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: N2NMQ

Calculation Name: 3DV8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DV8

Chain ID: A

ChEMBL ID:

UniProt ID: A5ZWV4

Base Structure: X-ray

Registration Date: 2023-09-27

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2593476.587811
FMO2-HF: Nuclear repulsion 2504830.473097
FMO2-HF: Total energy -88646.114714
FMO2-MP2: Total energy -88900.195619


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:4:GLU)


Summations of interaction energy for fragment #1(A:4:GLU)
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.
-17.973-15.85124.202-12.526-13.7960.086
Interaction energy analysis for fragmet #1(A:4:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.855 / q_NPA : -0.915
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].
3A6TYR00.0140.0012.953-8.242-5.0640.237-1.547-1.8690.010
4A7PHE00.0270.0182.877-5.321-4.3100.169-0.321-0.8590.001
5A8PRO00.0370.0214.5300.5800.674-0.001-0.010-0.0830.000
6A9LEU00.0380.0207.178-0.367-0.3670.0000.0000.0000.000
7A10TRP00.0050.0002.986-9.074-3.3963.154-2.300-6.5320.006
8A11ASN0-0.085-0.0575.1411.1441.188-0.001-0.001-0.0410.000
9A12ASP-1-0.860-0.9338.10022.08922.0890.0000.0000.0000.000
10A13LEU0-0.0510.0056.512-1.272-1.2720.0000.0000.0000.000
11A14ASN00.0400.0199.9522.1222.1220.0000.0000.0000.000
12A15THR00.036-0.0039.8862.1452.1450.0000.0000.0000.000
13A16ALA00.0080.0109.3822.6312.6310.0000.0000.0000.000
14A17GLN00.0150.00110.0811.7331.7330.0000.0000.0000.000
15A18LYS10.8430.9335.861-33.670-33.6700.0000.0000.0000.000
16A19LYS10.8080.8805.427-25.567-25.437-0.001-0.001-0.1280.000
17A20LEU00.0060.0106.9921.2561.2560.0000.0000.0000.000
18A21ILE00.0220.0105.063-1.925-1.9250.0000.0000.0000.000
19A22SER0-0.011-0.0341.571-26.012-35.26620.573-7.975-3.3440.068
20A23ASP-1-0.849-0.9084.24030.38530.4700.001-0.068-0.0190.000
21A24ASN0-0.094-0.0557.518-5.832-5.8320.0000.0000.0000.000
22A25LEU00.0000.0123.169-3.752-3.0620.067-0.213-0.5430.001
23A26ILE00.0080.0107.649-0.736-0.7360.0000.0000.0000.000
24A27THR0-0.015-0.0098.5630.5990.5990.0000.0000.0000.000
25A28GLN0-0.018-0.00810.129-1.439-1.4390.0000.0000.0000.000
26A29HIS00.0060.00012.624-0.520-0.5200.0000.0000.0000.000
27A30VAL00.0040.00615.267-0.739-0.7390.0000.0000.0000.000
28A31LYS10.8220.90117.996-13.885-13.8850.0000.0000.0000.000
29A32LYS10.9350.96121.300-11.365-11.3650.0000.0000.0000.000
30A33GLY0-0.029-0.01422.773-0.389-0.3890.0000.0000.0000.000
31A34THR0-0.071-0.04621.042-0.333-0.3330.0000.0000.0000.000
32A35ILE00.0070.00321.6550.4690.4690.0000.0000.0000.000
33A36ILE0-0.046-0.03816.0470.1150.1150.0000.0000.0000.000
34A37HIS0-0.034-0.01319.0281.2351.2350.0000.0000.0000.000
35A38ASN0-0.034-0.01821.115-0.355-0.3550.0000.0000.0000.000
36A39GLY00.0640.02824.918-0.293-0.2930.0000.0000.0000.000
37A40ASN0-0.085-0.08724.8310.7120.7120.0000.0000.0000.000
38A41MET0-0.101-0.03426.507-0.192-0.1920.0000.0000.0000.000
39A42ASP-1-0.827-0.88621.14013.19113.1910.0000.0000.0000.000
40A43CYS0-0.098-0.05220.175-0.340-0.3400.0000.0000.0000.000
41A44THR00.0540.03716.3260.6390.6390.0000.0000.0000.000
42A45GLY00.0250.00813.7960.8560.8560.0000.0000.0000.000
43A46LEU0-0.0370.01011.030-0.945-0.9450.0000.0000.0000.000
44A47LEU0-0.025-0.00110.6271.2981.2980.0000.0000.0000.000
45A48LEU0-0.015-0.0054.172-0.469-0.2830.004-0.064-0.1250.000
46A49VAL00.0280.0128.4590.9570.9570.0000.0000.0000.000
47A50LYS10.8490.9257.290-24.415-24.4150.0000.0000.0000.000
48A51SER0-0.063-0.0708.471-0.704-0.7040.0000.0000.0000.000
49A52GLY00.0290.01412.138-0.092-0.0920.0000.0000.0000.000
50A53GLN0-0.028-0.02815.574-0.046-0.0460.0000.0000.0000.000
51A54LEU0-0.018-0.00114.502-0.275-0.2750.0000.0000.0000.000
52A55ARG10.7610.85818.752-10.705-10.7050.0000.0000.0000.000
53A56THR00.0100.00719.9780.3190.3190.0000.0000.0000.000
54A57TYR0-0.063-0.06022.432-0.385-0.3850.0000.0000.0000.000
55A58ILE00.0300.02026.2010.1760.1760.0000.0000.0000.000
56A59LEU00.0250.00029.183-0.133-0.1330.0000.0000.0000.000
57A60SER0-0.060-0.04332.3580.0290.0290.0000.0000.0000.000
58A61ASP-1-0.878-0.94735.8977.7257.7250.0000.0000.0000.000
59A62GLU-1-0.927-0.94638.0177.3207.3200.0000.0000.0000.000
60A63GLY0-0.029-0.00935.681-0.072-0.0720.0000.0000.0000.000
61A64ARG10.8090.91335.834-7.634-7.6340.0000.0000.0000.000
62A65GLU-1-0.764-0.85930.1569.7409.7400.0000.0000.0000.000
63A66ILE0-0.041-0.02730.744-0.287-0.2870.0000.0000.0000.000
64A67THR0-0.014-0.02725.0880.2200.2200.0000.0000.0000.000
65A68LEU0-0.041-0.01924.729-0.224-0.2240.0000.0000.0000.000
66A69TYR00.021-0.00218.552-0.064-0.0640.0000.0000.0000.000
67A70ARG10.6850.78020.768-11.384-11.3840.0000.0000.0000.000
68A71LEU0-0.041-0.00514.9660.2610.2610.0000.0000.0000.000
69A72PHE00.021-0.00515.414-0.555-0.5550.0000.0000.0000.000
70A73ASP-1-0.760-0.86711.94119.50019.5000.0000.0000.0000.000
71A74MET0-0.052-0.0278.838-0.208-0.2080.0000.0000.0000.000
72A75ASP-1-0.788-0.8639.92317.49117.4910.0000.0000.0000.000
73A76MET0-0.0340.0008.6182.2452.2450.0000.0000.0000.000
74A77CYS0-0.0270.00011.701-2.013-2.0130.0000.0000.0000.000
75A78LEU00.0550.01013.4290.9640.9640.0000.0000.0000.000
76A79LEU00.0640.02416.042-0.211-0.2110.0000.0000.0000.000
77A80SER00.0430.02315.023-0.611-0.6110.0000.0000.0000.000
78A81ALA0-0.0080.00215.9240.1800.1800.0000.0000.0000.000
79A82SER00.045-0.01918.008-0.295-0.2950.0000.0000.0000.000
80A84ILE0-0.047-0.02316.996-0.524-0.5240.0000.0000.0000.000
81A85MET0-0.035-0.01018.707-0.126-0.1260.0000.0000.0000.000
82A86ARG10.9270.94423.005-11.883-11.8830.0000.0000.0000.000
83A87SER00.0230.01226.542-0.345-0.3450.0000.0000.0000.000
84A88ILE0-0.0290.00322.799-0.288-0.2880.0000.0000.0000.000
85A89GLN0-0.066-0.03626.285-0.218-0.2180.0000.0000.0000.000
86A90PHE0-0.017-0.01024.821-0.346-0.3460.0000.0000.0000.000
87A91GLU-1-0.842-0.89126.11210.53410.5340.0000.0000.0000.000
88A92VAL00.005-0.00422.556-0.254-0.2540.0000.0000.0000.000
89A93THR00.0080.01024.2540.2050.2050.0000.0000.0000.000
90A94ILE0-0.020-0.01318.1650.0670.0670.0000.0000.0000.000
91A95GLU-1-0.773-0.85821.11611.31411.3140.0000.0000.0000.000
92A96ALA00.0260.02718.9750.3030.3030.0000.0000.0000.000
93A97GLU-1-0.756-0.84820.37811.19611.1960.0000.0000.0000.000
94A98LYS10.7720.87219.327-13.101-13.1010.0000.0000.0000.000
95A99ASP-1-0.816-0.88518.99913.54213.5420.0000.0000.0000.000
96A100THR0-0.028-0.02513.7410.1410.1410.0000.0000.0000.000
97A101ASP-1-0.826-0.87310.63520.80220.8020.0000.0000.0000.000
98A102LEU0-0.030-0.0329.8530.2850.2850.0000.0000.0000.000
99A103TRP00.0030.0044.6801.6671.9470.000-0.026-0.2530.000
100A104ILE00.0080.0068.002-0.809-0.8090.0000.0000.0000.000
101A105ILE0-0.018-0.0056.4632.4652.4650.0000.0000.0000.000
102A106PRO00.0190.0109.731-2.015-2.0150.0000.0000.0000.000
103A107ALA00.0840.04113.3810.3730.3730.0000.0000.0000.000
104A108GLU-1-0.884-0.95515.93318.18518.1850.0000.0000.0000.000
105A109ILE0-0.0030.00311.240-0.328-0.3280.0000.0000.0000.000
106A110TYR0-0.013-0.01910.5510.6270.6270.0000.0000.0000.000
107A111LYS10.9310.96813.363-14.277-14.2770.0000.0000.0000.000
108A112GLY0-0.024-0.01416.497-0.741-0.7410.0000.0000.0000.000
109A113ILE0-0.016-0.01210.216-0.416-0.4160.0000.0000.0000.000
110A114MET0-0.038-0.02014.406-0.829-0.8290.0000.0000.0000.000
111A115LYS10.7550.86616.402-14.809-14.8090.0000.0000.0000.000
112A116ASP-1-0.814-0.88118.24613.92613.9260.0000.0000.0000.000
113A117SER0-0.015-0.00913.914-0.179-0.1790.0000.0000.0000.000
114A118ALA00.0530.02616.5830.2690.2690.0000.0000.0000.000
115A119PRO00.0440.01713.833-0.187-0.1870.0000.0000.0000.000
116A120VAL00.0430.03111.5910.2860.2860.0000.0000.0000.000
117A121ALA0-0.0030.02113.925-0.143-0.1430.0000.0000.0000.000
118A122ASN00.0230.00317.448-0.246-0.2460.0000.0000.0000.000
119A123TYR00.0340.0019.781-0.171-0.1710.0000.0000.0000.000
120A124THR00.001-0.01914.6170.3280.3280.0000.0000.0000.000
121A125ASN0-0.044-0.02116.025-0.436-0.4360.0000.0000.0000.000
122A126GLU-1-0.866-0.93516.29913.26213.2620.0000.0000.0000.000
123A127LEU0-0.0360.00512.859-0.317-0.3170.0000.0000.0000.000
124A128MET0-0.031-0.02716.439-0.634-0.6340.0000.0000.0000.000
125A129ALA00.0140.00419.803-0.565-0.5650.0000.0000.0000.000
126A130THR0-0.0210.00017.699-0.468-0.4680.0000.0000.0000.000
127A131ARG10.7990.88615.086-16.162-16.1620.0000.0000.0000.000
128A132PHE0-0.045-0.01621.303-0.570-0.5700.0000.0000.0000.000
129A133SER00.005-0.01923.551-0.618-0.6180.0000.0000.0000.000
130A134ASP-1-0.859-0.92620.68712.79912.7990.0000.0000.0000.000
131A135VAL00.010-0.00724.373-0.428-0.4280.0000.0000.0000.000
132A136MET0-0.047-0.01727.060-0.556-0.5560.0000.0000.0000.000
133A137TRP00.0600.03627.142-0.353-0.3530.0000.0000.0000.000
134A138LEU0-0.0120.00328.398-0.357-0.3570.0000.0000.0000.000
135A139ILE00.006-0.00430.251-0.354-0.3540.0000.0000.0000.000
136A140GLU-1-0.932-0.96932.1888.6298.6290.0000.0000.0000.000
137A141GLN0-0.048-0.01130.281-0.469-0.4690.0000.0000.0000.000
138A142ILE0-0.049-0.03233.014-0.241-0.2410.0000.0000.0000.000
139A143MET0-0.048-0.01636.239-0.297-0.2970.0000.0000.0000.000
140A144TRP0-0.0040.00136.727-0.329-0.3290.0000.0000.0000.000
141A145LYS10.8050.89436.005-7.977-7.9770.0000.0000.0000.000
142A146SER00.003-0.02239.0450.0580.0580.0000.0000.0000.000
143A147LEU00.0350.00037.9250.1020.1020.0000.0000.0000.000
144A148ASP-1-0.737-0.83938.9677.1587.1580.0000.0000.0000.000
145A149LYS10.8620.92438.626-6.859-6.8590.0000.0000.0000.000
146A150ARG10.8460.92332.948-8.290-8.2900.0000.0000.0000.000
147A151VAL0-0.001-0.00534.3890.2300.2300.0000.0000.0000.000
148A152ALA0-0.017-0.01235.2730.1530.1530.0000.0000.0000.000
149A153SER00.0210.01031.2210.1300.1300.0000.0000.0000.000
150A154PHE00.0260.01928.1350.0900.0900.0000.0000.0000.000
151A155LEU0-0.031-0.01930.7800.1610.1610.0000.0000.0000.000
152A156LEU0-0.0090.01131.7470.0700.0700.0000.0000.0000.000
153A157GLU-1-0.870-0.90425.87710.92810.9280.0000.0000.0000.000
154A158GLU-1-0.779-0.88826.90710.76010.7600.0000.0000.0000.000
155A159THR0-0.102-0.07327.6870.1450.1450.0000.0000.0000.000
156A160SER0-0.052-0.03126.0680.0460.0460.0000.0000.0000.000
157A161ILE0-0.038-0.00522.4220.3260.3260.0000.0000.0000.000
158A162GLU-1-0.889-0.94323.30311.86411.8640.0000.0000.0000.000
159A163GLY0-0.0080.01525.841-0.094-0.0940.0000.0000.0000.000
160A164THR0-0.033-0.01726.950-0.397-0.3970.0000.0000.0000.000
161A165ASN00.0160.00030.6080.1160.1160.0000.0000.0000.000
162A166GLU-1-0.870-0.92733.2077.7917.7910.0000.0000.0000.000
163A167LEU00.0620.03830.5520.1970.1970.0000.0000.0000.000
164A168LYS10.8620.91631.041-9.095-9.0950.0000.0000.0000.000
165A169ILE00.0560.04329.9520.1260.1260.0000.0000.0000.000
166A170THR0-0.037-0.02932.946-0.172-0.1720.0000.0000.0000.000
167A171HIS00.0440.02135.188-0.021-0.0210.0000.0000.0000.000
168A172GLU-1-0.788-0.89235.9067.7907.7900.0000.0000.0000.000
169A173THR00.0090.00830.3400.1790.1790.0000.0000.0000.000
170A174ILE00.0270.01131.8870.1440.1440.0000.0000.0000.000
171A175ALA0-0.058-0.03433.7490.0380.0380.0000.0000.0000.000
172A176ASN0-0.017-0.01931.841-0.263-0.2630.0000.0000.0000.000
173A177HIS00.0500.06825.6060.1000.1000.0000.0000.0000.000
174A178LEU0-0.010-0.00230.5520.0490.0490.0000.0000.0000.000
175A179GLY00.0640.05333.255-0.111-0.1110.0000.0000.0000.000
176A180SER0-0.081-0.03735.186-0.339-0.3390.0000.0000.0000.000
177A181HIS00.0840.02638.2380.0700.0700.0000.0000.0000.000
178A182ARG10.9130.95139.723-7.011-7.0110.0000.0000.0000.000
179A183GLU-1-0.810-0.88540.6026.4346.4340.0000.0000.0000.000
180A184VAL0-0.011-0.00642.092-0.125-0.1250.0000.0000.0000.000
181A185ILE00.0350.02637.629-0.080-0.0800.0000.0000.0000.000
182A186THR0-0.014-0.03940.818-0.054-0.0540.0000.0000.0000.000
183A187ARG10.8420.90543.174-6.373-6.3730.0000.0000.0000.000
184A188MET00.0040.03041.096-0.130-0.1300.0000.0000.0000.000
185A189LEU00.0280.01438.277-0.037-0.0370.0000.0000.0000.000
186A190ARG10.9200.95342.431-6.488-6.4880.0000.0000.0000.000
187A191TYR0-0.053-0.04145.446-0.056-0.0560.0000.0000.0000.000
188A192PHE00.036-0.00239.066-0.055-0.0550.0000.0000.0000.000
189A193GLN00.0140.02044.2940.1270.1270.0000.0000.0000.000
190A194VAL0-0.054-0.02245.825-0.083-0.0830.0000.0000.0000.000
191A195GLU-1-0.835-0.88846.0346.1646.1640.0000.0000.0000.000
192A196GLY00.0180.01646.4090.0250.0250.0000.0000.0000.000
193A197LEU0-0.007-0.00141.3980.0820.0820.0000.0000.0000.000
194A198VAL0-0.014-0.01039.1710.2130.2130.0000.0000.0000.000
195A199LYS10.9270.97040.802-7.395-7.3950.0000.0000.0000.000
196A200LEU00.0020.00040.8450.1920.1920.0000.0000.0000.000
197A201SER0-0.035-0.02941.062-0.148-0.1480.0000.0000.0000.000
198A202ARG10.9530.95941.007-6.717-6.7170.0000.0000.0000.000
199A203GLY00.0270.02537.8290.0810.0810.0000.0000.0000.000
200A204LYS10.8080.90336.231-7.547-7.5470.0000.0000.0000.000
201A205ILE00.0140.00435.970-0.277-0.2770.0000.0000.0000.000
202A206THR0-0.018-0.00536.2090.1190.1190.0000.0000.0000.000
203A207ILE00.0450.01735.008-0.248-0.2480.0000.0000.0000.000
204A208LEU0-0.076-0.02637.9780.0290.0290.0000.0000.0000.000
205A209ASP-1-0.792-0.89540.8606.9756.9750.0000.0000.0000.000
206A210SER00.0700.01735.2530.0730.0730.0000.0000.0000.000
207A211LYS10.9671.00237.362-6.812-6.8120.0000.0000.0000.000
208A212ARG10.8170.87939.532-6.536-6.5360.0000.0000.0000.000
209A213LEU00.0250.03036.872-0.030-0.0300.0000.0000.0000.000
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