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: V5K11

Calculation Name: 4U4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4U4H

Chain ID: A

ChEMBL ID:

UniProt ID: P10205

Base Structure: X-ray

Registration Date: 2023-06-22

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2215794.58507
FMO2-HF: Nuclear repulsion 2136851.78699
FMO2-HF: Total energy -78942.798079
FMO2-MP2: Total energy -79170.453861


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:MET)


Summations of interaction energy for fragment #1(A:-10:MET)
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.
-1.0681.406-0.018-1.221-1.2350.005
Interaction energy analysis for fragmet #1(A:-10:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.002
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].
3A-8SER0-0.0110.0003.817-0.3892.085-0.018-1.221-1.2350.005
4A-7HIS00.0330.0135.773-0.264-0.2640.0000.0000.0000.000
5A-6PRO00.0820.0378.3420.0920.0920.0000.0000.0000.000
6A-5GLN0-0.039-0.03711.5460.0460.0460.0000.0000.0000.000
7A-4PHE0-0.042-0.01911.1050.0850.0850.0000.0000.0000.000
8A-3GLU-1-0.933-0.94711.330-0.222-0.2220.0000.0000.0000.000
9A-2LYS10.8270.92414.0660.1960.1960.0000.0000.0000.000
10A-1GLY00.0350.02617.1290.0390.0390.0000.0000.0000.000
11A0SER0-0.023-0.02018.823-0.022-0.0220.0000.0000.0000.000
12A1MET0-0.057-0.01820.8150.0020.0020.0000.0000.0000.000
13A2GLU-1-0.825-0.92320.0300.2070.2070.0000.0000.0000.000
14A3LEU0-0.044-0.01624.323-0.006-0.0060.0000.0000.0000.000
15A4SER00.0040.00626.9650.0030.0030.0000.0000.0000.000
16A5TYR0-0.018-0.01625.963-0.012-0.0120.0000.0000.0000.000
17A6ALA0-0.048-0.01829.6420.0120.0120.0000.0000.0000.000
18A7THR0-0.028-0.01731.9210.0040.0040.0000.0000.0000.000
19A8THR00.0170.00530.8200.0000.0000.0000.0000.0000.000
20A9MET0-0.047-0.01733.1850.0000.0000.0000.0000.0000.000
21A10HIS00.0480.02932.927-0.004-0.0040.0000.0000.0000.000
22A11TYR0-0.087-0.09837.519-0.001-0.0010.0000.0000.0000.000
23A12ARG10.8980.94039.741-0.025-0.0250.0000.0000.0000.000
24A13ASP-1-0.872-0.92838.5180.0230.0230.0000.0000.0000.000
25A14VAL0-0.0050.01835.141-0.001-0.0010.0000.0000.0000.000
26A15VAL0-0.034-0.01930.9000.0050.0050.0000.0000.0000.000
27A16PHE00.010-0.00832.993-0.001-0.0010.0000.0000.0000.000
28A17TYR0-0.010-0.01328.2720.0050.0050.0000.0000.0000.000
29A18VAL00.0210.01432.300-0.004-0.0040.0000.0000.0000.000
30A19THR00.0250.00432.8920.0080.0080.0000.0000.0000.000
31A20THR00.040-0.00533.108-0.002-0.0020.0000.0000.0000.000
32A21ASP-1-0.901-0.95135.4020.0690.0690.0000.0000.0000.000
33A22ARG10.8590.94837.724-0.076-0.0760.0000.0000.0000.000
34A23ASN00.0170.00738.809-0.008-0.0080.0000.0000.0000.000
35A24ARG10.9520.96933.340-0.055-0.0550.0000.0000.0000.000
36A25ALA0-0.0030.01135.6470.0060.0060.0000.0000.0000.000
37A26TYR00.0030.00831.257-0.008-0.0080.0000.0000.0000.000
38A27PHE00.0270.01532.2520.0040.0040.0000.0000.0000.000
39A28VAL00.0260.01927.597-0.003-0.0030.0000.0000.0000.000
40A29CYS0-0.030-0.00230.581-0.002-0.0020.0000.0000.0000.000
41A30GLY00.1070.04330.915-0.002-0.0020.0000.0000.0000.000
42A31GLY0-0.0050.00426.788-0.008-0.0080.0000.0000.0000.000
43A32CYS0-0.162-0.06526.7320.0000.0000.0000.0000.0000.000
44A33VAL00.015-0.00327.5630.0060.0060.0000.0000.0000.000
45A34TYR00.026-0.01530.389-0.003-0.0030.0000.0000.0000.000
46A35SER0-0.027-0.02833.8300.0100.0100.0000.0000.0000.000
47A36VAL00.0120.00935.573-0.005-0.0050.0000.0000.0000.000
48A37GLY00.0050.00039.0010.0060.0060.0000.0000.0000.000
49A38ARG10.8410.91840.904-0.052-0.0520.0000.0000.0000.000
50A39PRO0-0.0010.01343.683-0.001-0.0010.0000.0000.0000.000
51A40CYS00.008-0.00547.0360.0030.0030.0000.0000.0000.000
52A41ALA00.010-0.01049.393-0.002-0.0020.0000.0000.0000.000
53A42SER0-0.027-0.01852.135-0.002-0.0020.0000.0000.0000.000
54A43GLN0-0.0060.01651.085-0.002-0.0020.0000.0000.0000.000
55A44PRO0-0.005-0.01647.6030.0020.0020.0000.0000.0000.000
56A45GLY00.0270.02444.1720.0000.0000.0000.0000.0000.000
57A46GLU-1-0.969-0.97940.9480.0320.0320.0000.0000.0000.000
58A47ILE0-0.0080.00239.4270.0030.0030.0000.0000.0000.000
59A48ALA0-0.009-0.00235.824-0.002-0.0020.0000.0000.0000.000
60A49LYS10.8040.90633.7010.0140.0140.0000.0000.0000.000
61A50PHE0-0.001-0.01628.9420.0000.0000.0000.0000.0000.000
62A51GLY00.0440.01226.8900.0020.0020.0000.0000.0000.000
63A52LEU00.0030.01422.629-0.001-0.0010.0000.0000.0000.000
64A53VAL0-0.025-0.00726.9970.0030.0030.0000.0000.0000.000
65A54VAL00.0160.00828.579-0.010-0.0100.0000.0000.0000.000
66A55ARG10.8010.83730.4460.0570.0570.0000.0000.0000.000
67A56GLY00.0320.01531.6400.0030.0030.0000.0000.0000.000
68A57THR0-0.012-0.00630.232-0.006-0.0060.0000.0000.0000.000
69A58GLY0-0.0070.00330.116-0.013-0.0130.0000.0000.0000.000
70A59PRO0-0.037-0.02330.3230.0050.0050.0000.0000.0000.000
71A60ASP-1-0.901-0.95331.811-0.061-0.0610.0000.0000.0000.000
72A61ASP-1-0.818-0.89934.397-0.094-0.0940.0000.0000.0000.000
73A62ARG10.8730.91834.5190.0620.0620.0000.0000.0000.000
74A63VAL00.0040.01334.5280.0050.0050.0000.0000.0000.000
75A64VAL00.0360.02930.7680.0020.0020.0000.0000.0000.000
76A65ALA0-0.007-0.00434.0170.0050.0050.0000.0000.0000.000
77A66ASN0-0.029-0.04135.6060.0080.0080.0000.0000.0000.000
78A67TYR0-0.015-0.01135.2950.0040.0040.0000.0000.0000.000
79A68VAL00.0770.03833.6920.0030.0030.0000.0000.0000.000
80A69ARG10.8480.91836.9670.0490.0490.0000.0000.0000.000
81A70SER0-0.117-0.06940.1970.0030.0030.0000.0000.0000.000
82A71GLU-1-0.775-0.88038.069-0.061-0.0610.0000.0000.0000.000
83A72LEU0-0.013-0.01037.8940.0030.0030.0000.0000.0000.000
84A73ARG10.9050.94941.4110.0440.0440.0000.0000.0000.000
85A74GLN0-0.048-0.01643.9500.0020.0020.0000.0000.0000.000
86A75ARG10.8200.90638.1580.0590.0590.0000.0000.0000.000
87A76GLY0-0.0240.00544.4490.0020.0020.0000.0000.0000.000
88A77LEU0-0.055-0.02441.1320.0040.0040.0000.0000.0000.000
89A86ASP-1-0.907-0.94939.235-0.023-0.0230.0000.0000.0000.000
90A87GLU-1-0.778-0.86733.952-0.044-0.0440.0000.0000.0000.000
91A88VAL0-0.0210.00333.6710.0040.0040.0000.0000.0000.000
92A89PHE00.015-0.00130.609-0.006-0.0060.0000.0000.0000.000
93A90LEU00.0580.01125.639-0.003-0.0030.0000.0000.0000.000
94A91ASP-1-0.718-0.82330.211-0.020-0.0200.0000.0000.0000.000
95A92SER0-0.023-0.01832.7890.0000.0000.0000.0000.0000.000
96A93VAL0-0.007-0.00430.317-0.003-0.0030.0000.0000.0000.000
97A94CYS0-0.0260.00631.091-0.003-0.0030.0000.0000.0000.000
98A95LEU0-0.0190.00833.175-0.001-0.0010.0000.0000.0000.000
99A96LEU0-0.040-0.00734.3610.0000.0000.0000.0000.0000.000
100A97ASN0-0.044-0.00931.8610.0000.0000.0000.0000.0000.000
101A98PRO00.0220.00735.4320.0050.0050.0000.0000.0000.000
102A99ASN0-0.088-0.05534.6930.0070.0070.0000.0000.0000.000
103A100VAL0-0.048-0.00934.3350.0050.0050.0000.0000.0000.000
104A101SER0-0.072-0.04037.661-0.001-0.0010.0000.0000.0000.000
105A102SER0-0.048-0.03839.7330.0020.0020.0000.0000.0000.000
106A103GLU-1-0.800-0.93237.150-0.015-0.0150.0000.0000.0000.000
107A104LEU0-0.032-0.01836.9020.0030.0030.0000.0000.0000.000
108A105ASP-1-0.793-0.88237.193-0.011-0.0110.0000.0000.0000.000
109A106VAL00.0030.00732.375-0.001-0.0010.0000.0000.0000.000
110A107ILE00.000-0.00632.6570.0030.0030.0000.0000.0000.000
111A108ASN0-0.070-0.06430.8000.0040.0040.0000.0000.0000.000
112A109THR0-0.0030.01728.4380.0030.0030.0000.0000.0000.000
113A110ASN0-0.028-0.02823.8780.0010.0010.0000.0000.0000.000
114A111ASP-1-0.875-0.92722.659-0.037-0.0370.0000.0000.0000.000
115A112VAL00.003-0.02225.2480.0060.0060.0000.0000.0000.000
116A113GLU-1-0.864-0.92426.366-0.091-0.0910.0000.0000.0000.000
117A114VAL0-0.028-0.02027.8210.0090.0090.0000.0000.0000.000
118A115LEU00.021-0.00129.207-0.011-0.0110.0000.0000.0000.000
119A116ASP-1-0.827-0.87731.813-0.092-0.0920.0000.0000.0000.000
120A117GLU-1-0.814-0.95231.186-0.131-0.1310.0000.0000.0000.000
121A118CYS0-0.0370.01131.416-0.012-0.0120.0000.0000.0000.000
122A119LEU00.007-0.00730.438-0.006-0.0060.0000.0000.0000.000
123A120ALA00.0110.00027.526-0.007-0.0070.0000.0000.0000.000
124A121GLU-1-0.932-0.95827.192-0.172-0.1720.0000.0000.0000.000
125A122TYR0-0.019-0.02428.290-0.012-0.0120.0000.0000.0000.000
126A123CYS0-0.082-0.03925.198-0.002-0.0020.0000.0000.0000.000
127A124THR0-0.017-0.00623.156-0.015-0.0150.0000.0000.0000.000
128A125SER0-0.063-0.05523.923-0.021-0.0210.0000.0000.0000.000
129A126LEU0-0.037-0.01622.374-0.011-0.0110.0000.0000.0000.000
130A127ARG10.9840.98826.6990.1820.1820.0000.0000.0000.000
131A128THR0-0.031-0.01225.562-0.024-0.0240.0000.0000.0000.000
132A129SER00.0090.03927.7360.0100.0100.0000.0000.0000.000
133A130PRO0-0.025-0.01727.496-0.015-0.0150.0000.0000.0000.000
134A131GLY00.0800.02327.8740.0120.0120.0000.0000.0000.000
135A132VAL0-0.066-0.03023.586-0.017-0.0170.0000.0000.0000.000
136A133LEU00.0100.01121.8530.0190.0190.0000.0000.0000.000
137A134ILE0-0.023-0.01821.999-0.024-0.0240.0000.0000.0000.000
138A135SER00.0170.00119.3820.0140.0140.0000.0000.0000.000
139A136GLY00.0260.00919.748-0.018-0.0180.0000.0000.0000.000
140A137LEU0-0.0400.00321.3170.0180.0180.0000.0000.0000.000
141A138ARG10.9590.98013.844-0.237-0.2370.0000.0000.0000.000
142A139VAL00.0210.01420.8710.0090.0090.0000.0000.0000.000
143A140ARG10.7850.90018.309-0.255-0.2550.0000.0000.0000.000
144A141ALA00.0190.00221.3150.0040.0040.0000.0000.0000.000
145A142GLN0-0.026-0.01821.137-0.024-0.0240.0000.0000.0000.000
146A143ASP-1-0.860-0.93219.2800.3270.3270.0000.0000.0000.000
147A144ARG10.8450.94222.868-0.187-0.1870.0000.0000.0000.000
148A145ILE00.0130.00721.984-0.012-0.0120.0000.0000.0000.000
149A146ILE0-0.047-0.01923.2840.0050.0050.0000.0000.0000.000
150A147GLU-1-0.833-0.93417.7300.2030.2030.0000.0000.0000.000
151A148LEU0-0.020-0.01021.807-0.016-0.0160.0000.0000.0000.000
152A149PHE00.005-0.01216.0600.0090.0090.0000.0000.0000.000
153A150GLU-1-0.846-0.93819.973-0.092-0.0920.0000.0000.0000.000
154A151HIS0-0.046-0.02715.420-0.067-0.0670.0000.0000.0000.000
155A152PRO00.0180.02017.7310.0070.0070.0000.0000.0000.000
156A153THR0-0.013-0.01615.800-0.058-0.0580.0000.0000.0000.000
157A154ILE0-0.0050.00717.6990.0380.0380.0000.0000.0000.000
158A155VAL00.0190.01517.375-0.050-0.0500.0000.0000.0000.000
159A156ASN0-0.016-0.00520.0070.0460.0460.0000.0000.0000.000
160A157VAL00.0040.00222.383-0.004-0.0040.0000.0000.0000.000
161A158SER0-0.045-0.01224.8330.0090.0090.0000.0000.0000.000
162A159SER0-0.010-0.02022.643-0.006-0.0060.0000.0000.0000.000
163A160HIS00.0060.00018.615-0.025-0.0250.0000.0000.0000.000
164A161PHE0-0.036-0.01517.682-0.039-0.0390.0000.0000.0000.000
165A162VAL00.0140.01013.9410.0400.0400.0000.0000.0000.000
166A163TYR00.000-0.00316.830-0.039-0.0390.0000.0000.0000.000
167A164THR0-0.035-0.02316.854-0.026-0.0260.0000.0000.0000.000
168A165PRO0-0.0080.00218.1160.0260.0260.0000.0000.0000.000
169A166SER00.0410.04521.217-0.029-0.0290.0000.0000.0000.000
170A167PRO0-0.003-0.01022.5740.0190.0190.0000.0000.0000.000
171A168TYR0-0.031-0.02124.3380.0110.0110.0000.0000.0000.000
172A169VAL0-0.0050.03026.4830.0160.0160.0000.0000.0000.000
173A170PHE00.009-0.00224.0690.0150.0150.0000.0000.0000.000
174A171ALA00.0070.00725.683-0.004-0.0040.0000.0000.0000.000
175A172LEU00.0010.00922.4520.0030.0030.0000.0000.0000.000
176A173ALA0-0.018-0.00326.6130.0000.0000.0000.0000.0000.000
177A174GLN00.014-0.01530.1040.0080.0080.0000.0000.0000.000
178A175ALA0-0.0220.00432.629-0.004-0.0040.0000.0000.0000.000
179A176HIS00.0290.01136.1480.0040.0040.0000.0000.0000.000
180A177LEU0-0.027-0.02437.658-0.005-0.0050.0000.0000.0000.000
181A178PRO0-0.011-0.00341.3010.0030.0030.0000.0000.0000.000
182A179ARG10.9140.95243.5690.0010.0010.0000.0000.0000.000
183A180LEU00.0220.02339.077-0.001-0.0010.0000.0000.0000.000
184A181PRO00.0590.03338.873-0.001-0.0010.0000.0000.0000.000
185A182SER00.001-0.01542.1820.0020.0020.0000.0000.0000.000
186A183SER0-0.0100.01141.6310.0030.0030.0000.0000.0000.000
187A184LEU00.0520.01537.5590.0020.0020.0000.0000.0000.000
188A185GLU-1-0.915-0.95141.6600.0110.0110.0000.0000.0000.000
189A186ALA00.010-0.00444.4910.0030.0030.0000.0000.0000.000
190A187LEU0-0.0020.01338.9530.0020.0020.0000.0000.0000.000
191A188VAL00.0330.00540.1460.0040.0040.0000.0000.0000.000
192A189SER0-0.0250.00042.8720.0010.0010.0000.0000.0000.000
193A190GLY00.0310.05646.3220.0000.0000.0000.0000.0000.000
194A191LEU0-0.0060.01839.2840.0020.0020.0000.0000.0000.000
195A192PHE0-0.016-0.04839.9110.0030.0030.0000.0000.0000.000
196A193ASP-1-0.891-0.93044.4540.0340.0340.0000.0000.0000.000
197A194GLY0-0.055-0.01544.8260.0010.0010.0000.0000.0000.000
198A195ILE0-0.061-0.02639.6920.0050.0050.0000.0000.0000.000
199A196PRO00.0250.00842.444-0.003-0.0030.0000.0000.0000.000
200A197ALA00.026-0.00243.5180.0020.0020.0000.0000.0000.000
201A198PRO0-0.0180.01242.5080.0030.0030.0000.0000.0000.000