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: GNKR1

Calculation Name: 4UV2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UV2

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEA2

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 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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2622906.33214
FMO2-HF: Nuclear repulsion 2532676.545231
FMO2-HF: Total energy -90229.786909
FMO2-MP2: Total energy -90494.329537


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:18:ALA)


Summations of interaction energy for fragment #1(A:18: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.
-7.193-3.0071.32-1.839-3.665-0.004
Interaction energy analysis for fragmet #1(A:18:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.005
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].
3A20SER00.0220.0093.050-1.5130.5840.072-0.940-1.2290.000
4A21TYR00.0390.0382.857-0.2330.7710.099-0.312-0.790-0.001
5A22LYS10.9660.9824.092-2.468-2.0830.000-0.098-0.2870.000
6A23ASP-1-0.703-0.8236.091-0.327-0.3270.0000.0000.0000.000
7A24LEU0-0.004-0.0057.5270.2550.2550.0000.0000.0000.000
8A25THR0-0.041-0.0347.5600.3100.3100.0000.0000.0000.000
9A26HIS0-0.139-0.0679.2540.2720.2720.0000.0000.0000.000
10A27LEU00.0030.01212.3380.0630.0630.0000.0000.0000.000
11A28PRO00.0170.01714.7290.0310.0310.0000.0000.0000.000
12A29ALA00.005-0.00418.453-0.025-0.0250.0000.0000.0000.000
13A30PRO00.0280.01719.6080.0190.0190.0000.0000.0000.000
14A31THR0-0.031-0.01222.6200.0060.0060.0000.0000.0000.000
15A32GLY00.0270.00825.1570.0110.0110.0000.0000.0000.000
16A33LYS10.8550.94718.4210.2530.2530.0000.0000.0000.000
17A34ILE00.0330.02121.5360.0170.0170.0000.0000.0000.000
18A35PHE0-0.030-0.01922.368-0.018-0.0180.0000.0000.0000.000
19A36VAL00.0290.01820.0620.0040.0040.0000.0000.0000.000
20A37SER0-0.029-0.01122.940-0.009-0.0090.0000.0000.0000.000
21A38VAL00.0260.01218.912-0.006-0.0060.0000.0000.0000.000
22A39TYR0-0.010-0.00521.9280.0180.0180.0000.0000.0000.000
23A40ASN0-0.010-0.02621.084-0.031-0.0310.0000.0000.0000.000
24A41ILE00.0040.01315.2300.0000.0000.0000.0000.0000.000
25A42GLN0-0.029-0.01219.377-0.007-0.0070.0000.0000.0000.000
26A43ASP-1-0.777-0.86819.932-0.231-0.2310.0000.0000.0000.000
27A44GLU-1-0.937-0.98120.847-0.161-0.1610.0000.0000.0000.000
28A45THR0-0.022-0.00618.9330.0180.0180.0000.0000.0000.000
29A46GLY00.0030.00622.2780.0150.0150.0000.0000.0000.000
30A47GLN0-0.075-0.03821.4860.0200.0200.0000.0000.0000.000
31A48PHE00.0210.00422.318-0.015-0.0150.0000.0000.0000.000
32A49LYS10.9060.96217.9820.1370.1370.0000.0000.0000.000
33A50PRO00.0410.02723.0300.0040.0040.0000.0000.0000.000
34A51TYR00.0270.03526.0380.0000.0000.0000.0000.0000.000
35A52PRO0-0.032-0.03226.1560.0020.0020.0000.0000.0000.000
36A53ALA0-0.013-0.01324.2830.0000.0000.0000.0000.0000.000
37A54SER00.0170.00926.1750.0030.0030.0000.0000.0000.000
38A55ASN00.032-0.00126.830-0.002-0.0020.0000.0000.0000.000
39A56PHE0-0.0020.00227.370-0.004-0.0040.0000.0000.0000.000
40A57SER0-0.061-0.03022.506-0.009-0.0090.0000.0000.0000.000
41A58THR00.0340.01519.4380.0100.0100.0000.0000.0000.000
42A59ALA0-0.037-0.02319.257-0.001-0.0010.0000.0000.0000.000
43A60VAL00.0410.03014.872-0.017-0.0170.0000.0000.0000.000
44A61PRO00.0050.01312.8620.0210.0210.0000.0000.0000.000
45A62GLN0-0.041-0.04716.028-0.003-0.0030.0000.0000.0000.000
46A63SER00.001-0.01014.4480.0070.0070.0000.0000.0000.000
47A64ALA00.0770.04013.827-0.046-0.0460.0000.0000.0000.000
48A65THR00.0500.02014.416-0.048-0.0480.0000.0000.0000.000
49A66ALA00.0360.01915.419-0.009-0.0090.0000.0000.0000.000
50A67MET0-0.0080.00610.450-0.048-0.0480.0000.0000.0000.000
51A68LEU00.0510.03411.495-0.088-0.0880.0000.0000.0000.000
52A69VAL00.0050.00513.690-0.009-0.0090.0000.0000.0000.000
53A70THR0-0.035-0.02410.4540.0450.0450.0000.0000.0000.000
54A71ALA00.0390.0259.947-0.017-0.0170.0000.0000.0000.000
55A72LEU00.005-0.00311.0440.0230.0230.0000.0000.0000.000
56A73LYS10.9250.96814.5490.3460.3460.0000.0000.0000.000
57A74ASP-1-0.869-0.9379.841-0.779-0.7790.0000.0000.0000.000
58A75SER0-0.029-0.01712.0670.0270.0270.0000.0000.0000.000
59A76ARG10.8410.90313.1400.3660.3660.0000.0000.0000.000
60A77TRP00.0340.00916.3630.0570.0570.0000.0000.0000.000
61A78PHE00.0000.02316.5490.0350.0350.0000.0000.0000.000
62A79ILE0-0.081-0.04119.084-0.011-0.0110.0000.0000.0000.000
63A80PRO00.0200.01418.1280.0150.0150.0000.0000.0000.000
64A81LEU0-0.085-0.03820.9620.0190.0190.0000.0000.0000.000
65A82GLU-1-0.806-0.91123.102-0.218-0.2180.0000.0000.0000.000
66A83ARG10.8490.91424.4610.1760.1760.0000.0000.0000.000
67A84GLN00.0680.04821.7230.0020.0020.0000.0000.0000.000
68A85GLY0-0.0030.00425.6890.0120.0120.0000.0000.0000.000
69A86LEU0-0.004-0.00827.8240.0090.0090.0000.0000.0000.000
70A87GLN00.0140.00430.3110.0060.0060.0000.0000.0000.000
71A88ASN00.0340.00629.1180.0130.0130.0000.0000.0000.000
72A89LEU00.0590.02928.9670.0070.0070.0000.0000.0000.000
73A90LEU0-0.046-0.02531.9850.0080.0080.0000.0000.0000.000
74A91ASN0-0.009-0.01235.3000.0080.0080.0000.0000.0000.000
75A92GLU-1-0.849-0.92132.687-0.082-0.0820.0000.0000.0000.000
76A93ARG10.8660.93434.0940.1010.1010.0000.0000.0000.000
77A94LYS10.8810.94737.2640.0790.0790.0000.0000.0000.000
78A95ILE00.0570.02837.7220.0040.0040.0000.0000.0000.000
79A96ILE00.0000.01035.7800.0030.0030.0000.0000.0000.000
80A97ARG10.9160.93938.9430.0760.0760.0000.0000.0000.000
81A98ALA00.0380.02542.9890.0030.0030.0000.0000.0000.000
82A99ALA0-0.0180.00442.7390.0030.0030.0000.0000.0000.000
83A100GLN0-0.053-0.03841.5050.0020.0020.0000.0000.0000.000
84A101GLU-1-0.953-0.96445.811-0.048-0.0480.0000.0000.0000.000
85A102ASN00.007-0.00348.2320.0020.0020.0000.0000.0000.000
86A103GLY0-0.036-0.00849.4940.0020.0020.0000.0000.0000.000
87A104THR0-0.016-0.01050.0800.0010.0010.0000.0000.0000.000
88A105VAL0-0.0210.01143.8110.0010.0010.0000.0000.0000.000
89A106ALA00.0380.00944.9500.0010.0010.0000.0000.0000.000
90A107ILE00.0340.01044.239-0.003-0.0030.0000.0000.0000.000
91A108ASN0-0.049-0.02541.664-0.004-0.0040.0000.0000.0000.000
92A109ASN00.0300.00740.109-0.003-0.0030.0000.0000.0000.000
93A110ARG10.8940.96740.6500.0460.0460.0000.0000.0000.000
94A111ILE00.0260.00336.088-0.002-0.0020.0000.0000.0000.000
95A112PRO0-0.018-0.01037.1690.0000.0000.0000.0000.0000.000
96A113LEU0-0.011-0.00136.406-0.005-0.0050.0000.0000.0000.000
97A114GLN00.0290.02533.8020.0000.0000.0000.0000.0000.000
98A115SER00.002-0.01336.5530.0000.0000.0000.0000.0000.000
99A116LEU0-0.034-0.02231.146-0.003-0.0030.0000.0000.0000.000
100A117THR00.0440.02428.6830.0060.0060.0000.0000.0000.000
101A118ALA0-0.0070.00230.061-0.007-0.0070.0000.0000.0000.000
102A119ALA00.006-0.01826.828-0.005-0.0050.0000.0000.0000.000
103A120ASN00.0330.02228.8590.0070.0070.0000.0000.0000.000
104A121ILE00.0280.04122.9080.0030.0030.0000.0000.0000.000
105A122MET0-0.030-0.01524.747-0.002-0.0020.0000.0000.0000.000
106A123VAL0-0.020-0.00918.468-0.001-0.0010.0000.0000.0000.000
107A124GLU-1-0.872-0.94421.281-0.182-0.1820.0000.0000.0000.000
108A125GLY00.017-0.01118.974-0.016-0.0160.0000.0000.0000.000
109A126SER0-0.0110.01319.4210.0130.0130.0000.0000.0000.000
110A127ILE0-0.025-0.00815.837-0.025-0.0250.0000.0000.0000.000
111A128ILE00.0350.00818.1040.0220.0220.0000.0000.0000.000
112A129GLY00.003-0.00618.2610.0250.0250.0000.0000.0000.000
113A130TYR0-0.049-0.04214.430-0.025-0.0250.0000.0000.0000.000
114A131GLU-1-0.900-0.93516.982-0.078-0.0780.0000.0000.0000.000
115A132SER0-0.022-0.00816.579-0.005-0.0050.0000.0000.0000.000
116A133ASN0-0.008-0.00818.2410.0000.0000.0000.0000.0000.000
117A134VAL00.0220.02718.7280.0040.0040.0000.0000.0000.000
118A135LYS10.8540.92019.686-0.050-0.0500.0000.0000.0000.000
119A136SER00.1050.04320.9310.0100.0100.0000.0000.0000.000
120A137GLY00.0340.03922.493-0.008-0.0080.0000.0000.0000.000
121A138GLY0-0.031-0.03221.4880.0000.0000.0000.0000.0000.000
122A139VAL00.0650.01718.2030.0130.0130.0000.0000.0000.000
123A140GLY00.0430.01916.8660.0190.0190.0000.0000.0000.000
124A141ALA00.0160.00517.2510.0310.0310.0000.0000.0000.000
125A142ARG10.9640.99819.319-0.125-0.1250.0000.0000.0000.000
126A143TYR0-0.061-0.03714.7500.0080.0080.0000.0000.0000.000
127A144PHE0-0.033-0.00711.2530.0600.0600.0000.0000.0000.000
128A145GLY0-0.0280.01615.6670.0280.0280.0000.0000.0000.000
129A146ILE0-0.054-0.01117.8020.0040.0040.0000.0000.0000.000
130A147GLY00.0410.01520.448-0.015-0.0150.0000.0000.0000.000
131A148ALA0-0.050-0.05123.0090.0000.0000.0000.0000.0000.000
132A149ASP-1-0.900-0.95525.0840.0580.0580.0000.0000.0000.000
133A150THR0-0.0490.00121.1810.0020.0020.0000.0000.0000.000
134A151GLN00.026-0.01121.472-0.004-0.0040.0000.0000.0000.000
135A152TYR0-0.086-0.05116.0930.0080.0080.0000.0000.0000.000
136A153GLN0-0.018-0.01114.5010.0070.0070.0000.0000.0000.000
137A154LEU0-0.020-0.01214.4010.0290.0290.0000.0000.0000.000
138A155ASP-1-0.803-0.90111.799-0.140-0.1400.0000.0000.0000.000
139A156GLN0-0.036-0.01912.243-0.029-0.0290.0000.0000.0000.000
140A157ILE00.0160.00611.9170.0060.0060.0000.0000.0000.000
141A158ALA00.0090.01513.316-0.021-0.0210.0000.0000.0000.000
142A159VAL0-0.014-0.01512.9710.0060.0060.0000.0000.0000.000
143A160ASN0-0.0210.00015.6340.0170.0170.0000.0000.0000.000
144A161LEU0-0.035-0.01314.065-0.009-0.0090.0000.0000.0000.000
145A162ARG10.8610.92018.4630.2210.2210.0000.0000.0000.000
146A163VAL0-0.001-0.00821.048-0.011-0.0110.0000.0000.0000.000
147A164VAL00.0330.01423.3550.0140.0140.0000.0000.0000.000
148A165ASN00.0190.00127.004-0.007-0.0070.0000.0000.0000.000
149A166VAL0-0.004-0.00229.1310.0070.0070.0000.0000.0000.000
150A167SER0-0.066-0.02731.6060.0090.0090.0000.0000.0000.000
151A168THR00.015-0.00733.6880.0030.0030.0000.0000.0000.000
152A169GLY00.0020.00532.3800.0040.0040.0000.0000.0000.000
153A170GLU-1-0.969-0.97031.993-0.103-0.1030.0000.0000.0000.000
154A171ILE0-0.022-0.02725.749-0.008-0.0080.0000.0000.0000.000
155A172LEU0-0.024-0.01126.2850.0040.0040.0000.0000.0000.000
156A173SER0-0.052-0.04421.861-0.008-0.0080.0000.0000.0000.000
157A174SER00.0050.00121.801-0.011-0.0110.0000.0000.0000.000
158A175VAL00.0120.03816.4620.0130.0130.0000.0000.0000.000
159A176ASN0-0.004-0.02117.467-0.006-0.0060.0000.0000.0000.000
160A177THR0-0.0380.00012.0980.0170.0170.0000.0000.0000.000
161A178SER00.0390.01613.3660.0070.0070.0000.0000.0000.000
162A179LYS10.8610.9416.5430.6490.6490.0000.0000.0000.000
163A180THR00.0640.02110.2210.0280.0280.0000.0000.0000.000
164A181ILE0-0.018-0.0156.1230.0380.0380.0000.0000.0000.000
165A182LEU0-0.0500.0049.939-0.006-0.0060.0000.0000.0000.000
166A183SER00.028-0.00610.2830.0770.0770.0000.0000.0000.000
167A184TYR00.0440.01212.113-0.017-0.0170.0000.0000.0000.000
168A185GLU-1-0.862-0.91613.6570.1450.1450.0000.0000.0000.000
169A186VAL0-0.071-0.02513.7310.0040.0040.0000.0000.0000.000
170A187GLN0-0.014-0.02715.604-0.019-0.0190.0000.0000.0000.000
171A188ALA00.0340.02016.098-0.007-0.0070.0000.0000.0000.000
172A189GLY00.0070.01814.7470.0120.0120.0000.0000.0000.000
173A190VAL0-0.050-0.02410.8200.0220.0220.0000.0000.0000.000
174A191PHE00.040-0.0029.598-0.022-0.0220.0000.0000.0000.000
175A192ARG10.9150.9569.435-0.365-0.3650.0000.0000.0000.000
176A193PHE0-0.012-0.0272.939-0.695-0.2670.071-0.119-0.380-0.001
177A194ILE0-0.042-0.0207.9160.2300.2300.0000.0000.0000.000
178A195ASP-1-0.867-0.9216.292-0.489-0.4890.0000.0000.0000.000
179A196TYR00.0100.0048.4140.0140.0140.0000.0000.0000.000
180A204VAL0-0.001-0.0338.398-0.074-0.0740.0000.0000.0000.000
181A205GLY0-0.0430.0015.7500.2740.2740.0000.0000.0000.000
182A206TYR00.0290.0146.181-0.597-0.5970.0000.0000.0000.000
183A207THR0-0.017-0.0095.4160.5760.5760.0000.0000.0000.000
184A208SER00.0280.0216.643-0.057-0.0570.0000.0000.0000.000
185A209ASN00.0080.0137.0160.1200.1200.0000.0000.0000.000
186A210GLU-1-0.897-0.9598.794-0.140-0.1400.0000.0000.0000.000
187A211PRO00.0230.0188.575-0.146-0.1460.0000.0000.0000.000
188A212VAL00.0550.0348.804-0.100-0.1000.0000.0000.0000.000
189A213MET0-0.012-0.0088.706-0.052-0.0520.0000.0000.0000.000
190A214LEU0-0.026-0.0062.393-0.613-0.5251.079-0.326-0.841-0.002
191A215CYS0-0.016-0.0105.600-0.206-0.2060.0000.0000.0000.000
192A216LEU00.0250.0227.995-0.065-0.0650.0000.0000.0000.000
193A217MET00.009-0.0085.691-0.087-0.0870.0000.0000.0000.000
194A218SER0-0.0150.0113.743-0.0310.0880.000-0.025-0.0940.000
195A219ALA00.020-0.0015.5060.0720.0720.0000.0000.0000.000
196A220ILE00.0040.0029.1440.0700.0700.0000.0000.0000.000
197A221GLU-1-0.852-0.9324.410-2.904-2.839-0.001-0.019-0.0440.000
198A222THR0-0.032-0.0287.4320.1140.1140.0000.0000.0000.000
199A223GLY00.0350.0159.5950.1090.1090.0000.0000.0000.000
200A224VAL00.0170.00411.5020.0890.0890.0000.0000.0000.000
201A225ILE0-0.0130.0049.2220.0800.0800.0000.0000.0000.000
202A226PHE0-0.024-0.02012.9400.0620.0620.0000.0000.0000.000
203A227LEU00.0110.00615.5100.0490.0490.0000.0000.0000.000
204A228ILE0-0.020-0.00714.4860.0380.0380.0000.0000.0000.000
205A229ASN0-0.008-0.02616.6850.0450.0450.0000.0000.0000.000
206A230ASP-1-0.799-0.88218.832-0.165-0.1650.0000.0000.0000.000
207A231GLY00.009-0.01120.8810.0230.0230.0000.0000.0000.000
208A232ILE0-0.039-0.02319.9250.0210.0210.0000.0000.0000.000
209A233ASP-1-0.899-0.92523.068-0.146-0.1460.0000.0000.0000.000
210A234ARG10.8420.92124.9200.1720.1720.0000.0000.0000.000
211A235GLY0-0.0210.00126.9740.0070.0070.0000.0000.0000.000
212A236LEU0-0.048-0.02024.5850.0040.0040.0000.0000.0000.000
213A237TRP0-0.065-0.03020.3480.0000.0000.0000.0000.0000.000
214A238ASP-1-0.883-0.94125.088-0.128-0.1280.0000.0000.0000.000
215A239LEU0-0.034-0.02420.273-0.007-0.0070.0000.0000.0000.000
216A240GLN0-0.027-0.00423.8900.0210.0210.0000.0000.0000.000
217A241ASN00.0460.03324.9420.0130.0130.0000.0000.0000.000
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