FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: V5461

Calculation Name: 5DUD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DUD

Chain ID: A

ChEMBL ID:

UniProt ID: P0AAV4

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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4391749.483933
FMO2-HF: Nuclear repulsion 4271904.749163
FMO2-HF: Total energy -119844.734769
FMO2-MP2: Total energy -120189.538


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-12.522-7.40315.949-8.557-12.511-0.05
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.025
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].
3A3LYS10.8490.9213.8712.1063.549-0.015-0.699-0.7290.002
4A4ILE00.0140.0025.692-0.184-0.1840.0000.0000.0000.000
5A5ILE0-0.069-0.0279.426-0.002-0.0020.0000.0000.0000.000
6A6ARG10.8430.91912.0550.0310.0310.0000.0000.0000.000
7A7ALA00.0550.02114.195-0.007-0.0070.0000.0000.0000.000
8A8GLY00.0050.02615.1080.0020.0020.0000.0000.0000.000
9A9MET0-0.023-0.01418.7160.0030.0030.0000.0000.0000.000
10A10TYR00.009-0.01320.7120.0070.0070.0000.0000.0000.000
11A11THR00.003-0.00414.554-0.017-0.0170.0000.0000.0000.000
12A12THR0-0.0010.01215.3250.0210.0210.0000.0000.0000.000
13A13VAL00.0450.04010.778-0.009-0.0090.0000.0000.0000.000
14A14GLN0-0.007-0.01413.588-0.035-0.0350.0000.0000.0000.000
15A15ASP-1-0.728-0.81815.0800.2480.2480.0000.0000.0000.000
16A16GLY00.0300.00517.177-0.019-0.0190.0000.0000.0000.000
17A17GLY0-0.0130.01120.081-0.018-0.0180.0000.0000.0000.000
18A18ARG10.8140.89318.843-0.217-0.2170.0000.0000.0000.000
19A19HIS0-0.054-0.05023.149-0.016-0.0160.0000.0000.0000.000
20A20GLY00.0280.01326.2630.0020.0020.0000.0000.0000.000
21A21PHE00.0330.02525.038-0.005-0.0050.0000.0000.0000.000
22A22ARG10.9310.96028.984-0.089-0.0890.0000.0000.0000.000
23A23GLN0-0.011-0.02431.625-0.001-0.0010.0000.0000.0000.000
24A24SER0-0.028-0.01331.242-0.005-0.0050.0000.0000.0000.000
25A25GLY0-0.020-0.00232.5570.0020.0020.0000.0000.0000.000
26A26ILE0-0.030-0.01026.0900.0030.0030.0000.0000.0000.000
27A27SER0-0.002-0.01826.786-0.003-0.0030.0000.0000.0000.000
28A28HIS00.0230.03324.7310.0010.0010.0000.0000.0000.000
29A29CYS0-0.0160.00121.6630.0140.0140.0000.0000.0000.000
30A30GLY00.0970.05919.946-0.014-0.0140.0000.0000.0000.000
31A31ALA0-0.023-0.00819.313-0.002-0.0020.0000.0000.0000.000
32A32LEU0-0.023-0.01420.993-0.011-0.0110.0000.0000.0000.000
33A33ASP-1-0.785-0.89322.8960.0660.0660.0000.0000.0000.000
34A34MET0-0.0080.01021.0020.0070.0070.0000.0000.0000.000
35A35PRO00.005-0.00422.3750.0030.0030.0000.0000.0000.000
36A36ALA00.0250.02321.2310.0000.0000.0000.0000.0000.000
37A37LEU0-0.0030.02016.481-0.003-0.0030.0000.0000.0000.000
38A38ARG10.8810.94317.924-0.096-0.0960.0000.0000.0000.000
39A39ILE0-0.0050.00019.687-0.003-0.0030.0000.0000.0000.000
40A40ALA0-0.017-0.00715.505-0.005-0.0050.0000.0000.0000.000
41A41ASN0-0.011-0.02614.1850.0110.0110.0000.0000.0000.000
42A42LEU00.0100.00215.850-0.001-0.0010.0000.0000.0000.000
43A43LEU0-0.052-0.00317.221-0.006-0.0060.0000.0000.0000.000
44A44VAL0-0.065-0.01812.000-0.010-0.0100.0000.0000.0000.000
45A45GLY00.0030.01213.5600.0110.0110.0000.0000.0000.000
46A46ASN0-0.064-0.03211.2170.0080.0080.0000.0000.0000.000
47A47ASP-1-0.762-0.88414.8700.1080.1080.0000.0000.0000.000
48A48ALA00.0090.00316.9040.0150.0150.0000.0000.0000.000
49A49ASN0-0.035-0.04118.811-0.001-0.0010.0000.0000.0000.000
50A50ALA00.0240.02413.3980.0150.0150.0000.0000.0000.000
51A51PRO00.0060.00410.870-0.017-0.0170.0000.0000.0000.000
52A52ALA00.0340.02011.1740.0250.0250.0000.0000.0000.000
53A53LEU0-0.009-0.01010.3260.0260.0260.0000.0000.0000.000
54A54GLU-1-0.749-0.84313.3550.1010.1010.0000.0000.0000.000
55A55ILE0-0.001-0.00214.6450.0210.0210.0000.0000.0000.000
56A56THR0-0.030-0.02318.131-0.023-0.0230.0000.0000.0000.000
57A57LEU0-0.041-0.04021.826-0.002-0.0020.0000.0000.0000.000
58A58GLY00.0450.01819.875-0.009-0.0090.0000.0000.0000.000
59A59GLN0-0.081-0.05419.5680.0100.0100.0000.0000.0000.000
60A60LEU00.0630.04912.7800.0010.0010.0000.0000.0000.000
61A61THR0-0.006-0.01012.569-0.011-0.0110.0000.0000.0000.000
62A62VAL00.0080.0138.7070.0600.0600.0000.0000.0000.000
63A63GLU-1-0.724-0.8357.703-0.530-0.5300.0000.0000.0000.000
64A64PHE00.0210.0155.349-0.482-0.4820.0000.0000.0000.000
65A65GLU-1-0.772-0.8521.915-9.980-12.09811.166-4.817-4.231-0.040
66A66THR0-0.017-0.0132.659-0.4310.8362.082-0.736-2.613-0.002
67A67ASP-1-0.857-0.9214.934-0.631-0.6020.002-0.0390.0080.000
68A68GLY0-0.038-0.0257.3550.2330.2330.0000.0000.0000.000
69A69TRP0-0.003-0.0039.277-0.070-0.0700.0000.0000.0000.000
70A70PHE00.004-0.0249.7650.0130.0130.0000.0000.0000.000
71A71ALA00.0300.02711.5140.0010.0010.0000.0000.0000.000
72A72LEU00.0190.01014.1870.0100.0100.0000.0000.0000.000
73A73THR0-0.023-0.03616.778-0.004-0.0040.0000.0000.0000.000
74A74GLY00.0150.01119.9220.0060.0060.0000.0000.0000.000
75A75ALA0-0.006-0.00722.736-0.008-0.0080.0000.0000.0000.000
76A76GLY00.0720.04322.7640.0000.0000.0000.0000.0000.000
77A77CYS0-0.086-0.04220.6770.0000.0000.0000.0000.0000.000
78A78GLU-1-0.865-0.91122.182-0.001-0.0010.0000.0000.0000.000
79A79ALA00.0140.01517.923-0.005-0.0050.0000.0000.0000.000
80A80ARG10.8540.93218.7690.0590.0590.0000.0000.0000.000
81A81LEU00.0110.00613.086-0.012-0.0120.0000.0000.0000.000
82A82ASP-1-0.772-0.87714.462-0.204-0.2040.0000.0000.0000.000
83A83ASP-1-0.841-0.90817.263-0.066-0.0660.0000.0000.0000.000
84A84ASN0-0.039-0.02819.6960.0220.0220.0000.0000.0000.000
85A85ALA0-0.039-0.01120.249-0.005-0.0050.0000.0000.0000.000
86A86VAL0-0.001-0.00316.9970.0000.0000.0000.0000.0000.000
87A87TRP00.004-0.00520.3630.0040.0040.0000.0000.0000.000
88A88THR0-0.031-0.01119.9630.0000.0000.0000.0000.0000.000
89A89GLY0-0.003-0.00819.950-0.002-0.0020.0000.0000.0000.000
90A90TRP00.010-0.00319.3790.0000.0000.0000.0000.0000.000
91A91ARG10.8170.92315.422-0.046-0.0460.0000.0000.0000.000
92A92LEU0-0.0060.01114.821-0.006-0.0060.0000.0000.0000.000
93A93PRO00.0120.00613.3870.0080.0080.0000.0000.0000.000
94A94MET0-0.046-0.0156.027-0.081-0.0810.0000.0000.0000.000
95A95LYS10.9450.96610.2560.1250.1250.0000.0000.0000.000
96A96ALA00.0020.0047.033-0.118-0.1180.0000.0000.0000.000
97A97GLY0-0.011-0.0137.6200.0360.0360.0000.0000.0000.000
98A98GLN0-0.048-0.0169.5720.0490.0490.0000.0000.0000.000
99A99ARG10.8130.8699.8250.1490.1490.0000.0000.0000.000
100A100LEU0-0.0040.01412.0160.0570.0570.0000.0000.0000.000
101A101THR0-0.066-0.05313.6960.0120.0120.0000.0000.0000.000
102A102LEU00.0310.02415.8230.0070.0070.0000.0000.0000.000
103A103LYS10.8850.92718.8280.0080.0080.0000.0000.0000.000
104A104ARG10.9560.97422.163-0.037-0.0370.0000.0000.0000.000
105A105PRO0-0.0180.00023.690-0.005-0.0050.0000.0000.0000.000
106A106GLN0-0.033-0.02726.1410.0030.0030.0000.0000.0000.000
107A107HIS0-0.012-0.01028.6930.0020.0020.0000.0000.0000.000
108A108GLY00.0020.00927.4420.0010.0010.0000.0000.0000.000
109A109MET0-0.034-0.00426.452-0.003-0.0030.0000.0000.0000.000
110A110ARG10.8670.93221.875-0.093-0.0930.0000.0000.0000.000
111A111SER0-0.0220.00619.336-0.011-0.0110.0000.0000.0000.000
112A112TYR0-0.028-0.05316.6480.0120.0120.0000.0000.0000.000
113A113LEU0-0.0030.00510.940-0.025-0.0250.0000.0000.0000.000
114A114ALA00.0190.02311.1750.0560.0560.0000.0000.0000.000
115A115VAL00.0630.0085.910-0.047-0.0470.0000.0000.0000.000
116A116ALA00.0460.0259.0740.0490.0490.0000.0000.0000.000
117A117GLY0-0.055-0.0278.2040.0470.0470.0000.0000.0000.000
118A118GLY00.0190.0289.167-0.003-0.0030.0000.0000.0000.000
119A119ILE0-0.049-0.0296.6270.0680.0680.0000.0000.0000.000
120A120ASP-1-0.895-0.9376.1010.2810.2810.0000.0000.0000.000
121A121VAL00.0320.0047.5360.2520.2520.0000.0000.0000.000
122A122PRO00.0480.01410.191-0.109-0.1090.0000.0000.0000.000
123A123PRO00.0430.02313.880-0.004-0.0040.0000.0000.0000.000
124A124VAL0-0.017-0.01516.258-0.040-0.0400.0000.0000.0000.000
125A125MET0-0.024-0.01419.133-0.012-0.0120.0000.0000.0000.000
126A126GLY00.0310.01920.336-0.010-0.0100.0000.0000.0000.000
127A127SER0-0.040-0.02618.182-0.001-0.0010.0000.0000.0000.000
128A128CYS0-0.025-0.00613.057-0.009-0.0090.0000.0000.0000.000
129A129SER0-0.045-0.03915.1830.0360.0360.0000.0000.0000.000
130A130THR0-0.027-0.02715.8630.0080.0080.0000.0000.0000.000
131A131ASP-1-0.785-0.89918.0180.1310.1310.0000.0000.0000.000
132A132LEU0-0.024-0.02519.6470.0050.0050.0000.0000.0000.000
133A133LYS10.8950.95522.743-0.110-0.1100.0000.0000.0000.000
134A134VAL0-0.050-0.03124.799-0.009-0.0090.0000.0000.0000.000
135A135GLY00.0190.03922.107-0.003-0.0030.0000.0000.0000.000
136A136ILE0-0.030-0.02419.8540.0130.0130.0000.0000.0000.000
137A137GLY00.0140.00716.519-0.010-0.0100.0000.0000.0000.000
138A138GLY0-0.019-0.02313.1300.0020.0020.0000.0000.0000.000
139A139LEU0-0.037-0.01110.3550.0920.0920.0000.0000.0000.000
140A140GLU-1-0.863-0.94013.0340.3780.3780.0000.0000.0000.000
141A141GLY00.0120.03216.320-0.045-0.0450.0000.0000.0000.000
142A142ARG10.7130.81913.128-0.498-0.4980.0000.0000.0000.000
143A143LEU0-0.013-0.01216.8260.0270.0270.0000.0000.0000.000
144A144LEU0-0.027-0.00411.0570.0260.0260.0000.0000.0000.000
145A145LYS10.8280.87912.985-0.425-0.4250.0000.0000.0000.000
146A146ASP-1-0.806-0.91112.8190.1820.1820.0000.0000.0000.000
147A147GLY00.0030.00910.7150.0090.0090.0000.0000.0000.000
148A148ASP-1-0.762-0.8359.5630.5830.5830.0000.0000.0000.000
149A149ARG10.7780.8392.5900.4821.3770.181-0.435-0.6410.001
150A150LEU00.0190.0064.915-0.512-0.337-0.001-0.021-0.1530.000
151A151PRO00.0230.0172.5400.4472.2260.628-1.081-1.325-0.007
152A152ILE00.0110.0162.367-2.817-1.5221.904-0.684-2.516-0.004
153A153GLY00.0360.0323.949-0.635-0.4000.003-0.044-0.1940.000
154A154LYS10.8210.8844.682-0.134-0.015-0.001-0.001-0.1170.000
155A155SER00.0300.0097.871-0.053-0.0530.0000.0000.0000.000
156A156LYS10.8420.91010.323-0.055-0.0550.0000.0000.0000.000
157A157ARG10.9310.9749.955-0.158-0.1580.0000.0000.0000.000
158A158ASP-1-0.764-0.86816.2860.0190.0190.0000.0000.0000.000
159A159SER0-0.118-0.08715.6000.0200.0200.0000.0000.0000.000
160A160MET00.0430.03117.884-0.004-0.0040.0000.0000.0000.000
161A161GLU-1-0.832-0.90619.8140.0110.0110.0000.0000.0000.000
162A162ALA00.0070.00619.1680.0070.0070.0000.0000.0000.000
163A163GLN0-0.043-0.02420.113-0.003-0.0030.0000.0000.0000.000
164A164GLY00.0620.03620.8120.0030.0030.0000.0000.0000.000
165A165VAL0-0.064-0.03422.517-0.001-0.0010.0000.0000.0000.000
166A166LYS10.9450.97024.949-0.023-0.0230.0000.0000.0000.000
167A167GLN00.0820.04422.8190.0090.0090.0000.0000.0000.000
168A168LEU00.0070.01726.286-0.004-0.0040.0000.0000.0000.000
169A169LEU00.0100.01528.4540.0010.0010.0000.0000.0000.000
170A170TRP0-0.033-0.01725.0300.0000.0000.0000.0000.0000.000
171A171GLY00.014-0.00231.764-0.004-0.0040.0000.0000.0000.000
172A172ASN00.0120.00434.5960.0020.0020.0000.0000.0000.000
173A173ARG10.8960.95337.282-0.030-0.0300.0000.0000.0000.000
174A174ILE00.0080.01134.8820.0010.0010.0000.0000.0000.000
175A175ARG10.8620.89436.468-0.041-0.0410.0000.0000.0000.000
176A176ALA0-0.019-0.02338.7770.0030.0030.0000.0000.0000.000
177A177LEU00.0010.01241.107-0.002-0.0020.0000.0000.0000.000
178A178PRO00.0220.00543.4850.0020.0020.0000.0000.0000.000
179A179GLY0-0.059-0.00846.017-0.001-0.0010.0000.0000.0000.000
180A180PRO0-0.012-0.02543.9390.0020.0020.0000.0000.0000.000
181A181GLU-1-0.719-0.82346.2030.0380.0380.0000.0000.0000.000
182A182TYR00.0480.02847.971-0.001-0.0010.0000.0000.0000.000
183A183HIS00.012-0.00349.604-0.001-0.0010.0000.0000.0000.000
184A184GLU-1-0.712-0.80051.6260.0310.0310.0000.0000.0000.000
185A185PHE0-0.0160.00548.2820.0000.0000.0000.0000.0000.000
186A186ASP-1-0.739-0.83552.9640.0240.0240.0000.0000.0000.000
187A187ARG10.8550.88154.443-0.023-0.0230.0000.0000.0000.000
188A188ALA00.0250.01955.1910.0000.0000.0000.0000.0000.000
189A189SER0-0.024-0.03051.2570.0010.0010.0000.0000.0000.000
190A190GLN0-0.015-0.01050.3450.0000.0000.0000.0000.0000.000
191A191ASP-1-0.793-0.86450.2110.0240.0240.0000.0000.0000.000
192A192ALA00.0000.00450.1420.0000.0000.0000.0000.0000.000
193A193PHE00.005-0.00242.1110.0010.0010.0000.0000.0000.000
194A194TRP0-0.005-0.01343.9290.0010.0010.0000.0000.0000.000
195A195ARG10.8270.90347.149-0.023-0.0230.0000.0000.0000.000
196A196SER0-0.025-0.00647.041-0.001-0.0010.0000.0000.0000.000
197A197PRO0-0.038-0.00944.0230.0010.0010.0000.0000.0000.000
198A198TRP0-0.021-0.00441.4310.0000.0000.0000.0000.0000.000
199A199GLN0-0.046-0.02339.5920.0010.0010.0000.0000.0000.000
200A200LEU0-0.028-0.00132.3730.0010.0010.0000.0000.0000.000
201A201SER0-0.005-0.00537.0100.0000.0000.0000.0000.0000.000
202A202SER00.0400.01134.2010.0040.0040.0000.0000.0000.000
203A203GLN00.0180.01733.2180.0050.0050.0000.0000.0000.000
204A204SER0-0.046-0.01232.4360.0040.0040.0000.0000.0000.000
205A205ASN0-0.009-0.01528.1250.0070.0070.0000.0000.0000.000
206A206ARG10.8280.87121.294-0.162-0.1620.0000.0000.0000.000
207A207MET0-0.0080.01626.733-0.001-0.0010.0000.0000.0000.000
208A208GLY00.017-0.00329.601-0.004-0.0040.0000.0000.0000.000
209A209TYR0-0.023-0.02429.1590.0030.0030.0000.0000.0000.000
210A210ARG10.8920.94334.097-0.061-0.0610.0000.0000.0000.000
211A211LEU00.009-0.00336.8820.0000.0000.0000.0000.0000.000
212A212GLN00.0390.03039.8990.0010.0010.0000.0000.0000.000
213A213GLY00.0430.00542.8380.0000.0000.0000.0000.0000.000
214A214GLN0-0.0150.00746.008-0.001-0.0010.0000.0000.0000.000
215A215ILE00.001-0.00448.3660.0010.0010.0000.0000.0000.000
216A216LEU0-0.053-0.02945.871-0.001-0.0010.0000.0000.0000.000
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