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: QVJVY

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 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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2004164.521115
FMO2-HF: Nuclear repulsion 1923627.87641
FMO2-HF: Total energy -80536.644705
FMO2-MP2: Total energy -80776.863798


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.
1.9817.10099999999993.456-3.835-4.7410.016
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 : -0.924 / q_NPA : -0.990
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].
3A56TRP0-0.008-0.0102.912-3.474-1.1990.111-0.948-1.439-0.001
4A57THR0-0.047-0.0266.404-1.941-1.9410.0000.0000.0000.000
5A58SER0-0.039-0.04310.111-0.985-0.9850.0000.0000.0000.000
6A59THR00.013-0.01712.753-0.171-0.1710.0000.0000.0000.000
7A60ALA00.0420.01616.330-0.203-0.2030.0000.0000.0000.000
8A61ILE0-0.0010.00119.7850.0330.0330.0000.0000.0000.000
9A62ILE00.0320.01923.256-0.280-0.2800.0000.0000.0000.000
10A63THR00.017-0.01725.943-0.104-0.1040.0000.0000.0000.000
11A64GLN00.0340.01929.6510.0260.0260.0000.0000.0000.000
12A65PRO00.0010.03232.8110.0010.0010.0000.0000.0000.000
13A66ASP-1-0.911-0.96233.9758.3478.3470.0000.0000.0000.000
14A67ALA00.0530.00236.665-0.022-0.0220.0000.0000.0000.000
15A68ALA00.0060.00238.742-0.081-0.0810.0000.0000.0000.000
16A69GLN00.0290.00532.4360.0330.0330.0000.0000.0000.000
17A70VAL00.0270.02237.2230.0610.0610.0000.0000.0000.000
18A71ALA0-0.022-0.00839.470-0.162-0.1620.0000.0000.0000.000
19A72THR00.0250.00341.111-0.190-0.1900.0000.0000.0000.000
20A73TYR00.0420.00440.521-0.195-0.1950.0000.0000.0000.000
21A74THR0-0.002-0.00142.635-0.090-0.0900.0000.0000.0000.000
22A75ASN0-0.0140.00344.654-0.153-0.1530.0000.0000.0000.000
23A76ALA00.002-0.00545.696-0.158-0.1580.0000.0000.0000.000
24A77LEU00.0290.02843.495-0.107-0.1070.0000.0000.0000.000
25A78ASN0-0.030-0.02247.665-0.094-0.0940.0000.0000.0000.000
26A79VAL00.0040.00450.840-0.126-0.1260.0000.0000.0000.000
27A80LEU00.009-0.00648.626-0.125-0.1250.0000.0000.0000.000
28A81TYR0-0.050-0.01948.623-0.010-0.0100.0000.0000.0000.000
29A82GLY0-0.050-0.03152.949-0.099-0.0990.0000.0000.0000.000
30A83GLY0-0.066-0.02353.7590.0380.0380.0000.0000.0000.000
31A84ASN0-0.011-0.01952.6280.1220.1220.0000.0000.0000.000
32A85ALA00.0000.01649.6210.1170.1170.0000.0000.0000.000
33A86PRO00.0530.03745.234-0.039-0.0390.0000.0000.0000.000
34A87LYS10.9290.96345.960-6.821-6.8210.0000.0000.0000.000
35A88ILE00.0700.02242.0380.1320.1320.0000.0000.0000.000
36A89SER0-0.032-0.01841.6650.0780.0780.0000.0000.0000.000
37A90GLU-1-0.894-0.95140.6617.2127.2120.0000.0000.0000.000
38A91VAL00.0170.03139.9100.1880.1880.0000.0000.0000.000
39A92GLN0-0.067-0.06537.5260.0190.0190.0000.0000.0000.000
40A93ALA00.0220.01636.1090.2950.2950.0000.0000.0000.000
41A94ASN0-0.022-0.01735.9270.3080.3080.0000.0000.0000.000
42A95PHE00.0500.02234.4760.2000.2000.0000.0000.0000.000
43A96ILE00.0360.02029.0520.2560.2560.0000.0000.0000.000
44A97SER0-0.057-0.02430.9570.4560.4560.0000.0000.0000.000
45A98ARG10.8270.89531.543-8.304-8.3040.0000.0000.0000.000
46A99PHE00.0280.02224.3130.3040.3040.0000.0000.0000.000
47A100SER0-0.073-0.04426.8380.4380.4380.0000.0000.0000.000
48A101SER00.0320.00926.7210.5120.5120.0000.0000.0000.000
49A102ALA00.0690.04527.1500.2780.2780.0000.0000.0000.000
50A103PHE00.032-0.00319.7470.5960.5960.0000.0000.0000.000
51A104SER0-0.101-0.05022.1790.7510.7510.0000.0000.0000.000
52A105ALA00.0400.02623.3670.2390.2390.0000.0000.0000.000
53A106LEU00.0190.00418.9780.4490.4490.0000.0000.0000.000
54A107SER0-0.096-0.07218.3450.7090.7090.0000.0000.0000.000
55A108GLU-1-0.890-0.95018.28715.29715.2970.0000.0000.0000.000
56A109VAL0-0.055-0.01519.6100.3740.3740.0000.0000.0000.000
57A110LEU00.004-0.02315.3340.4590.4590.0000.0000.0000.000
58A111ASP-1-0.874-0.91714.31322.11822.1180.0000.0000.0000.000
59A112ASN0-0.053-0.02615.6481.0891.0890.0000.0000.0000.000
60A113GLN0-0.033-0.01314.306-1.521-1.5210.0000.0000.0000.000
61A114LYS10.8590.91913.659-20.114-20.1140.0000.0000.0000.000
62A115GLU-1-0.948-0.97910.12025.46925.4690.0000.0000.0000.000
63A116ARG10.8630.94810.305-21.557-21.5570.0000.0000.0000.000
64A117GLU-1-0.754-0.82110.04923.92323.9230.0000.0000.0000.000
65A118LYS10.8510.93211.276-21.976-21.9760.0000.0000.0000.000
66A119LEU00.0530.02812.7720.9560.9560.0000.0000.0000.000
67A120THR0-0.0080.00915.715-0.587-0.5870.0000.0000.0000.000
68A121ILE00.0230.00618.350-0.097-0.0970.0000.0000.0000.000
69A122GLU-1-0.831-0.88720.66914.58614.5860.0000.0000.0000.000
70A123GLN00.0370.01423.331-0.056-0.0560.0000.0000.0000.000
71A124SER0-0.005-0.01724.3500.3840.3840.0000.0000.0000.000
72A125VAL0-0.0030.01025.4260.1550.1550.0000.0000.0000.000
73A126LYS10.8120.89421.935-13.980-13.9800.0000.0000.0000.000
74A127GLY00.0270.01428.195-0.266-0.2660.0000.0000.0000.000
75A128GLN0-0.065-0.02630.990-0.485-0.4850.0000.0000.0000.000
76A129ALA0-0.017-0.01730.8310.2660.2660.0000.0000.0000.000
77A130LEU0-0.0010.01730.3820.2540.2540.0000.0000.0000.000
78A131PRO0-0.017-0.00627.170-0.233-0.2330.0000.0000.0000.000
79A132LEU00.0300.02525.3870.1220.1220.0000.0000.0000.000
80A133SER0-0.014-0.02021.056-0.123-0.1230.0000.0000.0000.000
81A134VAL00.0190.02119.5340.2940.2940.0000.0000.0000.000
82A135SER0-0.046-0.02514.8350.6530.6530.0000.0000.0000.000
83A136TYR0-0.025-0.05011.1100.3410.3410.0000.0000.0000.000
84A137VAL00.0170.0217.2340.5530.5530.0000.0000.0000.000
85A138SER0-0.041-0.0167.0860.3580.3580.0000.0000.0000.000
86A139THR00.0590.0283.5084.5154.8080.009-0.104-0.1980.000
87A140THR00.0130.0033.2962.5943.4810.075-0.496-0.465-0.004
88A141ALA00.0540.0365.893-1.250-1.2500.0000.0000.0000.000
89A142GLU-1-0.853-0.9558.15322.28022.2800.0000.0000.0000.000
90A143GLY0-0.031-0.0139.032-1.447-1.4470.0000.0000.0000.000
91A144ALA00.0050.0018.907-1.345-1.3450.0000.0000.0000.000
92A145GLN0-0.001-0.00310.721-0.859-0.8590.0000.0000.0000.000
93A146ARG10.8860.95711.342-20.823-20.8230.0000.0000.0000.000
94A147ARG10.9670.96212.616-18.741-18.7410.0000.0000.0000.000
95A148LEU0-0.0220.01114.620-0.858-0.8580.0000.0000.0000.000
96A149ALA00.032-0.01216.328-0.792-0.7920.0000.0000.0000.000
97A150GLU-1-0.923-0.93717.06315.78515.7850.0000.0000.0000.000
98A151TYR00.004-0.03014.357-1.115-1.1150.0000.0000.0000.000
99A152ILE0-0.063-0.01119.556-0.497-0.4970.0000.0000.0000.000
100A153GLN0-0.057-0.02922.246-0.396-0.3960.0000.0000.0000.000
101A154GLN0-0.0020.00220.674-0.233-0.2330.0000.0000.0000.000
102A155VAL00.0250.01922.948-0.349-0.3490.0000.0000.0000.000
103A156ASP-1-0.853-0.94525.3579.9529.9520.0000.0000.0000.000
104A157GLU-1-0.915-0.95927.49610.63210.6320.0000.0000.0000.000
105A158GLU-1-0.970-0.97727.04310.82910.8290.0000.0000.0000.000
106A159VAL0-0.005-0.00829.066-0.358-0.3580.0000.0000.0000.000
107A160ALA00.0390.01431.321-0.374-0.3740.0000.0000.0000.000
108A161LYS10.7600.87032.614-8.784-8.7840.0000.0000.0000.000
109A162GLU-1-0.808-0.90033.5568.8038.8030.0000.0000.0000.000
110A163LEU00.0220.02135.091-0.302-0.3020.0000.0000.0000.000
111A164GLU-1-0.857-0.92737.2817.7257.7250.0000.0000.0000.000
112A165VAL00.019-0.00137.797-0.236-0.2360.0000.0000.0000.000
113A166ASP-1-0.799-0.91439.2667.8457.8450.0000.0000.0000.000
114A167LEU0-0.122-0.02841.250-0.221-0.2210.0000.0000.0000.000
115A168LYS10.9120.93342.982-7.184-7.1840.0000.0000.0000.000
116A169ASP-1-0.847-0.90343.7927.0537.0530.0000.0000.0000.000
117A170ASN0-0.016-0.02745.263-0.237-0.2370.0000.0000.0000.000
118A171ILE0-0.058-0.03246.558-0.177-0.1770.0000.0000.0000.000
119A172THR0-0.052-0.02048.201-0.198-0.1980.0000.0000.0000.000
120A173LEU00.007-0.00948.622-0.176-0.1760.0000.0000.0000.000
121A174GLN00.0200.02451.840-0.094-0.0940.0000.0000.0000.000
122A175THR0-0.019-0.01153.577-0.165-0.1650.0000.0000.0000.000
123A176LYS10.8600.93254.602-5.718-5.7180.0000.0000.0000.000
124A177THR00.0320.02656.088-0.114-0.1140.0000.0000.0000.000
125A178LEU00.0280.00056.929-0.123-0.1230.0000.0000.0000.000
126A179GLN00.0090.01058.875-0.027-0.0270.0000.0000.0000.000
127A180GLU-1-0.785-0.87860.0335.3035.3030.0000.0000.0000.000
128A181SER0-0.071-0.02762.342-0.104-0.1040.0000.0000.0000.000
129A182LEU0-0.014-0.02363.666-0.111-0.1110.0000.0000.0000.000
130A183GLU-1-0.893-0.93563.6234.9444.9440.0000.0000.0000.000
131A184THR0-0.023-0.01566.120-0.062-0.0620.0000.0000.0000.000
132A185GLN0-0.078-0.04768.226-0.139-0.1390.0000.0000.0000.000
133A186GLU-1-0.900-0.96168.9934.5934.5930.0000.0000.0000.000
134A187VAL00.0070.03271.124-0.048-0.0480.0000.0000.0000.000
135A188VAL00.0510.02272.888-0.066-0.0660.0000.0000.0000.000
136A189ALA0-0.087-0.05174.021-0.081-0.0810.0000.0000.0000.000
137A190GLN00.0220.01975.822-0.084-0.0840.0000.0000.0000.000
138A191GLU-1-0.806-0.91476.4124.1674.1670.0000.0000.0000.000
139A192GLN0-0.066-0.03278.639-0.048-0.0480.0000.0000.0000.000
140A193LYS10.8390.90477.336-4.191-4.1910.0000.0000.0000.000
141A194ASP-1-0.888-0.92881.7743.9103.9100.0000.0000.0000.000
142A195LEU0-0.003-0.00283.098-0.052-0.0520.0000.0000.0000.000
143A196ARG11.0150.97983.923-3.882-3.8820.0000.0000.0000.000
144A197ILE0-0.0120.01085.888-0.045-0.0450.0000.0000.0000.000
145A198LYS10.8780.91985.254-3.803-3.8030.0000.0000.0000.000
146A199GLN0-0.0270.00486.6460.0180.0180.0000.0000.0000.000
147A200ILE0-0.052-0.03189.612-0.024-0.0240.0000.0000.0000.000
148A201GLU-1-0.853-0.88991.7943.3773.3770.0000.0000.0000.000
149A202GLU-1-0.931-0.94493.5823.4243.4240.0000.0000.0000.000
150A203ALA0-0.033-0.02795.215-0.013-0.0130.0000.0000.0000.000
151A204LEU0-0.011-0.01698.134-0.027-0.0270.0000.0000.0000.000
152A205ARG10.9000.94394.965-3.386-3.3860.0000.0000.0000.000
153A206TYR0-0.030-0.02694.492-0.013-0.0130.0000.0000.0000.000
154A207ALA0-0.046-0.038101.0290.0060.0060.0000.0000.0000.000
155A208ASP-1-0.842-0.903100.9433.1163.1160.0000.0000.0000.000
156A209GLU-1-0.884-0.95297.7393.3013.3010.0000.0000.0000.000
157A210ALA0-0.028-0.01496.3200.0410.0410.0000.0000.0000.000
158A211LYS10.8610.93095.542-3.304-3.3040.0000.0000.0000.000
159A212ILE0-0.037-0.00795.2650.0170.0170.0000.0000.0000.000
160A213THR0-0.062-0.00391.1910.0390.0390.0000.0000.0000.000
161A214GLN0-0.044-0.03090.8340.0200.0200.0000.0000.0000.000
162A247PRO00.022-0.01880.6820.0120.0120.0000.0000.0000.000
163A248LEU0-0.040-0.01176.5540.0020.0020.0000.0000.0000.000
164A249VAL00.0290.03675.3610.0500.0500.0000.0000.0000.000
165A250PHE00.005-0.00172.079-0.020-0.0200.0000.0000.0000.000
166A251SER00.0260.00671.4760.0020.0020.0000.0000.0000.000
167A252PRO00.0490.01069.9030.0420.0420.0000.0000.0000.000
168A253ALA00.0070.01367.1800.0730.0730.0000.0000.0000.000
169A254TYR00.030-0.01366.0120.0500.0500.0000.0000.0000.000
170A255TYR0-0.025-0.00766.5200.0300.0300.0000.0000.0000.000
171A256GLN00.0060.01762.4030.0760.0760.0000.0000.0000.000
172A257THR00.0240.01461.4530.0810.0810.0000.0000.0000.000
173A258LYS10.8590.92161.271-4.670-4.6700.0000.0000.0000.000
174A259GLN0-0.0070.00160.695-0.024-0.0240.0000.0000.0000.000
175A260THR00.0200.01157.5130.0430.0430.0000.0000.0000.000
176A261LEU00.0130.00156.9480.1070.1070.0000.0000.0000.000
177A262LEU0-0.0180.00257.5050.0500.0500.0000.0000.0000.000
178A263ASP-1-0.835-0.93755.2135.6075.6070.0000.0000.0000.000
179A264ILE0-0.044-0.01452.4190.1330.1330.0000.0000.0000.000
180A265LYS10.8750.94752.295-5.457-5.4570.0000.0000.0000.000
181A266ASN0-0.119-0.05253.0970.0740.0740.0000.0000.0000.000
182A267LEU00.0680.06046.6680.0160.0160.0000.0000.0000.000
183A268LYS10.8020.87247.098-6.096-6.0960.0000.0000.0000.000
184A269VAL00.0270.00841.1690.0070.0070.0000.0000.0000.000
185A270THR0-0.0010.01839.1440.0050.0050.0000.0000.0000.000
186A271ALA00.0590.04736.3630.0340.0340.0000.0000.0000.000
187A272ASP-1-0.866-0.92635.0718.5838.5830.0000.0000.0000.000
188A273THR0-0.168-0.11736.105-0.051-0.0510.0000.0000.0000.000
189A274VAL0-0.032-0.01635.410-0.012-0.0120.0000.0000.0000.000
190A275HIS00.0240.02029.9860.1130.1130.0000.0000.0000.000
191A276VAL00.0250.01730.038-0.165-0.1650.0000.0000.0000.000
192A277TYR0-0.054-0.02925.8370.1460.1460.0000.0000.0000.000
193A278ARG10.9680.99629.663-9.377-9.3770.0000.0000.0000.000
194A279TYR0-0.024-0.01921.8960.3930.3930.0000.0000.0000.000
195A280VAL0-0.066-0.01725.867-0.423-0.4230.0000.0000.0000.000
196A281MET0-0.045-0.02819.122-0.263-0.2630.0000.0000.0000.000
197A282LYS10.9660.98321.260-12.031-12.0310.0000.0000.0000.000
198A283PRO00.0140.01016.7080.1030.1030.0000.0000.0000.000
199A284THR00.0000.01614.130-0.036-0.0360.0000.0000.0000.000
200A285LEU00.0100.02811.6570.8880.8880.0000.0000.0000.000
201A286PRO0-0.065-0.0219.003-0.650-0.6500.0000.0000.0000.000
202A287VAL00.0290.02110.1531.0391.0390.0000.0000.0000.000
203A288ARG10.8970.9569.807-23.592-23.5920.0000.0000.0000.000
204A289ARG10.9800.9892.233-66.175-64.5103.261-2.287-2.6390.021
205A290ASP-1-0.879-0.9406.84331.97931.9790.0000.0000.0000.000
206A291SER00.0460.0025.5058.5048.5040.0000.0000.0000.000
207A292PRO0-0.0260.0117.376-3.752-3.7520.0000.0000.0000.000