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: 855YY

Calculation Name: 5FMS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5FMS

Chain ID: A

ChEMBL ID:

UniProt ID: Q62559

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 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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2927103.318541
FMO2-HF: Nuclear repulsion 2837764.165733
FMO2-HF: Total energy -89339.152809
FMO2-MP2: Total energy -89600.870622


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:SER)


Summations of interaction energy for fragment #1(A:7:SER)
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.
-7.365-2.0519.738-7.662-7.39-0.044
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.030
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].
3A9ILE00.0020.0213.784-1.3451.535-0.031-1.528-1.3210.010
4A10LEU0-0.011-0.0116.389-0.029-0.0290.0000.0000.0000.000
5A11PHE0-0.017-0.0029.5210.2620.2620.0000.0000.0000.000
6A12ASN0-0.045-0.04113.034-0.109-0.1090.0000.0000.0000.000
7A13ALA0-0.045-0.05715.4820.0380.0380.0000.0000.0000.000
8A14TYR0-0.009-0.01216.6750.0190.0190.0000.0000.0000.000
9A15LYS10.8450.95020.3750.3610.3610.0000.0000.0000.000
10A16LYS10.8220.87122.3070.3360.3360.0000.0000.0000.000
11A17GLU-1-0.732-0.85418.908-0.430-0.4300.0000.0000.0000.000
12A18VAL0-0.056-0.01222.1310.0080.0080.0000.0000.0000.000
13A19PHE0-0.054-0.03119.8740.0060.0060.0000.0000.0000.000
14A20THR00.0540.03017.662-0.051-0.0510.0000.0000.0000.000
15A21THR00.0250.00213.6220.0310.0310.0000.0000.0000.000
16A22ASN0-0.027-0.01116.8010.0220.0220.0000.0000.0000.000
17A23THR0-0.027-0.02420.0690.0420.0420.0000.0000.0000.000
18A24GLY00.0280.00920.162-0.030-0.0300.0000.0000.0000.000
19A25THR00.0570.06416.8360.0240.0240.0000.0000.0000.000
20A26LYS10.9220.95517.1610.3170.3170.0000.0000.0000.000
21A27SER0-0.028-0.02917.715-0.031-0.0310.0000.0000.0000.000
22A28LEU00.0280.03014.1550.0120.0120.0000.0000.0000.000
23A29GLN0-0.036-0.03412.997-0.110-0.1100.0000.0000.0000.000
24A30LYS10.9090.97412.5420.1600.1600.0000.0000.0000.000
25A31ARG10.8130.86913.5830.2520.2520.0000.0000.0000.000
26A32LEU00.0350.0269.2140.0320.0320.0000.0000.0000.000
27A33ARG10.9050.9408.1450.5940.5940.0000.0000.0000.000
28A34SER0-0.0180.0059.291-0.019-0.0190.0000.0000.0000.000
29A35ASN0-0.006-0.0096.5180.2830.2830.0000.0000.0000.000
30A36TRP00.0490.0391.958-1.575-1.2185.434-3.093-2.698-0.015
31A37LYS10.8960.9564.0332.9163.182-0.001-0.053-0.2120.000
32A38ILE00.011-0.0035.763-0.340-0.3400.0000.0000.0000.000
33A39GLN00.0090.0098.9970.1360.1360.0000.0000.0000.000
34A40SER0-0.0080.00410.6980.0610.0610.0000.0000.0000.000
35A41LEU00.0550.02012.688-0.135-0.1350.0000.0000.0000.000
36A42LYS10.8870.92914.4130.7370.7370.0000.0000.0000.000
37A43ASP-1-0.868-0.92117.054-0.484-0.4840.0000.0000.0000.000
38A44GLU-1-0.860-0.94817.062-0.421-0.4210.0000.0000.0000.000
39A45ILE00.0170.02013.525-0.059-0.0590.0000.0000.0000.000
40A46THR00.0410.01614.7720.0530.0530.0000.0000.0000.000
41A47SER00.0410.02213.023-0.058-0.0580.0000.0000.0000.000
42A48GLU-1-0.881-0.95011.646-0.389-0.3890.0000.0000.0000.000
43A49LYS10.8380.91610.3630.4540.4540.0000.0000.0000.000
44A50LEU0-0.044-0.0248.391-0.338-0.3380.0000.0000.0000.000
45A51ILE0-0.0160.0097.233-0.112-0.1120.0000.0000.0000.000
46A52GLY00.0060.0033.8160.1610.4640.002-0.116-0.1880.000
47A53VAL0-0.070-0.0302.054-8.348-7.7064.200-2.551-2.291-0.037
48A54LYS10.8270.9362.883-0.5260.2670.135-0.312-0.617-0.002
49A55LEU00.0300.0194.7410.2930.366-0.001-0.009-0.0630.000
50A56TRP00.0060.0107.730-0.379-0.3790.0000.0000.0000.000
51A57ILE0-0.003-0.01210.6200.1610.1610.0000.0000.0000.000
52A58THR00.0060.00713.391-0.032-0.0320.0000.0000.0000.000
53A59ALA0-0.003-0.00817.0310.0540.0540.0000.0000.0000.000
54A60GLY00.0400.00119.0350.0060.0060.0000.0000.0000.000
55A61PRO0-0.027-0.01620.793-0.007-0.0070.0000.0000.0000.000
56A62ARG10.8590.91722.8940.2880.2880.0000.0000.0000.000
57A63GLU-1-0.817-0.85724.760-0.268-0.2680.0000.0000.0000.000
58A64LYS10.8020.89824.9710.1500.1500.0000.0000.0000.000
59A65PHE00.026-0.00118.906-0.025-0.0250.0000.0000.0000.000
60A66THR0-0.009-0.01623.2010.0310.0310.0000.0000.0000.000
61A67ALA00.0240.00423.117-0.014-0.0140.0000.0000.0000.000
62A68ALA00.0230.01122.9630.0050.0050.0000.0000.0000.000
63A69GLU-1-0.728-0.83919.389-0.334-0.3340.0000.0000.0000.000
64A70PHE00.0100.00318.532-0.024-0.0240.0000.0000.0000.000
65A71GLU-1-0.839-0.90919.174-0.121-0.1210.0000.0000.0000.000
66A72VAL0-0.070-0.03014.6770.0110.0110.0000.0000.0000.000
67A73LEU0-0.020-0.00513.754-0.031-0.0310.0000.0000.0000.000
68A74LYS10.8430.91015.1640.1290.1290.0000.0000.0000.000
69A75LYS10.9230.96314.6290.2010.2010.0000.0000.0000.000
70A76TYR0-0.033-0.0316.6450.1050.1050.0000.0000.0000.000
71A77LEU0-0.023-0.00411.7060.0500.0500.0000.0000.0000.000
72A78ASP-1-0.810-0.91413.8840.1350.1350.0000.0000.0000.000
73A79SER0-0.060-0.04511.4960.0320.0320.0000.0000.0000.000
74A80GLY00.0010.01911.0840.1140.1140.0000.0000.0000.000
75A81GLY0-0.019-0.0048.4060.1650.1650.0000.0000.0000.000
76A82ASP-1-0.795-0.9048.4350.4550.4550.0000.0000.0000.000
77A83ILE0-0.030-0.02510.592-0.193-0.1930.0000.0000.0000.000
78A84LEU0-0.0090.00013.0220.0710.0710.0000.0000.0000.000
79A85VAL00.0140.01514.881-0.059-0.0590.0000.0000.0000.000
80A86MET0-0.027-0.01017.9000.0230.0230.0000.0000.0000.000
81A87LEU00.0210.02620.519-0.025-0.0250.0000.0000.0000.000
82A88GLY00.0390.01823.9490.0120.0120.0000.0000.0000.000
83A89GLU-1-0.795-0.87227.019-0.115-0.1150.0000.0000.0000.000
84A90GLY00.001-0.00230.738-0.007-0.0070.0000.0000.0000.000
85A91GLY00.0670.02228.9540.0050.0050.0000.0000.0000.000
86A92GLU-1-0.758-0.89527.984-0.146-0.1460.0000.0000.0000.000
87A93SER0-0.073-0.02330.1660.0020.0020.0000.0000.0000.000
88A94ARG10.8090.90031.6080.1330.1330.0000.0000.0000.000
89A95PHE0-0.074-0.04725.650-0.010-0.0100.0000.0000.0000.000
90A96ASP-1-0.839-0.88128.993-0.167-0.1670.0000.0000.0000.000
91A97THR0-0.040-0.04325.078-0.011-0.0110.0000.0000.0000.000
92A98ASN00.0170.02425.984-0.004-0.0040.0000.0000.0000.000
93A99ILE00.0530.01720.155-0.001-0.0010.0000.0000.0000.000
94A100ASN00.023-0.01623.9200.0020.0020.0000.0000.0000.000
95A101PHE0-0.0190.00426.3320.0090.0090.0000.0000.0000.000
96A102LEU0-0.0110.02218.5910.0020.0020.0000.0000.0000.000
97A103LEU0-0.040-0.03120.7430.0120.0120.0000.0000.0000.000
98A104GLU-1-0.901-0.96023.636-0.063-0.0630.0000.0000.0000.000
99A105GLU-1-0.842-0.90823.780-0.076-0.0760.0000.0000.0000.000
100A106TYR0-0.072-0.05219.3400.0100.0100.0000.0000.0000.000
101A107GLY0-0.0080.00024.0220.0110.0110.0000.0000.0000.000
102A108ILE0-0.058-0.03521.8250.0030.0030.0000.0000.0000.000
103A109MET00.0470.02325.897-0.007-0.0070.0000.0000.0000.000
104A110VAL0-0.062-0.03424.8300.0070.0070.0000.0000.0000.000
105A111ASN00.0020.03227.862-0.001-0.0010.0000.0000.0000.000
106A112ASN00.018-0.00630.869-0.007-0.0070.0000.0000.0000.000
107A113ASP-1-0.836-0.90532.931-0.077-0.0770.0000.0000.0000.000
108A114ALA0-0.036-0.03932.855-0.008-0.0080.0000.0000.0000.000
109A115VAL00.0070.02031.3220.0070.0070.0000.0000.0000.000
110A116VAL0-0.045-0.02134.043-0.006-0.0060.0000.0000.0000.000
111A117ARG10.8530.92936.3390.0790.0790.0000.0000.0000.000
112A118ASN00.0190.00937.9830.0000.0000.0000.0000.0000.000
113A119VAL00.0290.00640.8560.0010.0010.0000.0000.0000.000
114A120TYR0-0.043-0.01740.677-0.003-0.0030.0000.0000.0000.000
115A121TYR00.0720.01237.1660.0030.0030.0000.0000.0000.000
116A122LYS10.8230.93134.3090.0560.0560.0000.0000.0000.000
117A123TYR0-0.060-0.05331.412-0.009-0.0090.0000.0000.0000.000
118A124PHE00.0100.02036.6140.0040.0040.0000.0000.0000.000
119A125HIS00.0430.02035.6420.0050.0050.0000.0000.0000.000
120A126PRO00.015-0.01736.9730.0000.0000.0000.0000.0000.000
121A127LYS10.8940.92833.5030.1020.1020.0000.0000.0000.000
122A128GLU-1-0.853-0.87632.061-0.118-0.1180.0000.0000.0000.000
123A129ALA00.0070.00732.1750.0070.0070.0000.0000.0000.000
124A130LEU00.0090.00631.542-0.005-0.0050.0000.0000.0000.000
125A131VAL00.008-0.00830.2570.0060.0060.0000.0000.0000.000
126A132SER0-0.024-0.00831.2360.0030.0030.0000.0000.0000.000
127A133ASP-1-0.787-0.86032.599-0.017-0.0170.0000.0000.0000.000
128A134GLY00.0680.03429.9280.0020.0020.0000.0000.0000.000
129A135VAL0-0.016-0.00426.109-0.003-0.0030.0000.0000.0000.000
130A136LEU0-0.0250.00927.2690.0040.0040.0000.0000.0000.000
131A137ASN0-0.003-0.00824.8910.0140.0140.0000.0000.0000.000
132A138ARG10.9710.96826.860-0.090-0.0900.0000.0000.0000.000
133A139GLU-1-0.813-0.89923.4390.1210.1210.0000.0000.0000.000
134A140ILE0-0.028-0.00321.4670.0080.0080.0000.0000.0000.000
135A141SER0-0.056-0.01623.556-0.014-0.0140.0000.0000.0000.000
136A142ARG10.8050.89519.979-0.168-0.1680.0000.0000.0000.000
137A143ALA0-0.0040.00422.5630.0020.0020.0000.0000.0000.000
138A144ALA0-0.016-0.02124.3840.0080.0080.0000.0000.0000.000
139A145GLY00.0380.03027.987-0.006-0.0060.0000.0000.0000.000
140A146LYS10.9340.95430.384-0.044-0.0440.0000.0000.0000.000
141A147ALA00.0320.02632.343-0.006-0.0060.0000.0000.0000.000
142A162GLN0-0.011-0.01033.075-0.001-0.0010.0000.0000.0000.000
143A163ALA0-0.033-0.02032.5390.0030.0030.0000.0000.0000.000
144A164LEU0-0.028-0.01625.1830.0020.0020.0000.0000.0000.000
145A165THR0-0.0090.01129.900-0.002-0.0020.0000.0000.0000.000
146A166PHE00.0130.01426.127-0.006-0.0060.0000.0000.0000.000
147A167VAL0-0.022-0.02827.4210.0030.0030.0000.0000.0000.000
148A168TYR0-0.017-0.03425.495-0.018-0.0180.0000.0000.0000.000
149A169PRO0-0.0140.00226.5750.0050.0050.0000.0000.0000.000
150A170PHE0-0.007-0.00628.067-0.011-0.0110.0000.0000.0000.000
151A171GLY00.0200.00328.354-0.013-0.0130.0000.0000.0000.000
152A172ALA00.0150.02428.2550.0100.0100.0000.0000.0000.000
153A173THR0-0.021-0.02128.7860.0020.0020.0000.0000.0000.000
154A174LEU0-0.051-0.02324.074-0.004-0.0040.0000.0000.0000.000
155A175SER0-0.005-0.02128.5820.0130.0130.0000.0000.0000.000
156A176VAL0-0.053-0.03526.204-0.004-0.0040.0000.0000.0000.000
157A177MET0-0.0090.01028.4630.0090.0090.0000.0000.0000.000
158A178LYS10.9270.97227.335-0.049-0.0490.0000.0000.0000.000
159A179PRO00.0170.00124.535-0.003-0.0030.0000.0000.0000.000
160A180ALA00.0160.02523.4690.0140.0140.0000.0000.0000.000
161A181VAL0-0.041-0.03623.6070.0050.0050.0000.0000.0000.000
162A182ALA00.0050.00824.037-0.006-0.0060.0000.0000.0000.000
163A183VAL00.000-0.01721.5520.0110.0110.0000.0000.0000.000
164A184LEU0-0.0120.00522.9990.0010.0010.0000.0000.0000.000
165A185SER0-0.004-0.01526.444-0.005-0.0050.0000.0000.0000.000
166A186THR00.007-0.03529.875-0.001-0.0010.0000.0000.0000.000
167A187GLY00.0340.02931.897-0.002-0.0020.0000.0000.0000.000
168A188SER0-0.066-0.07333.999-0.001-0.0010.0000.0000.0000.000
169A189VAL0-0.020-0.02036.7740.0000.0000.0000.0000.0000.000
170A190CYS0-0.058-0.01034.623-0.007-0.0070.0000.0000.0000.000
171A191PHE0-0.014-0.00636.6870.0050.0050.0000.0000.0000.000
172A192PRO00.0530.01434.944-0.004-0.0040.0000.0000.0000.000
173A193LEU00.0140.03835.739-0.001-0.0010.0000.0000.0000.000
174A194ASN0-0.017-0.01234.3730.0020.0020.0000.0000.0000.000
175A195ARG10.9020.96032.8580.0420.0420.0000.0000.0000.000
176A196PRO00.008-0.00528.231-0.002-0.0020.0000.0000.0000.000
177A197ILE00.0140.00125.888-0.007-0.0070.0000.0000.0000.000
178A198LEU00.0120.00419.392-0.018-0.0180.0000.0000.0000.000
179A199ALA0-0.0220.00722.1410.0190.0190.0000.0000.0000.000
180A200PHE00.023-0.00218.276-0.015-0.0150.0000.0000.0000.000
181A201TYR00.0580.00918.243-0.003-0.0030.0000.0000.0000.000
182A202HIS00.0110.00315.950-0.020-0.0200.0000.0000.0000.000
183A203SER0-0.035-0.01418.3190.0300.0300.0000.0000.0000.000
184A204LYS10.8900.95419.658-0.049-0.0490.0000.0000.0000.000
185A205ASN0-0.018-0.02018.8980.0480.0480.0000.0000.0000.000
186A206GLN0-0.070-0.00716.1430.0140.0140.0000.0000.0000.000
187A207GLY00.0490.02915.416-0.022-0.0220.0000.0000.0000.000
188A208PHE0-0.061-0.05814.0040.0450.0450.0000.0000.0000.000
189A209GLY00.1030.08113.0490.0640.0640.0000.0000.0000.000
190A210LYS10.7830.89312.608-0.361-0.3610.0000.0000.0000.000
191A211LEU0-0.0080.00213.641-0.059-0.0590.0000.0000.0000.000
192A212ALA0-0.017-0.01915.8880.0340.0340.0000.0000.0000.000
193A213VAL00.0110.01817.465-0.043-0.0430.0000.0000.0000.000
194A214LEU00.004-0.01719.6920.0250.0250.0000.0000.0000.000
195A215GLY00.0340.02221.659-0.016-0.0160.0000.0000.0000.000
196A216SER00.028-0.01723.565-0.007-0.0070.0000.0000.0000.000
197A217CYS00.0010.00821.4000.0000.0000.0000.0000.0000.000
198A218HIS00.0250.00121.730-0.030-0.0300.0000.0000.0000.000
199A219MET0-0.0030.02322.3670.0010.0010.0000.0000.0000.000
200A220PHE00.0510.00517.4280.0060.0060.0000.0000.0000.000
201A221SER0-0.059-0.01619.853-0.028-0.0280.0000.0000.0000.000
202A222ASP-1-0.729-0.89021.439-0.307-0.3070.0000.0000.0000.000
203A223GLN0-0.036-0.01423.3380.0240.0240.0000.0000.0000.000
204A224TYR0-0.033-0.06425.0120.0160.0160.0000.0000.0000.000
205A225LEU0-0.0440.01518.5030.0140.0140.0000.0000.0000.000
206A226ASP-1-0.830-0.92022.871-0.175-0.1750.0000.0000.0000.000
207A227LYS10.8480.94324.6650.1460.1460.0000.0000.0000.000
208A228GLU-1-0.730-0.86227.276-0.061-0.0610.0000.0000.0000.000
209A229GLU-1-0.821-0.88625.535-0.021-0.0210.0000.0000.0000.000
210A230ASN00.0130.01523.1100.0180.0180.0000.0000.0000.000
211A231SER00.005-0.00320.709-0.001-0.0010.0000.0000.0000.000
212A232LYS10.9290.95119.8540.0220.0220.0000.0000.0000.000
213A233ILE00.0230.02020.2460.0110.0110.0000.0000.0000.000
214A234MET0-0.040-0.00915.435-0.023-0.0230.0000.0000.0000.000
215A235ASP-1-0.888-0.95115.759-0.084-0.0840.0000.0000.0000.000
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