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: LNJN9

Calculation Name: 5XAY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XAY

Chain ID: A

ChEMBL ID:

UniProt ID: Q9XCC7

Base Structure: X-ray

Registration Date: 2023-09-20

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. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2458270.070144
FMO2-HF: Nuclear repulsion 2374414.619086
FMO2-HF: Total energy -83855.451058
FMO2-MP2: Total energy -84102.329998


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-15.478-8.3724.291-4.643-6.751-0.014
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.059 / 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].
3A4GLN00.0380.0102.652-1.9600.2910.252-0.944-1.5580.005
4A5GLU-1-0.857-0.9182.306-10.579-7.5523.878-2.976-3.929-0.024
5A6ARG10.9270.9632.996-3.977-2.2710.162-0.716-1.1510.005
6A7ALA00.0590.0225.3440.2280.350-0.001-0.007-0.1130.000
7A8ALA00.0130.0016.8880.1860.1860.0000.0000.0000.000
8A9GLN0-0.082-0.0398.097-0.084-0.0840.0000.0000.0000.000
9A10THR00.004-0.0329.7950.1070.1070.0000.0000.0000.000
10A11ARG10.7610.86311.5080.3170.3170.0000.0000.0000.000
11A12ARG10.9710.9918.8830.9300.9300.0000.0000.0000.000
12A13THR00.0160.01414.1390.0320.0320.0000.0000.0000.000
13A14ILE0-0.037-0.01115.2530.0340.0340.0000.0000.0000.000
14A15VAL00.0150.00517.2600.0260.0260.0000.0000.0000.000
15A16ALA00.0210.01018.5850.0190.0190.0000.0000.0000.000
16A17ALA0-0.015-0.00320.1430.0180.0180.0000.0000.0000.000
17A18ALA0-0.010-0.01921.6990.0150.0150.0000.0000.0000.000
18A19ALA0-0.011-0.00423.0160.0100.0100.0000.0000.0000.000
19A20ALA00.0260.02024.7690.0090.0090.0000.0000.0000.000
20A21VAL00.004-0.00626.1200.0090.0090.0000.0000.0000.000
21A22PHE0-0.008-0.00225.3300.0080.0080.0000.0000.0000.000
22A23ASP-1-0.786-0.86728.977-0.070-0.0700.0000.0000.0000.000
23A24GLU-1-0.848-0.89429.935-0.042-0.0420.0000.0000.0000.000
24A25LEU0-0.034-0.02132.1600.0050.0050.0000.0000.0000.000
25A26GLY00.0180.01633.1150.0040.0040.0000.0000.0000.000
26A27TYR00.0170.00329.1660.0020.0020.0000.0000.0000.000
27A28GLU-1-0.878-0.92732.482-0.022-0.0220.0000.0000.0000.000
28A29ALA00.008-0.00634.4850.0040.0040.0000.0000.0000.000
29A30THR00.0360.04328.2780.0040.0040.0000.0000.0000.000
30A31THR0-0.023-0.02130.0460.0030.0030.0000.0000.0000.000
31A32ILE00.0680.00824.175-0.003-0.0030.0000.0000.0000.000
32A33ALA0-0.006-0.00325.4180.0030.0030.0000.0000.0000.000
33A34GLU-1-0.775-0.87626.6580.0020.0020.0000.0000.0000.000
34A35ILE00.0450.02921.9690.0000.0000.0000.0000.0000.000
35A36LEU0-0.050-0.00720.683-0.005-0.0050.0000.0000.0000.000
36A37LYS10.8200.90622.1930.0020.0020.0000.0000.0000.000
37A38ARG10.7890.85924.0080.0460.0460.0000.0000.0000.000
38A39SER0-0.038-0.03618.4420.0000.0000.0000.0000.0000.000
39A40GLY00.0110.01018.7290.0000.0000.0000.0000.0000.000
40A41VAL0-0.034-0.00615.3100.0310.0310.0000.0000.0000.000
41A42THR00.0520.03816.430-0.014-0.0140.0000.0000.0000.000
42A43LYS10.9360.94518.793-0.085-0.0850.0000.0000.0000.000
43A44GLY0-0.0070.01518.344-0.018-0.0180.0000.0000.0000.000
44A45ALA00.0460.02114.580-0.016-0.0160.0000.0000.0000.000
45A46LEU00.017-0.00115.957-0.043-0.0430.0000.0000.0000.000
46A47TYR0-0.019-0.03218.611-0.015-0.0150.0000.0000.0000.000
47A48PHE0-0.0580.00011.464-0.002-0.0020.0000.0000.0000.000
48A49HIS0-0.018-0.00611.168-0.047-0.0470.0000.0000.0000.000
49A50PHE00.0040.00216.342-0.026-0.0260.0000.0000.0000.000
50A51THR0-0.023-0.02319.9840.0220.0220.0000.0000.0000.000
51A52SER00.011-0.01322.9280.0120.0120.0000.0000.0000.000
52A53LYS10.8510.92824.6940.0220.0220.0000.0000.0000.000
53A54GLU-1-0.808-0.89426.363-0.064-0.0640.0000.0000.0000.000
54A55GLN00.0710.05821.465-0.002-0.0020.0000.0000.0000.000
55A56LEU00.0100.01020.426-0.015-0.0150.0000.0000.0000.000
56A57ALA0-0.007-0.00423.133-0.012-0.0120.0000.0000.0000.000
57A58GLN0-0.033-0.03725.299-0.011-0.0110.0000.0000.0000.000
58A59GLU-1-0.788-0.85517.315-0.263-0.2630.0000.0000.0000.000
59A60VAL00.006-0.00522.134-0.017-0.0170.0000.0000.0000.000
60A61LEU0-0.070-0.04023.741-0.007-0.0070.0000.0000.0000.000
61A62THR0-0.0080.00123.317-0.004-0.0040.0000.0000.0000.000
62A63SER0-0.069-0.02720.472-0.015-0.0150.0000.0000.0000.000
63A64GLN0-0.009-0.00821.005-0.029-0.0290.0000.0000.0000.000
64A65LEU0-0.0060.02421.174-0.008-0.0080.0000.0000.0000.000
65A75ARG10.8810.92832.2380.1180.1180.0000.0000.0000.000
66A76LEU0-0.0250.00934.1040.0030.0030.0000.0000.0000.000
67A77VAL00.0320.01732.494-0.006-0.0060.0000.0000.0000.000
68A78LEU00.0300.00033.884-0.004-0.0040.0000.0000.0000.000
69A79GLN0-0.060-0.05033.8430.0070.0070.0000.0000.0000.000
70A80GLN0-0.039-0.02427.6450.0000.0000.0000.0000.0000.000
71A81ILE00.0670.02731.254-0.003-0.0030.0000.0000.0000.000
72A82ILE0-0.0330.00533.2070.0020.0020.0000.0000.0000.000
73A83ASP-1-0.745-0.83630.029-0.147-0.1470.0000.0000.0000.000
74A84GLU-1-0.815-0.88827.461-0.174-0.1740.0000.0000.0000.000
75A85THR0-0.022-0.02529.7160.0020.0020.0000.0000.0000.000
76A86LEU0-0.032-0.01932.7980.0050.0050.0000.0000.0000.000
77A87LEU00.0120.00725.4210.0030.0030.0000.0000.0000.000
78A88LEU00.0350.02427.713-0.001-0.0010.0000.0000.0000.000
79A89ALA00.0180.00630.1050.0050.0050.0000.0000.0000.000
80A90GLN0-0.039-0.01530.6500.0080.0080.0000.0000.0000.000
81A91LEU0-0.003-0.00625.5120.0050.0050.0000.0000.0000.000
82A92LEU0-0.042-0.02029.1990.0050.0050.0000.0000.0000.000
83A93SER0-0.025-0.00531.5030.0070.0070.0000.0000.0000.000
84A94LYS10.8920.94129.9320.1050.1050.0000.0000.0000.000
85A95GLY0-0.0120.00630.6540.0020.0020.0000.0000.0000.000
86A96ASP-1-0.802-0.89824.253-0.183-0.1830.0000.0000.0000.000
87A97PRO00.0470.00424.3280.0020.0020.0000.0000.0000.000
88A98LEU00.0150.01419.8020.0060.0060.0000.0000.0000.000
89A99VAL0-0.008-0.00224.3900.0070.0070.0000.0000.0000.000
90A100ARG10.7980.87727.4410.0900.0900.0000.0000.0000.000
91A101GLY00.0320.02927.5330.0090.0090.0000.0000.0000.000
92A102SER0-0.011-0.00927.0440.0090.0090.0000.0000.0000.000
93A103VAL00.0030.01228.7760.0080.0080.0000.0000.0000.000
94A104ARG10.8170.91531.9430.0580.0580.0000.0000.0000.000
95A105LEU0-0.043-0.01728.0530.0070.0070.0000.0000.0000.000
96A106THR0-0.089-0.05931.8640.0030.0030.0000.0000.0000.000
97A107VAL0-0.020-0.00133.8600.0040.0040.0000.0000.0000.000
98A108GLU-1-0.848-0.90934.964-0.047-0.0470.0000.0000.0000.000
99A109PRO00.021-0.00337.918-0.002-0.0020.0000.0000.0000.000
100A110GLY00.0120.00937.7540.0020.0020.0000.0000.0000.000
101A111ALA0-0.023-0.01138.4360.0000.0000.0000.0000.0000.000
102A112PRO0-0.016-0.02039.973-0.001-0.0010.0000.0000.0000.000
103A113ARG10.7580.87637.5210.0380.0380.0000.0000.0000.000
104A114ASP-1-0.750-0.86135.980-0.043-0.0430.0000.0000.0000.000
105A115GLY0-0.042-0.01435.5160.0010.0010.0000.0000.0000.000
106A116LEU00.0010.01629.6200.0000.0000.0000.0000.0000.000
107A117ASP-1-0.823-0.92631.957-0.070-0.0700.0000.0000.0000.000
108A118ARG10.8390.88731.4240.0510.0510.0000.0000.0000.000
109A119ARG10.8990.95632.6020.0520.0520.0000.0000.0000.000
110A120ALA0-0.011-0.00629.770-0.005-0.0050.0000.0000.0000.000
111A121PRO00.0870.03927.806-0.005-0.0050.0000.0000.0000.000
112A122MET00.0070.01329.084-0.009-0.0090.0000.0000.0000.000
113A123GLN0-0.072-0.04932.0980.0050.0050.0000.0000.0000.000
114A124GLU-1-0.905-0.94425.266-0.150-0.1500.0000.0000.0000.000
115A125TRP00.0120.01229.147-0.005-0.0050.0000.0000.0000.000
116A126ILE0-0.019-0.02930.140-0.001-0.0010.0000.0000.0000.000
117A127GLY0-0.040-0.03131.1190.0030.0030.0000.0000.0000.000
118A128HIS00.0190.00426.306-0.001-0.0010.0000.0000.0000.000
119A129GLY00.0130.01129.857-0.002-0.0020.0000.0000.0000.000
120A130ARG10.8520.90633.0630.1000.1000.0000.0000.0000.000
121A131ASP-1-0.884-0.94630.367-0.122-0.1220.0000.0000.0000.000
122A132LEU0-0.027-0.01228.8480.0010.0010.0000.0000.0000.000
123A133LEU00.0150.00032.5980.0040.0040.0000.0000.0000.000
124A134ARG10.8790.93934.1850.1050.1050.0000.0000.0000.000
125A135ARG10.9050.95728.3720.1620.1620.0000.0000.0000.000
126A136ALA00.0220.00935.1310.0020.0020.0000.0000.0000.000
127A137GLU-1-0.980-0.97937.464-0.074-0.0740.0000.0000.0000.000
128A138ALA00.0030.00237.5960.0030.0030.0000.0000.0000.000
129A139GLY0-0.051-0.01638.6940.0020.0020.0000.0000.0000.000
130A140GLY0-0.032-0.01539.5500.0010.0010.0000.0000.0000.000
131A141GLU-1-0.825-0.93637.381-0.109-0.1090.0000.0000.0000.000
132A142LEU0-0.029-0.00340.0310.0010.0010.0000.0000.0000.000
133A143LEU0-0.025-0.01443.5560.0030.0030.0000.0000.0000.000
134A144PRO00.0080.00146.271-0.001-0.0010.0000.0000.0000.000
135A145ARG10.9210.94847.4470.0550.0550.0000.0000.0000.000
136A146LEU00.0430.04344.2040.0020.0020.0000.0000.0000.000
137A147ASP-1-0.837-0.92842.974-0.070-0.0700.0000.0000.0000.000
138A148VAL00.0200.00537.958-0.001-0.0010.0000.0000.0000.000
139A149ASP-1-0.764-0.84338.128-0.084-0.0840.0000.0000.0000.000
140A150ALA00.0040.00539.734-0.001-0.0010.0000.0000.0000.000
141A151VAL00.0260.00039.9100.0000.0000.0000.0000.0000.000
142A152ALA0-0.002-0.00535.817-0.002-0.0020.0000.0000.0000.000
143A153ARG10.8110.88237.6150.0710.0710.0000.0000.0000.000
144A154MET0-0.019-0.00439.3450.0010.0010.0000.0000.0000.000
145A155LEU00.0040.01237.1650.0000.0000.0000.0000.0000.000
146A156VAL00.0150.01733.9790.0000.0000.0000.0000.0000.000
147A157GLY00.0210.01136.5050.0010.0010.0000.0000.0000.000
148A158GLY00.0450.02139.7350.0030.0030.0000.0000.0000.000
149A159PHE00.0250.00732.9830.0020.0020.0000.0000.0000.000
150A160THR0-0.045-0.02936.6090.0010.0010.0000.0000.0000.000
151A161GLY00.0010.00537.8850.0030.0030.0000.0000.0000.000
152A162ALA0-0.018-0.01640.0500.0030.0030.0000.0000.0000.000
153A163GLN00.0530.01135.4160.0050.0050.0000.0000.0000.000
154A164ILE0-0.033-0.01038.7320.0030.0030.0000.0000.0000.000
155A165LEU00.018-0.00440.7580.0030.0030.0000.0000.0000.000
156A166SER0-0.024-0.01740.4640.0010.0010.0000.0000.0000.000
157A167ASN0-0.053-0.03338.8990.0000.0000.0000.0000.0000.000
158A168ILE0-0.026-0.02141.1610.0030.0030.0000.0000.0000.000
159A169LEU0-0.055-0.00944.4840.0030.0030.0000.0000.0000.000
160A170THR0-0.035-0.01243.3840.0010.0010.0000.0000.0000.000
161A171GLY00.0620.03341.6320.0010.0010.0000.0000.0000.000
162A172HIS0-0.055-0.04535.838-0.004-0.0040.0000.0000.0000.000
163A173ALA0-0.024-0.00938.917-0.004-0.0040.0000.0000.0000.000
164A174ASP-1-0.794-0.86840.713-0.064-0.0640.0000.0000.0000.000
165A175LEU00.0080.02235.145-0.002-0.0020.0000.0000.0000.000
166A176LEU00.0200.00335.503-0.001-0.0010.0000.0000.0000.000
167A177GLU-1-0.818-0.87938.332-0.062-0.0620.0000.0000.0000.000
168A178ARG10.7820.86541.7020.0600.0600.0000.0000.0000.000
169A179VAL00.0080.00336.1040.0000.0000.0000.0000.0000.000
170A180THR0-0.029-0.03139.391-0.002-0.0020.0000.0000.0000.000
171A181ASP-1-0.820-0.91440.481-0.064-0.0640.0000.0000.0000.000
172A182MET0-0.0270.01941.5980.0030.0030.0000.0000.0000.000
173A183HIS00.010-0.00835.9380.0050.0050.0000.0000.0000.000
174A184ARG10.8650.93640.9860.0720.0720.0000.0000.0000.000
175A185HIS0-0.041-0.02743.4570.0030.0030.0000.0000.0000.000
176A186LEU00.0070.01041.4730.0010.0010.0000.0000.0000.000
177A187MET00.0520.02638.3930.0010.0010.0000.0000.0000.000
178A188THR0-0.082-0.04542.8980.0010.0010.0000.0000.0000.000
179A189SER0-0.100-0.04845.9570.0030.0030.0000.0000.0000.000
180A190VAL0-0.004-0.00941.3660.0010.0010.0000.0000.0000.000
181A191ALA00.0400.03042.577-0.001-0.0010.0000.0000.0000.000
182A192VAL00.0020.00244.1430.0040.0040.0000.0000.0000.000
183A193PRO00.0640.02346.060-0.003-0.0030.0000.0000.0000.000
184A194ALA00.005-0.00147.4140.0000.0000.0000.0000.0000.000
185A195VAL0-0.034-0.02641.281-0.002-0.0020.0000.0000.0000.000
186A196LEU00.0060.00743.210-0.003-0.0030.0000.0000.0000.000
187A197VAL0-0.035-0.01644.536-0.001-0.0010.0000.0000.0000.000
188A198ARG10.9240.96940.6690.0910.0910.0000.0000.0000.000
189A199LEU0-0.0460.00238.276-0.006-0.0060.0000.0000.0000.000
190A200ASP-1-0.815-0.88837.652-0.102-0.1020.0000.0000.0000.000
191A201PHE00.003-0.01537.903-0.005-0.0050.0000.0000.0000.000
192A202SER0-0.045-0.02838.9910.0020.0020.0000.0000.0000.000
193A203ALA00.0720.00537.664-0.006-0.0060.0000.0000.0000.000
194A204GLU-1-0.874-0.93236.367-0.094-0.0940.0000.0000.0000.000
195A205ARG10.7900.87231.6520.1330.1330.0000.0000.0000.000
196A206SER00.0070.00732.808-0.013-0.0130.0000.0000.0000.000
197A207ILE00.012-0.01231.809-0.008-0.0080.0000.0000.0000.000
198A208THR0-0.053-0.01930.132-0.008-0.0080.0000.0000.0000.000
199A209VAL0-0.006-0.00527.679-0.013-0.0130.0000.0000.0000.000
200A210TYR00.0280.00226.857-0.015-0.0150.0000.0000.0000.000
201A211ASP-1-0.818-0.88326.611-0.176-0.1760.0000.0000.0000.000
202A212GLU-1-0.922-0.94922.059-0.312-0.3120.0000.0000.0000.000
203A213ALA00.0390.01222.632-0.024-0.0240.0000.0000.0000.000
204A214MET0-0.036-0.02921.753-0.021-0.0210.0000.0000.0000.000
205A215ARG10.7780.87521.0130.1990.1990.0000.0000.0000.000
206A216ARG10.7800.88317.1410.3520.3520.0000.0000.0000.000
207A217ARG10.7700.87716.8140.1810.1810.0000.0000.0000.000
208A218GLU-1-0.910-0.93614.412-0.422-0.4220.0000.0000.0000.000
209A219ALA0-0.013-0.01617.343-0.019-0.0190.0000.0000.0000.000
210A220PRO0-0.0140.01414.490-0.007-0.0070.0000.0000.0000.000
211A221LEU00.0410.01613.5730.0640.0640.0000.0000.0000.000
212A222PRO00.0570.03012.236-0.085-0.0850.0000.0000.0000.000
213A223ALA0-0.016-0.0107.6020.0610.0610.0000.0000.0000.000
214A224ALA00.008-0.0099.4280.0870.0870.0000.0000.0000.000
215A225GLY0-0.061-0.0319.749-0.027-0.0270.0000.0000.0000.000
216A226ASP-1-0.855-0.90610.5900.1690.1690.0000.0000.0000.000
217A227LEU0-0.038-0.02213.188-0.072-0.0720.0000.0000.0000.000
218A228GLU-1-0.897-0.95315.8290.1980.1980.0000.0000.0000.000
219A229HIS0-0.060-0.01815.908-0.031-0.0310.0000.0000.0000.000