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: 1NJ8Z

Calculation Name: 3VUQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VUQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLX6

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1863533.477351
FMO2-HF: Nuclear repulsion 1791752.005858
FMO2-HF: Total energy -71781.471493
FMO2-MP2: Total energy -71992.904783


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:8:ALA)


Summations of interaction energy for fragment #1(A:8: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.
-3.797-2.083-0.007-0.779-0.9280.001
Interaction energy analysis for fragmet #1(A:8:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.057 / 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].
3A10VAL0-0.027-0.0223.7750.0131.636-0.006-0.774-0.8430.001
4A11LYS10.8970.9185.6420.8730.8730.0000.0000.0000.000
5A12ASP-1-0.831-0.8937.126-0.050-0.0500.0000.0000.0000.000
6A13LYS11.0201.0075.114-4.649-4.558-0.001-0.005-0.0850.000
7A14LYS10.8260.9169.219-0.142-0.1420.0000.0000.0000.000
8A15ARG10.8790.92611.250-0.269-0.2690.0000.0000.0000.000
9A16ALA00.0490.02612.128-0.030-0.0300.0000.0000.0000.000
10A17ILE00.0210.00311.570-0.050-0.0500.0000.0000.0000.000
11A18LEU0-0.0140.01815.002-0.045-0.0450.0000.0000.0000.000
12A19GLU-1-0.820-0.90016.9220.2020.2020.0000.0000.0000.000
13A20ALA00.0040.01017.583-0.025-0.0250.0000.0000.0000.000
14A21THR0-0.030-0.04418.752-0.027-0.0270.0000.0000.0000.000
15A22LEU00.0030.00221.080-0.020-0.0200.0000.0000.0000.000
16A23ALA00.0050.00622.314-0.016-0.0160.0000.0000.0000.000
17A24VAL0-0.019-0.01722.759-0.013-0.0130.0000.0000.0000.000
18A25LEU0-0.032-0.00325.036-0.016-0.0160.0000.0000.0000.000
19A26ARG10.9210.95726.906-0.105-0.1050.0000.0000.0000.000
20A27GLH0-0.055-0.03826.418-0.005-0.0050.0000.0000.0000.000
21A28ARG10.8340.90127.479-0.170-0.1700.0000.0000.0000.000
22A29GLY00.0830.05530.413-0.006-0.0060.0000.0000.0000.000
23A30LEU00.006-0.01427.8880.0110.0110.0000.0000.0000.000
24A31SER00.0050.00429.4580.0050.0050.0000.0000.0000.000
25A32GLY00.0020.00930.3310.0010.0010.0000.0000.0000.000
26A33LEU0-0.0160.00022.9310.0140.0140.0000.0000.0000.000
27A34LYS10.9510.97525.222-0.155-0.1550.0000.0000.0000.000
28A35MET00.0540.01719.1800.0060.0060.0000.0000.0000.000
29A36GLU-1-0.834-0.88319.8430.3010.3010.0000.0000.0000.000
30A37GLU-1-0.697-0.78620.5180.2340.2340.0000.0000.0000.000
31A38VAL00.0000.00017.4210.0160.0160.0000.0000.0000.000
32A39ALA0-0.019-0.01416.0930.0370.0370.0000.0000.0000.000
33A40ARG10.8120.86616.126-0.199-0.1990.0000.0000.0000.000
34A41ARG10.8460.90118.053-0.223-0.2230.0000.0000.0000.000
35A42ALA0-0.0160.01013.921-0.016-0.0160.0000.0000.0000.000
36A43GLU-1-0.943-0.95312.5980.8240.8240.0000.0000.0000.000
37A44VAL0-0.055-0.02310.1450.2620.2620.0000.0000.0000.000
38A45GLY00.0730.03812.736-0.145-0.1450.0000.0000.0000.000
39A46LYS10.9510.95014.580-0.269-0.2690.0000.0000.0000.000
40A47GLY0-0.005-0.00915.942-0.033-0.0330.0000.0000.0000.000
41A48THR00.0310.0109.624-0.033-0.0330.0000.0000.0000.000
42A49ILE00.0330.01711.7670.0040.0040.0000.0000.0000.000
43A50TYR0-0.033-0.02014.067-0.039-0.0390.0000.0000.0000.000
44A51LEU0-0.034-0.0049.630-0.032-0.0320.0000.0000.0000.000
45A52TYR0-0.085-0.0385.8190.1960.1960.0000.0000.0000.000
46A53PHE00.0320.01412.230-0.055-0.0550.0000.0000.0000.000
47A54ARG10.9510.98116.097-0.055-0.0550.0000.0000.0000.000
48A55ASP-1-0.834-0.94918.7930.1200.1200.0000.0000.0000.000
49A56LYS10.8770.93620.411-0.144-0.1440.0000.0000.0000.000
50A57ARG10.7890.85322.320-0.060-0.0600.0000.0000.0000.000
51A58ASP-1-0.817-0.89018.8210.0680.0680.0000.0000.0000.000
52A59LEU0-0.039-0.01717.085-0.006-0.0060.0000.0000.0000.000
53A60LEU0-0.029-0.02319.690-0.004-0.0040.0000.0000.0000.000
54A61LYS10.8420.91022.711-0.028-0.0280.0000.0000.0000.000
55A62ALA00.0470.02318.436-0.010-0.0100.0000.0000.0000.000
56A63LEU0-0.013-0.00120.552-0.008-0.0080.0000.0000.0000.000
57A64VAL00.0060.00421.653-0.009-0.0090.0000.0000.0000.000
58A65GLU-1-0.807-0.86523.0190.0030.0030.0000.0000.0000.000
59A66GLU-1-0.801-0.89417.5800.0330.0330.0000.0000.0000.000
60A67ARG10.7960.87122.221-0.062-0.0620.0000.0000.0000.000
61A68THR00.019-0.02024.876-0.005-0.0050.0000.0000.0000.000
62A69TRP0-0.010-0.00821.479-0.007-0.0070.0000.0000.0000.000
63A70ALA0-0.018-0.01024.111-0.007-0.0070.0000.0000.0000.000
64A71PHE00.0400.02625.898-0.004-0.0040.0000.0000.0000.000
65A72TYR0-0.042-0.06329.279-0.001-0.0010.0000.0000.0000.000
66A73ARG10.9570.99122.5120.0400.0400.0000.0000.0000.000
67A74GLU-1-0.859-0.91528.8160.0150.0150.0000.0000.0000.000
68A75VAL0-0.036-0.01430.939-0.001-0.0010.0000.0000.0000.000
69A76GLU-1-0.874-0.93630.075-0.041-0.0410.0000.0000.0000.000
70A77GLU-1-0.847-0.89130.679-0.017-0.0170.0000.0000.0000.000
71A78VAL00.0080.00332.783-0.001-0.0010.0000.0000.0000.000
72A79VAL0-0.039-0.02535.9110.0000.0000.0000.0000.0000.000
73A80ARG10.7430.83332.1500.0350.0350.0000.0000.0000.000
74A81ARG10.7330.84833.4360.0050.0050.0000.0000.0000.000
75A82LYS10.9530.97537.9560.0250.0250.0000.0000.0000.000
76A83ALA00.0140.00540.7240.0010.0010.0000.0000.0000.000
77A84PRO00.0370.01543.038-0.001-0.0010.0000.0000.0000.000
78A85PHE00.0660.03244.9210.0020.0020.0000.0000.0000.000
79A86PHE00.025-0.00545.0470.0010.0010.0000.0000.0000.000
80A87VAL00.0180.01642.3890.0020.0020.0000.0000.0000.000
81A88ARG10.7810.86939.9950.0170.0170.0000.0000.0000.000
82A89LEU0-0.012-0.00441.1280.0010.0010.0000.0000.0000.000
83A90GLU-1-0.779-0.89043.0840.0110.0110.0000.0000.0000.000
84A91GLU-1-0.830-0.90337.5740.0030.0030.0000.0000.0000.000
85A92VAL0-0.012-0.01037.9150.0020.0020.0000.0000.0000.000
86A93LEU00.000-0.00239.1550.0020.0020.0000.0000.0000.000
87A94ARG10.7730.84539.534-0.013-0.0130.0000.0000.0000.000
88A95ARG10.8020.88332.898-0.006-0.0060.0000.0000.0000.000
89A96ARG10.8430.94236.420-0.008-0.0080.0000.0000.0000.000
90A97LEU00.0210.00838.2660.0030.0030.0000.0000.0000.000
91A98ALA00.0390.02435.9510.0030.0030.0000.0000.0000.000
92A99TRP0-0.005-0.00428.9390.0060.0060.0000.0000.0000.000
93A100VAL0-0.019-0.00934.8570.0030.0030.0000.0000.0000.000
94A101GLN0-0.042-0.01837.4950.0050.0050.0000.0000.0000.000
95A102GLU-1-0.752-0.83529.5060.0660.0660.0000.0000.0000.000
96A103TRP0-0.021-0.02030.1890.0060.0060.0000.0000.0000.000
97A104ARG10.8560.90734.222-0.027-0.0270.0000.0000.0000.000
98A105GLY00.0070.02435.7910.0010.0010.0000.0000.0000.000
99A106LEU0-0.054-0.02527.9890.0080.0080.0000.0000.0000.000
100A107TRP00.006-0.03325.2140.0050.0050.0000.0000.0000.000
101A108ALA0-0.0100.00831.062-0.002-0.0020.0000.0000.0000.000
102A109ALA0-0.014-0.00232.875-0.002-0.0020.0000.0000.0000.000
103A110VAL0-0.006-0.01926.5280.0010.0010.0000.0000.0000.000
104A111ALA00.002-0.00428.9700.0010.0010.0000.0000.0000.000
105A112ARG10.8620.91830.334-0.059-0.0590.0000.0000.0000.000
106A113GLU-1-0.818-0.89229.1230.0650.0650.0000.0000.0000.000
107A114ALA0-0.055-0.01725.9950.0040.0040.0000.0000.0000.000
108A115MET0-0.039-0.01926.858-0.006-0.0060.0000.0000.0000.000
109A116ASP-1-0.781-0.85729.4210.0450.0450.0000.0000.0000.000
110A117ASP-1-0.838-0.91432.1620.0110.0110.0000.0000.0000.000
111A118PRO0-0.0030.00832.070-0.004-0.0040.0000.0000.0000.000
112A119THR0-0.002-0.01233.113-0.002-0.0020.0000.0000.0000.000
113A120PRO0-0.049-0.03733.627-0.003-0.0030.0000.0000.0000.000
114A121TRP00.004-0.01027.241-0.001-0.0010.0000.0000.0000.000
115A122LEU00.0200.00632.614-0.002-0.0020.0000.0000.0000.000
116A123LYS10.9220.97334.871-0.005-0.0050.0000.0000.0000.000
117A124GLY00.0300.02134.143-0.002-0.0020.0000.0000.0000.000
118A125LEU00.0170.01329.895-0.004-0.0040.0000.0000.0000.000
119A126HIS00.0130.02333.9950.0000.0000.0000.0000.0000.000
120A127GLU-1-0.777-0.87937.257-0.016-0.0160.0000.0000.0000.000
121A128HIS0-0.044-0.01531.225-0.004-0.0040.0000.0000.0000.000
122A129TYR00.0180.00835.577-0.001-0.0010.0000.0000.0000.000
123A130LEU0-0.0060.00637.428-0.001-0.0010.0000.0000.0000.000
124A131ARG10.8860.92434.8170.0190.0190.0000.0000.0000.000
125A132LEU00.0090.01533.598-0.001-0.0010.0000.0000.0000.000
126A133LEU00.0360.02038.2150.0000.0000.0000.0000.0000.000
127A134GLU-1-0.848-0.92341.641-0.016-0.0160.0000.0000.0000.000
128A135GLU-1-0.861-0.88737.018-0.029-0.0290.0000.0000.0000.000
129A136LEU00.0320.02041.004-0.001-0.0010.0000.0000.0000.000
130A137LEU0-0.028-0.01842.4740.0000.0000.0000.0000.0000.000
131A138ARG10.8690.92642.5360.0190.0190.0000.0000.0000.000
132A139SER0-0.0120.00142.871-0.001-0.0010.0000.0000.0000.000
133A140GLY00.0720.02844.9960.0000.0000.0000.0000.0000.000
134A141GLN0-0.105-0.06447.871-0.001-0.0010.0000.0000.0000.000
135A142SER0-0.094-0.05347.0850.0000.0000.0000.0000.0000.000
136A143GLU-1-0.792-0.87845.636-0.015-0.0150.0000.0000.0000.000
137A144GLY0-0.0100.00749.9330.0010.0010.0000.0000.0000.000
138A145ALA0-0.049-0.01449.9140.0010.0010.0000.0000.0000.000
139A146VAL0-0.012-0.00148.9980.0010.0010.0000.0000.0000.000
140A147ARG11.0000.98952.2810.0030.0030.0000.0000.0000.000
141A148THR00.0720.02253.1340.0000.0000.0000.0000.0000.000
142A149GLY00.0040.01754.222-0.001-0.0010.0000.0000.0000.000
143A150LEU0-0.049-0.00652.6590.0010.0010.0000.0000.0000.000
144A151SER00.0550.02250.836-0.001-0.0010.0000.0000.0000.000
145A152PRO00.0400.02346.4740.0010.0010.0000.0000.0000.000
146A153ARG10.8530.90941.2300.0130.0130.0000.0000.0000.000
147A154ALA00.0090.00446.9780.0010.0010.0000.0000.0000.000
148A155THR00.017-0.00949.0560.0020.0020.0000.0000.0000.000
149A156ALA00.0100.00443.7550.0010.0010.0000.0000.0000.000
150A157ALA0-0.008-0.01344.9820.0020.0020.0000.0000.0000.000
151A158VAL0-0.021-0.00646.5320.0020.0020.0000.0000.0000.000
152A159ILE00.0170.00644.0880.0020.0020.0000.0000.0000.000
153A160ALA0-0.020-0.01642.2250.0020.0020.0000.0000.0000.000
154A161ALA0-0.021-0.00143.0570.0020.0020.0000.0000.0000.000
155A162MET0-0.0190.01143.8670.0030.0030.0000.0000.0000.000
156A163GLY00.0460.00242.2890.0000.0000.0000.0000.0000.000
157A164CYS0-0.063-0.03342.8720.0020.0020.0000.0000.0000.000
158A165THR00.0390.01845.6290.0000.0000.0000.0000.0000.000
159A166PRO00.0160.02445.9870.0000.0000.0000.0000.0000.000
160A167SER0-0.031-0.02347.0870.0010.0010.0000.0000.0000.000
161A168LEU00.0170.00448.585-0.001-0.0010.0000.0000.0000.000
162A169GLU-1-0.849-0.92743.4940.0310.0310.0000.0000.0000.000
163A170VAL0-0.036-0.00945.3120.0000.0000.0000.0000.0000.000
164A171GLU-1-0.826-0.88444.2050.0190.0190.0000.0000.0000.000
165A172ALA00.0750.04447.548-0.001-0.0010.0000.0000.0000.000
166A173TYR0-0.015-0.00447.050-0.001-0.0010.0000.0000.0000.000
167A174LEU00.0080.00043.839-0.001-0.0010.0000.0000.0000.000
168A175GLU-1-0.901-0.95748.0460.0100.0100.0000.0000.0000.000
169A176HIS0-0.008-0.00750.722-0.002-0.0020.0000.0000.0000.000
170A177LEU0-0.025-0.00746.935-0.001-0.0010.0000.0000.0000.000
171A178MET0-0.014-0.00747.394-0.002-0.0020.0000.0000.0000.000
172A179GLU-1-0.827-0.89150.3290.0010.0010.0000.0000.0000.000
173A180VAL00.007-0.00153.652-0.001-0.0010.0000.0000.0000.000
174A181LEU0-0.048-0.02748.081-0.001-0.0010.0000.0000.0000.000
175A182ARG10.7700.88851.771-0.003-0.0030.0000.0000.0000.000
176A183LYS10.8780.93854.015-0.001-0.0010.0000.0000.0000.000
177A184GLY0-0.0140.01256.4740.0000.0000.0000.0000.0000.000
178A185VAL0-0.023-0.03558.0540.0010.0010.0000.0000.0000.000
179A186GLU-1-0.941-0.95660.7900.0020.0020.0000.0000.0000.000
180A187PRO0-0.037-0.01263.725-0.001-0.0010.0000.0000.0000.000