FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: JQNV9

Calculation Name: 5XI8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5XI8

Chain ID: A

ChEMBL ID:

UniProt ID: P66948

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:

Apendix: None


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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1674983.931136
FMO2-HF: Nuclear repulsion 1607632.85157
FMO2-HF: Total energy -67351.079566
FMO2-MP2: Total energy -67550.35255


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:308:GLY)


Summations of interaction energy for fragment #1(A:308:GLY)
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.
-0.4581.8190.68-1.108-1.8480.003
Interaction energy analysis for fragmet #1(A:308:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / 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].
3A310ALA00.0540.0303.8640.1931.177-0.001-0.426-0.5570.001
4A311ALA00.0000.0012.371-1.380-0.5870.682-0.575-0.9000.002
5A312GLN00.0180.0213.977-0.3330.0950.000-0.101-0.3270.000
6A313TYR00.048-0.0015.8370.4520.4520.0000.0000.0000.000
7A314GLY00.0380.0227.7060.1240.1240.0000.0000.0000.000
8A315ARG10.9020.9374.1101.0241.096-0.001-0.006-0.0640.000
9A316ALA0-0.002-0.0019.7620.0480.0480.0000.0000.0000.000
10A317LEU00.0150.01111.8070.0510.0510.0000.0000.0000.000
11A318GLN00.0220.01712.866-0.007-0.0070.0000.0000.0000.000
12A319ALA0-0.052-0.02713.8030.0140.0140.0000.0000.0000.000
13A320MET0-0.0120.00415.6160.0030.0030.0000.0000.0000.000
14A321GLU-1-0.943-0.96217.4150.0130.0130.0000.0000.0000.000
15A322ALA0-0.063-0.02618.4260.0110.0110.0000.0000.0000.000
16A323ASN0-0.007-0.02320.1750.0040.0040.0000.0000.0000.000
17A324LYS10.9360.98717.9810.1070.1070.0000.0000.0000.000
18A325TYR00.0450.01417.995-0.035-0.0350.0000.0000.0000.000
19A326ASP-1-0.832-0.91418.331-0.252-0.2520.0000.0000.0000.000
20A327GLU-1-0.859-0.90814.212-0.356-0.3560.0000.0000.0000.000
21A328ALA00.0210.01913.791-0.082-0.0820.0000.0000.0000.000
22A329ARG10.7780.87413.7140.1490.1490.0000.0000.0000.000
23A330LYS10.7480.84214.0340.2360.2360.0000.0000.0000.000
24A331THR0-0.061-0.0348.618-0.105-0.1050.0000.0000.0000.000
25A332LEU00.0030.0089.467-0.249-0.2490.0000.0000.0000.000
26A333GLN00.003-0.00611.4350.0030.0030.0000.0000.0000.000
27A334PRO00.001-0.0038.7310.0460.0460.0000.0000.0000.000
28A335LEU0-0.0080.0035.872-0.090-0.0900.0000.0000.0000.000
29A336LEU0-0.018-0.0129.5710.1280.1280.0000.0000.0000.000
30A337ALA0-0.011-0.00313.0390.0710.0710.0000.0000.0000.000
31A338ALA0-0.0190.00210.1280.0590.0590.0000.0000.0000.000
32A339GLU-1-0.826-0.8809.132-0.410-0.4100.0000.0000.0000.000
33A340PRO0-0.015-0.01213.4200.0230.0230.0000.0000.0000.000
34A341GLY0-0.034-0.02316.3420.0270.0270.0000.0000.0000.000
35A342ASN0-0.020-0.01311.4080.0680.0680.0000.0000.0000.000
36A343ALA00.027-0.00315.126-0.019-0.0190.0000.0000.0000.000
37A344TRP00.0750.04113.9500.0030.0030.0000.0000.0000.000
38A345TYR0-0.076-0.0588.340-0.103-0.1030.0000.0000.0000.000
39A346LEU0-0.027-0.01814.104-0.001-0.0010.0000.0000.0000.000
40A347ASP-1-0.862-0.89817.731-0.086-0.0860.0000.0000.0000.000
41A348LEU00.0550.02913.231-0.008-0.0080.0000.0000.0000.000
42A349ALA0-0.026-0.02616.505-0.004-0.0040.0000.0000.0000.000
43A350THR0-0.053-0.03217.9050.0130.0130.0000.0000.0000.000
44A351ASP-1-0.850-0.92720.088-0.090-0.0900.0000.0000.0000.000
45A352ILE0-0.008-0.02015.6800.0020.0020.0000.0000.0000.000
46A353ASP-1-0.815-0.88220.303-0.185-0.1850.0000.0000.0000.000
47A354LEU0-0.029-0.00622.8970.0110.0110.0000.0000.0000.000
48A355GLY00.0280.03123.7580.0100.0100.0000.0000.0000.000
49A356GLN0-0.021-0.01822.216-0.010-0.0100.0000.0000.0000.000
50A357ASN0-0.005-0.00225.8250.0060.0060.0000.0000.0000.000
51A358LYS10.8280.91723.2710.1560.1560.0000.0000.0000.000
52A359ALA00.0670.02526.322-0.007-0.0070.0000.0000.0000.000
53A360ASN00.0160.00028.1450.0030.0030.0000.0000.0000.000
54A361GLU-1-0.838-0.91024.527-0.122-0.1220.0000.0000.0000.000
55A362ALA00.0250.02123.578-0.008-0.0080.0000.0000.0000.000
56A363ILE00.0020.00624.6140.0000.0000.0000.0000.0000.000
57A364ASN0-0.013-0.01627.3680.0090.0090.0000.0000.0000.000
58A365ARG10.8260.90619.0690.1980.1980.0000.0000.0000.000
59A366LEU00.0190.00822.1240.0000.0000.0000.0000.0000.000
60A367LYS10.8840.93724.3260.0820.0820.0000.0000.0000.000
61A368ASN0-0.033-0.00723.2540.0170.0170.0000.0000.0000.000
62A369ALA00.0250.03321.778-0.002-0.0020.0000.0000.0000.000
63A370ARG10.9660.97220.2350.1220.1220.0000.0000.0000.000
64A371ASP-1-0.842-0.92721.499-0.062-0.0620.0000.0000.0000.000
65A372LEU0-0.0070.00823.9310.0090.0090.0000.0000.0000.000
66A373ARG10.8060.89125.7840.0670.0670.0000.0000.0000.000
67A374THR00.0000.00226.4580.0030.0030.0000.0000.0000.000
68A375ASN00.0380.02420.3860.0080.0080.0000.0000.0000.000
69A376PRO00.0590.01624.685-0.008-0.0080.0000.0000.0000.000
70A377VAL00.0520.04120.157-0.003-0.0030.0000.0000.0000.000
71A378LEU0-0.0040.01020.319-0.010-0.0100.0000.0000.0000.000
72A379GLN00.0040.01023.9740.0010.0010.0000.0000.0000.000
73A380LEU00.0370.02425.694-0.003-0.0030.0000.0000.0000.000
74A381ASN0-0.037-0.04821.869-0.011-0.0110.0000.0000.0000.000
75A382LEU0-0.032-0.00825.266-0.004-0.0040.0000.0000.0000.000
76A383ALA00.0050.00127.6880.0010.0010.0000.0000.0000.000
77A384ASN00.0590.03325.7780.0050.0050.0000.0000.0000.000
78A385ALA00.0170.00226.4700.0000.0000.0000.0000.0000.000
79A386TYR0-0.005-0.02628.515-0.003-0.0030.0000.0000.0000.000
80A387LEU0-0.036-0.01032.0390.0020.0020.0000.0000.0000.000
81A388GLN0-0.019-0.01329.6030.0030.0030.0000.0000.0000.000
82A389GLY0-0.034-0.01232.124-0.002-0.0020.0000.0000.0000.000
83A390GLY0-0.0100.00332.9910.0010.0010.0000.0000.0000.000
84A391GLN0-0.068-0.04233.8990.0030.0030.0000.0000.0000.000
85A392PRO00.0590.01936.1830.0000.0000.0000.0000.0000.000
86A393GLN00.0050.00937.7280.0030.0030.0000.0000.0000.000
87A394GLU-1-0.845-0.92734.728-0.038-0.0380.0000.0000.0000.000
88A395ALA0-0.0160.00433.6300.0000.0000.0000.0000.0000.000
89A396ALA00.0790.03634.6540.0020.0020.0000.0000.0000.000
90A397ASN0-0.063-0.03236.8480.0050.0050.0000.0000.0000.000
91A398ILE0-0.095-0.04130.6680.0020.0020.0000.0000.0000.000
92A399LEU00.0160.00731.9090.0030.0030.0000.0000.0000.000
93A400ASN0-0.042-0.01534.7440.0060.0060.0000.0000.0000.000
94A401ARG10.8610.93432.5140.0330.0330.0000.0000.0000.000
95A402TYR0-0.069-0.04627.7980.0020.0020.0000.0000.0000.000
96A403THR00.039-0.00432.9050.0040.0040.0000.0000.0000.000
97A404PHE0-0.053-0.01435.3320.0040.0040.0000.0000.0000.000
98A405ASN0-0.095-0.06232.6940.0050.0050.0000.0000.0000.000
99A406ASN0-0.068-0.03429.4350.0060.0060.0000.0000.0000.000
100A407LYS10.8670.92132.447-0.016-0.0160.0000.0000.0000.000
101A408ASP-1-0.809-0.88432.7460.0170.0170.0000.0000.0000.000
102A409ASP-1-0.778-0.85529.629-0.004-0.0040.0000.0000.0000.000
103A410SER0-0.019-0.02231.823-0.002-0.0020.0000.0000.0000.000
104A411ASN0-0.010-0.00828.605-0.007-0.0070.0000.0000.0000.000
105A412GLY00.0250.00531.110-0.005-0.0050.0000.0000.0000.000
106A413TRP0-0.012-0.02932.530-0.004-0.0040.0000.0000.0000.000
107A414ASP-1-0.871-0.92633.621-0.010-0.0100.0000.0000.0000.000
108A415LEU00.007-0.00429.493-0.003-0.0030.0000.0000.0000.000
109A416LEU0-0.040-0.01434.209-0.002-0.0020.0000.0000.0000.000
110A417ALA0-0.006-0.00837.1060.0000.0000.0000.0000.0000.000
111A418GLN0-0.025-0.01734.272-0.001-0.0010.0000.0000.0000.000
112A419ALA00.003-0.00136.443-0.001-0.0010.0000.0000.0000.000
113A420GLU-1-0.771-0.89638.366-0.022-0.0220.0000.0000.0000.000
114A421ALA0-0.037-0.01341.6330.0010.0010.0000.0000.0000.000
115A422ALA0-0.058-0.02440.0860.0000.0000.0000.0000.0000.000
116A423LEU0-0.041-0.01140.559-0.001-0.0010.0000.0000.0000.000
117A424ASN0-0.070-0.02844.0580.0010.0010.0000.0000.0000.000
118A425ASN0-0.028-0.01343.5350.0020.0020.0000.0000.0000.000
119A426ARG10.8960.92945.8680.0140.0140.0000.0000.0000.000
120A427ASP-1-0.820-0.90047.808-0.010-0.0100.0000.0000.0000.000
121A428GLN00.0750.03143.8010.0020.0020.0000.0000.0000.000
122A429GLU-1-0.802-0.86442.865-0.014-0.0140.0000.0000.0000.000
123A430LEU0-0.072-0.03643.5760.0010.0010.0000.0000.0000.000
124A431ALA00.0400.01144.7640.0020.0020.0000.0000.0000.000
125A432ALA00.0080.00639.5920.0020.0020.0000.0000.0000.000
126A433ARG10.8920.92240.4520.0140.0140.0000.0000.0000.000
127A434ALA0-0.043-0.00542.2820.0020.0020.0000.0000.0000.000
128A435GLU-1-0.766-0.85039.7570.0040.0040.0000.0000.0000.000
129A436GLY00.0530.03038.2140.0020.0020.0000.0000.0000.000
130A437TYR0-0.052-0.04939.2240.0010.0010.0000.0000.0000.000
131A438ALA0-0.015-0.00941.7920.0020.0020.0000.0000.0000.000
132A439LEU0-0.0160.00335.2870.0020.0020.0000.0000.0000.000
133A440ALA0-0.044-0.00938.1460.0020.0020.0000.0000.0000.000
134A441GLY00.0220.00839.4990.0010.0010.0000.0000.0000.000
135A442ARG10.8350.91942.409-0.003-0.0030.0000.0000.0000.000
136A443LEU00.0280.00044.276-0.002-0.0020.0000.0000.0000.000
137A444ASP-1-0.812-0.90346.9380.0060.0060.0000.0000.0000.000
138A445GLN00.0160.01946.6650.0000.0000.0000.0000.0000.000
139A446ALA00.0150.01144.958-0.001-0.0010.0000.0000.0000.000
140A447ILE00.0130.00946.765-0.001-0.0010.0000.0000.0000.000
141A448SER00.0050.02150.117-0.001-0.0010.0000.0000.0000.000
142A449LEU0-0.049-0.01245.773-0.001-0.0010.0000.0000.0000.000
143A450MET00.0200.03344.869-0.002-0.0020.0000.0000.0000.000
144A451SER0-0.020-0.04049.2720.0000.0000.0000.0000.0000.000
145A452SER0-0.048-0.03151.358-0.001-0.0010.0000.0000.0000.000
146A453ALA00.0040.02548.914-0.001-0.0010.0000.0000.0000.000
147A454SER0-0.053-0.06851.003-0.001-0.0010.0000.0000.0000.000
148A455SER0-0.097-0.05753.4940.0000.0000.0000.0000.0000.000
149A456GLN0-0.030-0.02851.964-0.001-0.0010.0000.0000.0000.000
150A457VAL0-0.0060.02251.222-0.001-0.0010.0000.0000.0000.000
151A458LYS10.9380.96754.3710.0070.0070.0000.0000.0000.000
152A459LEU00.0650.03357.0140.0000.0000.0000.0000.0000.000
153A460GLY0-0.013-0.00858.8270.0000.0000.0000.0000.0000.000
154A461SER0-0.068-0.03354.4280.0000.0000.0000.0000.0000.000
155A462LEU00.024-0.00650.1020.0000.0000.0000.0000.0000.000
156A463GLN00.0260.01146.1340.0010.0010.0000.0000.0000.000
157A464GLN00.0450.01950.6510.0000.0000.0000.0000.0000.000
158A465ALA00.0240.01352.7220.0010.0010.0000.0000.0000.000
159A466ARG10.8780.94046.1310.0060.0060.0000.0000.0000.000
160A467TYR0-0.001-0.03046.2770.0010.0010.0000.0000.0000.000
161A468ASP-1-0.762-0.85249.7530.0000.0000.0000.0000.0000.000
162A469ALA0-0.017-0.00749.5780.0010.0010.0000.0000.0000.000
163A470ARG10.7600.83043.061-0.003-0.0030.0000.0000.0000.000
164A471ILE0-0.0070.00547.8130.0010.0010.0000.0000.0000.000
165A472ASP-1-0.818-0.91250.4420.0050.0050.0000.0000.0000.000
166A473GLN0-0.020-0.00646.0060.0010.0010.0000.0000.0000.000
167A474LEU0-0.022-0.00644.3350.0020.0020.0000.0000.0000.000
168A475ARG10.9120.95747.921-0.003-0.0030.0000.0000.0000.000
169A476GLN0-0.028-0.02049.6930.0010.0010.0000.0000.0000.000
170A477LEU0-0.041-0.01543.0620.0020.0020.0000.0000.0000.000
171A478GLN0-0.011-0.02347.4240.0010.0010.0000.0000.0000.000
172A479GLU-1-0.822-0.88849.6890.0110.0110.0000.0000.0000.000
173A480ARG10.8590.94343.384-0.021-0.0210.0000.0000.0000.000
174A481PHE0-0.024-0.01443.0790.0020.0020.0000.0000.0000.000
175A482LYS10.8020.90549.132-0.010-0.0100.0000.0000.0000.000