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

tag_button

FMODB ID: 1NNJZ

Calculation Name: 3QV0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QV0

Chain ID: A

ChEMBL ID:

UniProt ID: P40513

Base Structure: X-ray

Registration Date: 2023-09-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1928167.312678
FMO2-HF: Nuclear repulsion 1854032.305312
FMO2-HF: Total energy -74135.007366
FMO2-MP2: Total energy -74354.483846


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:49:GLU)


Summations of interaction energy for fragment #1(A:49: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.
52.97152.53916.011-7.656-7.9260.071
Interaction energy analysis for fragmet #1(A:49:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.917 / q_NPA : -0.967
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].
3A51GLN00.0020.0011.703-37.189-39.83415.713-6.867-6.2020.069
4A52ARG11.0021.0032.725-50.424-48.6660.295-0.680-1.3740.002
5A53VAL0-0.0170.0003.525-5.929-5.4740.003-0.109-0.3500.000
6A54GLY00.0390.0155.984-3.740-3.7400.0000.0000.0000.000
7A55ASP-1-0.914-0.9677.28733.96433.9640.0000.0000.0000.000
8A56ILE0-0.031-0.0107.056-2.739-2.7390.0000.0000.0000.000
9A57LEU00.0460.02910.003-2.246-2.2460.0000.0000.0000.000
10A58GLN0-0.037-0.00711.678-3.210-3.2100.0000.0000.0000.000
11A59SER0-0.093-0.05613.272-0.949-0.9490.0000.0000.0000.000
12A60GLU-1-0.821-0.90014.17515.94515.9450.0000.0000.0000.000
13A61LEU0-0.067-0.04215.464-1.029-1.0290.0000.0000.0000.000
14A62LYS10.8060.90216.598-18.489-18.4890.0000.0000.0000.000
15A63ILE00.0430.01418.169-0.581-0.5810.0000.0000.0000.000
16A64GLU-1-0.842-0.92219.86212.61812.6180.0000.0000.0000.000
17A65LYS10.8140.90920.347-15.206-15.2060.0000.0000.0000.000
18A66GLU-1-0.999-0.98424.16111.86611.8660.0000.0000.0000.000
19A67THR0-0.037-0.03926.180-0.001-0.0010.0000.0000.0000.000
20A68LEU00.0480.02424.843-0.272-0.2720.0000.0000.0000.000
21A69PRO00.0010.01526.977-0.202-0.2020.0000.0000.0000.000
22A70GLU-1-0.941-0.96429.6339.2209.2200.0000.0000.0000.000
23A71SER0-0.059-0.03232.991-0.011-0.0110.0000.0000.0000.000
24A72THR0-0.019-0.01732.508-0.384-0.3840.0000.0000.0000.000
25A73SER0-0.042-0.03435.060-0.017-0.0170.0000.0000.0000.000
26A74LEU00.0280.00934.157-0.082-0.0820.0000.0000.0000.000
27A75ASP-1-0.890-0.92938.0477.5417.5410.0000.0000.0000.000
28A76SER00.0480.00940.251-0.236-0.2360.0000.0000.0000.000
29A77PHE0-0.022-0.00934.595-0.155-0.1550.0000.0000.0000.000
30A78ASN0-0.039-0.02240.470-0.094-0.0940.0000.0000.0000.000
31A79ASP-1-0.899-0.95243.0736.5186.5180.0000.0000.0000.000
32A80PHE0-0.016-0.00142.842-0.183-0.1830.0000.0000.0000.000
33A81LEU0-0.002-0.00940.346-0.143-0.1430.0000.0000.0000.000
34A82ASN0-0.019-0.01144.900-0.195-0.1950.0000.0000.0000.000
35A83LYS10.7680.87848.032-6.284-6.2840.0000.0000.0000.000
36A84TYR0-0.050-0.03747.496-0.203-0.2030.0000.0000.0000.000
37A85LYS10.8300.90749.604-5.722-5.7220.0000.0000.0000.000
38A86PHE00.0050.00044.341-0.046-0.0460.0000.0000.0000.000
39A87SER0-0.050-0.01943.8720.0050.0050.0000.0000.0000.000
40A88LEU00.000-0.00836.668-0.058-0.0580.0000.0000.0000.000
41A89VAL0-0.044-0.01737.4420.0230.0230.0000.0000.0000.000
42A90GLU-1-0.732-0.82731.8279.5379.5370.0000.0000.0000.000
43A91THR0-0.086-0.07031.149-0.147-0.1470.0000.0000.0000.000
44A92PRO00.0000.00327.8150.1580.1580.0000.0000.0000.000
45A93GLY0-0.080-0.04025.0280.0050.0050.0000.0000.0000.000
46A94LYS10.7790.87526.059-8.790-8.7900.0000.0000.0000.000
47A95ASN0-0.019-0.02126.5420.2240.2240.0000.0000.0000.000
48A96GLU-1-0.826-0.88628.8248.3218.3210.0000.0000.0000.000
49A97ALA00.0230.02032.6060.1370.1370.0000.0000.0000.000
50A98GLU-1-0.801-0.89235.0207.1357.1350.0000.0000.0000.000
51A99ILE0-0.026-0.00438.8140.0500.0500.0000.0000.0000.000
52A100VAL0-0.019-0.01341.691-0.134-0.1340.0000.0000.0000.000
53A101ARG10.8430.92545.185-6.114-6.1140.0000.0000.0000.000
54A102ARG10.7730.85348.666-5.788-5.7880.0000.0000.0000.000
55A103THR0-0.015-0.02152.356-0.021-0.0210.0000.0000.0000.000
56A104GLU-1-0.879-0.94354.8985.3705.3700.0000.0000.0000.000
57A105SER0-0.056-0.04358.099-0.099-0.0990.0000.0000.0000.000
58A106GLY0-0.031-0.01357.503-0.053-0.0530.0000.0000.0000.000
59A107GLU-1-0.769-0.81653.9785.5075.5070.0000.0000.0000.000
60A108THR0-0.033-0.03048.8660.0370.0370.0000.0000.0000.000
61A109VAL0-0.011-0.00147.6060.0150.0150.0000.0000.0000.000
62A110HIS10.8140.89243.971-6.627-6.6270.0000.0000.0000.000
63A111VAL00.0350.01541.155-0.103-0.1030.0000.0000.0000.000
64A112PHE00.0170.01037.8710.0900.0900.0000.0000.0000.000
65A113PHE00.0410.00734.380-0.126-0.1260.0000.0000.0000.000
66A114ASP-1-0.792-0.89129.8939.8699.8690.0000.0000.0000.000
67A115VAL00.0150.00128.265-0.027-0.0270.0000.0000.0000.000
68A116ALA0-0.0030.00525.9210.1140.1140.0000.0000.0000.000
69A117GLN0-0.083-0.03027.6510.0540.0540.0000.0000.0000.000
70A118ILE0-0.048-0.02930.291-0.235-0.2350.0000.0000.0000.000
71A119ALA0-0.073-0.06425.442-0.077-0.0770.0000.0000.0000.000
72A150PHE0-0.069-0.05235.7580.0010.0010.0000.0000.0000.000
73A151ALA00.0020.02134.4560.1990.1990.0000.0000.0000.000
74A152ASN0-0.032-0.01935.957-0.088-0.0880.0000.0000.0000.000
75A153VAL0-0.011-0.00837.1590.1620.1620.0000.0000.0000.000
76A154ASN0-0.0060.00439.848-0.310-0.3100.0000.0000.0000.000
77A155VAL00.0090.00742.0360.0510.0510.0000.0000.0000.000
78A156VAL0-0.007-0.00644.409-0.126-0.1260.0000.0000.0000.000
79A157ILE0-0.0030.00147.0790.0150.0150.0000.0000.0000.000
80A158SER00.0180.00350.590-0.027-0.0270.0000.0000.0000.000
81A159LYS10.9600.97852.710-5.262-5.2620.0000.0000.0000.000
82A160GLU-1-0.762-0.81954.5165.6765.6760.0000.0000.0000.000
83A161SER0-0.008-0.02950.8260.1230.1230.0000.0000.0000.000
84A162ALA0-0.017-0.01150.8960.0020.0020.0000.0000.0000.000
85A163SER0-0.060-0.05551.9690.0760.0760.0000.0000.0000.000
86A164GLU-1-0.885-0.90754.6875.2725.2720.0000.0000.0000.000
87A165PRO0-0.051-0.03153.9860.0980.0980.0000.0000.0000.000
88A166ALA0-0.028-0.01150.358-0.037-0.0370.0000.0000.0000.000
89A167VAL0-0.039-0.01251.2800.0120.0120.0000.0000.0000.000
90A168SER0-0.043-0.01745.2070.0750.0750.0000.0000.0000.000
91A169PHE00.030-0.00446.716-0.151-0.1510.0000.0000.0000.000
92A170GLU-1-0.785-0.86640.8557.4547.4540.0000.0000.0000.000
93A171LEU0-0.020-0.00842.811-0.164-0.1640.0000.0000.0000.000
94A172LEU00.0310.01439.8450.2140.2140.0000.0000.0000.000
95A173MET00.0030.01037.518-0.192-0.1920.0000.0000.0000.000
96A174ASN0-0.002-0.00638.8050.3570.3570.0000.0000.0000.000
97A175LEU00.0120.00033.483-0.076-0.0760.0000.0000.0000.000
98A176GLN0-0.047-0.01636.3820.2270.2270.0000.0000.0000.000
99A177GLU-1-0.969-0.99239.1956.7036.7030.0000.0000.0000.000
100A178GLY00.0200.02441.351-0.146-0.1460.0000.0000.0000.000
101A179SER00.007-0.00442.602-0.117-0.1170.0000.0000.0000.000
102A180PHE0-0.012-0.02541.8090.1700.1700.0000.0000.0000.000
103A181TYR00.0070.01044.183-0.169-0.1690.0000.0000.0000.000
104A182VAL0-0.0090.00045.3700.1460.1460.0000.0000.0000.000
105A183ASP-1-0.892-0.92144.1576.6346.6340.0000.0000.0000.000
106A184SER0-0.055-0.05245.654-0.133-0.1330.0000.0000.0000.000
107A185ALA00.0130.00147.8290.0590.0590.0000.0000.0000.000
108A186THR0-0.033-0.00148.519-0.072-0.0720.0000.0000.0000.000
109A187PRO0-0.022-0.00250.3920.0600.0600.0000.0000.0000.000
110A188TYR00.0790.03745.509-0.069-0.0690.0000.0000.0000.000
111A189PRO0-0.012-0.02351.249-0.070-0.0700.0000.0000.0000.000
112A190SER00.0110.00751.102-0.044-0.0440.0000.0000.0000.000
113A191VAL00.0560.01947.3170.0790.0790.0000.0000.0000.000
114A192ASP-1-0.885-0.91946.2846.7376.7370.0000.0000.0000.000
115A193ALA0-0.003-0.00745.9550.1420.1420.0000.0000.0000.000
116A194ALA0-0.020-0.00746.2970.0780.0780.0000.0000.0000.000
117A195LEU00.0070.01342.4290.0930.0930.0000.0000.0000.000
118A196ASN0-0.057-0.02441.3460.3590.3590.0000.0000.0000.000
119A197GLN00.0390.01235.9280.1390.1390.0000.0000.0000.000
120A198SER0-0.066-0.03237.7090.1650.1650.0000.0000.0000.000
121A199ALA00.0380.00737.901-0.058-0.0580.0000.0000.0000.000
122A200GLU-1-0.899-0.95739.4806.9626.9620.0000.0000.0000.000
123A201ALA0-0.0310.00942.642-0.177-0.1770.0000.0000.0000.000
124A202GLU-1-0.762-0.85438.5367.3427.3420.0000.0000.0000.000
125A203ILE00.0180.01340.575-0.109-0.1090.0000.0000.0000.000
126A204THR0-0.091-0.06243.302-0.207-0.2070.0000.0000.0000.000
127A205ARG10.7270.82240.581-7.284-7.2840.0000.0000.0000.000
128A206GLU-1-0.965-0.98639.9837.2477.2470.0000.0000.0000.000
129A207LEU0-0.066-0.03444.495-0.126-0.1260.0000.0000.0000.000
130A208VAL0-0.066-0.01547.902-0.178-0.1780.0000.0000.0000.000
131A209TYR0-0.024-0.01349.0780.0420.0420.0000.0000.0000.000
132A210HIS10.8710.91846.570-6.379-6.3790.0000.0000.0000.000
133A211GLY00.0630.04150.1630.0140.0140.0000.0000.0000.000
134A212PRO0-0.075-0.03651.9320.0570.0570.0000.0000.0000.000
135A213PRO00.0500.01349.6620.0500.0500.0000.0000.0000.000
136A214PHE00.0580.03749.938-0.137-0.1370.0000.0000.0000.000
137A215SER00.0310.00451.154-0.062-0.0620.0000.0000.0000.000
138A216ASN0-0.100-0.04752.857-0.028-0.0280.0000.0000.0000.000
139A217LEU0-0.049-0.00954.264-0.114-0.1140.0000.0000.0000.000
140A218ASP-1-0.883-0.95257.2514.8934.8930.0000.0000.0000.000
141A219GLU-1-0.906-0.95458.6095.1245.1240.0000.0000.0000.000
142A220GLU-1-0.898-0.93959.0224.9474.9470.0000.0000.0000.000
143A221LEU0-0.072-0.01857.8940.0380.0380.0000.0000.0000.000
144A222GLN0-0.042-0.02554.1470.1590.1590.0000.0000.0000.000
145A223GLU-1-0.852-0.92855.3755.2605.2600.0000.0000.0000.000
146A224SER0-0.077-0.05856.8310.0560.0560.0000.0000.0000.000
147A225LEU0-0.067-0.03654.0910.0380.0380.0000.0000.0000.000
148A226GLU-1-0.883-0.94950.9985.9695.9690.0000.0000.0000.000
149A227ALA00.0450.02653.1320.0680.0680.0000.0000.0000.000
150A228TYR0-0.104-0.06553.6660.0180.0180.0000.0000.0000.000
151A229LEU00.0300.01149.0780.0440.0440.0000.0000.0000.000
152A230GLU-1-0.919-0.94651.1485.7655.7650.0000.0000.0000.000
153A231SER0-0.101-0.05252.2790.0090.0090.0000.0000.0000.000
154A232ARG10.7870.85351.302-5.519-5.5190.0000.0000.0000.000
155A233GLY0-0.025-0.00849.2580.0740.0740.0000.0000.0000.000
156A234VAL0-0.026-0.00346.1100.1400.1400.0000.0000.0000.000
157A235ASN00.0460.01147.1750.0210.0210.0000.0000.0000.000
158A236GLU-1-0.830-0.92745.4426.4016.4010.0000.0000.0000.000
159A237GLU-1-0.813-0.84844.2106.4486.4480.0000.0000.0000.000
160A238LEU0-0.0080.00942.8320.1750.1750.0000.0000.0000.000
161A239ALA00.0540.02341.0450.1940.1940.0000.0000.0000.000
162A240SER0-0.041-0.02339.5130.2380.2380.0000.0000.0000.000
163A241PHE0-0.016-0.01138.7500.2300.2300.0000.0000.0000.000
164A242ILE00.0150.00436.7700.2100.2100.0000.0000.0000.000
165A243SER0-0.0030.00635.1280.2900.2900.0000.0000.0000.000
166A244ALA00.0350.01533.8200.2800.2800.0000.0000.0000.000
167A245TYR0-0.071-0.06533.5790.2240.2240.0000.0000.0000.000
168A246SER00.001-0.02231.3160.2770.2770.0000.0000.0000.000
169A247GLU-1-0.888-0.91929.3449.7639.7630.0000.0000.0000.000
170A248PHE0-0.004-0.00428.5180.4050.4050.0000.0000.0000.000
171A249LYS10.7770.89028.732-9.587-9.5870.0000.0000.0000.000
172A250GLU-1-0.858-0.89023.90512.26012.2600.0000.0000.0000.000
173A251ASN00.0610.02723.7100.2630.2630.0000.0000.0000.000
174A252ASN0-0.042-0.03223.5540.6940.6940.0000.0000.0000.000
175A253GLU-1-0.777-0.87023.73411.70311.7030.0000.0000.0000.000
176A254TYR0-0.031-0.02316.4501.0481.0480.0000.0000.0000.000
177A255ILE00.0200.00419.0741.1061.1060.0000.0000.0000.000
178A256SER0-0.055-0.04519.7080.6790.6790.0000.0000.0000.000
179A257TRP0-0.034-0.02613.3180.7910.7910.0000.0000.0000.000
180A258LEU00.0290.01714.4631.2741.2740.0000.0000.0000.000
181A259GLU-1-0.815-0.89315.03217.89617.8960.0000.0000.0000.000
182A260LYS10.8910.94316.972-13.145-13.1450.0000.0000.0000.000
183A261MET00.0120.01210.8640.9010.9010.0000.0000.0000.000
184A262LYS10.8570.91811.826-16.872-16.8720.0000.0000.0000.000
185A263LYS10.8640.93011.805-14.520-14.5200.0000.0000.0000.000
186A264PHE0-0.042-0.0029.656-0.040-0.0400.0000.0000.0000.000
187A265PHE0-0.003-0.0156.3111.4681.4680.0000.0000.0000.000
188A266HIS0-0.050-0.0057.5393.6703.6700.0000.0000.0000.000