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: ZVJ5N

Calculation Name: 3APQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3APQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9DC23

Base Structure: X-ray

Registration Date: 2023-09-24

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2420449.205569
FMO2-HF: Nuclear repulsion 2336083.970418
FMO2-HF: Total energy -84365.235151
FMO2-MP2: Total energy -84610.286136


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:33:ILE)


Summations of interaction energy for fragment #1(A:33:ILE)
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.
-1.2432.2430.253-1.806-1.934-0.002
Interaction energy analysis for fragmet #1(A:33:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.019
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].
3A35ASN00.0120.0032.895-2.3061.1320.254-1.803-1.889-0.002
4A36PHE00.0610.0065.3160.1580.206-0.001-0.003-0.0450.000
5A37TYR00.000-0.0018.8200.1840.1840.0000.0000.0000.000
6A38SER0-0.012-0.0236.415-0.046-0.0460.0000.0000.0000.000
7A39LEU0-0.088-0.0278.6060.2190.2190.0000.0000.0000.000
8A40LEU00.0190.01410.2400.2050.2050.0000.0000.0000.000
9A41GLY0-0.045-0.01811.7980.1330.1330.0000.0000.0000.000
10A42VAL0-0.027-0.01612.2660.1190.1190.0000.0000.0000.000
11A43SER00.0440.01111.555-0.188-0.1880.0000.0000.0000.000
12A44LYS10.8420.89210.3460.7810.7810.0000.0000.0000.000
13A45THR0-0.017-0.01212.7180.0470.0470.0000.0000.0000.000
14A46ALA0-0.0300.01715.6890.0560.0560.0000.0000.0000.000
15A47SER00.038-0.02717.585-0.002-0.0020.0000.0000.0000.000
16A48SER00.025-0.02919.861-0.040-0.0400.0000.0000.0000.000
17A49ARG10.8690.93921.3920.2150.2150.0000.0000.0000.000
18A50GLU-1-0.838-0.88418.922-0.360-0.3600.0000.0000.0000.000
19A51ILE0-0.0020.00115.872-0.024-0.0240.0000.0000.0000.000
20A52ARG10.7890.85418.3140.2320.2320.0000.0000.0000.000
21A53GLN00.008-0.00821.3780.0090.0090.0000.0000.0000.000
22A54ALA0-0.049-0.01616.6360.0110.0110.0000.0000.0000.000
23A55PHE00.0380.01818.092-0.014-0.0140.0000.0000.0000.000
24A56LYS10.8810.94419.0690.2240.2240.0000.0000.0000.000
25A57LYS10.8440.93216.2410.4590.4590.0000.0000.0000.000
26A58LEU0-0.015-0.00514.7800.0220.0220.0000.0000.0000.000
27A59ALA00.0390.01719.4910.0300.0300.0000.0000.0000.000
28A60LEU0-0.025-0.01822.1940.0250.0250.0000.0000.0000.000
29A61LYS10.9390.97921.2000.1970.1970.0000.0000.0000.000
30A62LEU0-0.054-0.03617.6820.0150.0150.0000.0000.0000.000
31A63HIS0-0.0010.01921.9730.0080.0080.0000.0000.0000.000
32A64PRO00.0620.03522.6050.0160.0160.0000.0000.0000.000
33A65ASP-1-0.822-0.92225.417-0.121-0.1210.0000.0000.0000.000
34A66LYS10.7810.88927.4430.1280.1280.0000.0000.0000.000
35A67ASN0-0.076-0.03124.6090.0070.0070.0000.0000.0000.000
36A68PRO00.0560.03126.1480.0010.0010.0000.0000.0000.000
37A69ASN0-0.019-0.01428.4600.0050.0050.0000.0000.0000.000
38A70ASN00.0050.00520.6380.0190.0190.0000.0000.0000.000
39A71PRO00.0380.02023.868-0.013-0.0130.0000.0000.0000.000
40A72ASN0-0.021-0.01717.2730.0140.0140.0000.0000.0000.000
41A73ALA0-0.0140.00219.666-0.025-0.0250.0000.0000.0000.000
42A74HIS00.0740.04120.564-0.031-0.0310.0000.0000.0000.000
43A75GLY00.0550.02518.609-0.019-0.0190.0000.0000.0000.000
44A76ASP-1-0.834-0.91414.859-0.285-0.2850.0000.0000.0000.000
45A77PHE00.0180.00915.706-0.070-0.0700.0000.0000.0000.000
46A78LEU00.0170.01517.270-0.031-0.0310.0000.0000.0000.000
47A79LYS10.8020.88911.6000.3970.3970.0000.0000.0000.000
48A80ILE0-0.026-0.00512.978-0.081-0.0810.0000.0000.0000.000
49A81ASN0-0.010-0.02014.849-0.015-0.0150.0000.0000.0000.000
50A82ARG10.8200.89210.2260.4640.4640.0000.0000.0000.000
51A83ALA0-0.0080.00011.533-0.018-0.0180.0000.0000.0000.000
52A84TYR00.030-0.00113.071-0.002-0.0020.0000.0000.0000.000
53A85GLU-1-0.900-0.97416.453-0.246-0.2460.0000.0000.0000.000
54A86VAL0-0.048-0.01113.0450.0250.0250.0000.0000.0000.000
55A87LEU0-0.025-0.02611.7630.0150.0150.0000.0000.0000.000
56A88LYS10.8310.92115.7030.2770.2770.0000.0000.0000.000
57A89ASP-1-0.860-0.91718.773-0.228-0.2280.0000.0000.0000.000
58A90GLU-1-0.749-0.84219.015-0.239-0.2390.0000.0000.0000.000
59A91ASP-1-0.841-0.92419.638-0.232-0.2320.0000.0000.0000.000
60A92LEU0-0.028-0.01016.923-0.014-0.0140.0000.0000.0000.000
61A93ARG10.8440.93414.8270.4500.4500.0000.0000.0000.000
62A94LYS10.7770.87814.6660.1830.1830.0000.0000.0000.000
63A95LYS10.8490.94115.1850.2870.2870.0000.0000.0000.000
64A96TYR00.0610.0366.864-0.117-0.1170.0000.0000.0000.000
65A97ASP-1-0.794-0.88610.671-0.772-0.7720.0000.0000.0000.000
66A98LYS10.9140.96812.1810.2060.2060.0000.0000.0000.000
67A99TYR0-0.050-0.03911.7070.0670.0670.0000.0000.0000.000
68A100GLY00.0590.0478.4360.0240.0240.0000.0000.0000.000
69A101GLU-1-0.840-0.9247.967-0.669-0.6690.0000.0000.0000.000
70A102LYS10.9440.98310.4820.2670.2670.0000.0000.0000.000
71A103GLY0-0.016-0.02113.1650.0010.0010.0000.0000.0000.000
72A104LEU0-0.041-0.01111.857-0.006-0.0060.0000.0000.0000.000
73A105GLU-1-0.833-0.90815.295-0.142-0.1420.0000.0000.0000.000
74A106ASP-1-0.923-0.96012.952-0.256-0.2560.0000.0000.0000.000
75A107ASN0-0.065-0.04514.729-0.018-0.0180.0000.0000.0000.000
76A108GLN00.0330.02315.7320.0220.0220.0000.0000.0000.000
77A109GLY00.0240.00617.078-0.028-0.0280.0000.0000.0000.000
78A110GLY0-0.0010.00018.863-0.012-0.0120.0000.0000.0000.000
79A111GLN0-0.067-0.02920.6680.0290.0290.0000.0000.0000.000
80A112TYR0-0.026-0.01921.437-0.005-0.0050.0000.0000.0000.000
81A113GLU-1-0.797-0.89323.491-0.128-0.1280.0000.0000.0000.000
82A114SER00.0170.00126.190-0.005-0.0050.0000.0000.0000.000
83A115TRP0-0.054-0.04826.744-0.003-0.0030.0000.0000.0000.000
84A116SER00.004-0.01928.343-0.001-0.0010.0000.0000.0000.000
85A117TYR0-0.0090.01326.151-0.004-0.0040.0000.0000.0000.000
86A118TYR00.0470.00722.5190.0030.0030.0000.0000.0000.000
87A119ARG10.8550.94627.1750.1280.1280.0000.0000.0000.000
88A120TYR0-0.029-0.02729.9650.0050.0050.0000.0000.0000.000
89A121ASP-1-0.773-0.86831.091-0.131-0.1310.0000.0000.0000.000
90A122PHE0-0.0260.00022.251-0.006-0.0060.0000.0000.0000.000
91A123GLY00.0140.00426.9430.0000.0000.0000.0000.0000.000
92A124ILE0-0.0410.00027.6820.0020.0020.0000.0000.0000.000
93A125TYR00.0500.01931.0770.0100.0100.0000.0000.0000.000
94A126ASP-1-0.737-0.82325.936-0.234-0.2340.0000.0000.0000.000
95A127ASP-1-0.934-0.96627.959-0.202-0.2020.0000.0000.0000.000
96A128ASP-1-0.796-0.89030.465-0.117-0.1170.0000.0000.0000.000
97A129PRO0-0.022-0.00731.801-0.003-0.0030.0000.0000.0000.000
98A130GLU-1-0.754-0.87033.046-0.116-0.1160.0000.0000.0000.000
99A131ILE0-0.055-0.02134.2990.0050.0050.0000.0000.0000.000
100A132ILE0-0.008-0.00531.162-0.011-0.0110.0000.0000.0000.000
101A133THR0-0.025-0.01128.7500.0070.0070.0000.0000.0000.000
102A134LEU0-0.071-0.02229.378-0.010-0.0100.0000.0000.0000.000
103A135GLU-1-0.740-0.84424.616-0.234-0.2340.0000.0000.0000.000
104A136ARG10.8700.91827.6660.1440.1440.0000.0000.0000.000
105A137ARG10.8250.88725.4900.1980.1980.0000.0000.0000.000
106A138GLU-1-0.843-0.93826.928-0.186-0.1860.0000.0000.0000.000
107A139PHE00.0550.01930.2690.0110.0110.0000.0000.0000.000
108A140ASP-1-0.784-0.87932.689-0.111-0.1110.0000.0000.0000.000
109A141ALA0-0.027-0.01532.2670.0080.0080.0000.0000.0000.000
110A142ALA00.0210.01834.1980.0070.0070.0000.0000.0000.000
111A143VAL0-0.035-0.00735.9790.0070.0070.0000.0000.0000.000
112A144ASN0-0.023-0.00937.2560.0090.0090.0000.0000.0000.000
113A145SER0-0.038-0.03237.4700.0060.0060.0000.0000.0000.000
114A146GLY00.0070.00139.1940.0030.0030.0000.0000.0000.000
115A147GLU-1-0.846-0.90338.143-0.100-0.1000.0000.0000.0000.000
116A148LEU0-0.034-0.01042.3060.0000.0000.0000.0000.0000.000
117A149TRP00.015-0.00334.483-0.006-0.0060.0000.0000.0000.000
118A150PHE0-0.007-0.01240.7010.0030.0030.0000.0000.0000.000
119A151VAL0-0.019-0.00436.238-0.005-0.0050.0000.0000.0000.000
120A152ASN00.000-0.00437.6980.0040.0040.0000.0000.0000.000
121A153PHE00.003-0.00535.970-0.009-0.0090.0000.0000.0000.000
122A154TYR00.0480.00130.8690.0060.0060.0000.0000.0000.000
123A155SER0-0.026-0.02833.717-0.005-0.0050.0000.0000.0000.000
124A156PRO00.0240.03130.5580.0040.0040.0000.0000.0000.000
125A157GLY00.010-0.00633.1380.0060.0060.0000.0000.0000.000
126A158CYS0-0.121-0.02635.9830.0100.0100.0000.0000.0000.000
127A159SER00.0270.00538.505-0.001-0.0010.0000.0000.0000.000
128A160HIS00.0630.03741.179-0.002-0.0020.0000.0000.0000.000
129A162HIS0-0.051-0.03534.7380.0010.0010.0000.0000.0000.000
130A163ASP-1-0.869-0.94739.384-0.079-0.0790.0000.0000.0000.000
131A164LEU0-0.031-0.00941.2080.0020.0020.0000.0000.0000.000
132A165ALA00.0110.02037.6920.0000.0000.0000.0000.0000.000
133A166PRO0-0.021-0.02239.725-0.002-0.0020.0000.0000.0000.000
134A167THR00.0750.04141.599-0.001-0.0010.0000.0000.0000.000
135A168TRP0-0.001-0.00237.8190.0040.0040.0000.0000.0000.000
136A169ARG10.8300.90534.1840.1220.1220.0000.0000.0000.000
137A170GLU-1-0.913-0.96139.835-0.074-0.0740.0000.0000.0000.000
138A171PHE00.015-0.00942.7700.0020.0020.0000.0000.0000.000
139A172ALA0-0.016-0.00939.3760.0020.0020.0000.0000.0000.000
140A173LYS10.7350.85337.4150.1100.1100.0000.0000.0000.000
141A174GLU-1-0.871-0.90641.978-0.064-0.0640.0000.0000.0000.000
142A175VAL0-0.046-0.03743.6420.0040.0040.0000.0000.0000.000
143A176ASP-1-0.842-0.91939.462-0.100-0.1000.0000.0000.0000.000
144A177GLY0-0.059-0.02040.9830.0050.0050.0000.0000.0000.000
145A178LEU0-0.079-0.03542.4750.0030.0030.0000.0000.0000.000
146A179LEU0-0.033-0.02343.1100.0030.0030.0000.0000.0000.000
147A180ARG10.8490.92134.7730.1100.1100.0000.0000.0000.000
148A181ILE00.0490.03238.3140.0010.0010.0000.0000.0000.000
149A182GLY00.0540.01235.417-0.007-0.0070.0000.0000.0000.000
150A183ALA0-0.047-0.02833.6610.0070.0070.0000.0000.0000.000
151A184VAL00.0170.01031.960-0.008-0.0080.0000.0000.0000.000
152A185ASN00.0480.01927.7970.0200.0200.0000.0000.0000.000
153A186CYS0-0.035-0.02030.3530.0010.0010.0000.0000.0000.000
154A187GLY0-0.047-0.04130.1340.0030.0030.0000.0000.0000.000
155A188ASP-1-0.853-0.89524.774-0.231-0.2310.0000.0000.0000.000
156A189ASP-1-0.806-0.90927.155-0.155-0.1550.0000.0000.0000.000
157A190ARG10.9260.94729.7370.1360.1360.0000.0000.0000.000
158A191MET0-0.038-0.01131.8520.0130.0130.0000.0000.0000.000
159A192LEU00.0270.01631.7480.0080.0080.0000.0000.0000.000
160A194ARG10.9610.98736.2800.0970.0970.0000.0000.0000.000
161A195MET0-0.058-0.03635.2900.0030.0030.0000.0000.0000.000
162A196LYS10.8110.91936.5260.1090.1090.0000.0000.0000.000
163A197GLY00.0230.02140.0320.0030.0030.0000.0000.0000.000
164A198VAL0-0.042-0.01838.6770.0030.0030.0000.0000.0000.000
165A199ASN0-0.022-0.00839.363-0.005-0.0050.0000.0000.0000.000
166A200SER0-0.032-0.02041.7000.0010.0010.0000.0000.0000.000
167A201TYR00.0160.01737.176-0.005-0.0050.0000.0000.0000.000
168A202PRO00.0490.01039.9830.0020.0020.0000.0000.0000.000
169A203SER0-0.068-0.04740.3740.0070.0070.0000.0000.0000.000
170A204LEU0-0.0240.01040.783-0.005-0.0050.0000.0000.0000.000
171A205PHE00.0380.00941.6900.0050.0050.0000.0000.0000.000
172A206ILE00.0030.01642.178-0.005-0.0050.0000.0000.0000.000
173A207PHE00.008-0.01740.3320.0020.0020.0000.0000.0000.000
174A208ARG10.9210.91543.5470.0650.0650.0000.0000.0000.000
175A209SER0-0.0060.01542.0890.0030.0030.0000.0000.0000.000
176A210GLY0-0.004-0.00443.7950.0030.0030.0000.0000.0000.000
177A211MET0-0.0390.02046.3920.0040.0040.0000.0000.0000.000
178A212ALA0-0.0020.00546.420-0.003-0.0030.0000.0000.0000.000
179A213ALA0-0.0120.00044.1600.0000.0000.0000.0000.0000.000
180A214VAL00.0120.00346.0810.0030.0030.0000.0000.0000.000
181A215LYS10.8780.95144.8250.0730.0730.0000.0000.0000.000
182A216TYR0-0.017-0.01446.5580.0020.0020.0000.0000.0000.000
183A217ASN0-0.072-0.05647.885-0.003-0.0030.0000.0000.0000.000
184A218GLY00.0500.03250.2320.0030.0030.0000.0000.0000.000
185A219ASP-1-0.795-0.86850.516-0.061-0.0610.0000.0000.0000.000
186A220ARG10.8820.92645.7290.0740.0740.0000.0000.0000.000
187A221SER0-0.019-0.01547.838-0.003-0.0030.0000.0000.0000.000
188A222LYS10.8490.90346.8110.0650.0650.0000.0000.0000.000
189A223GLU-1-0.830-0.91348.778-0.062-0.0620.0000.0000.0000.000
190A224SER0-0.018-0.01451.3050.0000.0000.0000.0000.0000.000
191A225LEU0-0.033-0.01645.0030.0000.0000.0000.0000.0000.000
192A226VAL00.0370.01648.313-0.001-0.0010.0000.0000.0000.000
193A227ALA0-0.017-0.00249.6450.0010.0010.0000.0000.0000.000
194A228PHE0-0.004-0.00546.9050.0010.0010.0000.0000.0000.000
195A229ALA00.0180.01046.8730.0000.0000.0000.0000.0000.000
196A230MET00.0400.01348.4880.0000.0000.0000.0000.0000.000
197A231GLN0-0.052-0.02151.2600.0030.0030.0000.0000.0000.000
198A232HIS0-0.045-0.02748.9570.0030.0030.0000.0000.0000.000
199A233VAL00.0010.00347.5030.0000.0000.0000.0000.0000.000
200A234ARG10.8890.94849.9380.0500.0500.0000.0000.0000.000
201A235SER0-0.0190.00252.2720.0020.0020.0000.0000.0000.000
202A236THR00.0180.02351.204-0.004-0.0040.0000.0000.0000.000
203A237VAL0-0.008-0.01251.0200.0000.0000.0000.0000.0000.000
204A238THR0-0.013-0.00952.9210.0010.0010.0000.0000.0000.000
205A239GLU-1-0.936-0.96556.581-0.045-0.0450.0000.0000.0000.000
206A240LEU0-0.036-0.01459.3970.0010.0010.0000.0000.0000.000