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: 85Z2Y

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 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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2357151.649638
FMO2-HF: Nuclear repulsion 2280065.293964
FMO2-HF: Total energy -77086.355673
FMO2-MP2: Total energy -77317.016228


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.
-285.473-314.529101.625-40.966-31.6080.184
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 : -0.756 / q_NPA : -0.826
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].
3A3ASN0-0.004-0.0102.551-14.579-10.2271.853-2.686-3.5200.015
4A4VAL0-0.0020.0163.7150.0150.1600.0040.040-0.1900.000
5A5THR00.011-0.0047.072-3.908-3.9080.0000.0000.0000.000
6A6LYS10.9190.9589.926-17.244-17.2440.0000.0000.0000.000
7A7VAL0-0.0080.00213.1810.8260.8260.0000.0000.0000.000
8A8LYS10.8450.91611.250-26.116-26.1160.0000.0000.0000.000
9A9ASP-1-0.766-0.89716.79213.42613.4260.0000.0000.0000.000
10A10THR0-0.076-0.03918.1870.8380.8380.0000.0000.0000.000
11A11ASN0-0.076-0.05919.912-0.613-0.6130.0000.0000.0000.000
12A12ILE00.0560.04717.985-0.572-0.5720.0000.0000.0000.000
13A13PHE00.0220.02418.1340.5180.5180.0000.0000.0000.000
14A14PRO00.016-0.00214.1870.2620.2620.0000.0000.0000.000
15A15TYR0-0.021-0.05112.100-1.097-1.0970.0000.0000.0000.000
16A16THR0-0.001-0.02118.047-0.344-0.3440.0000.0000.0000.000
17A17GLY00.0290.02920.231-0.814-0.8140.0000.0000.0000.000
18A18VAL0-0.035-0.01316.607-0.084-0.0840.0000.0000.0000.000
19A19VAL0-0.025-0.02419.961-0.754-0.7540.0000.0000.0000.000
20A20ALA0-0.0130.00221.2850.6360.6360.0000.0000.0000.000
21A21PHE00.0420.01422.824-0.702-0.7020.0000.0000.0000.000
22A22LYS10.8530.91023.950-11.031-11.0310.0000.0000.0000.000
23A23SER00.0240.00022.4310.0830.0830.0000.0000.0000.000
24A24ALA00.0000.01719.7200.5470.5470.0000.0000.0000.000
25A25THR00.0120.00716.6200.0030.0030.0000.0000.0000.000
26A26GLY00.0440.02519.543-0.499-0.4990.0000.0000.0000.000
27A27PHE0-0.021-0.00818.3670.5660.5660.0000.0000.0000.000
28A28VAL00.0240.01021.287-0.525-0.5250.0000.0000.0000.000
29A29VAL0-0.011-0.01323.0160.5370.5370.0000.0000.0000.000
30A30GLY00.0270.00725.168-0.149-0.1490.0000.0000.0000.000
31A31LYS10.9090.95128.672-8.829-8.8290.0000.0000.0000.000
32A32ASN0-0.044-0.02631.8610.0870.0870.0000.0000.0000.000
33A33THR0-0.001-0.01128.294-0.215-0.2150.0000.0000.0000.000
34A34ILE0-0.011-0.01024.7410.4280.4280.0000.0000.0000.000
35A35LEU0-0.018-0.00121.018-0.420-0.4200.0000.0000.0000.000
36A36THR00.017-0.01221.1360.4970.4970.0000.0000.0000.000
37A37ASN0-0.030-0.02918.0060.1500.1500.0000.0000.0000.000
38A38LYS10.8570.94021.737-11.621-11.6210.0000.0000.0000.000
39A39HIS10.7590.85317.976-14.534-14.5340.0000.0000.0000.000
40A40VAL0-0.016-0.00520.888-0.093-0.0930.0000.0000.0000.000
41A41SER00.002-0.03023.853-0.395-0.3950.0000.0000.0000.000
42A42LYS10.9090.95425.521-10.981-10.9810.0000.0000.0000.000
43A43ASN0-0.040-0.00426.402-0.357-0.3570.0000.0000.0000.000
44A44TYR0-0.033-0.01225.696-0.030-0.0300.0000.0000.0000.000
45A45LYS10.8900.93331.178-8.701-8.7010.0000.0000.0000.000
46A46VAL00.0270.00534.3110.1740.1740.0000.0000.0000.000
47A47GLY00.0120.02036.418-0.196-0.1960.0000.0000.0000.000
48A48ASP-1-0.836-0.89432.4179.0249.0240.0000.0000.0000.000
49A49ARG10.9020.94131.973-8.659-8.6590.0000.0000.0000.000
50A50ILE0-0.0030.02226.8230.2420.2420.0000.0000.0000.000
51A51THR0-0.012-0.00926.171-0.426-0.4260.0000.0000.0000.000
52A52ALA00.0130.01325.1160.6150.6150.0000.0000.0000.000
53A53HIS10.8770.94621.354-13.381-13.3810.0000.0000.0000.000
54A54PRO0-0.0130.00022.508-0.027-0.0270.0000.0000.0000.000
55A55ASN00.0560.00721.5580.3540.3540.0000.0000.0000.000
56A56SER00.004-0.00520.182-0.053-0.0530.0000.0000.0000.000
57A57ASP-1-0.879-0.92522.65312.06212.0620.0000.0000.0000.000
58A58LYS11.0010.97926.410-9.997-9.9970.0000.0000.0000.000
59A59GLY00.0000.02827.140-0.275-0.2750.0000.0000.0000.000
60A60ASN0-0.003-0.00925.8720.3720.3720.0000.0000.0000.000
61A61GLY00.0260.01526.791-0.269-0.2690.0000.0000.0000.000
62A62GLY00.0490.02528.201-0.235-0.2350.0000.0000.0000.000
63A63ILE0-0.036-0.01429.3920.4830.4830.0000.0000.0000.000
64A64TYR00.001-0.01129.791-0.446-0.4460.0000.0000.0000.000
65A65SER00.0320.01432.2580.1440.1440.0000.0000.0000.000
66A66ILE0-0.026-0.01729.8240.0420.0420.0000.0000.0000.000
67A67LYS10.8410.90933.505-8.899-8.8990.0000.0000.0000.000
68A68LYS10.9370.98234.202-9.088-9.0880.0000.0000.0000.000
69A69ILE00.0180.01229.9380.3330.3330.0000.0000.0000.000
70A70ILE0-0.026-0.01530.606-0.336-0.3360.0000.0000.0000.000
71A71ASN00.0430.03128.1780.6840.6840.0000.0000.0000.000
72A72TYR00.0300.01825.895-0.276-0.2760.0000.0000.0000.000
73A73PRO00.0020.00128.2750.0930.0930.0000.0000.0000.000
74A74GLY00.0380.02527.576-0.082-0.0820.0000.0000.0000.000
75A75LYS10.9240.96621.967-12.623-12.6230.0000.0000.0000.000
76A76GLU-1-0.774-0.86521.65012.40412.4040.0000.0000.0000.000
77A77ASP-1-0.725-0.84619.84712.67712.6770.0000.0000.0000.000
78A78VAL0-0.004-0.00821.0340.5300.5300.0000.0000.0000.000
79A79SER00.014-0.01223.216-0.684-0.6840.0000.0000.0000.000
80A80VAL00.0270.02325.4310.4710.4710.0000.0000.0000.000
81A81ILE0-0.034-0.02126.865-0.385-0.3850.0000.0000.0000.000
82A82GLN0-0.0070.00029.3060.0320.0320.0000.0000.0000.000
83A83VAL00.013-0.00630.411-0.090-0.0900.0000.0000.0000.000
84A84GLU-1-0.832-0.94033.1238.1558.1550.0000.0000.0000.000
85A85GLU-1-0.814-0.85934.8048.9848.9840.0000.0000.0000.000
86A86ARG10.8960.95935.839-7.677-7.6770.0000.0000.0000.000
87A87ALA00.002-0.00534.2830.0130.0130.0000.0000.0000.000
88A88ILE0-0.051-0.03335.441-0.307-0.3070.0000.0000.0000.000
89A89GLU-1-0.925-0.96234.4028.7998.7990.0000.0000.0000.000
90A90ARG10.8570.92533.923-8.340-8.3400.0000.0000.0000.000
91A91GLY00.0750.05331.4610.1510.1510.0000.0000.0000.000
92A92PRO0-0.014-0.02329.402-0.363-0.3630.0000.0000.0000.000
93A93LYS10.8570.91230.671-10.306-10.3060.0000.0000.0000.000
94A94GLY00.0130.01733.670-0.273-0.2730.0000.0000.0000.000
95A95PHE0-0.005-0.01934.8190.1830.1830.0000.0000.0000.000
96A96ASN00.0160.02434.8480.2900.2900.0000.0000.0000.000
97A97PHE00.0720.02727.6590.2490.2490.0000.0000.0000.000
98A98ASN0-0.021-0.04230.3650.6220.6220.0000.0000.0000.000
99A99ASP-1-0.857-0.89630.6699.4969.4960.0000.0000.0000.000
100A100ASN0-0.056-0.03429.2470.1810.1810.0000.0000.0000.000
101A101VAL0-0.0200.00325.4260.4910.4910.0000.0000.0000.000
102A102THR00.0280.01922.086-0.188-0.1880.0000.0000.0000.000
103A103PRO0-0.016-0.00522.7850.6620.6620.0000.0000.0000.000
104A104PHE00.0010.01316.9130.2130.2130.0000.0000.0000.000
105A105LYS10.8760.94420.510-15.889-15.8890.0000.0000.0000.000
106A106TYR00.004-0.01120.0990.6880.6880.0000.0000.0000.000
107A107ALA00.0000.00217.275-0.301-0.3010.0000.0000.0000.000
108A108ALA0-0.026-0.02119.421-0.645-0.6450.0000.0000.0000.000
109A109GLY00.0060.00119.310-0.753-0.7530.0000.0000.0000.000
110A110ALA0-0.052-0.02314.1510.8980.8980.0000.0000.0000.000
111A111LYS10.8110.88914.231-23.338-23.3380.0000.0000.0000.000
112A112ALA00.0320.01311.9841.8771.8770.0000.0000.0000.000
113A113GLY00.0050.0089.694-1.444-1.4440.0000.0000.0000.000
114A114GLU-1-0.817-0.8868.79627.68327.6830.0000.0000.0000.000
115A115ARG10.8180.8651.672-138.233-151.86634.025-12.393-8.0000.142
116A116ILE0-0.040-0.0136.242-6.324-6.3240.0000.0000.0000.000
117A117LYS10.8390.9096.035-20.943-20.9430.0000.0000.0000.000
118A118VAL00.0060.0077.898-4.532-4.5320.0000.0000.0000.000
119A119ILE0-0.0150.0009.8390.9270.9270.0000.0000.0000.000
120A120GLY00.033-0.00812.460-1.425-1.4250.0000.0000.0000.000
121A121TYR0-0.062-0.03214.7300.5450.5450.0000.0000.0000.000
122A122PRO00.0440.03911.944-1.206-1.2060.0000.0000.0000.000
123A123HIS00.0400.01812.719-0.556-0.5560.0000.0000.0000.000
124A124PRO0-0.007-0.02217.190-0.274-0.2740.0000.0000.0000.000
125A125TYR00.0480.01417.307-0.760-0.7600.0000.0000.0000.000
126A126LYS10.7690.91218.918-15.467-15.4670.0000.0000.0000.000
127A127ASN00.0210.01324.073-0.528-0.5280.0000.0000.0000.000
128A128LYS10.8750.94723.866-11.749-11.7490.0000.0000.0000.000
129A129TYR00.0280.02521.7350.3830.3830.0000.0000.0000.000
130A130VAL0-0.013-0.00716.7970.1050.1050.0000.0000.0000.000
131A131LEU00.0030.02215.2920.4210.4210.0000.0000.0000.000
132A132TYR00.006-0.01111.223-0.658-0.6580.0000.0000.0000.000
133A133GLU-1-0.783-0.8738.07429.45329.4530.0000.0000.0000.000
134A134SER0-0.038-0.0165.9732.7052.7050.0000.0000.0000.000
135A135THR0-0.040-0.0361.567-23.981-35.91222.793-7.720-3.1420.066
136A136GLY00.0700.0302.5380.1993.0185.440-4.351-3.9080.015
137A137PRO0-0.0230.0042.854-10.899-10.9220.4451.306-1.7290.008
138A138VAL0-0.008-0.0125.778-3.158-3.1580.0000.0000.0000.000
139A139MET0-0.035-0.0136.8620.3020.3020.0000.0000.0000.000
140A140SER00.0290.0059.549-1.938-1.9380.0000.0000.0000.000
141A141VAL0-0.047-0.03512.9190.7240.7240.0000.0000.0000.000
142A142GLU-1-0.851-0.91215.69313.50213.5020.0000.0000.0000.000
143A143GLY00.010-0.00318.840-0.036-0.0360.0000.0000.0000.000
144A144SER0-0.091-0.07820.7120.2360.2360.0000.0000.0000.000
145A145SER0-0.035-0.00515.3040.0800.0800.0000.0000.0000.000
146A146ILE0-0.027-0.01412.0470.0270.0270.0000.0000.0000.000
147A147VAL00.0260.0159.350-0.121-0.1210.0000.0000.0000.000
148A148TYR00.0490.0166.4990.6240.6240.0000.0000.0000.000
149A149SER00.0570.0311.819-10.056-14.48713.111-5.835-2.8450.019
150A150ALA00.0220.0051.9178.4284.22312.181-4.015-3.961-0.040
151A151HIS0-0.018-0.0013.622-3.376-2.9870.001-0.073-0.3170.000
152A152THR0-0.027-0.0185.5781.3701.3700.0000.0000.0000.000
153A153GLU-1-0.764-0.8599.19318.52318.5230.0000.0000.0000.000
154A154SER00.0400.01612.5620.0560.0560.0000.0000.0000.000
155A155GLY00.0260.03516.003-0.440-0.4400.0000.0000.0000.000
156A156ASN0-0.014-0.01511.9080.0610.0610.0000.0000.0000.000
157A157SER00.0000.00614.6930.1630.1630.0000.0000.0000.000
158A158GLY00.0500.02417.118-0.502-0.5020.0000.0000.0000.000
159A159SER0-0.023-0.03813.597-0.055-0.0550.0000.0000.0000.000
160A160PRO0-0.0270.00815.043-0.060-0.0600.0000.0000.0000.000
161A161VAL00.001-0.00110.2441.4661.4660.0000.0000.0000.000
162A162LEU0-0.036-0.01511.572-1.994-1.9940.0000.0000.0000.000
163A163ASN00.0620.01410.7553.3323.3320.0000.0000.0000.000
164A164SER00.0430.01210.509-0.366-0.3660.0000.0000.0000.000
165A165ASN0-0.057-0.02011.460-0.462-0.4620.0000.0000.0000.000
166A166ASN0-0.007-0.01713.263-0.121-0.1210.0000.0000.0000.000
167A167GLU-1-0.780-0.86014.59116.22816.2280.0000.0000.0000.000
168A168LEU0-0.018-0.01015.4621.4651.4650.0000.0000.0000.000
169A169VAL00.000-0.00812.902-1.111-1.1110.0000.0000.0000.000
170A170GLY00.021-0.00515.507-0.729-0.7290.0000.0000.0000.000
171A171ILE0-0.049-0.00115.9300.3660.3660.0000.0000.0000.000
172A172HIS0-0.003-0.00310.510-0.927-0.9270.0000.0000.0000.000
173A173PHE0-0.053-0.02214.139-1.167-1.1670.0000.0000.0000.000
174A174ALA00.0090.01313.758-0.923-0.9230.0000.0000.0000.000
175A175SER0-0.010-0.0029.2470.8220.8220.0000.0000.0000.000
176A176ASP-1-0.764-0.8379.14918.40318.4030.0000.0000.0000.000
177A177VAL0-0.005-0.01110.4770.4180.4180.0000.0000.0000.000
178A178LYS10.8090.9029.250-18.909-18.9090.0000.0000.0000.000
179A179ASN00.0350.0078.605-0.204-0.2040.0000.0000.0000.000
180A180ASP-1-0.883-0.9236.28320.44420.4440.0000.0000.0000.000
181A181ASP-1-0.807-0.9044.05123.85324.590-0.001-0.303-0.434-0.001
182A182ASN0-0.012-0.0201.831-7.764-11.15111.769-5.008-3.374-0.040
183A183ARG10.8060.9213.453-21.949-21.8680.0050.074-0.1600.000
184A184ASN0-0.036-0.0214.9993.7353.766-0.001-0.002-0.0280.000
185A185ALA0-0.001-0.0026.989-1.902-1.9020.0000.0000.0000.000
186A186TYR0-0.025-0.0398.3671.0451.0450.0000.0000.0000.000
187A187GLY0-0.010-0.02111.707-0.204-0.2040.0000.0000.0000.000
188A188VAL0-0.028-0.00314.063-0.371-0.3710.0000.0000.0000.000
189A189TYR00.0230.01116.6560.8000.8000.0000.0000.0000.000
190A190PHE0-0.001-0.00318.248-1.054-1.0540.0000.0000.0000.000
191A191THR00.0640.02521.361-0.213-0.2130.0000.0000.0000.000
192A192PRO00.0370.00224.107-0.073-0.0730.0000.0000.0000.000
193A193GLU-1-0.839-0.90127.5469.7519.7510.0000.0000.0000.000
194A194ILE0-0.0030.00422.653-0.205-0.2050.0000.0000.0000.000
195A195LYS10.8920.94922.292-14.233-14.2330.0000.0000.0000.000
196A196LYS10.8990.96526.736-9.794-9.7940.0000.0000.0000.000
197A197PHE00.0340.01728.046-0.196-0.1960.0000.0000.0000.000
198A198ILE0-0.005-0.01524.283-0.158-0.1580.0000.0000.0000.000
199A199ALA00.0010.00528.678-0.199-0.1990.0000.0000.0000.000
200A200GLU-1-0.892-0.94731.2479.0209.0200.0000.0000.0000.000
201A201ASN0-0.042-0.03531.340-0.526-0.5260.0000.0000.0000.000
202A202ILE0-0.0110.01228.128-0.027-0.0270.0000.0000.0000.000
203A203ASP-1-0.811-0.87531.9908.4508.4500.0000.0000.0000.000
204A204LYS10.7810.88134.461-9.179-9.1790.0000.0000.0000.000