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: 6NVRZ

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 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 255
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3540162.853953
FMO2-HF: Nuclear repulsion 3435918.847165
FMO2-HF: Total energy -104244.006788
FMO2-MP2: Total energy -104535.106649


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.
2.4344.664-0.008-0.789-1.4310.001
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 : -0.026 / q_NPA : -0.029
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].
3A11LYS10.8740.9443.5063.1005.159-0.007-0.756-1.2950.001
4A12HIS00.014-0.0015.7460.3980.3980.0000.0000.0000.000
5A13PHE00.017-0.0018.552-0.153-0.1530.0000.0000.0000.000
6A14VAL00.0170.00711.8380.1300.1300.0000.0000.0000.000
7A15LEU0-0.026-0.01615.196-0.075-0.0750.0000.0000.0000.000
8A16VAL00.0350.00317.9810.0450.0450.0000.0000.0000.000
9A17HIS0-0.0110.00521.281-0.019-0.0190.0000.0000.0000.000
10A18GLY00.0640.02224.563-0.004-0.0040.0000.0000.0000.000
11A19GLY00.0080.00527.5530.0160.0160.0000.0000.0000.000
12A20CYS0-0.0190.01731.131-0.006-0.0060.0000.0000.0000.000
13A21LEU00.0030.02128.3330.0040.0040.0000.0000.0000.000
14A22GLY00.0530.00027.5650.0080.0080.0000.0000.0000.000
15A23ALA00.0230.00123.228-0.014-0.0140.0000.0000.0000.000
16A24TRP00.0410.00923.731-0.003-0.0030.0000.0000.0000.000
17A25ILE00.0190.01023.888-0.001-0.0010.0000.0000.0000.000
18A26TRP0-0.024-0.02819.921-0.033-0.0330.0000.0000.0000.000
19A27TYR0-0.037-0.02920.6280.0200.0200.0000.0000.0000.000
20A28LYS10.7780.88721.5240.0340.0340.0000.0000.0000.000
21A29LEU00.005-0.00115.8220.0020.0020.0000.0000.0000.000
22A30LYS10.8410.90416.312-0.407-0.4070.0000.0000.0000.000
23A31PRO00.0870.04415.2940.0400.0400.0000.0000.0000.000
24A32LEU0-0.048-0.00515.0970.0370.0370.0000.0000.0000.000
25A33LEU0-0.010-0.01111.593-0.032-0.0320.0000.0000.0000.000
26A34GLU-1-0.810-0.89510.4030.5010.5010.0000.0000.0000.000
27A35SER0-0.060-0.03911.1010.1820.1820.0000.0000.0000.000
28A36ALA0-0.090-0.0368.5750.0750.0750.0000.0000.0000.000
29A37GLY00.0090.0136.835-0.047-0.0470.0000.0000.0000.000
30A38HIS0-0.0080.0084.4031.0691.240-0.001-0.033-0.1360.000
31A39LYS10.9240.9708.472-1.144-1.1440.0000.0000.0000.000
32A40VAL0-0.023-0.01610.918-0.236-0.2360.0000.0000.0000.000
33A41THR0-0.004-0.00213.9540.0860.0860.0000.0000.0000.000
34A42ALA0-0.024-0.01316.705-0.071-0.0710.0000.0000.0000.000
35A43VAL00.0030.00319.6620.0260.0260.0000.0000.0000.000
36A44ASP-1-0.813-0.89722.1330.0780.0780.0000.0000.0000.000
37A45LEU0-0.001-0.00624.2410.0100.0100.0000.0000.0000.000
38A46SER0-0.010-0.03127.3030.0120.0120.0000.0000.0000.000
39A47ALA0-0.072-0.03330.743-0.012-0.0120.0000.0000.0000.000
40A48ALA0-0.0280.00929.318-0.009-0.0090.0000.0000.0000.000
41A49GLY00.0610.02329.3970.0130.0130.0000.0000.0000.000
42A50ILE0-0.052-0.02128.993-0.005-0.0050.0000.0000.0000.000
43A51ASN00.0110.01828.6180.0060.0060.0000.0000.0000.000
44A52PRO00.0190.00631.189-0.011-0.0110.0000.0000.0000.000
45A53ARG10.8520.94633.324-0.096-0.0960.0000.0000.0000.000
46A54ARG10.8530.87635.515-0.048-0.0480.0000.0000.0000.000
47A55LEU00.0420.01235.928-0.001-0.0010.0000.0000.0000.000
48A56ASP-1-0.816-0.88037.9210.0330.0330.0000.0000.0000.000
49A57GLU-1-0.854-0.90837.7240.0680.0680.0000.0000.0000.000
50A58ILE0-0.040-0.01633.7790.0030.0030.0000.0000.0000.000
51A59HIS00.001-0.00636.930-0.010-0.0100.0000.0000.0000.000
52A60THR0-0.041-0.02834.624-0.008-0.0080.0000.0000.0000.000
53A61PHE00.019-0.01027.5250.0060.0060.0000.0000.0000.000
54A62ARG10.9490.96627.883-0.002-0.0020.0000.0000.0000.000
55A63ASP-1-0.806-0.88029.8460.0420.0420.0000.0000.0000.000
56A64TYR0-0.017-0.01328.8200.0140.0140.0000.0000.0000.000
57A65SER00.010-0.00925.7860.0000.0000.0000.0000.0000.000
58A66GLU-1-0.876-0.93625.4990.0860.0860.0000.0000.0000.000
59A67PRO00.0190.01925.2700.0140.0140.0000.0000.0000.000
60A68LEU0-0.045-0.01718.9840.0210.0210.0000.0000.0000.000
61A69MET0-0.055-0.02320.8550.0050.0050.0000.0000.0000.000
62A70GLU-1-0.896-0.95022.0690.1850.1850.0000.0000.0000.000
63A71VAL0-0.015-0.00517.1070.0410.0410.0000.0000.0000.000
64A72MET0-0.068-0.03215.5730.0470.0470.0000.0000.0000.000
65A73ALA0-0.014-0.00217.9490.0230.0230.0000.0000.0000.000
66A74SER0-0.075-0.02518.7330.0390.0390.0000.0000.0000.000
67A75ILE0-0.051-0.01412.6550.0960.0960.0000.0000.0000.000
68A76PRO00.0350.02412.308-0.086-0.0860.0000.0000.0000.000
69A77PRO00.031-0.00413.678-0.009-0.0090.0000.0000.0000.000
70A78ASP-1-0.927-0.9519.6941.0391.0390.0000.0000.0000.000
71A79GLU-1-0.878-0.9218.7731.3931.3930.0000.0000.0000.000
72A80LYS10.8280.8908.5280.0070.0070.0000.0000.0000.000
73A81VAL00.0240.0168.7290.1440.1440.0000.0000.0000.000
74A82VAL0-0.057-0.0218.364-0.189-0.1890.0000.0000.0000.000
75A83LEU00.0030.00811.1150.1120.1120.0000.0000.0000.000
76A84LEU00.0160.01514.946-0.085-0.0850.0000.0000.0000.000
77A85GLY00.0210.01517.0460.0620.0620.0000.0000.0000.000
78A86HIS00.0060.01620.773-0.015-0.0150.0000.0000.0000.000
79A87SER00.0760.04923.7890.0280.0280.0000.0000.0000.000
80A88PHE00.022-0.02126.604-0.012-0.0120.0000.0000.0000.000
81A89GLY00.0360.02424.2710.0060.0060.0000.0000.0000.000
82A90GLY0-0.032-0.01323.119-0.005-0.0050.0000.0000.0000.000
83A91MET0-0.012-0.00724.101-0.016-0.0160.0000.0000.0000.000
84A92SER0-0.0010.00123.9760.0020.0020.0000.0000.0000.000
85A93LEU00.0050.00818.5240.0140.0140.0000.0000.0000.000
86A94GLY00.0470.01721.219-0.006-0.0060.0000.0000.0000.000
87A95LEU00.002-0.00523.487-0.001-0.0010.0000.0000.0000.000
88A96ALA00.0290.01819.3690.0130.0130.0000.0000.0000.000
89A97MET0-0.047-0.01518.4330.0070.0070.0000.0000.0000.000
90A98GLU-1-0.742-0.84220.312-0.136-0.1360.0000.0000.0000.000
91A99THR0-0.085-0.04622.8060.0080.0080.0000.0000.0000.000
92A100TYR00.006-0.00818.2920.0190.0190.0000.0000.0000.000
93A101PRO00.0350.03717.509-0.009-0.0090.0000.0000.0000.000
94A102GLU-1-0.872-0.95815.782-0.063-0.0630.0000.0000.0000.000
95A103LYS10.8250.92013.340-0.352-0.3520.0000.0000.0000.000
96A104ILE00.0350.03312.6620.0460.0460.0000.0000.0000.000
97A105SER0-0.071-0.0328.654-0.169-0.1690.0000.0000.0000.000
98A106VAL0-0.034-0.03110.635-0.101-0.1010.0000.0000.0000.000
99A107ALA00.0240.02112.9110.0600.0600.0000.0000.0000.000
100A108VAL0-0.029-0.03414.104-0.036-0.0360.0000.0000.0000.000
101A109PHE00.0150.00016.9450.0650.0650.0000.0000.0000.000
102A110MET00.0060.00320.323-0.034-0.0340.0000.0000.0000.000
103A111SER00.0560.02722.1580.0230.0230.0000.0000.0000.000
104A112ALA0-0.028-0.00423.9260.0250.0250.0000.0000.0000.000
105A113MET0-0.0190.01825.955-0.018-0.0180.0000.0000.0000.000
106A114MET00.0040.01222.505-0.004-0.0040.0000.0000.0000.000
107A115PRO0-0.013-0.00724.6200.0040.0040.0000.0000.0000.000
108A116ASP-1-0.679-0.80426.286-0.212-0.2120.0000.0000.0000.000
109A117PRO00.0030.01526.6020.0180.0180.0000.0000.0000.000
110A118ASN0-0.081-0.04129.1480.0210.0210.0000.0000.0000.000
111A119HIS10.8060.88832.0320.1570.1570.0000.0000.0000.000
112A120SER00.0300.02032.811-0.003-0.0030.0000.0000.0000.000
113A121LEU00.020-0.00729.926-0.009-0.0090.0000.0000.0000.000
114A122THR00.001-0.00832.884-0.001-0.0010.0000.0000.0000.000
115A123TYR00.0220.02333.3220.0020.0020.0000.0000.0000.000
116A124PRO00.023-0.00330.730-0.001-0.0010.0000.0000.0000.000
117A125PHE00.0090.00031.356-0.001-0.0010.0000.0000.0000.000
118A126GLU-1-0.865-0.92235.744-0.081-0.0810.0000.0000.0000.000
119A127LYS10.8110.88535.4410.1190.1190.0000.0000.0000.000
120A128TYR0-0.008-0.03634.8360.0010.0010.0000.0000.0000.000
121A129ASN0-0.024-0.01836.8650.0030.0030.0000.0000.0000.000
122A130GLU-1-0.838-0.89640.108-0.110-0.1100.0000.0000.0000.000
123A131LYS10.8740.94236.7420.1340.1340.0000.0000.0000.000
124A132CYS0-0.057-0.00837.171-0.003-0.0030.0000.0000.0000.000
125A133PRO00.0340.03040.7180.0030.0030.0000.0000.0000.000
126A134ALA00.011-0.01342.8960.0000.0000.0000.0000.0000.000
127A135ASP-1-0.897-0.94644.876-0.053-0.0530.0000.0000.0000.000
128A136MET0-0.0230.00039.0020.0000.0000.0000.0000.0000.000
129A137MET0-0.004-0.01436.905-0.001-0.0010.0000.0000.0000.000
130A138LEU0-0.0090.00641.0840.0050.0050.0000.0000.0000.000
131A139ASP-1-0.783-0.89243.006-0.023-0.0230.0000.0000.0000.000
132A140SER0-0.022-0.01240.4200.0050.0050.0000.0000.0000.000
133A141GLN0-0.064-0.01742.5410.0020.0020.0000.0000.0000.000
134A142PHE00.026-0.01039.9090.0010.0010.0000.0000.0000.000
135A143SER0-0.0150.00043.8670.0020.0020.0000.0000.0000.000
136A144THR00.0230.00444.3220.0000.0000.0000.0000.0000.000
137A145TYR0-0.046-0.03238.3450.0010.0010.0000.0000.0000.000
138A146GLY00.0450.02144.151-0.003-0.0030.0000.0000.0000.000
139A147ASN0-0.067-0.03744.9640.0000.0000.0000.0000.0000.000
140A148PRO00.0330.00447.367-0.003-0.0030.0000.0000.0000.000
141A149GLU-1-0.863-0.92549.2420.0020.0020.0000.0000.0000.000
142A150ASN0-0.104-0.06043.769-0.005-0.0050.0000.0000.0000.000
143A151PRO00.0280.05644.6090.0010.0010.0000.0000.0000.000
144A152GLY00.0600.01841.694-0.005-0.0050.0000.0000.0000.000
145A153MET0-0.023-0.02040.7410.0010.0010.0000.0000.0000.000
146A154SER0-0.0400.00839.531-0.001-0.0010.0000.0000.0000.000
147A155MET0-0.016-0.02436.441-0.005-0.0050.0000.0000.0000.000
148A156ILE00.0280.01538.6850.0050.0050.0000.0000.0000.000
149A157LEU00.0370.00933.918-0.005-0.0050.0000.0000.0000.000
150A158GLY00.0440.03038.6750.0060.0060.0000.0000.0000.000
151A159PRO00.016-0.00640.044-0.004-0.0040.0000.0000.0000.000
152A160GLN00.007-0.00740.330-0.002-0.0020.0000.0000.0000.000
153A161PHE0-0.0050.00135.766-0.007-0.0070.0000.0000.0000.000
154A162MET0-0.016-0.00734.801-0.006-0.0060.0000.0000.0000.000
155A163ALA0-0.001-0.00836.027-0.005-0.0050.0000.0000.0000.000
156A164LEU0-0.026-0.01737.429-0.005-0.0050.0000.0000.0000.000
157A165LYS10.8410.91336.5460.0590.0590.0000.0000.0000.000
158A166MET0-0.063-0.01431.617-0.005-0.0050.0000.0000.0000.000
159A167PHE00.020-0.01530.447-0.006-0.0060.0000.0000.0000.000
160A168GLN0-0.0150.01432.8190.0070.0070.0000.0000.0000.000
161A169ASN0-0.055-0.03930.4220.0090.0090.0000.0000.0000.000
162A170CYS0-0.117-0.04629.794-0.003-0.0030.0000.0000.0000.000
163A171SER0-0.027-0.03131.0460.0020.0020.0000.0000.0000.000
164A172VAL00.0620.00832.9920.0000.0000.0000.0000.0000.000
165A173GLU-1-0.853-0.90632.5770.0120.0120.0000.0000.0000.000
166A174ASP-1-0.772-0.85728.9090.0020.0020.0000.0000.0000.000
167A175LEU00.0080.01731.8690.0030.0030.0000.0000.0000.000
168A176GLU-1-0.833-0.90634.8500.0180.0180.0000.0000.0000.000
169A177LEU00.0100.00729.3260.0060.0060.0000.0000.0000.000
170A178ALA0-0.001-0.01432.5480.0050.0050.0000.0000.0000.000
171A179LYS10.7850.86533.927-0.007-0.0070.0000.0000.0000.000
172A180MET0-0.064-0.01636.0840.0050.0050.0000.0000.0000.000
173A181LEU0-0.037-0.01831.1870.0080.0080.0000.0000.0000.000
174A182THR0-0.088-0.02833.9320.0010.0010.0000.0000.0000.000
175A183ARG10.8160.90033.731-0.059-0.0590.0000.0000.0000.000
176A184PRO00.009-0.00936.033-0.007-0.0070.0000.0000.0000.000
177A185GLY00.0250.00534.9260.0050.0050.0000.0000.0000.000
178A186SER0-0.014-0.03934.595-0.004-0.0040.0000.0000.0000.000
179A187LEU00.006-0.00333.090-0.001-0.0010.0000.0000.0000.000
180A188PHE0-0.013-0.00533.155-0.007-0.0070.0000.0000.0000.000
181A189PHE00.0340.03636.199-0.001-0.0010.0000.0000.0000.000
182A190GLN00.0630.02137.819-0.006-0.0060.0000.0000.0000.000
183A191ASP-1-0.836-0.91735.268-0.015-0.0150.0000.0000.0000.000
184A192LEU00.0230.00031.630-0.003-0.0030.0000.0000.0000.000
185A193ALA0-0.040-0.02735.436-0.006-0.0060.0000.0000.0000.000
186A194LYS10.8080.90138.1940.0210.0210.0000.0000.0000.000
187A195ALA0-0.0230.01333.2020.0030.0030.0000.0000.0000.000
188A196LYS10.9360.96332.0580.0400.0400.0000.0000.0000.000
189A197LYS10.8890.94231.8100.1250.1250.0000.0000.0000.000
190A198PHE00.001-0.00826.5050.0040.0040.0000.0000.0000.000
191A199SER0-0.040-0.05027.078-0.005-0.0050.0000.0000.0000.000
192A200THR0-0.002-0.03226.058-0.012-0.0120.0000.0000.0000.000
193A201GLU-1-0.905-0.94324.703-0.180-0.1800.0000.0000.0000.000
194A202ARG10.8500.93322.7520.0630.0630.0000.0000.0000.000
195A203TYR00.007-0.01021.682-0.039-0.0390.0000.0000.0000.000
196A204GLY0-0.055-0.03421.496-0.030-0.0300.0000.0000.0000.000
197A205SER0-0.070-0.02520.027-0.033-0.0330.0000.0000.0000.000
198A206VAL0-0.047-0.01515.712-0.059-0.0590.0000.0000.0000.000
199A207LYS10.9340.97910.8371.2841.2840.0000.0000.0000.000
200A208ARG10.9130.94516.1050.3820.3820.0000.0000.0000.000
201A209ALA0-0.019-0.01415.671-0.059-0.0590.0000.0000.0000.000
202A210TYR00.002-0.01617.7530.0560.0560.0000.0000.0000.000
203A211ILE0-0.020-0.01316.662-0.047-0.0470.0000.0000.0000.000
204A212PHE00.000-0.02320.9370.0320.0320.0000.0000.0000.000
205A213CYS00.0040.01524.114-0.014-0.0140.0000.0000.0000.000
206A214ASN0-0.032-0.05526.2570.0100.0100.0000.0000.0000.000
207A215GLU-1-0.812-0.88029.134-0.109-0.1090.0000.0000.0000.000
208A216ASP-1-0.782-0.88529.290-0.114-0.1140.0000.0000.0000.000
209A217LYS10.8540.89931.3140.1030.1030.0000.0000.0000.000
210A218SER0-0.090-0.03132.3250.0090.0090.0000.0000.0000.000
211A219PHE0-0.055-0.02728.3490.0020.0020.0000.0000.0000.000
212A220PRO00.1080.06031.381-0.014-0.0140.0000.0000.0000.000
213A221VAL00.0510.02229.094-0.010-0.0100.0000.0000.0000.000
214A222GLU-1-0.930-0.96831.114-0.160-0.1600.0000.0000.0000.000
215A223PHE0-0.031-0.01132.042-0.003-0.0030.0000.0000.0000.000
216A224GLN0-0.023-0.01727.276-0.028-0.0280.0000.0000.0000.000
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