Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4J28N

Calculation Name: 2WUI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WUI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RG61

Base Structure: X-ray

Registration Date: 2023-09-24

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134948.073754
FMO2-HF: Nuclear repulsion 2054817.224524
FMO2-HF: Total energy -80130.84923
FMO2-MP2: Total energy -80361.317857


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:9:SER)


Summations of interaction energy for fragment #1(A:9:SER)
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.
-9.893-4.6840.121-2.267-3.0640.008
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / q_NPA : 0.019
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].
3A11LYS10.9850.9913.023-7.606-4.1380.081-1.643-1.9070.007
4A12THR0-0.050-0.0483.277-1.813-0.6440.038-0.493-0.7130.001
5A13ARG10.8960.9695.366-1.115-0.989-0.001-0.016-0.1100.000
6A14ASP-1-0.872-0.9327.4230.7580.7580.0000.0000.0000.000
7A15GLY00.0200.0118.522-0.150-0.1500.0000.0000.0000.000
8A16ILE00.0510.0088.168-0.134-0.1340.0000.0000.0000.000
9A17LEU0-0.0310.00911.794-0.056-0.0560.0000.0000.0000.000
10A18ASP-1-0.870-0.93513.1540.4810.4810.0000.0000.0000.000
11A19ALA00.0020.02013.926-0.055-0.0550.0000.0000.0000.000
12A20ALA0-0.009-0.01215.383-0.045-0.0450.0000.0000.0000.000
13A21GLU-1-0.789-0.90017.3250.3300.3300.0000.0000.0000.000
14A22ARG10.9330.96419.149-0.267-0.2670.0000.0000.0000.000
15A23VAL00.0170.03718.418-0.016-0.0160.0000.0000.0000.000
16A24PHE00.013-0.01918.711-0.018-0.0180.0000.0000.0000.000
17A25LEU0-0.041-0.02422.987-0.010-0.0100.0000.0000.0000.000
18A26GLU-1-0.921-0.95224.2320.0690.0690.0000.0000.0000.000
19A27LYS10.7690.86425.223-0.079-0.0790.0000.0000.0000.000
20A28GLY00.0630.03825.6070.0070.0070.0000.0000.0000.000
21A29VAL00.0200.00923.337-0.003-0.0030.0000.0000.0000.000
22A30GLY0-0.012-0.00524.766-0.009-0.0090.0000.0000.0000.000
23A31THR0-0.073-0.04327.143-0.011-0.0110.0000.0000.0000.000
24A32THR0-0.052-0.00721.729-0.004-0.0040.0000.0000.0000.000
25A33ALA0-0.010-0.02021.722-0.008-0.0080.0000.0000.0000.000
26A34MET0-0.015-0.00614.0830.0220.0220.0000.0000.0000.000
27A35ALA0-0.080-0.05616.420-0.012-0.0120.0000.0000.0000.000
28A36ASP-1-0.710-0.86317.2500.0410.0410.0000.0000.0000.000
29A37LEU00.0200.03115.1160.0190.0190.0000.0000.0000.000
30A38ALA0-0.037-0.03413.2800.0220.0220.0000.0000.0000.000
31A39ASP-1-0.930-0.95414.143-0.040-0.0400.0000.0000.0000.000
32A40ALA00.0040.00916.0930.0150.0150.0000.0000.0000.000
33A41ALA0-0.057-0.03711.4400.0370.0370.0000.0000.0000.000
34A42GLY0-0.0120.01611.8270.0610.0610.0000.0000.0000.000
35A43VAL0-0.092-0.0377.552-0.098-0.0980.0000.0000.0000.000
36A44SER00.0640.02710.2300.0090.0090.0000.0000.0000.000
37A45ARG11.0270.97911.2750.1580.1580.0000.0000.0000.000
38A46GLY00.0010.00911.7960.0240.0240.0000.0000.0000.000
39A47ALA00.0110.0106.999-0.048-0.0480.0000.0000.0000.000
40A48VAL00.0400.0198.1770.0180.0180.0000.0000.0000.000
41A49TYR0-0.027-0.02510.2800.0640.0640.0000.0000.0000.000
42A50GLY0-0.0160.0148.2070.0110.0110.0000.0000.0000.000
43A51HIS0-0.063-0.0323.755-0.1660.2800.003-0.115-0.3340.000
44A52TYR0-0.001-0.0128.7020.1830.1830.0000.0000.0000.000
45A53LYS10.8890.95312.440-0.069-0.0690.0000.0000.0000.000
46A54ASN00.0180.00315.680-0.037-0.0370.0000.0000.0000.000
47A55LYS10.9430.95816.948-0.008-0.0080.0000.0000.0000.000
48A56ILE00.0280.01318.5720.0280.0280.0000.0000.0000.000
49A57GLU-1-0.876-0.93615.6950.0900.0900.0000.0000.0000.000
50A58VAL00.001-0.00613.2430.0390.0390.0000.0000.0000.000
51A59CYS00.0090.01615.7290.0450.0450.0000.0000.0000.000
52A60LEU0-0.0030.00619.0370.0210.0210.0000.0000.0000.000
53A61ALA00.0020.00314.2490.0240.0240.0000.0000.0000.000
54A62MET0-0.037-0.00516.2860.0520.0520.0000.0000.0000.000
55A63CYS0-0.049-0.03017.1410.0080.0080.0000.0000.0000.000
56A64ASP-1-0.827-0.87417.5050.2520.2520.0000.0000.0000.000
57A65ARG10.7870.88513.151-0.607-0.6070.0000.0000.0000.000
58A66ALA00.015-0.00117.0250.0050.0050.0000.0000.0000.000
59A67PHE00.018-0.01220.298-0.030-0.0300.0000.0000.0000.000
60A68GLY0-0.0300.00019.629-0.016-0.0160.0000.0000.0000.000
61A69GLN0-0.020-0.00418.7900.0310.0310.0000.0000.0000.000
62A70ILE0-0.0250.01621.742-0.015-0.0150.0000.0000.0000.000
63A71GLU-1-0.884-0.91525.4130.1860.1860.0000.0000.0000.000
64A72VAL0-0.002-0.00926.403-0.015-0.0150.0000.0000.0000.000
65A73PRO0-0.0040.00028.6770.0000.0000.0000.0000.0000.000
66A74ASP-1-0.846-0.93632.1310.1350.1350.0000.0000.0000.000
67A75GLU-1-0.808-0.88333.6690.1020.1020.0000.0000.0000.000
68A76ASN0-0.068-0.01435.760-0.014-0.0140.0000.0000.0000.000
69A77ALA00.1090.06836.8370.0010.0010.0000.0000.0000.000
70A78ARG10.8870.93838.711-0.087-0.0870.0000.0000.0000.000
71A79VAL0-0.004-0.00340.158-0.001-0.0010.0000.0000.0000.000
72A80PRO00.0110.01343.138-0.001-0.0010.0000.0000.0000.000
73A81ALA00.0330.00442.1210.0050.0050.0000.0000.0000.000
74A82LEU00.000-0.01141.6760.0050.0050.0000.0000.0000.000
75A83ASP-1-0.876-0.93841.6720.0940.0940.0000.0000.0000.000
76A84ILE0-0.079-0.03136.6070.0070.0070.0000.0000.0000.000
77A85LEU0-0.048-0.02837.6640.0060.0060.0000.0000.0000.000
78A86LEU00.0050.00438.4650.0040.0040.0000.0000.0000.000
79A87ARG10.8700.93031.732-0.157-0.1570.0000.0000.0000.000
80A88ALA00.0490.03033.7520.0060.0060.0000.0000.0000.000
81A89GLY00.0080.00934.1400.0060.0060.0000.0000.0000.000
82A90MET0-0.030-0.02136.2600.0010.0010.0000.0000.0000.000
83A91GLY0-0.010-0.00332.4350.0040.0040.0000.0000.0000.000
84A92PHE00.029-0.00328.9920.0070.0070.0000.0000.0000.000
85A93LEU00.0290.01831.5870.0030.0030.0000.0000.0000.000
86A94ARG00.0000.00231.1600.0030.0030.0000.0000.0000.000
87A95GLN00.014-0.01525.396-0.005-0.0050.0000.0000.0000.000
88A96CYS0-0.106-0.05028.2780.0080.0080.0000.0000.0000.000
89A97CYS0-0.053-0.02230.546-0.008-0.0080.0000.0000.0000.000
90A98GLU-1-0.912-0.92627.2790.2160.2160.0000.0000.0000.000
91A99PRO0-0.008-0.02326.9380.0020.0020.0000.0000.0000.000
92A100GLY00.0170.00123.3890.0150.0150.0000.0000.0000.000
93A101SER0-0.041-0.04519.432-0.025-0.0250.0000.0000.0000.000
94A102VAL00.0120.00921.528-0.018-0.0180.0000.0000.0000.000
95A103GLN00.0260.01824.008-0.018-0.0180.0000.0000.0000.000
96A104ARG10.8230.91019.824-0.307-0.3070.0000.0000.0000.000
97A105VAL0-0.0010.00420.948-0.019-0.0190.0000.0000.0000.000
98A106LEU00.0300.01523.875-0.018-0.0180.0000.0000.0000.000
99A107GLU-1-0.803-0.89427.5090.1120.1120.0000.0000.0000.000
100A108ILE0-0.064-0.03823.162-0.014-0.0140.0000.0000.0000.000
101A109LEU0-0.056-0.04325.038-0.013-0.0130.0000.0000.0000.000
102A110TYR0-0.085-0.06727.780-0.008-0.0080.0000.0000.0000.000
103A111LEU0-0.044-0.01430.848-0.010-0.0100.0000.0000.0000.000
104A112LYS10.8170.93127.769-0.118-0.1180.0000.0000.0000.000
105A113CYS00.026-0.00227.8580.0010.0010.0000.0000.0000.000
106A114GLU-1-0.861-0.91029.1800.0530.0530.0000.0000.0000.000
107A115ARG10.9410.94831.104-0.045-0.0450.0000.0000.0000.000
108A116SER0-0.035-0.02730.077-0.005-0.0050.0000.0000.0000.000
109A117ASP-1-0.843-0.92831.9750.0230.0230.0000.0000.0000.000
110A118GLU-1-0.871-0.94025.2000.0220.0220.0000.0000.0000.000
111A119ASN0-0.023-0.00826.3290.0030.0030.0000.0000.0000.000
112A120GLU-1-0.728-0.83928.0200.0590.0590.0000.0000.0000.000
113A121PRO0-0.034-0.02324.6180.0080.0080.0000.0000.0000.000
114A122LEU0-0.009-0.00322.7820.0120.0120.0000.0000.0000.000
115A123LEU00.0180.01626.3830.0090.0090.0000.0000.0000.000
116A124ARG10.8370.89128.264-0.049-0.0490.0000.0000.0000.000
117A125ARG10.8190.89220.351-0.182-0.1820.0000.0000.0000.000
118A126ARG10.9130.93227.015-0.085-0.0850.0000.0000.0000.000
119A127GLU-1-0.828-0.88829.3330.0720.0720.0000.0000.0000.000
120A128LEU0-0.078-0.02826.976-0.003-0.0030.0000.0000.0000.000
121A129LEU00.0360.03427.0960.0000.0000.0000.0000.0000.000
122A130GLU-1-0.718-0.81830.1610.0910.0910.0000.0000.0000.000
123A131LYS10.8520.90133.531-0.081-0.0810.0000.0000.0000.000
124A132GLN0-0.064-0.03127.244-0.005-0.0050.0000.0000.0000.000
125A133GLY00.0510.03132.796-0.001-0.0010.0000.0000.0000.000
126A134GLN00.0580.02234.3330.0000.0000.0000.0000.0000.000
127A135ARG10.8260.89232.696-0.102-0.1020.0000.0000.0000.000
128A136PHE00.0200.01534.587-0.003-0.0030.0000.0000.0000.000
129A137GLY00.0470.01836.715-0.002-0.0020.0000.0000.0000.000
130A138LEU0-0.026-0.02839.615-0.004-0.0040.0000.0000.0000.000
131A139ARG10.7780.87634.289-0.111-0.1110.0000.0000.0000.000
132A140GLN0-0.004-0.01338.030-0.007-0.0070.0000.0000.0000.000
133A141ILE00.0200.02741.648-0.003-0.0030.0000.0000.0000.000
134A142ARG10.8210.92244.315-0.066-0.0660.0000.0000.0000.000
135A143ARG10.8340.88939.034-0.097-0.0970.0000.0000.0000.000
136A144ALA00.0510.03345.470-0.003-0.0030.0000.0000.0000.000
137A145VAL0-0.020-0.01147.358-0.002-0.0020.0000.0000.0000.000
138A146GLU-1-0.924-0.95846.4460.0640.0640.0000.0000.0000.000
139A147ARG10.7980.91243.185-0.077-0.0770.0000.0000.0000.000
140A148GLY0-0.016-0.01749.4350.0000.0000.0000.0000.0000.000
141A149GLU-1-0.864-0.92646.6140.0760.0760.0000.0000.0000.000
142A150LEU0-0.006-0.01048.4040.0000.0000.0000.0000.0000.000
143A151PRO00.0290.02452.242-0.001-0.0010.0000.0000.0000.000
144A152ALA00.0710.03654.3830.0010.0010.0000.0000.0000.000
145A153ARG10.8670.91855.386-0.040-0.0400.0000.0000.0000.000
146A154LEU00.0360.02650.307-0.001-0.0010.0000.0000.0000.000
147A155ASP-1-0.934-0.99152.7090.0480.0480.0000.0000.0000.000
148A156VAL0-0.019-0.01747.1370.0020.0020.0000.0000.0000.000
149A157GLU-1-0.765-0.88546.2240.0630.0630.0000.0000.0000.000
150A158LEU00.0250.01947.9110.0030.0030.0000.0000.0000.000
151A159ALA00.0490.02748.6110.0020.0020.0000.0000.0000.000
152A160SER0-0.040-0.02043.5750.0030.0030.0000.0000.0000.000
153A161ILE00.0220.01444.9700.0020.0020.0000.0000.0000.000
154A162TYR0-0.0310.00946.2810.0000.0000.0000.0000.0000.000
155A163LEU00.023-0.00742.8340.0020.0020.0000.0000.0000.000
156A164GLN0-0.083-0.04238.9160.0070.0070.0000.0000.0000.000
157A165SER0-0.017-0.01842.0800.0010.0010.0000.0000.0000.000
158A166LEU0-0.066-0.01543.9780.0010.0010.0000.0000.0000.000
159A167TRP0-0.004-0.02334.1260.0010.0010.0000.0000.0000.000
160A168ASP-1-0.835-0.91139.0870.0900.0900.0000.0000.0000.000
161A169GLY0-0.013-0.00740.6290.0000.0000.0000.0000.0000.000
162A170ILE0-0.034-0.02040.587-0.001-0.0010.0000.0000.0000.000
163A171CYS0-0.0250.00436.0100.0040.0040.0000.0000.0000.000
164A172GLY00.0670.02638.5380.0020.0020.0000.0000.0000.000
165A173THR0-0.147-0.08440.443-0.005-0.0050.0000.0000.0000.000
166A174LEU0-0.0180.00337.437-0.001-0.0010.0000.0000.0000.000
167A175ALA0-0.0040.02335.6130.0000.0000.0000.0000.0000.000
168A176TRP00.0670.01735.6530.0010.0010.0000.0000.0000.000
169A177THR0-0.137-0.08039.699-0.008-0.0080.0000.0000.0000.000
170A178GLU-1-0.779-0.88741.6620.0850.0850.0000.0000.0000.000
171A179ARG10.9100.94843.810-0.063-0.0630.0000.0000.0000.000
172A180LEU0-0.022-0.00642.414-0.002-0.0020.0000.0000.0000.000
173A181ARG10.8940.95341.494-0.075-0.0750.0000.0000.0000.000
174A182ASP-1-0.863-0.91742.0670.0780.0780.0000.0000.0000.000
175A183ASP-1-0.831-0.92042.9400.0960.0960.0000.0000.0000.000
176A184PRO00.0550.04839.003-0.004-0.0040.0000.0000.0000.000
177A185TRP00.0240.00135.248-0.005-0.0050.0000.0000.0000.000
178A186ASN0-0.008-0.01840.1810.0000.0000.0000.0000.0000.000
179A187ARG10.7720.86643.233-0.082-0.0820.0000.0000.0000.000
180A188ALA00.0590.03040.955-0.003-0.0030.0000.0000.0000.000
181A189GLU-1-0.841-0.90241.4620.0930.0930.0000.0000.0000.000
182A190ARG10.9570.97343.132-0.077-0.0770.0000.0000.0000.000
183A191MET0-0.051-0.01645.359-0.003-0.0030.0000.0000.0000.000
184A192PHE00.0630.01539.421-0.003-0.0030.0000.0000.0000.000
185A193ARG10.8560.92343.574-0.093-0.0930.0000.0000.0000.000
186A194ALA0-0.005-0.00747.007-0.003-0.0030.0000.0000.0000.000
187A195GLY0-0.014-0.00747.615-0.003-0.0030.0000.0000.0000.000
188A196LEU0-0.003-0.02043.896-0.002-0.0020.0000.0000.0000.000
189A197ASP-1-0.813-0.87848.2820.0610.0610.0000.0000.0000.000
190A198SER0-0.060-0.01051.682-0.002-0.0020.0000.0000.0000.000
191A199LEU00.0280.00047.144-0.002-0.0020.0000.0000.0000.000
192A200ARG10.8010.87751.772-0.063-0.0630.0000.0000.0000.000
193A201SER0-0.047-0.03253.606-0.002-0.0020.0000.0000.0000.000
194A202SER00.0120.00755.726-0.003-0.0030.0000.0000.0000.000
195A203PRO00.027-0.00257.0510.0000.0000.0000.0000.0000.000
196A204TYR0-0.037-0.02457.664-0.001-0.0010.0000.0000.0000.000
197A205LEU00.0390.03551.6580.0000.0000.0000.0000.0000.000
198A206LEU0-0.0330.01354.7100.0010.0010.0000.0000.0000.000
199A207LEU00.0490.05055.067-0.001-0.0010.0000.0000.0000.000
200A208ALA0-0.088-0.04958.232-0.002-0.0020.0000.0000.0000.000