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: JLYR9

Calculation Name: 2YSW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YSW

Chain ID: A

ChEMBL ID:

UniProt ID: O66440

Base Structure: X-ray

Registration Date: 2023-06-22

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2786700.958387
FMO2-HF: Nuclear repulsion 2699968.910733
FMO2-HF: Total energy -86732.047654
FMO2-MP2: Total energy -86988.023912


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.
-20.295-11.50124.117-9.297-23.613-0.046
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 : -0.046 / q_NPA : -0.016
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].
3A3ILE0-0.012-0.0213.246-3.421-0.8640.076-1.184-1.449-0.002
4A4ALA00.0060.0095.1180.4760.554-0.001-0.004-0.0730.000
5A5VAL00.004-0.0138.489-0.067-0.0670.0000.0000.0000.000
6A6PRO0-0.044-0.02110.9950.0670.0670.0000.0000.0000.000
7A7LEU0-0.034-0.00714.2170.0250.0250.0000.0000.0000.000
8A8ASP-1-0.794-0.87617.653-0.173-0.1730.0000.0000.0000.000
9A9ASP-1-0.745-0.83621.222-0.114-0.1140.0000.0000.0000.000
10A10THR0-0.037-0.03623.8230.0190.0190.0000.0000.0000.000
11A11ASN0-0.049-0.03323.4160.0000.0000.0000.0000.0000.000
12A12PHE00.0020.02119.569-0.002-0.0020.0000.0000.0000.000
13A13SER00.040-0.00421.258-0.007-0.0070.0000.0000.0000.000
14A14GLU-1-0.896-0.95922.117-0.058-0.0580.0000.0000.0000.000
15A15ASN0-0.010-0.02719.0040.0130.0130.0000.0000.0000.000
16A16LEU00.0070.02016.695-0.012-0.0120.0000.0000.0000.000
17A17LYS10.7870.87817.3170.0050.0050.0000.0000.0000.000
18A18LYS10.8310.91117.8720.1010.1010.0000.0000.0000.000
19A19ALA00.0120.00013.5200.0160.0160.0000.0000.0000.000
20A20LYS10.9110.96213.0720.0000.0000.0000.0000.0000.000
21A21GLU-1-0.855-0.90814.3820.0390.0390.0000.0000.0000.000
22A22LYS10.7950.88613.3830.0520.0520.0000.0000.0000.000
23A23GLY0-0.0130.00011.0240.0850.0850.0000.0000.0000.000
24A24ALA0-0.026-0.0208.5730.0210.0210.0000.0000.0000.000
25A25ASP-1-0.777-0.8716.054-1.161-1.1610.0000.0000.0000.000
26A26ILE0-0.049-0.0267.7320.1410.1410.0000.0000.0000.000
27A27VAL00.0360.02610.452-0.062-0.0620.0000.0000.0000.000
28A28GLU-1-0.897-0.96312.719-0.496-0.4960.0000.0000.0000.000
29A29LEU00.0420.01814.2530.0100.0100.0000.0000.0000.000
30A30ARG10.7670.85416.6030.3040.3040.0000.0000.0000.000
31A31VAL00.0660.03019.4650.0180.0180.0000.0000.0000.000
32A32ASP-1-0.767-0.84921.118-0.226-0.2260.0000.0000.0000.000
33A33GLN0-0.070-0.07121.4750.0170.0170.0000.0000.0000.000
34A34PHE0-0.0340.00221.1320.0080.0080.0000.0000.0000.000
35A35SER0-0.084-0.07325.6560.0070.0070.0000.0000.0000.000
36A36ASP-1-0.773-0.85928.681-0.066-0.0660.0000.0000.0000.000
37A37THR0-0.033-0.03227.227-0.009-0.0090.0000.0000.0000.000
38A38SER0-0.025-0.03729.0600.0030.0030.0000.0000.0000.000
39A39LEU00.0380.02028.666-0.004-0.0040.0000.0000.0000.000
40A40ASN00.012-0.02028.7380.0000.0000.0000.0000.0000.000
41A41TYR0-0.026-0.01227.1050.0040.0040.0000.0000.0000.000
42A42VAL0-0.001-0.01023.825-0.006-0.0060.0000.0000.0000.000
43A43LYS10.8030.89124.2340.0290.0290.0000.0000.0000.000
44A44GLU-1-0.900-0.94124.857-0.041-0.0410.0000.0000.0000.000
45A45LYS10.8520.92422.0830.0860.0860.0000.0000.0000.000
46A46LEU0-0.018-0.01219.359-0.013-0.0130.0000.0000.0000.000
47A47GLU-1-0.815-0.88820.716-0.028-0.0280.0000.0000.0000.000
48A48GLU-1-0.749-0.84922.134-0.066-0.0660.0000.0000.0000.000
49A49VAL0-0.002-0.00115.8530.0070.0070.0000.0000.0000.000
50A50HIS10.8180.89616.8040.0540.0540.0000.0000.0000.000
51A51SER0-0.065-0.03019.3220.0180.0180.0000.0000.0000.000
52A52GLN00.0180.00218.5400.0230.0230.0000.0000.0000.000
53A53GLY0-0.032-0.01617.1050.0060.0060.0000.0000.0000.000
54A54LEU0-0.055-0.01312.2490.0070.0070.0000.0000.0000.000
55A55LYS10.8810.92210.880-0.098-0.0980.0000.0000.0000.000
56A56THR00.009-0.01713.534-0.057-0.0570.0000.0000.0000.000
57A57ILE0-0.034-0.02010.4750.0040.0040.0000.0000.0000.000
58A58LEU00.0240.02614.945-0.017-0.0170.0000.0000.0000.000
59A59THR0-0.031-0.02815.9150.0100.0100.0000.0000.0000.000
60A60ILE00.0400.01818.9320.0050.0050.0000.0000.0000.000
61A61ARG10.8460.93916.0760.3630.3630.0000.0000.0000.000
62A62SER00.007-0.01922.1540.0050.0050.0000.0000.0000.000
63A63PRO0-0.013-0.02024.384-0.016-0.0160.0000.0000.0000.000
64A64GLU-1-0.839-0.90125.685-0.156-0.1560.0000.0000.0000.000
65A65GLU-1-0.794-0.87420.909-0.255-0.2550.0000.0000.0000.000
66A66GLY0-0.024-0.00520.489-0.037-0.0370.0000.0000.0000.000
67A67GLY00.000-0.00121.166-0.022-0.0220.0000.0000.0000.000
68A68ARG10.8150.92823.3810.1520.1520.0000.0000.0000.000
69A69GLU-1-0.796-0.88227.078-0.091-0.0910.0000.0000.0000.000
70A70VAL00.0100.01526.3760.0010.0010.0000.0000.0000.000
71A71LYS10.7970.86929.5210.0810.0810.0000.0000.0000.000
72A72ASN00.004-0.00630.447-0.002-0.0020.0000.0000.0000.000
73A73ARG10.8260.87124.1050.1520.1520.0000.0000.0000.000
74A74GLU-1-0.863-0.90827.091-0.071-0.0710.0000.0000.0000.000
75A75GLU-1-0.817-0.90428.633-0.060-0.0600.0000.0000.0000.000
76A76LEU0-0.013-0.00425.8940.0020.0020.0000.0000.0000.000
77A77PHE0-0.014-0.02321.240-0.001-0.0010.0000.0000.0000.000
78A78GLU-1-0.857-0.92824.940-0.045-0.0450.0000.0000.0000.000
79A79GLU-1-0.908-0.95627.407-0.029-0.0290.0000.0000.0000.000
80A80LEU0-0.041-0.02523.7970.0050.0050.0000.0000.0000.000
81A81SER00.001-0.02621.109-0.003-0.0030.0000.0000.0000.000
82A82PRO0-0.0100.00020.8870.0090.0090.0000.0000.0000.000
83A83LEU0-0.018-0.00422.3580.0170.0170.0000.0000.0000.000
84A84SER0-0.005-0.00617.117-0.007-0.0070.0000.0000.0000.000
85A85ASP-1-0.819-0.88413.5330.0280.0280.0000.0000.0000.000
86A86TYR00.0070.0008.6990.0770.0770.0000.0000.0000.000
87A87THR00.0310.05514.903-0.013-0.0130.0000.0000.0000.000
88A88ASP-1-0.828-0.88015.122-0.390-0.3900.0000.0000.0000.000
89A89ILE00.0190.01217.3080.0170.0170.0000.0000.0000.000
90A90GLU-1-0.711-0.80519.613-0.200-0.2000.0000.0000.0000.000
91A91LEU0-0.014-0.02020.8950.0250.0250.0000.0000.0000.000
92A92SER0-0.024-0.03822.5160.0220.0220.0000.0000.0000.000
93A93SER00.0200.00924.4930.0200.0200.0000.0000.0000.000
94A94ARG10.7870.83825.8660.1260.1260.0000.0000.0000.000
95A95GLY0-0.0110.00027.5670.0060.0060.0000.0000.0000.000
96A96LEU00.0230.01225.6410.0070.0070.0000.0000.0000.000
97A97LEU0-0.0330.00521.9520.0070.0070.0000.0000.0000.000
98A98VAL00.0320.00123.9890.0070.0070.0000.0000.0000.000
99A99LYS10.7850.88326.4070.0680.0680.0000.0000.0000.000
100A100LEU00.0610.02122.0830.0070.0070.0000.0000.0000.000
101A101TYR00.0030.04220.5760.0140.0140.0000.0000.0000.000
102A102ASN0-0.034-0.02422.7280.0170.0170.0000.0000.0000.000
103A103ILE00.0670.04124.5510.0100.0100.0000.0000.0000.000
104A104THR0-0.037-0.04119.3990.0080.0080.0000.0000.0000.000
105A105LYS10.9020.94921.212-0.009-0.0090.0000.0000.0000.000
106A106GLU-1-0.981-0.98222.1460.0190.0190.0000.0000.0000.000
107A107ALA0-0.0110.01122.7440.0070.0070.0000.0000.0000.000
108A108GLY0-0.024-0.00320.7770.0060.0060.0000.0000.0000.000
109A109LYS10.7580.88017.372-0.006-0.0060.0000.0000.0000.000
110A110LYS10.8380.90010.415-0.410-0.4100.0000.0000.0000.000
111A111LEU00.0020.00715.838-0.032-0.0320.0000.0000.0000.000
112A112ILE0-0.041-0.02011.4810.0120.0120.0000.0000.0000.000
113A113ILE0-0.0050.00415.0050.0020.0020.0000.0000.0000.000
114A114SER0-0.029-0.04516.185-0.016-0.0160.0000.0000.0000.000
115A115TYR00.0110.01117.2140.0400.0400.0000.0000.0000.000
116A116HIS0-0.036-0.03416.196-0.105-0.1050.0000.0000.0000.000
117A117ASN00.0110.00918.3140.0350.0350.0000.0000.0000.000
118A118PHE00.0490.00818.018-0.041-0.0410.0000.0000.0000.000
119A119GLU-1-0.938-0.95020.763-0.174-0.1740.0000.0000.0000.000
120A120LEU0-0.045-0.03521.3500.0060.0060.0000.0000.0000.000
121A121THR00.0240.01517.286-0.037-0.0370.0000.0000.0000.000
122A122PRO00.0370.03218.9520.0280.0280.0000.0000.0000.000
123A123PRO00.0710.03421.421-0.009-0.0090.0000.0000.0000.000
124A124ASN00.0870.01821.453-0.018-0.0180.0000.0000.0000.000
125A125TRP0-0.0060.00422.375-0.004-0.0040.0000.0000.0000.000
126A126ILE00.0530.04122.0030.0030.0030.0000.0000.0000.000
127A127ILE0-0.0080.00617.113-0.004-0.0040.0000.0000.0000.000
128A128ARG10.9000.93019.0000.1370.1370.0000.0000.0000.000
129A129GLU-1-0.771-0.86420.878-0.095-0.0950.0000.0000.0000.000
130A130VAL00.0320.00918.0410.0120.0120.0000.0000.0000.000
131A131LEU0-0.0140.00014.607-0.001-0.0010.0000.0000.0000.000
132A132ARG10.8810.92417.9800.1270.1270.0000.0000.0000.000
133A133GLU-1-0.800-0.86521.013-0.092-0.0920.0000.0000.0000.000
134A134GLY00.0290.01517.8290.0120.0120.0000.0000.0000.000
135A135TYR0-0.011-0.04313.0890.0070.0070.0000.0000.0000.000
136A136ARG10.7480.85618.9750.1070.1070.0000.0000.0000.000
137A137TYR0-0.030-0.01021.5750.0070.0070.0000.0000.0000.000
138A138GLY0-0.0040.00619.9370.0010.0010.0000.0000.0000.000
139A139GLY00.009-0.00616.5180.0210.0210.0000.0000.0000.000
140A140ILE0-0.054-0.0189.7070.0010.0010.0000.0000.0000.000
141A141PRO0-0.0150.01413.387-0.052-0.0520.0000.0000.0000.000
142A142LYS10.7810.87912.2960.5230.5230.0000.0000.0000.000
143A143ILE0-0.018-0.00713.1020.0590.0590.0000.0000.0000.000
144A144ALA00.0220.00612.801-0.125-0.1250.0000.0000.0000.000
145A145VAL0-0.014-0.01614.0710.0840.0840.0000.0000.0000.000
146A146LYS10.8760.95915.3220.2000.2000.0000.0000.0000.000
147A147ALA00.0030.01515.3710.0180.0180.0000.0000.0000.000
148A148ASN0-0.050-0.04217.3700.0100.0100.0000.0000.0000.000
149A149SER00.003-0.00519.1390.0270.0270.0000.0000.0000.000
150A150TYR00.0620.00614.545-0.018-0.0180.0000.0000.0000.000
151A151GLU-1-0.867-0.92516.154-0.234-0.2340.0000.0000.0000.000
152A152ASP-1-0.805-0.88617.513-0.274-0.2740.0000.0000.0000.000
153A153VAL0-0.0010.00311.329-0.033-0.0330.0000.0000.0000.000
154A154ALA00.0140.01113.256-0.046-0.0460.0000.0000.0000.000
155A155ARG10.8070.87914.9810.2400.2400.0000.0000.0000.000
156A156LEU0-0.002-0.00512.3380.0220.0220.0000.0000.0000.000
157A157LEU0-0.0110.0058.784-0.017-0.0170.0000.0000.0000.000
158A158CYS0-0.015-0.01012.5300.0420.0420.0000.0000.0000.000
159A159ILE0-0.057-0.03415.5940.0410.0410.0000.0000.0000.000
160A160SER0-0.032-0.02813.1410.0230.0230.0000.0000.0000.000
161A161ARG10.9920.98713.3770.2030.2030.0000.0000.0000.000
162A162GLN0-0.035-0.00515.8930.0430.0430.0000.0000.0000.000
163A163VAL0-0.056-0.02317.5640.0210.0210.0000.0000.0000.000
164A164GLU-1-0.913-0.94514.779-0.029-0.0290.0000.0000.0000.000
165A165GLY00.0600.03413.6240.0140.0140.0000.0000.0000.000
166A166GLU-1-0.822-0.8968.5170.4710.4710.0000.0000.0000.000
167A167LYS10.8420.9298.9000.1880.1880.0000.0000.0000.000
168A168ILE0-0.0020.0177.902-0.081-0.0810.0000.0000.0000.000
169A169LEU0-0.015-0.0098.4600.1920.1920.0000.0000.0000.000
170A170ILE0-0.019-0.0116.745-0.351-0.3510.0000.0000.0000.000
171A171SER00.0290.0329.9190.1720.1720.0000.0000.0000.000
172A172MET0-0.077-0.03511.547-0.076-0.0760.0000.0000.0000.000
173A173GLY00.0760.03714.0680.0570.0570.0000.0000.0000.000
174A174ASP-1-0.804-0.92814.255-0.385-0.3850.0000.0000.0000.000
175A175TYR0-0.0260.00214.323-0.002-0.0020.0000.0000.0000.000
176A176GLY00.050-0.00112.547-0.012-0.0120.0000.0000.0000.000
177A177LYS10.8570.9459.9380.2090.2090.0000.0000.0000.000
178A178ILE00.0260.0167.611-0.180-0.1800.0000.0000.0000.000
179A179SER0-0.006-0.0136.745-0.242-0.2420.0000.0000.0000.000
180A180ARG10.8840.9404.9330.7140.7140.0000.0000.0000.000
181A181LEU00.0440.0392.182-3.387-2.7683.774-1.667-2.725-0.008
182A182ALA00.0300.0152.894-0.234-0.1090.2640.477-0.866-0.008
183A183GLY00.0450.0105.0720.2070.2070.0000.0000.0000.000
184A184TYR0-0.0060.0132.255-6.300-5.49910.465-3.427-7.839-0.021
185A185VAL0-0.009-0.0044.6240.4350.558-0.001-0.015-0.1080.000
186A186PHE0-0.063-0.0377.6600.2360.2360.0000.0000.0000.000
187A187GLY00.0200.0147.9570.1180.1180.0000.0000.0000.000
188A188SER0-0.055-0.0225.4570.3230.3230.0000.0000.0000.000
189A189VAL00.0280.0053.444-1.606-1.1070.010-0.092-0.4170.000
190A190ILE0-0.024-0.0013.051-1.2850.0500.207-0.857-0.686-0.007
191A191THR0-0.022-0.0242.2210.1680.7691.574-0.486-1.6890.000
192A192TYR00.0190.0094.5010.5540.626-0.001-0.016-0.0540.000
193A193CYS0-0.061-0.0216.485-0.056-0.0560.0000.0000.0000.000
194A194SER0-0.009-0.0108.6670.0720.0720.0000.0000.0000.000
195A195LEU00.0430.02911.7960.0160.0160.0000.0000.0000.000
196A196GLU-1-0.751-0.86013.996-0.031-0.0310.0000.0000.0000.000
197A197LYS10.8370.89214.2190.0180.0180.0000.0000.0000.000
198A198ALA00.0330.00812.665-0.004-0.0040.0000.0000.0000.000
199A199PHE00.0180.00314.7600.0160.0160.0000.0000.0000.000
200A200ALA0-0.0050.02515.8160.0130.0130.0000.0000.0000.000
201A201PRO00.0390.00015.371-0.040-0.0400.0000.0000.0000.000
202A202GLY0-0.022-0.00813.163-0.037-0.0370.0000.0000.0000.000
203A203GLN0-0.044-0.00810.707-0.142-0.1420.0000.0000.0000.000
204A204ILE00.009-0.0046.3130.0680.0680.0000.0000.0000.000
205A205PRO0-0.0150.0099.543-0.093-0.0930.0000.0000.0000.000
206A206LEU00.0290.0298.6050.0200.0200.0000.0000.0000.000
207A207GLU-1-0.803-0.8958.7200.2490.2490.0000.0000.0000.000
208A208GLU-1-0.821-0.9119.5050.0880.0880.0000.0000.0000.000
209A209MET00.0090.0042.958-0.665-0.9912.221-0.414-1.482-0.005
210A210VAL0-0.0010.0105.1491.2101.355-0.001-0.004-0.1390.000
211A211GLU-1-0.815-0.8767.5660.8150.8150.0000.0000.0000.000
212A212LEU0-0.025-0.0225.069-0.006-0.0060.0000.0000.0000.000
213A213ARG10.8290.8832.701-1.6160.2702.285-1.039-3.1310.004
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