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: 7G7JK

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2086952.247018
FMO2-HF: Nuclear repulsion 2013938.484277
FMO2-HF: Total energy -73013.762741
FMO2-MP2: Total energy -73232.344064


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.
-29.069-20.03929.948-11.968-27.011-0.081
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 : -0.047 / q_NPA : -0.013
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].
3A3LEU0-0.032-0.0173.8080.7693.027-0.013-1.056-1.1900.005
4A4THR00.0440.0175.755-0.180-0.1800.0000.0000.0000.000
5A5LYS10.9140.9679.2430.7270.7270.0000.0000.0000.000
6A6LEU00.0430.03012.274-0.063-0.0630.0000.0000.0000.000
7A7VAL0-0.0090.00014.9830.0840.0840.0000.0000.0000.000
8A8LEU00.0120.00217.326-0.017-0.0170.0000.0000.0000.000
9A9ASN00.0530.02420.3960.0220.0220.0000.0000.0000.000
10A10PRO00.0210.00024.0060.0120.0120.0000.0000.0000.000
11A11ALA00.0280.03126.4740.0150.0150.0000.0000.0000.000
12A12SER00.0280.02625.0770.0140.0140.0000.0000.0000.000
13A13ARG10.9430.95826.779-0.005-0.0050.0000.0000.0000.000
14A14ALA00.0370.01524.5220.0220.0220.0000.0000.0000.000
15A15ALA00.0920.04422.3750.0200.0200.0000.0000.0000.000
16A16ARG10.8670.91723.0320.0480.0480.0000.0000.0000.000
17A17ARG10.7680.87822.779-0.015-0.0150.0000.0000.0000.000
18A18ASP-1-0.714-0.82220.1390.0510.0510.0000.0000.0000.000
19A19LEU0-0.044-0.02620.3110.0350.0350.0000.0000.0000.000
20A20ALA0-0.0270.00022.2290.0250.0250.0000.0000.0000.000
21A21ASN00.0290.01523.4030.0420.0420.0000.0000.0000.000
22A22PRO00.0580.02019.003-0.008-0.0080.0000.0000.0000.000
23A23TYR00.0130.01118.8050.0060.0060.0000.0000.0000.000
24A24GLU-1-0.856-0.89420.1600.1040.1040.0000.0000.0000.000
25A25MET00.0260.02616.148-0.020-0.0200.0000.0000.0000.000
26A26HIS00.0200.02312.447-0.045-0.0450.0000.0000.0000.000
27A27ARG10.8490.92215.906-0.150-0.1500.0000.0000.0000.000
28A28THR0-0.034-0.04817.960-0.035-0.0350.0000.0000.0000.000
29A29LEU0-0.003-0.00612.325-0.067-0.0670.0000.0000.0000.000
30A30SER0-0.017-0.03513.385-0.054-0.0540.0000.0000.0000.000
31A31LYS10.9160.97014.3240.0460.0460.0000.0000.0000.000
32A32ALA00.0230.02712.262-0.022-0.0220.0000.0000.0000.000
33A33VAL00.0140.0078.307-0.139-0.1390.0000.0000.0000.000
34A34SER00.0130.01011.7170.1250.1250.0000.0000.0000.000
35A35ARG10.8520.91414.6840.1760.1760.0000.0000.0000.000
36A36ALA00.0190.0089.7740.0630.0630.0000.0000.0000.000
37A37LEU0-0.066-0.04111.3350.1790.1790.0000.0000.0000.000
38A38GLU-1-0.885-0.91313.1730.0940.0940.0000.0000.0000.000
39A39GLU-1-0.847-0.90814.331-0.045-0.0450.0000.0000.0000.000
40A40GLY0-0.0220.00013.6430.0370.0370.0000.0000.0000.000
41A41ARG10.8710.92010.0220.3060.3060.0000.0000.0000.000
42A42GLU-1-0.710-0.8266.6110.1210.1210.0000.0000.0000.000
43A43ARG10.8440.9136.053-1.822-1.8220.0000.0000.0000.000
44A44LEU00.0270.0366.3650.3500.3500.0000.0000.0000.000
45A45LEU0-0.052-0.0236.0680.0720.0720.0000.0000.0000.000
46A46TRP00.003-0.0078.216-0.207-0.2070.0000.0000.0000.000
47A47ARG10.7950.86010.554-0.699-0.6990.0000.0000.0000.000
48A48LEU00.0480.04613.248-0.103-0.1030.0000.0000.0000.000
49A49GLU-1-0.792-0.87813.7140.4040.4040.0000.0000.0000.000
50A50PRO0-0.027-0.02117.115-0.021-0.0210.0000.0000.0000.000
51A51ALA00.0100.01620.643-0.033-0.0330.0000.0000.0000.000
52A52ARG10.9630.97921.4680.0380.0380.0000.0000.0000.000
53A53GLY00.0350.01425.391-0.018-0.0180.0000.0000.0000.000
54A54LEU00.006-0.00827.9900.0130.0130.0000.0000.0000.000
55A55GLU-1-0.952-0.95825.226-0.081-0.0810.0000.0000.0000.000
56A56PRO0-0.012-0.00922.7400.0180.0180.0000.0000.0000.000
57A57PRO0-0.0040.00520.507-0.002-0.0020.0000.0000.0000.000
58A58VAL0-0.003-0.00115.103-0.042-0.0420.0000.0000.0000.000
59A59VAL00.006-0.00512.9360.0950.0950.0000.0000.0000.000
60A60LEU0-0.060-0.0168.633-0.159-0.1590.0000.0000.0000.000
61A61VAL00.012-0.0148.1730.3080.3080.0000.0000.0000.000
62A62GLN0-0.015-0.0252.758-1.737-0.4561.906-0.764-2.424-0.006
63A63THR0-0.010-0.0033.9340.4360.7360.000-0.067-0.2330.000
64A64LEU0-0.064-0.0522.363-4.845-2.2803.301-2.679-3.188-0.025
65A65THR0-0.081-0.0583.330-1.475-1.1130.015-0.020-0.357-0.002
66A66GLU-1-0.916-0.9595.745-2.529-2.5290.0000.0000.0000.000
67A67PRO0-0.031-0.0136.9260.4520.4520.0000.0000.0000.000
68A68ASP-1-0.791-0.8629.784-0.705-0.7050.0000.0000.0000.000
69A69TRP0-0.025-0.0639.8150.2520.2520.0000.0000.0000.000
70A70SER0-0.066-0.04215.1360.0990.0990.0000.0000.0000.000
71A71VAL0-0.022-0.00816.3240.0640.0640.0000.0000.0000.000
72A72LEU0-0.111-0.05015.9740.0640.0640.0000.0000.0000.000
73A73ASP-1-0.892-0.93919.836-0.144-0.1440.0000.0000.0000.000
74A74GLU-1-0.892-0.94822.727-0.221-0.2210.0000.0000.0000.000
75A75GLY0-0.017-0.01124.3550.0260.0260.0000.0000.0000.000
76A76TYR0-0.072-0.07018.2690.0250.0250.0000.0000.0000.000
77A77ALA00.000-0.02718.4070.0320.0320.0000.0000.0000.000
78A78GLN00.0080.03219.3240.0000.0000.0000.0000.0000.000
79A79VAL00.019-0.00614.3260.0010.0010.0000.0000.0000.000
80A80PHE0-0.046-0.01814.100-0.030-0.0300.0000.0000.0000.000
81A81PRO00.0230.00013.167-0.097-0.0970.0000.0000.0000.000
82A82PRO00.0380.0318.792-0.031-0.0310.0000.0000.0000.000
83A83LYS10.8790.9378.3321.5681.5680.0000.0000.0000.000
84A84PRO00.0460.0324.808-0.779-0.7790.0000.0000.0000.000
85A85PHE0-0.036-0.0342.369-1.1891.3174.355-1.754-5.106-0.005
86A86HIS00.0510.0181.988-13.095-12.75810.778-5.035-6.080-0.052
87A87PRO0-0.037-0.0082.8070.2851.1000.741-0.292-1.2630.000
88A88ALA00.0760.0445.6440.3850.3850.0000.0000.0000.000
89A89LEU0-0.048-0.0235.4600.0560.0560.0000.0000.0000.000
90A90LYS10.9270.9509.3290.2280.2280.0000.0000.0000.000
91A91PRO00.0560.01712.9790.0430.0430.0000.0000.0000.000
92A92GLY00.0250.02515.386-0.060-0.0600.0000.0000.0000.000
93A93GLN0-0.0120.00010.200-0.019-0.0190.0000.0000.0000.000
94A94ARG10.8690.92713.666-0.142-0.1420.0000.0000.0000.000
95A95LEU0-0.066-0.0308.806-0.084-0.0840.0000.0000.0000.000
96A96ARG10.9160.95012.9950.0410.0410.0000.0000.0000.000
97A97PHE0-0.021-0.01911.3050.0480.0480.0000.0000.0000.000
98A98ARG10.8440.89111.782-0.418-0.4180.0000.0000.0000.000
99A99LEU0-0.043-0.01811.4510.2130.2130.0000.0000.0000.000
100A100ARG10.9040.96013.704-0.535-0.5350.0000.0000.0000.000
101A101ALA00.009-0.01314.8550.1350.1350.0000.0000.0000.000
102A102ASN00.0530.02716.733-0.086-0.0860.0000.0000.0000.000
103A103PRO0-0.027-0.02719.3060.0510.0510.0000.0000.0000.000
104A104ALA00.0600.03620.364-0.062-0.0620.0000.0000.0000.000
105A105LYS10.9170.95620.089-0.492-0.4920.0000.0000.0000.000
106A106ARG10.9590.96420.146-0.519-0.5190.0000.0000.0000.000
107A107LEU00.0710.05019.994-0.023-0.0230.0000.0000.0000.000
108A117LYS10.9670.98730.945-0.245-0.2450.0000.0000.0000.000
109A118THR00.1110.03628.6350.0200.0200.0000.0000.0000.000
110A119PRO00.0390.01427.1970.0270.0270.0000.0000.0000.000
111A120ALA00.0350.00326.1020.0210.0210.0000.0000.0000.000
112A121GLU-1-0.877-0.93226.3230.3180.3180.0000.0000.0000.000
113A122LYS10.7590.87723.151-0.305-0.3050.0000.0000.0000.000
114A123VAL00.0110.00721.6910.0580.0580.0000.0000.0000.000
115A124ALA00.0610.03721.4750.0400.0400.0000.0000.0000.000
116A125TRP0-0.064-0.02816.3520.0650.0650.0000.0000.0000.000
117A126LEU0-0.031-0.02215.2000.0830.0830.0000.0000.0000.000
118A127GLU-1-0.853-0.93717.1550.5200.5200.0000.0000.0000.000
119A128ARG10.8440.90218.259-0.547-0.5470.0000.0000.0000.000
120A129ARG10.8330.93815.173-0.759-0.7590.0000.0000.0000.000
121A130LEU00.008-0.00212.3360.1620.1620.0000.0000.0000.000
122A131GLU-1-0.826-0.88713.8630.6200.6200.0000.0000.0000.000
123A132GLU-1-0.907-0.95316.0080.7180.7180.0000.0000.0000.000
124A133GLY0-0.077-0.03511.9880.0740.0740.0000.0000.0000.000
125A134GLY00.0190.02610.8030.2200.2200.0000.0000.0000.000
126A135PHE0-0.007-0.0176.752-0.067-0.0670.0000.0000.0000.000
127A136ARG10.9630.96612.888-0.446-0.4460.0000.0000.0000.000
128A137LEU0-0.0150.00716.118-0.009-0.0090.0000.0000.0000.000
129A138LEU0-0.027-0.01117.546-0.041-0.0410.0000.0000.0000.000
130A139GLU-1-0.906-0.95319.7600.2890.2890.0000.0000.0000.000
131A140GLY0-0.029-0.02023.517-0.022-0.0220.0000.0000.0000.000
132A141GLU-1-0.842-0.91325.7890.1260.1260.0000.0000.0000.000
133A142ARG10.8170.88328.237-0.141-0.1410.0000.0000.0000.000
134A143GLY00.0340.04127.0880.0080.0080.0000.0000.0000.000
135A144PRO00.0340.01222.086-0.006-0.0060.0000.0000.0000.000
136A145TRP00.0130.01120.069-0.023-0.0230.0000.0000.0000.000
137A146VAL0-0.058-0.05318.5300.0430.0430.0000.0000.0000.000
138A147GLN0-0.0010.00820.695-0.042-0.0420.0000.0000.0000.000
139A148ILE0-0.005-0.00621.0380.0400.0400.0000.0000.0000.000
140A149LEU0-0.0090.00419.837-0.030-0.0300.0000.0000.0000.000
141A150GLN00.0220.00922.395-0.003-0.0030.0000.0000.0000.000
142A151ASP-1-0.821-0.89723.0050.3830.3830.0000.0000.0000.000
143A152THR00.0060.00223.840-0.034-0.0340.0000.0000.0000.000
144A153PHE00.0200.00625.0800.0390.0390.0000.0000.0000.000
145A154LEU0-0.032-0.00619.627-0.015-0.0150.0000.0000.0000.000
146A155GLU-1-0.859-0.92624.2580.1880.1880.0000.0000.0000.000
147A170GLN00.0110.00827.8110.0050.0050.0000.0000.0000.000
148A171VAL0-0.068-0.03921.4700.0210.0210.0000.0000.0000.000
149A172GLN00.0190.01823.868-0.024-0.0240.0000.0000.0000.000
150A173ALA00.0100.00020.4780.0650.0650.0000.0000.0000.000
151A174VAL0-0.001-0.00420.172-0.046-0.0460.0000.0000.0000.000
152A175LEU0-0.049-0.02217.0510.0930.0930.0000.0000.0000.000
153A176PHE00.021-0.00316.630-0.061-0.0610.0000.0000.0000.000
154A177GLU-1-0.816-0.89116.4430.3470.3470.0000.0000.0000.000
155A178GLY00.0370.01516.348-0.039-0.0390.0000.0000.0000.000
156A179ARG10.8670.94515.770-0.188-0.1880.0000.0000.0000.000
157A180LEU00.0260.02210.8170.0250.0250.0000.0000.0000.000
158A181GLU-1-0.788-0.89414.1300.2470.2470.0000.0000.0000.000
159A182VAL0-0.022-0.0089.6850.1160.1160.0000.0000.0000.000
160A183VAL0-0.025-0.00512.448-0.102-0.1020.0000.0000.0000.000
161A184ASP-1-0.817-0.90413.1630.7820.7820.0000.0000.0000.000
162A185PRO00.018-0.0109.9350.1860.1860.0000.0000.0000.000
163A186GLU-1-0.842-0.9138.5671.3301.3300.0000.0000.0000.000
164A187ARG10.8270.8998.733-0.461-0.4610.0000.0000.0000.000
165A188ALA0-0.0160.0068.2070.4110.4110.0000.0000.0000.000
166A189LEU00.0700.0192.6660.2710.7170.508-0.108-0.8450.000
167A190ALA0-0.034-0.0144.5992.4002.6260.001-0.022-0.2060.000
168A191THR0-0.032-0.0386.7740.7310.7310.0000.0000.0000.000
169A192LEU0-0.0350.0022.867-1.397-0.3750.416-0.292-1.146-0.001
170A193ARG10.9740.9902.500-3.711-5.0307.889-1.966-4.6030.003
171A194ARG10.8770.9563.789-3.903-5.6720.0512.087-0.3700.002
172A195GLY00.0990.0577.203-0.829-0.8290.0000.0000.0000.000
173A196VAL0-0.079-0.0638.655-0.280-0.2800.0000.0000.0000.000
174A197GLY00.0270.01211.951-0.157-0.1570.0000.0000.0000.000
175A198PRO0-0.029-0.01814.4380.1410.1410.0000.0000.0000.000
176A199GLY00.0750.02616.5490.0080.0080.0000.0000.0000.000
177A200LYS10.7790.88710.523-2.032-2.0320.0000.0000.0000.000
178A201ALA0-0.0220.00413.1270.0210.0210.0000.0000.0000.000
179A202LEU0-0.025-0.02615.534-0.104-0.1040.0000.0000.0000.000
180A203GLY00.0480.03713.959-0.061-0.0610.0000.0000.0000.000
181A204LEU0-0.060-0.02914.785-0.012-0.0120.0000.0000.0000.000
182A205GLY0-0.003-0.00212.0200.1070.1070.0000.0000.0000.000
183A206LEU00.0130.0156.6050.4210.4210.0000.0000.0000.000
184A207LEU0-0.019-0.0017.869-0.445-0.4450.0000.0000.0000.000
185A208SER00.0300.0216.8580.4830.4830.0000.0000.0000.000
186A209VAL00.0300.0096.074-0.202-0.2020.0000.0000.0000.000
187A210ALA00.0060.0008.615-0.216-0.2160.0000.0000.0000.000
188A211PRO00.0700.06110.9060.0870.0870.0000.0000.0000.000