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: R8L58

Calculation Name: 2FM9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2FM9

Chain ID: A

ChEMBL ID:

UniProt ID: P0CL52

Base Structure: X-ray

Registration Date: 2023-09-23

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2187955.055962
FMO2-HF: Nuclear repulsion 2109730.82155
FMO2-HF: Total energy -78224.234411
FMO2-MP2: Total energy -78449.020537


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:49:PRO)


Summations of interaction energy for fragment #1(A:49:PRO)
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.
-0.2852.90.092-1.258-2.0190.001
Interaction energy analysis for fragmet #1(A:49:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.009
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].
3A51LEU00.0340.0003.730-0.4951.756-0.043-1.050-1.1580.002
4A52GLU-1-0.941-0.9736.537-0.731-0.7310.0000.0000.0000.000
5A53ASP-1-0.918-0.9394.5190.8961.071-0.001-0.016-0.1570.000
6A54PHE0-0.082-0.0432.988-0.5610.1980.136-0.192-0.704-0.001
7A55PRO00.0520.0208.139-0.098-0.0980.0000.0000.0000.000
8A56ALA0-0.019-0.01411.848-0.024-0.0240.0000.0000.0000.000
9A57LEU00.0450.0276.931-0.002-0.0020.0000.0000.0000.000
10A58ILE00.0450.02810.615-0.012-0.0120.0000.0000.0000.000
11A59LYS10.9030.93911.9950.1700.1700.0000.0000.0000.000
12A60GLN0-0.011-0.00413.675-0.016-0.0160.0000.0000.0000.000
13A61ALA00.0580.03312.3890.0150.0150.0000.0000.0000.000
14A62SER0-0.052-0.04314.5190.0220.0220.0000.0000.0000.000
15A63LEU0-0.029-0.02117.1970.0270.0270.0000.0000.0000.000
16A64ASP-1-0.915-0.93516.947-0.294-0.2940.0000.0000.0000.000
17A65ALA0-0.068-0.04018.1150.0180.0180.0000.0000.0000.000
18A66LEU0-0.0020.00319.9220.0200.0200.0000.0000.0000.000
19A67PHE00.0680.01422.6520.0170.0170.0000.0000.0000.000
20A68LYS10.9470.98121.0850.2840.2840.0000.0000.0000.000
21A69CYS0-0.120-0.02524.3590.0110.0110.0000.0000.0000.000
22A70GLY00.0380.01926.7500.0140.0140.0000.0000.0000.000
23A71LYS10.8540.91429.2840.0940.0940.0000.0000.0000.000
24A72ASP-1-0.829-0.92530.189-0.121-0.1210.0000.0000.0000.000
25A73ALA00.0030.00024.6550.0020.0020.0000.0000.0000.000
26A74GLU-1-0.879-0.93226.305-0.146-0.1460.0000.0000.0000.000
27A75ALA00.0510.03627.5100.0040.0040.0000.0000.0000.000
28A76LEU0-0.047-0.02226.8530.0060.0060.0000.0000.0000.000
29A77LYS10.9620.98020.3610.2020.2020.0000.0000.0000.000
30A78GLU-1-0.925-0.95325.656-0.097-0.0970.0000.0000.0000.000
31A79VAL0-0.027-0.01028.7040.0070.0070.0000.0000.0000.000
32A80PHE0-0.024-0.02022.4320.0050.0050.0000.0000.0000.000
33A81THR0-0.104-0.07423.7300.0080.0080.0000.0000.0000.000
34A82ASN00.0200.01426.3390.0060.0060.0000.0000.0000.000
35A83SER0-0.040-0.00229.1960.0090.0090.0000.0000.0000.000
36A84ASN00.002-0.01829.077-0.003-0.0030.0000.0000.0000.000
37A85ASN0-0.032-0.01131.1320.0050.0050.0000.0000.0000.000
38A86VAL00.0430.01226.708-0.007-0.0070.0000.0000.0000.000
39A87ALA00.0330.02327.491-0.005-0.0050.0000.0000.0000.000
40A88GLY00.0810.02628.706-0.005-0.0050.0000.0000.0000.000
41A89LYS10.8920.95025.0620.0790.0790.0000.0000.0000.000
42A90LYS10.9460.97222.7290.0560.0560.0000.0000.0000.000
43A91ALA00.0170.00724.502-0.007-0.0070.0000.0000.0000.000
44A92ILE00.0270.01824.385-0.009-0.0090.0000.0000.0000.000
45A93MET0-0.0150.00120.571-0.017-0.0170.0000.0000.0000.000
46A94GLU-1-0.916-0.94820.947-0.097-0.0970.0000.0000.0000.000
47A95PHE00.0130.01122.452-0.012-0.0120.0000.0000.0000.000
48A96ALA00.0160.00220.491-0.011-0.0110.0000.0000.0000.000
49A97GLY00.0000.00318.178-0.027-0.0270.0000.0000.0000.000
50A98LEU00.0130.00319.019-0.019-0.0190.0000.0000.0000.000
51A99PHE0-0.009-0.00521.483-0.004-0.0040.0000.0000.0000.000
52A100ARG10.9360.97311.4310.6280.6280.0000.0000.0000.000
53A101SER0-0.013-0.01218.108-0.025-0.0250.0000.0000.0000.000
54A102ALA00.0590.02819.0050.0020.0020.0000.0000.0000.000
55A103LEU0-0.051-0.02219.5180.0060.0060.0000.0000.0000.000
56A104ASN0-0.045-0.02315.013-0.009-0.0090.0000.0000.0000.000
57A105ALA00.0030.00518.8620.0080.0080.0000.0000.0000.000
58A106THR0-0.042-0.03221.6370.0170.0170.0000.0000.0000.000
59A107SER0-0.098-0.04120.5140.0110.0110.0000.0000.0000.000
60A108ASP-1-0.868-0.91622.827-0.197-0.1970.0000.0000.0000.000
61A109SER0-0.022-0.01625.2120.0170.0170.0000.0000.0000.000
62A110PRO00.0410.00428.195-0.004-0.0040.0000.0000.0000.000
63A111GLU-1-0.882-0.94230.284-0.100-0.1000.0000.0000.0000.000
64A112ALA00.0550.02928.4490.0030.0030.0000.0000.0000.000
65A113LYS10.9780.99423.1860.2200.2200.0000.0000.0000.000
66A114THR0-0.049-0.03028.147-0.003-0.0030.0000.0000.0000.000
67A115LEU0-0.024-0.00631.3390.0010.0010.0000.0000.0000.000
68A116LEU00.0250.01223.7190.0040.0040.0000.0000.0000.000
69A117MET0-0.031-0.02124.295-0.005-0.0050.0000.0000.0000.000
70A118LYS10.9560.98928.8950.0890.0890.0000.0000.0000.000
71A119VAL00.0120.00929.4600.0050.0050.0000.0000.0000.000
72A120GLY00.0480.00327.6680.0020.0020.0000.0000.0000.000
73A121ALA0-0.0120.00528.4370.0030.0030.0000.0000.0000.000
74A122GLU-1-0.960-0.97931.251-0.076-0.0760.0000.0000.0000.000
75A123TYR00.0170.01827.6960.0040.0040.0000.0000.0000.000
76A124THR00.010-0.02127.2270.0060.0060.0000.0000.0000.000
77A125ALA0-0.020-0.00630.1900.0040.0040.0000.0000.0000.000
78A126GLN0-0.065-0.03833.6110.0090.0090.0000.0000.0000.000
79A127ILE00.0090.00527.9740.0040.0040.0000.0000.0000.000
80A128ILE0-0.019-0.00331.3570.0050.0050.0000.0000.0000.000
81A129LYS10.9230.95634.0690.0670.0670.0000.0000.0000.000
82A130ASP-1-0.778-0.83534.773-0.058-0.0580.0000.0000.0000.000
83A131GLY0-0.027-0.01934.7510.0050.0050.0000.0000.0000.000
84A132LEU0-0.045-0.01928.882-0.001-0.0010.0000.0000.0000.000
85A133LYS10.9500.98733.4130.0550.0550.0000.0000.0000.000
86A134GLU-1-0.903-0.95335.463-0.033-0.0330.0000.0000.0000.000
87A135LYS10.9080.95936.9770.0350.0350.0000.0000.0000.000
88A136SER0-0.056-0.05934.383-0.003-0.0030.0000.0000.0000.000
89A137ALA00.0250.00436.3160.0030.0030.0000.0000.0000.000
90A138PHE0-0.030-0.01130.503-0.002-0.0020.0000.0000.0000.000
91A139GLY00.005-0.01630.8210.0020.0020.0000.0000.0000.000
92A140PRO0-0.017-0.01331.8540.0030.0030.0000.0000.0000.000
93A141TRP00.0570.02833.6060.0040.0040.0000.0000.0000.000
94A142LEU0-0.041-0.00527.700-0.002-0.0020.0000.0000.0000.000
95A143PRO00.0270.03328.3790.0040.0040.0000.0000.0000.000
96A144GLU-1-0.896-0.95729.818-0.017-0.0170.0000.0000.0000.000
97A145THR0-0.019-0.00931.0820.0060.0060.0000.0000.0000.000
98A146LYS10.9390.93723.818-0.014-0.0140.0000.0000.0000.000
99A147LYS10.9620.99329.495-0.006-0.0060.0000.0000.0000.000
100A148ALA0-0.007-0.01632.451-0.002-0.0020.0000.0000.0000.000
101A149GLU-1-0.827-0.90525.191-0.017-0.0170.0000.0000.0000.000
102A150ALA00.0310.01829.013-0.004-0.0040.0000.0000.0000.000
103A151LYS10.8920.94130.2060.0060.0060.0000.0000.0000.000
104A152LEU00.0330.02529.347-0.002-0.0020.0000.0000.0000.000
105A153GLU-1-0.878-0.93225.008-0.027-0.0270.0000.0000.0000.000
106A154ASN0-0.120-0.06329.096-0.001-0.0010.0000.0000.0000.000
107A155LEU00.0550.03632.121-0.001-0.0010.0000.0000.0000.000
108A156GLU-1-0.813-0.91228.110-0.066-0.0660.0000.0000.0000.000
109A157LYS10.9070.94827.2590.0130.0130.0000.0000.0000.000
110A158GLN0-0.018-0.02231.3490.0030.0030.0000.0000.0000.000
111A159LEU00.0270.01733.8640.0000.0000.0000.0000.0000.000
112A160LEU0-0.023-0.01229.051-0.002-0.0020.0000.0000.0000.000
113A161ASP-1-0.959-0.98933.002-0.027-0.0270.0000.0000.0000.000
114A162ILE00.0270.01635.2650.0010.0010.0000.0000.0000.000
115A163ILE00.003-0.00434.6100.0000.0000.0000.0000.0000.000
116A164LYS10.9040.95329.6250.0510.0510.0000.0000.0000.000
117A165ASN0-0.063-0.02436.2730.0010.0010.0000.0000.0000.000
118A166ASN0-0.079-0.03239.6480.0050.0050.0000.0000.0000.000
119A167THR00.024-0.02140.760-0.003-0.0030.0000.0000.0000.000
120A168GLY00.0030.00443.1410.0030.0030.0000.0000.0000.000
121A169GLY0-0.011-0.02245.7820.0000.0000.0000.0000.0000.000
122A170GLU-1-0.830-0.92346.523-0.023-0.0230.0000.0000.0000.000
123A171LEU00.0110.02239.7060.0010.0010.0000.0000.0000.000
124A172SER0-0.0020.00243.2370.0000.0000.0000.0000.0000.000
125A173LYS10.9160.97845.2440.0220.0220.0000.0000.0000.000
126A174LEU0-0.018-0.01042.7360.0010.0010.0000.0000.0000.000
127A175SER0-0.026-0.01840.4150.0000.0000.0000.0000.0000.000
128A176THR00.0470.01041.7410.0000.0000.0000.0000.0000.000
129A177ASN0-0.010-0.00644.4350.0010.0010.0000.0000.0000.000
130A178LEU00.0060.02836.6940.0010.0010.0000.0000.0000.000
131A179VAL00.022-0.00340.0260.0000.0000.0000.0000.0000.000
132A180MET0-0.017-0.01441.4240.0010.0010.0000.0000.0000.000
133A181GLN0-0.041-0.02643.2090.0010.0010.0000.0000.0000.000
134A182GLU-1-0.903-0.95137.839-0.020-0.0200.0000.0000.0000.000
135A183VAL0-0.012-0.00336.7090.0000.0000.0000.0000.0000.000
136A184MET0-0.0200.00338.779-0.001-0.0010.0000.0000.0000.000
137A185PRO0-0.022-0.01040.9020.0010.0010.0000.0000.0000.000
138A186TYR0-0.0350.00932.4020.0040.0040.0000.0000.0000.000
139A187ILE00.0420.01638.0380.0000.0000.0000.0000.0000.000
140A188ALA0-0.020-0.02239.2840.0010.0010.0000.0000.0000.000
141A189SER0-0.020-0.04438.5280.0020.0020.0000.0000.0000.000
142A190CYS0-0.081-0.01436.0380.0010.0010.0000.0000.0000.000
143A191ILE00.000-0.00638.3200.0000.0000.0000.0000.0000.000
144A192GLU-1-0.890-0.95041.578-0.011-0.0110.0000.0000.0000.000
145A193HIS0-0.025-0.01036.8990.0040.0040.0000.0000.0000.000
146A194ASN0-0.099-0.03438.7720.0000.0000.0000.0000.0000.000
147A195PHE00.006-0.00741.5370.0010.0010.0000.0000.0000.000
148A196GLY00.0060.02044.2130.0010.0010.0000.0000.0000.000
149A197CYS0-0.098-0.03545.8380.0010.0010.0000.0000.0000.000
150A198THR00.0320.00746.731-0.001-0.0010.0000.0000.0000.000
151A199LEU0-0.051-0.03045.299-0.001-0.0010.0000.0000.0000.000
152A200ASP-1-0.795-0.84048.653-0.018-0.0180.0000.0000.0000.000
153A201PRO00.023-0.01851.108-0.001-0.0010.0000.0000.0000.000
154A202LEU0-0.0090.01952.557-0.001-0.0010.0000.0000.0000.000
155A203THR0-0.010-0.06347.085-0.002-0.0020.0000.0000.0000.000
156A204ARG10.9870.99745.9420.0150.0150.0000.0000.0000.000
157A205SER0-0.0090.01048.334-0.002-0.0020.0000.0000.0000.000
158A206ASN00.020-0.00849.589-0.001-0.0010.0000.0000.0000.000
159A207LEU0-0.016-0.01042.933-0.002-0.0020.0000.0000.0000.000
160A208THR00.006-0.02444.743-0.002-0.0020.0000.0000.0000.000
161A209HIS0-0.0040.01445.840-0.001-0.0010.0000.0000.0000.000
162A210LEU0-0.057-0.01541.596-0.002-0.0020.0000.0000.0000.000
163A211VAL00.007-0.01339.965-0.003-0.0030.0000.0000.0000.000
164A212ASP-1-0.859-0.93041.774-0.036-0.0360.0000.0000.0000.000
165A213LYS10.9280.97543.6330.0430.0430.0000.0000.0000.000
166A214ALA0-0.051-0.03339.734-0.002-0.0020.0000.0000.0000.000
167A215ALA00.0410.01038.747-0.004-0.0040.0000.0000.0000.000
168A216ALA00.0440.02239.670-0.002-0.0020.0000.0000.0000.000
169A217LYS10.9170.95940.4310.0520.0520.0000.0000.0000.000
170A218ALA0-0.0020.00335.765-0.003-0.0030.0000.0000.0000.000
171A219VAL00.0230.01036.885-0.004-0.0040.0000.0000.0000.000
172A220GLU-1-0.931-0.95538.657-0.051-0.0510.0000.0000.0000.000
173A221ALA0-0.045-0.02636.503-0.002-0.0020.0000.0000.0000.000
174A222LEU0-0.025-0.02932.000-0.004-0.0040.0000.0000.0000.000
175A223ASP-1-0.769-0.85335.691-0.050-0.0500.0000.0000.0000.000
176A224MET0-0.032-0.02538.6860.0000.0000.0000.0000.0000.000
177A225CYS0-0.060-0.03232.721-0.005-0.0050.0000.0000.0000.000
178A226HIS00.020-0.00734.518-0.007-0.0070.0000.0000.0000.000
179A227GLN0-0.071-0.02335.5190.0010.0010.0000.0000.0000.000
180A228LYS10.8620.95934.2870.0740.0740.0000.0000.0000.000
181A243HIS00.0070.00125.489-0.007-0.0070.0000.0000.0000.000
182A244LEU0-0.006-0.00721.0070.0110.0110.0000.0000.0000.000
183A245GLU-1-0.842-0.92025.080-0.121-0.1210.0000.0000.0000.000
184A246MET00.0270.01126.817-0.001-0.0010.0000.0000.0000.000
185A247GLN0-0.032-0.01723.745-0.006-0.0060.0000.0000.0000.000
186A248THR0-0.037-0.01322.216-0.002-0.0020.0000.0000.0000.000
187A249LEU00.0170.00625.111-0.004-0.0040.0000.0000.0000.000
188A250ILE0-0.0150.00628.1150.0020.0020.0000.0000.0000.000
189A251PRO00.0500.02525.4990.0030.0030.0000.0000.0000.000
190A252LEU0-0.032-0.00324.5470.0020.0020.0000.0000.0000.000
191A253LEU00.005-0.01228.4330.0040.0040.0000.0000.0000.000
192A254LEU00.0000.01131.4260.0040.0040.0000.0000.0000.000
193A255ARG10.7810.86826.4760.0800.0800.0000.0000.0000.000
194A256ASN0-0.005-0.02531.4070.0000.0000.0000.0000.0000.000
195A257VAL00.0010.00733.1090.0030.0030.0000.0000.0000.000
196A258PHE00.0140.00332.4620.0030.0030.0000.0000.0000.000
197A259ALA0-0.043-0.01533.3890.0030.0030.0000.0000.0000.000
198A260GLN0-0.049-0.02135.4570.0040.0040.0000.0000.0000.000
199A261ILE0-0.043-0.00738.5680.0040.0040.0000.0000.0000.000
200A262PRO0-0.049-0.01139.710-0.002-0.0020.0000.0000.0000.000
201A263ALA0-0.002-0.00139.1220.0030.0030.0000.0000.0000.000