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: ZVVNN

Calculation Name: 4HA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HA7

Chain ID: A

ChEMBL ID:

UniProt ID: P33312

Base Structure: X-ray

Registration Date: 2023-09-21

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2763936.760373
FMO2-HF: Nuclear repulsion 2675794.101511
FMO2-HF: Total energy -88142.658862
FMO2-MP2: Total energy -88400.768311


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:8:GLU)


Summations of interaction energy for fragment #1(A:8: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.
-73.762-68.5685.598-4.129-6.6640.024
Interaction energy analysis for fragmet #1(A:8:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.973 / q_NPA : -1.008
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].
3A10LEU00.0200.0081.951-13.213-10.4065.219-3.327-4.6990.016
4A11PRO00.0080.0032.620-7.635-7.0150.296-0.120-0.7960.001
5A12GLN00.010-0.0025.727-2.236-2.2360.0000.0000.0000.000
6A13PHE0-0.0010.0076.636-2.308-2.3080.0000.0000.0000.000
7A14LEU00.015-0.0127.050-3.004-3.0040.0000.0000.0000.000
8A15GLN00.0070.0259.661-1.874-1.8740.0000.0000.0000.000
9A16ASN0-0.006-0.02211.411-1.568-1.5680.0000.0000.0000.000
10A17TYR0-0.074-0.05112.901-1.300-1.3000.0000.0000.0000.000
11A18LEU00.0090.02110.749-0.367-0.3670.0000.0000.0000.000
12A19PRO00.0360.00414.933-0.768-0.7680.0000.0000.0000.000
13A20ASN0-0.051-0.02717.139-1.233-1.2330.0000.0000.0000.000
14A21ALA00.0410.04315.8240.0700.0700.0000.0000.0000.000
15A22GLY0-0.061-0.03317.876-0.443-0.4430.0000.0000.0000.000
16A23GLN0-0.086-0.06220.246-1.000-1.0000.0000.0000.0000.000
17A24THR00.0370.01223.0080.0500.0500.0000.0000.0000.000
18A25GLU-1-0.956-0.94626.4169.4149.4140.0000.0000.0000.000
19A26ASN00.0150.01027.7360.5520.5520.0000.0000.0000.000
20A27THR0-0.013-0.00927.806-0.222-0.2220.0000.0000.0000.000
21A28ILE00.0520.01730.4000.0570.0570.0000.0000.0000.000
22A29VAL0-0.021-0.00328.080-0.069-0.0690.0000.0000.0000.000
23A30PRO0-0.0360.00425.2180.1750.1750.0000.0000.0000.000
24A31PHE00.0240.01618.152-0.073-0.0730.0000.0000.0000.000
25A32VAL00.006-0.00322.2380.2770.2770.0000.0000.0000.000
26A33THR0-0.025-0.01516.6430.2230.2230.0000.0000.0000.000
27A34LEU00.0010.00319.288-0.282-0.2820.0000.0000.0000.000
28A35THR0-0.062-0.03414.9411.0751.0750.0000.0000.0000.000
29A36TYR00.0570.01216.730-0.699-0.6990.0000.0000.0000.000
30A37ALA00.0040.00714.6061.0511.0510.0000.0000.0000.000
31A38GLN0-0.002-0.00316.181-1.576-1.5760.0000.0000.0000.000
32A39SER0-0.017-0.00917.1041.1591.1590.0000.0000.0000.000
33A40LEU00.0400.00718.196-0.076-0.0760.0000.0000.0000.000
34A41ASP-1-0.806-0.88920.53412.99212.9920.0000.0000.0000.000
35A42ALA00.0090.01821.794-0.583-0.5830.0000.0000.0000.000
36A43ARG10.8230.92122.390-12.346-12.3460.0000.0000.0000.000
37A44VAL00.0130.01520.1950.7500.7500.0000.0000.0000.000
38A45SER0-0.077-0.04721.7690.1490.1490.0000.0000.0000.000
39A46ARG10.9730.98021.206-14.404-14.4040.0000.0000.0000.000
40A47GLY00.0350.03625.707-0.459-0.4590.0000.0000.0000.000
41A57PRO00.020-0.0129.053-1.512-1.5120.0000.0000.0000.000
42A58GLU-1-0.863-0.9324.99741.49841.690-0.001-0.004-0.1870.000
43A59THR00.0390.0265.9392.3312.3310.0000.0000.0000.000
44A60LYS10.9500.9778.474-24.158-24.1580.0000.0000.0000.000
45A61THR0-0.001-0.0155.416-6.589-6.5890.0000.0000.0000.000
46A62MET00.0690.0556.376-1.126-1.1260.0000.0000.0000.000
47A63THR0-0.0020.0047.368-3.780-3.7800.0000.0000.0000.000
48A64HIS0-0.054-0.03310.261-2.345-2.3450.0000.0000.0000.000
49A65TYR00.1250.0677.448-2.243-2.2430.0000.0000.0000.000
50A66LEU0-0.0010.0139.874-2.108-2.1080.0000.0000.0000.000
51A67ARG10.7680.85512.206-20.797-20.7970.0000.0000.0000.000
52A68HIS0-0.029-0.01012.825-1.716-1.7160.0000.0000.0000.000
53A69HIS0-0.060-0.04110.654-1.247-1.2470.0000.0000.0000.000
54A70HIS0-0.007-0.01115.122-1.198-1.1980.0000.0000.0000.000
55A71ASP-1-0.776-0.83118.55713.22913.2290.0000.0000.0000.000
56A72GLY00.0000.00621.818-0.381-0.3810.0000.0000.0000.000
57A73ILE0-0.038-0.01018.2160.6200.6200.0000.0000.0000.000
58A74LEU0-0.0020.00221.426-0.598-0.5980.0000.0000.0000.000
59A75VAL0-0.001-0.00622.3210.5460.5460.0000.0000.0000.000
60A76GLY00.0470.02124.890-0.558-0.5580.0000.0000.0000.000
61A77SER00.001-0.00427.7100.2330.2330.0000.0000.0000.000
62A78GLY0-0.024-0.02230.295-0.116-0.1160.0000.0000.0000.000
63A79THR0-0.040-0.03324.4850.2160.2160.0000.0000.0000.000
64A80VAL00.0270.01025.7520.2690.2690.0000.0000.0000.000
65A81LEU0-0.065-0.03427.220-0.169-0.1690.0000.0000.0000.000
66A82ALA0-0.0280.00727.175-0.171-0.1710.0000.0000.0000.000
67A83ASP-1-0.941-0.96622.31914.27714.2770.0000.0000.0000.000
68A84ASN00.0710.02925.386-0.205-0.2050.0000.0000.0000.000
69A85PRO0-0.0070.01021.5330.3010.3010.0000.0000.0000.000
70A86GLY0-0.032-0.04121.095-0.362-0.3620.0000.0000.0000.000
71A87LEU00.005-0.01719.431-0.260-0.2600.0000.0000.0000.000
72A88ASN00.0160.02618.8510.3540.3540.0000.0000.0000.000
73A89CYS0-0.055-0.01513.6940.7050.7050.0000.0000.0000.000
74A90LYS10.9080.9629.770-30.067-30.0670.0000.0000.0000.000
75A91TRP0-0.015-0.04111.0461.1821.1820.0000.0000.0000.000
76A92GLY0-0.064-0.1557.7970.7790.7790.0000.0000.0000.000
77A93PRO0-0.0070.0937.4114.3204.3200.0000.0000.0000.000
78A94ASP-1-0.777-0.8597.29728.78328.7830.0000.0000.0000.000
79A95PRO0-0.074-0.03310.208-1.796-1.7960.0000.0000.0000.000
80A96ALA00.0360.00413.6230.0280.0280.0000.0000.0000.000
81A97ALA00.0430.01816.845-0.542-0.5420.0000.0000.0000.000
82A98ASN0-0.091-0.02919.500-0.559-0.5590.0000.0000.0000.000
83A99SER00.0230.00618.7160.5110.5110.0000.0000.0000.000
84A100PRO00.0110.01617.968-0.855-0.8550.0000.0000.0000.000
85A101ARG10.7930.85820.914-10.709-10.7090.0000.0000.0000.000
86A102PRO00.001-0.00423.4890.2100.2100.0000.0000.0000.000
87A103ILE00.0210.02924.713-0.557-0.5570.0000.0000.0000.000
88A104ILE0-0.0010.00026.3890.3430.3430.0000.0000.0000.000
89A105ILE0-0.008-0.00228.709-0.411-0.4110.0000.0000.0000.000
90A106ASP-1-0.770-0.90731.0169.2629.2620.0000.0000.0000.000
91A107THR00.0380.02634.060-0.223-0.2230.0000.0000.0000.000
92A108LYS10.9040.94736.892-8.455-8.4550.0000.0000.0000.000
93A109GLN00.0090.03237.495-0.216-0.2160.0000.0000.0000.000
94A110LYS10.8940.94035.638-8.918-8.9180.0000.0000.0000.000
95A111TRP0-0.037-0.02629.3830.0010.0010.0000.0000.0000.000
96A112ARG10.8630.94033.952-8.592-8.5920.0000.0000.0000.000
97A113PHE00.0150.00329.2430.3430.3430.0000.0000.0000.000
98A114ASP-1-0.953-0.97132.6248.7898.7890.0000.0000.0000.000
99A115GLY00.0350.01033.992-0.049-0.0490.0000.0000.0000.000
100A116SER0-0.077-0.03829.2040.3950.3950.0000.0000.0000.000
101A117LYS10.9690.97821.375-14.219-14.2190.0000.0000.0000.000
102A118MET00.0240.01725.1560.0700.0700.0000.0000.0000.000
103A119GLN00.0450.03526.6090.0950.0950.0000.0000.0000.000
104A120GLU-1-0.896-0.95827.30411.34711.3470.0000.0000.0000.000
105A121LEU0-0.074-0.04421.8520.1030.1030.0000.0000.0000.000
106A122PHE0-0.0230.01325.7790.0290.0290.0000.0000.0000.000
107A123ILE00.0290.02028.098-0.149-0.1490.0000.0000.0000.000
108A124LYS10.8470.92925.856-12.108-12.1080.0000.0000.0000.000
109A125ARG10.9250.96126.607-9.774-9.7740.0000.0000.0000.000
110A126GLN0-0.009-0.00522.1050.6300.6300.0000.0000.0000.000
111A127GLY0-0.016-0.00921.8490.8620.8620.0000.0000.0000.000
112A128LYS10.8780.94423.000-13.872-13.8720.0000.0000.0000.000
113A129PRO00.0410.04026.0550.1880.1880.0000.0000.0000.000
114A130PRO00.0300.01427.9800.2480.2480.0000.0000.0000.000
115A131ILE00.0000.01128.590-0.338-0.3380.0000.0000.0000.000
116A132VAL0-0.031-0.02129.9800.3220.3220.0000.0000.0000.000
117A133VAL00.0240.01331.029-0.270-0.2700.0000.0000.0000.000
118A134VAL0-0.030-0.01533.6540.0300.0300.0000.0000.0000.000
119A135THR00.011-0.01037.1630.1010.1010.0000.0000.0000.000
120A136SER0-0.044-0.01939.734-0.134-0.1340.0000.0000.0000.000
121A137GLU-1-0.861-0.93741.5947.3477.3470.0000.0000.0000.000
122A138PRO0-0.040-0.01339.7650.0180.0180.0000.0000.0000.000
123A139ILE0-0.018-0.01341.734-0.158-0.1580.0000.0000.0000.000
124A140ILE0-0.036-0.01840.995-0.166-0.1660.0000.0000.0000.000
125A141LYS10.9350.97439.822-7.189-7.1890.0000.0000.0000.000
126A142GLU-1-0.742-0.88236.0018.7808.7800.0000.0000.0000.000
127A143GLN00.006-0.01837.8030.0910.0910.0000.0000.0000.000
128A144HIS0-0.010-0.01433.9230.2650.2650.0000.0000.0000.000
129A145VAL0-0.0350.00233.1650.3760.3760.0000.0000.0000.000
130A146ASP-1-0.816-0.87132.8999.1149.1140.0000.0000.0000.000
131A147TYR0-0.009-0.01433.9720.1480.1480.0000.0000.0000.000
132A148ALA00.0470.02833.927-0.123-0.1230.0000.0000.0000.000
133A149ILE0-0.007-0.00635.8370.0850.0850.0000.0000.0000.000
134A150CYS0-0.0280.00835.7260.0020.0020.0000.0000.0000.000
135A151PRO00.0150.00337.863-0.090-0.0900.0000.0000.0000.000
136A152ILE00.0200.00338.8700.2570.2570.0000.0000.0000.000
137A153ASN00.0030.00238.494-0.249-0.2490.0000.0000.0000.000
138A154ASP-1-0.875-0.95040.5377.0827.0820.0000.0000.0000.000
139A155THR0-0.066-0.01141.500-0.145-0.1450.0000.0000.0000.000
140A156THR0-0.0160.00137.468-0.065-0.0650.0000.0000.0000.000
141A157LYS10.9480.97639.657-8.077-8.0770.0000.0000.0000.000
142A158LEU0-0.070-0.04635.2330.0300.0300.0000.0000.0000.000
143A159VAL00.0360.00633.159-0.150-0.1500.0000.0000.0000.000
144A160ASP-1-0.862-0.93235.4228.8228.8220.0000.0000.0000.000
145A161TRP00.009-0.02228.8940.1890.1890.0000.0000.0000.000
146A162LYS10.9420.98231.712-9.369-9.3690.0000.0000.0000.000
147A163LYS10.9990.99433.054-8.034-8.0340.0000.0000.0000.000
148A164LEU00.0380.01230.7090.0000.0000.0000.0000.0000.000
149A165PHE0-0.023-0.02625.9960.1740.1740.0000.0000.0000.000
150A166GLU-1-0.887-0.94630.1909.0839.0830.0000.0000.0000.000
151A167ILE00.0330.02732.701-0.010-0.0100.0000.0000.0000.000
152A168LEU0-0.029-0.01928.1710.0370.0370.0000.0000.0000.000
153A169LYS10.8380.91728.238-10.397-10.3970.0000.0000.0000.000
154A170GLU-1-1.004-1.00930.3568.6268.6260.0000.0000.0000.000
155A171GLU-1-0.951-0.97334.0198.3478.3470.0000.0000.0000.000
156A172PHE0-0.040-0.03130.9210.0510.0510.0000.0000.0000.000
157A173ASN0-0.050-0.01428.9640.2520.2520.0000.0000.0000.000
158A174ILE0-0.031-0.00924.8230.4870.4870.0000.0000.0000.000
159A175ARG10.8610.87022.448-12.917-12.9170.0000.0000.0000.000
160A176SER00.0030.00020.3930.3300.3300.0000.0000.0000.000
161A177VAL0-0.029-0.01721.809-0.013-0.0130.0000.0000.0000.000
162A178MET0-0.0040.02914.3750.2540.2540.0000.0000.0000.000
163A179VAL0-0.031-0.02619.606-0.407-0.4070.0000.0000.0000.000
164A180GLU-1-0.717-0.84416.66019.11219.1120.0000.0000.0000.000
165A181GLY00.0060.00019.8540.1670.1670.0000.0000.0000.000
166A182GLY00.0150.00022.785-0.596-0.5960.0000.0000.0000.000
167A183ALA00.0650.04525.2940.2020.2020.0000.0000.0000.000
168A184ASN00.013-0.00626.206-0.299-0.2990.0000.0000.0000.000
169A185VAL0-0.0040.00925.801-0.292-0.2920.0000.0000.0000.000
170A186ILE00.0210.01221.982-0.174-0.1740.0000.0000.0000.000
171A187ASN00.030-0.00825.3520.2110.2110.0000.0000.0000.000
172A188GLN0-0.0170.00628.339-0.463-0.4630.0000.0000.0000.000
173A189LEU00.0330.00625.333-0.163-0.1630.0000.0000.0000.000
174A190LEU00.0170.01423.1520.0770.0770.0000.0000.0000.000
175A191LEU0-0.033-0.01926.599-0.057-0.0570.0000.0000.0000.000
176A192ARG10.7760.85828.462-10.134-10.1340.0000.0000.0000.000
177A193SER00.0460.02227.2900.2170.2170.0000.0000.0000.000
178A194ASP-1-0.840-0.87928.11510.02010.0200.0000.0000.0000.000
179A195ILE0-0.089-0.04826.698-0.122-0.1220.0000.0000.0000.000
180A196VAL0-0.0050.00522.0720.3120.3120.0000.0000.0000.000
181A197ASN0-0.0060.01321.304-0.324-0.3240.0000.0000.0000.000
182A198SER0-0.052-0.04616.830-0.050-0.0500.0000.0000.0000.000
183A199LEU0-0.0150.01218.399-0.295-0.2950.0000.0000.0000.000
184A200ILE00.0210.00012.1440.6210.6210.0000.0000.0000.000
185A201ILE00.0050.01014.913-0.157-0.1570.0000.0000.0000.000
186A202THR00.0070.00710.9202.2742.2740.0000.0000.0000.000
187A203ILE0-0.047-0.02513.063-1.902-1.9020.0000.0000.0000.000
188A204GLY00.0520.03013.5931.4391.4390.0000.0000.0000.000
189A205SER0-0.043-0.04914.364-1.686-1.6860.0000.0000.0000.000
190A206THR0-0.037-0.02116.630-0.810-0.8100.0000.0000.0000.000
191A207PHE00.0110.00719.6590.1170.1170.0000.0000.0000.000
192A208LEU0-0.050-0.03321.203-0.107-0.1070.0000.0000.0000.000
193A209GLY00.0080.01624.289-0.460-0.4600.0000.0000.0000.000
194A210SER0-0.011-0.02827.7720.1400.1400.0000.0000.0000.000
195A211SER0-0.001-0.00130.144-0.081-0.0810.0000.0000.0000.000
196A212GLY00.0010.00927.072-0.086-0.0860.0000.0000.0000.000
197A213THR0-0.053-0.03026.399-0.268-0.2680.0000.0000.0000.000
198A214GLU-1-0.851-0.93925.69811.60611.6060.0000.0000.0000.000
199A215VAL0-0.060-0.02521.996-0.236-0.2360.0000.0000.0000.000
200A216SER00.012-0.00125.1320.3340.3340.0000.0000.0000.000
201A217PRO0-0.0400.00426.669-0.295-0.2950.0000.0000.0000.000
202A218PRO0-0.001-0.00729.581-0.132-0.1320.0000.0000.0000.000
203A219GLN0-0.027-0.01332.223-0.417-0.4170.0000.0000.0000.000
204A220THR0-0.013-0.00530.7020.3450.3450.0000.0000.0000.000
205A221VAL00.0610.02526.229-0.139-0.1390.0000.0000.0000.000
206A222ASN0-0.0210.00327.0810.4050.4050.0000.0000.0000.000
207A223LEU00.0320.00420.8960.0800.0800.0000.0000.0000.000
208A224LYS10.9340.95822.829-12.357-12.3570.0000.0000.0000.000
209A225ASP-1-0.827-0.91519.63414.17314.1730.0000.0000.0000.000
210A226MET0-0.0400.01617.7320.6410.6410.0000.0000.0000.000
211A227SER00.0130.00413.0560.3370.3370.0000.0000.0000.000
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213A229TRP00.0010.0153.108-6.837-5.2620.084-0.678-0.9820.007
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