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: M34JZ

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2333847.916222
FMO2-HF: Nuclear repulsion 2251489.783821
FMO2-HF: Total energy -82358.132401
FMO2-MP2: Total energy -82596.386356


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.
55.16964.6425.965-5.172-10.2660.005
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 : -0.982 / q_NPA : -0.991
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].
3A32MET0-0.036-0.0283.7163.1585.521-0.010-1.207-1.1470.006
4A33LEU00.0100.0206.488-3.361-3.3610.0000.0000.0000.000
5A34THR0-0.069-0.0498.7860.0840.0840.0000.0000.0000.000
6A35GLY00.0790.03811.936-0.597-0.5970.0000.0000.0000.000
7A36ARG10.8690.93015.501-13.656-13.6560.0000.0000.0000.000
8A37VAL00.0100.01718.719-0.023-0.0230.0000.0000.0000.000
9A38MET0-0.094-0.05320.890-0.417-0.4170.0000.0000.0000.000
10A39TYR00.0650.02324.106-0.058-0.0580.0000.0000.0000.000
11A40ASN0-0.056-0.02827.662-0.188-0.1880.0000.0000.0000.000
12A41GLY00.0140.01027.036-0.251-0.2510.0000.0000.0000.000
13A42GLU-1-0.882-0.91926.86710.26310.2630.0000.0000.0000.000
14A43ALA0-0.023-0.00222.6700.1060.1060.0000.0000.0000.000
15A44LEU00.0230.00524.067-0.488-0.4880.0000.0000.0000.000
16A45GLN0-0.020-0.00524.3730.2530.2530.0000.0000.0000.000
17A46LEU00.0140.00721.867-0.409-0.4090.0000.0000.0000.000
18A47ARG10.8610.91524.036-12.458-12.4580.0000.0000.0000.000
19A48GLY00.0130.01421.1740.3610.3610.0000.0000.0000.000
20A49ASN0-0.037-0.03919.811-0.704-0.7040.0000.0000.0000.000
21A50GLU-1-0.859-0.93616.68417.42917.4290.0000.0000.0000.000
22A51ALA0-0.056-0.01418.8800.0040.0040.0000.0000.0000.000
23A52VAL00.0290.02020.136-0.413-0.4130.0000.0000.0000.000
24A53GLN0-0.005-0.00216.4660.7250.7250.0000.0000.0000.000
25A54LEU0-0.023-0.00914.915-1.167-1.1670.0000.0000.0000.000
26A55GLN0-0.008-0.00114.5050.5160.5160.0000.0000.0000.000
27A56LEU00.0300.0189.334-0.916-0.9160.0000.0000.0000.000
28A57TYR0-0.032-0.03512.6680.6750.6750.0000.0000.0000.000
29A58GLN00.0800.0358.5580.2300.2300.0000.0000.0000.000
30A59HIS0-0.076-0.04513.405-0.022-0.0220.0000.0000.0000.000
31A60GLY00.0420.02516.889-1.108-1.1080.0000.0000.0000.000
32A61TYR00.0700.03219.0730.1950.1950.0000.0000.0000.000
33A62ALA00.001-0.00120.770-0.065-0.0650.0000.0000.0000.000
34A63LYS10.9290.97018.896-15.413-15.4130.0000.0000.0000.000
35A64HIS10.8040.90719.776-13.992-13.9920.0000.0000.0000.000
36A65ASP-1-0.845-0.91915.72918.64718.6470.0000.0000.0000.000
37A66PRO0-0.0350.00013.9521.0941.0940.0000.0000.0000.000
38A67ILE00.0470.0277.1690.1200.1200.0000.0000.0000.000
39A68ASN0-0.039-0.02510.926-3.127-3.1270.0000.0000.0000.000
40A69VAL00.0220.0149.8822.5512.5510.0000.0000.0000.000
41A70TYR00.0040.00712.070-1.520-1.5200.0000.0000.0000.000
42A71VAL0-0.0100.00014.5770.7500.7500.0000.0000.0000.000
43A72ASN00.0210.01317.363-1.091-1.0910.0000.0000.0000.000
44A73GLN00.004-0.02819.118-0.102-0.1020.0000.0000.0000.000
45A74ASP-1-0.893-0.93321.52012.27912.2790.0000.0000.0000.000
46A75GLY00.0450.04221.090-0.193-0.1930.0000.0000.0000.000
47A76MET0-0.042-0.02916.129-0.108-0.1080.0000.0000.0000.000
48A77TYR0-0.011-0.01611.2680.5730.5730.0000.0000.0000.000
49A78SER0-0.033-0.0359.6860.3700.3700.0000.0000.0000.000
50A79ALA00.0020.0067.583-0.200-0.2000.0000.0000.0000.000
51A80ASN0-0.023-0.0033.173-11.387-10.0650.121-0.723-0.7200.006
52A81LEU00.0180.0122.7796.2738.8491.114-0.955-2.7340.004
53A82PHE00.0400.0152.507-4.307-1.1454.726-2.326-5.562-0.011
54A83ASP-1-0.782-0.8543.65527.03427.0840.0140.039-0.1030.000
55A84GLY0-0.026-0.0186.3450.3210.3210.0000.0000.0000.000
56A85GLU-1-0.867-0.8969.87018.58318.5830.0000.0000.0000.000
57A86TYR0-0.078-0.0716.4151.2981.2980.0000.0000.0000.000
58A87GLN0-0.055-0.02112.825-1.337-1.3370.0000.0000.0000.000
59A88MET00.0030.01012.3610.6530.6530.0000.0000.0000.000
60A89ILE0-0.007-0.00315.704-1.160-1.1600.0000.0000.0000.000
61A90THR00.0830.04018.0030.7990.7990.0000.0000.0000.000
62A91LYS10.9200.97019.138-15.155-15.1550.0000.0000.0000.000
63A92SER0-0.013-0.02420.840-0.560-0.5600.0000.0000.0000.000
64A93GLY0-0.006-0.00724.4750.0740.0740.0000.0000.0000.000
65A94ASN0-0.095-0.05121.1390.5480.5480.0000.0000.0000.000
66A95GLY00.0510.00623.4760.5010.5010.0000.0000.0000.000
67A96PRO0-0.0700.00025.122-0.353-0.3530.0000.0000.0000.000
68A97TRP00.012-0.02921.832-0.115-0.1150.0000.0000.0000.000
69A98THR00.0230.02128.8630.1420.1420.0000.0000.0000.000
70A99SER0-0.031-0.03327.9790.2980.2980.0000.0000.0000.000
71A100GLU-1-0.945-0.97028.9069.6219.6210.0000.0000.0000.000
72A101GLY00.0250.01328.3040.2620.2620.0000.0000.0000.000
73A102ARG10.7800.90021.631-12.987-12.9870.0000.0000.0000.000
74A103ASP-1-0.843-0.92523.70312.00812.0080.0000.0000.0000.000
75A104THR0-0.143-0.07819.6950.6590.6590.0000.0000.0000.000
76A105ILE00.0220.01917.847-0.522-0.5220.0000.0000.0000.000
77A106ASN0-0.009-0.01616.9931.1341.1340.0000.0000.0000.000
78A107VAL00.0030.00211.961-0.379-0.3790.0000.0000.0000.000
79A108THR0-0.008-0.02012.5090.4030.4030.0000.0000.0000.000
80A109VAL0-0.081-0.0386.422-0.495-0.4950.0000.0000.0000.000
81A110ALA00.008-0.0028.6140.5490.5490.0000.0000.0000.000
82A111GLY00.0420.0266.358-1.827-1.8270.0000.0000.0000.000
83A112ASN0-0.023-0.0196.8092.6902.6900.0000.0000.0000.000
84A113THR0-0.021-0.0078.591-2.123-2.1230.0000.0000.0000.000
85A114VAL0-0.020-0.01511.2220.8550.8550.0000.0000.0000.000
86A115GLN0-0.021-0.01914.037-0.513-0.5130.0000.0000.0000.000
87A116ASP-1-0.804-0.88715.67015.91415.9140.0000.0000.0000.000
88A117VAL0-0.016-0.01017.456-0.017-0.0170.0000.0000.0000.000
89A118GLU-1-0.806-0.89620.22011.15011.1500.0000.0000.0000.000
90A119VAL0-0.027-0.01423.3950.0710.0710.0000.0000.0000.000
91A120THR00.0590.02326.100-0.366-0.3660.0000.0000.0000.000
92A121PRO0-0.0030.00028.702-0.009-0.0090.0000.0000.0000.000
93A122TYR00.0140.01830.356-0.393-0.3930.0000.0000.0000.000
94A123TYR0-0.035-0.05833.241-0.281-0.2810.0000.0000.0000.000
95A124LEU00.0020.00830.3110.4040.4040.0000.0000.0000.000
96A125VAL0-0.028-0.00833.337-0.337-0.3370.0000.0000.0000.000
97A126ARG10.7940.86732.356-9.000-9.0000.0000.0000.0000.000
98A127ASP-1-0.848-0.92037.1747.6067.6060.0000.0000.0000.000
99A128ALA0-0.0090.00036.246-0.149-0.1490.0000.0000.0000.000
100A129GLN0-0.040-0.01038.311-0.062-0.0620.0000.0000.0000.000
101A130MET0-0.031-0.01037.7610.0430.0430.0000.0000.0000.000
102A131THR0-0.015-0.01240.7760.1400.1400.0000.0000.0000.000
103A132LEU0-0.016-0.00842.687-0.016-0.0160.0000.0000.0000.000
104A133GLU-1-0.819-0.89944.8006.5516.5510.0000.0000.0000.000
105A134GLY0-0.009-0.00248.591-0.087-0.0870.0000.0000.0000.000
106A135ASN0-0.001-0.01947.5200.2320.2320.0000.0000.0000.000
107A136LYS10.8800.92347.414-6.096-6.0960.0000.0000.0000.000
108A137VAL0-0.0100.00341.5950.0680.0680.0000.0000.0000.000
109A138ASN00.0060.01145.022-0.057-0.0570.0000.0000.0000.000
110A139ALA00.0140.01341.0700.1300.1300.0000.0000.0000.000
111A140SER0-0.008-0.00442.228-0.152-0.1520.0000.0000.0000.000
112A141PHE00.011-0.00439.0720.2330.2330.0000.0000.0000.000
113A142LYS10.8990.94340.256-7.434-7.4340.0000.0000.0000.000
114A143VAL00.0140.01839.2500.2860.2860.0000.0000.0000.000
115A144GLU-1-0.808-0.88835.7328.6248.6240.0000.0000.0000.000
116A145LYS10.8120.87837.036-7.059-7.0590.0000.0000.0000.000
117A146VAL0-0.019-0.00633.023-0.073-0.0730.0000.0000.0000.000
118A147ALA0-0.036-0.01233.966-0.182-0.1820.0000.0000.0000.000
119A148GLY0-0.029-0.00635.975-0.232-0.2320.0000.0000.0000.000
120A149GLY00.0290.00537.2030.2010.2010.0000.0000.0000.000
121A150GLY0-0.0030.00139.430-0.115-0.1150.0000.0000.0000.000
122A151ILE0-0.026-0.01938.5800.2620.2620.0000.0000.0000.000
123A152ASP-1-0.899-0.94937.3538.1278.1270.0000.0000.0000.000
124A153ARG10.8500.91936.012-8.443-8.4430.0000.0000.0000.000
125A154VAL0-0.0060.01038.0020.2410.2410.0000.0000.0000.000
126A155PHE00.003-0.00832.861-0.114-0.1140.0000.0000.0000.000
127A156PHE00.0100.01536.7700.2120.2120.0000.0000.0000.000
128A157MET0-0.071-0.01932.8920.0810.0810.0000.0000.0000.000
129A158LEU00.0190.00735.898-0.025-0.0250.0000.0000.0000.000
130A159SER00.018-0.01031.4080.0980.0980.0000.0000.0000.000
131A160THR00.0280.00333.122-0.125-0.1250.0000.0000.0000.000
132A161THR0-0.101-0.05328.8700.1470.1470.0000.0000.0000.000
133A162GLN00.0480.01424.560-0.191-0.1910.0000.0000.0000.000
134A163PHE00.0060.01822.6330.0760.0760.0000.0000.0000.000
135A164VAL0-0.0050.00726.966-0.206-0.2060.0000.0000.0000.000
136A165ASN0-0.009-0.02625.912-0.017-0.0170.0000.0000.0000.000
137A166ASP-1-0.754-0.89628.82310.66710.6670.0000.0000.0000.000
138A167ALA0-0.029-0.00327.960-0.378-0.3780.0000.0000.0000.000
139A168GLU-1-0.884-0.90025.35612.50512.5050.0000.0000.0000.000
140A169HIS10.9190.94229.710-9.549-9.5490.0000.0000.0000.000
141A170ASN0-0.0040.00832.792-0.303-0.3030.0000.0000.0000.000
142A171VAL0-0.047-0.01234.593-0.211-0.2110.0000.0000.0000.000
143A172ASP-1-0.733-0.84437.1787.5447.5440.0000.0000.0000.000
144A173ARG10.7870.87233.704-8.727-8.7270.0000.0000.0000.000
145A174TYR0-0.069-0.04337.958-0.172-0.1720.0000.0000.0000.000
146A175ASP-1-0.759-0.87138.4718.5708.5700.0000.0000.0000.000
147A176GLU-1-0.770-0.83641.1126.8126.8120.0000.0000.0000.000
148A177THR00.040-0.01141.9110.1910.1910.0000.0000.0000.000
149A178ASP-1-0.899-0.92744.2696.5166.5160.0000.0000.0000.000
150A179ASN0-0.035-0.03647.3090.0140.0140.0000.0000.0000.000
151A180LEU00.0410.03441.691-0.019-0.0190.0000.0000.0000.000
152A181ASP-1-0.844-0.91544.9827.0747.0740.0000.0000.0000.000
153A182ALA0-0.048-0.01746.570-0.034-0.0340.0000.0000.0000.000
154A183TYR0-0.017-0.02044.475-0.085-0.0850.0000.0000.0000.000
155A184ASP-1-0.803-0.87342.0657.7637.7630.0000.0000.0000.000
156A185GLU-1-0.869-0.93343.7677.0617.0610.0000.0000.0000.000
157A186THR00.0490.02240.8450.0960.0960.0000.0000.0000.000
158A187GLY0-0.043-0.01342.233-0.183-0.1830.0000.0000.0000.000
159A188LYS10.8190.92044.107-6.820-6.8200.0000.0000.0000.000
160A189LEU0-0.013-0.00943.9030.1820.1820.0000.0000.0000.000
161A190TYR0-0.025-0.04142.931-0.135-0.1350.0000.0000.0000.000
162A191THR0-0.045-0.03944.2830.1210.1210.0000.0000.0000.000
163A192PHE0-0.030-0.00239.711-0.027-0.0270.0000.0000.0000.000
164A193ALA00.0030.00745.560-0.124-0.1240.0000.0000.0000.000
165A194THR0-0.051-0.04246.6990.0880.0880.0000.0000.0000.000
166A195ARG10.8310.92442.705-7.396-7.3960.0000.0000.0000.000
167A196ASP-1-0.809-0.87647.0536.4096.4090.0000.0000.0000.000
168A197TYR0-0.034-0.05642.2110.0280.0280.0000.0000.0000.000
169A198THR0-0.026-0.04446.5270.0680.0680.0000.0000.0000.000
170A199ASP-1-0.896-0.94148.6906.3816.3810.0000.0000.0000.000
171A200ASN0-0.0230.00841.0130.1640.1640.0000.0000.0000.000
172A201SER00.0730.02143.1760.0500.0500.0000.0000.0000.000
173A202MET0-0.0150.00637.3280.1320.1320.0000.0000.0000.000
174A203PHE00.0840.03539.9200.1520.1520.0000.0000.0000.000
175A204GLN0-0.017-0.00341.6900.0330.0330.0000.0000.0000.000
176A205THR0-0.107-0.06739.376-0.056-0.0560.0000.0000.0000.000
177A206ALA00.0020.00937.9860.0640.0640.0000.0000.0000.000
178A207LEU00.0560.02539.4000.0380.0380.0000.0000.0000.000
179A208LYS10.9080.97442.389-7.134-7.1340.0000.0000.0000.000
180A209ARG10.9400.96235.527-8.758-8.7580.0000.0000.0000.000
181A210GLY0-0.0050.01138.7600.0890.0890.0000.0000.0000.000
182A211THR0-0.104-0.05134.6240.1280.1280.0000.0000.0000.000
183A212LEU00.0210.01136.5260.0410.0410.0000.0000.0000.000
184A213PHE0-0.009-0.00331.162-0.039-0.0390.0000.0000.0000.000
185A214GLY00.0440.01034.516-0.149-0.1490.0000.0000.0000.000
186A215ARG10.7570.86826.344-11.171-11.1710.0000.0000.0000.000
187A216ILE00.0580.02034.011-0.205-0.2050.0000.0000.0000.000
188A217CYS0-0.073-0.01631.9960.3720.3720.0000.0000.0000.000
189A218ILE00.0450.03134.052-0.343-0.3430.0000.0000.0000.000
190A219TRP00.016-0.00329.8930.3880.3880.0000.0000.0000.000
191A220PRO0-0.0140.00532.516-0.320-0.3200.0000.0000.0000.000
192A221LYS10.8760.92734.879-7.296-7.2960.0000.0000.0000.000
193A222GLY0-0.002-0.00234.9570.0160.0160.0000.0000.0000.000
194A223SER0-0.029-0.01230.3270.3700.3700.0000.0000.0000.000
195A224ASP-1-0.792-0.88225.84611.94211.9420.0000.0000.0000.000
196A225GLN0-0.034-0.03225.0930.3880.3880.0000.0000.0000.000
197A226GLY00.0480.04628.595-0.332-0.3320.0000.0000.0000.000
198A227ILE0-0.028-0.01428.3150.4850.4850.0000.0000.0000.000
199A228TYR00.0360.00428.033-0.405-0.4050.0000.0000.0000.000
200A229SER00.0020.00031.105-0.019-0.0190.0000.0000.0000.000
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