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: N99MQ

Calculation Name: 5LON-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LON

Chain ID: A

ChEMBL ID:

UniProt ID: Q6CPV9

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 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 225
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2791033.011157
FMO2-HF: Nuclear repulsion 2700665.628676
FMO2-HF: Total energy -90367.382482
FMO2-MP2: Total energy -90633.736207


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-1.0160.518-0.004-0.779-0.7510.004
Interaction energy analysis for fragmet #1(A:2:SER)
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 : 0.010
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].
3A4PRO0-0.0120.0023.871-2.238-0.704-0.004-0.779-0.7510.004
4A5LEU0-0.0170.0005.7930.8570.8570.0000.0000.0000.000
5A6LEU00.0260.0057.946-0.152-0.1520.0000.0000.0000.000
6A7ARG10.7760.83910.8460.5550.5550.0000.0000.0000.000
7A8PRO00.0640.03212.9860.0480.0480.0000.0000.0000.000
8A9PHE00.0380.00915.3220.0300.0300.0000.0000.0000.000
9A10GLU-1-0.806-0.86615.694-0.419-0.4190.0000.0000.0000.000
10A11THR0-0.051-0.02817.9040.0130.0130.0000.0000.0000.000
11A12VAL0-0.0370.00819.7800.0160.0160.0000.0000.0000.000
12A13SER00.0340.01021.8460.0060.0060.0000.0000.0000.000
13A14LEU00.0120.00623.983-0.007-0.0070.0000.0000.0000.000
14A15GLU-1-0.841-0.94225.290-0.073-0.0730.0000.0000.0000.000
15A16ASN00.002-0.01721.646-0.004-0.0040.0000.0000.0000.000
16A17ALA0-0.036-0.01420.557-0.007-0.0070.0000.0000.0000.000
17A18VAL0-0.005-0.00521.3630.0020.0020.0000.0000.0000.000
18A19GLU-1-0.820-0.90422.066-0.065-0.0650.0000.0000.0000.000
19A20ASP-1-0.840-0.87415.833-0.185-0.1850.0000.0000.0000.000
20A21LEU0-0.021-0.02018.4200.0110.0110.0000.0000.0000.000
21A22VAL00.0290.00320.3500.0160.0160.0000.0000.0000.000
22A23VAL0-0.0160.00316.6910.0170.0170.0000.0000.0000.000
23A24ARG10.7320.82612.0450.2370.2370.0000.0000.0000.000
24A25PHE0-0.051-0.02517.7240.0120.0120.0000.0000.0000.000
25A26ILE0-0.049-0.02721.0770.0070.0070.0000.0000.0000.000
26A27LEU00.0440.01821.9580.0070.0070.0000.0000.0000.000
27A28ASN0-0.051-0.01818.218-0.003-0.0030.0000.0000.0000.000
28A29VAL0-0.0030.00320.3060.0100.0100.0000.0000.0000.000
29A30PRO0-0.0140.00023.1340.0020.0020.0000.0000.0000.000
30A31PRO00.0860.02025.636-0.008-0.0080.0000.0000.0000.000
31A32GLU-1-0.855-0.90329.1230.0670.0670.0000.0000.0000.000
32A33ASP-1-0.843-0.89426.7750.0420.0420.0000.0000.0000.000
33A34LEU0-0.006-0.01526.477-0.007-0.0070.0000.0000.0000.000
34A35SER0-0.073-0.04129.743-0.004-0.0040.0000.0000.0000.000
35A36THR0-0.021-0.01332.628-0.002-0.0020.0000.0000.0000.000
36A37VAL00.0360.01932.941-0.001-0.0010.0000.0000.0000.000
37A38GLU-1-0.882-0.96633.5350.0150.0150.0000.0000.0000.000
38A39ARG10.8320.91727.369-0.049-0.0490.0000.0000.0000.000
39A40VAL00.0550.03528.676-0.002-0.0020.0000.0000.0000.000
40A41LEU0-0.020-0.00129.159-0.007-0.0070.0000.0000.0000.000
41A42PHE0-0.052-0.02125.954-0.006-0.0060.0000.0000.0000.000
42A43HIS10.8280.87824.293-0.030-0.0300.0000.0000.0000.000
43A44PHE00.0430.02125.481-0.009-0.0090.0000.0000.0000.000
44A45GLU-1-0.788-0.87627.718-0.012-0.0120.0000.0000.0000.000
45A46GLU-1-0.888-0.93023.0220.0070.0070.0000.0000.0000.000
46A47ALA00.0270.02122.629-0.011-0.0110.0000.0000.0000.000
47A48SER00.0040.00723.700-0.013-0.0130.0000.0000.0000.000
48A49TRP0-0.014-0.01324.590-0.005-0.0050.0000.0000.0000.000
49A50PHE00.0020.00415.464-0.012-0.0120.0000.0000.0000.000
50A51TYR00.003-0.03021.104-0.023-0.0230.0000.0000.0000.000
51A52THR0-0.019-0.00723.217-0.012-0.0120.0000.0000.0000.000
52A53ASP-1-0.831-0.93021.672-0.076-0.0760.0000.0000.0000.000
53A54PHE0-0.060-0.04316.479-0.011-0.0110.0000.0000.0000.000
54A55VAL00.0100.01718.906-0.020-0.0200.0000.0000.0000.000
55A56LYS10.8300.93220.6050.1100.1100.0000.0000.0000.000
56A57LEU0-0.0130.00021.652-0.001-0.0010.0000.0000.0000.000
57A58MET0-0.057-0.02615.917-0.034-0.0340.0000.0000.0000.000
58A59ASN00.0180.00319.751-0.005-0.0050.0000.0000.0000.000
59A60PRO0-0.0030.00322.4500.0180.0180.0000.0000.0000.000
60A61TYR00.020-0.00325.0350.0180.0180.0000.0000.0000.000
61A62LEU0-0.0130.02823.1560.0110.0110.0000.0000.0000.000
62A63PRO00.0610.03327.3610.0010.0010.0000.0000.0000.000
63A64ASN00.0340.02228.912-0.011-0.0110.0000.0000.0000.000
64A65LEU0-0.0040.00428.3630.0060.0060.0000.0000.0000.000
65A66SER00.0160.01630.5080.0010.0010.0000.0000.0000.000
66A67ILE00.0650.02530.3770.0000.0000.0000.0000.0000.000
67A68LYS10.9350.97931.9670.0350.0350.0000.0000.0000.000
68A69SER00.0270.01233.8580.0020.0020.0000.0000.0000.000
69A70PHE00.0430.01924.5770.0000.0000.0000.0000.0000.000
70A71SER00.008-0.00730.1330.0010.0010.0000.0000.0000.000
71A72LYS10.8940.93831.5650.0270.0270.0000.0000.0000.000
72A73ILE00.0350.01729.1310.0010.0010.0000.0000.0000.000
73A74VAL0-0.0020.00126.684-0.001-0.0010.0000.0000.0000.000
74A75ILE0-0.061-0.03329.3060.0040.0040.0000.0000.0000.000
75A76ASP-1-0.950-0.97232.510-0.028-0.0280.0000.0000.0000.000
76A77ILE0-0.0020.00627.0520.0010.0010.0000.0000.0000.000
77A78CYS0-0.082-0.03826.6910.0010.0010.0000.0000.0000.000
78A79PRO00.0560.02529.3810.0060.0060.0000.0000.0000.000
79A80LEU0-0.025-0.01229.5970.0030.0030.0000.0000.0000.000
80A81ILE00.0010.00826.9200.0060.0060.0000.0000.0000.000
81A82TRP0-0.054-0.03730.3770.0020.0020.0000.0000.0000.000
82A83ASN0-0.028-0.01132.766-0.001-0.0010.0000.0000.0000.000
83A84TRP0-0.021-0.01833.6320.0030.0030.0000.0000.0000.000
84A85ASP-1-0.922-0.95739.153-0.001-0.0010.0000.0000.0000.000
85A86ILE0-0.0340.00139.788-0.002-0.0020.0000.0000.0000.000
86A87THR00.043-0.00539.4260.0000.0000.0000.0000.0000.000
87A88PRO00.0900.04234.8140.0020.0020.0000.0000.0000.000
88A89GLU-1-0.771-0.87236.685-0.018-0.0180.0000.0000.0000.000
89A90ASN0-0.003-0.00638.5290.0020.0020.0000.0000.0000.000
90A91ALA00.0390.03437.3550.0020.0020.0000.0000.0000.000
91A92LEU0-0.008-0.00334.4650.0020.0020.0000.0000.0000.000
92A93VAL0-0.039-0.01136.8730.0010.0010.0000.0000.0000.000
93A94LYS10.8500.91040.2910.0040.0040.0000.0000.0000.000
94A95PHE00.0340.02438.0500.0020.0020.0000.0000.0000.000
95A96SER00.014-0.00333.3830.0030.0030.0000.0000.0000.000
96A97ASN0-0.088-0.07036.3150.0010.0010.0000.0000.0000.000
97A98TYR00.0270.03338.6640.0000.0000.0000.0000.0000.000
98A99LYS10.7740.90032.080-0.003-0.0030.0000.0000.0000.000
99A100LYS10.9440.95337.773-0.004-0.0040.0000.0000.0000.000
100A101THR0-0.044-0.01135.3240.0000.0000.0000.0000.0000.000
101A102ILE0-0.002-0.00738.6630.0000.0000.0000.0000.0000.000
102A103PRO0-0.023-0.01237.6220.0000.0000.0000.0000.0000.000
103A104VAL0-0.025-0.00335.9620.0010.0010.0000.0000.0000.000
104A105ARG10.7940.87935.9660.0260.0260.0000.0000.0000.000
105A106GLY00.0840.02836.5790.0030.0030.0000.0000.0000.000
106A107ALA00.0210.01033.972-0.003-0.0030.0000.0000.0000.000
107A108ALA0-0.053-0.02929.8050.0020.0020.0000.0000.0000.000
108A109ILE00.0300.01831.857-0.005-0.0050.0000.0000.0000.000
109A110PHE0-0.010-0.03126.922-0.001-0.0010.0000.0000.0000.000
110A111ASN00.0600.02032.280-0.002-0.0020.0000.0000.0000.000
111A112ASP-1-0.753-0.88732.954-0.078-0.0780.0000.0000.0000.000
112A113SER0-0.042-0.01332.110-0.004-0.0040.0000.0000.0000.000
113A114LEU0-0.0030.01927.183-0.007-0.0070.0000.0000.0000.000
114A115SER0-0.051-0.03128.301-0.008-0.0080.0000.0000.0000.000
115A116LYS10.8000.87229.5700.0590.0590.0000.0000.0000.000
116A117ILE00.0020.01728.402-0.003-0.0030.0000.0000.0000.000
117A118LEU00.0330.03031.2800.0040.0040.0000.0000.0000.000
118A119LEU0-0.073-0.03229.7780.0010.0010.0000.0000.0000.000
119A120LEU00.0530.02734.4270.0010.0010.0000.0000.0000.000
120A121ARG10.8830.92636.1950.0120.0120.0000.0000.0000.000
121A122GLY00.0400.03538.2770.0000.0000.0000.0000.0000.000
122A123ILE00.0510.03341.0920.0010.0010.0000.0000.0000.000
123A124ASN00.0710.03442.5080.0000.0000.0000.0000.0000.000
124A125SER0-0.0030.01138.0560.0010.0010.0000.0000.0000.000
125A126LYS10.8930.91237.4410.0000.0000.0000.0000.0000.000
126A127HIS00.0000.02629.8590.0000.0000.0000.0000.0000.000
127A128TRP00.0260.01132.113-0.001-0.0010.0000.0000.0000.000
128A129SER0-0.082-0.06931.8210.0010.0010.0000.0000.0000.000
129A130PHE00.0880.04128.155-0.001-0.0010.0000.0000.0000.000
130A131PRO00.0380.03334.1390.0040.0040.0000.0000.0000.000
131A132ARG10.7900.89832.8710.0140.0140.0000.0000.0000.000
132A133GLY00.1040.05737.7560.0030.0030.0000.0000.0000.000
133A134LYS10.7690.86039.9740.0160.0160.0000.0000.0000.000
134A135ILE00.0100.01241.0720.0000.0000.0000.0000.0000.000
135A136GLY00.0080.00843.8140.0020.0020.0000.0000.0000.000
136A137LYS10.7620.84547.1010.0140.0140.0000.0000.0000.000
137A138ASP-1-0.822-0.88948.520-0.015-0.0150.0000.0000.0000.000
138A139GLU-1-0.802-0.87844.899-0.022-0.0220.0000.0000.0000.000
139A140ASP-1-0.817-0.90842.992-0.032-0.0320.0000.0000.0000.000
140A141ASP-1-0.813-0.90837.917-0.033-0.0330.0000.0000.0000.000
141A142VAL00.0090.00238.3030.0000.0000.0000.0000.0000.000
142A143ALA00.0070.00640.7870.0000.0000.0000.0000.0000.000
143A144CYS0-0.011-0.01441.9560.0020.0020.0000.0000.0000.000
144A145CYM-1-0.894-0.91438.166-0.039-0.0390.0000.0000.0000.000
145A146ILE0-0.008-0.01040.6100.0010.0010.0000.0000.0000.000
146A147ARG10.7880.88143.0570.0210.0210.0000.0000.0000.000
147A148GLU-1-0.778-0.87341.503-0.018-0.0180.0000.0000.0000.000
148A149VAL0-0.012-0.00239.6280.0010.0010.0000.0000.0000.000
149A150LYS10.8060.90541.7920.0280.0280.0000.0000.0000.000
150A151GLU-1-0.913-0.94245.337-0.016-0.0160.0000.0000.0000.000
151A152GLU-1-0.852-0.94840.413-0.019-0.0190.0000.0000.0000.000
152A153THR0-0.166-0.10540.018-0.001-0.0010.0000.0000.0000.000
153A154GLY00.0720.04543.505-0.001-0.0010.0000.0000.0000.000
154A155PHE0-0.049-0.03141.822-0.001-0.0010.0000.0000.0000.000
155A156ASP-1-0.806-0.88342.906-0.032-0.0320.0000.0000.0000.000
156A157LEU00.002-0.01438.084-0.001-0.0010.0000.0000.0000.000
157A158THR0-0.002-0.00940.848-0.002-0.0020.0000.0000.0000.000
158A159GLY00.0600.04837.889-0.001-0.0010.0000.0000.0000.000
159A160PHE0-0.009-0.01737.630-0.004-0.0040.0000.0000.0000.000
160A161ILE00.0420.02133.9990.0010.0010.0000.0000.0000.000
161A162ASH0-0.078-0.07333.8940.0010.0010.0000.0000.0000.000
162A163ALA00.0100.01934.5810.0010.0010.0000.0000.0000.000
163A164ASP-1-0.890-0.94432.741-0.061-0.0610.0000.0000.0000.000
164A165GLN0-0.075-0.02928.401-0.011-0.0110.0000.0000.0000.000
165A166TYR0-0.012-0.01830.4570.0040.0040.0000.0000.0000.000
166A167VAL0-0.021-0.01425.318-0.008-0.0080.0000.0000.0000.000
167A168GLU-1-0.883-0.94227.567-0.032-0.0320.0000.0000.0000.000
168A169ARG10.7980.88522.6260.0410.0410.0000.0000.0000.000
169A170ASN0-0.013-0.00128.593-0.001-0.0010.0000.0000.0000.000
170A171MET0-0.020-0.01426.9060.0030.0030.0000.0000.0000.000
171A172ASN0-0.005-0.01430.9210.0000.0000.0000.0000.0000.000
172A173GLY00.0540.02533.4840.0000.0000.0000.0000.0000.000
173A174LYS10.8920.96034.653-0.001-0.0010.0000.0000.0000.000
174A175ASN00.0360.03433.3040.0000.0000.0000.0000.0000.000
175A176PHE0-0.009-0.01431.1840.0000.0000.0000.0000.0000.000
176A177LYS10.8440.92531.5240.0410.0410.0000.0000.0000.000
177A178ILE0-0.036-0.01030.3670.0020.0020.0000.0000.0000.000
178A179PHE00.0470.01731.004-0.005-0.0050.0000.0000.0000.000
179A180LEU0-0.024-0.00827.2220.0000.0000.0000.0000.0000.000
180A181VAL00.0440.02731.5250.0000.0000.0000.0000.0000.000
181A182LYS10.8400.92531.3610.0860.0860.0000.0000.0000.000
182A183GLY0-0.017-0.00233.517-0.002-0.0020.0000.0000.0000.000
183A184VAL00.0100.01737.1750.0040.0040.0000.0000.0000.000
184A185PRO0-0.0020.01138.201-0.003-0.0030.0000.0000.0000.000
185A186GLU-1-0.804-0.91136.225-0.061-0.0610.0000.0000.0000.000
186A187ASP-1-0.942-0.96539.264-0.046-0.0460.0000.0000.0000.000
187A188PHE0-0.027-0.00542.5470.0030.0030.0000.0000.0000.000
188A189GLU-1-0.879-0.92943.410-0.027-0.0270.0000.0000.0000.000
189A190PHE0-0.030-0.01640.6610.0010.0010.0000.0000.0000.000
190A191LYS10.8500.91244.4260.0260.0260.0000.0000.0000.000
191A192PRO0-0.0180.00245.979-0.001-0.0010.0000.0000.0000.000
192A193GLU-1-0.886-0.93647.256-0.021-0.0210.0000.0000.0000.000
193A194HIS0-0.046-0.04048.9760.0020.0020.0000.0000.0000.000
194A195LYS10.9050.96150.8570.0110.0110.0000.0000.0000.000
195A196ASN0-0.0050.00047.5570.0000.0000.0000.0000.0000.000
196A204LYN00.0950.05430.849-0.001-0.0010.0000.0000.0000.000
197A205ASP-1-0.797-0.87729.067-0.063-0.0630.0000.0000.0000.000
198A206PHE00.0920.04921.9540.0030.0030.0000.0000.0000.000
199A207LYS10.8670.91724.3810.0740.0740.0000.0000.0000.000
200A208LYS10.8030.87924.5690.0430.0430.0000.0000.0000.000
201A209LEU00.0630.02425.1820.0060.0060.0000.0000.0000.000
202A210SER0-0.016-0.01020.1960.0080.0080.0000.0000.0000.000
203A211LYS10.9160.96820.0940.0940.0940.0000.0000.0000.000
204A212ALA0-0.031-0.00721.9930.0120.0120.0000.0000.0000.000
205A213ILE00.006-0.01120.3040.0100.0100.0000.0000.0000.000
206A214THR0-0.031-0.02116.6310.0100.0100.0000.0000.0000.000
207A215LYS10.8950.97118.1700.0180.0180.0000.0000.0000.000
208A216ASN00.0370.02618.6660.0140.0140.0000.0000.0000.000
209A224LEU00.0360.01328.8450.0010.0010.0000.0000.0000.000
210A225VAL00.0670.04626.541-0.002-0.0020.0000.0000.0000.000
211A226ASN00.025-0.00224.494-0.010-0.0100.0000.0000.0000.000
212A227SER0-0.073-0.03222.5360.0050.0050.0000.0000.0000.000
213A228MET00.0270.02322.730-0.004-0.0040.0000.0000.0000.000
214A229ILE00.0210.00319.510-0.013-0.0130.0000.0000.0000.000
215A230ARG10.9330.97011.9650.1170.1170.0000.0000.0000.000
216A231PRO00.0930.05619.189-0.018-0.0180.0000.0000.0000.000
217A232LEU00.0320.02021.717-0.009-0.0090.0000.0000.0000.000
218A233SER0-0.030-0.02019.067-0.017-0.0170.0000.0000.0000.000
219A234LEU0-0.0260.00417.467-0.024-0.0240.0000.0000.0000.000
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