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: 82Z7Y

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 OptHSide
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 -2623752.197036
FMO2-HF: Nuclear repulsion 2533521.32392
FMO2-HF: Total energy -90230.873116
FMO2-MP2: Total energy -90495.323842


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.
-17.547-12.1242.33-2.925-4.830.003
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 : 0.036 / q_NPA : 0.013
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].
3A20SER00.0300.0073.152-1.5990.5480.046-0.957-1.2370.000
4A21TYR0-0.014-0.0032.884-0.0780.9090.093-0.316-0.765-0.002
5A22LYS10.9320.9782.916-11.861-10.2160.618-0.984-1.2790.009
6A23ASP-1-0.727-0.8176.295-0.268-0.2680.0000.0000.0000.000
7A24LEU00.0040.0017.5550.1920.1920.0000.0000.0000.000
8A25THR0-0.024-0.0347.6170.2680.2680.0000.0000.0000.000
9A26HIS0-0.145-0.0699.4200.2250.2250.0000.0000.0000.000
10A27LEU0-0.0030.01412.4810.0390.0390.0000.0000.0000.000
11A28PRO00.0330.02514.7530.0320.0320.0000.0000.0000.000
12A29ALA00.011-0.00118.509-0.029-0.0290.0000.0000.0000.000
13A30PRO00.0360.02419.6920.0140.0140.0000.0000.0000.000
14A31THR0-0.025-0.02122.6350.0070.0070.0000.0000.0000.000
15A32GLY00.0160.00325.1580.0110.0110.0000.0000.0000.000
16A33LYS10.8210.91818.8970.1650.1650.0000.0000.0000.000
17A34ILE00.0210.01621.4740.0130.0130.0000.0000.0000.000
18A35PHE0-0.019-0.01222.364-0.018-0.0180.0000.0000.0000.000
19A36VAL00.0260.01520.0180.0030.0030.0000.0000.0000.000
20A37SER0-0.046-0.01022.929-0.002-0.0020.0000.0000.0000.000
21A38VAL0-0.002-0.00618.714-0.006-0.0060.0000.0000.0000.000
22A39TYR00.0180.00421.9160.0180.0180.0000.0000.0000.000
23A40ASN0-0.027-0.03121.075-0.028-0.0280.0000.0000.0000.000
24A41ILE0-0.0120.01015.2720.0020.0020.0000.0000.0000.000
25A42GLN0-0.015-0.00219.375-0.010-0.0100.0000.0000.0000.000
26A43ASP-1-0.756-0.84919.849-0.305-0.3050.0000.0000.0000.000
27A44GLU-1-0.889-0.92420.832-0.197-0.1970.0000.0000.0000.000
28A45THR0-0.033-0.02818.8490.0190.0190.0000.0000.0000.000
29A46GLY0-0.0010.00522.2320.0180.0180.0000.0000.0000.000
30A47GLN0-0.061-0.03121.4590.0220.0220.0000.0000.0000.000
31A48PHE00.0150.00022.335-0.019-0.0190.0000.0000.0000.000
32A49LYS10.8890.95717.2120.2460.2460.0000.0000.0000.000
33A50PRO00.0390.02723.0860.0080.0080.0000.0000.0000.000
34A51TYR00.0300.03226.0420.0000.0000.0000.0000.0000.000
35A52PRO0-0.033-0.02926.1460.0000.0000.0000.0000.0000.000
36A53ALA0-0.011-0.01124.2620.0010.0010.0000.0000.0000.000
37A54SER00.0240.00926.1660.0080.0080.0000.0000.0000.000
38A55ASN00.0350.00226.823-0.006-0.0060.0000.0000.0000.000
39A56PHE00.0010.00227.362-0.004-0.0040.0000.0000.0000.000
40A57SER0-0.052-0.02422.576-0.010-0.0100.0000.0000.0000.000
41A58THR00.0260.01619.5120.0110.0110.0000.0000.0000.000
42A59ALA0-0.046-0.03219.443-0.007-0.0070.0000.0000.0000.000
43A60VAL00.0370.03014.524-0.030-0.0300.0000.0000.0000.000
44A61PRO00.0160.01612.7750.0340.0340.0000.0000.0000.000
45A62GLN0-0.041-0.04416.0190.0050.0050.0000.0000.0000.000
46A63SER00.004-0.00814.5720.0110.0110.0000.0000.0000.000
47A64ALA00.0750.03713.810-0.048-0.0480.0000.0000.0000.000
48A65THR00.0590.02314.399-0.048-0.0480.0000.0000.0000.000
49A66ALA00.0360.01915.443-0.003-0.0030.0000.0000.0000.000
50A67MET0-0.0050.01310.407-0.051-0.0510.0000.0000.0000.000
51A68LEU00.0550.03311.479-0.080-0.0800.0000.0000.0000.000
52A69VAL00.0030.00413.6760.0070.0070.0000.0000.0000.000
53A70THR0-0.034-0.03110.6550.0520.0520.0000.0000.0000.000
54A71ALA00.0310.0209.8650.0030.0030.0000.0000.0000.000
55A72LEU00.0110.00111.0290.0450.0450.0000.0000.0000.000
56A73LYS10.9240.97514.5400.3250.3250.0000.0000.0000.000
57A74ASP-1-0.841-0.91410.084-0.571-0.5710.0000.0000.0000.000
58A75SER0-0.016-0.01012.0540.0540.0540.0000.0000.0000.000
59A76ARG10.8350.90413.1390.2060.2060.0000.0000.0000.000
60A77TRP00.0410.01516.3750.0490.0490.0000.0000.0000.000
61A78PHE0-0.0010.02116.4620.0260.0260.0000.0000.0000.000
62A79ILE0-0.065-0.03319.069-0.006-0.0060.0000.0000.0000.000
63A80PRO00.0110.01418.0250.0130.0130.0000.0000.0000.000
64A81LEU0-0.081-0.03920.9420.0190.0190.0000.0000.0000.000
65A82GLU-1-0.803-0.90822.962-0.228-0.2280.0000.0000.0000.000
66A83ARG10.8710.92124.4510.1750.1750.0000.0000.0000.000
67A84GLN00.0670.05421.931-0.003-0.0030.0000.0000.0000.000
68A85GLY0-0.011-0.00425.6610.0120.0120.0000.0000.0000.000
69A86LEU0-0.010-0.01127.7870.0110.0110.0000.0000.0000.000
70A87GLN00.0030.00030.2790.0090.0090.0000.0000.0000.000
71A88ASN00.0380.00729.1840.0130.0130.0000.0000.0000.000
72A89LEU00.0450.02628.7730.0080.0080.0000.0000.0000.000
73A90LEU0-0.022-0.01631.9450.0090.0090.0000.0000.0000.000
74A91ASN00.0100.00135.2480.0100.0100.0000.0000.0000.000
75A92GLU-1-0.836-0.91332.671-0.082-0.0820.0000.0000.0000.000
76A93ARG10.8460.91333.4980.0970.0970.0000.0000.0000.000
77A94LYS10.8420.91937.2220.0830.0830.0000.0000.0000.000
78A95ILE00.0550.02837.6230.0050.0050.0000.0000.0000.000
79A96ILE0-0.0010.00535.6200.0040.0040.0000.0000.0000.000
80A97ARG10.9050.94139.5540.0730.0730.0000.0000.0000.000
81A98ALA00.0440.03042.9460.0030.0030.0000.0000.0000.000
82A99ALA0-0.0200.00142.6290.0030.0030.0000.0000.0000.000
83A100GLN0-0.053-0.04141.1030.0020.0020.0000.0000.0000.000
84A101GLU-1-0.948-0.96445.764-0.046-0.0460.0000.0000.0000.000
85A102ASN0-0.014-0.01348.1880.0030.0030.0000.0000.0000.000
86A103GLY0-0.029-0.00449.4330.0020.0020.0000.0000.0000.000
87A104THR00.000-0.00649.9860.0010.0010.0000.0000.0000.000
88A105VAL0-0.0370.00343.7790.0010.0010.0000.0000.0000.000
89A106ALA00.0350.01444.8670.0010.0010.0000.0000.0000.000
90A107ILE00.0280.00944.170-0.002-0.0020.0000.0000.0000.000
91A108ASN0-0.015-0.01241.600-0.003-0.0030.0000.0000.0000.000
92A109ASN00.003-0.01040.040-0.001-0.0010.0000.0000.0000.000
93A110ARG10.9010.97540.5700.0360.0360.0000.0000.0000.000
94A111ILE00.0450.00435.955-0.001-0.0010.0000.0000.0000.000
95A112PRO0-0.031-0.00237.0430.0000.0000.0000.0000.0000.000
96A113LEU0-0.0030.00136.223-0.005-0.0050.0000.0000.0000.000
97A114GLN00.0360.02633.7590.0000.0000.0000.0000.0000.000
98A115SER00.0350.01436.527-0.001-0.0010.0000.0000.0000.000
99A116LEU0-0.047-0.02930.998-0.002-0.0020.0000.0000.0000.000
100A117THR00.0300.02228.6580.0030.0030.0000.0000.0000.000
101A118ALA00.0020.00230.044-0.008-0.0080.0000.0000.0000.000
102A119ALA00.010-0.01226.776-0.002-0.0020.0000.0000.0000.000
103A120ASN00.0140.01028.8540.0060.0060.0000.0000.0000.000
104A121ILE00.0280.03822.9570.0020.0020.0000.0000.0000.000
105A122MET0-0.053-0.02524.717-0.002-0.0020.0000.0000.0000.000
106A123VAL0-0.010-0.00718.524-0.001-0.0010.0000.0000.0000.000
107A124GLU-1-0.822-0.90221.273-0.201-0.2010.0000.0000.0000.000
108A125GLY00.026-0.00318.987-0.015-0.0150.0000.0000.0000.000
109A126SER0-0.029-0.02119.4380.0160.0160.0000.0000.0000.000
110A127ILE0-0.042-0.01815.703-0.030-0.0300.0000.0000.0000.000
111A128ILE00.0300.00318.0630.0260.0260.0000.0000.0000.000
112A129GLY00.005-0.00318.2350.0300.0300.0000.0000.0000.000
113A130TYR0-0.072-0.07014.377-0.036-0.0360.0000.0000.0000.000
114A131GLU-1-0.881-0.91116.960-0.151-0.1510.0000.0000.0000.000
115A132SER0-0.013-0.02816.161-0.013-0.0130.0000.0000.0000.000
116A133ASN0-0.029-0.00918.2090.0130.0130.0000.0000.0000.000
117A134VAL00.0250.02218.738-0.005-0.0050.0000.0000.0000.000
118A135LYS10.8840.94219.7240.0240.0240.0000.0000.0000.000
119A136SER00.1070.05620.9680.0040.0040.0000.0000.0000.000
120A137GLY00.0430.02722.481-0.003-0.0030.0000.0000.0000.000
121A138GLY0-0.027-0.00521.490-0.005-0.0050.0000.0000.0000.000
122A139VAL00.0420.00718.2330.0130.0130.0000.0000.0000.000
123A140GLY00.0570.02916.8700.0190.0190.0000.0000.0000.000
124A141ALA00.0100.01117.2520.0260.0260.0000.0000.0000.000
125A142ARG10.9520.99219.697-0.080-0.0800.0000.0000.0000.000
126A143TYR0-0.033-0.02814.6590.0130.0130.0000.0000.0000.000
127A144PHE0-0.0060.00911.4190.0530.0530.0000.0000.0000.000
128A145GLY0-0.0050.02515.6660.0330.0330.0000.0000.0000.000
129A146ILE0-0.048-0.01917.4220.0050.0050.0000.0000.0000.000
130A147GLY00.0430.02220.445-0.010-0.0100.0000.0000.0000.000
131A148ALA0-0.056-0.05223.007-0.005-0.0050.0000.0000.0000.000
132A149ASP-1-0.907-0.95625.0830.0140.0140.0000.0000.0000.000
133A150THR0-0.0170.00821.318-0.001-0.0010.0000.0000.0000.000
134A151GLN0-0.008-0.03021.495-0.006-0.0060.0000.0000.0000.000
135A152TYR0-0.103-0.08016.1990.0050.0050.0000.0000.0000.000
136A153GLN0-0.028-0.02314.1490.0240.0240.0000.0000.0000.000
137A154LEU0-0.019-0.00814.4020.0120.0120.0000.0000.0000.000
138A155ASP-1-0.750-0.83311.799-0.304-0.3040.0000.0000.0000.000
139A156GLN0-0.045-0.04012.231-0.045-0.0450.0000.0000.0000.000
140A157ILE0-0.005-0.00211.4120.0170.0170.0000.0000.0000.000
141A158ALA00.0150.02113.309-0.024-0.0240.0000.0000.0000.000
142A159VAL0-0.015-0.01712.8140.0070.0070.0000.0000.0000.000
143A160ASN0-0.009-0.00215.6150.0230.0230.0000.0000.0000.000
144A161LEU0-0.034-0.01214.037-0.010-0.0100.0000.0000.0000.000
145A162ARG10.8020.86818.4890.2500.2500.0000.0000.0000.000
146A163VAL00.000-0.00821.048-0.010-0.0100.0000.0000.0000.000
147A164VAL00.0210.00623.3750.0140.0140.0000.0000.0000.000
148A165ASN00.034-0.00427.021-0.006-0.0060.0000.0000.0000.000
149A166VAL0-0.003-0.00729.0590.0060.0060.0000.0000.0000.000
150A167SER0-0.072-0.01731.6140.0080.0080.0000.0000.0000.000
151A168THR0-0.032-0.06433.7100.0030.0030.0000.0000.0000.000
152A169GLY0-0.0070.00332.3960.0030.0030.0000.0000.0000.000
153A170GLU-1-0.877-0.88932.018-0.105-0.1050.0000.0000.0000.000
154A171ILE0-0.035-0.03625.825-0.007-0.0070.0000.0000.0000.000
155A172LEU0-0.017-0.00726.2910.0050.0050.0000.0000.0000.000
156A173SER0-0.048-0.05421.769-0.006-0.0060.0000.0000.0000.000
157A174SER00.003-0.00321.819-0.015-0.0150.0000.0000.0000.000
158A175VAL00.0070.03116.5270.0130.0130.0000.0000.0000.000
159A176ASN0-0.021-0.02217.472-0.011-0.0110.0000.0000.0000.000
160A177THR0-0.0290.00312.0550.0240.0240.0000.0000.0000.000
161A178SER00.0220.00013.395-0.006-0.0060.0000.0000.0000.000
162A179LYS10.8180.9106.4580.7990.7990.0000.0000.0000.000
163A180THR00.0760.02310.2370.0110.0110.0000.0000.0000.000
164A181ILE0-0.038-0.0235.8640.0240.0240.0000.0000.0000.000
165A182LEU0-0.0320.0129.9450.0160.0160.0000.0000.0000.000
166A183SER00.000-0.01610.3090.0430.0430.0000.0000.0000.000
167A184TYR00.0540.01712.1430.0110.0110.0000.0000.0000.000
168A185GLU-1-0.837-0.89813.6550.0110.0110.0000.0000.0000.000
169A186VAL0-0.072-0.03313.6040.0170.0170.0000.0000.0000.000
170A187GLN0-0.023-0.02315.4520.0060.0060.0000.0000.0000.000
171A188ALA00.0260.01615.988-0.018-0.0180.0000.0000.0000.000
172A189GLY00.0000.00514.6930.0160.0160.0000.0000.0000.000
173A190VAL0-0.061-0.03010.6420.0000.0000.0000.0000.0000.000
174A191PHE00.045-0.0019.6180.0000.0000.0000.0000.0000.000
175A192ARG10.8760.9379.334-0.287-0.2870.0000.0000.0000.000
176A193PHE0-0.025-0.0322.824-0.676-0.2100.110-0.144-0.433-0.001
177A194ILE0-0.027-0.0177.9170.2230.2230.0000.0000.0000.000
178A195ASP-1-0.818-0.8906.341-0.683-0.6830.0000.0000.0000.000
179A196TYR0-0.025-0.0078.4730.0760.0760.0000.0000.0000.000
180A204VAL00.0200.0047.972-0.096-0.0960.0000.0000.0000.000
181A205GLY0-0.052-0.0245.7450.3250.3250.0000.0000.0000.000
182A206TYR00.0120.0006.185-0.499-0.4990.0000.0000.0000.000
183A207THR0-0.021-0.0135.2900.2470.2470.0000.0000.0000.000
184A208SER00.0370.0266.5340.0210.0210.0000.0000.0000.000
185A209ASN0-0.0020.0086.8570.2150.2150.0000.0000.0000.000
186A210GLU-1-0.902-0.9588.754-0.323-0.3230.0000.0000.0000.000
187A211PRO00.0390.0188.555-0.194-0.1940.0000.0000.0000.000
188A212VAL00.0520.0368.823-0.134-0.1340.0000.0000.0000.000
189A213MET0-0.001-0.0038.642-0.034-0.0340.0000.0000.0000.000
190A214LEU0-0.027-0.0102.330-0.589-0.6611.463-0.444-0.947-0.003
191A215CYS0-0.025-0.0115.620-0.281-0.2810.0000.0000.0000.000
192A216LEU00.0420.0277.946-0.046-0.0460.0000.0000.0000.000
193A217MET00.001-0.0115.656-0.085-0.0850.0000.0000.0000.000
194A218SER0-0.0140.0023.9080.0890.1940.000-0.020-0.0840.000
195A219ALA00.0210.0115.4780.1740.1740.0000.0000.0000.000
196A220ILE00.0090.0019.1310.1150.1150.0000.0000.0000.000
197A221GLU-1-0.828-0.9054.130-3.557-3.4120.000-0.060-0.0850.000
198A222THR0-0.042-0.0427.5100.1700.1700.0000.0000.0000.000
199A223GLY00.0320.0219.6190.1320.1320.0000.0000.0000.000
200A224VAL00.0220.00411.5570.0990.0990.0000.0000.0000.000
201A225ILE0-0.0250.0049.1050.0930.0930.0000.0000.0000.000
202A226PHE0-0.013-0.01912.7410.0630.0630.0000.0000.0000.000
203A227LEU00.0250.01415.5470.0520.0520.0000.0000.0000.000
204A228ILE0-0.028-0.00814.4240.0390.0390.0000.0000.0000.000
205A229ASN0-0.001-0.03216.1350.0670.0670.0000.0000.0000.000
206A230ASP-1-0.775-0.83418.878-0.162-0.1620.0000.0000.0000.000
207A231GLY00.019-0.00320.9200.0220.0220.0000.0000.0000.000
208A232ILE0-0.041-0.02519.8750.0210.0210.0000.0000.0000.000
209A233ASP-1-0.862-0.90523.280-0.114-0.1140.0000.0000.0000.000
210A234ARG10.8130.89624.2220.1720.1720.0000.0000.0000.000
211A235GLY0-0.0210.00027.0150.0050.0050.0000.0000.0000.000
212A236LEU0-0.051-0.01724.8070.0040.0040.0000.0000.0000.000
213A237TRP0-0.056-0.03420.186-0.001-0.0010.0000.0000.0000.000
214A238ASP-1-0.886-0.93925.120-0.093-0.0930.0000.0000.0000.000
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