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: 39JQL

Calculation Name: 5VRE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5VRE

Chain ID: A

ChEMBL ID:

UniProt ID: K9UJK2

Base Structure: X-ray

Registration Date: 2023-06-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1983546.383293
FMO2-HF: Nuclear repulsion 1911642.621782
FMO2-HF: Total energy -71903.761511
FMO2-MP2: Total energy -72119.649004


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:7:GLN)


Summations of interaction energy for fragment #1(A:7:GLN)
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.
-10.455-5.7821.676-2.603-3.746-0.013
Interaction energy analysis for fragmet #1(A:7:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.000
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].
3A9GLU-1-0.770-0.8423.595-2.300-0.5980.001-0.778-0.9240.003
4A10THR00.0280.0042.443-5.187-3.1881.085-1.279-1.805-0.016
5A11GLY00.0820.0493.5950.4060.8670.002-0.184-0.2790.000
6A12ARG10.8000.8675.0830.3690.480-0.001-0.007-0.1030.000
7A13ILE0-0.067-0.0417.2850.1300.1300.0000.0000.0000.000
8A14GLU-1-0.799-0.8986.774-2.399-2.3990.0000.0000.0000.000
9A15ALA00.0350.0298.7270.2130.2130.0000.0000.0000.000
10A16PHE0-0.047-0.02110.4580.1420.1420.0000.0000.0000.000
11A17SER00.017-0.01212.1230.0400.0400.0000.0000.0000.000
12A18ASP-1-0.839-0.91112.370-0.906-0.9060.0000.0000.0000.000
13A19GLY0-0.030-0.01314.1770.0780.0780.0000.0000.0000.000
14A20VAL0-0.031-0.02316.7390.0470.0470.0000.0000.0000.000
15A21PHE00.0280.00315.6470.0450.0450.0000.0000.0000.000
16A22ALA00.0060.01518.4620.0360.0360.0000.0000.0000.000
17A23ILE0-0.001-0.00520.3530.0320.0320.0000.0000.0000.000
18A24ALA0-0.0060.00322.1680.0220.0220.0000.0000.0000.000
19A25ILE0-0.005-0.00620.9070.0210.0210.0000.0000.0000.000
20A26THR0-0.027-0.02924.5080.0280.0280.0000.0000.0000.000
21A27LEU00.0040.00426.5060.0200.0200.0000.0000.0000.000
22A28LEU0-0.0220.00327.4590.0150.0150.0000.0000.0000.000
23A29VAL0-0.020-0.01730.2030.0090.0090.0000.0000.0000.000
24A30LEU0-0.043-0.02731.6570.0110.0110.0000.0000.0000.000
25A31GLU-1-0.851-0.90733.660-0.121-0.1210.0000.0000.0000.000
26A32ILE00.0040.00335.0450.0060.0060.0000.0000.0000.000
27A33LYS10.8340.94037.5820.1110.1110.0000.0000.0000.000
28A34VAL00.0130.00340.656-0.001-0.0010.0000.0000.0000.000
29A35PRO00.0060.00443.1780.0030.0030.0000.0000.0000.000
30A36GLN00.0120.00046.6630.0070.0070.0000.0000.0000.000
31A37HIS00.0950.01948.986-0.001-0.0010.0000.0000.0000.000
32A38LYS10.9110.96052.0630.0450.0450.0000.0000.0000.000
33A39ILE00.0480.03150.3180.0000.0000.0000.0000.0000.000
34A40VAL00.0000.02050.9350.0000.0000.0000.0000.0000.000
35A41GLU-1-0.963-0.97452.982-0.045-0.0450.0000.0000.0000.000
36A42THR0-0.0340.00156.3620.0000.0000.0000.0000.0000.000
37A43VAL0-0.043-0.02253.5060.0000.0000.0000.0000.0000.000
38A44GLY00.0480.02654.983-0.001-0.0010.0000.0000.0000.000
39A45LEU00.021-0.02148.050-0.003-0.0030.0000.0000.0000.000
40A46VAL00.0110.00649.596-0.004-0.0040.0000.0000.0000.000
41A47SER00.0420.01449.503-0.005-0.0050.0000.0000.0000.000
42A48SER00.0250.01548.833-0.003-0.0030.0000.0000.0000.000
43A49LEU00.0330.01944.594-0.004-0.0040.0000.0000.0000.000
44A50LEU00.0010.01644.883-0.007-0.0070.0000.0000.0000.000
45A51SER0-0.067-0.04045.865-0.004-0.0040.0000.0000.0000.000
46A52LEU00.0240.00441.715-0.002-0.0020.0000.0000.0000.000
47A53TRP00.0070.01141.658-0.009-0.0090.0000.0000.0000.000
48A54PRO0-0.009-0.01440.396-0.010-0.0100.0000.0000.0000.000
49A55SER00.027-0.01538.202-0.005-0.0050.0000.0000.0000.000
50A56TYR0-0.082-0.05036.627-0.009-0.0090.0000.0000.0000.000
51A57LEU0-0.044-0.01435.798-0.011-0.0110.0000.0000.0000.000
52A58ALA00.0590.02634.722-0.014-0.0140.0000.0000.0000.000
53A59PHE00.0050.02830.673-0.018-0.0180.0000.0000.0000.000
54A60LEU00.0220.01230.961-0.018-0.0180.0000.0000.0000.000
55A61THR0-0.011-0.01630.330-0.017-0.0170.0000.0000.0000.000
56A62SER00.011-0.00528.981-0.020-0.0200.0000.0000.0000.000
57A63PHE00.0100.01725.891-0.029-0.0290.0000.0000.0000.000
58A64ALA0-0.006-0.00425.385-0.030-0.0300.0000.0000.0000.000
59A65SER0-0.020-0.01224.891-0.037-0.0370.0000.0000.0000.000
60A66ILE0-0.001-0.01821.579-0.038-0.0380.0000.0000.0000.000
61A67LEU00.0530.03520.418-0.046-0.0460.0000.0000.0000.000
62A68VAL0-0.0270.00119.939-0.065-0.0650.0000.0000.0000.000
63A69MET0-0.065-0.01819.688-0.054-0.0540.0000.0000.0000.000
64A70TRP0-0.0120.00413.685-0.015-0.0150.0000.0000.0000.000
65A71VAL0-0.009-0.00715.326-0.114-0.1140.0000.0000.0000.000
66A72ASN0-0.083-0.06615.199-0.128-0.1280.0000.0000.0000.000
67A73HIS0-0.027-0.00511.661-0.047-0.0470.0000.0000.0000.000
68A74HIS00.005-0.0058.988-0.054-0.0540.0000.0000.0000.000
69A75ARG10.8250.91310.3240.6760.6760.0000.0000.0000.000
70A76ILE0-0.091-0.04710.880-0.135-0.1350.0000.0000.0000.000
71A77PHE0-0.043-0.0306.680-0.010-0.0100.0000.0000.0000.000
72A78SER0-0.031-0.0186.541-0.614-0.6140.0000.0000.0000.000
73A79LEU0-0.052-0.0077.104-0.613-0.6130.0000.0000.0000.000
74A80VAL0-0.040-0.0307.261-0.094-0.0940.0000.0000.0000.000
75A81ALA00.0440.0172.580-0.654-0.2870.590-0.348-0.6100.000
76A82ARG10.9010.9454.4731.3681.401-0.001-0.007-0.0250.000
77A83THR00.0350.0245.857-0.191-0.1910.0000.0000.0000.000
78A84ASP-1-0.812-0.9108.4640.1980.1980.0000.0000.0000.000
79A85HIS00.0380.01312.149-0.087-0.0870.0000.0000.0000.000
80A86ALA0-0.015-0.00814.551-0.050-0.0500.0000.0000.0000.000
81A87PHE0-0.0060.0068.7080.0160.0160.0000.0000.0000.000
82A88PHE00.0260.01611.658-0.054-0.0540.0000.0000.0000.000
83A89TYR00.022-0.00713.114-0.016-0.0160.0000.0000.0000.000
84A90TRP0-0.026-0.01116.193-0.003-0.0030.0000.0000.0000.000
85A91ASN00.0410.01312.899-0.098-0.0980.0000.0000.0000.000
86A92GLY00.0070.01315.0840.0010.0010.0000.0000.0000.000
87A93LEU0-0.016-0.01317.4030.0160.0160.0000.0000.0000.000
88A94LEU0-0.014-0.00816.4740.0190.0190.0000.0000.0000.000
89A95LEU00.0370.01715.0410.0060.0060.0000.0000.0000.000
90A96MET0-0.032-0.00118.9760.0260.0260.0000.0000.0000.000
91A97LEU0-0.021-0.02022.3690.0180.0180.0000.0000.0000.000
92A98VAL00.0230.00819.7160.0140.0140.0000.0000.0000.000
93A99THR0-0.039-0.03221.6850.0240.0240.0000.0000.0000.000
94A100PHE0-0.023-0.01124.1530.0210.0210.0000.0000.0000.000
95A101VAL0-0.0010.00025.4170.0130.0130.0000.0000.0000.000
96A102PRO00.0360.01226.9530.0100.0100.0000.0000.0000.000
97A103PHE00.0230.03330.1990.0100.0100.0000.0000.0000.000
98A104PRO00.000-0.01730.8600.0070.0070.0000.0000.0000.000
99A105THR0-0.001-0.00731.2060.0000.0000.0000.0000.0000.000
100A106ALA00.0130.02433.4170.0060.0060.0000.0000.0000.000
101A107LEU0-0.055-0.02536.1700.0070.0070.0000.0000.0000.000
102A108LEU0-0.051-0.02336.1110.0050.0050.0000.0000.0000.000
103A109ALA00.0120.00237.3750.0030.0030.0000.0000.0000.000
104A110GLU-1-0.897-0.92239.089-0.087-0.0870.0000.0000.0000.000
105A111TYR0-0.097-0.07741.4270.0070.0070.0000.0000.0000.000
106A112LEU0-0.030-0.00340.3460.0010.0010.0000.0000.0000.000
107A113ILE0-0.016-0.01743.1990.0010.0010.0000.0000.0000.000
108A114HIS00.0210.03046.2410.0050.0050.0000.0000.0000.000
109A115PRO00.0600.01547.321-0.004-0.0040.0000.0000.0000.000
110A116GLN0-0.053-0.03145.903-0.004-0.0040.0000.0000.0000.000
111A117ALA00.0690.05343.519-0.004-0.0040.0000.0000.0000.000
112A118ARG10.8880.92141.9460.1000.1000.0000.0000.0000.000
113A119VAL00.0280.02940.877-0.006-0.0060.0000.0000.0000.000
114A120ALA00.0320.03138.910-0.006-0.0060.0000.0000.0000.000
115A121ALA00.010-0.00937.373-0.009-0.0090.0000.0000.0000.000
116A122SER0-0.033-0.00936.540-0.010-0.0100.0000.0000.0000.000
117A123VAL00.012-0.00634.205-0.009-0.0090.0000.0000.0000.000
118A124TYR0-0.030-0.02531.741-0.013-0.0130.0000.0000.0000.000
119A125ALA00.0390.00931.664-0.015-0.0150.0000.0000.0000.000
120A126GLY0-0.0010.01031.473-0.013-0.0130.0000.0000.0000.000
121A127ILE0-0.0110.00926.786-0.014-0.0140.0000.0000.0000.000
122A128PHE00.0310.00327.008-0.023-0.0230.0000.0000.0000.000
123A129LEU00.0060.00726.565-0.027-0.0270.0000.0000.0000.000
124A130ALA0-0.043-0.02026.725-0.018-0.0180.0000.0000.0000.000
125A131ILE00.0500.01621.476-0.017-0.0170.0000.0000.0000.000
126A132ALA00.0070.01522.122-0.039-0.0390.0000.0000.0000.000
127A133ILE0-0.044-0.03422.694-0.030-0.0300.0000.0000.0000.000
128A134VAL00.0090.00519.241-0.009-0.0090.0000.0000.0000.000
129A135PHE00.0560.03015.945-0.017-0.0170.0000.0000.0000.000
130A136ASN0-0.059-0.03618.199-0.025-0.0250.0000.0000.0000.000
131A137ARG10.8640.93419.8710.2770.2770.0000.0000.0000.000
132A138LEU00.0340.02113.0870.0210.0210.0000.0000.0000.000
133A139TRP00.0490.02113.505-0.021-0.0210.0000.0000.0000.000
134A140LYS10.8190.90616.1720.3540.3540.0000.0000.0000.000
135A141HIS0-0.014-0.02114.0650.0170.0170.0000.0000.0000.000
136A142ALA00.0300.02312.6290.0240.0240.0000.0000.0000.000
137A143ALA0-0.068-0.01814.208-0.001-0.0010.0000.0000.0000.000
138A144THR0-0.036-0.00916.8840.0610.0610.0000.0000.0000.000
139A154ASP-1-0.865-0.93412.806-1.279-1.2790.0000.0000.0000.000
140A155ARG10.8990.93014.6700.6860.6860.0000.0000.0000.000
141A156HIS00.0600.01817.7700.0430.0430.0000.0000.0000.000
142A157GLU-1-0.766-0.85014.380-1.212-1.2120.0000.0000.0000.000
143A158VAL00.0430.01815.2670.0510.0510.0000.0000.0000.000
144A159ASP-1-0.855-0.91217.677-0.463-0.4630.0000.0000.0000.000
145A160ALA0-0.018-0.01621.2240.0540.0540.0000.0000.0000.000
146A161ILE00.0290.02915.7880.0650.0650.0000.0000.0000.000
147A162THR0-0.034-0.01819.3950.0760.0760.0000.0000.0000.000
148A163LYS10.8150.89121.2950.5200.5200.0000.0000.0000.000
149A164GLN00.0370.01222.1640.0520.0520.0000.0000.0000.000
150A165TYR00.0350.01116.1480.0690.0690.0000.0000.0000.000
151A166ARG10.8860.95022.7240.3790.3790.0000.0000.0000.000
152A167PHE0-0.008-0.00225.9130.0270.0270.0000.0000.0000.000
153A168GLY00.0230.01925.8480.0210.0210.0000.0000.0000.000
154A169PRO00.016-0.00225.0870.0250.0250.0000.0000.0000.000
155A170GLY00.0240.02127.9170.0210.0210.0000.0000.0000.000
156A171LEU00.0350.02130.3910.0190.0190.0000.0000.0000.000
157A172TYR00.0420.00227.5600.0090.0090.0000.0000.0000.000
158A173LEU00.0180.00831.2670.0150.0150.0000.0000.0000.000
159A174VAL0-0.0260.00233.5420.0150.0150.0000.0000.0000.000
160A175ALA00.0290.00533.6010.0120.0120.0000.0000.0000.000
161A176PHE00.0030.00633.8660.0130.0130.0000.0000.0000.000
162A177ALA0-0.0060.01535.8080.0120.0120.0000.0000.0000.000
163A178LEU0-0.004-0.01438.3730.0100.0100.0000.0000.0000.000
164A179SER0-0.067-0.06538.2380.0100.0100.0000.0000.0000.000
165A180PHE0-0.005-0.00139.1970.0080.0080.0000.0000.0000.000
166A181ILE0-0.0160.00843.2060.0070.0070.0000.0000.0000.000
167A182SER0-0.014-0.02043.8110.0070.0070.0000.0000.0000.000
168A183VAL00.0910.04341.527-0.007-0.0070.0000.0000.0000.000
169A184TRP00.0170.00541.255-0.009-0.0090.0000.0000.0000.000
170A185LEU00.0190.01641.415-0.008-0.0080.0000.0000.0000.000
171A186SER0-0.0320.01137.458-0.011-0.0110.0000.0000.0000.000
172A187VAL00.0740.02136.813-0.012-0.0120.0000.0000.0000.000
173A188GLY00.0070.01436.476-0.011-0.0110.0000.0000.0000.000
174A189VAL0-0.023-0.00534.622-0.012-0.0120.0000.0000.0000.000
175A190CYS0-0.031-0.01532.676-0.018-0.0180.0000.0000.0000.000
176A191PHE00.0270.01431.881-0.018-0.0180.0000.0000.0000.000
177A192VAL00.009-0.00132.484-0.015-0.0150.0000.0000.0000.000
178A193LEU0-0.015-0.01130.116-0.019-0.0190.0000.0000.0000.000
179A194ALA00.0190.01827.935-0.028-0.0280.0000.0000.0000.000
180A195ILE00.0200.00827.584-0.027-0.0270.0000.0000.0000.000
181A196TYR0-0.050-0.02028.666-0.026-0.0260.0000.0000.0000.000
182A197PHE00.009-0.00623.608-0.023-0.0230.0000.0000.0000.000
183A198ALA00.0130.02323.981-0.049-0.0490.0000.0000.0000.000
184A199LEU0-0.027-0.01124.124-0.032-0.0320.0000.0000.0000.000
185A200ARG10.8960.95324.5300.4170.4170.0000.0000.0000.000
186A201SER0-0.039-0.02119.692-0.047-0.0470.0000.0000.0000.000
187A202ASN0-0.043-0.01819.400-0.056-0.0560.0000.0000.0000.000
188A203ALA00.0190.02118.092-0.063-0.0630.0000.0000.0000.000