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: 661MZ

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 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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2916358.965017
FMO2-HF: Nuclear repulsion 2823694.624921
FMO2-HF: Total energy -92664.340096
FMO2-MP2: Total energy -92935.494152


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.
-3.7660.3580.056-2.025-2.1570
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 : 0.078 / q_NPA : 0.035
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].
3B4SER00.1290.0423.022-3.016-0.7290.001-1.142-1.1470.004
4B5SER0-0.072-0.0333.100-3.099-2.0900.051-0.551-0.509-0.005
5B6HIS00.0500.0253.575-0.1210.2640.005-0.100-0.2910.000
6B7ASN00.0550.0185.7180.3560.3560.0000.0000.0000.000
7B8PRO00.0350.0168.847-0.017-0.0170.0000.0000.0000.000
8B9VAL00.1100.06510.6900.0340.0340.0000.0000.0000.000
9B10ILE0-0.045-0.01611.6040.0330.0330.0000.0000.0000.000
10B11LEU0-0.024-0.0109.2760.0090.0090.0000.0000.0000.000
11B12LEU00.0250.02211.9330.0420.0420.0000.0000.0000.000
12B13LYS10.9840.99115.3000.2400.2400.0000.0000.0000.000
13B14ARG10.8380.94711.5090.4640.4640.0000.0000.0000.000
14B15ILE00.0200.01313.4760.0200.0200.0000.0000.0000.000
15B16LEU00.0140.01216.9040.0240.0240.0000.0000.0000.000
16B17SER0-0.043-0.06118.6420.0130.0130.0000.0000.0000.000
17B18LEU0-0.012-0.01319.9260.0120.0120.0000.0000.0000.000
18B19THR0-0.039-0.06516.023-0.007-0.0070.0000.0000.0000.000
19B20GLU-1-0.953-0.94111.461-0.520-0.5200.0000.0000.0000.000
20B21SER0-0.088-0.04115.4600.0340.0340.0000.0000.0000.000
21B22SER00.034-0.00716.310-0.028-0.0280.0000.0000.0000.000
22B23PRO00.0060.01218.6620.0090.0090.0000.0000.0000.000
23B24PHE00.0310.02121.3550.0120.0120.0000.0000.0000.000
24B25ILE0-0.011-0.00819.893-0.010-0.0100.0000.0000.0000.000
25B26LEU0-0.0050.00822.1440.0090.0090.0000.0000.0000.000
26B27CYS0-0.041-0.03223.125-0.010-0.0100.0000.0000.0000.000
27B28LEU00.0010.01024.4040.0090.0090.0000.0000.0000.000
28B29ASP-1-0.768-0.85826.969-0.053-0.0530.0000.0000.0000.000
29B30SER00.0190.00429.6660.0060.0060.0000.0000.0000.000
30B31ILE00.0330.00732.786-0.003-0.0030.0000.0000.0000.000
31B32ALA00.0080.02032.994-0.001-0.0010.0000.0000.0000.000
32B33GLN0-0.032-0.03929.0670.0020.0020.0000.0000.0000.000
33B34THR00.0150.02330.883-0.004-0.0040.0000.0000.0000.000
34B35SER00.043-0.01228.689-0.003-0.0030.0000.0000.0000.000
35B36TYR0-0.012-0.00429.404-0.008-0.0080.0000.0000.0000.000
36B37LYS10.9300.97429.8130.0540.0540.0000.0000.0000.000
37B38LEU00.0560.03222.698-0.007-0.0070.0000.0000.0000.000
38B39ILE00.0170.00226.069-0.010-0.0100.0000.0000.0000.000
39B40GLN0-0.020-0.02027.872-0.006-0.0060.0000.0000.0000.000
40B41GLU-1-0.737-0.80124.110-0.120-0.1200.0000.0000.0000.000
41B42PHE00.0000.00521.223-0.012-0.0120.0000.0000.0000.000
42B43VAL0-0.052-0.02624.864-0.005-0.0050.0000.0000.0000.000
43B44HIS00.0080.01225.6710.0020.0020.0000.0000.0000.000
44B45GLN00.0450.01221.647-0.010-0.0100.0000.0000.0000.000
45B46SER0-0.128-0.05423.476-0.006-0.0060.0000.0000.0000.000
46B47LYS10.9730.97624.5670.0940.0940.0000.0000.0000.000
47B48SER0-0.045-0.01024.8930.0010.0010.0000.0000.0000.000
48B49LYS10.8750.94117.4450.2360.2360.0000.0000.0000.000
49B50GLY00.0080.00123.563-0.005-0.0050.0000.0000.0000.000
50B51ASN0-0.0560.04722.2300.0030.0030.0000.0000.0000.000
51B52GLU-1-0.874-0.95926.435-0.086-0.0860.0000.0000.0000.000
52B53TYR0-0.121-0.09323.0640.0010.0010.0000.0000.0000.000
53B54PRO0-0.024-0.00129.2900.0030.0030.0000.0000.0000.000
54B55ILE00.000-0.00929.976-0.004-0.0040.0000.0000.0000.000
55B56VAL00.0140.01132.2090.0050.0050.0000.0000.0000.000
56B57TYR0-0.020-0.02833.063-0.005-0.0050.0000.0000.0000.000
57B58ILE0-0.023-0.02333.6890.0040.0040.0000.0000.0000.000
58B59SER0-0.047-0.03335.925-0.001-0.0010.0000.0000.0000.000
59B60PHE00.035-0.00236.4910.0020.0020.0000.0000.0000.000
60B61GLU-1-0.799-0.88637.004-0.037-0.0370.0000.0000.0000.000
61B62THR0-0.025-0.01137.800-0.001-0.0010.0000.0000.0000.000
62B63VAL00.0390.00840.2430.0000.0000.0000.0000.0000.000
63B64ASN0-0.048-0.02341.5500.0010.0010.0000.0000.0000.000
64B65LYS10.9500.97340.2970.0410.0410.0000.0000.0000.000
65B66PRO00.0270.02635.7700.0000.0000.0000.0000.0000.000
66B67SER00.020-0.00137.302-0.001-0.0010.0000.0000.0000.000
67B68TYR0-0.027-0.01432.789-0.001-0.0010.0000.0000.0000.000
68B69CYS0-0.074-0.01634.262-0.002-0.0020.0000.0000.0000.000
69B70THR0-0.002-0.00135.0020.0010.0010.0000.0000.0000.000
70B71GLN00.0180.00836.7730.0050.0050.0000.0000.0000.000
71B72PHE0-0.025-0.01737.378-0.003-0.0030.0000.0000.0000.000
72B73ILE0-0.004-0.00137.7190.0020.0020.0000.0000.0000.000
73B74ASP-1-0.837-0.89540.071-0.035-0.0350.0000.0000.0000.000
74B75ALA0-0.034-0.02939.7350.0010.0010.0000.0000.0000.000
75B76THR0-0.055-0.04041.8420.0020.0020.0000.0000.0000.000
76B77GLN0-0.027-0.00144.4430.0030.0030.0000.0000.0000.000
77B78MET0-0.059-0.01041.9520.0010.0010.0000.0000.0000.000
78B79ASP-1-0.804-0.88844.659-0.027-0.0270.0000.0000.0000.000
79B80PHE00.0540.00236.664-0.002-0.0020.0000.0000.0000.000
80B81VAL00.008-0.00540.771-0.002-0.0020.0000.0000.0000.000
81B82HIS0-0.075-0.05242.017-0.002-0.0020.0000.0000.0000.000
82B83LEU00.0510.03637.841-0.002-0.0020.0000.0000.0000.000
83B84VAL00.0190.00636.557-0.003-0.0030.0000.0000.0000.000
84B85LYS10.9440.96738.1730.0270.0270.0000.0000.0000.000
85B86GLN0-0.0070.00940.123-0.001-0.0010.0000.0000.0000.000
86B87ILE00.0090.00533.975-0.002-0.0020.0000.0000.0000.000
87B88ILE00.0280.00735.334-0.003-0.0030.0000.0000.0000.000
88B89SER0-0.113-0.04336.664-0.002-0.0020.0000.0000.0000.000
89B90TYR0-0.029-0.02536.7400.0010.0010.0000.0000.0000.000
90B91LEU0-0.054-0.03231.065-0.005-0.0050.0000.0000.0000.000
91B92PRO0-0.050-0.02431.4560.0030.0030.0000.0000.0000.000
92B93ALA00.0530.02333.8950.0000.0000.0000.0000.0000.000
93B94ALA00.0060.01635.4430.0000.0000.0000.0000.0000.000
94B95THR0-0.053-0.04434.497-0.002-0.0020.0000.0000.0000.000
95B96ALA0-0.0100.01135.393-0.001-0.0010.0000.0000.0000.000
96B97THR00.021-0.00133.3270.0020.0020.0000.0000.0000.000
97B98GLN0-0.0170.01127.683-0.006-0.0060.0000.0000.0000.000
98B99ALA00.0510.03130.8170.0030.0030.0000.0000.0000.000
99B100LYS10.9630.97929.1290.0680.0680.0000.0000.0000.000
100B101LYS10.9280.96520.9340.1670.1670.0000.0000.0000.000
101B102HIS00.0230.00727.3650.0050.0050.0000.0000.0000.000
102B103MET0-0.0050.01325.920-0.005-0.0050.0000.0000.0000.000
103B104VAL00.0240.00328.0110.0070.0070.0000.0000.0000.000
104B105ILE0-0.0080.00128.814-0.004-0.0040.0000.0000.0000.000
105B106ILE00.0150.00830.4660.0050.0050.0000.0000.0000.000
106B107ASP-1-0.748-0.85831.573-0.050-0.0500.0000.0000.0000.000
107B108SER00.0100.00833.3630.0010.0010.0000.0000.0000.000
108B109LEU00.005-0.02729.1200.0020.0020.0000.0000.0000.000
109B110ASN0-0.037-0.02033.326-0.001-0.0010.0000.0000.0000.000
110B111TYR00.0270.03035.8320.0040.0040.0000.0000.0000.000
111B112ILE0-0.0420.00134.3600.0010.0010.0000.0000.0000.000
112B113SER00.000-0.01936.6260.0000.0000.0000.0000.0000.000
113B114THR00.0550.00634.110-0.003-0.0030.0000.0000.0000.000
114B115GLU-1-0.840-0.89835.137-0.021-0.0210.0000.0000.0000.000
115B116TYR0-0.046-0.01936.930-0.001-0.0010.0000.0000.0000.000
116B117ILE0-0.0040.01130.526-0.003-0.0030.0000.0000.0000.000
117B118THR00.009-0.01429.962-0.004-0.0040.0000.0000.0000.000
118B119ARG10.9310.97431.7410.0260.0260.0000.0000.0000.000
119B120PHE00.010-0.00331.871-0.003-0.0030.0000.0000.0000.000
120B121LEU0-0.009-0.02027.163-0.003-0.0030.0000.0000.0000.000
121B122SER0-0.075-0.02929.308-0.004-0.0040.0000.0000.0000.000
122B123GLU-1-0.898-0.94930.830-0.038-0.0380.0000.0000.0000.000
123B124ILE0-0.016-0.00330.106-0.001-0.0010.0000.0000.0000.000
124B125ALA0-0.0220.00627.073-0.005-0.0050.0000.0000.0000.000
125B126SER00.0430.00027.0440.0030.0030.0000.0000.0000.000
126B127PRO0-0.027-0.00224.719-0.008-0.0080.0000.0000.0000.000
127B128HIS0-0.054-0.04424.789-0.007-0.0070.0000.0000.0000.000
128B129CYS0-0.0350.00226.5240.0000.0000.0000.0000.0000.000
129B130THR0-0.0170.00722.065-0.008-0.0080.0000.0000.0000.000
130B131MET0-0.011-0.00124.6870.0060.0060.0000.0000.0000.000
131B132VAL0-0.028-0.01523.940-0.009-0.0090.0000.0000.0000.000
132B133ALA00.0120.00826.1690.0080.0080.0000.0000.0000.000
133B134THR00.0380.04727.199-0.006-0.0060.0000.0000.0000.000
134B135TYR0-0.034-0.01029.0070.0050.0050.0000.0000.0000.000
135B136HIS10.7900.83530.2620.0420.0420.0000.0000.0000.000
136B137LYS10.8670.91626.8680.0460.0460.0000.0000.0000.000
137B138ASP-1-0.837-0.92231.955-0.025-0.0250.0000.0000.0000.000
138B139ILE0-0.0140.00435.4650.0020.0020.0000.0000.0000.000
139B140LYS10.8920.94236.7020.0150.0150.0000.0000.0000.000
140B141ASP-1-0.800-0.90536.043-0.022-0.0220.0000.0000.0000.000
141B142GLU-1-0.851-0.93138.914-0.022-0.0220.0000.0000.0000.000
142B143ASN0-0.016-0.01942.3460.0010.0010.0000.0000.0000.000
143B144ARG10.8960.93135.6950.0120.0120.0000.0000.0000.000
144B145THR0-0.020-0.01241.8800.0010.0010.0000.0000.0000.000
145B146VAL0-0.030-0.01044.6750.0010.0010.0000.0000.0000.000
146B147ILE00.0170.01944.0670.0000.0000.0000.0000.0000.000
147B148PRO0-0.064-0.03141.1970.0000.0000.0000.0000.0000.000
148B149ASP-1-0.821-0.90743.4750.0000.0000.0000.0000.0000.000
149B150TRP0-0.021-0.02743.5210.0000.0000.0000.0000.0000.000
150B151ASN0-0.078-0.03342.8580.0030.0030.0000.0000.0000.000
151B152ASN00.0030.01739.8030.0000.0000.0000.0000.0000.000
152B153ASN0-0.019-0.02236.6220.0010.0010.0000.0000.0000.000
153B154TYR0-0.040-0.00833.4350.0000.0000.0000.0000.0000.000
154B155PRO00.0030.00630.7890.0010.0010.0000.0000.0000.000
155B156ASP-1-0.837-0.90531.700-0.014-0.0140.0000.0000.0000.000
156B157LYS10.8730.93231.6990.0260.0260.0000.0000.0000.000
157B158LEU00.0230.02127.255-0.005-0.0050.0000.0000.0000.000
158B159THR0-0.004-0.02627.369-0.005-0.0050.0000.0000.0000.000
159B160LEU0-0.018-0.00426.644-0.003-0.0030.0000.0000.0000.000
160B161LEU0-0.007-0.00926.712-0.006-0.0060.0000.0000.0000.000
161B162GLN00.012-0.01223.170-0.015-0.0150.0000.0000.0000.000
162B163PHE0-0.051-0.00422.159-0.008-0.0080.0000.0000.0000.000
163B164MET0-0.039-0.03222.479-0.005-0.0050.0000.0000.0000.000
164B165ALA0-0.0150.01621.634-0.010-0.0100.0000.0000.0000.000
165B166THR0-0.040-0.02717.6510.0030.0030.0000.0000.0000.000
166B167THR0-0.032-0.00916.189-0.031-0.0310.0000.0000.0000.000
167B168ILE00.0300.02918.0600.0160.0160.0000.0000.0000.000
168B169VAL0-0.008-0.01218.935-0.018-0.0180.0000.0000.0000.000
169B170ASP-1-0.796-0.86921.230-0.039-0.0390.0000.0000.0000.000
170B171ILE0-0.009-0.00722.953-0.005-0.0050.0000.0000.0000.000
171B172ASP-1-0.877-0.93725.313-0.032-0.0320.0000.0000.0000.000
172B173VAL0-0.023-0.01227.194-0.006-0.0060.0000.0000.0000.000
173B174VAL0-0.0040.00126.4890.0010.0010.0000.0000.0000.000
174B175LEU0-0.020-0.00429.309-0.001-0.0010.0000.0000.0000.000
175B176THR00.001-0.01032.0740.0010.0010.0000.0000.0000.000
176B177GLY0-0.048-0.01634.2570.0010.0010.0000.0000.0000.000
177B178THR0-0.006-0.02636.9120.0000.0000.0000.0000.0000.000
178B179LEU0-0.0580.00038.2410.0010.0010.0000.0000.0000.000
179B180ASP-1-0.840-0.92334.590-0.004-0.0040.0000.0000.0000.000
180B181THR0-0.006-0.04530.383-0.002-0.0020.0000.0000.0000.000
181B182GLU-1-0.917-0.95633.6170.0000.0000.0000.0000.0000.000
182B183GLU-1-0.811-0.89536.060-0.005-0.0050.0000.0000.0000.000
183B184VAL0-0.061-0.03835.748-0.001-0.0010.0000.0000.0000.000
184B185SER00.0010.00334.752-0.003-0.0030.0000.0000.0000.000
185B186GLU-1-0.937-0.95837.299-0.001-0.0010.0000.0000.0000.000
186B187LEU0-0.023-0.01640.894-0.001-0.0010.0000.0000.0000.000
187B188LEU0-0.056-0.03636.327-0.001-0.0010.0000.0000.0000.000
188B189ASN0-0.034-0.01139.134-0.002-0.0020.0000.0000.0000.000
189B190GLU-1-0.986-0.98541.890-0.005-0.0050.0000.0000.0000.000
190B191PHE0-0.063-0.03942.357-0.001-0.0010.0000.0000.0000.000
191B192ARG10.9000.96644.5350.0070.0070.0000.0000.0000.000
192B193ILE0-0.017-0.00940.5840.0000.0000.0000.0000.0000.000
193B194PRO00.0210.03339.0650.0000.0000.0000.0000.0000.000
194B195ARG10.9250.93740.7200.0150.0150.0000.0000.0000.000
195B196GLY00.0290.01137.6120.0010.0010.0000.0000.0000.000
196B197LEU00.0070.02034.895-0.001-0.0010.0000.0000.0000.000
197B198ASN0-0.043-0.03233.651-0.004-0.0040.0000.0000.0000.000
198B199ASN0-0.0100.01031.8370.0010.0010.0000.0000.0000.000
199B200ASP-1-0.833-0.92131.463-0.061-0.0610.0000.0000.0000.000
200B201ILE0-0.0360.01726.997-0.008-0.0080.0000.0000.0000.000
201B202PHE0-0.030-0.01524.9860.0040.0040.0000.0000.0000.000
202B203GLN00.0550.02522.114-0.008-0.0080.0000.0000.0000.000
203B204LEU0-0.028-0.02019.906-0.001-0.0010.0000.0000.0000.000
204B205ARG10.9090.96418.0480.0390.0390.0000.0000.0000.000
205B206LEU0-0.058-0.02313.652-0.011-0.0110.0000.0000.0000.000
206B207VAL00.0460.01815.089-0.004-0.0040.0000.0000.0000.000
207B208ASN0-0.007-0.01310.2990.0530.0530.0000.0000.0000.000
208B209LYS10.9220.97012.4900.0880.0880.0000.0000.0000.000
209B210ARG10.8610.9314.0211.8072.250-0.001-0.232-0.2100.001
210B211LYS11.0280.99811.0910.3220.3220.0000.0000.0000.000
211B212SER0-0.064-0.0299.0230.0140.0140.0000.0000.0000.000
212B213GLY00.0550.03311.1440.0560.0560.0000.0000.0000.000
213B214ARG10.8460.9206.658-0.143-0.1430.0000.0000.0000.000
214B215SER00.0420.02111.950-0.083-0.0830.0000.0000.0000.000
215B216LEU0-0.109-0.0537.5300.0190.0190.0000.0000.0000.000
216B217GLU-1-0.844-0.93211.460-0.056-0.0560.0000.0000.0000.000
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