GLU-1-0.877-0.95217.2790.0990.0990.0000.0000.0000.000
34A34ASP-1-0.814-0.89514.089-0.007-0.0070.0000.0000.0000.000
35A35LEU0-0.064-0.04412.589-0.021-0.0210.0000.0000.0000.000
36A36GLU-1-0.975-0.98011.6830.5430.5430.0000.0000.0000.000
37A37GLY00.0370.0199.152-0.098-0.0980.0000.0000.0000.000
38A38ILE0-0.078-0.0246.365-0.041-0.0410.0000.0000.0000.000
39A39ASP-1-0.825-0.9222.6790.0552.6883.135-2.698-3.070-0.026
40A40ALA0-0.035-0.0304.996-0.1070.100-0.001-0.022-0.1840.000
41A41LEU0-0.033-0.0066.569-0.521-0.5210.0000.0000.0000.000
42A42ILE00.0190.0187.9330.0750.0750.0000.0000.0000.000
43A43ILE0-0.037-0.03310.916-0.044-0.0440.0000.0000.0000.000
44A44PRO00.0820.05713.8960.0210.0210.0000.0000.0000.000
45A45GLY00.0540.01016.5570.0150.0150.0000.0000.0000.000
46A46GLY00.010-0.00320.1940.0050.0050.0000.0000.0000.000
47A47GLU-1-0.822-0.90423.701-0.005-0.0050.0000.0000.0000.000
48A48SER00.0710.03623.9970.0020.0020.0000.0000.0000.000
49A49THR0-0.095-0.06725.0190.0070.0070.0000.0000.0000.000
50A50ALA00.000-0.00826.6010.0050.0050.0000.0000.0000.000
51A51ILE00.0560.02720.2940.0030.0030.0000.0000.0000.000
52A52GLY00.0810.03923.1390.0080.0080.0000.0000.0000.000
53A53LYS10.9070.94124.671-0.002-0.0020.0000.0000.0000.000
54A54LEU0-0.0190.00223.4350.0060.0060.0000.0000.0000.000
55A55MET00.0400.02018.4520.0010.0010.0000.0000.0000.000
56A56LYS10.9590.98722.536-0.039-0.0390.0000.0000.0000.000
57A57LYS10.8850.95125.6790.0030.0030.0000.0000.0000.000
58A58TYR0-0.034-0.03623.038-0.004-0.0040.0000.0000.0000.000
59A59GLY00.0490.03323.1230.0040.0040.0000.0000.0000.000
60A60LEU00.0080.00317.0840.0130.0130.0000.0000.0000.000
61A61LEU0-0.045-0.01919.4320.0160.0160.0000.0000.0000.000
62A62GLU-1-0.916-0.97021.0080.1060.1060.0000.0000.0000.000
63A63LYS10.9390.98217.466-0.189-0.1890.0000.0000.0000.000
64A64ILE00.0300.00915.2760.0250.0250.0000.0000.0000.000
65A65LYS10.9270.98016.767-0.071-0.0710.0000.0000.0000.000
66A66ASN0-0.037-0.00119.3020.0050.0050.0000.0000.0000.000
67A67SER0-0.058-0.01613.8020.0380.0380.0000.0000.0000.000
68A68ASN00.015-0.01113.054-0.046-0.0460.0000.0000.0000.000
69A69LEU00.0140.0058.5060.0610.0610.0000.0000.0000.000
70A70PRO00.0010.0076.729-0.192-0.1920.0000.0000.0000.000
71A71ILE0-0.041-0.0229.3680.0170.0170.0000.0000.0000.000
72A72LEU00.0250.02510.609-0.029-0.0290.0000.0000.0000.000
73A73GLY0-0.011-0.01512.263-0.050-0.0500.0000.0000.0000.000
74A74THR00.0130.00014.5130.0000.0000.0000.0000.0000.000
75A75CYS00.0410.02817.209-0.005-0.0050.0000.0000.0000.000
76A76ALA0-0.063-0.02320.5850.0180.0180.0000.0000.0000.000
77A77GLY00.0470.00917.5160.0150.0150.0000.0000.0000.000
78A78MET0-0.0410.00618.5060.0230.0230.0000.0000.0000.000
79A79VAL0-0.050-0.03120.1990.0100.0100.0000.0000.0000.000
80A80LEU0-0.023-0.01520.0080.0080.0080.0000.0000.0000.000
81A81LEU00.0630.03415.5430.0080.0080.0000.0000.0000.000
82A82SER0-0.065-0.01219.9090.0100.0100.0000.0000.0000.000
83A83LYS10.9170.94923.078-0.105-0.1050.0000.0000.0000.000
84A84GLY0-0.010-0.00425.984-0.004-0.0040.0000.0000.0000.000
85A85THR00.000-0.00827.376-0.001-0.0010.0000.0000.0000.000
86A86GLY0-0.023-0.00130.003-0.005-0.0050.0000.0000.0000.000
87A87ILE0-0.040-0.01431.423-0.003-0.0030.0000.0000.0000.000
88A88ASN0-0.029-0.01432.0800.0040.0040.0000.0000.0000.000
89A89GLN00.0570.01727.105-0.007-0.0070.0000.0000.0000.000
90A90ILE0-0.028-0.01125.2320.0040.0040.0000.0000.0000.000
91A91LEU0-0.027-0.00324.343-0.007-0.0070.0000.0000.0000.000
92A92LEU0-0.028-0.02817.8730.0010.0010.0000.0000.0000.000
93A93GLU-1-0.974-0.98921.9740.0860.0860.0000.0000.0000.000
94A94LEU0-0.025-0.01216.7800.0050.0050.0000.0000.0000.000
95A95MET0-0.030-0.00217.2710.0060.0060.0000.0000.0000.000
96A96ASP-1-0.790-0.87620.3420.0900.0900.0000.0000.0000.000
97A97ILE00.0010.00321.641-0.011-0.0110.0000.0000.0000.000
98A98THR0-0.030-0.00224.916-0.001-0.0010.0000.0000.0000.000
99A99VAL00.021-0.00724.034-0.003-0.0030.0000.0000.0000.000
100A100LYS10.9851.00227.382-0.005-0.0050.0000.0000.0000.000
101A101ARG10.9330.95627.906-0.005-0.0050.0000.0000.0000.000
102A102ASN0-0.014-0.01728.9550.0040.0040.0000.0000.0000.000
103A103ALA00.0430.03429.5680.0000.0000.0000.0000.0000.000
104A104TYR0-0.037-0.04527.5250.0020.0020.0000.0000.0000.000
105A105GLY0-0.0020.01232.534-0.001-0.0010.0000.0000.0000.000
106A106ARG10.8190.88233.1330.0130.0130.0000.0000.0000.000
107A107GLN00.0140.00635.016-0.002-0.0020.0000.0000.0000.000
108A108VAL00.0060.02333.038-0.001-0.0010.0000.0000.0000.000
109A109ASP-1-0.908-0.94732.309-0.051-0.0510.0000.0000.0000.000
110A110SER0-0.084-0.06727.552-0.004-0.0040.0000.0000.0000.000
111A111PHE0-0.034-0.01027.6870.0040.0040.0000.0000.0000.000
112A112GLU-1-0.855-0.89326.024-0.109-0.1090.0000.0000.0000.000
113A113LYS10.8560.92525.5340.0570.0570.0000.0000.0000.000
114A114GLU-1-0.906-0.95023.863-0.102-0.1020.0000.0000.0000.000
115A115ILE0-0.080-0.04121.5420.0120.0120.0000.0000.0000.000
116A116GLU-1-0.858-0.93021.603-0.076-0.0760.0000.0000.0000.000
117A117PHE0-0.025-0.02415.2260.0100.0100.0000.0000.0000.000
118A118LYS10.8460.88518.399-0.028-0.0280.0000.0000.0000.000
119A119ASP-1-0.915-0.95616.815-0.013-0.0130.0000.0000.0000.000
120A120LEU0-0.052-0.01214.195-0.012-0.0120.0000.0000.0000.000
121A121GLY00.0170.00817.371-0.010-0.0100.0000.0000.0000.000
122A122LYS10.8410.92420.2260.0810.0810.0000.0000.0000.000
123A123VAL0-0.0330.00016.635-0.017-0.0170.0000.0000.0000.000
124A124TYR0-0.012-0.04419.7350.0200.0200.0000.0000.0000.000
125A125GLY0-0.0010.01120.249-0.015-0.0150.0000.0000.0000.000
126A126VAL00.0790.03521.5070.0120.0120.0000.0000.0000.000
127A127PHE00.000-0.01522.7450.0030.0030.0000.0000.0000.000
128A128ILE00.0640.03124.6610.0030.0030.0000.0000.0000.000
129A129ARG10.9120.93925.5880.0620.0620.0000.0000.0000.000
130A130ALA00.0470.03225.1930.0040.0040.0000.0000.0000.000
131A131PRO0-0.088-0.01923.7680.0040.0040.0000.0000.0000.000
132A132VAL00.0560.02325.253-0.004-0.0040.0000.0000.0000.000
133A133VAL00.0190.00523.2970.0040.0040.0000.0000.0000.000
134A134ASP-1-0.989-0.98826.3110.0140.0140.0000.0000.0000.000
135A135LYS10.8730.93829.623-0.031-0.0310.0000.0000.0000.000
136A136ILE00.0310.00624.7470.0030.0030.0000.0000.0000.000
137A137LEU0-0.073-0.05825.972-0.004-0.0040.0000.0000.0000.000
138A138SER00.001-0.00722.601-0.001-0.0010.0000.0000.0000.000
139A139ASP-1-0.878-0.93924.7040.0550.0550.0000.0000.0000.000
140A140ASP-1-0.904-0.91819.6930.1170.1170.0000.0000.0000.000
141A141VAL0-0.070-0.02719.5870.0120.0120.0000.0000.0000.000
142A142GLU-1-0.814-0.89217.3990.0460.0460.0000.0000.0000.000
143A143VAL0-0.054-0.03719.7170.0030.0030.0000.0000.0000.000
144A144ILE0-0.004-0.00715.602-0.004-0.0040.0000.0000.0000.000
145A145ALA00.0490.03119.471-0.015-0.0150.0000.0000.0000.000
146A146ARG10.9200.95521.7100.0070.0070.0000.0000.0000.000
147A147ASP-1-0.758-0.84225.394-0.048-0.0480.0000.0000.0000.000
148A148GLY0-0.012-0.00627.7760.0030.0030.0000.0000.0000.000
149A149ASP-1-0.940-0.98730.154-0.008-0.0080.0000.0000.0000.000
150A150LYS10.9250.98428.5210.0240.0240.0000.0000.0000.000
151A151ILE00.0020.00423.629-0.004-0.0040.0000.0000.0000.000
152A152VAL00.018-0.00622.3090.0040.0040.0000.0000.0000.000
153A153GLY00.0360.01519.657-0.007-0.0070.0000.0000.0000.000
154A154VAL0-0.019-0.00418.920-0.003-0.0030.0000.0000.0000.000
155A155LYS10.9480.96412.075-0.171-0.1710.0000.0000.0000.000
156A156GLN00.0240.00715.648-0.016-0.0160.0000.0000.0000.000
157A157GLY00.0150.01614.0350.0280.0280.0000.0000.0000.000
158A158LYS10.9460.9799.953-0.419-0.4190.0000.0000.0000.000
159A159TYR00.0140.00611.0630.0720.0720.0000.0000.0000.000
160A160MET00.0130.01412.000-0.040-0.0400.0000.0000.0000.000
161A161ALA0-0.0010.01314.553-0.003-0.0030.0000.0000.0000.000
162A162LEU0-0.007-0.00714.685-0.010-0.0100.0000.0000.0000.000
163A163SER0-0.008-0.03218.583-0.001-0.0010.0000.0000.0000.000
164A164PHE0-0.019-0.00917.6780.0030.0030.0000.0000.0000.000
165A165HIS0-0.022-0.01718.3660.0050.0050.0000.0000.0000.000
166A166PRO0-0.039-0.03114.469-0.008-0.0080.0000.0000.0000.000
167A167GLU-1-0.831-0.93614.899-0.202-0.2020.0000.0000.0000.000
168A168LEU0-0.022-0.00116.186-0.005-0.0050.0000.0000.0000.000
169A169SER0-0.0090.00518.5870.0070.0070.0000.0000.0000.000
170A170GLU-1-0.892-0.95117.789-0.222-0.2220.0000.0000.0000.000
171A171ASP-1-0.816-0.91016.692-0.227-0.2270.0000.0000.0000.000
172A172GLY00.0210.01914.562-0.005-0.0050.0000.0000.0000.000
173A173TYR0-0.006-0.02310.8080.0150.0150.0000.0000.0000.000
174A174LYS10.8740.95010.1410.1760.1760.0000.0000.0000.000
175A175VAL00.0080.01511.4910.0290.0290.0000.0000.0000.000
176A176TYR00.000-0.0137.8340.0720.0720.0000.0000.0000.000
177A177LYS10.9570.9876.6830.6440.6440.0000.0000.0000.000
178A178TYR0-0.012-0.0037.5570.1070.1070.0000.0000.0000.000
179A179PHE00.0360.0027.3920.1100.1100.0000.0000.0000.000
180A180VAL00.0240.0052.394-0.944-0.1251.293-0.338-1.774-0.002
181A181GLU-1-0.974-1.0044.835-0.404-0.284-0.001-0.005-0.1150.000
182A182ASN0-0.041-0.0176.232-0.021-0.0210.0000.0000.0000.000
183A183CYS0-0.147-0.0537.790-0.080-0.0800.0000.0000.0000.000
184A184VAL0-0.021-0.0022.644-0.857-0.4251.665-0.486-1.6110.000
185A185LYS10.9210.9792.561-0.8380.0021.362-0.322-1.8800.003