FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 9GZK2

Calculation Name: 3HN5-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3HN5

Chain ID: A

ChEMBL ID:
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UniProt ID: Q5LIG1

Base Structure: X-ray

Registration Date: 2023-06-19

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 OptH
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 -2332557.863615
FMO2-HF: Nuclear repulsion 2250200.444212
FMO2-HF: Total energy -82357.419403
FMO2-MP2: Total energy -82595.662882


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:30:GLU)


Summations of interaction energy for fragment #1(A:30:GLU)
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.
63.85969.1179.219-4.205-10.273-0.003
Interaction energy analysis for fragmet #1(A:30:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -1.012 / q_NPA : -1.016
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].
3A32MET0-0.031-0.0203.4942.5994.3240.013-0.838-0.9000.002
4A33LEU00.0200.0246.249-2.828-2.8280.0000.0000.0000.000
5A34THR0-0.078-0.0478.553-0.256-0.2560.0000.0000.0000.000
6A35GLY00.0870.03711.642-0.502-0.5020.0000.0000.0000.000
7A36ARG10.8910.93515.214-13.754-13.7540.0000.0000.0000.000
8A37VAL00.0160.02418.4130.0150.0150.0000.0000.0000.000
9A38MET0-0.080-0.04720.593-0.456-0.4560.0000.0000.0000.000
10A39TYR00.0580.01723.793-0.080-0.0800.0000.0000.0000.000
11A40ASN0-0.040-0.01327.384-0.125-0.1250.0000.0000.0000.000
12A41GLY00.0070.00726.776-0.243-0.2430.0000.0000.0000.000
13A42GLU-1-0.966-0.97326.58010.17710.1770.0000.0000.0000.000
14A43ALA0-0.024-0.00922.3640.1300.1300.0000.0000.0000.000
15A44LEU00.0160.00423.734-0.481-0.4810.0000.0000.0000.000
16A45GLN0-0.018-0.00424.0190.2920.2920.0000.0000.0000.000
17A46LEU00.0200.00821.521-0.395-0.3950.0000.0000.0000.000
18A47ARG10.8920.94024.760-12.184-12.1840.0000.0000.0000.000
19A48GLY00.0240.02321.1920.3500.3500.0000.0000.0000.000
20A49ASN0-0.063-0.04520.313-0.716-0.7160.0000.0000.0000.000
21A50GLU-1-0.852-0.94316.93517.37117.3710.0000.0000.0000.000
22A51ALA0-0.069-0.02619.266-0.009-0.0090.0000.0000.0000.000
23A52VAL00.0240.01619.989-0.380-0.3800.0000.0000.0000.000
24A53GLN0-0.024-0.01516.7500.9450.9450.0000.0000.0000.000
25A54LEU0-0.027-0.01414.712-1.094-1.0940.0000.0000.0000.000
26A55GLN0-0.010-0.00914.4650.4790.4790.0000.0000.0000.000
27A56LEU00.0260.0169.125-0.923-0.9230.0000.0000.0000.000
28A57TYR0-0.027-0.02512.4460.6800.6800.0000.0000.0000.000
29A58GLN00.0840.0338.322-0.165-0.1650.0000.0000.0000.000
30A59HIS0-0.054-0.01712.683-0.318-0.3180.0000.0000.0000.000
31A60GLY00.0410.02316.415-1.168-1.1680.0000.0000.0000.000
32A61TYR00.0640.03318.6970.2090.2090.0000.0000.0000.000
33A62ALA00.0060.00320.449-0.080-0.0800.0000.0000.0000.000
34A63LYS10.9350.96718.579-15.318-15.3180.0000.0000.0000.000
35A64HIS10.8060.91019.481-14.170-14.1700.0000.0000.0000.000
36A65ASP-1-0.863-0.94215.32819.05919.0590.0000.0000.0000.000
37A66PRO0-0.0290.00513.7291.1561.1560.0000.0000.0000.000
38A67ILE00.0430.0247.0140.0960.0960.0000.0000.0000.000
39A68ASN0-0.040-0.02410.817-2.946-2.9460.0000.0000.0000.000
40A69VAL00.0150.01510.1112.4352.4350.0000.0000.0000.000
41A70TYR00.0020.00312.292-2.048-2.0480.0000.0000.0000.000
42A71VAL0-0.0110.00214.4150.7350.7350.0000.0000.0000.000
43A72ASN00.0150.00817.134-1.088-1.0880.0000.0000.0000.000
44A73GLN00.051-0.00418.8380.0860.0860.0000.0000.0000.000
45A74ASP-1-0.927-0.96321.18212.13812.1380.0000.0000.0000.000
46A75GLY00.0410.03820.737-0.161-0.1610.0000.0000.0000.000
47A76MET0-0.038-0.02515.960-0.081-0.0810.0000.0000.0000.000
48A77TYR0-0.009-0.02411.0680.4870.4870.0000.0000.0000.000
49A78SER0-0.039-0.0409.4600.4340.4340.0000.0000.0000.000
50A79ALA00.0130.0147.203-0.286-0.2860.0000.0000.0000.000
51A80ASN0-0.028-0.0062.811-7.388-6.6820.135-0.229-0.6120.002
52A81LEU00.0110.0102.5565.6177.7032.373-1.226-3.2330.005
53A82PHE00.0470.0192.476-1.186-0.3256.676-2.163-5.374-0.012
54A83ASP-1-0.803-0.8693.35430.09829.9780.0220.251-0.1540.000
55A84GLY0-0.026-0.0176.3360.2970.2970.0000.0000.0000.000
56A85GLU-1-0.851-0.8509.63419.18319.1830.0000.0000.0000.000
57A86TYR0-0.068-0.0596.1321.3791.3790.0000.0000.0000.000
58A87GLN0-0.059-0.02312.810-1.323-1.3230.0000.0000.0000.000
59A88MET00.0060.01412.0850.6300.6300.0000.0000.0000.000
60A89ILE0-0.0040.00215.579-1.174-1.1740.0000.0000.0000.000
61A90THR00.0820.03817.8900.7540.7540.0000.0000.0000.000
62A91LYS10.9721.00119.269-15.170-15.1700.0000.0000.0000.000
63A92SER0-0.035-0.03220.874-0.563-0.5630.0000.0000.0000.000
64A93GLY00.003-0.00724.4790.0680.0680.0000.0000.0000.000
65A94ASN0-0.091-0.03621.2240.5100.5100.0000.0000.0000.000
66A95GLY00.0400.00023.5850.5020.5020.0000.0000.0000.000
67A96PRO0-0.0700.00125.163-0.343-0.3430.0000.0000.0000.000
68A97TRP00.002-0.03621.757-0.107-0.1070.0000.0000.0000.000
69A98THR00.0250.03228.5870.1420.1420.0000.0000.0000.000
70A99SER0-0.021-0.03227.7770.3060.3060.0000.0000.0000.000
71A100GLU-1-0.966-0.98528.7269.6319.6310.0000.0000.0000.000
72A101GLY00.0300.01628.1280.2460.2460.0000.0000.0000.000
73A102ARG10.7780.89621.781-12.938-12.9380.0000.0000.0000.000
74A103ASP-1-0.852-0.93323.56512.12012.1200.0000.0000.0000.000
75A104THR0-0.137-0.06719.5540.6300.6300.0000.0000.0000.000
76A105ILE00.0290.02217.438-0.528-0.5280.0000.0000.0000.000
77A106ASN0-0.007-0.02016.9311.2071.2070.0000.0000.0000.000
78A107VAL00.000-0.00111.896-0.416-0.4160.0000.0000.0000.000
79A108THR0-0.025-0.07012.4290.4370.4370.0000.0000.0000.000
80A109VAL0-0.086-0.0386.383-0.595-0.5950.0000.0000.0000.000
81A110ALA00.0130.0018.5910.7360.7360.0000.0000.0000.000
82A111GLY00.0360.0246.516-2.041-2.0410.0000.0000.0000.000
83A112ASN0-0.021-0.0226.8502.5982.5980.0000.0000.0000.000
84A113THR0-0.030-0.0098.591-2.135-2.1350.0000.0000.0000.000
85A114VAL0-0.010-0.01411.0830.7640.7640.0000.0000.0000.000
86A115GLN0-0.016-0.01113.849-0.348-0.3480.0000.0000.0000.000
87A116ASP-1-0.844-0.89715.48415.80415.8040.0000.0000.0000.000
88A117VAL0-0.020-0.01417.2560.0190.0190.0000.0000.0000.000
89A118GLU-1-0.818-0.90719.99211.17311.1730.0000.0000.0000.000
90A119VAL0-0.030-0.01523.1270.0750.0750.0000.0000.0000.000
91A120THR00.0610.02125.853-0.360-0.3600.0000.0000.0000.000
92A121PRO00.0080.00828.7220.0020.0020.0000.0000.0000.000
93A122TYR00.0140.01230.357-0.367-0.3670.0000.0000.0000.000
94A123TYR0-0.046-0.06732.931-0.267-0.2670.0000.0000.0000.000
95A124LEU00.0040.00830.1330.3910.3910.0000.0000.0000.000
96A125VAL0-0.027-0.00833.119-0.328-0.3280.0000.0000.0000.000
97A126ARG10.8200.89732.033-8.907-8.9070.0000.0000.0000.000
98A127ASP-1-0.908-0.96436.8237.5977.5970.0000.0000.0000.000
99A128ALA0-0.017-0.00235.882-0.142-0.1420.0000.0000.0000.000
100A129GLN0-0.023-0.00737.937-0.007-0.0070.0000.0000.0000.000
101A130MET0-0.036-0.01037.5310.0310.0310.0000.0000.0000.000
102A131THR0-0.0030.00840.6560.0260.0260.0000.0000.0000.000
103A132LEU0-0.004-0.00442.309-0.016-0.0160.0000.0000.0000.000
104A133GLU-1-0.882-0.95244.7546.3336.3330.0000.0000.0000.000
105A134GLY0-0.010-0.00248.545-0.087-0.0870.0000.0000.0000.000
106A135ASN00.007-0.00447.4800.2370.2370.0000.0000.0000.000
107A136LYS10.8860.92247.376-6.068-6.0680.0000.0000.0000.000
108A137VAL00.0010.01041.5320.0640.0640.0000.0000.0000.000
109A138ASN00.0260.03644.925-0.061-0.0610.0000.0000.0000.000
110A139ALA00.0000.00240.7510.1260.1260.0000.0000.0000.000
111A140SER0-0.007-0.00541.822-0.158-0.1580.0000.0000.0000.000
112A141PHE00.005-0.00638.7020.2230.2230.0000.0000.0000.000
113A142LYS10.9690.99139.894-7.246-7.2460.0000.0000.0000.000
114A143VAL00.0120.02238.9020.2880.2880.0000.0000.0000.000
115A144GLU-1-0.842-0.91035.9938.3998.3990.0000.0000.0000.000
116A145LYS10.9250.95436.719-7.162-7.1620.0000.0000.0000.000
117A146VAL0-0.018-0.00532.792-0.066-0.0660.0000.0000.0000.000
118A147ALA0-0.033-0.01133.699-0.181-0.1810.0000.0000.0000.000
119A148GLY0-0.039-0.01535.711-0.239-0.2390.0000.0000.0000.000
120A149GLY00.0290.00736.9610.2000.2000.0000.0000.0000.000
121A150GLY00.0020.00639.288-0.115-0.1150.0000.0000.0000.000
122A151ILE0-0.023-0.01838.6370.2670.2670.0000.0000.0000.000
123A152ASP-1-0.963-0.98237.6098.0388.0380.0000.0000.0000.000
124A153ARG10.8940.93236.597-8.378-8.3780.0000.0000.0000.000
125A154VAL00.0090.02138.0540.2440.2440.0000.0000.0000.000
126A155PHE0-0.016-0.01833.134-0.102-0.1020.0000.0000.0000.000
127A156PHE00.0060.01536.7130.2060.2060.0000.0000.0000.000
128A157MET0-0.073-0.01932.9740.0760.0760.0000.0000.0000.000
129A158LEU00.0190.00335.926-0.026-0.0260.0000.0000.0000.000
130A159SER00.009-0.02131.5430.0900.0900.0000.0000.0000.000
131A160THR00.0160.00733.8440.0010.0010.0000.0000.0000.000
132A161THR0-0.065-0.03328.7960.1580.1580.0000.0000.0000.000
133A162GLN00.0490.01224.159-0.186-0.1860.0000.0000.0000.000
134A163PHE0-0.0140.01322.3850.0920.0920.0000.0000.0000.000
135A164VAL00.0080.02026.929-0.206-0.2060.0000.0000.0000.000
136A165ASN00.0260.00725.975-0.031-0.0310.0000.0000.0000.000
137A166ASP-1-0.758-0.89929.06010.58710.5870.0000.0000.0000.000
138A167ALA0-0.045-0.01828.415-0.371-0.3710.0000.0000.0000.000
139A168GLU-1-0.922-0.94725.56112.16212.1620.0000.0000.0000.000
140A169HIS10.9150.94130.176-9.367-9.3670.0000.0000.0000.000
141A170ASN0-0.032-0.00132.801-0.428-0.4280.0000.0000.0000.000
142A171VAL0-0.0210.00034.998-0.209-0.2090.0000.0000.0000.000
143A172ASP-1-0.741-0.84337.4337.4317.4310.0000.0000.0000.000
144A173ARG10.7610.84734.219-8.586-8.5860.0000.0000.0000.000
145A174TYR0-0.064-0.03638.262-0.174-0.1740.0000.0000.0000.000
146A175ASP-1-0.732-0.84338.9208.4618.4610.0000.0000.0000.000
147A176GLU-1-0.759-0.82741.3546.7366.7360.0000.0000.0000.000
148A177THR00.030-0.02142.1140.1840.1840.0000.0000.0000.000
149A178ASP-1-0.888-0.91044.4806.4536.4530.0000.0000.0000.000
150A179ASN0-0.036-0.04247.3320.0220.0220.0000.0000.0000.000
151A180LEU00.0150.01741.735-0.012-0.0120.0000.0000.0000.000
152A181ASP-1-0.948-0.97044.8116.7656.7650.0000.0000.0000.000
153A182ALA0-0.0040.00546.440-0.024-0.0240.0000.0000.0000.000
154A183TYR0-0.056-0.04544.093-0.063-0.0630.0000.0000.0000.000
155A184ASP-1-0.813-0.87641.6937.7537.7530.0000.0000.0000.000
156A185GLU-1-0.947-0.97743.4786.9516.9510.0000.0000.0000.000
157A186THR00.0480.01240.5000.0910.0910.0000.0000.0000.000
158A187GLY0-0.036-0.00941.905-0.183-0.1830.0000.0000.0000.000
159A188LYS10.8710.94843.779-6.770-6.7700.0000.0000.0000.000
160A189LEU0-0.026-0.01543.5580.1770.1770.0000.0000.0000.000
161A190TYR0-0.018-0.04142.552-0.124-0.1240.0000.0000.0000.000
162A191THR0-0.044-0.04143.9140.1200.1200.0000.0000.0000.000
163A192PHE0-0.022-0.00339.677-0.028-0.0280.0000.0000.0000.000
164A193ALA00.0120.01645.389-0.121-0.1210.0000.0000.0000.000
165A194THR0-0.052-0.04546.6310.0910.0910.0000.0000.0000.000
166A195ARG10.8250.91243.385-7.254-7.2540.0000.0000.0000.000
167A196ASP-1-0.813-0.85447.0326.3376.3370.0000.0000.0000.000
168A197TYR0-0.038-0.06542.3980.0360.0360.0000.0000.0000.000
169A198THR0-0.031-0.06946.6320.0750.0750.0000.0000.0000.000
170A199ASP-1-0.891-0.93648.8926.3026.3020.0000.0000.0000.000
171A200ASN0-0.0310.00341.4740.1670.1670.0000.0000.0000.000
172A201SER00.0560.01043.5410.0210.0210.0000.0000.0000.000
173A202MET0-0.017-0.00337.2240.1330.1330.0000.0000.0000.000
174A203PHE00.0840.03339.9040.1430.1430.0000.0000.0000.000
175A204GLN0-0.028-0.01141.6600.0220.0220.0000.0000.0000.000
176A205THR0-0.098-0.05339.260-0.045-0.0450.0000.0000.0000.000
177A206ALA00.0180.01337.9030.0620.0620.0000.0000.0000.000
178A207LEU00.0380.01339.3700.0400.0400.0000.0000.0000.000
179A208LYS10.8940.96142.355-7.009-7.0090.0000.0000.0000.000
180A209ARG10.9460.95735.283-8.583-8.5830.0000.0000.0000.000
181A210GLY00.0100.02238.7290.0930.0930.0000.0000.0000.000
182A211THR0-0.099-0.06534.5880.1300.1300.0000.0000.0000.000
183A212LEU00.0270.02936.4900.0440.0440.0000.0000.0000.000
184A213PHE0-0.001-0.00230.924-0.031-0.0310.0000.0000.0000.000
185A214GLY00.0390.00634.473-0.149-0.1490.0000.0000.0000.000
186A215ARG10.7650.87726.088-10.978-10.9780.0000.0000.0000.000
187A216ILE00.0700.02833.747-0.205-0.2050.0000.0000.0000.000
188A217CYS0-0.042-0.00132.3740.3660.3660.0000.0000.0000.000
189A218ILE00.0410.03233.828-0.342-0.3420.0000.0000.0000.000
190A219TRP0-0.011-0.01730.3090.3580.3580.0000.0000.0000.000
191A220PRO0-0.0160.00332.482-0.314-0.3140.0000.0000.0000.000
192A221LYS10.9510.96935.020-7.297-7.2970.0000.0000.0000.000
193A222GLY0-0.007-0.00335.1190.0170.0170.0000.0000.0000.000
194A223SER0-0.033-0.01530.3630.3720.3720.0000.0000.0000.000
195A224ASP-1-0.786-0.88326.03511.78711.7870.0000.0000.0000.000
196A225GLN0-0.035-0.02825.3690.2590.2590.0000.0000.0000.000
197A226GLY00.0480.04828.841-0.321-0.3210.0000.0000.0000.000
198A227ILE0-0.021-0.00727.9520.4740.4740.0000.0000.0000.000
199A228TYR00.020-0.01428.044-0.437-0.4370.0000.0000.0000.000
200A229SER00.0050.00530.742-0.014-0.0140.0000.0000.0000.000
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204A233ARG10.7990.86832.925-8.872-8.8720.0000.0000.0000.000
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206A235LYS10.9391.01237.450-7.290-7.2900.0000.0000.0000.000