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

tag_button

FMODB ID: JLQ39

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1984946.488695
FMO2-HF: Nuclear repulsion 1913044.002157
FMO2-HF: Total energy -71902.486538
FMO2-MP2: Total energy -72118.505649


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.
-11.165-6.1791.326-2.631-3.682-0.013
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 : 0.028 / q_NPA : 0.003
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-1-0.812-0.8813.679-2.171-0.4560.000-0.801-0.9140.003
4A10THR00.014-0.0052.525-5.624-3.3470.794-1.301-1.771-0.016
5A11GLY00.0950.0563.6270.3270.7900.002-0.185-0.2810.000
6A12ARG10.8330.9065.0620.3050.418-0.001-0.008-0.1030.000
7A13ILE0-0.053-0.0357.3280.1240.1240.0000.0000.0000.000
8A14GLU-1-0.821-0.9177.052-2.318-2.3180.0000.0000.0000.000
9A15ALA00.0450.0418.6900.2110.2110.0000.0000.0000.000
10A16PHE0-0.052-0.02210.4380.1430.1430.0000.0000.0000.000
11A17SER00.014-0.01912.2750.0350.0350.0000.0000.0000.000
12A18ASP-1-0.868-0.92711.337-1.003-1.0030.0000.0000.0000.000
13A19GLY0-0.029-0.01514.1600.0780.0780.0000.0000.0000.000
14A20VAL0-0.015-0.01616.7190.0470.0470.0000.0000.0000.000
15A21PHE00.0300.00115.4850.0460.0460.0000.0000.0000.000
16A22ALA00.0050.01718.4440.0360.0360.0000.0000.0000.000
17A23ILE0-0.005-0.00720.3360.0320.0320.0000.0000.0000.000
18A24ALA0-0.0050.00522.1490.0220.0220.0000.0000.0000.000
19A25ILE0-0.010-0.01121.1080.0210.0210.0000.0000.0000.000
20A26THR0-0.018-0.02724.4380.0280.0280.0000.0000.0000.000
21A27LEU00.0000.00226.5040.0210.0210.0000.0000.0000.000
22A28LEU0-0.0310.00127.2040.0150.0150.0000.0000.0000.000
23A29VAL0-0.015-0.01030.1870.0090.0090.0000.0000.0000.000
24A30LEU0-0.043-0.03331.7620.0110.0110.0000.0000.0000.000
25A31GLU-1-0.951-0.97033.403-0.135-0.1350.0000.0000.0000.000
26A32ILE00.0310.01135.3210.0070.0070.0000.0000.0000.000
27A33LYS10.8480.94637.5660.1050.1050.0000.0000.0000.000
28A34VAL00.0360.01640.639-0.001-0.0010.0000.0000.0000.000
29A35PRO0-0.014-0.00743.1620.0030.0030.0000.0000.0000.000
30A36GLN0-0.016-0.01446.6470.0070.0070.0000.0000.0000.000
31A37HIS00.0960.01648.969-0.001-0.0010.0000.0000.0000.000
32A38LYS10.9440.97652.0450.0420.0420.0000.0000.0000.000
33A39ILE00.0550.03650.0670.0010.0010.0000.0000.0000.000
34A40VAL0-0.0060.01150.9370.0000.0000.0000.0000.0000.000
35A41GLU-1-0.935-0.97152.966-0.045-0.0450.0000.0000.0000.000
36A42THR0-0.0490.00656.4230.0000.0000.0000.0000.0000.000
37A43VAL0-0.046-0.01653.3860.0000.0000.0000.0000.0000.000
38A44GLY00.0470.02154.968-0.001-0.0010.0000.0000.0000.000
39A45LEU00.016-0.01748.065-0.003-0.0030.0000.0000.0000.000
40A46VAL00.0230.01049.581-0.004-0.0040.0000.0000.0000.000
41A47SER00.0320.00949.489-0.005-0.0050.0000.0000.0000.000
42A48SER00.0430.01748.755-0.003-0.0030.0000.0000.0000.000
43A49LEU00.0040.00144.896-0.004-0.0040.0000.0000.0000.000
44A50LEU00.0050.02244.869-0.007-0.0070.0000.0000.0000.000
45A51SER0-0.055-0.02845.853-0.004-0.0040.0000.0000.0000.000
46A52LEU00.0260.00741.358-0.002-0.0020.0000.0000.0000.000
47A53TRP00.009-0.01441.645-0.009-0.0090.0000.0000.0000.000
48A54PRO0-0.011-0.01040.384-0.010-0.0100.0000.0000.0000.000
49A55SER00.0610.02238.170-0.006-0.0060.0000.0000.0000.000
50A56TYR0-0.076-0.02736.614-0.009-0.0090.0000.0000.0000.000
51A57LEU0-0.051-0.02035.786-0.012-0.0120.0000.0000.0000.000
52A58ALA00.0350.01234.704-0.014-0.0140.0000.0000.0000.000
53A59PHE00.0230.02230.332-0.017-0.0170.0000.0000.0000.000
54A60LEU00.0020.00430.949-0.019-0.0190.0000.0000.0000.000
55A61THR00.012-0.01230.320-0.017-0.0170.0000.0000.0000.000
56A62SER0-0.0030.01528.968-0.026-0.0260.0000.0000.0000.000
57A63PHE00.0260.02625.334-0.030-0.0300.0000.0000.0000.000
58A64ALA0-0.015-0.00925.375-0.031-0.0310.0000.0000.0000.000
59A65SER0-0.021-0.01324.883-0.038-0.0380.0000.0000.0000.000
60A66ILE00.008-0.01921.572-0.039-0.0390.0000.0000.0000.000
61A67LEU00.0230.02320.300-0.047-0.0470.0000.0000.0000.000
62A68VAL0-0.0260.00219.932-0.066-0.0660.0000.0000.0000.000
63A69MET0-0.078-0.02519.683-0.050-0.0500.0000.0000.0000.000
64A70TRP00.0210.02813.585-0.016-0.0160.0000.0000.0000.000
65A71VAL0-0.006-0.00615.318-0.118-0.1180.0000.0000.0000.000
66A72ASN0-0.032-0.02515.196-0.144-0.1440.0000.0000.0000.000
67A73HIS0-0.050-0.01611.241-0.034-0.0340.0000.0000.0000.000
68A74HIS0-0.007-0.0088.753-0.071-0.0710.0000.0000.0000.000
69A75ARG10.9120.97610.3230.6720.6720.0000.0000.0000.000
70A76ILE0-0.086-0.05010.895-0.157-0.1570.0000.0000.0000.000
71A77PHE0-0.044-0.0246.5590.0040.0040.0000.0000.0000.000
72A78SER0-0.058-0.0076.491-0.653-0.6530.0000.0000.0000.000
73A79LEU0-0.0100.0147.033-0.660-0.6600.0000.0000.0000.000
74A80VAL0-0.046-0.0357.302-0.135-0.1350.0000.0000.0000.000
75A81ALA00.0500.0212.620-0.648-0.2620.532-0.330-0.5880.000
76A82ARG10.8980.9414.4341.5691.601-0.001-0.006-0.0250.000
77A83THR00.0240.0145.739-0.171-0.1710.0000.0000.0000.000
78A84ASP-1-0.811-0.9028.4820.1840.1840.0000.0000.0000.000
79A85HIS00.0450.01512.177-0.085-0.0850.0000.0000.0000.000
80A86ALA0-0.017-0.00714.586-0.048-0.0480.0000.0000.0000.000
81A87PHE0-0.011-0.0038.5980.0110.0110.0000.0000.0000.000
82A88PHE00.0180.01711.981-0.055-0.0550.0000.0000.0000.000
83A89TYR00.021-0.00713.142-0.014-0.0140.0000.0000.0000.000
84A90TRP0-0.027-0.01016.149-0.002-0.0020.0000.0000.0000.000
85A91ASN00.0540.02112.942-0.082-0.0820.0000.0000.0000.000
86A92GLY00.0050.01115.0960.0040.0040.0000.0000.0000.000
87A93LEU0-0.012-0.01317.4280.0160.0160.0000.0000.0000.000
88A94LEU00.005-0.00216.4180.0200.0200.0000.0000.0000.000
89A95LEU00.0300.01215.1840.0050.0050.0000.0000.0000.000
90A96MET0-0.0220.00418.9900.0270.0270.0000.0000.0000.000
91A97LEU0-0.024-0.02522.3770.0190.0190.0000.0000.0000.000
92A98VAL00.0310.01119.5910.0140.0140.0000.0000.0000.000
93A99THR0-0.062-0.03521.8000.0240.0240.0000.0000.0000.000
94A100PHE0-0.003-0.00524.1660.0210.0210.0000.0000.0000.000
95A101VAL00.0250.01625.5610.0150.0150.0000.0000.0000.000
96A102PRO00.0240.00426.9290.0110.0110.0000.0000.0000.000
97A103PHE00.0280.03830.2040.0100.0100.0000.0000.0000.000
98A104PRO0-0.001-0.01830.7810.0080.0080.0000.0000.0000.000
99A105THR00.0060.00530.741-0.004-0.0040.0000.0000.0000.000
100A106ALA00.0220.02733.4150.0060.0060.0000.0000.0000.000
101A107LEU0-0.041-0.02036.1340.0070.0070.0000.0000.0000.000
102A108LEU0-0.057-0.02136.1320.0060.0060.0000.0000.0000.000
103A109ALA00.0260.00537.4460.0030.0030.0000.0000.0000.000
104A110GLU-1-0.959-0.96139.077-0.089-0.0890.0000.0000.0000.000
105A111TYR0-0.063-0.04741.5690.0080.0080.0000.0000.0000.000
106A112LEU0-0.032-0.00940.1050.0010.0010.0000.0000.0000.000
107A113ILE0-0.016-0.01443.1890.0010.0010.0000.0000.0000.000
108A114HIS00.0390.02946.4270.0030.0030.0000.0000.0000.000
109A115PRO00.0470.02447.313-0.004-0.0040.0000.0000.0000.000
110A116GLN0-0.038-0.03745.987-0.005-0.0050.0000.0000.0000.000
111A117ALA00.0650.05543.510-0.004-0.0040.0000.0000.0000.000
112A118ARG10.9440.95441.9370.1020.1020.0000.0000.0000.000
113A119VAL00.0230.02940.919-0.006-0.0060.0000.0000.0000.000
114A120ALA00.0290.02138.938-0.006-0.0060.0000.0000.0000.000
115A121ALA00.015-0.00737.367-0.009-0.0090.0000.0000.0000.000
116A122SER0-0.015-0.00236.528-0.010-0.0100.0000.0000.0000.000
117A123VAL00.0010.00034.300-0.010-0.0100.0000.0000.0000.000
118A124TYR0-0.050-0.05231.985-0.013-0.0130.0000.0000.0000.000
119A125ALA00.0380.00931.654-0.016-0.0160.0000.0000.0000.000
120A126GLY0-0.0100.00531.458-0.013-0.0130.0000.0000.0000.000
121A127ILE0-0.0130.00726.828-0.014-0.0140.0000.0000.0000.000
122A128PHE00.0430.01226.826-0.023-0.0230.0000.0000.0000.000
123A129LEU0-0.0050.00226.548-0.028-0.0280.0000.0000.0000.000
124A130ALA0-0.039-0.02126.709-0.019-0.0190.0000.0000.0000.000
125A131ILE00.0430.01021.545-0.018-0.0180.0000.0000.0000.000
126A132ALA00.0040.01622.107-0.040-0.0400.0000.0000.0000.000
127A133ILE0-0.045-0.03422.672-0.031-0.0310.0000.0000.0000.000
128A134VAL00.0070.00019.225-0.010-0.0100.0000.0000.0000.000
129A135PHE00.0480.02815.959-0.022-0.0220.0000.0000.0000.000
130A136ASN0-0.084-0.05018.175-0.034-0.0340.0000.0000.0000.000
131A137ARG10.8470.93219.8470.2970.2970.0000.0000.0000.000
132A138LEU00.0430.02713.2610.0200.0200.0000.0000.0000.000
133A139TRP00.0520.02413.638-0.025-0.0250.0000.0000.0000.000
134A140LYS10.8530.92416.1450.3510.3510.0000.0000.0000.000
135A141HIS0-0.014-0.02314.2320.0240.0240.0000.0000.0000.000
136A142ALA00.0270.02312.6250.0250.0250.0000.0000.0000.000
137A143ALA0-0.065-0.01614.184-0.006-0.0060.0000.0000.0000.000
138A144THR0-0.041-0.01216.8220.0640.0640.0000.0000.0000.000
139A154ASP-1-0.867-0.92812.577-1.470-1.4700.0000.0000.0000.000
140A155ARG10.9370.94314.3970.7660.7660.0000.0000.0000.000
141A156HIS00.0730.02917.4890.0400.0400.0000.0000.0000.000
142A157GLU-1-0.851-0.91614.134-1.326-1.3260.0000.0000.0000.000
143A158VAL00.0310.01415.3950.0470.0470.0000.0000.0000.000
144A159ASP-1-0.926-0.96417.733-0.538-0.5380.0000.0000.0000.000
145A160ALA0-0.066-0.04021.1630.0590.0590.0000.0000.0000.000
146A161ILE00.0280.02415.6850.0690.0690.0000.0000.0000.000
147A162THR0-0.032-0.01919.1950.0820.0820.0000.0000.0000.000
148A163LYS10.9050.94921.2460.5300.5300.0000.0000.0000.000
149A164GLN00.0610.02021.8470.0450.0450.0000.0000.0000.000
150A165TYR00.0380.01016.5170.0560.0560.0000.0000.0000.000
151A166ARG10.8940.94722.6840.3910.3910.0000.0000.0000.000
152A167PHE0-0.024-0.00625.8720.0290.0290.0000.0000.0000.000
153A168GLY00.0190.01625.8140.0210.0210.0000.0000.0000.000
154A169PRO00.013-0.00324.9920.0270.0270.0000.0000.0000.000
155A170GLY00.0300.02727.8890.0220.0220.0000.0000.0000.000
156A171LEU00.0360.02430.3550.0190.0190.0000.0000.0000.000
157A172TYR00.0430.00127.3820.0100.0100.0000.0000.0000.000
158A173LEU00.0060.00231.2400.0160.0160.0000.0000.0000.000
159A174VAL0-0.0250.00633.5170.0160.0160.0000.0000.0000.000
160A175ALA00.0300.00433.6480.0120.0120.0000.0000.0000.000
161A176PHE00.0180.01933.8640.0130.0130.0000.0000.0000.000
162A177ALA0-0.0010.03535.7890.0130.0130.0000.0000.0000.000
163A178LEU0-0.010-0.01637.9200.0100.0100.0000.0000.0000.000
164A179SER0-0.079-0.09038.2280.0100.0100.0000.0000.0000.000
165A180PHE0-0.016-0.01039.3120.0080.0080.0000.0000.0000.000
166A181ILE0-0.040-0.00643.1890.0070.0070.0000.0000.0000.000
167A182SER0-0.025-0.02543.7870.0060.0060.0000.0000.0000.000
168A183VAL00.0790.03241.496-0.007-0.0070.0000.0000.0000.000
169A184TRP00.0210.00841.234-0.009-0.0090.0000.0000.0000.000
170A185LEU00.0130.01341.399-0.008-0.0080.0000.0000.0000.000
171A186SER0-0.0330.00737.478-0.011-0.0110.0000.0000.0000.000
172A187VAL00.0640.01036.792-0.012-0.0120.0000.0000.0000.000
173A188GLY00.0090.01436.470-0.011-0.0110.0000.0000.0000.000
174A189VAL0-0.031-0.00434.342-0.012-0.0120.0000.0000.0000.000
175A190CYS0-0.007-0.00732.656-0.019-0.0190.0000.0000.0000.000
176A191PHE00.0220.01731.876-0.018-0.0180.0000.0000.0000.000
177A192VAL00.007-0.00232.480-0.015-0.0150.0000.0000.0000.000
178A193LEU0-0.013-0.01030.258-0.020-0.0200.0000.0000.0000.000
179A194ALA00.0260.02127.934-0.028-0.0280.0000.0000.0000.000
180A195ILE00.0180.00927.581-0.027-0.0270.0000.0000.0000.000
181A196TYR0-0.049-0.02428.664-0.027-0.0270.0000.0000.0000.000
182A197PHE00.005-0.00923.503-0.025-0.0250.0000.0000.0000.000
183A198ALA00.0130.01123.982-0.048-0.0480.0000.0000.0000.000
184A199LEU0-0.028-0.01424.123-0.032-0.0320.0000.0000.0000.000
185A200ARG10.8930.95124.4980.4250.4250.0000.0000.0000.000
186A201SER0-0.062-0.03219.652-0.052-0.0520.0000.0000.0000.000
187A202ASN0-0.081-0.04119.403-0.046-0.0460.0000.0000.0000.000
188A203ALA00.0550.04318.097-0.058-0.0580.0000.0000.0000.000