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: 8576Y

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 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 -2778730.684672
FMO2-HF: Nuclear repulsion 2692000.633387
FMO2-HF: Total energy -86730.051285
FMO2-MP2: Total energy -86986.061074


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.
-18.043-5.74617.539-8.583-21.254-0.05
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 : -0.039 / 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].
3A3ILE00.000-0.0173.159-2.689-0.2330.118-0.944-1.6310.000
4A4ALA00.0060.0074.5640.2620.363-0.001-0.015-0.0860.000
5A5VAL00.003-0.0087.9590.0960.0960.0000.0000.0000.000
6A6PRO0-0.038-0.01011.0180.0120.0120.0000.0000.0000.000
7A7LEU0-0.049-0.02014.0930.0360.0360.0000.0000.0000.000
8A8ASP-1-0.805-0.86917.337-0.088-0.0880.0000.0000.0000.000
9A9ASP-1-0.754-0.86220.961-0.058-0.0580.0000.0000.0000.000
10A10THR0-0.054-0.04223.3230.0140.0140.0000.0000.0000.000
11A11ASN0-0.027-0.02723.0020.0050.0050.0000.0000.0000.000
12A12PHE0-0.0220.00518.9630.0030.0030.0000.0000.0000.000
13A13SER00.0810.04020.8620.0000.0000.0000.0000.0000.000
14A14GLU-1-0.901-0.95021.659-0.001-0.0010.0000.0000.0000.000
15A15ASN00.003-0.01718.3020.0220.0220.0000.0000.0000.000
16A16LEU0-0.0090.00916.4080.0010.0010.0000.0000.0000.000
17A17LYS10.8910.95316.894-0.032-0.0320.0000.0000.0000.000
18A18LYS10.9020.94917.129-0.011-0.0110.0000.0000.0000.000
19A19ALA00.008-0.00613.0100.0220.0220.0000.0000.0000.000
20A20LYS10.9710.98812.593-0.038-0.0380.0000.0000.0000.000
21A21GLU-1-0.978-0.99114.0820.0700.0700.0000.0000.0000.000
22A22LYS10.8580.93512.803-0.084-0.0840.0000.0000.0000.000
23A23GLY0-0.021-0.00810.1560.0840.0840.0000.0000.0000.000
24A24ALA0-0.035-0.0078.198-0.076-0.0760.0000.0000.0000.000
25A25ASP-1-0.793-0.8845.751-1.170-1.1700.0000.0000.0000.000
26A26ILE0-0.059-0.0377.8290.1170.1170.0000.0000.0000.000
27A27VAL00.0320.02810.195-0.013-0.0130.0000.0000.0000.000
28A28GLU-1-0.925-0.96912.439-0.383-0.3830.0000.0000.0000.000
29A29LEU00.0110.00414.0090.0210.0210.0000.0000.0000.000
30A30ARG10.8160.87116.6120.1940.1940.0000.0000.0000.000
31A31VAL00.0860.03819.2310.0160.0160.0000.0000.0000.000
32A32ASP-1-0.773-0.84821.213-0.154-0.1540.0000.0000.0000.000
33A33GLN0-0.124-0.09121.4000.0130.0130.0000.0000.0000.000
34A34PHE0-0.042-0.00220.9720.0070.0070.0000.0000.0000.000
35A35SER0-0.109-0.07425.4830.0020.0020.0000.0000.0000.000
36A36ASP-1-0.835-0.92228.166-0.039-0.0390.0000.0000.0000.000
37A37THR0-0.026-0.02927.108-0.004-0.0040.0000.0000.0000.000
38A38SER00.0020.00728.6880.0000.0000.0000.0000.0000.000
39A39LEU00.0870.02728.561-0.003-0.0030.0000.0000.0000.000
40A40ASN0-0.009-0.03428.4210.0000.0000.0000.0000.0000.000
41A41TYR0-0.0330.00326.6100.0040.0040.0000.0000.0000.000
42A42VAL00.019-0.00423.216-0.002-0.0020.0000.0000.0000.000
43A43LYS10.8850.94523.8740.0130.0130.0000.0000.0000.000
44A44GLU-1-0.898-0.94324.634-0.016-0.0160.0000.0000.0000.000
45A45LYS10.9160.96821.5770.0450.0450.0000.0000.0000.000
46A46LEU0-0.016-0.02019.052-0.006-0.0060.0000.0000.0000.000
47A47GLU-1-0.912-0.95520.275-0.009-0.0090.0000.0000.0000.000
48A48GLU-1-0.824-0.91721.990-0.019-0.0190.0000.0000.0000.000
49A49VAL0-0.021-0.00115.5400.0060.0060.0000.0000.0000.000
50A50HIS10.8200.89816.7650.0310.0310.0000.0000.0000.000
51A51SER0-0.085-0.03618.9700.0160.0160.0000.0000.0000.000
52A52GLN00.005-0.01017.7360.0170.0170.0000.0000.0000.000
53A53GLY0-0.058-0.02616.5850.0050.0050.0000.0000.0000.000
54A54LEU0-0.051-0.00811.9890.0110.0110.0000.0000.0000.000
55A55LYS10.9220.95110.526-0.127-0.1270.0000.0000.0000.000
56A56THR00.017-0.01513.206-0.038-0.0380.0000.0000.0000.000
57A57ILE0-0.026-0.01110.283-0.010-0.0100.0000.0000.0000.000
58A58LEU0-0.0090.00314.7500.0000.0000.0000.0000.0000.000
59A59THR0-0.005-0.02915.651-0.006-0.0060.0000.0000.0000.000
60A60ILE00.0190.01418.7180.0140.0140.0000.0000.0000.000
61A61ARG10.8670.95616.1700.2730.2730.0000.0000.0000.000
62A62SER00.0140.00921.7690.0150.0150.0000.0000.0000.000
63A63PRO0-0.014-0.01924.168-0.010-0.0100.0000.0000.0000.000
64A64GLU-1-0.859-0.93025.600-0.123-0.1230.0000.0000.0000.000
65A65GLU-1-0.894-0.94619.822-0.244-0.2440.0000.0000.0000.000
66A66GLY0-0.016-0.01720.652-0.025-0.0250.0000.0000.0000.000
67A67GLY0-0.037-0.00422.406-0.002-0.0020.0000.0000.0000.000
68A68ARG10.8970.94223.5650.0960.0960.0000.0000.0000.000
69A69GLU-1-0.906-0.96627.063-0.073-0.0730.0000.0000.0000.000
70A70VAL0-0.0130.01526.2020.0030.0030.0000.0000.0000.000
71A71LYS10.9410.95329.3900.0560.0560.0000.0000.0000.000
72A72ASN0-0.0090.00330.360-0.003-0.0030.0000.0000.0000.000
73A73ARG10.8910.93523.7800.1240.1240.0000.0000.0000.000
74A74GLU-1-0.947-0.96627.182-0.064-0.0640.0000.0000.0000.000
75A75GLU-1-0.821-0.91228.751-0.044-0.0440.0000.0000.0000.000
76A76LEU0-0.027-0.00725.8570.0010.0010.0000.0000.0000.000
77A77PHE0-0.030-0.02420.9940.0010.0010.0000.0000.0000.000
78A78GLU-1-0.900-0.96624.682-0.051-0.0510.0000.0000.0000.000
79A79GLU-1-0.907-0.95427.115-0.027-0.0270.0000.0000.0000.000
80A80LEU0-0.035-0.02823.7500.0060.0060.0000.0000.0000.000
81A81SER0-0.038-0.01621.246-0.007-0.0070.0000.0000.0000.000
82A82PRO0-0.0140.00020.7690.0030.0030.0000.0000.0000.000
83A83LEU0-0.040-0.02722.2340.0140.0140.0000.0000.0000.000
84A84SER00.0150.01217.1060.0000.0000.0000.0000.0000.000
85A85ASP-1-0.868-0.92313.6720.0100.0100.0000.0000.0000.000
86A86TYR0-0.014-0.0178.8490.0500.0500.0000.0000.0000.000
87A87THR00.0410.03414.791-0.007-0.0070.0000.0000.0000.000
88A88ASP-1-0.906-0.91814.773-0.355-0.3550.0000.0000.0000.000
89A89ILE00.008-0.00216.9700.0220.0220.0000.0000.0000.000
90A90GLU-1-0.728-0.86019.338-0.193-0.1930.0000.0000.0000.000
91A91LEU0-0.004-0.01620.3750.0220.0220.0000.0000.0000.000
92A92SER0-0.034-0.02821.9960.0160.0160.0000.0000.0000.000
93A93SER00.0380.03024.3480.0180.0180.0000.0000.0000.000
94A94ARG10.8220.85525.4690.1330.1330.0000.0000.0000.000
95A95GLY0-0.0140.00327.7500.0050.0050.0000.0000.0000.000
96A96LEU00.0120.00025.9240.0060.0060.0000.0000.0000.000
97A97LEU0-0.0200.01322.1710.0040.0040.0000.0000.0000.000
98A98VAL00.0210.00824.2930.0040.0040.0000.0000.0000.000
99A99LYS10.9410.97426.5640.0640.0640.0000.0000.0000.000
100A100LEU00.0690.02322.4320.0060.0060.0000.0000.0000.000
101A101TYR0-0.0110.03020.4980.0100.0100.0000.0000.0000.000
102A102ASN0-0.036-0.03423.0460.0120.0120.0000.0000.0000.000
103A103ILE00.0410.03124.4640.0080.0080.0000.0000.0000.000
104A104THR0-0.018-0.02219.6990.0080.0080.0000.0000.0000.000
105A105LYS10.9360.97921.3460.0170.0170.0000.0000.0000.000
106A106GLU-1-0.987-0.98722.3410.0080.0080.0000.0000.0000.000
107A107ALA0-0.0090.00822.5140.0070.0070.0000.0000.0000.000
108A108GLY0-0.048-0.01920.5130.0090.0090.0000.0000.0000.000
109A109LYS10.8240.92717.3730.0020.0020.0000.0000.0000.000
110A110LYS10.9460.96311.087-0.242-0.2420.0000.0000.0000.000
111A111LEU00.0450.03315.837-0.024-0.0240.0000.0000.0000.000
112A112ILE0-0.0180.00611.223-0.011-0.0110.0000.0000.0000.000
113A113ILE0-0.0190.00214.8460.0170.0170.0000.0000.0000.000
114A114SER0-0.045-0.06315.354-0.028-0.0280.0000.0000.0000.000
115A115TYR00.0200.02616.1990.0440.0440.0000.0000.0000.000
116A116HIS0-0.031-0.02915.744-0.090-0.0900.0000.0000.0000.000
117A117ASN00.0290.01117.7890.0350.0350.0000.0000.0000.000
118A118PHE00.006-0.01917.949-0.030-0.0300.0000.0000.0000.000
119A119GLU-1-0.930-0.94920.214-0.130-0.1300.0000.0000.0000.000
120A120LEU0-0.047-0.03020.5150.0070.0070.0000.0000.0000.000
121A121THR00.0290.02516.932-0.032-0.0320.0000.0000.0000.000
122A122PRO00.0280.01918.3840.0240.0240.0000.0000.0000.000
123A123PRO00.0710.03020.737-0.014-0.0140.0000.0000.0000.000
124A124ASN00.0970.02320.838-0.024-0.0240.0000.0000.0000.000
125A125TRP0-0.017-0.00921.510-0.012-0.0120.0000.0000.0000.000
126A126ILE00.0530.04021.0300.0010.0010.0000.0000.0000.000
127A127ILE00.0140.01616.229-0.007-0.0070.0000.0000.0000.000
128A128ARG10.8990.92418.2610.1570.1570.0000.0000.0000.000
129A129GLU-1-0.893-0.94520.179-0.132-0.1320.0000.0000.0000.000
130A130VAL00.0310.01617.1080.0080.0080.0000.0000.0000.000
131A131LEU0-0.022-0.00514.063-0.005-0.0050.0000.0000.0000.000
132A132ARG10.9050.95517.8270.1570.1570.0000.0000.0000.000
133A133GLU-1-0.814-0.89221.086-0.120-0.1200.0000.0000.0000.000
134A134GLY00.0480.02318.1350.0130.0130.0000.0000.0000.000
135A135TYR0-0.012-0.04913.1630.0080.0080.0000.0000.0000.000
136A136ARG10.8850.96418.9090.1210.1210.0000.0000.0000.000
137A137TYR0-0.067-0.03721.6390.0140.0140.0000.0000.0000.000
138A138GLY0-0.0010.00219.9570.0050.0050.0000.0000.0000.000
139A139GLY00.0060.00516.6960.0170.0170.0000.0000.0000.000
140A140ILE0-0.055-0.03010.084-0.002-0.0020.0000.0000.0000.000
141A141PRO0-0.0250.00213.479-0.042-0.0420.0000.0000.0000.000
142A142LYS10.9470.97410.8630.4800.4800.0000.0000.0000.000
143A143ILE0-0.022-0.01011.9580.0840.0840.0000.0000.0000.000
144A144ALA00.0100.00811.741-0.125-0.1250.0000.0000.0000.000
145A145VAL0-0.018-0.02213.3180.0780.0780.0000.0000.0000.000
146A146LYS10.9320.99514.6020.1410.1410.0000.0000.0000.000
147A147ALA0-0.0060.01214.6540.0090.0090.0000.0000.0000.000
148A148ASN0-0.078-0.06116.5550.0230.0230.0000.0000.0000.000
149A149SER00.0280.00518.1890.0210.0210.0000.0000.0000.000
150A150TYR00.0690.01414.557-0.028-0.0280.0000.0000.0000.000
151A151GLU-1-0.883-0.93415.831-0.221-0.2210.0000.0000.0000.000
152A152ASP-1-0.851-0.91916.920-0.239-0.2390.0000.0000.0000.000
153A153VAL0-0.044-0.01511.041-0.041-0.0410.0000.0000.0000.000
154A154ALA00.0080.00513.067-0.059-0.0590.0000.0000.0000.000
155A155ARG10.8500.91514.7500.2130.2130.0000.0000.0000.000
156A156LEU0-0.002-0.00211.5890.0130.0130.0000.0000.0000.000
157A157LEU0-0.009-0.0038.479-0.029-0.0290.0000.0000.0000.000
158A158CYS0-0.0050.00012.0960.0170.0170.0000.0000.0000.000
159A159ILE0-0.057-0.03015.0110.0330.0330.0000.0000.0000.000
160A160SER0-0.017-0.02012.5720.0130.0130.0000.0000.0000.000
161A161ARG10.9640.98213.2750.2810.2810.0000.0000.0000.000
162A162GLN0-0.0160.00515.4060.0380.0380.0000.0000.0000.000
163A163VAL0-0.060-0.02017.2640.0320.0320.0000.0000.0000.000
164A164GLU-1-0.917-0.96015.672-0.130-0.1300.0000.0000.0000.000
165A165GLY00.0590.03213.7880.0250.0250.0000.0000.0000.000
166A166GLU-1-0.921-0.9478.5840.1980.1980.0000.0000.0000.000
167A167LYS10.8610.9499.0050.4160.4160.0000.0000.0000.000
168A168ILE0-0.0080.0287.495-0.204-0.2040.0000.0000.0000.000
169A169LEU0-0.020-0.0147.3370.2440.2440.0000.0000.0000.000
170A170ILE0-0.028-0.0176.777-0.267-0.2670.0000.0000.0000.000
171A171SER00.0310.0339.4830.1300.1300.0000.0000.0000.000
172A172MET0-0.064-0.04611.079-0.008-0.0080.0000.0000.0000.000
173A173GLY00.0460.01513.2840.0270.0270.0000.0000.0000.000
174A174ASP-1-0.860-0.95313.418-0.154-0.1540.0000.0000.0000.000
175A175TYR0-0.038-0.01213.909-0.003-0.0030.0000.0000.0000.000
176A176GLY00.0430.00711.705-0.012-0.0120.0000.0000.0000.000
177A177LYS10.9791.0239.386-0.100-0.1000.0000.0000.0000.000
178A178ILE00.0220.0117.524-0.091-0.0910.0000.0000.0000.000
179A179SER0-0.008-0.0156.400-0.229-0.2290.0000.0000.0000.000
180A180ARG10.9390.9804.670-0.0780.073-0.001-0.041-0.1080.000
181A181LEU00.0320.0392.386-3.606-2.4772.476-1.276-2.329-0.015
182A182ALA00.026-0.0012.675-0.605-0.4781.123-0.107-1.143-0.008
183A183GLY00.0460.0194.6060.0480.154-0.001-0.012-0.0930.000
184A184TYR0-0.0040.0122.019-3.947-3.4999.860-3.035-7.273-0.019
185A185VAL0-0.014-0.0033.8090.2490.5090.013-0.059-0.2150.000
186A186PHE0-0.085-0.0516.8270.2840.2840.0000.0000.0000.000
187A187GLY00.0140.0127.5800.1350.1350.0000.0000.0000.000
188A188SER0-0.058-0.0214.7050.2170.291-0.001-0.006-0.0670.000
189A189VAL00.0480.0013.687-1.485-1.0730.003-0.057-0.3590.000
190A190ILE0-0.0200.0003.078-1.674-0.2160.171-0.881-0.747-0.008
191A191THR0-0.038-0.0332.493-1.298-0.2442.113-0.729-2.4380.000
192A192TYR00.007-0.0084.5730.3020.375-0.001-0.014-0.0580.000
193A193CYS0-0.057-0.0226.6500.2200.2200.0000.0000.0000.000
194A194SER00.1790.1069.485-0.066-0.0660.0000.0000.0000.000
195A195LEU00.0250.01212.6180.0570.0570.0000.0000.0000.000
196A196GLU-1-0.829-0.92214.3800.0970.0970.0000.0000.0000.000
197A197LYS10.9500.95615.552-0.100-0.1000.0000.0000.0000.000
198A198ALA0-0.046-0.04113.276-0.015-0.0150.0000.0000.0000.000
199A199PHE0-0.079-0.05415.3950.0080.0080.0000.0000.0000.000
200A200ALA00.0130.03216.213-0.003-0.0030.0000.0000.0000.000
201A201PRO00.0360.00615.435-0.001-0.0010.0000.0000.0000.000
202A202GLY00.0020.00012.767-0.034-0.0340.0000.0000.0000.000
203A203GLN0-0.046-0.03010.625-0.027-0.0270.0000.0000.0000.000
204A204ILE0-0.023-0.0126.305-0.001-0.0010.0000.0000.0000.000
205A205PRO0-0.035-0.0029.9060.0010.0010.0000.0000.0000.000
206A206LEU00.0320.0248.2650.1450.1450.0000.0000.0000.000
207A207GLU-1-0.880-0.9489.3410.3630.3630.0000.0000.0000.000
208A208GLU-1-0.925-0.97410.4980.3110.3110.0000.0000.0000.000
209A209MET00.002-0.0074.230-0.0300.7130.312-0.213-0.842-0.001
210A210VAL0-0.0040.0205.7130.9191.049-0.001-0.005-0.1240.000
211A211GLU-1-0.951-0.9717.8330.5220.5220.0000.0000.0000.000
212A212LEU0-0.033-0.0366.431-0.037-0.0370.0000.0000.0000.000
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