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: LZNJ9

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1985818.740271
FMO2-HF: Nuclear repulsion 1913914.220735
FMO2-HF: Total energy -71904.519536
FMO2-MP2: Total energy -72120.075609


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.
-7.65-3.482.889-3.02-4.039-0.012
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 : 0.015 / q_NPA : -0.008
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-1-0.761-0.8353.627-2.253-0.690-0.004-0.693-0.8660.002
4A10THR00.0200.0042.553-4.711-2.5920.786-1.213-1.692-0.014
5A11GLY00.0840.0463.6770.9371.2900.002-0.144-0.2110.000
6A12ARG10.7810.8525.2820.5490.647-0.001-0.005-0.0930.000
7A13ILE0-0.056-0.0317.5200.2120.2120.0000.0000.0000.000
8A14GLU-1-0.819-0.9016.688-2.023-2.0230.0000.0000.0000.000
9A15ALA00.0440.0209.0140.2160.2160.0000.0000.0000.000
10A16PHE0-0.043-0.01410.9200.1440.1440.0000.0000.0000.000
11A17SER00.015-0.01012.3770.0260.0260.0000.0000.0000.000
12A18ASP-1-0.832-0.90912.622-0.688-0.6880.0000.0000.0000.000
13A19GLY00.0040.00614.6940.0660.0660.0000.0000.0000.000
14A20VAL0-0.026-0.01716.9570.0390.0390.0000.0000.0000.000
15A21PHE00.019-0.00415.6640.0280.0280.0000.0000.0000.000
16A22ALA00.0130.01218.7030.0270.0270.0000.0000.0000.000
17A23ILE0-0.0020.01120.5700.0270.0270.0000.0000.0000.000
18A24ALA0-0.015-0.00622.2650.0150.0150.0000.0000.0000.000
19A25ILE0-0.023-0.01921.0490.0130.0130.0000.0000.0000.000
20A26THR0-0.039-0.04024.5390.0210.0210.0000.0000.0000.000
21A27LEU0-0.002-0.00526.3720.0150.0150.0000.0000.0000.000
22A28LEU0-0.039-0.00327.4610.0100.0100.0000.0000.0000.000
23A29VAL0-0.007-0.00830.3080.0060.0060.0000.0000.0000.000
24A30LEU0-0.025-0.01231.6430.0080.0080.0000.0000.0000.000
25A31GLU-1-0.799-0.87834.180-0.088-0.0880.0000.0000.0000.000
26A32ILE0-0.013-0.00134.9660.0030.0030.0000.0000.0000.000
27A33LYS10.7900.89038.1120.0850.0850.0000.0000.0000.000
28A34VAL00.0300.01741.316-0.001-0.0010.0000.0000.0000.000
29A35PRO00.0020.00843.7050.0020.0020.0000.0000.0000.000
30A36GLN00.0480.01647.2520.0060.0060.0000.0000.0000.000
31A37HIS00.0580.00249.384-0.002-0.0020.0000.0000.0000.000
32A38LYS10.9320.96852.5350.0290.0290.0000.0000.0000.000
33A39ILE00.0240.03450.4890.0000.0000.0000.0000.0000.000
34A40VAL0-0.0020.00351.0160.0000.0000.0000.0000.0000.000
35A41GLU-1-0.979-0.98753.083-0.028-0.0280.0000.0000.0000.000
36A42THR0-0.005-0.00656.638-0.001-0.0010.0000.0000.0000.000
37A43VAL0-0.027-0.00753.573-0.001-0.0010.0000.0000.0000.000
38A44GLY00.0600.05955.099-0.001-0.0010.0000.0000.0000.000
39A45LEU00.0240.01548.501-0.002-0.0020.0000.0000.0000.000
40A46VAL00.0210.00649.886-0.003-0.0030.0000.0000.0000.000
41A47SER00.010-0.01049.773-0.004-0.0040.0000.0000.0000.000
42A48SER00.004-0.01649.455-0.003-0.0030.0000.0000.0000.000
43A49LEU00.0240.01544.990-0.003-0.0030.0000.0000.0000.000
44A50LEU00.0070.01245.275-0.005-0.0050.0000.0000.0000.000
45A51SER0-0.082-0.05846.312-0.004-0.0040.0000.0000.0000.000
46A52LEU00.0280.01742.278-0.002-0.0020.0000.0000.0000.000
47A53TRP00.000-0.00141.778-0.008-0.0080.0000.0000.0000.000
48A54PRO0-0.005-0.00440.706-0.008-0.0080.0000.0000.0000.000
49A55SER00.013-0.01738.239-0.006-0.0060.0000.0000.0000.000
50A56TYR0-0.077-0.04836.761-0.007-0.0070.0000.0000.0000.000
51A57LEU0-0.022-0.00136.002-0.009-0.0090.0000.0000.0000.000
52A58ALA00.0530.02434.992-0.011-0.0110.0000.0000.0000.000
53A59PHE00.0160.03230.606-0.014-0.0140.0000.0000.0000.000
54A60LEU00.0090.00931.188-0.014-0.0140.0000.0000.0000.000
55A61THR0-0.007-0.02830.527-0.013-0.0130.0000.0000.0000.000
56A62SER00.0060.00429.048-0.020-0.0200.0000.0000.0000.000
57A63PHE00.0090.00826.617-0.023-0.0230.0000.0000.0000.000
58A64ALA0-0.0070.00225.586-0.022-0.0220.0000.0000.0000.000
59A65SER0-0.002-0.00824.955-0.030-0.0300.0000.0000.0000.000
60A66ILE0-0.001-0.00721.781-0.036-0.0360.0000.0000.0000.000
61A67LEU00.0320.02520.829-0.040-0.0400.0000.0000.0000.000
62A68VAL0-0.024-0.00620.097-0.051-0.0510.0000.0000.0000.000
63A69MET0-0.063-0.02119.974-0.049-0.0490.0000.0000.0000.000
64A70TRP0-0.026-0.00713.817-0.023-0.0230.0000.0000.0000.000
65A71VAL00.0100.00415.429-0.096-0.0960.0000.0000.0000.000
66A72ASN0-0.070-0.04015.390-0.118-0.1180.0000.0000.0000.000
67A73HIS00.0130.00512.048-0.053-0.0530.0000.0000.0000.000
68A74HIS0-0.011-0.0119.460-0.036-0.0360.0000.0000.0000.000
69A75ARG10.8120.89210.3570.5860.5860.0000.0000.0000.000
70A76ILE0-0.088-0.04411.112-0.116-0.1160.0000.0000.0000.000
71A77PHE0-0.049-0.0287.018-0.057-0.0570.0000.0000.0000.000
72A78SER0-0.020-0.0146.262-0.690-0.6900.0000.0000.0000.000
73A79LEU0-0.034-0.0086.786-0.591-0.5910.0000.0000.0000.000
74A80VAL0-0.041-0.0327.193-0.002-0.0020.0000.0000.0000.000
75A81ALA00.0290.0152.155-0.490-0.6482.106-0.891-1.0570.000
76A82ARG10.9040.9553.8951.7311.9260.000-0.074-0.1200.000
77A83THR00.0360.0205.499-0.135-0.1350.0000.0000.0000.000
78A84ASP-1-0.817-0.9178.1940.0530.0530.0000.0000.0000.000
79A85HIS00.0360.01811.830-0.095-0.0950.0000.0000.0000.000
80A86ALA0-0.010-0.00314.479-0.029-0.0290.0000.0000.0000.000
81A87PHE0-0.0120.0048.3600.0360.0360.0000.0000.0000.000
82A88PHE00.0340.01511.557-0.032-0.0320.0000.0000.0000.000
83A89TYR00.0360.00613.0170.0030.0030.0000.0000.0000.000
84A90TRP0-0.016-0.01116.1040.0170.0170.0000.0000.0000.000
85A91ASN00.015-0.00512.997-0.068-0.0680.0000.0000.0000.000
86A92GLY00.0080.01215.1280.0160.0160.0000.0000.0000.000
87A93LEU0-0.018-0.01417.5250.0220.0220.0000.0000.0000.000
88A94LEU0-0.014-0.00316.6770.0240.0240.0000.0000.0000.000
89A95LEU00.0400.02215.1550.0190.0190.0000.0000.0000.000
90A96MET0-0.0150.01519.3200.0310.0310.0000.0000.0000.000
91A97LEU0-0.024-0.01622.5300.0190.0190.0000.0000.0000.000
92A98VAL00.004-0.01220.0900.0170.0170.0000.0000.0000.000
93A99THR0-0.033-0.04222.0600.0220.0220.0000.0000.0000.000
94A100PHE0-0.0080.00724.5530.0210.0210.0000.0000.0000.000
95A101VAL00.000-0.00125.8470.0120.0120.0000.0000.0000.000
96A102PRO00.0550.01627.2630.0080.0080.0000.0000.0000.000
97A103PHE00.0000.02130.4550.0110.0110.0000.0000.0000.000
98A104PRO00.000-0.01531.1190.0060.0060.0000.0000.0000.000
99A105THR0-0.021-0.02131.3210.0010.0010.0000.0000.0000.000
100A106ALA00.0170.01433.6260.0050.0050.0000.0000.0000.000
101A107LEU0-0.062-0.02136.2020.0060.0060.0000.0000.0000.000
102A108LEU0-0.041-0.02636.3050.0040.0040.0000.0000.0000.000
103A109ALA0-0.004-0.00737.3930.0030.0030.0000.0000.0000.000
104A110GLU-1-0.867-0.90339.177-0.067-0.0670.0000.0000.0000.000
105A111TYR0-0.067-0.06541.5880.0060.0060.0000.0000.0000.000
106A112LEU0-0.0290.00240.5490.0010.0010.0000.0000.0000.000
107A113ILE0-0.017-0.01343.255-0.001-0.0010.0000.0000.0000.000
108A114HIS00.0200.03046.4570.0040.0040.0000.0000.0000.000
109A115PRO00.024-0.00447.562-0.004-0.0040.0000.0000.0000.000
110A116GLN0-0.014-0.01146.169-0.004-0.0040.0000.0000.0000.000
111A117ALA00.0230.02643.618-0.004-0.0040.0000.0000.0000.000
112A118ARG10.8670.91042.1490.0870.0870.0000.0000.0000.000
113A119VAL00.0350.02840.902-0.007-0.0070.0000.0000.0000.000
114A120ALA00.0380.03539.053-0.006-0.0060.0000.0000.0000.000
115A121ALA00.0210.00037.483-0.008-0.0080.0000.0000.0000.000
116A122SER0-0.060-0.02636.685-0.009-0.0090.0000.0000.0000.000
117A123VAL00.026-0.00334.002-0.010-0.0100.0000.0000.0000.000
118A124TYR0-0.022-0.00631.601-0.012-0.0120.0000.0000.0000.000
119A125ALA00.0330.00631.875-0.014-0.0140.0000.0000.0000.000
120A126GLY0-0.003-0.00231.450-0.015-0.0150.0000.0000.0000.000
121A127ILE0-0.0180.00226.895-0.012-0.0120.0000.0000.0000.000
122A128PHE00.0440.01426.931-0.021-0.0210.0000.0000.0000.000
123A129LEU0-0.0070.00426.591-0.025-0.0250.0000.0000.0000.000
124A130ALA0-0.016-0.00626.972-0.017-0.0170.0000.0000.0000.000
125A131ILE00.0320.01321.518-0.019-0.0190.0000.0000.0000.000
126A132ALA00.0040.01022.160-0.038-0.0380.0000.0000.0000.000
127A133ILE0-0.040-0.03022.987-0.028-0.0280.0000.0000.0000.000
128A134VAL00.0110.00619.356-0.016-0.0160.0000.0000.0000.000
129A135PHE00.0460.02316.186-0.022-0.0220.0000.0000.0000.000
130A136ASN0-0.041-0.02818.418-0.031-0.0310.0000.0000.0000.000
131A137ARG10.8540.93520.2620.2890.2890.0000.0000.0000.000
132A138LEU00.0370.02413.0940.0110.0110.0000.0000.0000.000
133A139TRP00.0350.01313.193-0.019-0.0190.0000.0000.0000.000
134A140LYS10.8450.91416.3600.3600.3600.0000.0000.0000.000
135A141HIS0-0.001-0.00113.722-0.004-0.0040.0000.0000.0000.000
136A142ALA00.0180.01712.3460.0120.0120.0000.0000.0000.000
137A143ALA0-0.054-0.01613.746-0.041-0.0410.0000.0000.0000.000
138A144THR0-0.079-0.03316.5300.0750.0750.0000.0000.0000.000
139A154ASP-1-0.810-0.91512.086-1.006-1.0060.0000.0000.0000.000
140A155ARG10.8760.90514.1130.7130.7130.0000.0000.0000.000
141A156HIS00.0390.02017.4100.0730.0730.0000.0000.0000.000
142A157GLU-1-0.803-0.86213.879-1.100-1.1000.0000.0000.0000.000
143A158VAL00.0300.01015.0000.0630.0630.0000.0000.0000.000
144A159ASP-1-0.813-0.87417.462-0.466-0.4660.0000.0000.0000.000
145A160ALA0-0.008-0.00620.5600.0610.0610.0000.0000.0000.000
146A161ILE00.0280.01815.8110.0720.0720.0000.0000.0000.000
147A162THR0-0.032-0.02919.3130.0770.0770.0000.0000.0000.000
148A163LYS10.7990.89521.2350.5120.5120.0000.0000.0000.000
149A164GLN00.0260.00522.2150.0540.0540.0000.0000.0000.000
150A165TYR00.014-0.00917.0220.0270.0270.0000.0000.0000.000
151A166ARG10.9030.96822.9380.3770.3770.0000.0000.0000.000
152A167PHE00.001-0.00426.2550.0230.0230.0000.0000.0000.000
153A168GLY00.0400.02325.9180.0210.0210.0000.0000.0000.000
154A169PRO0-0.007-0.01325.0760.0230.0230.0000.0000.0000.000
155A170GLY00.0200.02127.7830.0200.0200.0000.0000.0000.000
156A171LEU00.0160.00630.5990.0170.0170.0000.0000.0000.000
157A172TYR00.0590.01127.4990.0090.0090.0000.0000.0000.000
158A173LEU0-0.0010.00531.3670.0150.0150.0000.0000.0000.000
159A174VAL0-0.0200.00033.5400.0140.0140.0000.0000.0000.000
160A175ALA00.0210.00733.6450.0110.0110.0000.0000.0000.000
161A176PHE00.0110.01034.1290.0110.0110.0000.0000.0000.000
162A177ALA0-0.0010.01336.0680.0110.0110.0000.0000.0000.000
163A178LEU00.002-0.01238.6240.0090.0090.0000.0000.0000.000
164A179SER0-0.055-0.03638.6400.0090.0090.0000.0000.0000.000
165A180PHE00.0060.00239.1690.0080.0080.0000.0000.0000.000
166A181ILE00.0030.02643.5440.0070.0070.0000.0000.0000.000
167A182SER0-0.038-0.03243.9720.0070.0070.0000.0000.0000.000
168A183VAL00.0760.03742.110-0.007-0.0070.0000.0000.0000.000
169A184TRP00.0390.01341.286-0.007-0.0070.0000.0000.0000.000
170A185LEU00.0260.02441.376-0.006-0.0060.0000.0000.0000.000
171A186SER0-0.0320.00137.776-0.009-0.0090.0000.0000.0000.000
172A187VAL00.0610.02236.902-0.011-0.0110.0000.0000.0000.000
173A188GLY00.0240.01736.500-0.008-0.0080.0000.0000.0000.000
174A189VAL0-0.011-0.00935.006-0.009-0.0090.0000.0000.0000.000
175A190CYS0-0.031-0.01832.846-0.016-0.0160.0000.0000.0000.000
176A191PHE00.0140.01231.867-0.015-0.0150.0000.0000.0000.000
177A192VAL00.008-0.00432.393-0.012-0.0120.0000.0000.0000.000
178A193LEU0-0.031-0.01629.991-0.016-0.0160.0000.0000.0000.000
179A194ALA00.0340.02727.873-0.024-0.0240.0000.0000.0000.000
180A195ILE00.0120.00827.582-0.021-0.0210.0000.0000.0000.000
181A196TYR0-0.032-0.01428.583-0.023-0.0230.0000.0000.0000.000
182A197PHE00.005-0.01123.795-0.021-0.0210.0000.0000.0000.000
183A198ALA00.0280.04123.953-0.042-0.0420.0000.0000.0000.000
184A199LEU0-0.025-0.00923.925-0.028-0.0280.0000.0000.0000.000
185A200ARG10.8870.93024.4320.3550.3550.0000.0000.0000.000
186A201SER0-0.011-0.02119.928-0.052-0.0520.0000.0000.0000.000
187A202ASN0-0.082-0.01819.320-0.047-0.0470.0000.0000.0000.000
188A203ALA00.0230.02317.968-0.036-0.0360.0000.0000.0000.000