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: G5QK1

Calculation Name: 4UDS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UDS

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-20

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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2003367.169588
FMO2-HF: Nuclear repulsion 1928944.611067
FMO2-HF: Total energy -74422.558521
FMO2-MP2: Total energy -74638.435029


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:15:ALA)


Summations of interaction energy for fragment #1(A:15: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.
-14.094-12.2178.735-5.235-5.377-0.036
Interaction energy analysis for fragmet #1(A:15: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 : 0.004
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].
3A17THR00.0170.0092.911-3.298-0.7660.158-1.242-1.4480.006
4A18GLU-1-0.818-0.9141.906-13.241-14.3538.577-3.824-3.641-0.042
5A19ASN0-0.039-0.0133.9580.9701.4270.000-0.169-0.2880.000
6A20ILE0-0.0010.0085.8990.4540.4540.0000.0000.0000.000
7A21LEU00.0040.0036.0650.2130.2130.0000.0000.0000.000
8A22GLY00.0390.0177.9510.2000.2000.0000.0000.0000.000
9A23CYS0-0.047-0.0169.2670.2280.2280.0000.0000.0000.000
10A24ALA0-0.004-0.01111.6400.1090.1090.0000.0000.0000.000
11A25LEU0-0.0070.00112.5550.0730.0730.0000.0000.0000.000
12A26ASP-1-0.782-0.87213.664-0.357-0.3570.0000.0000.0000.000
13A27LEU0-0.023-0.00215.5200.0520.0520.0000.0000.0000.000
14A28PHE0-0.008-0.02715.4410.0390.0390.0000.0000.0000.000
15A29VAL0-0.0110.00318.3920.0280.0280.0000.0000.0000.000
16A30LYS10.7560.88017.2570.3180.3180.0000.0000.0000.000
17A31ASN0-0.047-0.02621.1900.0070.0070.0000.0000.0000.000
18A32GLY00.0770.05522.4090.0180.0180.0000.0000.0000.000
19A33TYR0-0.025-0.02818.467-0.004-0.0040.0000.0000.0000.000
20A34ARG10.8890.94021.8310.0750.0750.0000.0000.0000.000
21A35ALA00.0290.01624.3330.0090.0090.0000.0000.0000.000
22A36THR00.0320.02217.8370.0000.0000.0000.0000.0000.000
23A37THR00.023-0.00820.2220.0150.0150.0000.0000.0000.000
24A38ILE00.0530.01515.500-0.024-0.0240.0000.0000.0000.000
25A39ASP-1-0.822-0.88616.718-0.009-0.0090.0000.0000.0000.000
26A40MET00.0270.02517.8170.0010.0010.0000.0000.0000.000
27A41ILE00.0230.01412.604-0.017-0.0170.0000.0000.0000.000
28A42ALA00.001-0.00413.199-0.040-0.0400.0000.0000.0000.000
29A43ALA0-0.011-0.00413.7880.0010.0010.0000.0000.0000.000
30A44ARG10.8310.90613.1900.3330.3330.0000.0000.0000.000
31A45ALA00.0420.0179.506-0.043-0.0430.0000.0000.0000.000
32A46GLY00.0010.01610.0130.0070.0070.0000.0000.0000.000
33A47LEU0-0.037-0.0178.8060.1010.1010.0000.0000.0000.000
34A48THR00.0380.00412.867-0.026-0.0260.0000.0000.0000.000
35A49LYS10.8240.87615.2030.0010.0010.0000.0000.0000.000
36A50GLY0-0.0070.00917.124-0.015-0.0150.0000.0000.0000.000
37A51ALA00.005-0.00111.9160.0150.0150.0000.0000.0000.000
38A52ILE00.0280.01611.6400.0860.0860.0000.0000.0000.000
39A53TYR0-0.027-0.01712.510-0.004-0.0040.0000.0000.0000.000
40A54PHE0-0.033-0.01012.422-0.038-0.0380.0000.0000.0000.000
41A55TYR0-0.0260.0046.131-0.168-0.1680.0000.0000.0000.000
42A56PHE00.0390.0057.987-0.058-0.0580.0000.0000.0000.000
43A57LYS10.9630.98712.901-0.120-0.1200.0000.0000.0000.000
44A58THR0-0.056-0.06516.390-0.003-0.0030.0000.0000.0000.000
45A59LYS10.8810.92615.9630.0910.0910.0000.0000.0000.000
46A60ASP-1-0.767-0.85516.479-0.091-0.0910.0000.0000.0000.000
47A61ALA00.0040.01014.603-0.021-0.0210.0000.0000.0000.000
48A62ILE0-0.0040.00711.103-0.029-0.0290.0000.0000.0000.000
49A63MET0-0.0030.00913.174-0.080-0.0800.0000.0000.0000.000
50A64LEU0-0.016-0.00615.923-0.026-0.0260.0000.0000.0000.000
51A65MET00.0660.0427.8980.0150.0150.0000.0000.0000.000
52A66LEU0-0.033-0.02311.080-0.071-0.0710.0000.0000.0000.000
53A67LEU0-0.019-0.00913.313-0.007-0.0070.0000.0000.0000.000
54A68GLU-1-0.806-0.88413.577-0.176-0.1760.0000.0000.0000.000
55A69GLU-1-0.840-0.9039.231-1.128-1.1280.0000.0000.0000.000
56A70ALA0-0.003-0.00612.8690.0020.0020.0000.0000.0000.000
57A71GLU-1-0.837-0.91116.339-0.165-0.1650.0000.0000.0000.000
58A72LYS10.8930.9509.3420.8970.8970.0000.0000.0000.000
59A73TYR0-0.102-0.0779.3210.0050.0050.0000.0000.0000.000
60A74ILE0-0.039-0.02016.1380.0180.0180.0000.0000.0000.000
61A75VAL0-0.027-0.02819.6730.0240.0240.0000.0000.0000.000
62A76ASP-1-0.798-0.88418.293-0.203-0.2030.0000.0000.0000.000
63A77PRO0-0.058-0.03318.8880.0190.0190.0000.0000.0000.000
64A78ILE0-0.041-0.00421.6040.0140.0140.0000.0000.0000.000
65A79ASP-1-0.858-0.93124.989-0.102-0.1020.0000.0000.0000.000
66A80GLU-1-0.840-0.90424.574-0.144-0.1440.0000.0000.0000.000
67A81TYR00.0260.00923.3340.0150.0150.0000.0000.0000.000
68A82MET00.0040.01226.9820.0040.0040.0000.0000.0000.000
69A83ALA00.0070.01529.8760.0090.0090.0000.0000.0000.000
70A84ASN0-0.054-0.05628.3080.0150.0150.0000.0000.0000.000
71A85ALA0-0.058-0.00531.2990.0000.0000.0000.0000.0000.000
72A86GLY00.0260.02932.8720.0040.0040.0000.0000.0000.000
73A87PRO0-0.056-0.03936.723-0.003-0.0030.0000.0000.0000.000
74A88LEU00.0270.01839.4430.0020.0020.0000.0000.0000.000
75A89ALA00.0440.01037.502-0.006-0.0060.0000.0000.0000.000
76A90ASP-1-0.825-0.91237.077-0.080-0.0800.0000.0000.0000.000
77A91ALA0-0.020-0.00436.230-0.006-0.0060.0000.0000.0000.000
78A92LYS10.8340.90833.2690.0810.0810.0000.0000.0000.000
79A93LEU00.0450.02832.390-0.010-0.0100.0000.0000.0000.000
80A94VAL0-0.028-0.02232.760-0.008-0.0080.0000.0000.0000.000
81A95LYS10.8190.91326.9420.1340.1340.0000.0000.0000.000
82A96PHE00.0680.01427.567-0.014-0.0140.0000.0000.0000.000
83A97ILE00.0100.01127.938-0.013-0.0130.0000.0000.0000.000
84A98ASN0-0.043-0.02028.395-0.007-0.0070.0000.0000.0000.000
85A99MET0-0.035-0.00522.405-0.011-0.0110.0000.0000.0000.000
86A100GLN00.0650.03723.462-0.035-0.0350.0000.0000.0000.000
87A101ALA00.0290.02324.060-0.013-0.0130.0000.0000.0000.000
88A102LEU0-0.042-0.00820.6370.0000.0000.0000.0000.0000.000
89A103LEU00.0500.04118.389-0.029-0.0290.0000.0000.0000.000
90A104GLY00.007-0.00319.689-0.022-0.0220.0000.0000.0000.000
91A105VAL0-0.064-0.03120.7100.0130.0130.0000.0000.0000.000
92A106THR0-0.067-0.05016.350-0.024-0.0240.0000.0000.0000.000
93A107LYS10.9040.96712.5400.5200.5200.0000.0000.0000.000
94A108PRO00.0680.04516.5390.0080.0080.0000.0000.0000.000
95A109GLN00.0100.00714.6020.0660.0660.0000.0000.0000.000
96A110HIS00.012-0.01511.5020.0900.0900.0000.0000.0000.000
97A111VAL00.0300.00716.9250.0290.0290.0000.0000.0000.000
98A112LEU00.0100.01020.5660.0240.0240.0000.0000.0000.000
99A113LEU0-0.035-0.01816.1750.0230.0230.0000.0000.0000.000
100A114LEU00.0240.01019.8520.0230.0230.0000.0000.0000.000
101A115ILE0-0.0060.02322.4870.0190.0190.0000.0000.0000.000
102A116LEU0-0.009-0.00324.2430.0150.0150.0000.0000.0000.000
103A117VAL0-0.027-0.02020.4800.0110.0110.0000.0000.0000.000
104A118SER0-0.015-0.00823.8130.0150.0150.0000.0000.0000.000
105A119ILE00.0040.00326.2950.0140.0140.0000.0000.0000.000
106A120ASP-1-0.806-0.87528.023-0.082-0.0820.0000.0000.0000.000
107A121PHE0-0.019-0.00529.8350.0020.0020.0000.0000.0000.000
108A122SER0-0.0190.00624.609-0.002-0.0020.0000.0000.0000.000
109A123GLY0-0.008-0.01325.661-0.003-0.0030.0000.0000.0000.000
110A124THR0-0.030-0.02522.2480.0080.0080.0000.0000.0000.000
111A125GLY00.0370.01724.6260.0080.0080.0000.0000.0000.000
112A126ASP-1-0.816-0.89625.762-0.064-0.0640.0000.0000.0000.000
113A127ASP-1-0.914-0.95122.602-0.073-0.0730.0000.0000.0000.000
114A128ILE00.0390.01020.080-0.010-0.0100.0000.0000.0000.000
115A129GLH0-0.015-0.03922.568-0.013-0.0130.0000.0000.0000.000
116A130LYS10.8070.88625.4100.0540.0540.0000.0000.0000.000
117A131ARG10.8440.90716.7390.1540.1540.0000.0000.0000.000
118A132ALA00.0380.01922.131-0.009-0.0090.0000.0000.0000.000
119A133LYS10.8460.90723.1870.0880.0880.0000.0000.0000.000
120A134ALA0-0.056-0.00924.7210.0030.0030.0000.0000.0000.000
121A135ILE00.0280.02219.4580.0020.0020.0000.0000.0000.000
122A136TYR0-0.038-0.04123.5930.0010.0010.0000.0000.0000.000
123A137ARG10.9450.97026.0630.0850.0850.0000.0000.0000.000
124A138ARG10.7900.87621.2200.1730.1730.0000.0000.0000.000
125A139MET0-0.029-0.01424.711-0.002-0.0020.0000.0000.0000.000
126A140TYR0-0.033-0.02926.5610.0040.0040.0000.0000.0000.000
127A141GLY00.0400.01829.9390.0060.0060.0000.0000.0000.000
128A142HIS0-0.022-0.00926.775-0.001-0.0010.0000.0000.0000.000
129A143VAL0-0.036-0.01530.0460.0030.0030.0000.0000.0000.000
130A144GLU-1-0.859-0.91832.575-0.067-0.0670.0000.0000.0000.000
131A145GLN00.0200.00032.3820.0070.0070.0000.0000.0000.000
132A146LEU0-0.046-0.00732.9290.0030.0030.0000.0000.0000.000
133A147ILE0-0.027-0.00935.6880.0040.0040.0000.0000.0000.000
134A148ALA00.0600.02738.6680.0040.0040.0000.0000.0000.000
135A149GLN0-0.063-0.02738.2410.0050.0050.0000.0000.0000.000
136A150GLY00.042-0.01139.7960.0030.0030.0000.0000.0000.000
137A151GLN0-0.095-0.06141.4800.0030.0030.0000.0000.0000.000
138A152THR0-0.063-0.03343.4120.0040.0040.0000.0000.0000.000
139A153GLU-1-0.836-0.90840.826-0.066-0.0660.0000.0000.0000.000
140A154GLY0-0.0220.00045.2830.0020.0020.0000.0000.0000.000
141A155VAL0-0.062-0.01842.0650.0000.0000.0000.0000.0000.000
142A156PHE0-0.079-0.03838.196-0.002-0.0020.0000.0000.0000.000
143A157ARG10.8650.92244.1140.0580.0580.0000.0000.0000.000
144A158SER00.0480.01545.214-0.002-0.0020.0000.0000.0000.000
145A159ASP-1-0.881-0.91947.568-0.050-0.0500.0000.0000.0000.000
146A160SER0-0.024-0.03844.4500.0010.0010.0000.0000.0000.000
147A161GLY00.0110.01243.6040.0000.0000.0000.0000.0000.000
148A162SER0-0.014-0.04239.331-0.001-0.0010.0000.0000.0000.000
149A163ASP-1-0.815-0.91437.854-0.067-0.0670.0000.0000.0000.000
150A164GLU-1-0.841-0.87638.034-0.061-0.0610.0000.0000.0000.000
151A165LEU00.006-0.00939.169-0.004-0.0040.0000.0000.0000.000
152A166ALA00.0230.01434.544-0.005-0.0050.0000.0000.0000.000
153A167SER0-0.054-0.03334.414-0.008-0.0080.0000.0000.0000.000
154A168ILE0-0.034-0.01035.219-0.005-0.0050.0000.0000.0000.000
155A169VAL00.0100.00232.532-0.005-0.0050.0000.0000.0000.000
156A170MET0-0.0180.00727.342-0.009-0.0090.0000.0000.0000.000
157A171ALA00.0460.02631.123-0.007-0.0070.0000.0000.0000.000
158A172ALA0-0.0080.00233.072-0.002-0.0020.0000.0000.0000.000
159A173HIS0-0.046-0.05228.230-0.008-0.0080.0000.0000.0000.000
160A174ASP-1-0.806-0.89328.097-0.148-0.1480.0000.0000.0000.000
161A175GLY00.001-0.00329.007-0.004-0.0040.0000.0000.0000.000
162A176VAL0-0.027-0.01428.8780.0000.0000.0000.0000.0000.000
163A177LEU0-0.027-0.01222.530-0.005-0.0050.0000.0000.0000.000
164A178ILE0-0.004-0.01126.669-0.005-0.0050.0000.0000.0000.000
165A179GLU-1-0.852-0.91128.423-0.103-0.1030.0000.0000.0000.000
166A180TRP0-0.040-0.01321.109-0.004-0.0040.0000.0000.0000.000
167A181TYR0-0.017-0.04720.475-0.010-0.0100.0000.0000.0000.000
168A182ARG10.8240.91426.5090.1100.1100.0000.0000.0000.000
169A183ARG10.8540.91129.8040.0990.0990.0000.0000.0000.000
170A184PRO00.0310.02125.8130.0020.0020.0000.0000.0000.000
171A185ASN0-0.045-0.02927.672-0.010-0.0100.0000.0000.0000.000
172A186GLU-1-0.890-0.92229.896-0.089-0.0890.0000.0000.0000.000
173A187LEU0-0.047-0.01029.3330.0050.0050.0000.0000.0000.000
174A188THR00.031-0.00626.288-0.011-0.0110.0000.0000.0000.000
175A189GLY00.0590.01524.9300.0070.0070.0000.0000.0000.000
176A190LYS10.8490.90624.7450.1860.1860.0000.0000.0000.000
177A191THR0-0.0310.00828.3140.0050.0050.0000.0000.0000.000
178A192LEU00.0710.03730.9000.0080.0080.0000.0000.0000.000
179A193THR00.0140.01529.1470.0030.0030.0000.0000.0000.000
180A194LYS10.9650.98431.6700.0860.0860.0000.0000.0000.000
181A195ALA00.0170.02535.0750.0050.0050.0000.0000.0000.000
182A196LEU00.0460.02330.9660.0040.0040.0000.0000.0000.000
183A197ARG10.9370.95132.2760.1130.1130.0000.0000.0000.000
184A198SER0-0.060-0.04335.6460.0050.0050.0000.0000.0000.000
185A199VAL0-0.001-0.00338.7000.0040.0040.0000.0000.0000.000
186A200LEU0-0.012-0.01434.3850.0030.0030.0000.0000.0000.000
187A201LEU0-0.0360.00137.7750.0010.0010.0000.0000.0000.000
188A202ASN0-0.020-0.01340.8130.0060.0060.0000.0000.0000.000
189A203GLY0-0.0090.01842.6820.0030.0030.0000.0000.0000.000
190A204LEU0-0.032-0.04142.689-0.002-0.0020.0000.0000.0000.000
191A205ILE0-0.028-0.00145.9950.0020.0020.0000.0000.0000.000
192A206VAL00.0240.02049.4410.0000.0000.0000.0000.0000.000