Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 434VN

Calculation Name: 5BVL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5BVL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2195645.02949
FMO2-HF: Nuclear repulsion 2120655.644336
FMO2-HF: Total energy -74989.385154
FMO2-MP2: Total energy -75212.276847


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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
155.894162.6380.458-2.438-4.7650.022
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.888 / q_NPA : -0.958
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].
3A3ASP-1-0.956-0.9942.68427.39432.5810.436-2.019-3.6040.020
4A4GLU-1-0.954-0.9683.41624.98125.8700.020-0.317-0.5930.002
5A5ALA00.0220.0035.027-6.690-6.527-0.001-0.015-0.1470.000
6A6TRP0-0.055-0.0276.914-4.729-4.7290.0000.0000.0000.000
7A7LYS10.8110.9008.030-24.179-24.1790.0000.0000.0000.000
8A8CYS00.0130.0049.763-3.530-3.5300.0000.0000.0000.000
9A9VAL00.0810.04611.515-2.216-2.2160.0000.0000.0000.000
10A10GLU-1-0.875-0.90412.92217.44917.4490.0000.0000.0000.000
11A11GLN00.0150.02114.364-2.515-2.5150.0000.0000.0000.000
12A12LEU00.011-0.00215.338-1.255-1.2550.0000.0000.0000.000
13A13ARG10.9670.99117.517-16.033-16.0330.0000.0000.0000.000
14A14ARG10.7510.86218.686-15.770-15.7700.0000.0000.0000.000
15A15GLU-1-0.892-0.94919.96912.97612.9760.0000.0000.0000.000
16A16GLY0-0.0180.00522.312-0.510-0.5100.0000.0000.0000.000
17A17ALA0-0.027-0.02120.3660.0580.0580.0000.0000.0000.000
18A18THR0-0.0070.00921.907-0.364-0.3640.0000.0000.0000.000
19A19GLN0-0.031-0.01621.430-0.589-0.5890.0000.0000.0000.000
20A20ILE0-0.027-0.00515.2000.3290.3290.0000.0000.0000.000
21A21ALA0-0.001-0.00115.515-0.335-0.3350.0000.0000.0000.000
22A22TYR0-0.051-0.0285.5631.1681.1680.0000.0000.0000.000
23A23ARG10.9290.9729.793-25.365-25.3650.0000.0000.0000.000
24A24SER0-0.047-0.0487.7743.0803.0800.0000.0000.0000.000
25A25ASP-1-0.823-0.9177.81326.88726.8870.0000.0000.0000.000
26A26ASP-1-0.828-0.9058.88324.64124.6410.0000.0000.0000.000
27A27TRP00.0430.01410.512-0.700-0.7000.0000.0000.0000.000
28A28ARG10.8780.93912.745-20.009-20.0090.0000.0000.0000.000
29A29ASP-1-0.840-0.9067.50936.50636.5060.0000.0000.0000.000
30A30LEU00.0800.05210.602-1.060-1.0600.0000.0000.0000.000
31A31LYS10.8820.94112.652-17.141-17.1410.0000.0000.0000.000
32A32GLU-1-0.865-0.94912.52118.07918.0790.0000.0000.0000.000
33A33ALA00.0430.02611.444-0.870-0.8700.0000.0000.0000.000
34A34TRP00.0160.04913.531-0.972-0.9720.0000.0000.0000.000
35A35LYS10.8500.91416.929-17.863-17.8630.0000.0000.0000.000
36A36LYS10.7030.80713.784-21.177-21.1770.0000.0000.0000.000
37A37GLY0-0.079-0.05517.065-0.660-0.6600.0000.0000.0000.000
38A38ALA00.0040.04614.0410.5290.5290.0000.0000.0000.000
39A39ASP-1-0.836-0.91916.18414.99814.9980.0000.0000.0000.000
40A40ILE0-0.050-0.01917.382-0.495-0.4950.0000.0000.0000.000
41A41LEU0-0.006-0.00714.6191.3891.3890.0000.0000.0000.000
42A42ILE0-0.030-0.01713.401-1.249-1.2490.0000.0000.0000.000
43A43VAL00.0230.01112.8681.8861.8860.0000.0000.0000.000
44A44ASP-1-0.855-0.92511.05525.91125.9110.0000.0000.0000.000
45A45ALA0-0.069-0.03113.214-0.428-0.4280.0000.0000.0000.000
46A46THR00.0360.01412.352-0.050-0.0500.0000.0000.0000.000
47A47ASP-1-0.877-0.92715.18116.44716.4470.0000.0000.0000.000
48A48LYS10.8930.94218.107-13.929-13.9290.0000.0000.0000.000
49A49ASP-1-0.945-0.96020.41613.84713.8470.0000.0000.0000.000
50A50GLU-1-0.860-0.93215.64218.02518.0250.0000.0000.0000.000
51A51ALA00.009-0.00116.7850.1380.1380.0000.0000.0000.000
52A52TRP0-0.025-0.03317.708-0.478-0.4780.0000.0000.0000.000
53A53LYS11.0021.00620.060-14.635-14.6350.0000.0000.0000.000
54A54GLN0-0.037-0.02913.182-0.074-0.0740.0000.0000.0000.000
55A55VAL00.0080.01918.172-0.173-0.1730.0000.0000.0000.000
56A56GLU-1-0.945-0.97220.29312.14112.1410.0000.0000.0000.000
57A57GLN0-0.056-0.02319.401-0.958-0.9580.0000.0000.0000.000
58A58LEU00.007-0.01416.172-0.352-0.3520.0000.0000.0000.000
59A59ARG11.0030.99320.498-11.848-11.8480.0000.0000.0000.000
60A60ARG10.8260.91023.990-13.352-13.3520.0000.0000.0000.000
61A61GLU-1-0.893-0.94120.41214.39914.3990.0000.0000.0000.000
62A62GLY0-0.0210.00423.455-0.117-0.1170.0000.0000.0000.000
63A63ALA0-0.034-0.02520.072-0.107-0.1070.0000.0000.0000.000
64A64THR0-0.032-0.02821.993-0.052-0.0520.0000.0000.0000.000
65A65GLN00.0310.02321.211-0.189-0.1890.0000.0000.0000.000
66A66ILE0-0.0130.01518.9321.0061.0060.0000.0000.0000.000
67A67ALA00.0130.00117.714-0.744-0.7440.0000.0000.0000.000
68A68TYR0-0.006-0.00817.7140.4860.4860.0000.0000.0000.000
69A69ARG10.8380.91312.930-22.746-22.7460.0000.0000.0000.000
70A70SER0-0.032-0.02318.1950.4240.4240.0000.0000.0000.000
71A71ASP-1-0.855-0.92020.34614.29714.2970.0000.0000.0000.000
72A72ASP-1-0.752-0.85122.70811.15011.1500.0000.0000.0000.000
73A73TRP00.025-0.01425.0400.0870.0870.0000.0000.0000.000
74A74ARG10.7620.87127.327-11.231-11.2310.0000.0000.0000.000
75A75ASP-1-0.831-0.92522.73113.58813.5880.0000.0000.0000.000
76A76LEU0-0.014-0.00221.8860.1420.1420.0000.0000.0000.000
77A77LYS10.8700.92924.634-9.834-9.8340.0000.0000.0000.000
78A78GLU-1-0.908-0.97125.89111.06511.0650.0000.0000.0000.000
79A79ALA00.0050.00722.1770.0010.0010.0000.0000.0000.000
80A80TRP0-0.032-0.00624.059-0.059-0.0590.0000.0000.0000.000
81A81LYS10.8390.92326.594-10.470-10.4700.0000.0000.0000.000
82A82LYS10.8350.93524.569-12.239-12.2390.0000.0000.0000.000
83A83GLY0-0.055-0.03525.2580.2410.2410.0000.0000.0000.000
84A84ALA0-0.0140.01522.1470.1900.1900.0000.0000.0000.000
85A85ASP-1-0.880-0.94823.31012.02712.0270.0000.0000.0000.000
86A86ILE0-0.029-0.01821.231-0.325-0.3250.0000.0000.0000.000
87A87LEU0-0.043-0.03021.6980.7160.7160.0000.0000.0000.000
88A88ILE0-0.013-0.01417.687-0.308-0.3080.0000.0000.0000.000
89A89VAL00.0280.01620.9820.4190.4190.0000.0000.0000.000
90A90ASP-1-0.880-0.96517.70718.08618.0860.0000.0000.0000.000
91A91ALA0-0.011-0.00321.008-0.369-0.3690.0000.0000.0000.000
92A92THR00.0000.00020.3140.2290.2290.0000.0000.0000.000
93A93ASP-1-0.865-0.94123.41510.78310.7830.0000.0000.0000.000
94A94LYS10.8850.94326.973-11.233-11.2330.0000.0000.0000.000
95A95ASP-1-0.892-0.96329.0059.4089.4080.0000.0000.0000.000
96A96GLU-1-0.876-0.92728.72710.19310.1930.0000.0000.0000.000
97A97ALA00.0090.02526.4130.1040.1040.0000.0000.0000.000
98A98TRP0-0.021-0.02927.909-0.145-0.1450.0000.0000.0000.000
99A99LYS11.0021.01430.817-9.586-9.5860.0000.0000.0000.000
100A100GLN0-0.040-0.01426.494-0.122-0.1220.0000.0000.0000.000
101A101VAL00.0190.01227.920-0.022-0.0220.0000.0000.0000.000
102A102GLU-1-0.896-0.95029.9118.9078.9070.0000.0000.0000.000
103A103GLN0-0.030-0.00431.564-0.393-0.3930.0000.0000.0000.000
104A104LEU00.021-0.00126.605-0.231-0.2310.0000.0000.0000.000
105A105ARG10.9831.01531.200-9.123-9.1230.0000.0000.0000.000
106A106ARG10.7490.86133.686-9.326-9.3260.0000.0000.0000.000
107A107GLU-1-0.878-0.92232.5469.1049.1040.0000.0000.0000.000
108A108GLY0-0.007-0.00734.668-0.023-0.0230.0000.0000.0000.000
109A109ALA0-0.042-0.02529.1810.0520.0520.0000.0000.0000.000
110A110THR0-0.024-0.01629.681-0.064-0.0640.0000.0000.0000.000
111A111GLN00.0270.01526.250-0.027-0.0270.0000.0000.0000.000
112A112ILE00.0030.02425.7530.5580.5580.0000.0000.0000.000
113A113ALA00.011-0.00122.278-0.143-0.1430.0000.0000.0000.000
114A114TYR00.007-0.01523.751-0.050-0.0500.0000.0000.0000.000
115A115ARG10.8500.94114.886-19.304-19.3040.0000.0000.0000.000
116A116SER00.028-0.00521.283-0.199-0.1990.0000.0000.0000.000
117A117ASP-1-0.857-0.92421.19413.88213.8820.0000.0000.0000.000
118A118ASP-1-0.757-0.85822.57910.67110.6710.0000.0000.0000.000
119A119TRP00.030-0.00726.362-0.268-0.2680.0000.0000.0000.000
120A120ARG10.8160.90928.189-10.557-10.5570.0000.0000.0000.000
121A121ASP-1-0.797-0.90727.66010.95310.9530.0000.0000.0000.000
122A122LEU00.0060.01124.164-0.216-0.2160.0000.0000.0000.000
123A123LYS10.8950.95128.173-9.109-9.1090.0000.0000.0000.000
124A124GLU-1-0.928-0.97031.7588.7748.7740.0000.0000.0000.000
125A125ALA00.0220.00228.580-0.223-0.2230.0000.0000.0000.000
126A126TRP0-0.026-0.00730.555-0.209-0.2090.0000.0000.0000.000
127A127LYS10.8500.93531.541-9.050-9.0500.0000.0000.0000.000
128A128LYS10.8060.91732.873-9.459-9.4590.0000.0000.0000.000
129A129GLY0-0.046-0.03432.860-0.100-0.1000.0000.0000.0000.000
130A130ALA0-0.0310.00627.3540.1580.1580.0000.0000.0000.000
131A131ASP-1-0.863-0.93928.49210.12210.1220.0000.0000.0000.000
132A132ILE0-0.079-0.03922.4540.1590.1590.0000.0000.0000.000
133A133LEU0-0.032-0.02124.8080.2120.2120.0000.0000.0000.000
134A134ILE0-0.024-0.02618.2570.2830.2830.0000.0000.0000.000
135A135VAL00.0080.00620.976-0.077-0.0770.0000.0000.0000.000
136A136ASP-1-0.896-0.95916.16320.47820.4780.0000.0000.0000.000
137A137ALA00.0140.02216.688-0.648-0.6480.0000.0000.0000.000
138A138THR0-0.052-0.03413.7291.3471.3470.0000.0000.0000.000
139A139ASP-1-0.919-0.95715.76215.27915.2790.0000.0000.0000.000
140A140LYS10.8470.90112.392-22.529-22.5290.0000.0000.0000.000
141A141ASP-1-0.931-0.95317.61212.58712.5870.0000.0000.0000.000
142A142GLU-1-0.848-0.92720.61612.15512.1550.0000.0000.0000.000
143A143ALA00.0630.03620.059-0.469-0.4690.0000.0000.0000.000
144A144TRP0-0.020-0.02019.970-0.736-0.7360.0000.0000.0000.000
145A145LYS10.9180.96423.868-11.310-11.3100.0000.0000.0000.000
146A146GLN0-0.026-0.01723.331-0.577-0.5770.0000.0000.0000.000
147A147VAL00.0200.01623.311-0.234-0.2340.0000.0000.0000.000
148A148GLU-1-0.896-0.95226.27510.28710.2870.0000.0000.0000.000
149A149GLN0-0.063-0.03229.465-0.599-0.5990.0000.0000.0000.000
150A150LEU00.0150.00926.723-0.384-0.3840.0000.0000.0000.000
151A151ARG10.9350.97429.229-10.824-10.8240.0000.0000.0000.000
152A152ARG10.8830.95031.595-8.902-8.9020.0000.0000.0000.000
153A153GLU-1-0.952-0.98633.6548.6458.6450.0000.0000.0000.000
154A154GLY0-0.0060.00934.387-0.241-0.2410.0000.0000.0000.000
155A155ALA0-0.031-0.00429.910-0.030-0.0300.0000.0000.0000.000
156A156THR0-0.030-0.03330.9790.1670.1670.0000.0000.0000.000
157A157GLN00.0150.01726.087-0.053-0.0530.0000.0000.0000.000
158A158ILE00.0010.01524.4750.1920.1920.0000.0000.0000.000
159A159ALA00.0070.00019.7530.1710.1710.0000.0000.0000.000
160A160TYR00.030-0.00517.500-0.090-0.0900.0000.0000.0000.000
161A161ARG10.8330.92611.513-24.050-24.0500.0000.0000.0000.000
162A162SER00.0260.00813.552-0.212-0.2120.0000.0000.0000.000
163A163ASP-1-0.841-0.9098.32627.07627.0760.0000.0000.0000.000
164A164ASP-1-0.858-0.9349.85420.62120.6210.0000.0000.0000.000
165A165TRP00.020-0.01112.532-1.973-1.9730.0000.0000.0000.000
166A166ARG10.8790.93714.669-18.602-18.6020.0000.0000.0000.000
167A167ASP-1-0.774-0.90316.04916.15816.1580.0000.0000.0000.000
168A168LEU0-0.029-0.01213.407-0.952-0.9520.0000.0000.0000.000
169A169LYS10.8990.95417.747-14.202-14.2020.0000.0000.0000.000
170A170GLU-1-0.937-0.97320.42311.62311.6230.0000.0000.0000.000
171A171ALA00.0100.00820.600-0.720-0.7200.0000.0000.0000.000
172A172TRP0-0.020-0.00621.857-0.724-0.7240.0000.0000.0000.000
173A173LYS10.8750.94323.469-12.446-12.4460.0000.0000.0000.000
174A174LYS10.8150.92625.537-12.209-12.2090.0000.0000.0000.000
175A175GLY0-0.022-0.01426.486-0.390-0.3900.0000.0000.0000.000
176A176ALA0-0.036-0.00822.516-0.107-0.1070.0000.0000.0000.000
177A177ASP-1-0.902-0.96124.51911.64611.6460.0000.0000.0000.000
178A178ILE0-0.052-0.02819.0830.2780.2780.0000.0000.0000.000
179A179LEU0-0.018-0.01117.5400.1260.1260.0000.0000.0000.000
180A180ILE0-0.007-0.01713.0200.6100.6100.0000.0000.0000.000
181A181CYS0-0.032-0.01810.659-0.244-0.2440.0000.0000.0000.000
182A182ASP-1-0.846-0.9339.17131.93631.9360.0000.0000.0000.000
183A183ALA00.005-0.0025.415-2.066-2.0660.0000.0000.0000.000
184A184THR00.0030.0173.8399.90210.4070.003-0.087-0.4210.000