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: J31V9

Calculation Name: 1B78-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B78

Chain ID: A

ChEMBL ID:

UniProt ID: Q57679

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2044399.87055
FMO2-HF: Nuclear repulsion 1971631.740885
FMO2-HF: Total energy -72768.129664
FMO2-MP2: Total energy -72985.394603


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:10:LYS)


Summations of interaction energy for fragment #1(A:10:LYS)
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.
-173.369-171.95637.051-18.564-19.902-0.196
Interaction energy analysis for fragmet #1(A:10:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.903
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].
3A12TYR00.002-0.0082.503-13.557-9.6113.726-2.595-5.078-0.015
4A13PHE00.027-0.0105.0845.6755.736-0.001-0.002-0.0570.000
5A14ALA00.0200.0258.294-0.659-0.6590.0000.0000.0000.000
6A15THR00.007-0.00411.2362.8752.8750.0000.0000.0000.000
7A16GLY00.0420.03712.798-1.363-1.3630.0000.0000.0000.000
8A17ASN00.0080.00215.453-0.640-0.6400.0000.0000.0000.000
9A18PRO00.0560.01212.251-0.820-0.8200.0000.0000.0000.000
10A19ASN00.006-0.01212.395-1.849-1.8490.0000.0000.0000.000
11A20LYS10.8810.95313.24618.21218.2120.0000.0000.0000.000
12A21ILE00.0130.0167.5360.2350.2350.0000.0000.0000.000
13A22LYS10.9110.96510.36922.26122.2610.0000.0000.0000.000
14A23GLU-1-0.806-0.88212.555-16.632-16.6320.0000.0000.0000.000
15A24ALA00.0280.01310.0490.5080.5080.0000.0000.0000.000
16A25ASN00.030-0.0076.4380.5100.5100.0000.0000.0000.000
17A26ILE0-0.037-0.01010.0460.8720.8720.0000.0000.0000.000
18A27ILE0-0.043-0.01813.4151.3401.3400.0000.0000.0000.000
19A28LEU00.015-0.0068.3910.7410.7410.0000.0000.0000.000
20A29LYS10.8020.90410.11516.98316.9830.0000.0000.0000.000
21A30ASP-1-0.815-0.89011.133-16.288-16.2880.0000.0000.0000.000
22A31LEU0-0.0210.0029.0420.8920.8920.0000.0000.0000.000
23A32LYS10.8760.9268.43717.18717.1870.0000.0000.0000.000
24A33ASP-1-0.931-0.9627.206-21.055-21.0550.0000.0000.0000.000
25A34VAL0-0.037-0.0184.083-1.747-1.5310.000-0.030-0.1860.000
26A35GLU-1-0.839-0.9032.426-40.605-39.1580.937-0.677-1.707-0.002
27A36ILE0-0.038-0.0202.659-9.257-6.3361.550-2.071-2.401-0.023
28A37GLU-1-0.803-0.8831.720-148.984-156.23630.840-13.178-10.410-0.156
29A38GLN0-0.055-0.0494.5752.8012.875-0.001-0.011-0.0630.000
30A39ILE00.0060.0055.986-2.352-2.3520.0000.0000.0000.000
31A40LYS10.9030.9507.80731.61231.6120.0000.0000.0000.000
32A41ILE00.0080.00310.1741.0761.0760.0000.0000.0000.000
33A42SER0-0.0070.00212.971-0.255-0.2550.0000.0000.0000.000
34A43TYR0-0.036-0.04215.390-0.742-0.7420.0000.0000.0000.000
35A44PRO00.0130.00918.2250.2930.2930.0000.0000.0000.000
36A45GLU-1-0.822-0.88120.240-15.127-15.1270.0000.0000.0000.000
37A46ILE0-0.052-0.01722.8390.5400.5400.0000.0000.0000.000
38A47GLN00.0120.00025.6650.1300.1300.0000.0000.0000.000
39A48GLY00.0420.02727.8470.0710.0710.0000.0000.0000.000
40A49THR0-0.059-0.05726.924-0.112-0.1120.0000.0000.0000.000
41A50LEU00.028-0.00322.688-0.292-0.2920.0000.0000.0000.000
42A51GLU-1-0.756-0.86221.909-12.505-12.5050.0000.0000.0000.000
43A52GLU-1-0.801-0.85121.927-11.462-11.4620.0000.0000.0000.000
44A53VAL00.0060.01120.351-0.462-0.4620.0000.0000.0000.000
45A54ALA0-0.005-0.00117.997-0.769-0.7690.0000.0000.0000.000
46A55GLU-1-0.844-0.91417.426-14.544-14.5440.0000.0000.0000.000
47A56PHE0-0.019-0.01218.682-0.588-0.5880.0000.0000.0000.000
48A57GLY00.0470.00817.452-0.398-0.3980.0000.0000.0000.000
49A58ALA0-0.010-0.00213.955-1.040-1.0400.0000.0000.0000.000
50A59LYS10.8720.91514.37713.03213.0320.0000.0000.0000.000
51A60TRP0-0.014-0.00116.5280.0890.0890.0000.0000.0000.000
52A61VAL00.017-0.00811.033-0.407-0.4070.0000.0000.0000.000
53A62TYR0-0.037-0.0259.864-0.735-0.7350.0000.0000.0000.000
54A63ASN00.0080.00213.289-0.204-0.2040.0000.0000.0000.000
55A64ILE0-0.020-0.00513.0590.3700.3700.0000.0000.0000.000
56A65LEU0-0.025-0.0146.749-0.190-0.1900.0000.0000.0000.000
57A66LYS10.8350.91810.02818.24218.2420.0000.0000.0000.000
58A67LYS10.9040.9565.67836.73336.7330.0000.0000.0000.000
59A68PRO00.0190.0095.0540.8470.8470.0000.0000.0000.000
60A69VAL0-0.035-0.0036.369-5.504-5.5040.0000.0000.0000.000
61A70ILE0-0.020-0.0048.2402.9412.9410.0000.0000.0000.000
62A71VAL00.0090.01010.512-1.207-1.2070.0000.0000.0000.000
63A72GLU-1-0.759-0.84913.545-16.754-16.7540.0000.0000.0000.000
64A73ASP-1-0.809-0.88215.968-14.055-14.0550.0000.0000.0000.000
65A74SER0-0.034-0.04419.6300.1530.1530.0000.0000.0000.000
66A75GLY0-0.0050.00922.3190.0830.0830.0000.0000.0000.000
67A76PHE00.0080.00126.130-0.055-0.0550.0000.0000.0000.000
68A77PHE0-0.0340.00527.166-0.005-0.0050.0000.0000.0000.000
69A78VAL00.0770.03032.3430.0520.0520.0000.0000.0000.000
70A79GLU-1-0.809-0.88536.076-8.063-8.0630.0000.0000.0000.000
71A80ALA00.0260.01938.4500.0970.0970.0000.0000.0000.000
72A81LEU0-0.018-0.00838.2540.1710.1710.0000.0000.0000.000
73A82ASN0-0.031-0.01938.436-0.093-0.0930.0000.0000.0000.000
74A83GLY0-0.0050.00334.695-0.126-0.1260.0000.0000.0000.000
75A84PHE00.0120.02133.236-0.386-0.3860.0000.0000.0000.000
76A85PRO00.005-0.00731.2950.1270.1270.0000.0000.0000.000
77A86GLY00.0740.02029.662-0.100-0.1000.0000.0000.0000.000
78A87THR0-0.028-0.02225.207-0.132-0.1320.0000.0000.0000.000
79A88TYR0-0.0050.00626.882-0.435-0.4350.0000.0000.0000.000
80A89SER0-0.006-0.02227.2070.2300.2300.0000.0000.0000.000
81A90LYS10.8210.90622.17613.85713.8570.0000.0000.0000.000
82A91PHE00.1100.05127.8590.2560.2560.0000.0000.0000.000
83A92VAL00.0080.02530.9010.3080.3080.0000.0000.0000.000
84A93GLN0-0.033-0.03230.5430.4740.4740.0000.0000.0000.000
85A94GLU-1-0.940-0.98428.241-11.027-11.0270.0000.0000.0000.000
86A95THR0-0.079-0.04432.9060.2730.2730.0000.0000.0000.000
87A96ILE0-0.038-0.01836.1880.2990.2990.0000.0000.0000.000
88A97GLY00.0350.03234.9190.1570.1570.0000.0000.0000.000
89A98ASN0-0.017-0.02833.559-0.024-0.0240.0000.0000.0000.000
90A99GLU-1-0.853-0.92236.741-7.616-7.6160.0000.0000.0000.000
91A100GLY0-0.0010.00439.3670.2140.2140.0000.0000.0000.000
92A101ILE0-0.055-0.03335.1960.1060.1060.0000.0000.0000.000
93A102LEU00.006-0.00138.7580.1200.1200.0000.0000.0000.000
94A103LYS10.8000.88541.5306.7946.7940.0000.0000.0000.000
95A104LEU0-0.039-0.03239.9450.1670.1670.0000.0000.0000.000
96A105LEU0-0.059-0.02539.6800.0540.0540.0000.0000.0000.000
97A106GLU-1-0.782-0.86543.209-6.451-6.4510.0000.0000.0000.000
98A107GLY0-0.033-0.01846.6940.0390.0390.0000.0000.0000.000
99A108LYS10.8270.92143.9757.1427.1420.0000.0000.0000.000
100A109ASP-1-0.861-0.92345.663-6.461-6.4610.0000.0000.0000.000
101A110ASN0-0.054-0.03441.030-0.155-0.1550.0000.0000.0000.000
102A111ARG10.8540.91441.1297.1817.1810.0000.0000.0000.000
103A112ASN0-0.036-0.00937.773-0.209-0.2090.0000.0000.0000.000
104A113ALA0-0.012-0.01633.986-0.013-0.0130.0000.0000.0000.000
105A114TYR0-0.068-0.04029.070-0.080-0.0800.0000.0000.0000.000
106A115PHE00.0270.03826.184-0.071-0.0710.0000.0000.0000.000
107A116LYS10.8220.88524.43111.58111.5810.0000.0000.0000.000
108A117THR0-0.010-0.02118.726-0.017-0.0170.0000.0000.0000.000
109A118VAL0-0.053-0.03319.3110.3360.3360.0000.0000.0000.000
110A119ILE00.0230.02212.940-0.390-0.3900.0000.0000.0000.000
111A120GLY0-0.0020.00015.3330.9330.9330.0000.0000.0000.000
112A121TYR0-0.050-0.0727.811-1.941-1.9410.0000.0000.0000.000
113A122CYS0-0.020-0.01411.6312.2402.2400.0000.0000.0000.000
114A123ASP-1-0.734-0.8139.048-24.354-24.3540.0000.0000.0000.000
115A124GLU-1-0.804-0.8888.462-24.114-24.1140.0000.0000.0000.000
116A125ASN0-0.086-0.04411.7342.1092.1090.0000.0000.0000.000
117A126GLY0-0.0120.00014.2961.1551.1550.0000.0000.0000.000
118A127VAL0-0.004-0.02114.340-1.024-1.0240.0000.0000.0000.000
119A128ARG10.8960.96214.59415.67215.6720.0000.0000.0000.000
120A129LEU0-0.0020.01015.990-0.706-0.7060.0000.0000.0000.000
121A130PHE0-0.013-0.00813.1340.5800.5800.0000.0000.0000.000
122A131LYS10.8880.92117.71712.01712.0170.0000.0000.0000.000
123A132GLY00.0250.01120.5890.0050.0050.0000.0000.0000.000
124A133ILE0-0.058-0.04322.370-0.038-0.0380.0000.0000.0000.000
125A134VAL00.0310.03825.951-0.078-0.0780.0000.0000.0000.000
126A135LYS10.9080.93428.3188.8158.8150.0000.0000.0000.000
127A136GLY00.0760.02632.052-0.112-0.1120.0000.0000.0000.000
128A137ARG10.8210.91634.7257.9887.9880.0000.0000.0000.000
129A138VAL0-0.015-0.01136.281-0.185-0.1850.0000.0000.0000.000
130A139SER00.008-0.01738.0280.1450.1450.0000.0000.0000.000
131A140GLU-1-0.847-0.92640.221-7.007-7.0070.0000.0000.0000.000
132A141GLU-1-0.861-0.92142.326-7.338-7.3380.0000.0000.0000.000
133A142ILE0-0.0040.01937.391-0.235-0.2350.0000.0000.0000.000
134A143ARG10.7970.88037.9457.9527.9520.0000.0000.0000.000
135A144SER00.016-0.02434.311-0.357-0.3570.0000.0000.0000.000
136A145LYS10.8360.89534.6708.4988.4980.0000.0000.0000.000
137A146GLY00.0030.01332.855-0.006-0.0060.0000.0000.0000.000
138A147TYR0-0.032-0.00829.199-0.271-0.2710.0000.0000.0000.000
139A148GLY00.0440.01427.665-0.320-0.3200.0000.0000.0000.000
140A149PHE0-0.058-0.01722.4290.0270.0270.0000.0000.0000.000
141A150ALA00.0500.01928.0740.0270.0270.0000.0000.0000.000
142A151TYR00.0510.00329.0410.2680.2680.0000.0000.0000.000
143A152ASP-1-0.818-0.91827.802-11.076-11.0760.0000.0000.0000.000
144A153SER0-0.053-0.03530.6700.2700.2700.0000.0000.0000.000
145A154ILE00.0130.01233.9830.2560.2560.0000.0000.0000.000
146A155PHE0-0.0330.00430.2430.1660.1660.0000.0000.0000.000
147A156ILE00.0090.02333.455-0.185-0.1850.0000.0000.0000.000
148A157PRO0-0.073-0.01831.0580.0050.0050.0000.0000.0000.000
149A158GLU-1-0.970-1.01931.124-9.432-9.4320.0000.0000.0000.000
150A159GLU-1-0.913-0.94934.554-7.596-7.5960.0000.0000.0000.000
151A160GLU-1-0.819-0.87534.008-8.423-8.4230.0000.0000.0000.000
152A161GLU-1-0.858-0.93436.841-7.216-7.2160.0000.0000.0000.000
153A162ARG10.6940.82933.5519.0309.0300.0000.0000.0000.000
154A163THR00.0350.00934.767-0.167-0.1670.0000.0000.0000.000
155A164PHE00.0440.00326.915-0.162-0.1620.0000.0000.0000.000
156A165ALA0-0.0270.00730.476-0.282-0.2820.0000.0000.0000.000
157A166GLU-1-0.821-0.88032.097-8.121-8.1210.0000.0000.0000.000
158A167MET0-0.035-0.00130.4920.1240.1240.0000.0000.0000.000
159A168THR00.000-0.03328.357-0.374-0.3740.0000.0000.0000.000
160A169THR0-0.002-0.01122.194-0.142-0.1420.0000.0000.0000.000
161A170GLU-1-0.850-0.93924.290-12.152-12.1520.0000.0000.0000.000
162A171GLU-1-0.782-0.81625.414-9.588-9.5880.0000.0000.0000.000
163A172LYS10.8140.89925.61511.24011.2400.0000.0000.0000.000
164A173SER0-0.099-0.05621.748-0.308-0.3080.0000.0000.0000.000
165A174GLN0-0.023-0.03621.472-0.723-0.7230.0000.0000.0000.000
166A175ILE00.0440.03223.9690.0130.0130.0000.0000.0000.000
167A176SER00.0240.02621.8200.0620.0620.0000.0000.0000.000
168A177HIS00.0420.02022.783-0.212-0.2120.0000.0000.0000.000
169A178ARG10.7740.83416.45916.16116.1610.0000.0000.0000.000
170A179LYS10.8560.93218.25313.13913.1390.0000.0000.0000.000
171A180LYS10.8630.91218.46112.49112.4910.0000.0000.0000.000
172A181ALA00.0280.02517.872-0.045-0.0450.0000.0000.0000.000
173A182PHE00.025-0.01011.981-0.765-0.7650.0000.0000.0000.000
174A183GLU-1-0.783-0.87714.265-15.819-15.8190.0000.0000.0000.000
175A184GLU-1-0.854-0.88716.674-12.835-12.8350.0000.0000.0000.000
176A185PHE0-0.025-0.0138.185-0.193-0.1930.0000.0000.0000.000
177A186LYS10.8830.93311.93915.59615.5960.0000.0000.0000.000
178A187LYS10.8540.91812.99812.92712.9270.0000.0000.0000.000
179A188PHE00.011-0.00510.7130.0190.0190.0000.0000.0000.000
180A189LEU0-0.054-0.0327.224-0.402-0.4020.0000.0000.0000.000
181A190LEU0-0.008-0.00210.696-0.161-0.1610.0000.0000.0000.000
182A191ASP-1-0.941-0.96113.242-13.428-13.4280.0000.0000.0000.000
183A192ARG10.7980.9007.47922.08722.0870.0000.0000.0000.000
184A193ILE0-0.019-0.00112.4990.2370.2370.0000.0000.0000.000