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: VQ211

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1994933.502677
FMO2-HF: Nuclear repulsion 1920512.915545
FMO2-HF: Total energy -74420.587132
FMO2-MP2: Total energy -74635.379615


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.
-6.161-1.6930.722-2.163-3.0260.004
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 : 0.037 / q_NPA : 0.012
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].
3A17THR00.0310.0013.237-3.779-1.2090.104-1.239-1.4350.007
4A18GLU-1-0.910-0.9502.741-3.399-2.2310.612-0.599-1.180-0.004
5A19ASN0-0.043-0.0223.5350.0200.7500.006-0.325-0.4110.001
6A20ILE0-0.024-0.0065.4140.3300.3300.0000.0000.0000.000
7A21LEU00.0120.0077.0910.0810.0810.0000.0000.0000.000
8A22GLY00.0480.0277.6860.0740.0740.0000.0000.0000.000
9A23CYS0-0.027-0.0109.0880.1150.1150.0000.0000.0000.000
10A24ALA0-0.001-0.00711.2220.0630.0630.0000.0000.0000.000
11A25LEU0-0.025-0.00412.3090.0340.0340.0000.0000.0000.000
12A26ASP-1-0.804-0.89113.519-0.297-0.2970.0000.0000.0000.000
13A27LEU0-0.055-0.04615.3100.0320.0320.0000.0000.0000.000
14A28PHE0-0.012-0.00516.1250.0250.0250.0000.0000.0000.000
15A29VAL0-0.007-0.00818.1060.0130.0130.0000.0000.0000.000
16A30LYS10.8890.95919.6340.1540.1540.0000.0000.0000.000
17A31ASN0-0.043-0.01621.2130.0020.0020.0000.0000.0000.000
18A32GLY00.0550.04822.2880.0100.0100.0000.0000.0000.000
19A33TYR0-0.095-0.11619.7450.0020.0020.0000.0000.0000.000
20A34ARG10.8780.92022.2310.0030.0030.0000.0000.0000.000
21A35ALA00.0060.01424.3810.0080.0080.0000.0000.0000.000
22A36THR00.0240.01617.716-0.003-0.0030.0000.0000.0000.000
23A37THR00.017-0.00720.1100.0130.0130.0000.0000.0000.000
24A38ILE00.0890.03215.342-0.013-0.0130.0000.0000.0000.000
25A39ASP-1-0.885-0.92716.4990.0480.0480.0000.0000.0000.000
26A40MET00.0250.01617.6600.0000.0000.0000.0000.0000.000
27A41ILE00.002-0.00712.435-0.018-0.0180.0000.0000.0000.000
28A42ALA00.0050.00213.020-0.022-0.0220.0000.0000.0000.000
29A43ALA0-0.040-0.02013.566-0.009-0.0090.0000.0000.0000.000
30A44ARG10.8430.91813.1280.2270.2270.0000.0000.0000.000
31A45ALA00.0300.0109.189-0.045-0.0450.0000.0000.0000.000
32A46GLY00.0090.0299.398-0.043-0.0430.0000.0000.0000.000
33A47LEU0-0.044-0.0238.7310.0920.0920.0000.0000.0000.000
34A48THR00.0500.01812.694-0.032-0.0320.0000.0000.0000.000
35A49LYS10.8740.90414.953-0.038-0.0380.0000.0000.0000.000
36A50GLY00.0060.00717.138-0.006-0.0060.0000.0000.0000.000
37A51ALA0-0.0080.00011.6710.0330.0330.0000.0000.0000.000
38A52ILE00.0270.01611.7790.0880.0880.0000.0000.0000.000
39A53TYR0-0.019-0.01812.8580.0230.0230.0000.0000.0000.000
40A54PHE0-0.038-0.01612.662-0.042-0.0420.0000.0000.0000.000
41A55TYR0-0.0530.0046.8130.2740.2740.0000.0000.0000.000
42A56PHE00.0460.0118.484-0.051-0.0510.0000.0000.0000.000
43A57LYS10.9720.99513.261-0.217-0.2170.0000.0000.0000.000
44A58THR00.012-0.01716.649-0.021-0.0210.0000.0000.0000.000
45A59LYS10.9190.95416.450-0.007-0.0070.0000.0000.0000.000
46A60ASP-1-0.761-0.82817.2870.0350.0350.0000.0000.0000.000
47A61ALA00.0200.02915.316-0.013-0.0130.0000.0000.0000.000
48A62ILE0-0.021-0.00112.379-0.007-0.0070.0000.0000.0000.000
49A63MET00.0130.01214.001-0.040-0.0400.0000.0000.0000.000
50A64LEU0-0.041-0.02116.748-0.022-0.0220.0000.0000.0000.000
51A65MET00.0560.0458.4690.0150.0150.0000.0000.0000.000
52A66LEU0-0.038-0.03211.604-0.046-0.0460.0000.0000.0000.000
53A67LEU0-0.023-0.01614.011-0.023-0.0230.0000.0000.0000.000
54A68GLU-1-0.860-0.93614.1910.0150.0150.0000.0000.0000.000
55A69GLU-1-0.904-0.9539.084-0.487-0.4870.0000.0000.0000.000
56A70ALA0-0.019-0.01713.542-0.017-0.0170.0000.0000.0000.000
57A71GLU-1-0.880-0.93216.849-0.060-0.0600.0000.0000.0000.000
58A72LYS10.9650.99410.5410.3490.3490.0000.0000.0000.000
59A73TYR0-0.055-0.05410.093-0.010-0.0100.0000.0000.0000.000
60A74ILE0-0.031-0.01616.8720.0040.0040.0000.0000.0000.000
61A75VAL0-0.020-0.02420.3060.0100.0100.0000.0000.0000.000
62A76ASP-1-0.820-0.89618.527-0.096-0.0960.0000.0000.0000.000
63A77PRO0-0.064-0.04419.7250.0080.0080.0000.0000.0000.000
64A78ILE0-0.033-0.00122.4490.0040.0040.0000.0000.0000.000
65A79ASP-1-0.876-0.94025.787-0.056-0.0560.0000.0000.0000.000
66A80GLU-1-0.888-0.93924.673-0.100-0.1000.0000.0000.0000.000
67A81TYR0-0.021-0.03023.9390.0050.0050.0000.0000.0000.000
68A82MET0-0.033-0.00527.8880.0010.0010.0000.0000.0000.000
69A83ALA00.0090.01130.6040.0050.0050.0000.0000.0000.000
70A84ASN0-0.007-0.01528.9060.0080.0080.0000.0000.0000.000
71A85ALA0-0.0600.00031.861-0.001-0.0010.0000.0000.0000.000
72A86GLY00.0050.03033.4430.0030.0030.0000.0000.0000.000
73A87PRO0-0.035-0.04337.177-0.002-0.0020.0000.0000.0000.000
74A88LEU00.0560.02339.9270.0010.0010.0000.0000.0000.000
75A89ALA00.0470.02538.301-0.004-0.0040.0000.0000.0000.000
76A90ASP-1-0.835-0.91037.704-0.053-0.0530.0000.0000.0000.000
77A91ALA0-0.018-0.01936.551-0.004-0.0040.0000.0000.0000.000
78A92LYS10.8230.90033.8190.0510.0510.0000.0000.0000.000
79A93LEU00.0370.03132.926-0.005-0.0050.0000.0000.0000.000
80A94VAL0-0.021-0.01633.082-0.005-0.0050.0000.0000.0000.000
81A95LYS10.9140.96527.3520.0940.0940.0000.0000.0000.000
82A96PHE00.0590.01427.567-0.009-0.0090.0000.0000.0000.000
83A97ILE00.0180.02028.332-0.006-0.0060.0000.0000.0000.000
84A98ASN0-0.061-0.05028.563-0.006-0.0060.0000.0000.0000.000
85A99MET0-0.0240.00122.611-0.009-0.0090.0000.0000.0000.000
86A100GLN00.0290.01423.715-0.017-0.0170.0000.0000.0000.000
87A101ALA00.0000.00524.471-0.006-0.0060.0000.0000.0000.000
88A102LEU0-0.061-0.03120.513-0.006-0.0060.0000.0000.0000.000
89A103LEU00.0130.01718.586-0.019-0.0190.0000.0000.0000.000
90A104GLY00.0360.02520.013-0.011-0.0110.0000.0000.0000.000
91A105VAL0-0.075-0.04020.8910.0000.0000.0000.0000.0000.000
92A106THR0-0.069-0.05316.767-0.016-0.0160.0000.0000.0000.000
93A107LYS10.8980.96812.8270.3310.3310.0000.0000.0000.000
94A108PRO00.0740.05116.7860.0140.0140.0000.0000.0000.000
95A109GLN0-0.036-0.03114.2520.0430.0430.0000.0000.0000.000
96A110HIS00.0140.00512.1570.0380.0380.0000.0000.0000.000
97A111VAL00.0300.01217.3470.0190.0190.0000.0000.0000.000
98A112LEU0-0.009-0.00820.8560.0150.0150.0000.0000.0000.000
99A113LEU0-0.038-0.01016.6840.0150.0150.0000.0000.0000.000
100A114LEU00.0170.00620.4960.0140.0140.0000.0000.0000.000
101A115ILE0-0.0070.01422.8610.0100.0100.0000.0000.0000.000
102A116LEU0-0.016-0.01424.7700.0080.0080.0000.0000.0000.000
103A117VAL0-0.011-0.00321.3550.0070.0070.0000.0000.0000.000
104A118SER0-0.0100.01224.6820.0100.0100.0000.0000.0000.000
105A119ILE0-0.023-0.01327.2530.0050.0050.0000.0000.0000.000
106A120ASP-1-0.798-0.89229.024-0.014-0.0140.0000.0000.0000.000
107A121PHE0-0.062-0.02530.6080.0020.0020.0000.0000.0000.000
108A122SER0-0.0200.00025.4640.0010.0010.0000.0000.0000.000
109A123GLY0-0.0010.00426.3070.0000.0000.0000.0000.0000.000
110A124THR00.013-0.01223.0290.0030.0030.0000.0000.0000.000
111A125GLY00.0020.01125.2790.0070.0070.0000.0000.0000.000
112A126ASP-1-0.917-0.97626.6010.0040.0040.0000.0000.0000.000
113A127ASP-1-0.897-0.94123.7150.0340.0340.0000.0000.0000.000
114A128ILE00.007-0.00920.919-0.005-0.0050.0000.0000.0000.000
115A129GLH0-0.039-0.03323.409-0.010-0.0100.0000.0000.0000.000
116A130LYS10.9580.98526.158-0.011-0.0110.0000.0000.0000.000
117A131ARG10.9200.96417.523-0.013-0.0130.0000.0000.0000.000
118A132ALA00.0560.02522.859-0.007-0.0070.0000.0000.0000.000
119A133LYS10.8770.92423.9310.0180.0180.0000.0000.0000.000
120A134ALA0-0.071-0.02425.275-0.002-0.0020.0000.0000.0000.000
121A135ILE00.0420.02820.159-0.001-0.0010.0000.0000.0000.000
122A136TYR0-0.048-0.04024.313-0.003-0.0030.0000.0000.0000.000
123A137ARG10.9490.96126.8250.0240.0240.0000.0000.0000.000
124A138ARG10.8530.92321.7210.0700.0700.0000.0000.0000.000
125A139MET0-0.0040.01125.421-0.003-0.0030.0000.0000.0000.000
126A140TYR0-0.019-0.01127.4840.0000.0000.0000.0000.0000.000
127A141GLY00.0200.00030.9030.0010.0010.0000.0000.0000.000
128A142HIS0-0.030-0.00727.8650.0000.0000.0000.0000.0000.000
129A143VAL0-0.015-0.00430.8080.0000.0000.0000.0000.0000.000
130A144GLU-1-0.874-0.92633.352-0.033-0.0330.0000.0000.0000.000
131A145GLN00.0550.01934.3690.0000.0000.0000.0000.0000.000
132A146LEU0-0.060-0.01833.4380.0010.0010.0000.0000.0000.000
133A147ILE0-0.042-0.02836.5160.0010.0010.0000.0000.0000.000
134A148ALA00.0650.02839.2030.0020.0020.0000.0000.0000.000
135A149GLN0-0.075-0.02939.3200.0030.0030.0000.0000.0000.000
136A150GLY00.0660.00240.7110.0010.0010.0000.0000.0000.000
137A151GLN0-0.086-0.04842.3110.0010.0010.0000.0000.0000.000
138A152THR0-0.053-0.00844.3270.0020.0020.0000.0000.0000.000
139A153GLU-1-0.881-0.95842.193-0.041-0.0410.0000.0000.0000.000
140A154GLY0-0.0160.00646.2500.0000.0000.0000.0000.0000.000
141A155VAL0-0.046-0.01542.7260.0000.0000.0000.0000.0000.000
142A156PHE0-0.060-0.02238.861-0.001-0.0010.0000.0000.0000.000
143A157ARG10.8700.92344.6840.0340.0340.0000.0000.0000.000
144A158SER00.0410.00646.009-0.001-0.0010.0000.0000.0000.000
145A159ASP-1-0.870-0.91148.424-0.028-0.0280.0000.0000.0000.000
146A160SER00.005-0.00645.0070.0000.0000.0000.0000.0000.000
147A161GLY00.0370.02944.718-0.001-0.0010.0000.0000.0000.000
148A162SER0-0.005-0.02740.299-0.001-0.0010.0000.0000.0000.000
149A163ASP-1-0.864-0.92238.939-0.030-0.0300.0000.0000.0000.000
150A164GLU-1-0.950-0.99238.963-0.029-0.0290.0000.0000.0000.000
151A165LEU0-0.012-0.02039.964-0.002-0.0020.0000.0000.0000.000
152A166ALA00.0150.00835.402-0.003-0.0030.0000.0000.0000.000
153A167SER0-0.015-0.01035.173-0.004-0.0040.0000.0000.0000.000
154A168ILE0-0.0280.00135.696-0.002-0.0020.0000.0000.0000.000
155A169VAL0-0.0030.00832.848-0.003-0.0030.0000.0000.0000.000
156A170MET0-0.0120.00628.077-0.006-0.0060.0000.0000.0000.000
157A171ALA00.0160.00931.427-0.004-0.0040.0000.0000.0000.000
158A172ALA0-0.012-0.00633.071-0.002-0.0020.0000.0000.0000.000
159A173HIS0-0.050-0.05228.701-0.008-0.0080.0000.0000.0000.000
160A174ASP-1-0.818-0.89528.205-0.076-0.0760.0000.0000.0000.000
161A175GLY0-0.006-0.01129.021-0.003-0.0030.0000.0000.0000.000
162A176VAL0-0.017-0.01528.958-0.001-0.0010.0000.0000.0000.000
163A177LEU0-0.0100.00522.788-0.005-0.0050.0000.0000.0000.000
164A178ILE0-0.010-0.01526.716-0.003-0.0030.0000.0000.0000.000
165A179GLU-1-0.869-0.94228.239-0.067-0.0670.0000.0000.0000.000
166A180TRP0-0.056-0.01321.321-0.004-0.0040.0000.0000.0000.000
167A181TYR0-0.018-0.03320.298-0.008-0.0080.0000.0000.0000.000
168A182ARG10.8550.94326.4430.0650.0650.0000.0000.0000.000
169A183ARG10.9550.97729.8720.0630.0630.0000.0000.0000.000
170A184PRO00.0360.02625.9750.0000.0000.0000.0000.0000.000
171A185ASN0-0.058-0.04027.931-0.009-0.0090.0000.0000.0000.000
172A186GLU-1-0.968-0.97430.141-0.061-0.0610.0000.0000.0000.000
173A187LEU0-0.0260.00229.0020.0010.0010.0000.0000.0000.000
174A188THR00.0290.00626.329-0.009-0.0090.0000.0000.0000.000
175A189GLY00.0550.01424.9680.0050.0050.0000.0000.0000.000
176A190LYS10.9310.95425.1100.1350.1350.0000.0000.0000.000
177A191THR0-0.0060.01828.4570.0020.0020.0000.0000.0000.000
178A192LEU00.0550.01231.0810.0050.0050.0000.0000.0000.000
179A193THR00.0440.03829.5450.0020.0020.0000.0000.0000.000
180A194LYS10.9480.97032.0830.0630.0630.0000.0000.0000.000
181A195ALA00.0300.00835.4320.0030.0030.0000.0000.0000.000
182A196LEU00.0440.03431.5820.0030.0030.0000.0000.0000.000
183A197ARG10.9680.97732.3890.0800.0800.0000.0000.0000.000
184A198SER0-0.061-0.03736.1750.0030.0030.0000.0000.0000.000
185A199VAL0-0.0050.00439.0350.0030.0030.0000.0000.0000.000
186A200LEU0-0.0060.00134.7630.0020.0020.0000.0000.0000.000
187A201LEU0-0.044-0.02338.4970.0010.0010.0000.0000.0000.000
188A202ASN0-0.023-0.02140.9890.0040.0040.0000.0000.0000.000
189A203GLY00.0010.03242.9380.0020.0020.0000.0000.0000.000
190A204LEU0-0.019-0.03343.257-0.001-0.0010.0000.0000.0000.000
191A205ILE0-0.0300.00446.1060.0000.0000.0000.0000.0000.000
192A206VAL00.0380.02549.3040.0000.0000.0000.0000.0000.000