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: G6KN1

Calculation Name: 2VID-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VID

Chain ID: A

ChEMBL ID:

UniProt ID: Q2FXC3

Base Structure: X-ray

Registration Date: 2023-09-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357240.718378
FMO2-HF: Nuclear repulsion 2280155.288971
FMO2-HF: Total energy -77085.429407
FMO2-MP2: Total energy -77316.245615


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:1:GLU)


Summations of interaction energy for fragment #1(A:1:GLU)
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.
-284.71-304.58788.87-37.974-31.0210.191
Interaction energy analysis for fragmet #1(A:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.769 / q_NPA : -0.833
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].
3A3ASN0-0.024-0.0132.563-17.184-12.6532.731-3.193-4.0690.021
4A4VAL00.0080.0173.5661.6241.7110.0050.123-0.2150.000
5A5THR0-0.006-0.0126.899-4.115-4.1150.0000.0000.0000.000
6A6LYS10.9520.9769.861-17.286-17.2860.0000.0000.0000.000
7A7VAL0-0.014-0.00313.0100.4780.4780.0000.0000.0000.000
8A8LYS10.8520.91811.572-25.525-25.5250.0000.0000.0000.000
9A9ASP-1-0.804-0.90917.08413.54713.5470.0000.0000.0000.000
10A10THR0-0.039-0.02417.9710.5370.5370.0000.0000.0000.000
11A11ASN0-0.059-0.03719.716-0.487-0.4870.0000.0000.0000.000
12A12ILE00.0530.03818.267-0.550-0.5500.0000.0000.0000.000
13A13PHE00.0250.03118.4270.6240.6240.0000.0000.0000.000
14A14PRO00.005-0.00714.5140.2370.2370.0000.0000.0000.000
15A15TYR0-0.021-0.05512.344-0.954-0.9540.0000.0000.0000.000
16A16THR0-0.011-0.02618.114-0.379-0.3790.0000.0000.0000.000
17A17GLY00.0380.03120.161-0.815-0.8150.0000.0000.0000.000
18A18VAL0-0.034-0.01016.725-0.089-0.0890.0000.0000.0000.000
19A19VAL0-0.021-0.01820.149-0.706-0.7060.0000.0000.0000.000
20A20ALA0-0.013-0.00521.4350.6350.6350.0000.0000.0000.000
21A21PHE00.0390.01822.657-0.702-0.7020.0000.0000.0000.000
22A22LYS10.8730.92523.957-11.156-11.1560.0000.0000.0000.000
23A23SER0-0.015-0.04021.6460.0290.0290.0000.0000.0000.000
24A24ALA0-0.0170.00619.4150.3050.3050.0000.0000.0000.000
25A25THR0-0.0060.00116.738-0.105-0.1050.0000.0000.0000.000
26A26GLY00.0460.03419.452-0.455-0.4550.0000.0000.0000.000
27A27PHE0-0.022-0.01318.1830.4760.4760.0000.0000.0000.000
28A28VAL00.0110.00521.425-0.522-0.5220.0000.0000.0000.000
29A29VAL0-0.015-0.02023.1200.4990.4990.0000.0000.0000.000
30A30GLY00.0230.00825.291-0.154-0.1540.0000.0000.0000.000
31A31LYS10.9060.95228.739-8.789-8.7890.0000.0000.0000.000
32A32ASN0-0.059-0.03531.7170.0480.0480.0000.0000.0000.000
33A33THR00.006-0.00928.218-0.239-0.2390.0000.0000.0000.000
34A34ILE0-0.0020.00124.6710.4310.4310.0000.0000.0000.000
35A35LEU0-0.0160.00321.090-0.428-0.4280.0000.0000.0000.000
36A36THR00.018-0.01721.1760.4600.4600.0000.0000.0000.000
37A37ASN0-0.023-0.02517.9040.1870.1870.0000.0000.0000.000
38A38LYS10.8420.93321.681-11.551-11.5510.0000.0000.0000.000
39A39HIS10.7420.84518.057-14.458-14.4580.0000.0000.0000.000
40A40VAL00.006-0.00620.891-0.138-0.1380.0000.0000.0000.000
41A41SER0-0.013-0.02323.802-0.368-0.3680.0000.0000.0000.000
42A42LYS10.9030.95725.411-10.956-10.9560.0000.0000.0000.000
43A43ASN0-0.037-0.00926.008-0.471-0.4710.0000.0000.0000.000
44A44TYR0-0.030-0.00625.7450.0280.0280.0000.0000.0000.000
45A45LYS10.9100.94930.720-8.777-8.7770.0000.0000.0000.000
46A46VAL00.030-0.00133.9610.1790.1790.0000.0000.0000.000
47A47GLY0-0.0060.00536.012-0.208-0.2080.0000.0000.0000.000
48A48ASP-1-0.854-0.90832.0999.0749.0740.0000.0000.0000.000
49A49ARG10.9430.96632.059-8.612-8.6120.0000.0000.0000.000
50A50ILE0-0.0120.01126.9270.2620.2620.0000.0000.0000.000
51A51THR0-0.022-0.01126.317-0.411-0.4110.0000.0000.0000.000
52A52ALA00.0190.01425.2250.5840.5840.0000.0000.0000.000
53A53HIS10.8710.93821.743-13.289-13.2890.0000.0000.0000.000
54A54PRO0-0.005-0.00222.594-0.127-0.1270.0000.0000.0000.000
55A55ASN00.006-0.01921.7140.4130.4130.0000.0000.0000.000
56A56SER00.011-0.00320.7020.0050.0050.0000.0000.0000.000
57A57ASP-1-0.891-0.91923.04511.86511.8650.0000.0000.0000.000
58A58LYS10.9970.97426.799-9.878-9.8780.0000.0000.0000.000
59A59GLY0-0.0080.02127.476-0.282-0.2820.0000.0000.0000.000
60A60ASN00.0060.00426.1900.3970.3970.0000.0000.0000.000
61A61GLY00.0130.00026.826-0.286-0.2860.0000.0000.0000.000
62A62GLY00.0540.03028.184-0.247-0.2470.0000.0000.0000.000
63A63ILE0-0.036-0.00929.4430.4620.4620.0000.0000.0000.000
64A64TYR00.002-0.00929.799-0.410-0.4100.0000.0000.0000.000
65A65SER00.0560.02732.3790.1200.1200.0000.0000.0000.000
66A66ILE0-0.033-0.01229.7310.0540.0540.0000.0000.0000.000
67A67LYS10.8860.92633.488-8.899-8.8990.0000.0000.0000.000
68A68LYS10.9310.97034.062-8.960-8.9600.0000.0000.0000.000
69A69ILE00.0320.02129.8450.3300.3300.0000.0000.0000.000
70A70ILE0-0.030-0.01830.713-0.345-0.3450.0000.0000.0000.000
71A71ASN00.0500.04028.4810.6600.6600.0000.0000.0000.000
72A72TYR00.0100.00725.614-0.302-0.3020.0000.0000.0000.000
73A73PRO00.0060.00328.4800.0850.0850.0000.0000.0000.000
74A74GLY00.0620.03627.834-0.022-0.0220.0000.0000.0000.000
75A75LYS10.9240.96322.025-12.547-12.5470.0000.0000.0000.000
76A76GLU-1-0.784-0.86521.45612.44912.4490.0000.0000.0000.000
77A77ASP-1-0.698-0.82819.79112.66412.6640.0000.0000.0000.000
78A78VAL0-0.014-0.01120.9550.5640.5640.0000.0000.0000.000
79A79SER0-0.005-0.02823.212-0.657-0.6570.0000.0000.0000.000
80A80VAL00.0280.01125.4850.4850.4850.0000.0000.0000.000
81A81ILE0-0.018-0.00826.801-0.384-0.3840.0000.0000.0000.000
82A82GLN0-0.010-0.00629.2470.0230.0230.0000.0000.0000.000
83A83VAL0-0.005-0.00930.349-0.100-0.1000.0000.0000.0000.000
84A84GLU-1-0.890-0.96133.1478.1428.1420.0000.0000.0000.000
85A85GLU-1-0.771-0.84835.0228.9568.9560.0000.0000.0000.000
86A86ARG10.8930.95735.680-7.614-7.6140.0000.0000.0000.000
87A87ALA0-0.006-0.01334.275-0.042-0.0420.0000.0000.0000.000
88A88ILE0-0.055-0.03235.423-0.299-0.2990.0000.0000.0000.000
89A89GLU-1-0.941-0.96934.3318.8328.8320.0000.0000.0000.000
90A90ARG10.9220.96134.073-8.178-8.1780.0000.0000.0000.000
91A91GLY00.0840.05031.6020.1510.1510.0000.0000.0000.000
92A92PRO0-0.046-0.03629.331-0.362-0.3620.0000.0000.0000.000
93A93LYS10.8110.89630.456-10.317-10.3170.0000.0000.0000.000
94A94GLY0-0.0150.00033.487-0.205-0.2050.0000.0000.0000.000
95A95PHE00.001-0.02434.7560.1790.1790.0000.0000.0000.000
96A96ASN00.0360.03534.9570.3030.3030.0000.0000.0000.000
97A97PHE00.0980.04127.6110.2770.2770.0000.0000.0000.000
98A98ASN0-0.035-0.05130.3510.6440.6440.0000.0000.0000.000
99A99ASP-1-0.848-0.88630.7859.5549.5540.0000.0000.0000.000
100A100ASN0-0.055-0.03829.1630.2560.2560.0000.0000.0000.000
101A101VAL0-0.0160.01125.4370.5240.5240.0000.0000.0000.000
102A102THR00.0060.01222.357-0.233-0.2330.0000.0000.0000.000
103A103PRO0-0.0090.00122.9480.6460.6460.0000.0000.0000.000
104A104PHE0-0.0160.00617.2080.2770.2770.0000.0000.0000.000
105A105LYS10.9020.95320.685-15.911-15.9110.0000.0000.0000.000
106A106TYR0-0.013-0.02020.2110.7140.7140.0000.0000.0000.000
107A107ALA00.0220.01717.321-0.387-0.3870.0000.0000.0000.000
108A108ALA0-0.037-0.02519.444-0.635-0.6350.0000.0000.0000.000
109A109GLY0-0.005-0.00419.083-0.801-0.8010.0000.0000.0000.000
110A110ALA0-0.043-0.02114.0440.9310.9310.0000.0000.0000.000
111A111LYS10.8590.92313.964-23.737-23.7370.0000.0000.0000.000
112A112ALA00.0480.01111.8291.9821.9820.0000.0000.0000.000
113A113GLY0-0.0080.0049.454-1.509-1.5090.0000.0000.0000.000
114A114GLU-1-0.842-0.9018.40728.24428.2440.0000.0000.0000.000
115A115ARG10.8240.8681.676-139.557-152.80533.865-12.554-8.0630.145
116A116ILE0-0.039-0.0116.278-6.239-6.2390.0000.0000.0000.000
117A117LYS10.8460.9216.166-21.994-21.9940.0000.0000.0000.000
118A118VAL0-0.0010.0047.645-4.796-4.7960.0000.0000.0000.000
119A119ILE0-0.011-0.0049.9610.8120.8120.0000.0000.0000.000
120A120GLY00.0640.01612.566-1.543-1.5430.0000.0000.0000.000
121A121TYR0-0.044-0.02214.8190.4500.4500.0000.0000.0000.000
122A122PRO00.0530.04911.723-1.292-1.2920.0000.0000.0000.000
123A123HIS00.0630.01912.516-0.258-0.2580.0000.0000.0000.000
124A124PRO0-0.038-0.04917.162-0.202-0.2020.0000.0000.0000.000
125A125TYR00.0950.05917.201-0.786-0.7860.0000.0000.0000.000
126A126LYS10.7800.91218.768-15.435-15.4350.0000.0000.0000.000
127A127ASN00.0510.01824.275-0.530-0.5300.0000.0000.0000.000
128A128LYS10.8570.94423.733-11.648-11.6480.0000.0000.0000.000
129A129TYR00.0380.04721.6400.3760.3760.0000.0000.0000.000
130A130VAL0-0.021-0.01916.780-0.145-0.1450.0000.0000.0000.000
131A131LEU0-0.0080.01715.1360.4090.4090.0000.0000.0000.000
132A132TYR00.012-0.01311.079-0.504-0.5040.0000.0000.0000.000
133A133GLU-1-0.785-0.8798.05929.28429.2840.0000.0000.0000.000
134A134SER0-0.034-0.0336.0943.7863.7860.0000.0000.0000.000
135A135THR0-0.036-0.0221.609-23.727-33.06619.069-6.567-3.1640.063
136A136GLY00.0560.0232.5762.1145.3134.773-4.052-3.9200.012
137A137PRO0-0.0290.0062.856-12.597-11.7330.5340.477-1.8750.010
138A138VAL00.014-0.0025.709-3.328-3.319-0.0010.000-0.0090.000
139A139MET0-0.060-0.0306.8850.2350.2350.0000.0000.0000.000
140A140SER00.0290.0029.541-1.619-1.6190.0000.0000.0000.000
141A141VAL0-0.039-0.02713.0160.7280.7280.0000.0000.0000.000
142A142GLU-1-0.880-0.93015.78813.47113.4710.0000.0000.0000.000
143A143GLY00.0470.03218.750-0.124-0.1240.0000.0000.0000.000
144A144SER0-0.099-0.10020.1350.5260.5260.0000.0000.0000.000
145A145SER0-0.031-0.00515.2520.2200.2200.0000.0000.0000.000
146A146ILE0-0.033-0.00911.9350.1620.1620.0000.0000.0000.000
147A147VAL00.0270.0188.986-0.108-0.1080.0000.0000.0000.000
148A148TYR00.0440.0146.6570.9180.9180.0000.0000.0000.000
149A149SER00.0460.0211.790-8.893-12.70111.193-4.864-2.5220.011
150A150ALA00.0220.0091.9937.0064.8949.012-3.348-3.552-0.037
151A151HIS0-0.0260.0043.699-3.571-3.2530.000-0.033-0.2860.000
152A152THR0-0.0180.0035.6231.1691.1690.0000.0000.0000.000
153A153GLU-1-0.772-0.8789.17918.24518.2450.0000.0000.0000.000
154A154SER00.0550.02612.6660.1320.1320.0000.0000.0000.000
155A155GLY00.0000.01515.860-0.381-0.3810.0000.0000.0000.000
156A156ASN0-0.009-0.01211.7700.0940.0940.0000.0000.0000.000
157A157SER00.0100.02014.5420.2220.2220.0000.0000.0000.000
158A158GLY00.0330.01716.845-0.448-0.4480.0000.0000.0000.000
159A159SER0-0.030-0.05013.506-0.083-0.0830.0000.0000.0000.000
160A160PRO0-0.0280.01815.1140.0290.0290.0000.0000.0000.000
161A161VAL00.0110.00210.0651.3801.3800.0000.0000.0000.000
162A162LEU0-0.033-0.01311.581-1.829-1.8290.0000.0000.0000.000
163A163ASN00.0700.01610.8013.3203.3200.0000.0000.0000.000
164A164SER00.0270.00310.666-0.333-0.3330.0000.0000.0000.000
165A165ASN0-0.055-0.02511.707-0.618-0.6180.0000.0000.0000.000
166A166ASN0-0.022-0.02113.480-0.088-0.0880.0000.0000.0000.000
167A167GLU-1-0.769-0.85615.06916.13816.1380.0000.0000.0000.000
168A168LEU0-0.035-0.02115.4711.5911.5910.0000.0000.0000.000
169A169VAL0-0.002-0.01512.646-0.911-0.9110.0000.0000.0000.000
170A170GLY00.0280.00515.350-0.507-0.5070.0000.0000.0000.000
171A171ILE0-0.074-0.01215.8020.3080.3080.0000.0000.0000.000
172A172HIS00.009-0.01210.475-1.037-1.0370.0000.0000.0000.000
173A173PHE0-0.071-0.03714.057-1.159-1.1590.0000.0000.0000.000
174A174ALA00.0120.01313.590-0.923-0.9230.0000.0000.0000.000
175A175SER00.0000.0069.5330.9100.9100.0000.0000.0000.000
176A176ASP-1-0.801-0.8559.57717.63817.6380.0000.0000.0000.000
177A177VAL00.0620.03110.2670.5700.5700.0000.0000.0000.000
178A178LYS10.7620.8689.055-18.970-18.9700.0000.0000.0000.000
179A179ASN00.0200.0048.158-0.244-0.2440.0000.0000.0000.000
180A180ASP-1-0.867-0.9006.51120.62020.6200.0000.0000.0000.000
181A181ASP-1-0.766-0.8913.87524.55325.2530.000-0.239-0.460-0.001
182A182ASN0-0.093-0.0621.929-6.799-8.0017.690-3.827-2.661-0.033
183A183ARG10.8490.9443.434-21.869-21.7900.0000.112-0.1910.000
184A184ASN00.0340.0114.5414.5734.618-0.001-0.009-0.0340.000
185A185ALA0-0.020-0.0116.940-1.973-1.9730.0000.0000.0000.000
186A186TYR0-0.034-0.0468.5050.7130.7130.0000.0000.0000.000
187A187GLY0-0.014-0.02011.800-0.168-0.1680.0000.0000.0000.000
188A188VAL0-0.052-0.01713.917-0.510-0.5100.0000.0000.0000.000
189A189TYR00.0400.02016.4970.6410.6410.0000.0000.0000.000
190A190PHE0-0.008-0.00918.132-1.010-1.0100.0000.0000.0000.000
191A191THR00.0630.03221.395-0.175-0.1750.0000.0000.0000.000
192A192PRO00.046-0.00123.881-0.110-0.1100.0000.0000.0000.000
193A193GLU-1-0.854-0.91127.4089.7939.7930.0000.0000.0000.000
194A194ILE00.0020.00322.601-0.179-0.1790.0000.0000.0000.000
195A195LYS10.8840.94522.674-14.035-14.0350.0000.0000.0000.000
196A196LYS10.9030.96726.871-9.800-9.8000.0000.0000.0000.000
197A197PHE00.0570.04027.818-0.180-0.1800.0000.0000.0000.000
198A198ILE0-0.005-0.01324.228-0.135-0.1350.0000.0000.0000.000
199A199ALA0-0.0010.00528.640-0.195-0.1950.0000.0000.0000.000
200A200GLU-1-0.877-0.94531.1169.0349.0340.0000.0000.0000.000
201A201ASN0-0.076-0.05431.284-0.513-0.5130.0000.0000.0000.000
202A202ILE0-0.0020.01828.0820.0360.0360.0000.0000.0000.000
203A203ASP-1-0.839-0.88632.0218.4448.4440.0000.0000.0000.000
204A204LYS10.8110.89934.367-9.159-9.1590.0000.0000.0000.000