Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4J8JN

Calculation Name: 3B8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q04866

Base Structure: X-ray

Registration Date: 2023-09-23

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2006852.440368
FMO2-HF: Nuclear repulsion 1926312.949955
FMO2-HF: Total energy -80539.490413
FMO2-MP2: Total energy -80779.55274


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:54:GLU)


Summations of interaction energy for fragment #1(A:54: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.
-7.502-4.89813.552-7.624-8.5330.031
Interaction energy analysis for fragmet #1(A:54:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.842 / q_NPA : -0.909
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].
3A56TRP00.007-0.0052.300-6.269-3.7131.207-1.591-2.173-0.004
4A57THR00.0000.0056.359-1.995-1.9950.0000.0000.0000.000
5A58SER0-0.0110.00010.118-1.355-1.3550.0000.0000.0000.000
6A59THR00.032-0.01612.4410.0090.0090.0000.0000.0000.000
7A60ALA00.0230.01916.072-0.272-0.2720.0000.0000.0000.000
8A61ILE00.0010.00019.4990.0200.0200.0000.0000.0000.000
9A62ILE00.0220.02323.091-0.288-0.2880.0000.0000.0000.000
10A63THR0-0.003-0.01225.932-0.146-0.1460.0000.0000.0000.000
11A64GLN00.0440.02329.6600.0840.0840.0000.0000.0000.000
12A65PRO0-0.0060.03232.672-0.004-0.0040.0000.0000.0000.000
13A66ASP-1-0.803-0.89333.9048.4218.4210.0000.0000.0000.000
14A67ALA00.049-0.00536.862-0.020-0.0200.0000.0000.0000.000
15A68ALA0-0.034-0.00938.705-0.146-0.1460.0000.0000.0000.000
16A69GLN0-0.028-0.03431.709-0.078-0.0780.0000.0000.0000.000
17A70VAL00.0400.02637.0280.0260.0260.0000.0000.0000.000
18A71ALA0-0.0100.01039.313-0.161-0.1610.0000.0000.0000.000
19A72THR0-0.005-0.02540.899-0.225-0.2250.0000.0000.0000.000
20A73TYR00.011-0.01140.232-0.184-0.1840.0000.0000.0000.000
21A74THR00.000-0.00142.462-0.112-0.1120.0000.0000.0000.000
22A75ASN0-0.0110.00244.667-0.194-0.1940.0000.0000.0000.000
23A76ALA00.0130.01245.216-0.176-0.1760.0000.0000.0000.000
24A77LEU00.0270.01543.582-0.142-0.1420.0000.0000.0000.000
25A78ASN0-0.031-0.03747.696-0.078-0.0780.0000.0000.0000.000
26A79VAL0-0.015-0.00950.336-0.152-0.1520.0000.0000.0000.000
27A80LEU0-0.009-0.00648.311-0.126-0.1260.0000.0000.0000.000
28A81TYR0-0.0030.01248.443-0.045-0.0450.0000.0000.0000.000
29A82GLY00.0000.00352.908-0.091-0.0910.0000.0000.0000.000
30A83GLY0-0.048-0.02753.3280.0780.0780.0000.0000.0000.000
31A84ASN0-0.053-0.03053.0690.0630.0630.0000.0000.0000.000
32A85ALA00.0170.02849.1770.1130.1130.0000.0000.0000.000
33A86PRO0-0.0090.00345.184-0.041-0.0410.0000.0000.0000.000
34A87LYS10.8810.93045.252-7.107-7.1070.0000.0000.0000.000
35A88ILE00.0400.00741.5940.1570.1570.0000.0000.0000.000
36A89SER00.0010.00141.1290.1090.1090.0000.0000.0000.000
37A90GLU-1-0.794-0.89440.3837.3887.3880.0000.0000.0000.000
38A91VAL00.0020.01539.7920.1770.1770.0000.0000.0000.000
39A92GLN0-0.048-0.03637.0930.0160.0160.0000.0000.0000.000
40A93ALA00.0320.01535.8540.3230.3230.0000.0000.0000.000
41A94ASN0-0.015-0.00435.8610.2670.2670.0000.0000.0000.000
42A95PHE00.0400.01834.3520.2090.2090.0000.0000.0000.000
43A96ILE00.0290.01229.0990.2980.2980.0000.0000.0000.000
44A97SER0-0.062-0.00430.8720.3620.3620.0000.0000.0000.000
45A98ARG10.8030.86431.329-8.502-8.5020.0000.0000.0000.000
46A99PHE00.0290.01624.4670.3720.3720.0000.0000.0000.000
47A100SER0-0.033-0.04726.6080.4480.4480.0000.0000.0000.000
48A101SER0-0.0240.00726.3760.4380.4380.0000.0000.0000.000
49A102ALA00.0870.05126.7500.3700.3700.0000.0000.0000.000
50A103PHE00.029-0.00519.6620.6450.6450.0000.0000.0000.000
51A104SER0-0.103-0.06421.9260.7110.7110.0000.0000.0000.000
52A105ALA00.0330.01822.5530.4580.4580.0000.0000.0000.000
53A106LEU00.0180.00018.9180.5110.5110.0000.0000.0000.000
54A107SER0-0.101-0.06817.7820.8430.8430.0000.0000.0000.000
55A108GLU-1-0.912-0.96317.61716.58416.5840.0000.0000.0000.000
56A109VAL0-0.041-0.01919.0760.3920.3920.0000.0000.0000.000
57A110LEU00.004-0.00514.6970.5150.5150.0000.0000.0000.000
58A111ASP-1-0.795-0.85613.92823.40023.4000.0000.0000.0000.000
59A112ASN0-0.037-0.01215.3390.3490.3490.0000.0000.0000.000
60A113GLN0-0.067-0.02813.556-1.911-1.9110.0000.0000.0000.000
61A114LYS10.8420.90213.066-21.020-21.0200.0000.0000.0000.000
62A115GLU-1-0.915-0.9539.86726.98326.9830.0000.0000.0000.000
63A116ARG10.8240.89910.464-21.981-21.9810.0000.0000.0000.000
64A117GLU-1-0.755-0.8319.49427.11727.1170.0000.0000.0000.000
65A118LYS10.8660.92410.900-22.105-22.1050.0000.0000.0000.000
66A119LEU00.0520.03812.6180.9520.9520.0000.0000.0000.000
67A120THR0-0.028-0.00315.362-0.511-0.5110.0000.0000.0000.000
68A121ILE00.0280.00318.074-0.107-0.1070.0000.0000.0000.000
69A122GLU-1-0.823-0.87921.27714.76214.7620.0000.0000.0000.000
70A123GLN00.0590.02423.945-0.038-0.0380.0000.0000.0000.000
71A124SER0-0.010-0.03024.2030.2020.2020.0000.0000.0000.000
72A125VAL0-0.014-0.00125.6060.1420.1420.0000.0000.0000.000
73A126LYS10.7840.88322.438-14.317-14.3170.0000.0000.0000.000
74A127GLY00.0500.02828.845-0.268-0.2680.0000.0000.0000.000
75A128GLN0-0.083-0.04131.376-0.413-0.4130.0000.0000.0000.000
76A129ALA0-0.009-0.01131.2190.3040.3040.0000.0000.0000.000
77A130LEU00.0150.01930.4470.2450.2450.0000.0000.0000.000
78A131PRO0-0.016-0.01027.494-0.293-0.2930.0000.0000.0000.000
79A132LEU00.0190.01425.6150.0590.0590.0000.0000.0000.000
80A133SER0-0.0010.01020.884-0.190-0.1900.0000.0000.0000.000
81A134VAL00.0040.01019.3100.1050.1050.0000.0000.0000.000
82A135SER0-0.055-0.03514.7590.7330.7330.0000.0000.0000.000
83A136TYR0-0.013-0.02810.8750.2940.2940.0000.0000.0000.000
84A137VAL0-0.0060.0097.4140.7790.7790.0000.0000.0000.000
85A138SER00.0140.0167.1310.5730.5730.0000.0000.0000.000
86A139THR00.016-0.0032.6925.9966.7100.228-0.254-0.6890.000
87A140THR0-0.047-0.0532.9640.7452.5630.313-0.992-1.138-0.010
88A141ALA00.0560.0335.506-1.484-1.4840.0000.0000.0000.000
89A142GLU-1-0.704-0.8417.93323.63723.6370.0000.0000.0000.000
90A143GLY0-0.0050.0088.973-1.589-1.5890.0000.0000.0000.000
91A144ALA00.004-0.0048.594-1.115-1.1150.0000.0000.0000.000
92A145GLN0-0.070-0.05110.408-1.121-1.1210.0000.0000.0000.000
93A146ARG10.8160.89411.235-22.343-22.3430.0000.0000.0000.000
94A147ARG10.9100.94012.251-20.182-20.1820.0000.0000.0000.000
95A148LEU0-0.0270.00014.329-0.796-0.7960.0000.0000.0000.000
96A149ALA0-0.018-0.01616.082-1.036-1.0360.0000.0000.0000.000
97A150GLU-1-0.877-0.92515.81517.33217.3320.0000.0000.0000.000
98A151TYR00.015-0.02114.147-1.141-1.1410.0000.0000.0000.000
99A152ILE0-0.048-0.02419.402-0.633-0.6330.0000.0000.0000.000
100A153GLN0-0.056-0.03921.954-0.535-0.5350.0000.0000.0000.000
101A154GLN00.0150.01520.9250.0400.0400.0000.0000.0000.000
102A155VAL00.0320.01723.108-0.441-0.4410.0000.0000.0000.000
103A156ASP-1-0.799-0.89725.64410.16310.1630.0000.0000.0000.000
104A157GLU-1-0.856-0.92426.86511.16511.1650.0000.0000.0000.000
105A158GLU-1-0.962-0.97026.44311.62411.6240.0000.0000.0000.000
106A159VAL00.007-0.00729.232-0.414-0.4140.0000.0000.0000.000
107A160ALA00.0260.02531.485-0.412-0.4120.0000.0000.0000.000
108A161LYS10.7990.89832.784-9.055-9.0550.0000.0000.0000.000
109A162GLU-1-0.830-0.90733.4619.2379.2370.0000.0000.0000.000
110A163LEU00.0330.01434.829-0.342-0.3420.0000.0000.0000.000
111A164GLU-1-0.831-0.89837.2807.8117.8110.0000.0000.0000.000
112A165VAL00.003-0.00238.087-0.265-0.2650.0000.0000.0000.000
113A166ASP-1-0.757-0.86239.2578.0318.0310.0000.0000.0000.000
114A167LEU0-0.055-0.01241.363-0.256-0.2560.0000.0000.0000.000
115A168LYS10.8700.92041.533-7.839-7.8390.0000.0000.0000.000
116A169ASP-1-0.856-0.91244.0377.0547.0540.0000.0000.0000.000
117A170ASN0-0.046-0.04044.616-0.324-0.3240.0000.0000.0000.000
118A171ILE0-0.012-0.00446.788-0.177-0.1770.0000.0000.0000.000
119A172THR0-0.043-0.01348.387-0.225-0.2250.0000.0000.0000.000
120A173LEU00.010-0.00348.332-0.187-0.1870.0000.0000.0000.000
121A174GLN00.0150.00651.432-0.152-0.1520.0000.0000.0000.000
122A175THR0-0.048-0.03653.291-0.180-0.1800.0000.0000.0000.000
123A176LYS10.7870.88654.460-5.767-5.7670.0000.0000.0000.000
124A177THR0-0.015-0.00955.454-0.108-0.1080.0000.0000.0000.000
125A178LEU00.0290.00956.608-0.129-0.1290.0000.0000.0000.000
126A179GLN0-0.0150.00059.270-0.015-0.0150.0000.0000.0000.000
127A180GLU-1-0.771-0.86059.8525.3595.3590.0000.0000.0000.000
128A181SER0-0.053-0.02761.976-0.115-0.1150.0000.0000.0000.000
129A182LEU0-0.018-0.01563.031-0.108-0.1080.0000.0000.0000.000
130A183GLU-1-0.867-0.93563.3315.0685.0680.0000.0000.0000.000
131A184THR0-0.024-0.01565.678-0.086-0.0860.0000.0000.0000.000
132A185GLN0-0.061-0.03567.864-0.148-0.1480.0000.0000.0000.000
133A186GLU-1-0.855-0.94268.9414.6644.6640.0000.0000.0000.000
134A187VAL00.0170.03170.885-0.071-0.0710.0000.0000.0000.000
135A188VAL00.0570.03172.381-0.080-0.0800.0000.0000.0000.000
136A189ALA0-0.060-0.02573.789-0.084-0.0840.0000.0000.0000.000
137A190GLN0-0.007-0.00475.472-0.035-0.0350.0000.0000.0000.000
138A191GLU-1-0.870-0.93576.0854.2244.2240.0000.0000.0000.000
139A192GLN0-0.036-0.02578.404-0.054-0.0540.0000.0000.0000.000
140A193LYS10.8440.90377.185-4.272-4.2720.0000.0000.0000.000
141A194ASP-1-0.816-0.88881.2083.9063.9060.0000.0000.0000.000
142A195LEU00.0120.02182.849-0.057-0.0570.0000.0000.0000.000
143A196ARG10.9480.97683.414-3.952-3.9520.0000.0000.0000.000
144A197ILE0-0.013-0.00986.018-0.049-0.0490.0000.0000.0000.000
145A198LYS10.8170.88985.216-3.854-3.8540.0000.0000.0000.000
146A199GLN00.011-0.00686.550-0.001-0.0010.0000.0000.0000.000
147A200ILE0-0.039-0.00789.685-0.025-0.0250.0000.0000.0000.000
148A201GLU-1-0.817-0.88792.0273.3913.3910.0000.0000.0000.000
149A202GLU-1-0.865-0.88892.9753.4743.4740.0000.0000.0000.000
150A203ALA0-0.008-0.01195.095-0.016-0.0160.0000.0000.0000.000
151A204LEU0-0.035-0.02598.003-0.017-0.0170.0000.0000.0000.000
152A205ARG10.8120.87494.682-3.443-3.4430.0000.0000.0000.000
153A206TYR0-0.028-0.03294.483-0.008-0.0080.0000.0000.0000.000
154A207ALA0-0.018-0.010100.7240.0020.0020.0000.0000.0000.000
155A208ASP-1-0.859-0.926100.7063.1673.1670.0000.0000.0000.000
156A209GLU-1-0.880-0.94797.5913.3483.3480.0000.0000.0000.000
157A210ALA0-0.029-0.00596.2750.0460.0460.0000.0000.0000.000
158A211LYS10.8010.88195.472-3.354-3.3540.0000.0000.0000.000
159A212ILE0-0.0140.00995.4460.0270.0270.0000.0000.0000.000
160A213THR0-0.065-0.01591.3030.0390.0390.0000.0000.0000.000
161A214GLN0-0.051-0.02390.8680.0240.0240.0000.0000.0000.000
162A247PRO00.017-0.01980.1520.0160.0160.0000.0000.0000.000
163A248LEU0-0.0200.00877.035-0.008-0.0080.0000.0000.0000.000
164A249VAL00.0110.01375.4600.0470.0470.0000.0000.0000.000
165A250PHE00.011-0.00272.111-0.015-0.0150.0000.0000.0000.000
166A251SER00.0280.01771.1700.0040.0040.0000.0000.0000.000
167A252PRO00.0620.01869.4750.0510.0510.0000.0000.0000.000
168A253ALA00.0360.02866.6210.0750.0750.0000.0000.0000.000
169A254TYR00.0470.01765.7030.0540.0540.0000.0000.0000.000
170A255TYR0-0.0310.00166.6190.0210.0210.0000.0000.0000.000
171A256GLN00.0170.00262.2260.0610.0610.0000.0000.0000.000
172A257THR0-0.010-0.01561.7250.0880.0880.0000.0000.0000.000
173A258LYS10.8410.90661.457-4.756-4.7560.0000.0000.0000.000
174A259GLN0-0.051-0.02659.140-0.020-0.0200.0000.0000.0000.000
175A260THR00.0390.00757.5860.0610.0610.0000.0000.0000.000
176A261LEU00.0110.01656.9060.1170.1170.0000.0000.0000.000
177A262LEU0-0.024-0.00757.1960.0780.0780.0000.0000.0000.000
178A263ASP-1-0.831-0.91554.8975.7285.7280.0000.0000.0000.000
179A264ILE0-0.009-0.00452.3340.1400.1400.0000.0000.0000.000
180A265LYS10.8380.92252.187-5.546-5.5460.0000.0000.0000.000
181A266ASN0-0.064-0.03152.8740.0570.0570.0000.0000.0000.000
182A267LEU00.0390.04346.3230.0580.0580.0000.0000.0000.000
183A268LYS10.8010.88846.915-6.167-6.1670.0000.0000.0000.000
184A269VAL00.0130.00241.2210.0520.0520.0000.0000.0000.000
185A270THR00.0090.00839.2500.0180.0180.0000.0000.0000.000
186A271ALA00.0530.02936.3190.0740.0740.0000.0000.0000.000
187A272ASP-1-0.905-0.94934.8848.7698.7690.0000.0000.0000.000
188A273THR0-0.089-0.05035.696-0.036-0.0360.0000.0000.0000.000
189A274VAL0-0.049-0.01436.056-0.084-0.0840.0000.0000.0000.000
190A275HIS0-0.049-0.02730.1140.0460.0460.0000.0000.0000.000
191A276VAL0-0.001-0.00429.860-0.236-0.2360.0000.0000.0000.000
192A277TYR0-0.055-0.04525.2910.2430.2430.0000.0000.0000.000
193A278ARG10.8670.92629.298-9.646-9.6460.0000.0000.0000.000
194A279TYR00.014-0.00221.8940.3640.3640.0000.0000.0000.000
195A280VAL0-0.045-0.02525.920-0.474-0.4740.0000.0000.0000.000
196A281MET0-0.049-0.02018.760-0.230-0.2300.0000.0000.0000.000
197A282LYS10.9570.98120.725-12.298-12.2980.0000.0000.0000.000
198A283PRO00.0400.02316.1950.1010.1010.0000.0000.0000.000
199A284THR00.0020.02114.195-0.229-0.2290.0000.0000.0000.000
200A285LEU00.0150.02611.3771.1761.1760.0000.0000.0000.000
201A286PRO0-0.069-0.0248.732-0.807-0.8070.0000.0000.0000.000
202A287VAL00.0250.0089.6241.4441.4440.0000.0000.0000.000
203A288ARG10.7950.9099.362-25.697-25.6970.0000.0000.0000.000
204A289ARG10.8940.9321.988-73.203-75.68711.804-4.787-4.5330.045
205A290ASP-1-0.775-0.8946.37431.50531.5050.0000.0000.0000.000
206A291SER00.000-0.0225.9656.8026.8020.0000.0000.0000.000
207A292PRO0-0.0160.0208.008-3.125-3.1250.0000.0000.0000.000