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: N987Q

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 OptHSide
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 -2780902.028782
FMO2-HF: Nuclear repulsion 2694170.262256
FMO2-HF: Total energy -86731.766526
FMO2-MP2: Total energy -86987.746511


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.
-17.668-6.09419.026-8.118-22.478-0.051
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 : -0.041 / q_NPA : -0.010
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].
3A3ILE00.002-0.0193.172-2.979-0.2780.166-1.057-1.810-0.001
4A4ALA00.0000.0084.5920.3160.414-0.001-0.013-0.0840.000
5A5VAL0-0.002-0.0117.9360.0560.0560.0000.0000.0000.000
6A6PRO0-0.033-0.00711.0400.0200.0200.0000.0000.0000.000
7A7LEU0-0.041-0.01714.0790.0360.0360.0000.0000.0000.000
8A8ASP-1-0.805-0.87817.342-0.102-0.1020.0000.0000.0000.000
9A9ASP-1-0.754-0.85820.958-0.061-0.0610.0000.0000.0000.000
10A10THR0-0.049-0.03723.5820.0150.0150.0000.0000.0000.000
11A11ASN0-0.042-0.03023.0480.0040.0040.0000.0000.0000.000
12A12PHE0-0.0140.00819.1310.0040.0040.0000.0000.0000.000
13A13SER00.0660.02820.9160.0010.0010.0000.0000.0000.000
14A14GLU-1-0.881-0.94321.7380.0030.0030.0000.0000.0000.000
15A15ASN0-0.021-0.03318.4500.0220.0220.0000.0000.0000.000
16A16LEU0-0.0020.01316.3920.0040.0040.0000.0000.0000.000
17A17LYS10.8010.88416.976-0.052-0.0520.0000.0000.0000.000
18A18LYS10.8390.90217.379-0.001-0.0010.0000.0000.0000.000
19A19ALA00.012-0.00713.0960.0290.0290.0000.0000.0000.000
20A20LYS10.8970.95212.713-0.052-0.0520.0000.0000.0000.000
21A21GLU-1-0.858-0.90914.2120.1000.1000.0000.0000.0000.000
22A22LYS10.8200.90412.967-0.098-0.0980.0000.0000.0000.000
23A23GLY0-0.017-0.00610.3280.1110.1110.0000.0000.0000.000
24A24ALA0-0.033-0.0078.306-0.035-0.0350.0000.0000.0000.000
25A25ASP-1-0.791-0.8795.856-0.995-0.9950.0000.0000.0000.000
26A26ILE0-0.040-0.0307.5530.1100.1100.0000.0000.0000.000
27A27VAL00.0280.02510.165-0.020-0.0200.0000.0000.0000.000
28A28GLU-1-0.913-0.96212.369-0.402-0.4020.0000.0000.0000.000
29A29LEU00.0120.00513.9440.0170.0170.0000.0000.0000.000
30A30ARG10.8080.87116.5710.2240.2240.0000.0000.0000.000
31A31VAL00.0750.03019.1660.0150.0150.0000.0000.0000.000
32A32ASP-1-0.767-0.84221.160-0.174-0.1740.0000.0000.0000.000
33A33GLN0-0.096-0.08421.4140.0160.0160.0000.0000.0000.000
34A34PHE0-0.029-0.00420.8260.0070.0070.0000.0000.0000.000
35A35SER0-0.098-0.06525.4440.0020.0020.0000.0000.0000.000
36A36ASP-1-0.801-0.89328.128-0.039-0.0390.0000.0000.0000.000
37A37THR0-0.029-0.02526.906-0.005-0.0050.0000.0000.0000.000
38A38SER0-0.014-0.01628.6160.0010.0010.0000.0000.0000.000
39A39LEU00.0670.02428.559-0.002-0.0020.0000.0000.0000.000
40A40ASN0-0.003-0.03028.3390.0010.0010.0000.0000.0000.000
41A41TYR0-0.031-0.00326.3710.0050.0050.0000.0000.0000.000
42A42VAL00.008-0.01223.159-0.002-0.0020.0000.0000.0000.000
43A43LYS10.8220.89723.8100.0060.0060.0000.0000.0000.000
44A44GLU-1-0.929-0.95324.575-0.005-0.0050.0000.0000.0000.000
45A45LYS10.8720.93121.5930.0380.0380.0000.0000.0000.000
46A46LEU0-0.012-0.01119.147-0.004-0.0040.0000.0000.0000.000
47A47GLU-1-0.835-0.90520.2300.0030.0030.0000.0000.0000.000
48A48GLU-1-0.755-0.86421.788-0.010-0.0100.0000.0000.0000.000
49A49VAL0-0.012-0.00115.5280.0090.0090.0000.0000.0000.000
50A50HIS10.8400.90916.7190.0160.0160.0000.0000.0000.000
51A51SER0-0.078-0.03418.9450.0190.0190.0000.0000.0000.000
52A52GLN00.0150.00217.9030.0220.0220.0000.0000.0000.000
53A53GLY0-0.032-0.01916.5400.0080.0080.0000.0000.0000.000
54A54LEU0-0.051-0.00512.0590.0160.0160.0000.0000.0000.000
55A55LYS10.8840.92110.620-0.158-0.1580.0000.0000.0000.000
56A56THR00.021-0.00513.155-0.040-0.0400.0000.0000.0000.000
57A57ILE0-0.038-0.02110.098-0.007-0.0070.0000.0000.0000.000
58A58LEU0-0.0030.00714.634-0.005-0.0050.0000.0000.0000.000
59A59THR0-0.020-0.03615.699-0.004-0.0040.0000.0000.0000.000
60A60ILE00.0270.01818.7420.0130.0130.0000.0000.0000.000
61A61ARG10.8540.94815.9170.3060.3060.0000.0000.0000.000
62A62SER0-0.002-0.02021.8670.0080.0080.0000.0000.0000.000
63A63PRO00.001-0.01224.163-0.012-0.0120.0000.0000.0000.000
64A64GLU-1-0.837-0.89825.692-0.138-0.1380.0000.0000.0000.000
65A65GLU-1-0.829-0.90620.297-0.254-0.2540.0000.0000.0000.000
66A66GLY0-0.020-0.01520.592-0.029-0.0290.0000.0000.0000.000
67A67GLY0-0.0290.00122.146-0.003-0.0030.0000.0000.0000.000
68A68ARG10.8530.93223.4020.1090.1090.0000.0000.0000.000
69A69GLU-1-0.806-0.89126.999-0.075-0.0750.0000.0000.0000.000
70A70VAL00.0150.02226.2270.0030.0030.0000.0000.0000.000
71A71LYS10.8120.87429.4270.0640.0640.0000.0000.0000.000
72A72ASN0-0.012-0.01130.130-0.004-0.0040.0000.0000.0000.000
73A73ARG10.8560.90324.0070.1330.1330.0000.0000.0000.000
74A74GLU-1-0.877-0.92627.253-0.064-0.0640.0000.0000.0000.000
75A75GLU-1-0.836-0.90728.772-0.043-0.0430.0000.0000.0000.000
76A76LEU0-0.005-0.00425.6670.0020.0020.0000.0000.0000.000
77A77PHE0-0.034-0.03621.1200.0010.0010.0000.0000.0000.000
78A78GLU-1-0.859-0.93424.703-0.043-0.0430.0000.0000.0000.000
79A79GLU-1-0.922-0.96327.136-0.018-0.0180.0000.0000.0000.000
80A80LEU0-0.036-0.02423.8010.0070.0070.0000.0000.0000.000
81A81SER0-0.002-0.01021.076-0.001-0.0010.0000.0000.0000.000
82A82PRO0-0.019-0.00720.7900.0060.0060.0000.0000.0000.000
83A83LEU0-0.011-0.00722.2570.0160.0160.0000.0000.0000.000
84A84SER00.0030.00217.0830.0010.0010.0000.0000.0000.000
85A85ASP-1-0.839-0.89113.6480.0560.0560.0000.0000.0000.000
86A86TYR00.005-0.0088.7040.0400.0400.0000.0000.0000.000
87A87THR00.0390.05614.812-0.007-0.0070.0000.0000.0000.000
88A88ASP-1-0.830-0.88114.724-0.390-0.3900.0000.0000.0000.000
89A89ILE00.0150.00517.0380.0170.0170.0000.0000.0000.000
90A90GLU-1-0.708-0.83419.484-0.192-0.1920.0000.0000.0000.000
91A91LEU0-0.002-0.01520.7520.0250.0250.0000.0000.0000.000
92A92SER0-0.045-0.04322.3170.0220.0220.0000.0000.0000.000
93A93SER00.0170.02224.6160.0190.0190.0000.0000.0000.000
94A94ARG10.8180.85225.7610.1370.1370.0000.0000.0000.000
95A95GLY0-0.0180.00127.7620.0060.0060.0000.0000.0000.000
96A96LEU00.0180.00725.9530.0070.0070.0000.0000.0000.000
97A97LEU0-0.0220.00722.1090.0060.0060.0000.0000.0000.000
98A98VAL00.0180.00324.3070.0060.0060.0000.0000.0000.000
99A99LYS10.8090.89726.5770.0620.0620.0000.0000.0000.000
100A100LEU00.0730.02422.2330.0070.0070.0000.0000.0000.000
101A101TYR0-0.0020.04320.4960.0140.0140.0000.0000.0000.000
102A102ASN0-0.034-0.03123.0600.0140.0140.0000.0000.0000.000
103A103ILE00.0520.03524.5780.0090.0090.0000.0000.0000.000
104A104THR0-0.016-0.02519.6980.0090.0090.0000.0000.0000.000
105A105LYS10.9040.95721.3640.0070.0070.0000.0000.0000.000
106A106GLU-1-0.984-0.98022.3560.0210.0210.0000.0000.0000.000
107A107ALA0-0.0100.00622.5790.0070.0070.0000.0000.0000.000
108A108GLY0-0.030-0.01120.5290.0110.0110.0000.0000.0000.000
109A109LYS10.7660.89117.404-0.016-0.0160.0000.0000.0000.000
110A110LYS10.8790.92010.461-0.280-0.2800.0000.0000.0000.000
111A111LEU00.0240.02315.854-0.028-0.0280.0000.0000.0000.000
112A112ILE0-0.0240.00111.263-0.006-0.0060.0000.0000.0000.000
113A113ILE0-0.0080.00814.8600.0110.0110.0000.0000.0000.000
114A114SER0-0.032-0.04915.672-0.029-0.0290.0000.0000.0000.000
115A115TYR00.0240.02416.6350.0440.0440.0000.0000.0000.000
116A116HIS0-0.030-0.03215.733-0.101-0.1010.0000.0000.0000.000
117A117ASN00.0270.01517.8260.0360.0360.0000.0000.0000.000
118A118PHE00.010-0.01717.621-0.037-0.0370.0000.0000.0000.000
119A119GLU-1-0.920-0.94320.139-0.158-0.1580.0000.0000.0000.000
120A120LEU0-0.042-0.03120.6630.0070.0070.0000.0000.0000.000
121A121THR00.0110.01617.033-0.034-0.0340.0000.0000.0000.000
122A122PRO00.0340.02518.6580.0260.0260.0000.0000.0000.000
123A123PRO00.0720.03521.050-0.016-0.0160.0000.0000.0000.000
124A124ASN00.0970.02121.360-0.023-0.0230.0000.0000.0000.000
125A125TRP0-0.026-0.01222.135-0.012-0.0120.0000.0000.0000.000
126A126ILE00.0440.03821.3940.0030.0030.0000.0000.0000.000
127A127ILE00.0100.01516.782-0.006-0.0060.0000.0000.0000.000
128A128ARG10.9140.93518.9790.1780.1780.0000.0000.0000.000
129A129GLU-1-0.779-0.87620.962-0.132-0.1320.0000.0000.0000.000
130A130VAL00.0200.00817.9750.0110.0110.0000.0000.0000.000
131A131LEU0-0.0070.00514.635-0.002-0.0020.0000.0000.0000.000
132A132ARG10.8770.92218.2160.1670.1670.0000.0000.0000.000
133A133GLU-1-0.817-0.87421.084-0.112-0.1120.0000.0000.0000.000
134A134GLY00.0360.01918.1390.0130.0130.0000.0000.0000.000
135A135TYR0-0.015-0.04913.2090.0070.0070.0000.0000.0000.000
136A136ARG10.7780.88918.9120.1370.1370.0000.0000.0000.000
137A137TYR0-0.051-0.02221.6380.0130.0130.0000.0000.0000.000
138A138GLY0-0.003-0.00119.9650.0050.0050.0000.0000.0000.000
139A139GLY00.0090.00616.7070.0200.0200.0000.0000.0000.000
140A140ILE0-0.074-0.0349.8390.0030.0030.0000.0000.0000.000
141A141PRO0-0.0290.00013.487-0.047-0.0470.0000.0000.0000.000
142A142LYS10.8250.89111.8250.4730.4730.0000.0000.0000.000
143A143ILE0-0.022-0.00912.5240.0830.0830.0000.0000.0000.000
144A144ALA00.0200.01312.079-0.134-0.1340.0000.0000.0000.000
145A145VAL0-0.022-0.02513.4400.0870.0870.0000.0000.0000.000
146A146LYS10.8870.97014.6880.1770.1770.0000.0000.0000.000
147A147ALA00.0060.01914.9770.0140.0140.0000.0000.0000.000
148A148ASN0-0.049-0.04016.8610.0190.0190.0000.0000.0000.000
149A149SER00.0270.00618.6390.0260.0260.0000.0000.0000.000
150A150TYR00.0670.00914.422-0.022-0.0220.0000.0000.0000.000
151A151GLU-1-0.879-0.93116.172-0.280-0.2800.0000.0000.0000.000
152A152ASP-1-0.817-0.89617.388-0.285-0.2850.0000.0000.0000.000
153A153VAL0-0.029-0.00811.355-0.042-0.0420.0000.0000.0000.000
154A154ALA00.0080.00613.393-0.064-0.0640.0000.0000.0000.000
155A155ARG10.8230.88514.9450.2550.2550.0000.0000.0000.000
156A156LEU0-0.009-0.00411.9670.0180.0180.0000.0000.0000.000
157A157LEU0-0.006-0.0028.672-0.026-0.0260.0000.0000.0000.000
158A158CYS0-0.012-0.00712.2770.0230.0230.0000.0000.0000.000
159A159ILE0-0.048-0.02915.2320.0420.0420.0000.0000.0000.000
160A160SER0-0.011-0.01212.9990.0250.0250.0000.0000.0000.000
161A161ARG10.9680.98113.0670.3320.3320.0000.0000.0000.000
162A162GLN0-0.031-0.00415.6450.0490.0490.0000.0000.0000.000
163A163VAL0-0.060-0.02017.7570.0340.0340.0000.0000.0000.000
164A164GLU-1-0.914-0.95315.648-0.119-0.1190.0000.0000.0000.000
165A165GLY00.0670.03713.7800.0260.0260.0000.0000.0000.000
166A166GLU-1-0.837-0.9018.5650.2650.2650.0000.0000.0000.000
167A167LYS10.8580.9359.0050.3900.3900.0000.0000.0000.000
168A168ILE0-0.0070.0227.819-0.174-0.1740.0000.0000.0000.000
169A169LEU0-0.017-0.0098.0410.2280.2280.0000.0000.0000.000
170A170ILE0-0.024-0.0226.561-0.303-0.3030.0000.0000.0000.000
171A171SER00.0340.0369.5280.1550.1550.0000.0000.0000.000
172A172MET0-0.065-0.04311.281-0.024-0.0240.0000.0000.0000.000
173A173GLY00.0510.01913.3700.0340.0340.0000.0000.0000.000
174A174ASP-1-0.822-0.93713.729-0.245-0.2450.0000.0000.0000.000
175A175TYR0-0.037-0.00714.015-0.011-0.0110.0000.0000.0000.000
176A176GLY00.0480.00712.109-0.016-0.0160.0000.0000.0000.000
177A177LYS10.9291.0039.736-0.012-0.0120.0000.0000.0000.000
178A178ILE00.0230.0107.387-0.132-0.1320.0000.0000.0000.000
179A179SER00.000-0.0136.483-0.265-0.2650.0000.0000.0000.000
180A180ARG10.9180.9694.8030.2440.2440.0000.0000.0000.000
181A181LEU00.0200.0262.007-2.258-2.0753.944-1.705-2.422-0.010
182A182ALA00.0340.0142.7730.267-0.7671.2850.891-1.141-0.009
183A183GLY00.0460.0184.8720.1540.1540.0000.0000.0000.000
184A184TYR0-0.0050.0102.204-6.000-4.2358.586-2.941-7.411-0.022
185A185VAL0-0.011-0.0014.0790.5160.7550.002-0.060-0.1810.000
186A186PHE0-0.082-0.0487.1030.3590.3590.0000.0000.0000.000
187A187GLY00.0150.0127.8390.1660.1660.0000.0000.0000.000
188A188SER0-0.050-0.0145.4330.3930.3930.0000.0000.0000.000
189A189VAL00.038-0.0043.653-1.417-1.0120.003-0.057-0.3500.000
190A190ILE0-0.030-0.0053.093-1.428-0.0510.159-0.827-0.709-0.007
191A191THR0-0.029-0.0262.391-0.7520.2042.168-0.655-2.468-0.001
192A192TYR00.0310.0184.4770.4180.505-0.001-0.022-0.0630.000
193A193CYS0-0.057-0.0237.1470.1570.1570.0000.0000.0000.000
194A194SER0-0.009-0.0019.109-0.037-0.0370.0000.0000.0000.000
195A195LEU00.0330.02612.6100.0610.0610.0000.0000.0000.000
196A196GLU-1-0.760-0.86514.4860.1020.1020.0000.0000.0000.000
197A197LYS10.8670.89615.368-0.102-0.1020.0000.0000.0000.000
198A198ALA00.0320.02313.303-0.022-0.0220.0000.0000.0000.000
199A199PHE0-0.017-0.02715.3100.0030.0030.0000.0000.0000.000
200A200ALA0-0.0090.02415.9890.0000.0000.0000.0000.0000.000
201A201PRO00.0410.00515.500-0.012-0.0120.0000.0000.0000.000
202A202GLY0-0.011-0.00912.917-0.038-0.0380.0000.0000.0000.000
203A203GLN0-0.066-0.03310.733-0.061-0.0610.0000.0000.0000.000
204A204ILE00.0190.0026.3630.0190.0190.0000.0000.0000.000
205A205PRO0-0.0180.0069.783-0.011-0.0110.0000.0000.0000.000
206A206LEU00.0360.0288.5580.1460.1460.0000.0000.0000.000
207A207GLU-1-0.828-0.9209.2170.4260.4260.0000.0000.0000.000
208A208GLU-1-0.863-0.92610.0260.2710.2710.0000.0000.0000.000
209A209MET00.003-0.0063.593-0.7560.0510.519-0.246-1.080-0.002
210A210VAL00.0030.0195.3651.2201.406-0.001-0.010-0.1750.000
211A211GLU-1-0.818-0.8797.4140.6560.6560.0000.0000.0000.000
212A212LEU0-0.028-0.0325.702-0.057-0.0570.0000.0000.0000.000
213A213ARG10.8690.9152.685-1.4070.9411.227-0.917-2.6580.002
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