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: KG9M3

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2053081.914063
FMO2-HF: Nuclear repulsion 1981311.929621
FMO2-HF: Total energy -71769.984442
FMO2-MP2: Total energy -71978.990552


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.
-13.597-4.41615.113-7.442-16.853-0.04
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 : 0.004
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].
3A3ILE0-0.018-0.0102.4750.8793.2092.634-1.480-3.4840.004
4A4GLY00.0490.0194.920-0.346-0.325-0.001-0.006-0.0150.000
5A5VAL0-0.001-0.0038.6800.2980.2980.0000.0000.0000.000
6A6LEU0-0.031-0.01711.363-0.059-0.0590.0000.0000.0000.000
7A7ALA00.0590.02114.7800.0180.0180.0000.0000.0000.000
8A8ILE0-0.0180.00717.566-0.023-0.0230.0000.0000.0000.000
9A9GLN0-0.093-0.06720.4440.0000.0000.0000.0000.0000.000
10A10GLY00.0080.01020.9540.0100.0100.0000.0000.0000.000
11A11ASP-1-0.921-0.94519.688-0.201-0.2010.0000.0000.0000.000
12A12VAL0-0.018-0.02214.3060.0270.0270.0000.0000.0000.000
13A13GLU-1-0.787-0.90014.593-0.340-0.3400.0000.0000.0000.000
14A14GLU-1-0.939-0.95715.251-0.161-0.1610.0000.0000.0000.000
15A15HIS00.017-0.00812.256-0.047-0.0470.0000.0000.0000.000
16A16GLU-1-0.877-0.96010.517-0.664-0.6640.0000.0000.0000.000
17A17GLU-1-0.855-0.90210.456-0.586-0.5860.0000.0000.0000.000
18A18ALA00.0060.00411.664-0.018-0.0180.0000.0000.0000.000
19A19ILE0-0.024-0.0205.3360.1200.1200.0000.0000.0000.000
20A20LYS10.9150.9577.0090.5570.5570.0000.0000.0000.000
21A21LYS10.8440.9178.7920.3130.3130.0000.0000.0000.000
22A22ALA0-0.082-0.0356.9010.1280.1280.0000.0000.0000.000
23A23GLY0-0.046-0.0176.3740.2740.2740.0000.0000.0000.000
24A24TYR0-0.048-0.0342.322-2.295-0.5014.278-1.391-4.681-0.012
25A25GLU-1-0.894-0.9433.641-2.693-1.7400.002-0.279-0.6760.000
26A26ALA0-0.020-0.0075.051-0.222-0.230-0.001-0.0150.0240.000
27A27LYS10.9120.9517.6690.8970.8970.0000.0000.0000.000
28A28LYS10.8950.9639.9090.5590.5590.0000.0000.0000.000
29A29VAL0-0.006-0.00311.7130.0040.0040.0000.0000.0000.000
30A30LYS10.8710.92514.4520.2760.2760.0000.0000.0000.000
31A31ARG10.8470.89718.0650.2110.2110.0000.0000.0000.000
32A32VAL00.0250.00717.750-0.020-0.0200.0000.0000.0000.000
33A33GLU-1-0.864-0.94717.312-0.181-0.1810.0000.0000.0000.000
34A34ASP-1-0.800-0.88314.224-0.425-0.4250.0000.0000.0000.000
35A35LEU0-0.065-0.02812.623-0.086-0.0860.0000.0000.0000.000
36A36GLU-1-0.955-0.97411.714-0.437-0.4370.0000.0000.0000.000
37A37GLY00.0350.0199.182-0.093-0.0930.0000.0000.0000.000
38A38ILE0-0.082-0.0246.394-0.493-0.4930.0000.0000.0000.000
39A39ASP-1-0.820-0.9132.440-4.436-2.3044.780-3.254-3.657-0.032
40A40ALA0-0.030-0.0325.0350.0120.232-0.001-0.030-0.1900.000
41A41LEU0-0.046-0.0126.426-0.584-0.601-0.001-0.0020.0200.000
42A42ILE00.0270.0197.9280.1270.1270.0000.0000.0000.000
43A43ILE0-0.039-0.03111.039-0.138-0.1380.0000.0000.0000.000
44A44PRO00.0780.05914.0120.0330.0330.0000.0000.0000.000
45A45GLY00.0460.00616.605-0.018-0.0180.0000.0000.0000.000
46A46GLY00.0150.00020.2320.0160.0160.0000.0000.0000.000
47A47GLU-1-0.773-0.87223.7230.0280.0280.0000.0000.0000.000
48A48SER00.0530.03424.096-0.003-0.0030.0000.0000.0000.000
49A49THR0-0.095-0.08025.139-0.002-0.0020.0000.0000.0000.000
50A50ALA0-0.008-0.01426.721-0.003-0.0030.0000.0000.0000.000
51A51ILE00.0550.02620.459-0.009-0.0090.0000.0000.0000.000
52A52GLY00.0820.04023.330-0.002-0.0020.0000.0000.0000.000
53A53LYS10.9120.94424.8720.0000.0000.0000.0000.0000.000
54A54LEU0-0.026-0.00223.570-0.006-0.0060.0000.0000.0000.000
55A55MET00.0410.01918.693-0.012-0.0120.0000.0000.0000.000
56A56LYS10.8900.94922.776-0.003-0.0030.0000.0000.0000.000
57A57LYS10.8910.95825.8850.0610.0610.0000.0000.0000.000
58A58TYR0-0.028-0.03523.316-0.005-0.0050.0000.0000.0000.000
59A59GLY00.0520.03523.402-0.014-0.0140.0000.0000.0000.000
60A60LEU00.001-0.00117.2420.0080.0080.0000.0000.0000.000
61A61LEU0-0.038-0.01419.4020.0210.0210.0000.0000.0000.000
62A62GLU-1-0.829-0.92920.9050.0220.0220.0000.0000.0000.000
63A63LYS10.9510.99817.2810.1020.1020.0000.0000.0000.000
64A64ILE00.0300.01315.2220.0100.0100.0000.0000.0000.000
65A65LYS10.8250.92416.709-0.047-0.0470.0000.0000.0000.000
66A66ASN0-0.085-0.03819.2810.0130.0130.0000.0000.0000.000
67A67SER0-0.049-0.01313.8220.0060.0060.0000.0000.0000.000
68A68ASN00.013-0.00712.8370.0370.0370.0000.0000.0000.000
69A69LEU00.0300.0158.5590.0610.0610.0000.0000.0000.000
70A70PRO00.0060.0066.351-0.153-0.1530.0000.0000.0000.000
71A71ILE0-0.046-0.0279.2280.0290.0290.0000.0000.0000.000
72A72LEU00.0250.02610.605-0.028-0.0280.0000.0000.0000.000
73A73GLY0-0.007-0.01312.169-0.089-0.0890.0000.0000.0000.000
74A74THR00.0160.00014.7450.0150.0150.0000.0000.0000.000
75A75CYS00.0330.02117.236-0.037-0.0370.0000.0000.0000.000
76A76ALA0-0.051-0.01120.6140.0090.0090.0000.0000.0000.000
77A77GLY00.0390.00717.6270.0000.0000.0000.0000.0000.000
78A78MET0-0.0350.00818.6240.0170.0170.0000.0000.0000.000
79A79VAL0-0.056-0.03620.190-0.001-0.0010.0000.0000.0000.000
80A80LEU0-0.022-0.00820.127-0.002-0.0020.0000.0000.0000.000
81A81LEU00.0620.03815.341-0.010-0.0100.0000.0000.0000.000
82A82SER0-0.062-0.01519.7190.0000.0000.0000.0000.0000.000
83A83LYS10.8890.93822.214-0.174-0.1740.0000.0000.0000.000
84A84GLY0-0.008-0.00425.833-0.011-0.0110.0000.0000.0000.000
85A85THR00.0100.00327.2340.0060.0060.0000.0000.0000.000
86A86GLY0-0.0200.00029.787-0.004-0.0040.0000.0000.0000.000
87A87ILE0-0.034-0.01331.547-0.006-0.0060.0000.0000.0000.000
88A88ASN0-0.026-0.01131.9680.0050.0050.0000.0000.0000.000
89A89GLN00.0480.02026.918-0.006-0.0060.0000.0000.0000.000
90A90ILE0-0.018-0.00425.2220.0040.0040.0000.0000.0000.000
91A91LEU0-0.0160.00624.201-0.001-0.0010.0000.0000.0000.000
92A92LEU00.021-0.00417.704-0.013-0.0130.0000.0000.0000.000
93A93GLU-1-0.939-0.97021.8260.0780.0780.0000.0000.0000.000
94A94LEU0-0.007-0.00116.766-0.002-0.0020.0000.0000.0000.000
95A95MET0-0.024-0.00417.2560.0080.0080.0000.0000.0000.000
96A96ASP-1-0.809-0.88120.2120.1450.1450.0000.0000.0000.000
97A97ILE00.0030.00221.216-0.005-0.0050.0000.0000.0000.000
98A98THR0-0.027-0.00324.762-0.012-0.0120.0000.0000.0000.000
99A99VAL00.000-0.01623.7520.0040.0040.0000.0000.0000.000
100A100LYS10.8990.94727.155-0.083-0.0830.0000.0000.0000.000
101A101ARG10.8960.92227.848-0.039-0.0390.0000.0000.0000.000
102A102ASN0-0.030-0.01828.995-0.006-0.0060.0000.0000.0000.000
103A103ALA00.0440.03529.481-0.005-0.0050.0000.0000.0000.000
104A104TYR0-0.025-0.03227.7610.0010.0010.0000.0000.0000.000
105A105GLY0-0.0010.01232.503-0.005-0.0050.0000.0000.0000.000
106A106ARG10.8270.88033.164-0.024-0.0240.0000.0000.0000.000
107A107GLN00.0090.00535.002-0.005-0.0050.0000.0000.0000.000
108A108VAL00.0100.02233.082-0.003-0.0030.0000.0000.0000.000
109A109ASP-1-0.912-0.94732.2450.0020.0020.0000.0000.0000.000
110A110SER0-0.087-0.07727.4600.0000.0000.0000.0000.0000.000
111A111PHE0-0.025-0.00927.715-0.001-0.0010.0000.0000.0000.000
112A112GLU-1-0.850-0.89526.0950.0140.0140.0000.0000.0000.000
113A113LYS10.8310.89825.601-0.074-0.0740.0000.0000.0000.000
114A114GLU-1-0.891-0.94923.8880.0840.0840.0000.0000.0000.000
115A115ILE0-0.086-0.04521.645-0.001-0.0010.0000.0000.0000.000
116A116GLU-1-0.826-0.90321.6320.1400.1400.0000.0000.0000.000
117A117PHE0-0.029-0.02815.3660.0040.0040.0000.0000.0000.000
118A118LYS10.8730.90519.181-0.264-0.2640.0000.0000.0000.000
119A119ASP-1-0.914-0.95517.6230.2880.2880.0000.0000.0000.000
120A120LEU0-0.051-0.01314.4180.0250.0250.0000.0000.0000.000
121A121GLY00.0180.01417.805-0.020-0.0200.0000.0000.0000.000
122A122LYS10.8370.91720.221-0.093-0.0930.0000.0000.0000.000
123A123VAL0-0.035-0.01016.5490.0020.0020.0000.0000.0000.000
124A124TYR0-0.017-0.03219.7430.0020.0020.0000.0000.0000.000
125A125GLY00.0060.01820.2960.0010.0010.0000.0000.0000.000
126A126VAL00.0760.03521.512-0.005-0.0050.0000.0000.0000.000
127A127PHE00.004-0.01322.6300.0100.0100.0000.0000.0000.000
128A128ILE00.0560.03524.306-0.009-0.0090.0000.0000.0000.000
129A129ARG10.9180.94825.5540.0040.0040.0000.0000.0000.000
130A130ALA00.0460.03525.1600.0030.0030.0000.0000.0000.000
131A131PRO0-0.077-0.01423.766-0.006-0.0060.0000.0000.0000.000
132A132VAL00.0500.02825.2690.0070.0070.0000.0000.0000.000
133A133VAL00.0320.00923.225-0.006-0.0060.0000.0000.0000.000
134A134ASP-1-0.902-0.92526.1390.0730.0730.0000.0000.0000.000
135A135LYS10.8510.91829.383-0.084-0.0840.0000.0000.0000.000
136A136ILE00.0320.00724.9010.0070.0070.0000.0000.0000.000
137A137LEU0-0.069-0.05726.016-0.010-0.0100.0000.0000.0000.000
138A138SER00.009-0.01322.843-0.012-0.0120.0000.0000.0000.000
139A139ASP-1-0.890-0.94424.8200.1420.1420.0000.0000.0000.000
140A140ASP-1-0.895-0.91019.4750.2440.2440.0000.0000.0000.000
141A141VAL0-0.075-0.02719.7490.0320.0320.0000.0000.0000.000
142A142GLU-1-0.836-0.90917.5080.3060.3060.0000.0000.0000.000
143A143VAL0-0.054-0.03820.1630.0150.0150.0000.0000.0000.000
144A144ILE0-0.010-0.00416.188-0.006-0.0060.0000.0000.0000.000
145A145ALA00.0500.03320.151-0.004-0.0040.0000.0000.0000.000
146A146ARG10.9190.95322.020-0.142-0.1420.0000.0000.0000.000
147A147ASP-1-0.747-0.82325.6030.0800.0800.0000.0000.0000.000
148A148GLY00.0100.00627.875-0.007-0.0070.0000.0000.0000.000
149A149ASP-1-0.856-0.92830.4090.0830.0830.0000.0000.0000.000
150A150LYS10.8320.91628.650-0.071-0.0710.0000.0000.0000.000
151A151ILE00.0030.00123.9890.0050.0050.0000.0000.0000.000
152A152VAL00.023-0.00222.392-0.003-0.0030.0000.0000.0000.000
153A153GLY00.0380.01619.8370.0080.0080.0000.0000.0000.000
154A154VAL0-0.020-0.01019.041-0.016-0.0160.0000.0000.0000.000
155A155LYS10.9020.94111.948-0.556-0.5560.0000.0000.0000.000
156A156GLN00.0270.00715.755-0.039-0.0390.0000.0000.0000.000
157A157GLY00.0510.03514.1620.0190.0190.0000.0000.0000.000
158A158LYS10.9250.9709.816-0.388-0.3880.0000.0000.0000.000
159A159TYR00.0070.00011.0130.1220.1220.0000.0000.0000.000
160A160MET00.0140.01912.278-0.023-0.0230.0000.0000.0000.000
161A161ALA0-0.0020.01314.403-0.014-0.0140.0000.0000.0000.000
162A162LEU0-0.005-0.00414.886-0.010-0.0100.0000.0000.0000.000
163A163SER0-0.010-0.03618.701-0.014-0.0140.0000.0000.0000.000
164A164PHE0-0.020-0.01417.726-0.017-0.0170.0000.0000.0000.000
165A165HIS0-0.023-0.02218.2780.0190.0190.0000.0000.0000.000
166A166PRO0-0.027-0.02214.309-0.016-0.0160.0000.0000.0000.000
167A167GLU-1-0.798-0.90714.7340.0220.0220.0000.0000.0000.000
168A168LEU0-0.025-0.00716.018-0.024-0.0240.0000.0000.0000.000
169A169SER0-0.0070.00318.4370.0000.0000.0000.0000.0000.000
170A170GLU-1-0.871-0.94017.723-0.030-0.0300.0000.0000.0000.000
171A171ASP-1-0.822-0.91216.6690.0790.0790.0000.0000.0000.000
172A172GLY00.0220.02114.6010.0430.0430.0000.0000.0000.000
173A173TYR0-0.006-0.02110.7880.0680.0680.0000.0000.0000.000
174A174LYS10.8620.93410.116-0.025-0.0250.0000.0000.0000.000
175A175VAL0-0.0070.00311.4800.0980.0980.0000.0000.0000.000
176A176TYR0-0.021-0.0317.9480.1270.1270.0000.0000.0000.000
177A177LYS10.9380.9846.6610.0990.0990.0000.0000.0000.000
178A178TYR0-0.007-0.0087.7090.2600.2600.0000.0000.0000.000
179A179PHE00.0470.0057.2090.1340.1340.0000.0000.0000.000
180A180VAL00.0210.0042.412-0.719-0.4061.786-0.372-1.7270.001
181A181GLU-1-0.882-0.9355.4640.7890.7890.0000.0000.0000.000
182A182ASN0-0.029-0.0116.888-0.233-0.2330.0000.0000.0000.000
183A183CYS0-0.141-0.0558.334-0.268-0.2680.0000.0000.0000.000
184A184VAL0-0.0150.0022.554-1.156-0.5361.442-0.464-1.598-0.001
185A185LYS10.8260.9142.818-2.744-1.9210.195-0.149-0.8690.000