FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZVV5N

Calculation Name: 5X15-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5X15

Chain ID: A

ChEMBL ID:

UniProt ID: Q9FBS9

Base Structure: X-ray

Registration Date: 2023-09-21

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2079236.083954
FMO2-HF: Nuclear repulsion 2003898.246995
FMO2-HF: Total energy -75337.836959
FMO2-MP2: Total energy -75557.865464


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:34:ARG)


Summations of interaction energy for fragment #1(A:34:ARG)
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.
-140.861-140.168.616-4.762-4.556-0.003
Interaction energy analysis for fragmet #1(A:34:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.974 / q_NPA : 0.990
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].
3A36ASP-1-0.792-0.9053.733-26.542-24.946-0.008-0.853-0.7350.002
4A37GLY00.0100.0046.4640.5560.5560.0000.0000.0000.000
5A38GLU-1-0.871-0.9317.704-15.676-15.6760.0000.0000.0000.000
6A39LEU00.0020.0229.2481.2331.2330.0000.0000.0000.000
7A40VAL0-0.007-0.0026.7601.1411.1410.0000.0000.0000.000
8A41ARG10.8520.91510.00520.44720.4470.0000.0000.0000.000
9A42SER0-0.011-0.01913.1031.0601.0600.0000.0000.0000.000
10A43LEU00.0360.00212.5850.8700.8700.0000.0000.0000.000
11A44ASN0-0.069-0.03814.2971.3061.3060.0000.0000.0000.000
12A45ARG10.8870.94115.91013.07113.0710.0000.0000.0000.000
13A46VAL00.0120.03418.4810.5810.5810.0000.0000.0000.000
14A47SER0-0.025-0.01419.862-0.255-0.2550.0000.0000.0000.000
15A48SER00.019-0.00819.973-0.069-0.0690.0000.0000.0000.000
16A49ALA00.0420.02720.962-0.090-0.0900.0000.0000.0000.000
17A50THR0-0.022-0.03222.8290.1960.1960.0000.0000.0000.000
18A51ALA00.0140.00218.242-0.075-0.0750.0000.0000.0000.000
19A52CYS0-0.057-0.02920.330-0.028-0.0280.0000.0000.0000.000
20A53ALA00.0100.00421.8830.1300.1300.0000.0000.0000.000
21A54LYS10.8670.92321.56711.31711.3170.0000.0000.0000.000
22A55LEU00.0050.00216.738-0.199-0.1990.0000.0000.0000.000
23A56HIS0-0.037-0.01820.854-0.092-0.0920.0000.0000.0000.000
24A57GLU-1-0.932-0.96224.352-9.892-9.8920.0000.0000.0000.000
25A58LEU0-0.064-0.02319.2970.0410.0410.0000.0000.0000.000
26A59GLY0-0.022-0.00122.540-0.243-0.2430.0000.0000.0000.000
27A60ILE0-0.071-0.04417.917-0.090-0.0900.0000.0000.0000.000
28A61ARG10.9930.98921.8309.9699.9690.0000.0000.0000.000
29A62ARG10.6830.83322.43312.21412.2140.0000.0000.0000.000
30A63SER00.1190.06518.615-0.333-0.3330.0000.0000.0000.000
31A64TYR00.0580.03718.886-0.414-0.4140.0000.0000.0000.000
32A65LEU00.007-0.00317.0530.3470.3470.0000.0000.0000.000
33A66SER0-0.022-0.01521.2340.3640.3640.0000.0000.0000.000
34A67GLY00.008-0.00224.5880.1580.1580.0000.0000.0000.000
35A68PRO0-0.057-0.02120.4410.2870.2870.0000.0000.0000.000
36A69THR0-0.028-0.01023.2570.1320.1320.0000.0000.0000.000
37A70ALA00.0350.02223.742-0.202-0.2020.0000.0000.0000.000
38A71LEU0-0.022-0.00824.3210.4870.4870.0000.0000.0000.000
39A72ASP-1-0.881-0.95724.969-10.680-10.6800.0000.0000.0000.000
40A73LEU0-0.0140.00325.670-0.281-0.2810.0000.0000.0000.000
41A74GLY0-0.044-0.01926.0900.0980.0980.0000.0000.0000.000
42A75ASN0-0.065-0.04021.238-0.414-0.4140.0000.0000.0000.000
43A76LYS10.7900.87917.96912.91012.9100.0000.0000.0000.000
44A77VAL0-0.036-0.01413.246-0.263-0.2630.0000.0000.0000.000
45A78THR0-0.0110.00311.8970.5240.5240.0000.0000.0000.000
46A79GLY00.0250.0088.269-0.251-0.2510.0000.0000.0000.000
47A80PRO0-0.055-0.0113.9650.8951.051-0.001-0.020-0.1350.000
48A81ALA00.0100.0056.8280.7060.7060.0000.0000.0000.000
49A82ARG10.8010.9054.37835.64335.785-0.001-0.005-0.1360.000
50A83THR0-0.038-0.0509.5951.6261.6260.0000.0000.0000.000
51A84LEU00.0130.02012.1250.2490.2490.0000.0000.0000.000
52A85GLN0-0.027-0.02615.0560.8430.8430.0000.0000.0000.000
53A86PHE00.0160.00517.909-0.056-0.0560.0000.0000.0000.000
54A87MET0-0.0170.00521.1070.1860.1860.0000.0000.0000.000
55A88PRO00.040-0.00224.3880.1410.1410.0000.0000.0000.000
56A89GLN0-0.080-0.04828.001-0.419-0.4190.0000.0000.0000.000
57A90ARG10.8910.94728.98910.18910.1890.0000.0000.0000.000
58A91GLU-1-0.874-0.94130.411-9.279-9.2790.0000.0000.0000.000
59A92ASP-1-0.937-0.95831.240-9.214-9.2140.0000.0000.0000.000
60A93VAL0-0.087-0.03727.2110.1410.1410.0000.0000.0000.000
61A105SER00.0540.00922.4720.1390.1390.0000.0000.0000.000
62A106THR00.013-0.00618.793-0.521-0.5210.0000.0000.0000.000
63A107ALA00.0390.03316.742-0.873-0.8730.0000.0000.0000.000
64A108LEU00.0310.01115.778-0.980-0.9800.0000.0000.0000.000
65A109TRP0-0.028-0.02216.110-0.306-0.3060.0000.0000.0000.000
66A110ALA0-0.0010.00412.554-0.602-0.6020.0000.0000.0000.000
67A111VAL00.0370.02911.527-1.482-1.4820.0000.0000.0000.000
68A112LEU0-0.017-0.00611.619-1.189-1.1890.0000.0000.0000.000
69A113GLU-1-0.822-0.89512.128-19.655-19.6550.0000.0000.0000.000
70A114GLU-1-0.839-0.8786.500-38.964-38.9640.0000.0000.0000.000
71A115VAL0-0.072-0.0157.519-3.713-3.7130.0000.0000.0000.000
72A116GLN0-0.021-0.0152.054-12.710-13.9798.627-3.875-3.484-0.005
73A117PRO0-0.037-0.0387.3120.7700.7700.0000.0000.0000.000
74A118GLY00.0060.0077.213-1.372-1.3720.0000.0000.0000.000
75A119ASP-1-0.793-0.8865.907-34.949-34.9490.0000.0000.0000.000
76A120VAL0-0.018-0.0057.9922.4192.4190.0000.0000.0000.000
77A121LEU0-0.038-0.00411.054-0.930-0.9300.0000.0000.0000.000
78A122VAL00.0200.00912.4961.5391.5390.0000.0000.0000.000
79A123VAL0-0.012-0.01514.655-0.519-0.5190.0000.0000.0000.000
80A124GLN00.0550.03817.7160.0500.0500.0000.0000.0000.000
81A125ALA00.002-0.01719.905-0.069-0.0690.0000.0000.0000.000
82A126TYR0-0.023-0.03022.7060.4960.4960.0000.0000.0000.000
83A127GLY00.0400.02725.3820.4390.4390.0000.0000.0000.000
84A128SER0-0.070-0.04827.2660.4580.4580.0000.0000.0000.000
85A129ALA0-0.019-0.01929.126-0.097-0.0970.0000.0000.0000.000
86A130PHE0-0.004-0.00731.2140.2590.2590.0000.0000.0000.000
87A131THR00.0220.02227.250-0.131-0.1310.0000.0000.0000.000
88A132GLY00.0430.03826.9680.0520.0520.0000.0000.0000.000
89A133CYS0-0.101-0.04721.557-0.135-0.1350.0000.0000.0000.000
90A134LEU00.0450.01918.004-0.500-0.5000.0000.0000.0000.000
91A135GLY00.0540.02022.6500.5830.5830.0000.0000.0000.000
92A136ASP-1-0.791-0.89823.884-11.619-11.6190.0000.0000.0000.000
93A137MET0-0.005-0.00923.902-0.335-0.3350.0000.0000.0000.000
94A138LEU0-0.0160.00220.233-0.349-0.3490.0000.0000.0000.000
95A139VAL00.0490.02919.349-0.840-0.8400.0000.0000.0000.000
96A140ARG10.8660.92919.43511.09911.0990.0000.0000.0000.000
97A141TYR0-0.092-0.08315.4950.3800.3800.0000.0000.0000.000
98A142PHE00.0160.02012.407-0.739-0.7390.0000.0000.0000.000
99A143LYN00.0590.04814.760-0.703-0.7030.0000.0000.0000.000
100A144ARG10.8780.95016.07315.39215.3920.0000.0000.0000.000
101A145LYS10.7320.87011.69522.85522.8550.0000.0000.0000.000
102A146GLY00.0100.00811.737-1.539-1.5390.0000.0000.0000.000
103A147GLY0-0.002-0.00911.194-1.172-1.1720.0000.0000.0000.000
104A148ALA0-0.013-0.01011.2061.3651.3650.0000.0000.0000.000
105A149GLY00.0520.01812.9161.1691.1690.0000.0000.0000.000
106A150ILE0-0.055-0.02514.210-1.058-1.0580.0000.0000.0000.000
107A151VAL00.0260.01116.2820.8840.8840.0000.0000.0000.000
108A152VAL0-0.004-0.00617.823-0.556-0.5560.0000.0000.0000.000
109A153ASP-1-0.822-0.90620.586-11.793-11.7930.0000.0000.0000.000
110A154GLY00.0260.00322.5680.0990.0990.0000.0000.0000.000
111A155ARG10.8790.98125.0299.8819.8810.0000.0000.0000.000
112A156ILE00.0560.03422.245-0.393-0.3930.0000.0000.0000.000
113A157ARG10.8400.90325.92110.92310.9230.0000.0000.0000.000
114A158ASP-1-0.850-0.90627.399-10.353-10.3530.0000.0000.0000.000
115A159ALA00.0910.03728.753-0.102-0.1020.0000.0000.0000.000
116A160PRO0-0.062-0.03729.802-0.036-0.0360.0000.0000.0000.000
117A161ARG10.9140.96329.0629.6539.6530.0000.0000.0000.000
118A162VAL00.022-0.00223.703-0.143-0.1430.0000.0000.0000.000
119A163ARG10.9180.96524.9359.5329.5320.0000.0000.0000.000
120A164GLU-1-0.970-0.96926.748-9.664-9.6640.0000.0000.0000.000
121A165LEU0-0.082-0.04022.791-0.132-0.1320.0000.0000.0000.000
122A166GLY00.0170.00121.9640.0450.0450.0000.0000.0000.000
123A167VAL0-0.047-0.03916.843-0.585-0.5850.0000.0000.0000.000
124A168PRO00.0350.05517.7370.3430.3430.0000.0000.0000.000
125A169ILE0-0.026-0.03418.531-0.803-0.8030.0000.0000.0000.000
126A170TRP00.0030.00518.2150.4140.4140.0000.0000.0000.000
127A171CYS0-0.079-0.02021.614-0.352-0.3520.0000.0000.0000.000
128A172THR00.0610.02524.2610.4110.4110.0000.0000.0000.000
129A173GLY00.011-0.01227.5040.4950.4950.0000.0000.0000.000
130A174THR0-0.067-0.05227.993-0.276-0.2760.0000.0000.0000.000
131A175THR0-0.010-0.03529.1300.2650.2650.0000.0000.0000.000
132A176PRO0-0.014-0.00730.983-0.205-0.2050.0000.0000.0000.000
133A177HIS0-0.007-0.00531.7100.1240.1240.0000.0000.0000.000
134A178TYR00.019-0.01027.918-0.256-0.2560.0000.0000.0000.000
135A179ALA0-0.038-0.02224.0430.1720.1720.0000.0000.0000.000
136A180SER00.0670.02326.076-0.080-0.0800.0000.0000.0000.000
137A181GLN0-0.0430.01227.8350.0700.0700.0000.0000.0000.000
138A182SER0-0.006-0.02430.7180.4270.4270.0000.0000.0000.000
139A183GLU-1-0.767-0.86230.520-10.139-10.1390.0000.0000.0000.000
140A184LEU0-0.058-0.00525.550-0.209-0.2090.0000.0000.0000.000
141A185PHE00.0250.00525.2560.1480.1480.0000.0000.0000.000
142A186PRO0-0.051-0.02619.921-0.247-0.2470.0000.0000.0000.000
143A187TRP0-0.043-0.00619.4700.4870.4870.0000.0000.0000.000
144A188ALA0-0.007-0.01415.222-0.302-0.3020.0000.0000.0000.000
145A189TYR0-0.068-0.0747.8042.5742.5740.0000.0000.0000.000
146A190ASP-1-0.762-0.8908.290-32.747-32.7470.0000.0000.0000.000
147A191VAL0-0.054-0.00810.492-0.703-0.7030.0000.0000.0000.000
148A192PRO0-0.002-0.00312.633-0.014-0.0140.0000.0000.0000.000
149A193VAL0-0.0140.00514.2310.9330.9330.0000.0000.0000.000
150A194ALA0-0.026-0.01716.255-0.008-0.0080.0000.0000.0000.000
151A195ALA00.0290.01917.8890.6290.6290.0000.0000.0000.000
152A196GLY00.0420.01819.778-0.055-0.0550.0000.0000.0000.000
153A197GLY0-0.040-0.01922.122-0.167-0.1670.0000.0000.0000.000
154A198VAL0-0.039-0.02117.0520.3320.3320.0000.0000.0000.000
155A199LEU0-0.0150.00415.419-0.206-0.2060.0000.0000.0000.000
156A200THR0-0.012-0.00311.860-0.098-0.0980.0000.0000.0000.000
157A201LEU00.000-0.00910.3510.3150.3150.0000.0000.0000.000
158A202PRO00.008-0.0026.865-0.278-0.2780.0000.0000.0000.000
159A203GLY0-0.022-0.0054.800-2.646-2.570-0.001-0.009-0.0660.000
160A204ASP-1-0.832-0.9185.453-22.974-22.9740.0000.0000.0000.000
161A205LEU0-0.020-0.0107.735-0.493-0.4930.0000.0000.0000.000
162A206VAL0-0.004-0.00110.0761.7111.7110.0000.0000.0000.000
163A207VAL00.007-0.00212.856-0.175-0.1750.0000.0000.0000.000
164A208ALA0-0.025-0.01415.7000.6580.6580.0000.0000.0000.000
165A209ASP-1-0.702-0.85518.109-12.352-12.3520.0000.0000.0000.000
166A210ASP-1-0.784-0.88721.628-10.813-10.8130.0000.0000.0000.000
167A211ASP-1-0.932-0.95324.268-10.426-10.4260.0000.0000.0000.000
168A212GLY0-0.042-0.02522.9390.1730.1730.0000.0000.0000.000
169A213ALA0-0.003-0.00317.469-0.332-0.3320.0000.0000.0000.000
170A214VAL0-0.025-0.02017.8000.4180.4180.0000.0000.0000.000
171A215VAL0-0.0140.00212.642-0.645-0.6450.0000.0000.0000.000
172A216VAL00.0240.01113.2350.8150.8150.0000.0000.0000.000
173A217PRO00.0120.00711.514-1.398-1.3980.0000.0000.0000.000
174A218VAL00.020-0.0086.3670.7430.7430.0000.0000.0000.000
175A219SER0-0.079-0.0409.6710.5010.5010.0000.0000.0000.000
176A220LYS10.8000.88212.51615.56615.5660.0000.0000.0000.000
177A221ALA00.0310.02911.1460.7290.7290.0000.0000.0000.000
178A222GLN0-0.002-0.02313.277-0.041-0.0410.0000.0000.0000.000
179A223GLU-1-0.812-0.89115.751-13.926-13.9260.0000.0000.0000.000
180A224ILE0-0.027-0.00617.0000.8360.8360.0000.0000.0000.000
181A225VAL00.0030.00314.7710.5780.5780.0000.0000.0000.000
182A226ASP-1-0.833-0.91418.035-13.775-13.7750.0000.0000.0000.000
183A227SER00.0230.00720.9930.7730.7730.0000.0000.0000.000
184A228ALA00.0010.01020.7660.5730.5730.0000.0000.0000.000
185A229PHE0-0.014-0.00718.9630.4260.4260.0000.0000.0000.000
186A230ASP-1-0.887-0.93923.836-10.216-10.2160.0000.0000.0000.000
187A231HIS0-0.075-0.04025.8600.3060.3060.0000.0000.0000.000
188A232GLU-1-0.762-0.86823.432-11.197-11.1970.0000.0000.0000.000
189A233GLN0-0.013-0.00125.8590.5380.5380.0000.0000.0000.000
190A234TRP0-0.018-0.00829.3260.5310.5310.0000.0000.0000.000
191A235GLU-1-0.835-0.89430.204-9.116-9.1160.0000.0000.0000.000
192A236GLU-1-0.833-0.89030.428-8.762-8.7620.0000.0000.0000.000
193A237PHE0-0.013-0.01532.5320.3480.3480.0000.0000.0000.000
194A238SER0-0.125-0.08434.9890.3030.3030.0000.0000.0000.000
195A239ARG10.8340.89028.6669.5159.5150.0000.0000.0000.000
196A240MET0-0.024-0.00736.4540.1410.1410.0000.0000.0000.000
197A241ARG10.8580.93838.2497.4257.4250.0000.0000.0000.000
198A242ILE0-0.0330.00239.6360.1510.1510.0000.0000.0000.000