Manual

About

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: R53G8

Calculation Name: 2HZS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HZS

Chain ID: B

ChEMBL ID:

UniProt ID: P32585

Base Structure: X-ray

Registration Date: 2023-06-21

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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2794419.919989
FMO2-HF: Nuclear repulsion 2700773.327979
FMO2-HF: Total energy -93646.59201
FMO2-MP2: Total energy -93918.040711


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(B:2:VAL)


Summations of interaction energy for fragment #1(B:2:VAL)
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.
-13.318-4.2466.598-6.251-9.42-0.04
Interaction energy analysis for fragmet #1(B:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.010
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].
3B4GLN00.0160.0082.881-0.6042.3320.953-1.574-2.3160.000
4B5LEU0-0.001-0.0014.153-0.100-0.0220.001-0.021-0.0570.000
5B6SER0-0.023-0.0267.8070.1770.1770.0000.0000.0000.000
6B7LEU0-0.0030.00710.533-0.008-0.0080.0000.0000.0000.000
7B8PHE00.014-0.00711.8570.0070.0070.0000.0000.0000.000
8B9GLY00.0480.02216.5460.0160.0160.0000.0000.0000.000
9B10SER0-0.067-0.02620.120-0.008-0.0080.0000.0000.0000.000
10B11ILE00.0170.02022.7530.0080.0080.0000.0000.0000.000
11B12GLY00.0620.03226.049-0.005-0.0050.0000.0000.0000.000
12B13ASP-1-0.792-0.90328.125-0.106-0.1060.0000.0000.0000.000
13B14ASP-1-0.935-0.96429.783-0.072-0.0720.0000.0000.0000.000
14B15GLY0-0.034-0.01229.4460.0050.0050.0000.0000.0000.000
15B16TYR0-0.008-0.01024.3860.0000.0000.0000.0000.0000.000
16B17ASP-1-0.855-0.93527.590-0.048-0.0480.0000.0000.0000.000
17B18LEU00.0040.01029.5710.0060.0060.0000.0000.0000.000
18B19LEU0-0.0100.02022.6290.0020.0020.0000.0000.0000.000
19B20ILE00.0560.02223.8060.0030.0030.0000.0000.0000.000
20B21SER00.0070.01725.8830.0100.0100.0000.0000.0000.000
21B22THR0-0.048-0.02125.3730.0070.0070.0000.0000.0000.000
22B23LEU00.0130.00220.1370.0040.0040.0000.0000.0000.000
23B24THR0-0.025-0.01322.9080.0120.0120.0000.0000.0000.000
24B25THR0-0.100-0.06425.0200.0090.0090.0000.0000.0000.000
25B26ILE0-0.0180.00721.8690.0080.0080.0000.0000.0000.000
26B27SER0-0.044-0.04620.4880.0120.0120.0000.0000.0000.000
27B28GLY0-0.028-0.00222.1610.0160.0160.0000.0000.0000.000
28B29ASN0-0.081-0.04621.4730.0160.0160.0000.0000.0000.000
29B30PRO00.0340.01523.290-0.011-0.0110.0000.0000.0000.000
30B31PRO0-0.0110.00621.5280.0050.0050.0000.0000.0000.000
31B32LEU0-0.020-0.01318.1360.0090.0090.0000.0000.0000.000
32B33LEU0-0.005-0.00319.469-0.014-0.0140.0000.0000.0000.000
33B34TYR0-0.073-0.04114.7480.0280.0280.0000.0000.0000.000
34B35ASN0-0.015-0.03718.320-0.017-0.0170.0000.0000.0000.000
35B36SER00.0040.00914.1380.0120.0120.0000.0000.0000.000
36B37LEU00.0410.04117.175-0.023-0.0230.0000.0000.0000.000
37B38CYS0-0.048-0.01014.987-0.026-0.0260.0000.0000.0000.000
38B39THR00.0410.01916.7950.0030.0030.0000.0000.0000.000
39B40VAL0-0.007-0.00316.179-0.037-0.0370.0000.0000.0000.000
40B41TRP0-0.008-0.01417.0170.0610.0610.0000.0000.0000.000
41B42LYS10.8840.92517.4800.1660.1660.0000.0000.0000.000
42B43PRO00.0630.02618.6940.0320.0320.0000.0000.0000.000
43B44ASN00.0300.01721.448-0.004-0.0040.0000.0000.0000.000
44B45PRO00.0090.01125.0000.0030.0030.0000.0000.0000.000
45B46SER0-0.067-0.03927.3700.0090.0090.0000.0000.0000.000
46B47TYR0-0.101-0.05725.8460.0140.0140.0000.0000.0000.000
47B48ASP-1-0.854-0.92326.878-0.158-0.1580.0000.0000.0000.000
48B49VAL0-0.066-0.03623.1310.0150.0150.0000.0000.0000.000
49B50GLU-1-0.894-0.93725.359-0.118-0.1180.0000.0000.0000.000
50B51ASN0-0.033-0.01122.066-0.024-0.0240.0000.0000.0000.000
51B52VAL0-0.019-0.00921.782-0.021-0.0210.0000.0000.0000.000
52B53ASN00.0140.02218.0460.0330.0330.0000.0000.0000.000
53B54SER00.0380.00621.0250.0040.0040.0000.0000.0000.000
54B55ARG10.8800.93317.4520.0620.0620.0000.0000.0000.000
55B56ASN00.0060.00123.070-0.006-0.0060.0000.0000.0000.000
56B57GLN0-0.014-0.00118.3200.0120.0120.0000.0000.0000.000
57B58LEU00.0480.01020.7330.0020.0020.0000.0000.0000.000
58B59VAL0-0.041-0.02616.175-0.024-0.0240.0000.0000.0000.000
59B60GLU-1-0.837-0.89416.126-0.505-0.5050.0000.0000.0000.000
60B61PRO00.0110.01516.314-0.038-0.0380.0000.0000.0000.000
61B62ASN00.0360.01311.3460.0800.0800.0000.0000.0000.000
62B63ARG10.8080.88614.8700.4740.4740.0000.0000.0000.000
63B64ILE0-0.019-0.00212.540-0.085-0.0850.0000.0000.0000.000
64B65LYS10.8520.92010.2110.6690.6690.0000.0000.0000.000
65B66LEU00.0070.00712.037-0.030-0.0300.0000.0000.0000.000
66B67SER0-0.080-0.06012.547-0.029-0.0290.0000.0000.0000.000
67B68LYS10.8560.91414.2400.0760.0760.0000.0000.0000.000
68B69GLU-1-0.873-0.93016.0890.0130.0130.0000.0000.0000.000
69B70VAL0-0.005-0.00318.0220.0040.0040.0000.0000.0000.000
70B71PRO00.0200.01521.804-0.001-0.0010.0000.0000.0000.000
71B72PHE00.0580.01321.974-0.007-0.0070.0000.0000.0000.000
72B73SER0-0.014-0.00926.008-0.006-0.0060.0000.0000.0000.000
73B74TYR00.0400.01526.5220.0010.0010.0000.0000.0000.000
74B75LEU0-0.0130.01323.089-0.006-0.0060.0000.0000.0000.000
75B76ILE00.0220.02626.941-0.009-0.0090.0000.0000.0000.000
76B77ASP-1-0.735-0.86230.164-0.025-0.0250.0000.0000.0000.000
77B78GLU-1-0.848-0.92223.440-0.040-0.0400.0000.0000.0000.000
78B79THR0-0.097-0.06925.517-0.013-0.0130.0000.0000.0000.000
79B80MET0-0.028-0.01128.238-0.003-0.0030.0000.0000.0000.000
80B81MET0-0.048-0.01331.8910.0030.0030.0000.0000.0000.000
81B82ASP-1-0.765-0.84728.754-0.068-0.0680.0000.0000.0000.000
82B83LYS10.8080.89728.8530.0800.0800.0000.0000.0000.000
83B84PRO0-0.011-0.01433.2800.0040.0040.0000.0000.0000.000
84B85LEU00.0320.04232.6710.0060.0060.0000.0000.0000.000
85B86ASN0-0.028-0.02834.7240.0050.0050.0000.0000.0000.000
86B87PHE0-0.047-0.01537.5600.0030.0030.0000.0000.0000.000
87B88ARG10.8740.93633.3130.0050.0050.0000.0000.0000.000
88B89ILE00.002-0.00834.2010.0030.0030.0000.0000.0000.000
89B90LEU0-0.123-0.06931.0430.0070.0070.0000.0000.0000.000
90B159GLU-1-0.916-0.94928.5060.0520.0520.0000.0000.0000.000
91B160SER0-0.070-0.03623.955-0.003-0.0030.0000.0000.0000.000
92B161CYS0-0.112-0.04120.965-0.006-0.0060.0000.0000.0000.000
93B162SER00.0460.01220.0080.0110.0110.0000.0000.0000.000
94B163PRO00.028-0.00116.086-0.001-0.0010.0000.0000.0000.000
95B164TRP0-0.023-0.01514.932-0.044-0.0440.0000.0000.0000.000
96B165SER0-0.041-0.0248.8310.0100.0100.0000.0000.0000.000
97B166LEU00.005-0.00610.491-0.066-0.0660.0000.0000.0000.000
98B167GLN00.003-0.0116.2320.0090.0090.0000.0000.0000.000
99B168ILE00.010-0.0017.4850.2170.2170.0000.0000.0000.000
100B169SER0-0.0140.0106.819-0.536-0.5360.0000.0000.0000.000
101B170ASP-1-0.869-0.9237.560-1.547-1.5470.0000.0000.0000.000
102B171ILE0-0.042-0.0229.598-0.017-0.0170.0000.0000.0000.000
103B172PRO0-0.030-0.01310.678-0.096-0.0960.0000.0000.0000.000
104B173ALA00.0220.01711.2080.1610.1610.0000.0000.0000.000
105B174ALA0-0.030-0.02312.8710.0950.0950.0000.0000.0000.000
106B175GLY00.0430.01316.5170.0080.0080.0000.0000.0000.000
107B176ASN0-0.055-0.02218.940-0.024-0.0240.0000.0000.0000.000
108B177ASN0-0.024-0.03320.945-0.005-0.0050.0000.0000.0000.000
109B178ARG10.8750.95713.7540.6360.6360.0000.0000.0000.000
110B179SER0-0.011-0.03815.636-0.012-0.0120.0000.0000.0000.000
111B180VAL00.0340.00811.4210.0250.0250.0000.0000.0000.000
112B181SER0-0.017-0.02611.463-0.045-0.0450.0000.0000.0000.000
113B182MET00.0290.0407.408-0.084-0.0840.0000.0000.0000.000
114B183GLN0-0.043-0.0326.9460.2330.2330.0000.0000.0000.000
115B184THR00.0190.0033.760-0.440-0.2600.000-0.058-0.1220.000
116B185ILE0-0.024-0.0213.2121.0602.1590.029-0.316-0.8120.000
117B186ALA00.0270.0342.060-8.031-7.2574.179-2.497-2.457-0.032
118B187GLU-1-0.819-0.8904.332-0.301-0.138-0.001-0.010-0.1510.000
119B188THR0-0.043-0.0176.3020.6670.6670.0000.0000.0000.000
120B189ILE00.0110.0038.169-0.162-0.1620.0000.0000.0000.000
121B190ILE00.0020.01211.3770.0250.0250.0000.0000.0000.000
122B191LEU0-0.002-0.00614.3170.0020.0020.0000.0000.0000.000
123B192SER00.0190.00917.191-0.013-0.0130.0000.0000.0000.000
124B193SER0-0.019-0.02720.4770.0040.0040.0000.0000.0000.000
125B194ALA00.0540.01823.250-0.001-0.0010.0000.0000.0000.000
126B195GLY00.0260.01426.925-0.004-0.0040.0000.0000.0000.000
127B196LYS10.9130.93229.820-0.009-0.0090.0000.0000.0000.000
128B197ASN0-0.004-0.00328.082-0.002-0.0020.0000.0000.0000.000
129B198SER00.0290.03025.906-0.008-0.0080.0000.0000.0000.000
130B199SER00.0620.04224.5530.0000.0000.0000.0000.0000.000
131B200VAL00.0870.02319.0960.0000.0000.0000.0000.0000.000
132B201SER00.0240.01721.537-0.017-0.0170.0000.0000.0000.000
133B202SER0-0.046-0.01123.672-0.005-0.0050.0000.0000.0000.000
134B203LEU0-0.0150.00020.4880.0020.0020.0000.0000.0000.000
135B204MET00.0200.02216.3320.0070.0070.0000.0000.0000.000
136B205ASN0-0.043-0.03620.673-0.002-0.0020.0000.0000.0000.000
137B206GLY0-0.024-0.00223.838-0.002-0.0020.0000.0000.0000.000
138B207LEU0-0.038-0.02216.4890.0080.0080.0000.0000.0000.000
139B208GLY00.0000.01520.324-0.020-0.0200.0000.0000.0000.000
140B209TYR0-0.053-0.04116.186-0.005-0.0050.0000.0000.0000.000
141B210VAL0-0.042-0.02221.3630.0280.0280.0000.0000.0000.000
142B211PHE00.0230.01821.722-0.029-0.0290.0000.0000.0000.000
143B212GLU-1-0.832-0.87721.301-0.284-0.2840.0000.0000.0000.000
144B213PHE00.0260.00318.6860.0110.0110.0000.0000.0000.000
145B214GLN0-0.011-0.01220.255-0.012-0.0120.0000.0000.0000.000
146B215TYR00.002-0.00614.438-0.007-0.0070.0000.0000.0000.000
147B216LEU00.0190.02119.7030.0000.0000.0000.0000.0000.000
148B217THR0-0.027-0.02115.6640.0060.0060.0000.0000.0000.000
149B218ILE00.024-0.00619.1620.0230.0230.0000.0000.0000.000
150B219GLY00.0290.01619.715-0.014-0.0140.0000.0000.0000.000
151B220VAL0-0.0250.00019.9810.0200.0200.0000.0000.0000.000
152B221LYS10.8390.91611.2930.0430.0430.0000.0000.0000.000
153B222PHE00.0420.02416.5430.0170.0170.0000.0000.0000.000
154B223PHE00.0120.00511.897-0.013-0.0130.0000.0000.0000.000
155B224MET00.0130.00314.791-0.007-0.0070.0000.0000.0000.000
156B225LYS10.9740.97615.141-0.025-0.0250.0000.0000.0000.000
157B226HIS00.0200.00313.6130.0010.0010.0000.0000.0000.000
158B227GLY00.0330.03310.3820.0340.0340.0000.0000.0000.000
159B228LEU0-0.040-0.01010.147-0.015-0.0150.0000.0000.0000.000
160B229ILE0-0.043-0.0148.7750.0390.0390.0000.0000.0000.000
161B230LEU00.013-0.00112.309-0.063-0.0630.0000.0000.0000.000
162B231GLU-1-0.806-0.86612.018-0.203-0.2030.0000.0000.0000.000
163B232LEU00.0140.01316.032-0.026-0.0260.0000.0000.0000.000
164B233GLN0-0.010-0.00414.5220.0070.0070.0000.0000.0000.000
165B234LYS10.7740.87019.9320.1120.1120.0000.0000.0000.000
166B235ILE00.014-0.00717.668-0.001-0.0010.0000.0000.0000.000
167B236TRP0-0.033-0.02221.8130.0070.0070.0000.0000.0000.000
168B237GLN0-0.026-0.01523.182-0.029-0.0290.0000.0000.0000.000
169B238ILE0-0.054-0.02323.9830.0160.0160.0000.0000.0000.000
170B239GLU-1-0.860-0.92426.219-0.150-0.1500.0000.0000.0000.000
171B240GLU-1-0.864-0.94729.181-0.063-0.0630.0000.0000.0000.000
172B241ALA0-0.056-0.01832.5080.0050.0050.0000.0000.0000.000
173B242GLY00.0000.00332.1890.0030.0030.0000.0000.0000.000
174B243ASN0-0.013-0.01428.113-0.012-0.0120.0000.0000.0000.000
175B244SER00.0430.02428.2440.0000.0000.0000.0000.0000.000
176B245GLN00.014-0.00126.102-0.015-0.0150.0000.0000.0000.000
177B246ILE00.0290.00822.0060.0030.0030.0000.0000.0000.000
178B247THR0-0.0140.00521.680-0.009-0.0090.0000.0000.0000.000
179B248SER0-0.035-0.01424.7810.0140.0140.0000.0000.0000.000
180B249GLY00.0280.02128.624-0.004-0.0040.0000.0000.0000.000
181B250GLY00.0230.00526.8220.0060.0060.0000.0000.0000.000
182B251PHE0-0.0170.01322.496-0.002-0.0020.0000.0000.0000.000
183B252LEU00.0040.00316.667-0.004-0.0040.0000.0000.0000.000
184B253LEU0-0.015-0.00518.4800.0130.0130.0000.0000.0000.000
185B254LYS10.8580.9368.5700.5850.5850.0000.0000.0000.000
186B255ALA00.0410.02613.6460.0480.0480.0000.0000.0000.000
187B256TYR0-0.054-0.0846.990-0.095-0.0950.0000.0000.0000.000
188B257ILE00.0630.0456.8540.1110.1110.0000.0000.0000.000
189B258ASN00.0040.0112.735-1.738-0.8170.312-0.384-0.8500.001
190B259VAL00.001-0.0092.887-0.4870.2440.122-0.236-0.616-0.001
191B260SER00.003-0.0042.501-2.807-0.6400.990-1.411-1.746-0.008
192B261ARG0-0.042-0.0363.450-0.312-0.2890.0130.256-0.2930.000
193B262GLY00.0040.0136.5950.5420.5420.0000.0000.0000.000
194B263THR0-0.047-0.0728.972-0.058-0.0580.0000.0000.0000.000
195B264ASP-1-0.882-0.8939.8800.0020.0020.0000.0000.0000.000
196B265ILE00.0320.00410.724-0.046-0.0460.0000.0000.0000.000
197B266ASP-1-0.857-0.92013.0740.0000.0000.0000.0000.0000.000
198B267ARG00.0470.0348.0840.1740.1740.0000.0000.0000.000
199B268ILE00.0210.0277.160-0.044-0.0440.0000.0000.0000.000
200B269ASN00.0540.02210.652-0.075-0.0750.0000.0000.0000.000
201B270TYR0-0.046-0.01712.911-0.009-0.0090.0000.0000.0000.000
202B271THR0-0.002-0.0258.2730.0230.0230.0000.0000.0000.000
203B272GLU-1-0.864-0.90811.481-0.418-0.4180.0000.0000.0000.000
204B273THR0-0.047-0.02713.7450.0130.0130.0000.0000.0000.000
205B274VAL0-0.012-0.00513.5200.0110.0110.0000.0000.0000.000
206B275LEU0-0.009-0.00210.8850.0090.0090.0000.0000.0000.000
207B276MET00.004-0.00414.9850.0000.0000.0000.0000.0000.000
208B277ASN0-0.089-0.04318.2930.0280.0280.0000.0000.0000.000
209B278LEU00.0610.03716.4020.0040.0040.0000.0000.0000.000
210B279LYS10.7980.88218.8550.2200.2200.0000.0000.0000.000
211B280LYS10.7960.88220.4690.1020.1020.0000.0000.0000.000
212B281GLU-1-0.922-0.96022.184-0.041-0.0410.0000.0000.0000.000
213B282LEU00.0300.01820.5510.0060.0060.0000.0000.0000.000
214B283GLN00.0010.00624.2930.0050.0050.0000.0000.0000.000
215B284GLY0-0.029-0.01625.9820.0100.0100.0000.0000.0000.000
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