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: 7G38K

Calculation Name: 3WVZ-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WVZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q53FT3

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 200
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1866167.496999
FMO2-HF: Nuclear repulsion 1789050.38563
FMO2-HF: Total energy -77117.111369
FMO2-MP2: Total energy -77338.659093


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:-3:ALA )


Summations of interaction energy for fragment #1(A:-3:ALA )
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.
-8.528-3.8820.552-2.505-2.6920.006
Interaction energy analysis for fragmet #1(A:-3:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.003
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].
3A-1GLY 0-0.0170.0012.840-5.328-2.1950.264-1.786-1.6110.011
4A0SER 00.016-0.0014.4540.0310.1150.000-0.020-0.0650.000
5A1MET 00.0050.0267.432-0.389-0.3890.0000.0000.0000.000
6A2PHE 0-0.004-0.0128.664-0.303-0.3030.0000.0000.0000.000
7A3GLY 00.0350.01212.3670.0540.0540.0000.0000.0000.000
8A4CYS 0-0.053-0.01615.705-0.046-0.0460.0000.0000.0000.000
9A5LEU 00.0110.00518.472-0.008-0.0080.0000.0000.0000.000
10A6VAL 00.0620.03522.128-0.011-0.0110.0000.0000.0000.000
11A7ALA 00.009-0.00425.320-0.004-0.0040.0000.0000.0000.000
12A8GLY 00.0150.00728.482-0.005-0.0050.0000.0000.0000.000
13A9ARG 10.8250.91525.368-0.177-0.1770.0000.0000.0000.000
14A10LEU 00.0150.00022.920-0.002-0.0020.0000.0000.0000.000
15A11VAL 0-0.035-0.01218.4100.0110.0110.0000.0000.0000.000
16A12GLN 0-0.024-0.01217.2690.0350.0350.0000.0000.0000.000
17A13THR 00.020-0.01313.5710.0060.0060.0000.0000.0000.000
18A14ALA 0-0.017-0.00311.8760.1430.1430.0000.0000.0000.000
19A15ALA 0-0.0080.01010.883-0.088-0.0880.0000.0000.0000.000
20A16GLN 00.0260.00910.6980.1570.1570.0000.0000.0000.000
21A17GLN 0-0.033-0.0224.482-0.390-0.3360.000-0.011-0.0420.000
22A18VAL 0-0.040-0.0158.786-0.142-0.1420.0000.0000.0000.000
23A19ALA 00.015-0.0018.171-0.223-0.2230.0000.0000.0000.000
24A20GLU -1-0.962-0.9702.794-1.549-0.8520.263-0.291-0.668-0.002
25A21ASP -1-0.868-0.9353.4410.1400.8180.025-0.397-0.306-0.003
26A22LYS 10.8590.9386.086-0.450-0.4500.0000.0000.0000.000
27A23PHE 0-0.006-0.0065.2310.0630.0630.0000.0000.0000.000
28A24VAL 00.0210.00610.391-0.185-0.1850.0000.0000.0000.000
29A25PHE 0-0.026-0.01013.4950.0550.0550.0000.0000.0000.000
30A26ASP -1-0.793-0.89916.6320.2760.2760.0000.0000.0000.000
31A27LEU 0-0.086-0.05519.849-0.003-0.0030.0000.0000.0000.000
32A28PRO 00.0360.01222.806-0.020-0.0200.0000.0000.0000.000
33A29ASP -1-0.845-0.90925.9280.1380.1380.0000.0000.0000.000
34A30TYR 00.049-0.00326.819-0.003-0.0030.0000.0000.0000.000
35A31GLU -1-0.885-0.95328.5520.1200.1200.0000.0000.0000.000
36A32SER 0-0.122-0.04631.310-0.008-0.0080.0000.0000.0000.000
37A33ILE 0-0.0140.00226.0880.0050.0050.0000.0000.0000.000
38A34ASN 00.0160.00229.927-0.005-0.0050.0000.0000.0000.000
39A35HIS 0-0.026-0.02527.761-0.001-0.0010.0000.0000.0000.000
40A36VAL 00.0140.01321.3650.0060.0060.0000.0000.0000.000
41A37VAL 0-0.031-0.00821.645-0.011-0.0110.0000.0000.0000.000
42A38VAL 00.0240.01416.2420.0270.0270.0000.0000.0000.000
43A39PHE 0-0.014-0.02516.989-0.037-0.0370.0000.0000.0000.000
44A40MET 0-0.0130.01311.9680.0540.0540.0000.0000.0000.000
45A41LEU 0-0.047-0.02411.533-0.066-0.0660.0000.0000.0000.000
46A42GLY 0-0.015-0.00113.969-0.046-0.0460.0000.0000.0000.000
47A43THR 0-0.041-0.0179.816-0.077-0.0770.0000.0000.0000.000
48A44ILE 00.0180.0066.820-0.120-0.1200.0000.0000.0000.000
49A45PRO 0-0.022-0.01110.5770.0960.0960.0000.0000.0000.000
50A46PHE 00.007-0.0099.693-0.034-0.0340.0000.0000.0000.000
51A47PRO 00.0310.0047.032-0.032-0.0320.0000.0000.0000.000
52A48GLU -1-0.917-0.9649.876-0.101-0.1010.0000.0000.0000.000
53A49GLY 00.0230.01512.862-0.011-0.0110.0000.0000.0000.000
54A50MET 0-0.046-0.0148.8600.0210.0210.0000.0000.0000.000
55A51GLY 0-0.002-0.01612.8770.0000.0000.0000.0000.0000.000
56A52GLY 00.0240.01812.2440.0340.0340.0000.0000.0000.000
57A53SER 00.010-0.00413.500-0.034-0.0340.0000.0000.0000.000
58A54VAL 0-0.014-0.01015.0550.0510.0510.0000.0000.0000.000
59A55TYR 00.0190.00516.305-0.043-0.0430.0000.0000.0000.000
60A56PHE 00.0260.00519.0270.0300.0300.0000.0000.0000.000
61A57SER 00.0570.06521.144-0.022-0.0220.0000.0000.0000.000
62A58TYR 0-0.078-0.03523.0370.0060.0060.0000.0000.0000.000
63A59PRO 00.0400.01126.559-0.003-0.0030.0000.0000.0000.000
64A60ASP -1-1.016-0.93529.4790.0920.0920.0000.0000.0000.000
65A61SER 00.025-0.05031.941-0.003-0.0030.0000.0000.0000.000
66A62ASN 00.036-0.01429.1980.0050.0050.0000.0000.0000.000
67A63GLY 00.1010.06126.4070.0030.0030.0000.0000.0000.000
68A64MET 0-0.021-0.04923.4750.0000.0000.0000.0000.0000.000
69A65PRO 00.1540.04021.3210.0250.0250.0000.0000.0000.000
70A66VAL 0-0.150-0.00422.061-0.011-0.0110.0000.0000.0000.000
71A67TRP 00.032-0.00517.6140.0220.0220.0000.0000.0000.000
72A68GLN 00.1010.07922.051-0.015-0.0150.0000.0000.0000.000
73A69LEU 0-0.049-0.02119.4610.0200.0200.0000.0000.0000.000
74A70LEU 0-0.033-0.01921.183-0.017-0.0170.0000.0000.0000.000
75A71GLY 00.007-0.00520.908-0.018-0.0180.0000.0000.0000.000
76A72PHE 00.0130.01318.1180.0160.0160.0000.0000.0000.000
77A73VAL 0-0.0170.01014.500-0.009-0.0090.0000.0000.0000.000
78A74THR 00.0380.00815.6480.0020.0020.0000.0000.0000.000
79A75ASN 00.0920.03013.4570.0440.0440.0000.0000.0000.000
80A76GLY 0-0.0210.00916.746-0.004-0.0040.0000.0000.0000.000
81A77LYS 10.8480.91919.403-0.124-0.1240.0000.0000.0000.000
82A78PRO 00.0520.03417.1960.0170.0170.0000.0000.0000.000
83A79SER 0-0.009-0.00617.4620.0380.0380.0000.0000.0000.000
84A80ALA 0-0.014-0.00819.926-0.026-0.0260.0000.0000.0000.000
85A81ILE 00.0030.00722.0930.0170.0170.0000.0000.0000.000
86A82PHE 00.0060.00320.080-0.014-0.0140.0000.0000.0000.000
87A83LYS 10.9020.94525.410-0.091-0.0910.0000.0000.0000.000
88A84ILE 00.0160.00524.5700.0000.0000.0000.0000.0000.000
89A85SER 0-0.030-0.00227.747-0.002-0.0020.0000.0000.0000.000
90A86GLY 0-0.015-0.01531.420-0.004-0.0040.0000.0000.0000.000
91A87LEU 0-0.051-0.01327.056-0.005-0.0050.0000.0000.0000.000
92A88LYS 10.9710.98331.347-0.065-0.0650.0000.0000.0000.000
93A89SER 00.015-0.05130.6380.0010.0010.0000.0000.0000.000
94A90GLY 0-0.032-0.01929.962-0.006-0.0060.0000.0000.0000.000
95A91GLU -1-0.937-0.96430.1430.0680.0680.0000.0000.0000.000
96A92GLY 0-0.006-0.00226.5530.0080.0080.0000.0000.0000.000
97A93SER 0-0.037-0.01222.663-0.004-0.0040.0000.0000.0000.000
98A94GLN 00.0360.02022.9050.0080.0080.0000.0000.0000.000
99A95HIS 0-0.024-0.00818.8140.0170.0170.0000.0000.0000.000
100A96PRO 00.0400.02714.425-0.015-0.0150.0000.0000.0000.000
101A97PHE 0-0.033-0.01912.6620.0130.0130.0000.0000.0000.000
102A98GLY 00.0330.02015.227-0.022-0.0220.0000.0000.0000.000
103A99ALA 0-0.026-0.00414.405-0.012-0.0120.0000.0000.0000.000
104A100MET 00.012-0.00915.993-0.018-0.0180.0000.0000.0000.000
105A101ASN 0-0.049-0.02015.8450.0170.0170.0000.0000.0000.000
106A102ILE 00.0600.03415.9490.0370.0370.0000.0000.0000.000
107A103VAL 0-0.024-0.01618.750-0.032-0.0320.0000.0000.0000.000
108A104ARG 10.7580.89421.497-0.182-0.1820.0000.0000.0000.000
109A105THR 0-0.007-0.01624.009-0.016-0.0160.0000.0000.0000.000
110A106PRO 00.027-0.00927.3260.0070.0070.0000.0000.0000.000
111A107SER 00.0660.04229.726-0.001-0.0010.0000.0000.0000.000
112A108VAL 0-0.0360.00123.1750.0050.0050.0000.0000.0000.000
113A109ALA 0-0.028-0.00624.086-0.001-0.0010.0000.0000.0000.000
114A110GLN 00.0370.03718.560-0.002-0.0020.0000.0000.0000.000
115A111ILE 0-0.024-0.00116.587-0.030-0.0300.0000.0000.0000.000
116A112GLY 00.0180.01114.8860.0600.0600.0000.0000.0000.000
117A113ILE 0-0.055-0.02711.579-0.072-0.0720.0000.0000.0000.000
118A114SER 00.0110.00710.7530.1390.1390.0000.0000.0000.000
119A115VAL 0-0.022-0.0177.033-0.049-0.0490.0000.0000.0000.000
120A116GLU -1-0.894-0.9519.9220.0910.0910.0000.0000.0000.000
121A117LEU 00.0440.01512.799-0.019-0.0190.0000.0000.0000.000
122A118LEU 00.008-0.01714.9420.0240.0240.0000.0000.0000.000
123A119ASP -1-0.904-0.94617.496-0.024-0.0240.0000.0000.0000.000
124A120SER 0-0.047-0.03417.2700.0000.0000.0000.0000.0000.000
125A121MET 0-0.055-0.00415.9980.0090.0090.0000.0000.0000.000
126A122ALA 0-0.033-0.00619.3160.0060.0060.0000.0000.0000.000
127A123GLN 0-0.039-0.01822.268-0.003-0.0030.0000.0000.0000.000
128A124GLN 0-0.019-0.00218.7110.0080.0080.0000.0000.0000.000
129A125THR 0-0.028-0.02923.270-0.005-0.0050.0000.0000.0000.000
130A126PRO 0-0.040-0.01923.4130.0050.0050.0000.0000.0000.000
131A127VAL 00.0090.02325.329-0.009-0.0090.0000.0000.0000.000
132A128GLY 00.0300.01928.0430.0010.0010.0000.0000.0000.000
133A129ASN 0-0.081-0.06130.6850.0020.0020.0000.0000.0000.000
134A130ALA 00.0730.05725.7930.0040.0040.0000.0000.0000.000
135A131ALA 00.0220.01426.8420.0070.0070.0000.0000.0000.000
136A132VAL 0-0.050-0.02027.744-0.008-0.0080.0000.0000.0000.000
137A133SER 00.023-0.00329.503-0.001-0.0010.0000.0000.0000.000
138A134SER 00.0020.00332.3150.0000.0000.0000.0000.0000.000
139A135VAL 00.0360.00434.9180.0000.0000.0000.0000.0000.000
140A136ASP -1-0.885-0.94836.2330.0530.0530.0000.0000.0000.000
141A137SER 0-0.0130.00036.459-0.001-0.0010.0000.0000.0000.000
142A138PHE 00.0210.00238.350-0.002-0.0020.0000.0000.0000.000
143A139THR 00.0380.01841.208-0.003-0.0030.0000.0000.0000.000
144A140GLN 00.0140.01338.429-0.002-0.0020.0000.0000.0000.000
145A141PHE 0-0.013-0.00742.542-0.002-0.0020.0000.0000.0000.000
146A142THR 0-0.003-0.00744.492-0.003-0.0030.0000.0000.0000.000
147A143GLN 00.0170.00344.4600.0000.0000.0000.0000.0000.000
148A144LYS 10.9670.98942.893-0.052-0.0520.0000.0000.0000.000
149A145MET 0-0.025-0.00747.323-0.001-0.0010.0000.0000.0000.000
150A146LEU 0-0.0230.00850.275-0.002-0.0020.0000.0000.0000.000
151A147ASP -1-0.829-0.90350.1590.0340.0340.0000.0000.0000.000
152A148ASN 0-0.101-0.04450.877-0.002-0.0020.0000.0000.0000.000
153A149PHE 00.0330.01352.991-0.001-0.0010.0000.0000.0000.000
154A150TYR 00.0430.02755.820-0.002-0.0020.0000.0000.0000.000
155A151ASN 0-0.008-0.00453.823-0.002-0.0020.0000.0000.0000.000
156A152PHE 00.0060.01456.972-0.001-0.0010.0000.0000.0000.000
157A153ALA 00.0030.00058.655-0.001-0.0010.0000.0000.0000.000
158A154SER 0-0.039-0.04160.573-0.001-0.0010.0000.0000.0000.000
159A155SER 0-0.103-0.04360.691-0.001-0.0010.0000.0000.0000.000
160A156PHE 0-0.009-0.00661.7000.0000.0000.0000.0000.0000.000
161A157ALA 0-0.060-0.01365.715-0.001-0.0010.0000.0000.0000.000
162A158VAL 00.0300.01467.6120.0000.0000.0000.0000.0000.000
163A159SER 0-0.051-0.03471.224-0.001-0.0010.0000.0000.0000.000
164A160GLN 00.064-0.01074.3350.0000.0000.0000.0000.0000.000
165A161ALA 0-0.018-0.00577.6560.0000.0000.0000.0000.0000.000
166A162GLN 0-0.0220.00272.2070.0000.0000.0000.0000.0000.000
167A163MET 0-0.0280.01274.1210.0000.0000.0000.0000.0000.000
168A164THR 00.0190.01875.6890.0000.0000.0000.0000.0000.000
169A165PRO 0-0.045-0.03777.4760.0000.0000.0000.0000.0000.000
170A166SER 00.0070.00275.1370.0000.0000.0000.0000.0000.000
171A167PRO 0-0.004-0.00477.7780.0000.0000.0000.0000.0000.000
172A168SER 0-0.004-0.00476.0930.0000.0000.0000.0000.0000.000
173A169GLU -1-0.920-0.94071.6040.0210.0210.0000.0000.0000.000
174A170MET 0-0.043-0.01772.241-0.001-0.0010.0000.0000.0000.000
175A171PHE 00.0470.01871.2780.0010.0010.0000.0000.0000.000
176A172ILE 0-0.022-0.01366.664-0.001-0.0010.0000.0000.0000.000
177A173PRO 00.0090.00669.6740.0000.0000.0000.0000.0000.000
178A174ALA 00.1120.03966.9980.0000.0000.0000.0000.0000.000
179A175ASN 00.006-0.00566.1650.0010.0010.0000.0000.0000.000
180A176VAL 0-0.0010.00466.4720.0000.0000.0000.0000.0000.000
181A177VAL 00.0220.00962.1540.0000.0000.0000.0000.0000.000
182A178LEU 00.0270.02460.9060.0010.0010.0000.0000.0000.000
183A179LYS 10.9590.98561.430-0.018-0.0180.0000.0000.0000.000
184A180TRP 0-0.040-0.02056.7900.0000.0000.0000.0000.0000.000
185A181TYR 0-0.014-0.02853.5910.0000.0000.0000.0000.0000.000
186A182GLU -1-0.865-0.93556.8750.0220.0220.0000.0000.0000.000
187A183ASN 0-0.047-0.03057.1630.0000.0000.0000.0000.0000.000
188A184PHE 0-0.0110.00152.6290.0000.0000.0000.0000.0000.000
189A185GLN 00.0410.01452.3080.0000.0000.0000.0000.0000.000
190A186ARG 10.8940.94352.242-0.020-0.0200.0000.0000.0000.000
191A187ARG 10.9320.95653.145-0.023-0.0230.0000.0000.0000.000
192A188LEU 00.006-0.00848.6950.0000.0000.0000.0000.0000.000
193A189ALA 0-0.018-0.00248.2290.0010.0010.0000.0000.0000.000
194A190GLN 0-0.049-0.02648.464-0.001-0.0010.0000.0000.0000.000
195A191ASN 0-0.007-0.00448.7470.0010.0010.0000.0000.0000.000
196A192PRO 00.0590.03444.8680.0000.0000.0000.0000.0000.000
197A193LEU 00.0030.00244.3560.0020.0020.0000.0000.0000.000
198A194PHE 0-0.073-0.02248.511-0.001-0.0010.0000.0000.0000.000
199A195TRP 0-0.086-0.02847.314-0.001-0.0010.0000.0000.0000.000
200A196NME 00.0380.02052.2500.0010.0010.0000.0000.0000.000