FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: Z65GN

Calculation Name: 2WFM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WFM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9SE93

Base Structure: X-ray

Registration Date: 2023-09-19

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 255
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3549482.043007
FMO2-HF: Nuclear repulsion 3445237.452209
FMO2-HF: Total energy -104244.590798
FMO2-MP2: Total energy -104535.825107


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:GLN)


Summations of interaction energy for fragment #1(A:9:GLN)
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.
1.5524.210.037-0.907-1.7870.001
Interaction energy analysis for fragmet #1(A:9:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.021
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].
3A11LYS10.7930.8833.0924.1736.3800.036-0.788-1.4550.001
4A12HIS00.0160.0085.7180.5660.5660.0000.0000.0000.000
5A13PHE00.0230.0028.565-0.217-0.2170.0000.0000.0000.000
6A14VAL00.0090.00311.5160.1440.1440.0000.0000.0000.000
7A15LEU0-0.018-0.00814.871-0.083-0.0830.0000.0000.0000.000
8A16VAL00.0210.00217.8660.0450.0450.0000.0000.0000.000
9A17HIS0-0.007-0.00521.263-0.018-0.0180.0000.0000.0000.000
10A18GLY00.0510.02324.556-0.008-0.0080.0000.0000.0000.000
11A19GLY00.0160.00727.5990.0160.0160.0000.0000.0000.000
12A20CYS0-0.040-0.00731.083-0.006-0.0060.0000.0000.0000.000
13A21LEU00.0150.03128.2800.0060.0060.0000.0000.0000.000
14A22GLY00.0940.02227.5120.0080.0080.0000.0000.0000.000
15A23ALA0-0.029-0.02123.149-0.012-0.0120.0000.0000.0000.000
16A24TRP00.0410.01823.5230.0040.0040.0000.0000.0000.000
17A25ILE00.0240.01323.6190.0030.0030.0000.0000.0000.000
18A26TRP0-0.009-0.01619.670-0.025-0.0250.0000.0000.0000.000
19A27TYR0-0.049-0.03920.2830.0230.0230.0000.0000.0000.000
20A28LYS10.7930.88521.2110.0070.0070.0000.0000.0000.000
21A29LEU0-0.010-0.00115.7470.0050.0050.0000.0000.0000.000
22A30LYS10.8330.90115.888-0.481-0.4810.0000.0000.0000.000
23A31PRO00.0810.04514.9070.0560.0560.0000.0000.0000.000
24A32LEU0-0.031-0.00114.8140.0610.0610.0000.0000.0000.000
25A33LEU0-0.009-0.00411.251-0.001-0.0010.0000.0000.0000.000
26A34GLU-1-0.820-0.91210.0820.6790.6790.0000.0000.0000.000
27A35SER0-0.071-0.04910.9560.2220.2220.0000.0000.0000.000
28A36ALA0-0.074-0.0298.3790.0820.0820.0000.0000.0000.000
29A37GLY0-0.0010.0106.6340.0210.0210.0000.0000.0000.000
30A38HIS0-0.0060.0113.9611.0261.251-0.001-0.038-0.1860.000
31A39LYS10.8850.9498.404-1.301-1.3010.0000.0000.0000.000
32A40VAL0-0.027-0.01610.889-0.249-0.2490.0000.0000.0000.000
33A41THR00.009-0.01013.7310.0470.0470.0000.0000.0000.000
34A42ALA0-0.021-0.00416.490-0.075-0.0750.0000.0000.0000.000
35A43VAL00.0020.00319.3980.0310.0310.0000.0000.0000.000
36A44ASP-1-0.770-0.88921.7910.0860.0860.0000.0000.0000.000
37A45LEU0-0.0170.00124.2350.0100.0100.0000.0000.0000.000
38A46SER0-0.021-0.03327.3120.0120.0120.0000.0000.0000.000
39A47ALA0-0.049-0.01830.797-0.013-0.0130.0000.0000.0000.000
40A48ALA0-0.040-0.00328.867-0.007-0.0070.0000.0000.0000.000
41A49GLY00.008-0.01929.4030.0120.0120.0000.0000.0000.000
42A50ILE0-0.058-0.02128.405-0.003-0.0030.0000.0000.0000.000
43A51ASN00.0140.01528.4600.0040.0040.0000.0000.0000.000
44A52PRO0-0.001-0.00530.973-0.011-0.0110.0000.0000.0000.000
45A53ARG10.8390.93033.315-0.096-0.0960.0000.0000.0000.000
46A54ARG10.8630.87235.382-0.052-0.0520.0000.0000.0000.000
47A55LEU00.0350.00736.077-0.001-0.0010.0000.0000.0000.000
48A56ASP-1-0.807-0.87437.9810.0360.0360.0000.0000.0000.000
49A57GLU-1-0.846-0.89037.3730.0720.0720.0000.0000.0000.000
50A58ILE0-0.043-0.01433.6160.0030.0030.0000.0000.0000.000
51A59HIS0-0.021-0.01536.647-0.011-0.0110.0000.0000.0000.000
52A60THR0-0.030-0.02134.658-0.008-0.0080.0000.0000.0000.000
53A61PHE00.004-0.01927.4750.0050.0050.0000.0000.0000.000
54A62ARG10.8640.93026.948-0.010-0.0100.0000.0000.0000.000
55A63ASP-1-0.781-0.87429.8730.0380.0380.0000.0000.0000.000
56A64TYR00.0050.00728.4020.0140.0140.0000.0000.0000.000
57A65SER00.0400.00325.9360.0040.0040.0000.0000.0000.000
58A66GLU-1-0.820-0.90825.4360.0580.0580.0000.0000.0000.000
59A67PRO00.0460.02925.2330.0130.0130.0000.0000.0000.000
60A68LEU0-0.036-0.01018.7640.0260.0260.0000.0000.0000.000
61A69MET0-0.071-0.01820.7340.0070.0070.0000.0000.0000.000
62A70GLU-1-0.893-0.93522.2240.1830.1830.0000.0000.0000.000
63A71VAL0-0.003-0.00217.2410.0380.0380.0000.0000.0000.000
64A72MET0-0.051-0.01615.5540.0530.0530.0000.0000.0000.000
65A73ALA0-0.013-0.00317.8650.0230.0230.0000.0000.0000.000
66A74SER0-0.086-0.04318.2020.0430.0430.0000.0000.0000.000
67A75ILE0-0.051-0.01312.6300.0990.0990.0000.0000.0000.000
68A76PRO00.0340.02412.278-0.079-0.0790.0000.0000.0000.000
69A77PRO00.004-0.00613.564-0.011-0.0110.0000.0000.0000.000
70A78ASP-1-0.899-0.9529.8860.7560.7560.0000.0000.0000.000
71A79GLU-1-0.832-0.8858.8951.3321.3320.0000.0000.0000.000
72A80LYS10.7970.8708.4470.0830.0830.0000.0000.0000.000
73A81VAL00.0250.0158.6010.1330.1330.0000.0000.0000.000
74A82VAL0-0.045-0.0068.168-0.245-0.2450.0000.0000.0000.000
75A83LEU00.0130.00810.9490.1160.1160.0000.0000.0000.000
76A84LEU00.0120.00114.741-0.094-0.0940.0000.0000.0000.000
77A85GLY00.0180.01016.8140.0690.0690.0000.0000.0000.000
78A86HIS0-0.0010.00320.623-0.019-0.0190.0000.0000.0000.000
79A87SER00.0510.02223.8670.0260.0260.0000.0000.0000.000
80A88PHE00.012-0.01226.806-0.014-0.0140.0000.0000.0000.000
81A89GLY00.0610.04224.2050.0000.0000.0000.0000.0000.000
82A90GLY0-0.0010.00022.862-0.005-0.0050.0000.0000.0000.000
83A91MET0-0.0100.00523.894-0.019-0.0190.0000.0000.0000.000
84A92SER0-0.004-0.00824.0050.0010.0010.0000.0000.0000.000
85A93LEU0-0.015-0.00418.4120.0130.0130.0000.0000.0000.000
86A94GLY00.0410.00920.883-0.011-0.0110.0000.0000.0000.000
87A95LEU00.0060.00123.259-0.003-0.0030.0000.0000.0000.000
88A96ALA00.0310.01619.3220.0120.0120.0000.0000.0000.000
89A97MET0-0.061-0.01818.3400.0020.0020.0000.0000.0000.000
90A98GLU-1-0.739-0.84220.217-0.166-0.1660.0000.0000.0000.000
91A99THR0-0.065-0.03922.7300.0100.0100.0000.0000.0000.000
92A100TYR0-0.012-0.02218.3030.0120.0120.0000.0000.0000.000
93A101PRO00.0310.02817.285-0.007-0.0070.0000.0000.0000.000
94A102GLU-1-0.875-0.95815.739-0.121-0.1210.0000.0000.0000.000
95A103LYS10.8340.93613.378-0.317-0.3170.0000.0000.0000.000
96A104ILE00.0240.02612.6240.0440.0440.0000.0000.0000.000
97A105SER0-0.049-0.0308.623-0.186-0.1860.0000.0000.0000.000
98A106VAL0-0.031-0.02110.585-0.182-0.1820.0000.0000.0000.000
99A107ALA00.0270.02112.7860.0780.0780.0000.0000.0000.000
100A108VAL0-0.027-0.01713.811-0.033-0.0330.0000.0000.0000.000
101A109PHE00.006-0.00116.8080.0720.0720.0000.0000.0000.000
102A110MET00.0090.00220.204-0.037-0.0370.0000.0000.0000.000
103A111SER00.016-0.02222.0940.0240.0240.0000.0000.0000.000
104A112ALA0-0.0320.00023.7400.0250.0250.0000.0000.0000.000
105A113MET0-0.0200.02225.756-0.020-0.0200.0000.0000.0000.000
106A114MET0-0.0020.01422.503-0.007-0.0070.0000.0000.0000.000
107A115PRO0-0.009-0.01124.4570.0090.0090.0000.0000.0000.000
108A116ASP-1-0.696-0.81526.287-0.225-0.2250.0000.0000.0000.000
109A117PRO0-0.0100.01926.5450.0190.0190.0000.0000.0000.000
110A118ASN0-0.066-0.04129.2540.0180.0180.0000.0000.0000.000
111A119HIS10.8070.88432.0590.1650.1650.0000.0000.0000.000
112A120SER00.0410.01632.868-0.004-0.0040.0000.0000.0000.000
113A121LEU00.008-0.00629.533-0.009-0.0090.0000.0000.0000.000
114A122THR0-0.003-0.01132.585-0.001-0.0010.0000.0000.0000.000
115A123TYR00.0470.02532.8520.0030.0030.0000.0000.0000.000
116A124PRO00.010-0.00930.306-0.001-0.0010.0000.0000.0000.000
117A125PHE00.0290.00031.0040.0000.0000.0000.0000.0000.000
118A126GLU-1-0.863-0.90835.358-0.087-0.0870.0000.0000.0000.000
119A127LYS10.8260.89935.0540.1260.1260.0000.0000.0000.000
120A128TYR0-0.006-0.00834.483-0.001-0.0010.0000.0000.0000.000
121A129ASN0-0.004-0.01836.4160.0040.0040.0000.0000.0000.000
122A130GLU-1-0.841-0.89039.527-0.115-0.1150.0000.0000.0000.000
123A131LYS10.8180.89736.9760.1300.1300.0000.0000.0000.000
124A132CYS0-0.039-0.00436.678-0.003-0.0030.0000.0000.0000.000
125A133PRO00.0320.03340.2170.0030.0030.0000.0000.0000.000
126A134ALA00.037-0.00742.7380.0010.0010.0000.0000.0000.000
127A135ASP-1-0.898-0.94444.356-0.051-0.0510.0000.0000.0000.000
128A136MET0-0.039-0.00638.8970.0010.0010.0000.0000.0000.000
129A137MET00.0170.00136.600-0.001-0.0010.0000.0000.0000.000
130A138LEU0-0.033-0.01940.5640.0060.0060.0000.0000.0000.000
131A139ASP-1-0.769-0.87542.643-0.015-0.0150.0000.0000.0000.000
132A140SER0-0.021-0.01839.9710.0060.0060.0000.0000.0000.000
133A141GLN0-0.070-0.02042.0710.0010.0010.0000.0000.0000.000
134A142PHE00.026-0.00839.7560.0010.0010.0000.0000.0000.000
135A143SER0-0.0230.00043.5980.0020.0020.0000.0000.0000.000
136A144THR00.0190.02044.000-0.001-0.0010.0000.0000.0000.000
137A145TYR0-0.043-0.03238.0320.0010.0010.0000.0000.0000.000
138A146GLY00.0560.01744.013-0.003-0.0030.0000.0000.0000.000
139A147ASN0-0.079-0.04544.7670.0010.0010.0000.0000.0000.000
140A148PRO00.026-0.00647.331-0.003-0.0030.0000.0000.0000.000
141A149GLU-1-0.848-0.90948.9380.0000.0000.0000.0000.0000.000
142A150ASN0-0.102-0.05643.242-0.005-0.0050.0000.0000.0000.000
143A151PRO00.0200.05143.9790.0010.0010.0000.0000.0000.000
144A152GLY00.0820.04541.238-0.005-0.0050.0000.0000.0000.000
145A153MET0-0.027-0.01840.4670.0020.0020.0000.0000.0000.000
146A154SER0-0.047-0.01039.506-0.002-0.0020.0000.0000.0000.000
147A155MET0-0.007-0.01635.971-0.006-0.0060.0000.0000.0000.000
148A156ILE00.0290.00938.3870.0060.0060.0000.0000.0000.000
149A157LEU00.0410.00933.522-0.006-0.0060.0000.0000.0000.000
150A158GLY00.0420.03538.2680.0060.0060.0000.0000.0000.000
151A159PRO0-0.007-0.01339.723-0.003-0.0030.0000.0000.0000.000
152A160GLN00.006-0.01140.1640.0000.0000.0000.0000.0000.000
153A161PHE0-0.010-0.00835.534-0.006-0.0060.0000.0000.0000.000
154A162MET0-0.013-0.00934.584-0.005-0.0050.0000.0000.0000.000
155A163ALA00.004-0.01135.809-0.005-0.0050.0000.0000.0000.000
156A164LEU0-0.043-0.02437.540-0.004-0.0040.0000.0000.0000.000
157A165LYS10.8460.93136.2670.0530.0530.0000.0000.0000.000
158A166MET0-0.050-0.00731.391-0.006-0.0060.0000.0000.0000.000
159A167PHE00.030-0.01630.178-0.006-0.0060.0000.0000.0000.000
160A168GLN0-0.051-0.01932.6290.0070.0070.0000.0000.0000.000
161A169ASN0-0.030-0.01830.2340.0050.0050.0000.0000.0000.000
162A170CYS0-0.131-0.05529.253-0.001-0.0010.0000.0000.0000.000
163A171SER0-0.034-0.03830.3370.0000.0000.0000.0000.0000.000
164A172VAL00.0420.00232.193-0.001-0.0010.0000.0000.0000.000
165A173GLU-1-0.837-0.89932.0500.0360.0360.0000.0000.0000.000
166A174ASP-1-0.764-0.84828.3350.0290.0290.0000.0000.0000.000
167A175LEU00.0170.01531.1560.0020.0020.0000.0000.0000.000
168A176GLU-1-0.828-0.89634.2980.0320.0320.0000.0000.0000.000
169A177LEU00.003-0.00128.7510.0050.0050.0000.0000.0000.000
170A178ALA0-0.001-0.01131.8370.0040.0040.0000.0000.0000.000
171A179LYS10.7770.85333.246-0.022-0.0220.0000.0000.0000.000
172A180MET0-0.065-0.02135.6530.0040.0040.0000.0000.0000.000
173A181LEU0-0.029-0.00730.7550.0100.0100.0000.0000.0000.000
174A182THR0-0.092-0.03633.292-0.001-0.0010.0000.0000.0000.000
175A183ARG10.8160.90933.358-0.072-0.0720.0000.0000.0000.000
176A184PRO00.001-0.01035.775-0.008-0.0080.0000.0000.0000.000
177A185GLY00.0210.01634.6910.0060.0060.0000.0000.0000.000
178A186SER0-0.020-0.04134.500-0.004-0.0040.0000.0000.0000.000
179A187LEU00.0230.00632.924-0.002-0.0020.0000.0000.0000.000
180A188PHE0-0.003-0.00533.161-0.008-0.0080.0000.0000.0000.000
181A189PHE00.0480.04335.918-0.003-0.0030.0000.0000.0000.000
182A190GLN00.020-0.01337.428-0.008-0.0080.0000.0000.0000.000
183A191ASP-1-0.816-0.90835.675-0.017-0.0170.0000.0000.0000.000
184A192LEU00.007-0.00231.502-0.003-0.0030.0000.0000.0000.000
185A193ALA0-0.017-0.00835.105-0.008-0.0080.0000.0000.0000.000
186A194LYS10.7590.87537.6930.0240.0240.0000.0000.0000.000
187A195ALA0-0.0200.00333.0150.0010.0010.0000.0000.0000.000
188A196LYS10.9270.95731.9900.0560.0560.0000.0000.0000.000
189A197LYS10.8670.93631.6870.1430.1430.0000.0000.0000.000
190A198PHE00.0060.00126.4100.0050.0050.0000.0000.0000.000
191A199SER0-0.047-0.05626.861-0.004-0.0040.0000.0000.0000.000
192A200THR00.010-0.03425.970-0.013-0.0130.0000.0000.0000.000
193A201GLU-1-0.892-0.93524.603-0.210-0.2100.0000.0000.0000.000
194A202ARG10.8110.91722.4050.1030.1030.0000.0000.0000.000
195A203TYR00.024-0.00421.493-0.042-0.0420.0000.0000.0000.000
196A204GLY0-0.037-0.02521.422-0.032-0.0320.0000.0000.0000.000
197A205SER0-0.079-0.03520.153-0.040-0.0400.0000.0000.0000.000
198A206VAL0-0.037-0.00515.669-0.063-0.0630.0000.0000.0000.000
199A207LYS10.8860.94610.6021.3311.3310.0000.0000.0000.000
200A208ARG10.8840.93615.9010.4100.4100.0000.0000.0000.000
201A209ALA0-0.005-0.01515.449-0.070-0.0700.0000.0000.0000.000
202A210TYR00.011-0.02017.5230.0630.0630.0000.0000.0000.000
203A211ILE0-0.019-0.01216.478-0.047-0.0470.0000.0000.0000.000
204A212PHE00.0280.00020.7730.0330.0330.0000.0000.0000.000
205A213CYS0-0.029-0.01023.966-0.012-0.0120.0000.0000.0000.000
206A214ASN0-0.029-0.04426.1560.0080.0080.0000.0000.0000.000
207A215GLU-1-0.740-0.84029.125-0.096-0.0960.0000.0000.0000.000
208A216ASP-1-0.760-0.84329.340-0.102-0.1020.0000.0000.0000.000
209A217LYS10.8070.89831.3620.0910.0910.0000.0000.0000.000
210A218SER0-0.069-0.03432.1550.0080.0080.0000.0000.0000.000
211A219PHE0-0.031-0.02728.2910.0020.0020.0000.0000.0000.000
212A220PRO00.0770.04531.258-0.013-0.0130.0000.0000.0000.000
213A221VAL00.0400.03129.109-0.012-0.0120.0000.0000.0000.000
214A222GLU-1-0.862-0.94930.630-0.162-0.1620.0000.0000.0000.000
215A223PHE0-0.028-0.00632.039-0.007-0.0070.0000.0000.0000.000
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