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: R52R8

Calculation Name: 2YVS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YVS

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SM78

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2544352.214172
FMO2-HF: Nuclear repulsion 2462086.912256
FMO2-HF: Total energy -82265.301916
FMO2-MP2: Total energy -82513.784606


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-19.501-11.80621.009-8.234-20.471-0.027
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : -0.012
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].
3A3VAL00.005-0.0093.0770.6722.6060.023-0.691-1.2660.000
4A4HIS0-0.0070.0105.076-0.281-0.201-0.001-0.008-0.0700.000
5A5ALA00.020-0.0128.7500.1530.1530.0000.0000.0000.000
6A6ALA0-0.005-0.01010.4060.0280.0280.0000.0000.0000.000
7A7ASP-1-0.902-0.93812.4670.0370.0370.0000.0000.0000.000
8A8GLN0-0.084-0.04411.6160.0160.0160.0000.0000.0000.000
9A9TYR0-0.011-0.0058.2590.0920.0920.0000.0000.0000.000
10A10LEU00.002-0.0082.414-1.256-0.7102.385-0.629-2.3020.001
11A11VAL00.0040.0154.098-0.1180.186-0.001-0.075-0.2280.000
12A12ALA00.0230.0052.413-3.723-2.2274.340-2.444-3.392-0.021
13A13PRO00.0850.0372.485-1.102-0.4130.790-0.093-1.3850.000
14A14GLY0-0.031-0.0275.6360.2670.2670.0000.0000.0000.000
15A15GLU-1-0.998-1.0177.313-0.708-0.7080.0000.0000.0000.000
16A16ALA00.0000.0352.529-0.477-0.0900.565-0.232-0.720-0.001
17A17ASP-1-0.868-0.9664.448-0.0290.074-0.001-0.008-0.0940.000
18A18LEU0-0.060-0.0574.157-0.413-0.288-0.001-0.030-0.0940.000
19A19LEU0-0.010-0.0246.0710.4740.4740.0000.0000.0000.000
20A20GLU-1-0.867-0.8832.151-5.112-3.3121.792-1.505-2.088-0.016
21A21VAL0-0.021-0.0182.491-0.9380.4563.406-1.465-3.336-0.001
22A22HIS0-0.046-0.0343.1262.5091.9210.0460.924-0.3820.000
23A23ALA0-0.014-0.0016.1420.1000.1000.0000.0000.0000.000
24A24ARG10.8920.9552.165-5.996-6.6997.667-1.947-5.0180.011
25A25LEU00.0060.0015.249-0.870-0.742-0.001-0.031-0.0960.000
26A26ALA00.0110.0347.394-0.713-0.7130.0000.0000.0000.000
27A27GLY0-0.012-0.00710.499-0.049-0.0490.0000.0000.0000.000
28A28THR0-0.029-0.0388.659-0.166-0.1660.0000.0000.0000.000
29A29GLY0-0.058-0.01812.059-0.140-0.1400.0000.0000.0000.000
30A30LEU0-0.026-0.01510.216-0.158-0.1580.0000.0000.0000.000
31A31PHE0-0.0060.00110.5190.2090.2090.0000.0000.0000.000
32A32PRO00.0500.0367.551-0.100-0.1000.0000.0000.0000.000
33A33PRO0-0.034-0.0169.608-0.256-0.2560.0000.0000.0000.000
34A34PHE00.014-0.0306.120-0.142-0.1420.0000.0000.0000.000
35A35PRO00.0280.02911.4420.1360.1360.0000.0000.0000.000
36A36PRO0-0.0040.01010.8770.0310.0310.0000.0000.0000.000
37A37VAL00.002-0.01311.588-0.093-0.0930.0000.0000.0000.000
38A38GLU-1-0.771-0.8738.3350.0150.0150.0000.0000.0000.000
39A39LEU0-0.003-0.01611.216-0.012-0.0120.0000.0000.0000.000
40A40PRO00.0230.00811.864-0.036-0.0360.0000.0000.0000.000
41A41GLY0-0.015-0.02112.6570.0430.0430.0000.0000.0000.000
42A42GLY00.1050.0828.388-0.039-0.0390.0000.0000.0000.000
43A43VAL0-0.003-0.0125.4730.1670.1670.0000.0000.0000.000
44A44GLY00.002-0.0068.3340.0330.0330.0000.0000.0000.000
45A45GLY0-0.028-0.01210.6970.0120.0120.0000.0000.0000.000
46A46LEU0-0.0060.00410.4090.0010.0010.0000.0000.0000.000
47A47VAL00.000-0.00211.166-0.001-0.0010.0000.0000.0000.000
48A48ALA0-0.005-0.00613.875-0.027-0.0270.0000.0000.0000.000
49A49ARG10.9360.99313.446-0.166-0.1660.0000.0000.0000.000
50A50GLY00.0130.00217.003-0.005-0.0050.0000.0000.0000.000
51A51GLY0-0.039-0.01214.9700.0150.0150.0000.0000.0000.000
52A52PHE00.010-0.00614.525-0.052-0.0520.0000.0000.0000.000
53A53ALA00.0190.00016.1810.0580.0580.0000.0000.0000.000
54A54GLN0-0.0420.00217.7580.0240.0240.0000.0000.0000.000
55A55THR0-0.015-0.01619.250-0.032-0.0320.0000.0000.0000.000
56A56PHE0-0.063-0.02216.084-0.026-0.0260.0000.0000.0000.000
57A57PHE00.032-0.00921.2950.0010.0010.0000.0000.0000.000
58A58PHE00.0390.01413.021-0.004-0.0040.0000.0000.0000.000
59A59PRO00.0520.02016.7940.0380.0380.0000.0000.0000.000
60A60ALA0-0.0140.00517.131-0.008-0.0080.0000.0000.0000.000
61A61GLU-1-0.793-0.86413.9600.5280.5280.0000.0000.0000.000
62A62VAL0-0.0050.01412.0460.1200.1200.0000.0000.0000.000
63A63LEU0-0.004-0.01411.771-0.097-0.0970.0000.0000.0000.000
64A64GLY00.011-0.01012.036-0.089-0.0890.0000.0000.0000.000
65A65LEU0-0.0240.02311.1820.0880.0880.0000.0000.0000.000
66A66THR00.0250.01711.258-0.031-0.0310.0000.0000.0000.000
67A67PHE00.0140.02212.539-0.016-0.0160.0000.0000.0000.000
68A68ARG10.9831.00015.1990.2290.2290.0000.0000.0000.000
69A69THR0-0.008-0.01617.5400.0140.0140.0000.0000.0000.000
70A70PRO00.0390.00621.075-0.018-0.0180.0000.0000.0000.000
71A71LYS10.8300.91123.5450.0810.0810.0000.0000.0000.000
72A72GLY00.0130.01821.968-0.001-0.0010.0000.0000.0000.000
73A73ARG10.8870.95521.1390.1050.1050.0000.0000.0000.000
74A74ARG10.8820.92713.9540.4150.4150.0000.0000.0000.000
75A75VAL0-0.025-0.01117.4340.0050.0050.0000.0000.0000.000
76A76ARG10.9310.97510.5170.4360.4360.0000.0000.0000.000
77A77ALA00.001-0.01015.1100.0200.0200.0000.0000.0000.000
78A78GLY0-0.029-0.02314.9320.0080.0080.0000.0000.0000.000
79A79GLY00.019-0.00713.726-0.046-0.0460.0000.0000.0000.000
80A80VAL0-0.019-0.02012.899-0.005-0.0050.0000.0000.0000.000
81A81VAL00.0120.01815.751-0.024-0.0240.0000.0000.0000.000
82A82VAL00.0550.02817.710-0.021-0.0210.0000.0000.0000.000
83A83LYS10.8910.95517.675-0.011-0.0110.0000.0000.0000.000
84A84ASN0-0.023-0.01319.439-0.013-0.0130.0000.0000.0000.000
85A85VAL00.0440.02223.1750.0080.0080.0000.0000.0000.000
86A86GLN0-0.056-0.02623.268-0.008-0.0080.0000.0000.0000.000
87A87GLY00.0900.04324.1350.0080.0080.0000.0000.0000.000
88A88TYR0-0.038-0.02124.279-0.006-0.0060.0000.0000.0000.000
89A89ASP-1-0.781-0.86920.6720.0860.0860.0000.0000.0000.000
90A90LEU00.026-0.00219.9140.0070.0070.0000.0000.0000.000
91A91VAL0-0.0110.00115.592-0.009-0.0090.0000.0000.0000.000
92A92ARG10.8230.87317.209-0.155-0.1550.0000.0000.0000.000
93A93LEU0-0.0500.01320.1280.0000.0000.0000.0000.0000.000
94A94PHE00.0000.00015.211-0.005-0.0050.0000.0000.0000.000
95A95VAL0-0.0040.00815.6590.0080.0080.0000.0000.0000.000
96A96GLY00.0230.01418.062-0.006-0.0060.0000.0000.0000.000
97A97SER0-0.091-0.05619.660-0.024-0.0240.0000.0000.0000.000
98A98PHE00.001-0.02719.660-0.018-0.0180.0000.0000.0000.000
99A99GLY00.0290.02919.127-0.012-0.0120.0000.0000.0000.000
100A100LEU0-0.039-0.00119.961-0.022-0.0220.0000.0000.0000.000
101A101LEU00.010-0.01721.159-0.012-0.0120.0000.0000.0000.000
102A102GLY0-0.020-0.00919.644-0.019-0.0190.0000.0000.0000.000
103A103ARG10.9510.97810.6940.4300.4300.0000.0000.0000.000
104A104ALA00.0060.00711.762-0.031-0.0310.0000.0000.0000.000
105A105GLU-1-0.843-0.91910.905-0.471-0.4710.0000.0000.0000.000
106A106GLU-1-0.876-0.9416.219-1.039-1.0390.0000.0000.0000.000
107A107VAL0-0.018-0.0056.8700.0510.0510.0000.0000.0000.000
108A108VAL00.0110.0086.6220.1220.1220.0000.0000.0000.000
109A109LEU0-0.018-0.0177.503-0.107-0.1070.0000.0000.0000.000
110A110ARG10.9480.9759.032-0.406-0.4060.0000.0000.0000.000
111A111LEU0-0.0170.0067.3320.1480.1480.0000.0000.0000.000
112A112ARG10.7570.84611.415-0.750-0.7500.0000.0000.0000.000
113A113PRO00.0350.02214.0180.0960.0960.0000.0000.0000.000
114A114GLY0-0.029-0.02916.111-0.057-0.0570.0000.0000.0000.000
115A115ARG10.9140.95416.977-0.435-0.4350.0000.0000.0000.000
116A116ALA00.0320.02419.335-0.029-0.0290.0000.0000.0000.000
117A117GLN00.0500.01614.4250.0300.0300.0000.0000.0000.000
118A118ALA00.016-0.00318.983-0.038-0.0380.0000.0000.0000.000
119A119PHE0-0.0110.00816.4560.0290.0290.0000.0000.0000.000
120A120LEU00.0220.03219.440-0.015-0.0150.0000.0000.0000.000
121A121ARG10.8560.92422.566-0.163-0.1630.0000.0000.0000.000
122A122ARG10.9110.96124.743-0.177-0.1770.0000.0000.0000.000
123A123PRO00.0680.04028.2510.0040.0040.0000.0000.0000.000
124A124PHE0-0.035-0.00928.6550.0030.0030.0000.0000.0000.000
125A125SER00.018-0.00130.438-0.006-0.0060.0000.0000.0000.000
126A126GLY00.0350.01832.295-0.008-0.0080.0000.0000.0000.000
127A127SER0-0.069-0.02932.087-0.003-0.0030.0000.0000.0000.000
128A128PHE00.0030.00025.2240.0050.0050.0000.0000.0000.000
129A129PRO0-0.0080.01528.789-0.006-0.0060.0000.0000.0000.000
130A130ARG10.9610.96829.695-0.142-0.1420.0000.0000.0000.000
131A131LEU0-0.010-0.00427.506-0.006-0.0060.0000.0000.0000.000
132A132VAL0-0.0160.01529.8940.0040.0040.0000.0000.0000.000
133A133PRO00.023-0.00427.080-0.008-0.0080.0000.0000.0000.000
134A134THR00.0200.00325.124-0.001-0.0010.0000.0000.0000.000
135A135PRO0-0.0020.01521.9580.0160.0160.0000.0000.0000.000
136A136ARG10.8890.95318.163-0.504-0.5040.0000.0000.0000.000
137A137PHE0-0.003-0.00514.6140.0240.0240.0000.0000.0000.000
138A138LEU0-0.004-0.01319.348-0.012-0.0120.0000.0000.0000.000
139A139PHE0-0.032-0.02017.7590.0010.0010.0000.0000.0000.000
140A140ALA00.0370.02622.2390.0020.0020.0000.0000.0000.000
141A141LEU0-0.028-0.02920.3400.0010.0010.0000.0000.0000.000
142A142GLU-1-0.915-0.95223.9580.0930.0930.0000.0000.0000.000
143A143ASP-1-0.900-0.94224.3980.1400.1400.0000.0000.0000.000
144A144GLU-1-0.949-0.98427.1080.0640.0640.0000.0000.0000.000
145A145GLU-1-0.964-0.98029.1400.1170.1170.0000.0000.0000.000
146A146GLY00.0500.03130.007-0.005-0.0050.0000.0000.0000.000
147A147PRO0-0.037-0.01828.3160.0090.0090.0000.0000.0000.000
148A148TRP00.0430.02425.3840.0090.0090.0000.0000.0000.000
149A149LEU0-0.042-0.03425.4640.0040.0040.0000.0000.0000.000
150A150TYR00.0510.01020.233-0.001-0.0010.0000.0000.0000.000
151A151ALA0-0.002-0.00421.4570.0000.0000.0000.0000.0000.000
152A152TYR0-0.037-0.01113.8010.0430.0430.0000.0000.0000.000
153A153HIS00.0330.01218.8060.0290.0290.0000.0000.0000.000
154A154PHE00.0350.01214.9330.0170.0170.0000.0000.0000.000
155A155GLY00.008-0.00218.674-0.027-0.0270.0000.0000.0000.000
156A156HIS00.0210.01220.2770.0300.0300.0000.0000.0000.000
157A157PRO00.0650.01423.080-0.006-0.0060.0000.0000.0000.000
158A158LYS10.9880.99324.655-0.191-0.1910.0000.0000.0000.000
159A159GLU-1-0.965-0.98524.4130.2430.2430.0000.0000.0000.000
160A160VAL0-0.054-0.03421.290-0.009-0.0090.0000.0000.0000.000
161A161GLU-1-0.921-0.95024.4470.2230.2230.0000.0000.0000.000
162A162ARG10.9930.99127.602-0.200-0.2000.0000.0000.0000.000
163A163PHE0-0.027-0.00823.136-0.007-0.0070.0000.0000.0000.000
164A164ARG10.8880.93221.702-0.335-0.3350.0000.0000.0000.000
165A165GLU-1-0.945-0.95427.4390.1540.1540.0000.0000.0000.000
166A166ALA0-0.022-0.00330.342-0.010-0.0100.0000.0000.0000.000
167A167PHE0-0.111-0.05425.812-0.009-0.0090.0000.0000.0000.000
168A168GLY00.0620.04329.208-0.012-0.0120.0000.0000.0000.000
169A169GLY0-0.044-0.03528.2530.0140.0140.0000.0000.0000.000
170A170GLU-1-0.852-0.90625.7360.1680.1680.0000.0000.0000.000
171A171GLU-1-0.875-0.95521.6710.3400.3400.0000.0000.0000.000
172A172ALA00.0030.00320.348-0.019-0.0190.0000.0000.0000.000
173A173ARG10.9430.95417.809-0.200-0.2000.0000.0000.0000.000
174A174PRO0-0.009-0.01512.627-0.016-0.0160.0000.0000.0000.000
175A175LEU0-0.0120.01514.456-0.046-0.0460.0000.0000.0000.000
176A176ASP-1-0.737-0.86513.5710.0710.0710.0000.0000.0000.000
177A177LEU00.006-0.01414.671-0.019-0.0190.0000.0000.0000.000
178A178ARG10.8800.92711.0070.0880.0880.0000.0000.0000.000
179A179PRO0-0.007-0.00916.219-0.012-0.0120.0000.0000.0000.000
180A180ARG10.8700.92819.389-0.104-0.1040.0000.0000.0000.000
181A181PHE0-0.074-0.02518.5520.0060.0060.0000.0000.0000.000
182A182PRO00.0440.02919.313-0.012-0.0120.0000.0000.0000.000
183A183ARG10.8350.90820.648-0.020-0.0200.0000.0000.0000.000
184A184GLY0-0.0020.00218.793-0.007-0.0070.0000.0000.0000.000
185A185LEU0-0.040-0.03016.5430.0100.0100.0000.0000.0000.000
186A186GLY00.0070.02019.4810.0070.0070.0000.0000.0000.000
187A187LEU0-0.048-0.03622.6250.0160.0160.0000.0000.0000.000
188A188GLY00.021-0.00825.347-0.012-0.0120.0000.0000.0000.000
189A189GLU-1-0.963-0.98127.7880.0620.0620.0000.0000.0000.000
190A190GLY0-0.001-0.00326.159-0.005-0.0050.0000.0000.0000.000
191A191PRO00.0100.00123.8970.0050.0050.0000.0000.0000.000
192A192LEU00.0140.02118.6080.0120.0120.0000.0000.0000.000
193A193TRP0-0.0120.00123.284-0.010-0.0100.0000.0000.0000.000
194A194ASP-1-0.746-0.85020.1400.2350.2350.0000.0000.0000.000
195A195LEU0-0.029-0.02623.085-0.016-0.0160.0000.0000.0000.000
196A196ARG10.7920.91119.242-0.214-0.2140.0000.0000.0000.000
197A197PHE0-0.022-0.01121.284-0.020-0.0200.0000.0000.0000.000
198A198ARG10.9500.99224.297-0.072-0.0720.0000.0000.0000.000
199A199TYR0-0.060-0.06519.660-0.010-0.0100.0000.0000.0000.000
200A200GLN00.0090.00123.508-0.003-0.0030.0000.0000.0000.000
201A201ASP-1-0.752-0.86122.7340.0040.0040.0000.0000.0000.000
202A202GLY0-0.030-0.01422.950-0.003-0.0030.0000.0000.0000.000
203A203GLY0-0.0350.00424.478-0.003-0.0030.0000.0000.0000.000
204A204ALA00.0110.00325.122-0.007-0.0070.0000.0000.0000.000
205A205SER00.0380.01124.2990.0110.0110.0000.0000.0000.000
206A206PRO0-0.0100.00124.066-0.004-0.0040.0000.0000.0000.000
207A207PRO0-0.0090.00027.225-0.008-0.0080.0000.0000.0000.000
208A208PRO00.0210.00327.4090.0060.0060.0000.0000.0000.000
209A209PRO00.0350.03129.092-0.004-0.0040.0000.0000.0000.000
210A210PRO00.0870.01231.834-0.005-0.0050.0000.0000.0000.000
211A211ALA0-0.032-0.02732.092-0.006-0.0060.0000.0000.0000.000
212A212PHE00.066-0.01624.050-0.007-0.0070.0000.0000.0000.000
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