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: 17G4Z

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357619.351796
FMO2-HF: Nuclear repulsion 2280534.455946
FMO2-HF: Total energy -77084.89585
FMO2-MP2: Total energy -77315.74311


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.
-274.536-282.40773.606-35.792-29.9440.198
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 : -0.725 / q_NPA : -0.818
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].
3A3ASN0-0.014-0.0032.587-18.697-13.3771.963-3.273-4.0110.021
4A4VAL00.0100.0153.5870.1980.2690.0050.107-0.1830.000
5A5THR0-0.013-0.0126.996-3.602-3.6020.0000.0000.0000.000
6A6LYS10.9430.9719.913-17.216-17.2160.0000.0000.0000.000
7A7VAL00.002-0.00113.3680.5170.5170.0000.0000.0000.000
8A8LYS10.8610.92411.779-25.081-25.0810.0000.0000.0000.000
9A9ASP-1-0.823-0.91917.32913.38313.3830.0000.0000.0000.000
10A10THR0-0.020-0.02018.3070.5490.5490.0000.0000.0000.000
11A11ASN0-0.053-0.02720.086-0.453-0.4530.0000.0000.0000.000
12A12ILE00.0510.03718.206-0.564-0.5640.0000.0000.0000.000
13A13PHE00.0130.02619.0050.6320.6320.0000.0000.0000.000
14A14PRO00.003-0.01414.9360.2230.2230.0000.0000.0000.000
15A15TYR0-0.021-0.05712.589-1.009-1.0090.0000.0000.0000.000
16A16THR0-0.019-0.02318.540-0.399-0.3990.0000.0000.0000.000
17A17GLY00.0460.03320.609-0.791-0.7910.0000.0000.0000.000
18A18VAL0-0.033-0.00617.165-0.099-0.0990.0000.0000.0000.000
19A19VAL0-0.020-0.01420.580-0.672-0.6720.0000.0000.0000.000
20A20ALA0-0.016-0.01021.3330.6170.6170.0000.0000.0000.000
21A21PHE00.0310.01222.517-0.671-0.6710.0000.0000.0000.000
22A22LYS10.8900.93623.836-10.997-10.9970.0000.0000.0000.000
23A23SER0-0.020-0.05121.7730.0340.0340.0000.0000.0000.000
24A24ALA0-0.0130.01419.3830.2920.2920.0000.0000.0000.000
25A25THR0-0.0090.00116.704-0.081-0.0810.0000.0000.0000.000
26A26GLY00.0400.03019.364-0.448-0.4480.0000.0000.0000.000
27A27PHE0-0.025-0.01318.3740.4620.4620.0000.0000.0000.000
28A28VAL00.0190.01221.367-0.504-0.5040.0000.0000.0000.000
29A29VAL0-0.016-0.02223.1070.4700.4700.0000.0000.0000.000
30A30GLY00.0200.00525.363-0.149-0.1490.0000.0000.0000.000
31A31LYS10.9751.00728.979-8.523-8.5230.0000.0000.0000.000
32A32ASN0-0.066-0.03131.9620.0550.0550.0000.0000.0000.000
33A33THR0-0.001-0.01828.170-0.243-0.2430.0000.0000.0000.000
34A34ILE00.0000.00324.6890.4150.4150.0000.0000.0000.000
35A35LEU0-0.0060.00621.333-0.419-0.4190.0000.0000.0000.000
36A36THR00.014-0.01821.1490.4660.4660.0000.0000.0000.000
37A37ASN0-0.021-0.02117.9920.1600.1600.0000.0000.0000.000
38A38LYS10.8610.94621.744-11.332-11.3320.0000.0000.0000.000
39A39HIS10.7200.82318.221-14.202-14.2020.0000.0000.0000.000
40A40VAL0-0.007-0.00721.028-0.126-0.1260.0000.0000.0000.000
41A41SER00.010-0.01623.907-0.346-0.3460.0000.0000.0000.000
42A42LYS10.9310.97725.579-10.940-10.9400.0000.0000.0000.000
43A43ASN0-0.062-0.03025.901-0.519-0.5190.0000.0000.0000.000
44A44TYR0-0.0180.00926.0370.0470.0470.0000.0000.0000.000
45A45LYS10.9000.93930.837-8.539-8.5390.0000.0000.0000.000
46A46VAL00.024-0.00533.9200.1750.1750.0000.0000.0000.000
47A47GLY0-0.0030.00035.941-0.207-0.2070.0000.0000.0000.000
48A48ASP-1-0.843-0.88931.9639.0359.0350.0000.0000.0000.000
49A49ARG10.9470.96431.956-8.488-8.4880.0000.0000.0000.000
50A50ILE0-0.0100.01426.7720.2450.2450.0000.0000.0000.000
51A51THR0-0.018-0.01126.522-0.423-0.4230.0000.0000.0000.000
52A52ALA00.0150.01425.4880.5580.5580.0000.0000.0000.000
53A53HIS10.8620.93422.285-13.007-13.0070.0000.0000.0000.000
54A54PRO0-0.020-0.00622.571-0.143-0.1430.0000.0000.0000.000
55A55ASN00.006-0.02322.1220.3940.3940.0000.0000.0000.000
56A56SER00.009-0.00220.773-0.011-0.0110.0000.0000.0000.000
57A57ASP-1-0.902-0.92323.15011.75511.7550.0000.0000.0000.000
58A58LYS10.9900.97026.897-9.860-9.8600.0000.0000.0000.000
59A59GLY0-0.0090.02327.812-0.277-0.2770.0000.0000.0000.000
60A60ASN00.0240.01326.5940.3780.3780.0000.0000.0000.000
61A61GLY00.012-0.00927.267-0.267-0.2670.0000.0000.0000.000
62A62GLY00.0600.04428.617-0.232-0.2320.0000.0000.0000.000
63A63ILE0-0.044-0.00729.9000.4350.4350.0000.0000.0000.000
64A64TYR00.001-0.01930.159-0.400-0.4000.0000.0000.0000.000
65A65SER00.0500.02332.2800.1190.1190.0000.0000.0000.000
66A66ILE0-0.021-0.00729.7170.0500.0500.0000.0000.0000.000
67A67LYS10.8820.92033.419-8.805-8.8050.0000.0000.0000.000
68A68LYS10.9370.96634.017-8.689-8.6890.0000.0000.0000.000
69A69ILE00.0270.02429.8790.3180.3180.0000.0000.0000.000
70A70ILE0-0.029-0.01330.770-0.329-0.3290.0000.0000.0000.000
71A71ASN00.0270.00628.5140.5500.5500.0000.0000.0000.000
72A72TYR00.0150.01025.656-0.312-0.3120.0000.0000.0000.000
73A73PRO0-0.002-0.00128.4810.0830.0830.0000.0000.0000.000
74A74GLY00.0850.04827.803-0.029-0.0290.0000.0000.0000.000
75A75LYS10.9250.96021.998-12.205-12.2050.0000.0000.0000.000
76A76GLU-1-0.784-0.86121.64612.18412.1840.0000.0000.0000.000
77A77ASP-1-0.708-0.83719.79412.43212.4320.0000.0000.0000.000
78A78VAL0-0.014-0.01320.9850.5410.5410.0000.0000.0000.000
79A79SER0-0.020-0.01623.232-0.597-0.5970.0000.0000.0000.000
80A80VAL00.0390.01725.4910.4720.4720.0000.0000.0000.000
81A81ILE0-0.023-0.00126.783-0.372-0.3720.0000.0000.0000.000
82A82GLN00.007-0.01229.2090.0240.0240.0000.0000.0000.000
83A83VAL0-0.005-0.00630.275-0.101-0.1010.0000.0000.0000.000
84A84GLU-1-0.920-0.97533.0837.9867.9860.0000.0000.0000.000
85A85GLU-1-0.827-0.89535.1448.7898.7890.0000.0000.0000.000
86A86ARG10.9100.96336.143-7.538-7.5380.0000.0000.0000.000
87A87ALA0-0.011-0.01534.644-0.038-0.0380.0000.0000.0000.000
88A88ILE0-0.056-0.03535.654-0.290-0.2900.0000.0000.0000.000
89A89GLU-1-0.944-0.97534.7048.7428.7420.0000.0000.0000.000
90A90ARG10.9270.96434.524-8.050-8.0500.0000.0000.0000.000
91A91GLY00.0810.04932.0330.1500.1500.0000.0000.0000.000
92A92PRO0-0.046-0.03629.870-0.351-0.3510.0000.0000.0000.000
93A93LYS10.8780.94730.404-10.423-10.4230.0000.0000.0000.000
94A94GLY0-0.0080.00433.889-0.199-0.1990.0000.0000.0000.000
95A95PHE0-0.012-0.02835.1930.1680.1680.0000.0000.0000.000
96A96ASN00.0350.03135.4020.3010.3010.0000.0000.0000.000
97A97PHE00.0750.02727.7000.2880.2880.0000.0000.0000.000
98A98ASN0-0.010-0.03930.8120.6770.6770.0000.0000.0000.000
99A99ASP-1-0.890-0.90731.2279.3709.3700.0000.0000.0000.000
100A100ASN0-0.056-0.05029.4930.3000.3000.0000.0000.0000.000
101A101VAL0-0.0220.01525.9220.5210.5210.0000.0000.0000.000
102A102THR0-0.0010.00022.793-0.208-0.2080.0000.0000.0000.000
103A103PRO00.0040.00923.4000.6280.6280.0000.0000.0000.000
104A104PHE0-0.0230.00117.9720.2780.2780.0000.0000.0000.000
105A105LYS10.9050.95221.226-15.672-15.6720.0000.0000.0000.000
106A106TYR0-0.010-0.02020.6200.6680.6680.0000.0000.0000.000
107A107ALA00.0230.01817.670-0.357-0.3570.0000.0000.0000.000
108A108ALA0-0.035-0.02619.769-0.625-0.6250.0000.0000.0000.000
109A109GLY0-0.014-0.00919.269-0.789-0.7890.0000.0000.0000.000
110A110ALA0-0.030-0.01514.1570.8920.8920.0000.0000.0000.000
111A111LYS10.8670.93013.820-23.608-23.6080.0000.0000.0000.000
112A112ALA00.0530.01011.8031.9501.9500.0000.0000.0000.000
113A113GLY0-0.0130.0019.392-1.425-1.4250.0000.0000.0000.000
114A114GLU-1-0.858-0.9088.40928.11628.1160.0000.0000.0000.000
115A115ARG10.7870.8371.621-145.298-161.98543.034-17.017-9.3300.186
116A116ILE0-0.040-0.0126.393-5.840-5.8400.0000.0000.0000.000
117A117LYS10.8640.9226.599-21.660-21.6600.0000.0000.0000.000
118A118VAL0-0.0110.0037.653-4.434-4.4340.0000.0000.0000.000
119A119ILE0-0.0060.0019.8950.7300.7300.0000.0000.0000.000
120A120GLY00.0550.01012.798-1.449-1.4490.0000.0000.0000.000
121A121TYR0-0.050-0.02314.9840.4410.4410.0000.0000.0000.000
122A122PRO00.0530.04311.900-1.280-1.2800.0000.0000.0000.000
123A123HIS00.0730.02812.643-0.374-0.3740.0000.0000.0000.000
124A124PRO0-0.030-0.04817.319-0.203-0.2030.0000.0000.0000.000
125A125TYR00.0880.05517.247-0.807-0.8070.0000.0000.0000.000
126A126LYS10.7880.91418.731-15.238-15.2380.0000.0000.0000.000
127A127ASN00.0380.01524.418-0.541-0.5410.0000.0000.0000.000
128A128LYS10.8720.95623.720-11.611-11.6110.0000.0000.0000.000
129A129TYR00.0140.02321.7980.4000.4000.0000.0000.0000.000
130A130VAL0-0.016-0.01516.889-0.130-0.1300.0000.0000.0000.000
131A131LEU0-0.0070.01515.5470.3900.3900.0000.0000.0000.000
132A132TYR0-0.002-0.01711.185-0.516-0.5160.0000.0000.0000.000
133A133GLU-1-0.809-0.8948.32528.79928.7990.0000.0000.0000.000
134A134SER0-0.047-0.0385.8553.7673.7670.0000.0000.0000.000
135A135THR00.0010.0021.962-18.522-18.0365.298-2.931-2.8530.044
136A136GLY00.0450.0192.5272.4455.9982.950-3.549-2.9540.004
137A137PRO0-0.0210.0132.732-12.416-11.0140.482-0.127-1.7570.010
138A138VAL00.0180.0005.685-3.765-3.7650.0000.0000.0000.000
139A139MET0-0.074-0.0396.6390.6250.6250.0000.0000.0000.000
140A140SER00.000-0.0089.347-2.072-2.0720.0000.0000.0000.000
141A141VAL0-0.010-0.01512.8650.7090.7090.0000.0000.0000.000
142A142GLU-1-0.885-0.92715.63313.36713.3670.0000.0000.0000.000
143A143GLY00.0410.02518.606-0.142-0.1420.0000.0000.0000.000
144A144SER0-0.113-0.10620.0200.5530.5530.0000.0000.0000.000
145A145SER0-0.035-0.00415.5040.4810.4810.0000.0000.0000.000
146A146ILE00.0060.00611.6820.1650.1650.0000.0000.0000.000
147A147VAL00.0240.0168.8190.0180.0180.0000.0000.0000.000
148A148TYR00.0460.0166.5360.8000.8000.0000.0000.0000.000
149A149SER00.0240.0202.503-1.407-0.3922.722-1.790-1.946-0.011
150A150ALA00.0390.0221.8995.0452.06410.137-3.794-3.362-0.030
151A151HIS0-0.031-0.0033.784-3.449-3.1360.001-0.042-0.2720.000
152A152THR0-0.0130.0105.8211.0871.0870.0000.0000.0000.000
153A153GLU-1-0.830-0.9039.35118.23918.2390.0000.0000.0000.000
154A154SER00.0350.00912.8510.0650.0650.0000.0000.0000.000
155A155GLY00.0040.00316.023-0.375-0.3750.0000.0000.0000.000
156A156ASN00.003-0.01211.6620.1410.1410.0000.0000.0000.000
157A157SER00.0130.03514.5190.1240.1240.0000.0000.0000.000
158A158GLY00.0350.01416.956-0.419-0.4190.0000.0000.0000.000
159A159SER0-0.016-0.02613.519-0.063-0.0630.0000.0000.0000.000
160A160PRO0-0.0200.02415.093-0.030-0.0300.0000.0000.0000.000
161A161VAL00.0220.00210.1921.3051.3050.0000.0000.0000.000
162A162LEU0-0.046-0.01611.839-1.704-1.7040.0000.0000.0000.000
163A163ASN00.0830.02411.2153.1503.1500.0000.0000.0000.000
164A164SER00.024-0.00310.801-0.304-0.3040.0000.0000.0000.000
165A165ASN0-0.049-0.02011.955-0.439-0.4390.0000.0000.0000.000
166A166ASN00.0130.01413.8560.0890.0890.0000.0000.0000.000
167A167GLU-1-0.780-0.86315.43615.95815.9580.0000.0000.0000.000
168A168LEU0-0.033-0.01815.8731.5241.5240.0000.0000.0000.000
169A169VAL00.003-0.01312.768-0.851-0.8510.0000.0000.0000.000
170A170GLY00.0210.00315.422-0.468-0.4680.0000.0000.0000.000
171A171ILE0-0.083-0.00815.8280.2770.2770.0000.0000.0000.000
172A172HIS00.003-0.01910.454-0.943-0.9430.0000.0000.0000.000
173A173PHE0-0.068-0.03614.098-1.136-1.1360.0000.0000.0000.000
174A174ALA00.0220.02013.652-0.846-0.8460.0000.0000.0000.000
175A175SER00.0120.0019.6281.2481.2480.0000.0000.0000.000
176A176ASP-1-0.803-0.8299.61917.08617.0860.0000.0000.0000.000
177A177VAL00.0510.03110.2070.6160.6160.0000.0000.0000.000
178A178LYS10.7700.8608.907-19.403-19.4030.0000.0000.0000.000
179A179ASN00.0230.0008.223-0.446-0.4460.0000.0000.0000.000
180A180ASP-1-0.873-0.9106.48321.22121.2210.0000.0000.0000.000
181A181ASP-1-0.786-0.8813.93024.86625.5010.000-0.206-0.4290.000
182A182ASN0-0.051-0.0451.956-2.191-3.2937.016-3.276-2.638-0.026
183A183ARG10.8790.9723.450-22.039-21.980-0.0010.118-0.1770.000
184A184ASN00.0430.0064.4664.0404.085-0.001-0.012-0.0320.000
185A185ALA0-0.0060.0006.915-1.755-1.7550.0000.0000.0000.000
186A186TYR0-0.066-0.0808.5240.7060.7060.0000.0000.0000.000
187A187GLY0-0.010-0.02411.785-0.176-0.1760.0000.0000.0000.000
188A188VAL0-0.049-0.01213.897-0.467-0.4670.0000.0000.0000.000
189A189TYR00.0420.02016.2530.6060.6060.0000.0000.0000.000
190A190PHE00.002-0.01118.055-0.961-0.9610.0000.0000.0000.000
191A191THR00.0690.03621.388-0.144-0.1440.0000.0000.0000.000
192A192PRO00.036-0.00423.788-0.135-0.1350.0000.0000.0000.000
193A193GLU-1-0.959-0.97527.39910.03410.0340.0000.0000.0000.000
194A194ILE00.0330.02322.682-0.187-0.1870.0000.0000.0000.000
195A195LYS10.8880.94923.456-13.526-13.5260.0000.0000.0000.000
196A196LYS10.9700.99726.940-9.840-9.8400.0000.0000.0000.000
197A197PHE00.0500.04027.683-0.187-0.1870.0000.0000.0000.000
198A198ILE0-0.002-0.01024.203-0.127-0.1270.0000.0000.0000.000
199A199ALA0-0.0080.00028.675-0.190-0.1900.0000.0000.0000.000
200A200GLU-1-0.902-0.95731.1528.8578.8570.0000.0000.0000.000
201A201ASN0-0.070-0.04731.302-0.493-0.4930.0000.0000.0000.000
202A202ILE0-0.0120.01528.0440.0450.0450.0000.0000.0000.000
203A203ASP-1-0.816-0.88032.0208.3318.3310.0000.0000.0000.000
204A204LYS10.8210.91134.540-9.030-9.0300.0000.0000.0000.000