FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZY4JN

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:


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 231
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2917836.235771
FMO2-HF: Nuclear repulsion 2825170.888255
FMO2-HF: Total energy -92665.347516
FMO2-MP2: Total energy -92936.483837


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.
-3.7220.5980.073-2.136-2.257-0.003
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 : 0.080 / 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].
3B4SER00.0990.0502.951-2.673-0.5090.005-1.073-1.0950.003
4B5SER0-0.056-0.0343.071-3.341-2.2460.058-0.609-0.544-0.006
5B6HIS00.0490.0283.553-0.3270.1710.010-0.145-0.363-0.001
6B7ASN00.0540.0195.7530.3540.3540.0000.0000.0000.000
7B8PRO00.0330.0138.757-0.008-0.0080.0000.0000.0000.000
8B9VAL00.1000.06310.6920.0410.0410.0000.0000.0000.000
9B10ILE0-0.043-0.01411.7010.0360.0360.0000.0000.0000.000
10B11LEU0-0.039-0.0169.1200.0180.0180.0000.0000.0000.000
11B12LEU00.0330.02711.9390.0470.0470.0000.0000.0000.000
12B13LYS10.9890.99515.3070.2480.2480.0000.0000.0000.000
13B14ARG10.7940.90311.1920.4810.4810.0000.0000.0000.000
14B15ILE00.0180.00913.4510.0230.0230.0000.0000.0000.000
15B16LEU00.0300.01716.9150.0250.0250.0000.0000.0000.000
16B17SER0-0.044-0.05418.6870.0150.0150.0000.0000.0000.000
17B18LEU0-0.011-0.00819.8560.0130.0130.0000.0000.0000.000
18B19THR0-0.057-0.02416.959-0.007-0.0070.0000.0000.0000.000
19B20GLU-1-0.871-0.91811.180-0.500-0.5000.0000.0000.0000.000
20B21SER0-0.056-0.02515.4730.0270.0270.0000.0000.0000.000
21B22SER00.031-0.00916.327-0.010-0.0100.0000.0000.0000.000
22B23PRO00.0350.02318.6790.0080.0080.0000.0000.0000.000
23B24PHE00.0320.02221.3740.0120.0120.0000.0000.0000.000
24B25ILE0-0.016-0.00419.960-0.010-0.0100.0000.0000.0000.000
25B26LEU0-0.0030.00822.1570.0100.0100.0000.0000.0000.000
26B27CYS0-0.049-0.03523.140-0.012-0.0120.0000.0000.0000.000
27B28LEU00.0110.01124.5440.0090.0090.0000.0000.0000.000
28B29ASP-1-0.755-0.86926.935-0.062-0.0620.0000.0000.0000.000
29B30SER00.0170.01029.6310.0060.0060.0000.0000.0000.000
30B31ILE00.027-0.00132.749-0.003-0.0030.0000.0000.0000.000
31B32ALA00.0100.02032.9490.0000.0000.0000.0000.0000.000
32B33GLN0-0.033-0.03729.0190.0020.0020.0000.0000.0000.000
33B34THR00.0280.02930.854-0.004-0.0040.0000.0000.0000.000
34B35SER00.038-0.01028.719-0.003-0.0030.0000.0000.0000.000
35B36TYR0-0.006-0.00329.414-0.008-0.0080.0000.0000.0000.000
36B37LYS10.9070.95529.8020.0610.0610.0000.0000.0000.000
37B38LEU00.0480.02722.742-0.007-0.0070.0000.0000.0000.000
38B39ILE00.008-0.00126.078-0.010-0.0100.0000.0000.0000.000
39B40GLN0-0.010-0.01827.881-0.005-0.0050.0000.0000.0000.000
40B41GLU-1-0.755-0.83224.175-0.125-0.1250.0000.0000.0000.000
41B42PHE00.0130.01321.037-0.013-0.0130.0000.0000.0000.000
42B43VAL0-0.0330.00524.873-0.005-0.0050.0000.0000.0000.000
43B44HIS00.0160.01725.3710.0040.0040.0000.0000.0000.000
44B45GLN00.018-0.00121.562-0.012-0.0120.0000.0000.0000.000
45B46SER0-0.104-0.07823.482-0.004-0.0040.0000.0000.0000.000
46B47LYS10.9490.97024.5750.0970.0970.0000.0000.0000.000
47B48SER0-0.0220.00824.7880.0040.0040.0000.0000.0000.000
48B49LYS10.8670.93317.5330.2410.2410.0000.0000.0000.000
49B50GLY00.0100.00523.566-0.004-0.0040.0000.0000.0000.000
50B51ASN0-0.090-0.01322.6180.0000.0000.0000.0000.0000.000
51B52GLU-1-0.890-0.95926.442-0.082-0.0820.0000.0000.0000.000
52B53TYR0-0.076-0.04122.8110.0040.0040.0000.0000.0000.000
53B54PRO0-0.022-0.00429.3010.0030.0030.0000.0000.0000.000
54B55ILE0-0.002-0.00830.035-0.005-0.0050.0000.0000.0000.000
55B56VAL00.0130.01132.2220.0050.0050.0000.0000.0000.000
56B57TYR0-0.019-0.03233.078-0.005-0.0050.0000.0000.0000.000
57B58ILE0-0.017-0.02033.8050.0040.0040.0000.0000.0000.000
58B59SER0-0.039-0.02835.940-0.002-0.0020.0000.0000.0000.000
59B60PHE00.028-0.00936.1620.0030.0030.0000.0000.0000.000
60B61GLU-1-0.798-0.87137.219-0.041-0.0410.0000.0000.0000.000
61B62THR0-0.032-0.01637.784-0.001-0.0010.0000.0000.0000.000
62B63VAL00.0370.00840.2560.0000.0000.0000.0000.0000.000
63B64ASN0-0.042-0.01941.5660.0020.0020.0000.0000.0000.000
64B65LYS10.9460.97840.3080.0430.0430.0000.0000.0000.000
65B66PRO00.0340.02835.7950.0000.0000.0000.0000.0000.000
66B67SER00.0250.00637.251-0.001-0.0010.0000.0000.0000.000
67B68TYR0-0.023-0.01232.7920.0000.0000.0000.0000.0000.000
68B69CYS0-0.091-0.03034.272-0.002-0.0020.0000.0000.0000.000
69B70THR00.001-0.00635.0560.0010.0010.0000.0000.0000.000
70B71GLN00.0120.00536.7800.0050.0050.0000.0000.0000.000
71B72PHE0-0.024-0.01837.391-0.003-0.0030.0000.0000.0000.000
72B73ILE00.0040.00337.7720.0020.0020.0000.0000.0000.000
73B74ASP-1-0.821-0.88240.086-0.037-0.0370.0000.0000.0000.000
74B75ALA0-0.033-0.03039.7350.0010.0010.0000.0000.0000.000
75B76THR0-0.055-0.03641.8590.0020.0020.0000.0000.0000.000
76B77GLN0-0.041-0.01544.4590.0030.0030.0000.0000.0000.000
77B78MET0-0.058-0.01642.0430.0020.0020.0000.0000.0000.000
78B79ASP-1-0.772-0.87344.471-0.028-0.0280.0000.0000.0000.000
79B80PHE00.0540.00936.686-0.002-0.0020.0000.0000.0000.000
80B81VAL00.002-0.00540.790-0.002-0.0020.0000.0000.0000.000
81B82HIS0-0.046-0.04942.036-0.001-0.0010.0000.0000.0000.000
82B83LEU00.0600.04138.095-0.002-0.0020.0000.0000.0000.000
83B84VAL00.0250.00836.579-0.003-0.0030.0000.0000.0000.000
84B85LYS10.8550.93438.1920.0270.0270.0000.0000.0000.000
85B86GLN0-0.0070.00640.1410.0000.0000.0000.0000.0000.000
86B87ILE00.0080.00633.994-0.002-0.0020.0000.0000.0000.000
87B88ILE00.0390.01335.108-0.003-0.0030.0000.0000.0000.000
88B89SER0-0.108-0.04636.682-0.001-0.0010.0000.0000.0000.000
89B90TYR0-0.035-0.02336.7530.0010.0010.0000.0000.0000.000
90B91LEU0-0.050-0.02731.323-0.005-0.0050.0000.0000.0000.000
91B92PRO0-0.047-0.02231.4360.0040.0040.0000.0000.0000.000
92B93ALA00.0450.01833.9120.0000.0000.0000.0000.0000.000
93B94ALA00.0050.01735.3380.0000.0000.0000.0000.0000.000
94B95THR0-0.047-0.04334.285-0.002-0.0020.0000.0000.0000.000
95B96ALA0-0.0130.01035.312-0.001-0.0010.0000.0000.0000.000
96B97THR00.018-0.00133.2820.0020.0020.0000.0000.0000.000
97B98GLN0-0.0240.00527.793-0.006-0.0060.0000.0000.0000.000
98B99ALA00.0510.03330.8560.0020.0020.0000.0000.0000.000
99B100LYS10.9570.98029.1350.0680.0680.0000.0000.0000.000
100B101LYS10.9000.95220.9870.1670.1670.0000.0000.0000.000
101B102HIS00.009-0.01027.3780.0050.0050.0000.0000.0000.000
102B103MET0-0.0050.01326.034-0.005-0.0050.0000.0000.0000.000
103B104VAL00.0200.00128.0310.0070.0070.0000.0000.0000.000
104B105ILE0-0.013-0.00328.796-0.004-0.0040.0000.0000.0000.000
105B106ILE00.0190.01230.4780.0060.0060.0000.0000.0000.000
106B107ASP-1-0.739-0.84331.588-0.053-0.0530.0000.0000.0000.000
107B108SER00.0030.00433.403-0.001-0.0010.0000.0000.0000.000
108B109LEU00.018-0.01628.9610.0020.0020.0000.0000.0000.000
109B110ASN0-0.019-0.00633.343-0.001-0.0010.0000.0000.0000.000
110B111TYR00.004-0.00235.8490.0040.0040.0000.0000.0000.000
111B112ILE0-0.042-0.00234.2760.0020.0020.0000.0000.0000.000
112B113SER00.017-0.01736.6450.0000.0000.0000.0000.0000.000
113B114THR00.0550.01134.182-0.003-0.0030.0000.0000.0000.000
114B115GLU-1-0.837-0.89635.158-0.024-0.0240.0000.0000.0000.000
115B116TYR0-0.047-0.01736.9500.0000.0000.0000.0000.0000.000
116B117ILE0-0.0110.00730.589-0.003-0.0030.0000.0000.0000.000
117B118THR00.020-0.01029.773-0.004-0.0040.0000.0000.0000.000
118B119ARG10.8790.94031.7840.0280.0280.0000.0000.0000.000
119B120PHE00.0270.00431.786-0.003-0.0030.0000.0000.0000.000
120B121LEU0-0.007-0.01627.130-0.003-0.0030.0000.0000.0000.000
121B122SER0-0.096-0.04129.328-0.003-0.0030.0000.0000.0000.000
122B123GLU-1-0.853-0.92330.906-0.037-0.0370.0000.0000.0000.000
123B124ILE0-0.015-0.00330.288-0.001-0.0010.0000.0000.0000.000
124B125ALA0-0.0170.01227.214-0.005-0.0050.0000.0000.0000.000
125B126SER00.0450.00327.0560.0030.0030.0000.0000.0000.000
126B127PRO0-0.024-0.00424.761-0.008-0.0080.0000.0000.0000.000
127B128HIS0-0.056-0.04624.805-0.007-0.0070.0000.0000.0000.000
128B129CYS0-0.0340.00326.567-0.001-0.0010.0000.0000.0000.000
129B130THR0-0.025-0.00422.004-0.008-0.0080.0000.0000.0000.000
130B131MET0-0.013-0.00124.7040.0060.0060.0000.0000.0000.000
131B132VAL0-0.028-0.01924.061-0.010-0.0100.0000.0000.0000.000
132B133ALA00.0080.00626.1840.0080.0080.0000.0000.0000.000
133B134THR00.0300.04027.214-0.007-0.0070.0000.0000.0000.000
134B135TYR0-0.036-0.02129.0410.0050.0050.0000.0000.0000.000
135B136HIS10.7980.85230.2730.0470.0470.0000.0000.0000.000
136B137LYS10.8330.89426.6360.0580.0580.0000.0000.0000.000
137B138ASP-1-0.800-0.89831.909-0.032-0.0320.0000.0000.0000.000
138B139ILE0-0.0100.01035.4190.0030.0030.0000.0000.0000.000
139B140LYS10.8470.91036.6540.0210.0210.0000.0000.0000.000
140B141ASP-1-0.786-0.89236.039-0.026-0.0260.0000.0000.0000.000
141B142GLU-1-0.813-0.89438.931-0.025-0.0250.0000.0000.0000.000
142B143ASN0-0.010-0.01742.3630.0010.0010.0000.0000.0000.000
143B144ARG10.8990.92435.7210.0160.0160.0000.0000.0000.000
144B145THR0-0.019-0.01041.7480.0010.0010.0000.0000.0000.000
145B146VAL0-0.032-0.01544.5590.0010.0010.0000.0000.0000.000
146B147ILE00.0080.01844.2790.0000.0000.0000.0000.0000.000
147B148PRO0-0.050-0.01941.0920.0000.0000.0000.0000.0000.000
148B149ASP-1-0.837-0.91943.376-0.002-0.0020.0000.0000.0000.000
149B150TRP0-0.013-0.01943.521-0.001-0.0010.0000.0000.0000.000
150B151ASN0-0.081-0.03342.8910.0020.0020.0000.0000.0000.000
151B152ASN00.0060.01239.6930.0000.0000.0000.0000.0000.000
152B153ASN0-0.025-0.02636.5950.0010.0010.0000.0000.0000.000
153B154TYR0-0.033-0.00233.8820.0000.0000.0000.0000.0000.000
154B155PRO0-0.0010.00530.7370.0010.0010.0000.0000.0000.000
155B156ASP-1-0.802-0.87631.800-0.021-0.0210.0000.0000.0000.000
156B157LYS10.8080.88531.6990.0290.0290.0000.0000.0000.000
157B158LEU00.0250.02827.258-0.005-0.0050.0000.0000.0000.000
158B159THR0-0.043-0.05927.437-0.005-0.0050.0000.0000.0000.000
159B160LEU0-0.028-0.00626.644-0.003-0.0030.0000.0000.0000.000
160B161LEU0-0.003-0.00626.732-0.006-0.0060.0000.0000.0000.000
161B162GLN00.017-0.01023.148-0.014-0.0140.0000.0000.0000.000
162B163PHE0-0.050-0.00722.178-0.008-0.0080.0000.0000.0000.000
163B164MET0-0.041-0.03322.499-0.004-0.0040.0000.0000.0000.000
164B165ALA0-0.0220.01721.695-0.009-0.0090.0000.0000.0000.000
165B166THR0-0.053-0.05017.6720.0060.0060.0000.0000.0000.000
166B167THR0-0.037-0.00716.011-0.030-0.0300.0000.0000.0000.000
167B168ILE00.0120.02218.0760.0180.0180.0000.0000.0000.000
168B169VAL0-0.015-0.01718.949-0.021-0.0210.0000.0000.0000.000
169B170ASP-1-0.778-0.85521.210-0.051-0.0510.0000.0000.0000.000
170B171ILE0-0.014-0.00522.918-0.007-0.0070.0000.0000.0000.000
171B172ASP-1-0.849-0.92125.452-0.043-0.0430.0000.0000.0000.000
172B173VAL0-0.018-0.00527.159-0.006-0.0060.0000.0000.0000.000
173B174VAL0-0.0020.00126.3840.0010.0010.0000.0000.0000.000
174B175LEU0-0.0090.00029.2820.0000.0000.0000.0000.0000.000
175B176THR0-0.005-0.01432.0480.0010.0010.0000.0000.0000.000
176B177GLY0-0.041-0.01234.2360.0020.0020.0000.0000.0000.000
177B178THR0-0.004-0.02336.8850.0000.0000.0000.0000.0000.000
178B179LEU0-0.060-0.00138.2780.0020.0020.0000.0000.0000.000
179B180ASP-1-0.850-0.92634.461-0.011-0.0110.0000.0000.0000.000
180B181THR0-0.005-0.04130.408-0.002-0.0020.0000.0000.0000.000
181B182GLU-1-0.868-0.92133.573-0.008-0.0080.0000.0000.0000.000
182B183GLU-1-0.838-0.91336.010-0.011-0.0110.0000.0000.0000.000
183B184VAL0-0.054-0.03635.669-0.001-0.0010.0000.0000.0000.000
184B185SER0-0.016-0.01334.894-0.003-0.0030.0000.0000.0000.000
185B186GLU-1-0.955-0.97237.251-0.007-0.0070.0000.0000.0000.000
186B187LEU0-0.017-0.01140.8450.0000.0000.0000.0000.0000.000
187B188LEU0-0.042-0.02936.428-0.001-0.0010.0000.0000.0000.000
188B189ASN0-0.036-0.01638.791-0.001-0.0010.0000.0000.0000.000
189B190GLU-1-0.855-0.88141.841-0.010-0.0100.0000.0000.0000.000
190B191PHE0-0.066-0.04142.203-0.001-0.0010.0000.0000.0000.000
191B192ARG10.7740.87044.5160.0110.0110.0000.0000.0000.000
192B193ILE0-0.024-0.01440.5500.0000.0000.0000.0000.0000.000
193B194PRO00.0220.03339.0400.0000.0000.0000.0000.0000.000
194B195ARG10.9310.94040.6910.0200.0200.0000.0000.0000.000
195B196GLY00.0250.00737.5920.0010.0010.0000.0000.0000.000
196B197LEU00.0090.02434.870-0.002-0.0020.0000.0000.0000.000
197B198ASN0-0.039-0.03233.601-0.003-0.0030.0000.0000.0000.000
198B199ASN0-0.0200.00631.8620.0010.0010.0000.0000.0000.000
199B200ASP-1-0.843-0.91831.499-0.067-0.0670.0000.0000.0000.000
200B201ILE0-0.0170.00726.894-0.008-0.0080.0000.0000.0000.000
201B202PHE0-0.024-0.01225.2470.0050.0050.0000.0000.0000.000
202B203GLN00.0290.01521.431-0.006-0.0060.0000.0000.0000.000
203B204LEU0-0.055-0.02419.4200.0000.0000.0000.0000.0000.000
204B205ARG10.8800.92518.2270.0560.0560.0000.0000.0000.000
205B206LEU0-0.052-0.02113.697-0.009-0.0090.0000.0000.0000.000
206B207VAL00.0420.01415.025-0.011-0.0110.0000.0000.0000.000
207B208ASN00.000-0.01010.5810.0480.0480.0000.0000.0000.000
208B209LYS10.9100.96412.5080.0810.0810.0000.0000.0000.000
209B210ARG10.8760.9273.8011.9462.5090.000-0.309-0.2550.001
210B211LYS11.0110.98911.2300.2900.2900.0000.0000.0000.000
211B212SER0-0.044-0.0208.5720.0160.0160.0000.0000.0000.000
212B213GLY00.0480.03111.2050.0550.0550.0000.0000.0000.000
213B214ARG10.8570.9226.956-0.066-0.0660.0000.0000.0000.000
214B215SER00.0370.01811.950-0.079-0.0790.0000.0000.0000.000
215B216LEU0-0.114-0.0547.4150.0260.0260.0000.0000.0000.000
216B217GLU-1-0.821-0.89611.403-0.084-0.0840.0000.0000.0000.000
217B218TYR0-0.037-0.0357.410-0.158-0.1580.0000.0000.0000.000
218B219ASP-1-0.813-0.88913.687-0.078-0.0780.0000.0000.0000.000
219B220PHE0-0.061-0.06013.289-0.035-0.0350.0000.0000.0000.000
220B221ILE00.0650.04918.5400.0160.0160.0000.0000.0000.000
221B222VAL0-0.025-0.02421.401-0.019-0.0190.0000.0000.0000.000
222B223ASN00.0330.00923.4400.0160.0160.0000.0000.0000.000
223B224SER0-0.025-0.04226.514-0.005-0.0050.0000.0000.0000.000
224B225ASN0-0.030-0.00928.1890.0020.0020.0000.0000.0000.000
225B226THR0-0.072-0.06627.473-0.001-0.0010.0000.0000.0000.000
226B227HIS10.8060.88525.2030.1010.1010.0000.0000.0000.000
227B228GLU-1-0.879-0.88622.839-0.117-0.1170.0000.0000.0000.000
228B229TYR0-0.069-0.08518.767-0.007-0.0070.0000.0000.0000.000
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230B231LEU0-0.062-0.04112.361-0.016-0.0160.0000.0000.0000.000
231B232LEU00.0150.02316.6250.0200.0200.0000.0000.0000.000