FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: R57Z8

Calculation Name: 4A8J-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4A8J

Chain ID: B

ChEMBL ID:

UniProt ID: Q02884

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2928318.819181
FMO2-HF: Nuclear repulsion 2835652.945972
FMO2-HF: Total energy -92665.873209
FMO2-MP2: Total energy -92937.012938


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:ALA)


Summations of interaction energy for fragment #1(B:2:ALA)
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.
-5.659-0.2350.79-2.872-3.342-0.016
Interaction energy analysis for fragmet #1(B:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.034
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].
3B4SER00.0940.0542.669-2.234-0.1470.063-1.028-1.1220.003
4B5SER0-0.028-0.0192.557-5.718-3.8910.601-1.194-1.234-0.016
5B6HIS00.0470.0163.116-0.9580.1100.125-0.434-0.759-0.004
6B7ASN00.0380.0175.4660.4510.4510.0000.0000.0000.000
7B8PRO00.0320.0178.280-0.014-0.0140.0000.0000.0000.000
8B9VAL00.0870.06210.3140.0460.0460.0000.0000.0000.000
9B10ILE0-0.015-0.00611.4850.0350.0350.0000.0000.0000.000
10B11LEU0-0.053-0.0178.7050.0140.0140.0000.0000.0000.000
11B12LEU00.0440.03111.6790.0500.0500.0000.0000.0000.000
12B13LYS10.9370.97515.1010.2640.2640.0000.0000.0000.000
13B14ARG10.7400.86810.7200.5500.5500.0000.0000.0000.000
14B15ILE00.000-0.00113.0560.0320.0320.0000.0000.0000.000
15B16LEU00.0420.01716.5330.0300.0300.0000.0000.0000.000
16B17SER0-0.036-0.03918.4020.0190.0190.0000.0000.0000.000
17B18LEU0-0.022-0.01119.3660.0150.0150.0000.0000.0000.000
18B19THR0-0.016-0.01217.242-0.003-0.0030.0000.0000.0000.000
19B20GLU-1-0.827-0.88711.146-0.594-0.5940.0000.0000.0000.000
20B21SER0-0.050-0.03115.1910.0300.0300.0000.0000.0000.000
21B22SER00.0080.00216.8120.0050.0050.0000.0000.0000.000
22B23PRO00.0290.00918.3600.0110.0110.0000.0000.0000.000
23B24PHE00.0260.00921.2330.0150.0150.0000.0000.0000.000
24B25ILE0-0.024-0.00419.734-0.014-0.0140.0000.0000.0000.000
25B26LEU00.0020.01021.9810.0130.0130.0000.0000.0000.000
26B27CYS0-0.050-0.02423.007-0.013-0.0130.0000.0000.0000.000
27B28LEU00.0160.00523.9780.0100.0100.0000.0000.0000.000
28B29ASP-1-0.731-0.85026.307-0.083-0.0830.0000.0000.0000.000
29B30SER00.0460.02129.0880.0060.0060.0000.0000.0000.000
30B31ILE00.009-0.01032.252-0.003-0.0030.0000.0000.0000.000
31B32ALA00.0240.02632.5840.0010.0010.0000.0000.0000.000
32B33GLN0-0.064-0.04728.4710.0040.0040.0000.0000.0000.000
33B34THR00.0370.01730.085-0.006-0.0060.0000.0000.0000.000
34B35SER0-0.017-0.03228.357-0.003-0.0030.0000.0000.0000.000
35B36TYR0-0.002-0.00128.795-0.010-0.0100.0000.0000.0000.000
36B37LYS10.8960.95329.1570.0740.0740.0000.0000.0000.000
37B38LEU00.0350.01822.120-0.008-0.0080.0000.0000.0000.000
38B39ILE0-0.001-0.00425.664-0.011-0.0110.0000.0000.0000.000
39B40GLN0-0.002-0.01327.900-0.003-0.0030.0000.0000.0000.000
40B41GLU-1-0.742-0.82323.666-0.147-0.1470.0000.0000.0000.000
41B42PHE00.0120.01420.593-0.014-0.0140.0000.0000.0000.000
42B43VAL0-0.0330.00324.478-0.005-0.0050.0000.0000.0000.000
43B44HIS00.0020.01924.9450.0070.0070.0000.0000.0000.000
44B45GLN0-0.012-0.02321.063-0.013-0.0130.0000.0000.0000.000
45B46SER0-0.062-0.03822.925-0.003-0.0030.0000.0000.0000.000
46B47LYS10.9810.99924.0320.1050.1050.0000.0000.0000.000
47B48SER0-0.030-0.00924.6590.0060.0060.0000.0000.0000.000
48B49LYS10.8530.92517.2670.2730.2730.0000.0000.0000.000
49B50GLY00.0160.01823.665-0.004-0.0040.0000.0000.0000.000
50B51ASN0-0.069-0.01922.0120.0010.0010.0000.0000.0000.000
51B52GLU-1-0.900-0.96226.077-0.091-0.0910.0000.0000.0000.000
52B53TYR0-0.054-0.04622.5290.0040.0040.0000.0000.0000.000
53B54PRO0-0.033-0.00728.9940.0020.0020.0000.0000.0000.000
54B55ILE00.002-0.00629.617-0.006-0.0060.0000.0000.0000.000
55B56VAL00.0380.02331.9990.0060.0060.0000.0000.0000.000
56B57TYR0-0.041-0.03832.565-0.008-0.0080.0000.0000.0000.000
57B58ILE0-0.008-0.00533.3560.0050.0050.0000.0000.0000.000
58B59SER0-0.045-0.03435.497-0.003-0.0030.0000.0000.0000.000
59B60PHE00.0380.00135.8830.0030.0030.0000.0000.0000.000
60B61GLU-1-0.773-0.85337.049-0.056-0.0560.0000.0000.0000.000
61B62THR0-0.050-0.03337.102-0.001-0.0010.0000.0000.0000.000
62B63VAL00.0210.00739.5380.0000.0000.0000.0000.0000.000
63B64ASN0-0.028-0.00941.2880.0020.0020.0000.0000.0000.000
64B65LYS10.9520.97839.9480.0530.0530.0000.0000.0000.000
65B66PRO00.0300.02435.4800.0010.0010.0000.0000.0000.000
66B67SER00.0120.00037.446-0.002-0.0020.0000.0000.0000.000
67B68TYR00.0130.01032.3420.0000.0000.0000.0000.0000.000
68B69CYS0-0.103-0.04033.749-0.003-0.0030.0000.0000.0000.000
69B70THR0-0.026-0.02434.7640.0000.0000.0000.0000.0000.000
70B71GLN00.0030.00436.3610.0050.0050.0000.0000.0000.000
71B72PHE0-0.015-0.01436.895-0.004-0.0040.0000.0000.0000.000
72B73ILE0-0.006-0.00137.2540.0030.0030.0000.0000.0000.000
73B74ASP-1-0.803-0.87039.755-0.047-0.0470.0000.0000.0000.000
74B75ALA0-0.009-0.02139.3570.0010.0010.0000.0000.0000.000
75B76THR0-0.074-0.04641.4880.0020.0020.0000.0000.0000.000
76B77GLN0-0.045-0.02144.2900.0040.0040.0000.0000.0000.000
77B78MET0-0.054-0.01441.9630.0020.0020.0000.0000.0000.000
78B79ASP-1-0.767-0.86044.480-0.039-0.0390.0000.0000.0000.000
79B80PHE00.0490.00936.253-0.002-0.0020.0000.0000.0000.000
80B81VAL0-0.0010.00240.322-0.003-0.0030.0000.0000.0000.000
81B82HIS0-0.042-0.04541.921-0.001-0.0010.0000.0000.0000.000
82B83LEU00.0540.03137.771-0.002-0.0020.0000.0000.0000.000
83B84VAL00.0120.00236.354-0.003-0.0030.0000.0000.0000.000
84B85LYS10.8390.91538.0360.0370.0370.0000.0000.0000.000
85B86GLN00.0170.01540.1210.0000.0000.0000.0000.0000.000
86B87ILE00.0060.00733.668-0.003-0.0030.0000.0000.0000.000
87B88ILE00.007-0.00135.220-0.003-0.0030.0000.0000.0000.000
88B89SER0-0.116-0.05936.6500.0000.0000.0000.0000.0000.000
89B90TYR0-0.039-0.02836.2870.0020.0020.0000.0000.0000.000
90B91LEU0-0.002-0.00130.865-0.006-0.0060.0000.0000.0000.000
91B92PRO0-0.038-0.01631.1750.0040.0040.0000.0000.0000.000
92B93ALA00.0320.01433.114-0.001-0.0010.0000.0000.0000.000
93B94ALA00.0120.01735.0130.0010.0010.0000.0000.0000.000
94B95THR0-0.041-0.04034.006-0.002-0.0020.0000.0000.0000.000
95B96ALA0-0.0190.00735.443-0.001-0.0010.0000.0000.0000.000
96B97THR00.014-0.00133.3140.0020.0020.0000.0000.0000.000
97B98GLN0-0.0240.00227.928-0.008-0.0080.0000.0000.0000.000
98B99ALA00.0580.03630.1970.0040.0040.0000.0000.0000.000
99B100LYS10.9060.95828.9260.0860.0860.0000.0000.0000.000
100B101LYS10.8840.94621.2940.1900.1900.0000.0000.0000.000
101B102HIS0-0.031-0.03027.2140.0070.0070.0000.0000.0000.000
102B103MET0-0.022-0.00325.748-0.008-0.0080.0000.0000.0000.000
103B104VAL00.0170.00227.8840.0090.0090.0000.0000.0000.000
104B105ILE00.0160.01128.595-0.004-0.0040.0000.0000.0000.000
105B106ILE0-0.001-0.00530.1530.0070.0070.0000.0000.0000.000
106B107ASP-1-0.717-0.83431.161-0.069-0.0690.0000.0000.0000.000
107B108SER0-0.032-0.01333.272-0.001-0.0010.0000.0000.0000.000
108B109LEU00.026-0.00728.8100.0030.0030.0000.0000.0000.000
109B110ASN0-0.008-0.00133.231-0.001-0.0010.0000.0000.0000.000
110B111TYR0-0.022-0.00635.5120.0050.0050.0000.0000.0000.000
111B112ILE0-0.0210.00633.9660.0020.0020.0000.0000.0000.000
112B113SER00.011-0.01936.4700.0000.0000.0000.0000.0000.000
113B114THR00.0370.00333.892-0.003-0.0030.0000.0000.0000.000
114B115GLU-1-0.806-0.88934.772-0.038-0.0380.0000.0000.0000.000
115B116TYR0-0.052-0.01836.641-0.001-0.0010.0000.0000.0000.000
116B117ILE0-0.0200.00830.352-0.004-0.0040.0000.0000.0000.000
117B118THR00.016-0.00629.917-0.005-0.0050.0000.0000.0000.000
118B119ARG10.8250.89331.5280.0410.0410.0000.0000.0000.000
119B120PHE00.0270.01631.467-0.002-0.0020.0000.0000.0000.000
120B121LEU00.001-0.01026.900-0.003-0.0030.0000.0000.0000.000
121B122SER0-0.094-0.04628.894-0.004-0.0040.0000.0000.0000.000
122B123GLU-1-0.770-0.87530.800-0.051-0.0510.0000.0000.0000.000
123B124ILE0-0.013-0.00230.2310.0000.0000.0000.0000.0000.000
124B125ALA0-0.0180.00927.345-0.007-0.0070.0000.0000.0000.000
125B126SER00.0390.00627.2890.0040.0040.0000.0000.0000.000
126B127PRO0-0.018-0.00924.769-0.010-0.0100.0000.0000.0000.000
127B128HIS0-0.051-0.03824.814-0.007-0.0070.0000.0000.0000.000
128B129CYS0-0.029-0.00526.0510.0020.0020.0000.0000.0000.000
129B130THR0-0.015-0.00121.927-0.010-0.0100.0000.0000.0000.000
130B131MET00.0010.00924.5140.0060.0060.0000.0000.0000.000
131B132VAL0-0.031-0.01823.747-0.013-0.0130.0000.0000.0000.000
132B133ALA00.0030.00325.8780.0090.0090.0000.0000.0000.000
133B134THR00.0230.02926.987-0.009-0.0090.0000.0000.0000.000
134B135TYR0-0.050-0.04528.8050.0050.0050.0000.0000.0000.000
135B136HIS10.8020.85629.7990.0640.0640.0000.0000.0000.000
136B137LYS10.8130.88726.2260.0850.0850.0000.0000.0000.000
137B138ASP-1-0.816-0.89931.363-0.048-0.0480.0000.0000.0000.000
138B139ILE0-0.0160.00535.0150.0050.0050.0000.0000.0000.000
139B140LYS10.8790.91836.2960.0330.0330.0000.0000.0000.000
140B141ASP-1-0.764-0.86235.466-0.044-0.0440.0000.0000.0000.000
141B142GLU-1-0.789-0.88038.342-0.038-0.0380.0000.0000.0000.000
142B143ASN0-0.021-0.02341.7570.0010.0010.0000.0000.0000.000
143B144ARG10.9150.94035.3840.0330.0330.0000.0000.0000.000
144B145THR0-0.028-0.01541.5660.0000.0000.0000.0000.0000.000
145B146VAL0-0.037-0.01644.3730.0020.0020.0000.0000.0000.000
146B147ILE00.0020.01344.0380.0000.0000.0000.0000.0000.000
147B148PRO0-0.049-0.02140.9830.0010.0010.0000.0000.0000.000
148B149ASP-1-0.805-0.89143.262-0.012-0.0120.0000.0000.0000.000
149B150TRP0-0.025-0.01943.464-0.001-0.0010.0000.0000.0000.000
150B151ASN0-0.057-0.03742.7630.0030.0030.0000.0000.0000.000
151B152ASN0-0.0060.00639.604-0.001-0.0010.0000.0000.0000.000
152B153ASN0-0.051-0.03536.5500.0000.0000.0000.0000.0000.000
153B154TYR0-0.031-0.00133.938-0.001-0.0010.0000.0000.0000.000
154B155PRO0-0.016-0.00230.7640.0010.0010.0000.0000.0000.000
155B156ASP-1-0.806-0.88131.585-0.043-0.0430.0000.0000.0000.000
156B157LYS10.7780.85531.4420.0440.0440.0000.0000.0000.000
157B158LEU00.0300.02627.128-0.007-0.0070.0000.0000.0000.000
158B159THR0-0.046-0.06127.202-0.009-0.0090.0000.0000.0000.000
159B160LEU0-0.039-0.01326.467-0.007-0.0070.0000.0000.0000.000
160B161LEU00.0130.00226.655-0.008-0.0080.0000.0000.0000.000
161B162GLN00.004-0.01022.864-0.019-0.0190.0000.0000.0000.000
162B163PHE0-0.039-0.00321.909-0.013-0.0130.0000.0000.0000.000
163B164MET0-0.019-0.01322.212-0.008-0.0080.0000.0000.0000.000
164B165ALA00.0030.01421.597-0.011-0.0110.0000.0000.0000.000
165B166THR0-0.047-0.04117.4630.0010.0010.0000.0000.0000.000
166B167THR0-0.052-0.02215.787-0.037-0.0370.0000.0000.0000.000
167B168ILE00.0150.02317.8470.0250.0250.0000.0000.0000.000
168B169VAL0-0.014-0.02518.637-0.029-0.0290.0000.0000.0000.000
169B170ASP-1-0.764-0.85720.810-0.081-0.0810.0000.0000.0000.000
170B171ILE0-0.0170.00322.331-0.010-0.0100.0000.0000.0000.000
171B172ASP-1-0.831-0.91025.081-0.064-0.0640.0000.0000.0000.000
172B173VAL0-0.0030.00026.809-0.007-0.0070.0000.0000.0000.000
173B174VAL00.0000.01226.0180.0010.0010.0000.0000.0000.000
174B175LEU00.0090.01028.8110.0000.0000.0000.0000.0000.000
175B176THR0-0.020-0.02231.5290.0000.0000.0000.0000.0000.000
176B177GLY0-0.0010.00033.9690.0010.0010.0000.0000.0000.000
177B178THR0-0.078-0.04336.5660.0000.0000.0000.0000.0000.000
178B179LEU0-0.0180.00037.3660.0020.0020.0000.0000.0000.000
179B180ASP-1-0.853-0.91633.955-0.022-0.0220.0000.0000.0000.000
180B181THR0-0.007-0.04129.935-0.002-0.0020.0000.0000.0000.000
181B182GLU-1-0.878-0.91033.055-0.023-0.0230.0000.0000.0000.000
182B183GLU-1-0.828-0.91235.627-0.019-0.0190.0000.0000.0000.000
183B184VAL0-0.047-0.03134.987-0.001-0.0010.0000.0000.0000.000
184B185SER0-0.010-0.02734.543-0.003-0.0030.0000.0000.0000.000
185B186GLU-1-0.954-0.96236.937-0.015-0.0150.0000.0000.0000.000
186B187LEU0-0.007-0.00840.4990.0000.0000.0000.0000.0000.000
187B188LEU0-0.036-0.02636.084-0.001-0.0010.0000.0000.0000.000
188B189ASN0-0.073-0.04138.258-0.001-0.0010.0000.0000.0000.000
189B190GLU-1-0.846-0.87741.535-0.017-0.0170.0000.0000.0000.000
190B191PHE0-0.045-0.02841.8090.0000.0000.0000.0000.0000.000
191B192ARG10.7680.86044.0480.0180.0180.0000.0000.0000.000
192B193ILE0-0.030-0.02240.0110.0000.0000.0000.0000.0000.000
193B194PRO00.0250.03538.4440.0000.0000.0000.0000.0000.000
194B195ARG10.9180.93639.7950.0270.0270.0000.0000.0000.000
195B196GLY00.0160.01836.8780.0010.0010.0000.0000.0000.000
196B197LEU00.0390.02734.415-0.002-0.0020.0000.0000.0000.000
197B198ASN0-0.033-0.02433.015-0.003-0.0030.0000.0000.0000.000
198B199ASN0-0.0040.00831.5160.0010.0010.0000.0000.0000.000
199B200ASP-1-0.860-0.92031.172-0.079-0.0790.0000.0000.0000.000
200B201ILE0-0.017-0.00326.563-0.009-0.0090.0000.0000.0000.000
201B202PHE0-0.031-0.01624.7190.0060.0060.0000.0000.0000.000
202B203GLN00.010-0.00221.187-0.004-0.0040.0000.0000.0000.000
203B204LEU0-0.048-0.03418.794-0.001-0.0010.0000.0000.0000.000
204B205ARG10.8840.92818.2430.0890.0890.0000.0000.0000.000
205B206LEU0-0.044-0.01413.417-0.008-0.0080.0000.0000.0000.000
206B207VAL00.0360.00614.807-0.013-0.0130.0000.0000.0000.000
207B208ASN0-0.004-0.00310.9050.0630.0630.0000.0000.0000.000
208B209LYS10.8570.93612.3700.1030.1030.0000.0000.0000.000
209B210ARG10.8800.9363.6532.4142.8560.001-0.216-0.2270.001
210B211LYS10.9910.97911.4710.3430.3430.0000.0000.0000.000
211B212SER0-0.024-0.0038.8980.0190.0190.0000.0000.0000.000
212B213GLY00.0330.02511.8270.0510.0510.0000.0000.0000.000
213B214ARG10.8780.9207.0340.1460.1460.0000.0000.0000.000
214B215SER00.0410.02711.569-0.092-0.0920.0000.0000.0000.000
215B216LEU0-0.122-0.0547.102-0.013-0.0130.0000.0000.0000.000
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