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: 22QKR

Calculation Name: 1WJ9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WJ9

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WG9

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2089053.2219
FMO2-HF: Nuclear repulsion 2016039.088167
FMO2-HF: Total energy -73014.133733
FMO2-MP2: Total energy -73232.724821


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.
-27.584-19.8632.612-11.621-28.716-0.085
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 : -0.044 / q_NPA : -0.009
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].
3A3LEU0-0.029-0.0173.6200.5232.8740.002-1.204-1.1480.003
4A4THR00.0260.0105.961-0.204-0.2040.0000.0000.0000.000
5A5LYS10.9200.9679.5620.6150.6150.0000.0000.0000.000
6A6LEU00.0490.03712.706-0.066-0.0660.0000.0000.0000.000
7A7VAL0-0.021-0.01015.3690.0790.0790.0000.0000.0000.000
8A8LEU00.0220.00617.405-0.021-0.0210.0000.0000.0000.000
9A9ASN00.0240.00620.8050.0260.0260.0000.0000.0000.000
10A10PRO00.0380.00924.4350.0130.0130.0000.0000.0000.000
11A11ALA00.0350.03026.9500.0140.0140.0000.0000.0000.000
12A12SER00.0450.03624.9410.0140.0140.0000.0000.0000.000
13A13ARG10.9370.95626.936-0.007-0.0070.0000.0000.0000.000
14A14ALA00.0310.02424.4620.0200.0200.0000.0000.0000.000
15A15ALA00.0800.03722.5010.0200.0200.0000.0000.0000.000
16A16ARG10.8440.90023.4280.0440.0440.0000.0000.0000.000
17A17ARG10.7640.87122.734-0.021-0.0210.0000.0000.0000.000
18A18ASP-1-0.706-0.80820.2900.0510.0510.0000.0000.0000.000
19A19LEU0-0.034-0.03320.7730.0350.0350.0000.0000.0000.000
20A20ALA0-0.0230.00922.6650.0200.0200.0000.0000.0000.000
21A21ASN00.0540.02623.6650.0390.0390.0000.0000.0000.000
22A22PRO00.0360.01918.849-0.006-0.0060.0000.0000.0000.000
23A23TYR00.0300.01918.8620.0020.0020.0000.0000.0000.000
24A24GLU-1-0.841-0.86620.1740.1010.1010.0000.0000.0000.000
25A25MET00.0270.02116.481-0.018-0.0180.0000.0000.0000.000
26A26HIS00.0290.03012.546-0.037-0.0370.0000.0000.0000.000
27A27ARG10.8410.90716.006-0.134-0.1340.0000.0000.0000.000
28A28THR0-0.038-0.04918.009-0.034-0.0340.0000.0000.0000.000
29A29LEU0-0.029-0.02012.490-0.066-0.0660.0000.0000.0000.000
30A30SER0-0.025-0.03913.547-0.052-0.0520.0000.0000.0000.000
31A31LYS10.8380.93314.7730.1040.1040.0000.0000.0000.000
32A32ALA00.0280.03312.685-0.010-0.0100.0000.0000.0000.000
33A33VAL00.0240.0138.379-0.127-0.1270.0000.0000.0000.000
34A34SER0-0.0060.00111.7420.1080.1080.0000.0000.0000.000
35A35ARG10.8150.87514.5060.1690.1690.0000.0000.0000.000
36A36ALA00.0290.0149.8290.0500.0500.0000.0000.0000.000
37A37LEU0-0.072-0.04211.2420.1740.1740.0000.0000.0000.000
38A38GLU-1-0.873-0.90013.2160.0810.0810.0000.0000.0000.000
39A39GLU-1-0.826-0.89414.161-0.088-0.0880.0000.0000.0000.000
40A40GLY0-0.0140.00013.5380.0330.0330.0000.0000.0000.000
41A41ARG10.8470.9119.6890.4260.4260.0000.0000.0000.000
42A42GLU-1-0.700-0.8256.725-0.055-0.0550.0000.0000.0000.000
43A43ARG10.8300.9035.583-1.753-1.7530.0000.0000.0000.000
44A44LEU00.0370.0386.3510.3990.3990.0000.0000.0000.000
45A45LEU0-0.057-0.0265.9230.1550.1550.0000.0000.0000.000
46A46TRP0-0.001-0.0078.315-0.253-0.2530.0000.0000.0000.000
47A47ARG10.7690.84410.411-0.686-0.6860.0000.0000.0000.000
48A48LEU00.0530.04313.385-0.102-0.1020.0000.0000.0000.000
49A49GLU-1-0.764-0.85213.7900.4070.4070.0000.0000.0000.000
50A50PRO0-0.039-0.03617.321-0.018-0.0180.0000.0000.0000.000
51A51ALA00.0080.01920.950-0.035-0.0350.0000.0000.0000.000
52A52ARG10.9530.96721.8710.0250.0250.0000.0000.0000.000
53A53GLY00.0280.02126.029-0.013-0.0130.0000.0000.0000.000
54A54LEU0-0.004-0.00529.0330.0150.0150.0000.0000.0000.000
55A55GLU-1-0.909-0.94625.340-0.060-0.0600.0000.0000.0000.000
56A56PRO0-0.020-0.02323.2350.0160.0160.0000.0000.0000.000
57A57PRO00.0140.01921.157-0.005-0.0050.0000.0000.0000.000
58A58VAL0-0.016-0.00115.780-0.034-0.0340.0000.0000.0000.000
59A59VAL00.013-0.00213.2370.0860.0860.0000.0000.0000.000
60A60LEU0-0.052-0.0129.008-0.151-0.1510.0000.0000.0000.000
61A61VAL00.016-0.0088.4340.2530.2530.0000.0000.0000.000
62A62GLN0-0.034-0.0342.909-1.435-0.0791.434-0.676-2.114-0.005
63A63THR0-0.004-0.0063.8900.3220.575-0.001-0.049-0.2030.000
64A64LEU0-0.066-0.0492.277-4.792-1.9872.998-2.480-3.324-0.024
65A65THR0-0.089-0.0603.325-1.338-1.0360.0140.013-0.329-0.002
66A66GLU-1-0.891-0.9445.816-2.294-2.2940.0000.0000.0000.000
67A67PRO0-0.034-0.0117.2810.4120.4120.0000.0000.0000.000
68A68ASP-1-0.783-0.86410.104-0.622-0.6220.0000.0000.0000.000
69A69TRP0-0.031-0.0629.9260.2340.2340.0000.0000.0000.000
70A70SER0-0.054-0.04115.4410.0960.0960.0000.0000.0000.000
71A71VAL00.0020.01216.5610.0610.0610.0000.0000.0000.000
72A72LEU0-0.084-0.04315.9350.0660.0660.0000.0000.0000.000
73A73ASP-1-0.841-0.92519.854-0.125-0.1250.0000.0000.0000.000
74A74GLU-1-0.898-0.95123.203-0.194-0.1940.0000.0000.0000.000
75A75GLY00.0120.00824.6190.0230.0230.0000.0000.0000.000
76A76TYR0-0.096-0.08018.5030.0210.0210.0000.0000.0000.000
77A77ALA00.018-0.01418.7100.0330.0330.0000.0000.0000.000
78A78GLN00.0000.02319.3980.0010.0010.0000.0000.0000.000
79A79VAL00.0320.00914.4330.0050.0050.0000.0000.0000.000
80A80PHE0-0.038-0.02014.596-0.029-0.0290.0000.0000.0000.000
81A81PRO00.004-0.00413.430-0.096-0.0960.0000.0000.0000.000
82A82PRO00.0340.0249.183-0.035-0.0350.0000.0000.0000.000
83A83LYS10.8780.9358.4111.5651.5650.0000.0000.0000.000
84A84PRO00.0490.0374.935-0.655-0.6550.0000.0000.0000.000
85A85PHE0-0.034-0.0292.313-1.4810.9524.253-1.689-4.997-0.004
86A86HIS00.0600.0241.993-13.561-14.02812.942-5.710-6.766-0.057
87A87PRO0-0.034-0.0032.9200.4881.3200.344-0.217-0.9590.000
88A88ALA00.0820.0305.8510.5000.5000.0000.0000.0000.000
89A89LEU0-0.063-0.0245.5180.0850.0850.0000.0000.0000.000
90A90LYS10.9300.9599.2200.2450.2450.0000.0000.0000.000
91A91PRO00.0410.00612.8710.0320.0320.0000.0000.0000.000
92A92GLY00.0330.02915.211-0.060-0.0600.0000.0000.0000.000
93A93GLN0-0.008-0.0079.737-0.045-0.0450.0000.0000.0000.000
94A94ARG10.8670.91913.131-0.134-0.1340.0000.0000.0000.000
95A95LEU0-0.073-0.0279.199-0.086-0.0860.0000.0000.0000.000
96A96ARG10.9270.95213.3640.0630.0630.0000.0000.0000.000
97A97PHE0-0.035-0.02011.3680.0430.0430.0000.0000.0000.000
98A98ARG10.8040.86011.733-0.400-0.4000.0000.0000.0000.000
99A99LEU0-0.037-0.01711.4450.2230.2230.0000.0000.0000.000
100A100ARG10.8870.95413.545-0.516-0.5160.0000.0000.0000.000
101A101ALA00.014-0.00714.5340.1510.1510.0000.0000.0000.000
102A102ASN00.0520.01716.507-0.080-0.0800.0000.0000.0000.000
103A103PRO0-0.023-0.02219.1970.0490.0490.0000.0000.0000.000
104A104ALA00.0530.04120.249-0.063-0.0630.0000.0000.0000.000
105A105LYS10.9400.96520.171-0.495-0.4950.0000.0000.0000.000
106A106ARG10.9390.95420.405-0.519-0.5190.0000.0000.0000.000
107A107LEU00.0710.05520.056-0.028-0.0280.0000.0000.0000.000
108A117LYS10.9190.95130.507-0.243-0.2430.0000.0000.0000.000
109A118THR00.0790.03228.4690.0170.0170.0000.0000.0000.000
110A119PRO00.026-0.00126.9170.0270.0270.0000.0000.0000.000
111A120ALA00.0470.02325.6710.0210.0210.0000.0000.0000.000
112A121GLU-1-0.839-0.91225.6420.3100.3100.0000.0000.0000.000
113A122LYS10.7860.88222.843-0.301-0.3010.0000.0000.0000.000
114A123VAL0-0.0010.00521.2860.0580.0580.0000.0000.0000.000
115A124ALA00.0730.04021.0340.0430.0430.0000.0000.0000.000
116A125TRP0-0.088-0.04316.1190.0670.0670.0000.0000.0000.000
117A126LEU0-0.015-0.00814.9220.0810.0810.0000.0000.0000.000
118A127GLU-1-0.852-0.94516.7430.5140.5140.0000.0000.0000.000
119A128ARG10.8320.88017.718-0.536-0.5360.0000.0000.0000.000
120A129ARG10.7780.88514.957-0.724-0.7240.0000.0000.0000.000
121A130LEU0-0.016-0.00812.0770.1800.1800.0000.0000.0000.000
122A131GLU-1-0.824-0.88113.6090.6080.6080.0000.0000.0000.000
123A132GLU-1-0.785-0.86915.6460.7290.7290.0000.0000.0000.000
124A133GLY0-0.060-0.01511.8630.1080.1080.0000.0000.0000.000
125A134GLY00.0260.02610.4050.2450.2450.0000.0000.0000.000
126A135PHE0-0.003-0.0156.719-0.075-0.0750.0000.0000.0000.000
127A136ARG10.9550.96512.774-0.427-0.4270.0000.0000.0000.000
128A137LEU0-0.025-0.00915.907-0.004-0.0040.0000.0000.0000.000
129A138LEU0-0.048-0.01517.495-0.038-0.0380.0000.0000.0000.000
130A139GLU-1-0.881-0.93719.7250.2730.2730.0000.0000.0000.000
131A140GLY0-0.014-0.02123.525-0.017-0.0170.0000.0000.0000.000
132A141GLU-1-0.845-0.90726.0570.1220.1220.0000.0000.0000.000
133A142ARG10.8250.89428.504-0.134-0.1340.0000.0000.0000.000
134A143GLY00.0230.02827.1070.0060.0060.0000.0000.0000.000
135A144PRO00.0410.01521.969-0.008-0.0080.0000.0000.0000.000
136A145TRP00.0210.01219.904-0.021-0.0210.0000.0000.0000.000
137A146VAL0-0.066-0.05318.6100.0340.0340.0000.0000.0000.000
138A147GLN00.0050.00820.642-0.042-0.0420.0000.0000.0000.000
139A148ILE0-0.007-0.00720.8710.0380.0380.0000.0000.0000.000
140A149LEU00.0040.01019.854-0.029-0.0290.0000.0000.0000.000
141A150GLN00.0230.01222.465-0.004-0.0040.0000.0000.0000.000
142A151ASP-1-0.826-0.90022.9340.3770.3770.0000.0000.0000.000
143A152THR00.0120.01223.708-0.036-0.0360.0000.0000.0000.000
144A153PHE00.0010.00125.0790.0350.0350.0000.0000.0000.000
145A154LEU0-0.0180.00020.091-0.009-0.0090.0000.0000.0000.000
146A155GLU-1-0.878-0.92824.5460.1890.1890.0000.0000.0000.000
147A170GLN00.0210.00727.6350.0060.0060.0000.0000.0000.000
148A171VAL0-0.059-0.04621.1020.0200.0200.0000.0000.0000.000
149A172GLN00.0140.01323.714-0.020-0.0200.0000.0000.0000.000
150A173ALA0-0.016-0.01120.4700.0620.0620.0000.0000.0000.000
151A174VAL0-0.003-0.00319.988-0.046-0.0460.0000.0000.0000.000
152A175LEU0-0.034-0.01916.9420.0890.0890.0000.0000.0000.000
153A176PHE00.0220.00416.440-0.057-0.0570.0000.0000.0000.000
154A177GLU-1-0.761-0.84616.3630.3600.3600.0000.0000.0000.000
155A178GLY00.0410.01016.464-0.028-0.0280.0000.0000.0000.000
156A179ARG10.8340.93115.771-0.180-0.1800.0000.0000.0000.000
157A180LEU00.0190.01810.7860.0220.0220.0000.0000.0000.000
158A181GLU-1-0.766-0.87014.0020.2300.2300.0000.0000.0000.000
159A182VAL0-0.020-0.0039.5350.1190.1190.0000.0000.0000.000
160A183VAL0-0.028-0.01312.284-0.105-0.1050.0000.0000.0000.000
161A184ASP-1-0.812-0.88912.7910.8070.8070.0000.0000.0000.000
162A185PRO00.0290.0049.7760.1880.1880.0000.0000.0000.000
163A186GLU-1-0.749-0.8568.2261.6821.6820.0000.0000.0000.000
164A187ARG10.8120.8778.306-0.415-0.4150.0000.0000.0000.000
165A188ALA00.0020.0187.9510.4410.4410.0000.0000.0000.000
166A189LEU00.0560.0112.5200.2880.4601.147-0.120-1.2000.000
167A190ALA0-0.046-0.0044.1802.7153.0940.012-0.080-0.3110.000
168A191THR0-0.053-0.0516.6710.5600.5600.0000.0000.0000.000
169A192LEU0-0.053-0.0142.528-1.797-0.9531.720-0.597-1.9670.001
170A193ARG10.8830.9122.506-3.416-4.1857.712-1.961-4.9810.002
171A194ARG10.8750.9553.679-3.115-5.8820.0353.149-0.4170.001
172A195GLY00.0990.0376.656-0.972-0.9720.0000.0000.0000.000
173A196VAL0-0.057-0.0378.306-0.342-0.3420.0000.0000.0000.000
174A197GLY00.0130.00511.698-0.130-0.1300.0000.0000.0000.000
175A198PRO0-0.030-0.01214.3140.1380.1380.0000.0000.0000.000
176A199GLY00.0580.00916.2760.0260.0260.0000.0000.0000.000
177A200LYS10.7840.90510.578-1.971-1.9710.0000.0000.0000.000
178A201ALA0-0.0120.01113.6010.0030.0030.0000.0000.0000.000
179A202LEU0-0.005-0.01215.874-0.098-0.0980.0000.0000.0000.000
180A203GLY00.0390.02714.208-0.044-0.0440.0000.0000.0000.000
181A204LEU0-0.056-0.03214.540-0.017-0.0170.0000.0000.0000.000
182A205GLY00.019-0.00411.9630.1110.1110.0000.0000.0000.000
183A206LEU00.0050.0116.6640.4480.4480.0000.0000.0000.000
184A207LEU0-0.031-0.0027.798-0.465-0.4650.0000.0000.0000.000
185A208SER00.0110.0077.0130.4620.4620.0000.0000.0000.000
186A209VAL00.0350.0116.243-0.147-0.1470.0000.0000.0000.000
187A210ALA00.0000.0028.593-0.216-0.2160.0000.0000.0000.000
188A211PRO00.0640.05111.1510.0900.0900.0000.0000.0000.000