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: KGYM3

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134868.573474
FMO2-HF: Nuclear repulsion 2054740.657521
FMO2-HF: Total energy -80127.915953
FMO2-MP2: Total energy -80358.757146


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.
-11.603-5.7140.252-2.532-3.6080.01
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 : 0.062 / q_NPA : 0.020
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].
3A11LYS10.9660.9842.724-7.182-3.6740.202-1.572-2.1380.007
4A12THR0-0.090-0.0813.282-1.520-0.0890.025-0.637-0.8190.001
5A13ARG10.9520.9805.367-2.525-2.362-0.001-0.019-0.1430.000
6A14ASP-1-0.860-0.9297.4230.5250.5250.0000.0000.0000.000
7A15GLY00.0340.0158.571-0.134-0.1340.0000.0000.0000.000
8A16ILE00.0520.0228.350-0.063-0.0630.0000.0000.0000.000
9A17LEU0-0.0320.01111.249-0.041-0.0410.0000.0000.0000.000
10A18ASP-1-0.801-0.88913.0650.3390.3390.0000.0000.0000.000
11A19ALA0-0.058-0.02313.772-0.055-0.0550.0000.0000.0000.000
12A20ALA0-0.012-0.02315.408-0.044-0.0440.0000.0000.0000.000
13A21GLU-1-0.766-0.87517.3410.3270.3270.0000.0000.0000.000
14A22ARG10.9140.96018.890-0.183-0.1830.0000.0000.0000.000
15A23VAL00.0240.05618.102-0.014-0.0140.0000.0000.0000.000
16A24PHE00.012-0.01718.606-0.011-0.0110.0000.0000.0000.000
17A25LEU0-0.047-0.05522.999-0.012-0.0120.0000.0000.0000.000
18A26GLU-1-0.972-0.99424.2010.0500.0500.0000.0000.0000.000
19A27LYS10.8390.91025.239-0.073-0.0730.0000.0000.0000.000
20A28GLY00.0600.03925.6150.0110.0110.0000.0000.0000.000
21A29VAL00.0440.00923.813-0.001-0.0010.0000.0000.0000.000
22A30GLY0-0.017-0.00324.9330.0010.0010.0000.0000.0000.000
23A31THR0-0.081-0.04927.450-0.010-0.0100.0000.0000.0000.000
24A32THR0-0.0280.03321.605-0.003-0.0030.0000.0000.0000.000
25A33ALA00.0330.01921.9840.0040.0040.0000.0000.0000.000
26A34MET0-0.029-0.03814.2640.0090.0090.0000.0000.0000.000
27A35ALA0-0.079-0.05016.713-0.001-0.0010.0000.0000.0000.000
28A36ASP-1-0.723-0.88017.4260.0760.0760.0000.0000.0000.000
29A37LEU00.0120.02115.1670.0100.0100.0000.0000.0000.000
30A38ALA0-0.036-0.03413.2750.0040.0040.0000.0000.0000.000
31A39ASP-1-0.938-0.95014.138-0.084-0.0840.0000.0000.0000.000
32A40ALA00.0090.00716.098-0.019-0.0190.0000.0000.0000.000
33A41ALA0-0.061-0.03411.4310.0070.0070.0000.0000.0000.000
34A42GLY0-0.0130.01611.846-0.029-0.0290.0000.0000.0000.000
35A43VAL0-0.075-0.0257.677-0.110-0.1100.0000.0000.0000.000
36A44SER00.0470.01810.3270.0370.0370.0000.0000.0000.000
37A45ARG11.0270.97811.4530.1410.1410.0000.0000.0000.000
38A46GLY00.0040.00811.9370.0490.0490.0000.0000.0000.000
39A47ALA00.0320.0147.3620.0200.0200.0000.0000.0000.000
40A48VAL00.0300.0078.4820.2010.2010.0000.0000.0000.000
41A49TYR0-0.028-0.02110.5970.1240.1240.0000.0000.0000.000
42A50GLY0-0.0250.0118.4950.0130.0130.0000.0000.0000.000
43A51HIS0-0.064-0.0333.406-1.081-0.2940.026-0.304-0.5080.002
44A52TYR0-0.054-0.0298.4660.1530.1530.0000.0000.0000.000
45A53LYS10.8850.94812.213-0.365-0.3650.0000.0000.0000.000
46A54ASN00.0460.01315.506-0.056-0.0560.0000.0000.0000.000
47A55LYS10.9650.96516.858-0.071-0.0710.0000.0000.0000.000
48A56ILE00.0510.02418.6410.0330.0330.0000.0000.0000.000
49A57GLU-1-0.912-0.95015.1070.3910.3910.0000.0000.0000.000
50A58VAL00.0220.00813.5280.0560.0560.0000.0000.0000.000
51A59CYS0-0.038-0.00615.4650.0370.0370.0000.0000.0000.000
52A60LEU0-0.004-0.00418.5110.0060.0060.0000.0000.0000.000
53A61ALA00.0040.00813.6770.0200.0200.0000.0000.0000.000
54A62MET0-0.009-0.01715.8190.0520.0520.0000.0000.0000.000
55A63CYS0-0.040-0.02416.923-0.022-0.0220.0000.0000.0000.000
56A64ASP-1-0.841-0.88116.9420.4610.4610.0000.0000.0000.000
57A65ARG10.7840.89313.111-0.650-0.6500.0000.0000.0000.000
58A66ALA00.0210.00017.023-0.018-0.0180.0000.0000.0000.000
59A67PHE00.029-0.00220.322-0.043-0.0430.0000.0000.0000.000
60A68GLY0-0.033-0.00320.004-0.023-0.0230.0000.0000.0000.000
61A69GLN0-0.058-0.03518.3220.0350.0350.0000.0000.0000.000
62A70ILE0-0.0180.01221.918-0.030-0.0300.0000.0000.0000.000
63A71GLU-1-0.963-0.97325.6500.2070.2070.0000.0000.0000.000
64A72VAL0-0.009-0.00626.615-0.013-0.0130.0000.0000.0000.000
65A73PRO0-0.0030.00229.146-0.004-0.0040.0000.0000.0000.000
66A74ASP-1-0.857-0.94032.6140.1700.1700.0000.0000.0000.000
67A75GLU-1-0.850-0.93334.2220.1410.1410.0000.0000.0000.000
68A76ASN0-0.111-0.04236.416-0.017-0.0170.0000.0000.0000.000
69A77ALA00.1020.05937.3950.0000.0000.0000.0000.0000.000
70A78ARG10.8800.93339.266-0.106-0.1060.0000.0000.0000.000
71A79VAL0-0.005-0.00140.731-0.003-0.0030.0000.0000.0000.000
72A80PRO00.0280.01943.5530.0000.0000.0000.0000.0000.000
73A81ALA00.017-0.00642.6320.0050.0050.0000.0000.0000.000
74A82LEU00.005-0.00942.1110.0060.0060.0000.0000.0000.000
75A83ASP-1-0.889-0.93841.8290.1000.1000.0000.0000.0000.000
76A84ILE0-0.057-0.02037.0430.0050.0050.0000.0000.0000.000
77A85LEU0-0.052-0.03337.9890.0060.0060.0000.0000.0000.000
78A86LEU00.0040.00338.7310.0040.0040.0000.0000.0000.000
79A87ARG10.9810.99632.647-0.155-0.1550.0000.0000.0000.000
80A88ALA00.0500.02833.9820.0050.0050.0000.0000.0000.000
81A89GLY0-0.0070.00434.2850.0060.0060.0000.0000.0000.000
82A90MET0-0.0270.00536.292-0.002-0.0020.0000.0000.0000.000
83A91GLY0-0.0060.00332.4600.0000.0000.0000.0000.0000.000
84A92PHE00.029-0.00429.2640.0050.0050.0000.0000.0000.000
85A93LEU00.0120.00531.5480.0030.0030.0000.0000.0000.000
86A94ARG00.0190.00030.496-0.005-0.0050.0000.0000.0000.000
87A95GLN00.002-0.01125.347-0.010-0.0100.0000.0000.0000.000
88A96CYS0-0.106-0.04128.1020.0100.0100.0000.0000.0000.000
89A97CYS0-0.036-0.02130.476-0.007-0.0070.0000.0000.0000.000
90A98GLU-1-0.906-0.91727.0790.1890.1890.0000.0000.0000.000
91A99PRO00.0010.01626.2880.0080.0080.0000.0000.0000.000
92A100GLY0-0.021-0.04622.9620.0010.0010.0000.0000.0000.000
93A101SER0-0.047-0.04919.315-0.023-0.0230.0000.0000.0000.000
94A102VAL00.0380.02421.422-0.009-0.0090.0000.0000.0000.000
95A103GLN00.0420.02724.008-0.006-0.0060.0000.0000.0000.000
96A104ARG10.8250.89819.631-0.268-0.2680.0000.0000.0000.000
97A105VAL0-0.0090.00521.137-0.012-0.0120.0000.0000.0000.000
98A106LEU00.0190.01423.875-0.011-0.0110.0000.0000.0000.000
99A107GLU-1-0.819-0.90327.5090.1140.1140.0000.0000.0000.000
100A108ILE0-0.071-0.00923.477-0.013-0.0130.0000.0000.0000.000
101A109LEU0-0.032-0.03425.286-0.010-0.0100.0000.0000.0000.000
102A110TYR0-0.099-0.06727.620-0.005-0.0050.0000.0000.0000.000
103A111LEU0-0.033-0.00830.855-0.011-0.0110.0000.0000.0000.000
104A112LYS10.8200.93527.771-0.130-0.1300.0000.0000.0000.000
105A113CYS00.030-0.00827.5990.0120.0120.0000.0000.0000.000
106A114GLU-1-0.864-0.90829.2390.1010.1010.0000.0000.0000.000
107A115ARG10.9530.95030.890-0.082-0.0820.0000.0000.0000.000
108A116SER0-0.0270.01529.584-0.002-0.0020.0000.0000.0000.000
109A117ASP-1-0.796-0.91131.6800.0870.0870.0000.0000.0000.000
110A118GLU-1-0.981-0.99725.5070.1170.1170.0000.0000.0000.000
111A119ASN0-0.080-0.05926.6070.0120.0120.0000.0000.0000.000
112A120GLU-1-0.835-0.90027.6950.1330.1330.0000.0000.0000.000
113A121PRO0-0.046-0.03324.0040.0080.0080.0000.0000.0000.000
114A122LEU00.0010.00422.5000.0190.0190.0000.0000.0000.000
115A123LEU00.0170.01925.8130.0060.0060.0000.0000.0000.000
116A124ARG10.9630.96527.768-0.138-0.1380.0000.0000.0000.000
117A125ARG10.8250.90019.661-0.361-0.3610.0000.0000.0000.000
118A126ARG11.0131.00826.458-0.140-0.1400.0000.0000.0000.000
119A127GLU-1-0.871-0.93228.7670.1300.1300.0000.0000.0000.000
120A128LEU0-0.085-0.03326.153-0.008-0.0080.0000.0000.0000.000
121A129LEU00.0370.03326.549-0.003-0.0030.0000.0000.0000.000
122A130GLU-1-0.812-0.90329.6700.1340.1340.0000.0000.0000.000
123A131LYS10.8740.94133.043-0.148-0.1480.0000.0000.0000.000
124A132GLN0-0.068-0.04126.853-0.006-0.0060.0000.0000.0000.000
125A133GLY00.0560.03332.428-0.004-0.0040.0000.0000.0000.000
126A134GLN00.0740.03034.174-0.003-0.0030.0000.0000.0000.000
127A135ARG10.8300.89532.252-0.167-0.1670.0000.0000.0000.000
128A136PHE00.0220.01534.665-0.005-0.0050.0000.0000.0000.000
129A137GLY00.0620.02836.752-0.005-0.0050.0000.0000.0000.000
130A138LEU00.054-0.02739.718-0.007-0.0070.0000.0000.0000.000
131A139ARG10.7700.87334.782-0.156-0.1560.0000.0000.0000.000
132A140GLN0-0.025-0.03338.527-0.008-0.0080.0000.0000.0000.000
133A141ILE00.0070.07041.981-0.005-0.0050.0000.0000.0000.000
134A142ARG10.9270.97044.098-0.098-0.0980.0000.0000.0000.000
135A143ARG10.9140.96238.734-0.129-0.1290.0000.0000.0000.000
136A144ALA00.0460.03045.825-0.004-0.0040.0000.0000.0000.000
137A145VAL0-0.0010.00447.843-0.003-0.0030.0000.0000.0000.000
138A146GLU-1-0.949-0.96946.8980.0880.0880.0000.0000.0000.000
139A147ARG10.7770.90344.019-0.098-0.0980.0000.0000.0000.000
140A148GLY0-0.006-0.01250.011-0.001-0.0010.0000.0000.0000.000
141A149GLU-1-0.869-0.93047.1770.0910.0910.0000.0000.0000.000
142A150LEU0-0.011-0.01948.906-0.001-0.0010.0000.0000.0000.000
143A151PRO00.0340.02952.712-0.001-0.0010.0000.0000.0000.000
144A152ALA00.0680.03654.6110.0020.0020.0000.0000.0000.000
145A153ARG10.8480.90355.449-0.057-0.0570.0000.0000.0000.000
146A154LEU00.0390.01950.722-0.002-0.0020.0000.0000.0000.000
147A155ASP-1-0.930-0.98152.1920.0700.0700.0000.0000.0000.000
148A156VAL0-0.031-0.02146.8640.0020.0020.0000.0000.0000.000
149A157GLU-1-0.890-0.94445.5200.0920.0920.0000.0000.0000.000
150A158LEU00.0440.05747.6770.0030.0030.0000.0000.0000.000
151A159ALA00.0240.01448.4150.0010.0010.0000.0000.0000.000
152A160SER0-0.067-0.05943.5820.0030.0030.0000.0000.0000.000
153A161ILE00.0280.01744.8860.0020.0020.0000.0000.0000.000
154A162TYR0-0.053-0.01546.114-0.001-0.0010.0000.0000.0000.000
155A163LEU00.021-0.01243.4290.0010.0010.0000.0000.0000.000
156A164GLN0-0.091-0.04938.9180.0080.0080.0000.0000.0000.000
157A165SER00.0000.00842.0060.0010.0010.0000.0000.0000.000
158A166LEU0-0.060-0.01243.9780.0000.0000.0000.0000.0000.000
159A167TRP00.007-0.03334.282-0.001-0.0010.0000.0000.0000.000
160A168ASP-1-0.830-0.91039.5010.1110.1110.0000.0000.0000.000
161A169GLY0-0.025-0.01240.629-0.001-0.0010.0000.0000.0000.000
162A170ILE0-0.053-0.01440.427-0.003-0.0030.0000.0000.0000.000
163A171CYS0-0.0050.00136.3830.0020.0020.0000.0000.0000.000
164A172GLY00.0330.01638.5380.0000.0000.0000.0000.0000.000
165A173THR0-0.158-0.09140.443-0.007-0.0070.0000.0000.0000.000
166A174LEU0-0.030-0.01137.367-0.003-0.0030.0000.0000.0000.000
167A175ALA00.0060.02735.645-0.003-0.0030.0000.0000.0000.000
168A176TRP00.0570.01335.8400.0030.0030.0000.0000.0000.000
169A177THR0-0.105-0.04139.737-0.007-0.0070.0000.0000.0000.000
170A178GLU-1-0.798-0.90541.2230.0730.0730.0000.0000.0000.000
171A179ARG10.8440.91043.740-0.061-0.0610.0000.0000.0000.000
172A180LEU0-0.059-0.02242.170-0.002-0.0020.0000.0000.0000.000
173A181ARG11.0091.02741.216-0.056-0.0560.0000.0000.0000.000
174A182ASP-1-0.899-0.96341.6620.0630.0630.0000.0000.0000.000
175A183ASP-1-0.882-0.92742.4210.0820.0820.0000.0000.0000.000
176A184PRO00.0600.03838.619-0.002-0.0020.0000.0000.0000.000
177A185TRP00.0480.01835.1150.0000.0000.0000.0000.0000.000
178A186ASN00.025-0.00939.7950.0030.0030.0000.0000.0000.000
179A187ARG10.7820.90142.877-0.071-0.0710.0000.0000.0000.000
180A188ALA00.0930.04240.723-0.001-0.0010.0000.0000.0000.000
181A189GLU-1-0.850-0.93941.4910.0930.0930.0000.0000.0000.000
182A190ARG10.9180.95742.979-0.069-0.0690.0000.0000.0000.000
183A191MET0-0.037-0.01645.238-0.002-0.0020.0000.0000.0000.000
184A192PHE00.0760.01639.805-0.001-0.0010.0000.0000.0000.000
185A193ARG10.8690.93843.604-0.091-0.0910.0000.0000.0000.000
186A194ALA00.0080.00247.039-0.002-0.0020.0000.0000.0000.000
187A195GLY00.0140.00947.722-0.003-0.0030.0000.0000.0000.000
188A196LEU00.008-0.01544.136-0.001-0.0010.0000.0000.0000.000
189A197ASP-1-0.858-0.92248.4860.0680.0680.0000.0000.0000.000
190A198SER0-0.096-0.03051.306-0.002-0.0020.0000.0000.0000.000
191A199LEU00.0370.00147.804-0.002-0.0020.0000.0000.0000.000
192A200ARG10.8520.93152.172-0.069-0.0690.0000.0000.0000.000
193A201SER0-0.100-0.05253.936-0.003-0.0030.0000.0000.0000.000
194A202SER00.0440.01356.113-0.003-0.0030.0000.0000.0000.000
195A203PRO00.0230.00057.2600.0010.0010.0000.0000.0000.000
196A204TYR0-0.029-0.02357.7470.0000.0000.0000.0000.0000.000
197A205LEU00.0610.04752.0040.0010.0010.0000.0000.0000.000
198A206LEU0-0.0300.01054.7050.0020.0020.0000.0000.0000.000
199A207LEU00.0280.03454.867-0.001-0.0010.0000.0000.0000.000
200A208ALA0-0.043-0.01558.073-0.002-0.0020.0000.0000.0000.000