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: R9N88

Calculation Name: 3NB6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NB6

Chain ID: A

ChEMBL ID:

UniProt ID: O66874

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2062694.082031
FMO2-HF: Nuclear repulsion 1990443.547555
FMO2-HF: Total energy -72250.534476
FMO2-MP2: Total energy -72467.352637


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:61:GLN)


Summations of interaction energy for fragment #1(A:61:GLN)
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.
-32.851-44.49535.688-12.27-11.7750
Interaction energy analysis for fragmet #1(A:61:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.014 / q_NPA : 0.001
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].
3A63ARG10.9050.9291.769-20.437-35.66331.649-9.980-6.4440.024
4A64PHE00.0670.0345.415-0.051-0.0510.0000.0000.0000.000
5A65TYR0-0.023-0.0197.764-1.042-1.0420.0000.0000.0000.000
6A66VAL0-0.060-0.0329.8820.5560.5560.0000.0000.0000.000
7A67SER0-0.010-0.04013.261-0.228-0.2280.0000.0000.0000.000
8A68ILE00.007-0.04215.5390.0270.0270.0000.0000.0000.000
9A69ASP-1-0.878-0.90016.909-0.842-0.8420.0000.0000.0000.000
10A70LYS10.9000.96816.2560.8940.8940.0000.0000.0000.000
11A71ILE0-0.046-0.01813.843-0.051-0.0510.0000.0000.0000.000
12A72PRO00.0250.02617.9870.0620.0620.0000.0000.0000.000
13A73GLU-1-0.846-0.94219.987-0.715-0.7150.0000.0000.0000.000
14A74HIS00.0340.01722.371-0.043-0.0430.0000.0000.0000.000
15A75VAL00.0180.00415.942-0.022-0.0220.0000.0000.0000.000
16A76ILE00.0030.00117.609-0.092-0.0920.0000.0000.0000.000
17A77ASN00.0330.01018.729-0.067-0.0670.0000.0000.0000.000
18A78ALA00.0250.02019.3460.0370.0370.0000.0000.0000.000
19A79PHE0-0.021-0.03113.028-0.014-0.0140.0000.0000.0000.000
20A80VAL0-0.0080.00917.8550.0190.0190.0000.0000.0000.000
21A81ALA00.0200.00820.1650.0540.0540.0000.0000.0000.000
22A82THR0-0.095-0.04818.9970.1070.1070.0000.0000.0000.000
23A83GLU-1-0.927-0.98115.697-1.079-1.0790.0000.0000.0000.000
24A84ASP-1-0.768-0.86618.410-0.842-0.8420.0000.0000.0000.000
25A85ARG10.9550.97920.3310.5000.5000.0000.0000.0000.000
26A86ASN00.0220.00623.5080.0360.0360.0000.0000.0000.000
27A87PHE0-0.0220.01317.0510.0090.0090.0000.0000.0000.000
28A88TRP00.021-0.01920.667-0.022-0.0220.0000.0000.0000.000
29A89HIS00.0070.00723.6900.0310.0310.0000.0000.0000.000
30A90HIS0-0.063-0.00719.6040.0820.0820.0000.0000.0000.000
31A91PHE00.0470.01523.581-0.021-0.0210.0000.0000.0000.000
32A92GLY00.0210.00219.5490.0070.0070.0000.0000.0000.000
33A93ILE0-0.055-0.02119.640-0.032-0.0320.0000.0000.0000.000
34A94ASP-1-0.774-0.91222.281-0.497-0.4970.0000.0000.0000.000
35A95PRO00.0200.00324.3910.0150.0150.0000.0000.0000.000
36A96VAL00.0770.03727.6340.0180.0180.0000.0000.0000.000
37A97ALA00.0020.01724.1910.0180.0180.0000.0000.0000.000
38A98ILE0-0.004-0.01224.1570.0060.0060.0000.0000.0000.000
39A99VAL00.0250.01726.3490.0250.0250.0000.0000.0000.000
40A100ARG10.9310.95028.7190.3270.3270.0000.0000.0000.000
41A101ALA0-0.002-0.03525.3390.0040.0040.0000.0000.0000.000
42A102ALA00.009-0.00127.3570.0160.0160.0000.0000.0000.000
43A103ILE0-0.007-0.01630.0420.0190.0190.0000.0000.0000.000
44A104VAL0-0.083-0.02929.4980.0170.0170.0000.0000.0000.000
45A105ASN00.0370.01928.2440.0090.0090.0000.0000.0000.000
46A106TYR00.0390.00430.7000.0040.0040.0000.0000.0000.000
47A107ARG10.9010.97234.1300.2140.2140.0000.0000.0000.000
48A108ALA0-0.008-0.00531.233-0.001-0.0010.0000.0000.0000.000
49A109GLY00.0370.03531.993-0.004-0.0040.0000.0000.0000.000
50A110ARG10.9110.94229.3670.1520.1520.0000.0000.0000.000
51A111ILE0-0.050-0.02524.578-0.001-0.0010.0000.0000.0000.000
52A112ALA00.0250.02026.5740.0030.0030.0000.0000.0000.000
53A113GLN0-0.0670.01424.423-0.011-0.0110.0000.0000.0000.000
54A114GLY00.0660.03120.6390.0150.0150.0000.0000.0000.000
55A115GLY0-0.030-0.01221.1530.0160.0160.0000.0000.0000.000
56A116SER0-0.108-0.05516.6960.0040.0040.0000.0000.0000.000
57A117THR00.0280.02618.081-0.084-0.0840.0000.0000.0000.000
58A118ILE00.018-0.01213.604-0.063-0.0630.0000.0000.0000.000
59A119THR0-0.008-0.01113.402-0.256-0.2560.0000.0000.0000.000
60A120GLN00.0390.02013.838-0.044-0.0440.0000.0000.0000.000
61A121GLN0-0.073-0.01711.370-0.161-0.1610.0000.0000.0000.000
62A122LEU00.0280.0238.421-0.211-0.2110.0000.0000.0000.000
63A123ALA00.0180.0019.107-0.112-0.1120.0000.0000.0000.000
64A124LYS10.8820.95410.4771.2201.2200.0000.0000.0000.000
65A125ASN0-0.075-0.0485.3810.1500.1500.0000.0000.0000.000
66A126LEU0-0.0030.0095.921-0.035-0.0350.0000.0000.0000.000
67A127PHE0-0.085-0.0358.2660.4210.4210.0000.0000.0000.000
68A128LEU00.0390.0267.1480.2570.2570.0000.0000.0000.000
69A129THR00.0070.0108.3730.4180.4180.0000.0000.0000.000
70A130ARG10.9930.9799.866-1.264-1.2640.0000.0000.0000.000
71A131GLU-1-0.891-0.93811.7360.2250.2250.0000.0000.0000.000
72A132ARG10.7900.83114.5890.2250.2250.0000.0000.0000.000
73A133THR00.0890.04217.009-0.063-0.0630.0000.0000.0000.000
74A134LEU00.0550.02519.790-0.049-0.0490.0000.0000.0000.000
75A135GLU-1-0.864-0.94420.9920.0020.0020.0000.0000.0000.000
76A136ARG10.8530.94712.461-0.268-0.2680.0000.0000.0000.000
77A137LYS10.9320.97017.1820.1910.1910.0000.0000.0000.000
78A138ILE00.0190.01918.461-0.064-0.0640.0000.0000.0000.000
79A139LYS10.9590.97717.306-0.085-0.0850.0000.0000.0000.000
80A140GLU-1-0.751-0.85513.723-0.492-0.4920.0000.0000.0000.000
81A141ALA00.0110.00616.103-0.098-0.0980.0000.0000.0000.000
82A142LEU0-0.005-0.00819.173-0.021-0.0210.0000.0000.0000.000
83A143LEU00.0000.00813.048-0.012-0.0120.0000.0000.0000.000
84A144ALA00.028-0.00416.212-0.054-0.0540.0000.0000.0000.000
85A145ILE00.0280.02217.073-0.018-0.0180.0000.0000.0000.000
86A146LYS10.9250.97019.0020.3940.3940.0000.0000.0000.000
87A147ILE0-0.005-0.00213.5550.0050.0050.0000.0000.0000.000
88A148GLU-1-0.783-0.88117.632-0.845-0.8450.0000.0000.0000.000
89A149ARG10.8660.95020.1400.3880.3880.0000.0000.0000.000
90A150THR0-0.094-0.05318.9670.0690.0690.0000.0000.0000.000
91A151PHE0-0.025-0.01616.276-0.013-0.0130.0000.0000.0000.000
92A152ASP-1-0.810-0.90619.568-0.813-0.8130.0000.0000.0000.000
93A153LYS10.8410.89718.9770.6430.6430.0000.0000.0000.000
94A154LYS11.0171.00618.1200.6410.6410.0000.0000.0000.000
95A155LYS10.9320.98315.1061.1061.1060.0000.0000.0000.000
96A156ILE0-0.007-0.00114.381-0.288-0.2880.0000.0000.0000.000
97A157MET0-0.0050.00413.337-0.387-0.3870.0000.0000.0000.000
98A158GLU-1-0.785-0.85612.998-1.819-1.8190.0000.0000.0000.000
99A159LEU00.0040.00410.060-0.465-0.4650.0000.0000.0000.000
100A160TYR0-0.036-0.0448.595-1.090-1.0900.0000.0000.0000.000
101A161LEU00.026-0.0018.881-0.768-0.7680.0000.0000.0000.000
102A162ASN0-0.039-0.0207.667-0.109-0.1090.0000.0000.0000.000
103A163GLN0-0.063-0.0174.181-2.986-2.920-0.001-0.009-0.0560.000
104A164ILE0-0.0060.0074.409-2.773-2.611-0.001-0.016-0.1440.000
105A165TYR0-0.0050.0165.2750.1980.1980.0000.0000.0000.000
106A166LEU0-0.003-0.0047.1080.9840.9840.0000.0000.0000.000
107A167GLY00.0170.0038.9920.4980.4980.0000.0000.0000.000
108A168SER00.0400.0169.618-0.150-0.1500.0000.0000.0000.000
109A169GLY00.0040.0096.4520.2050.2050.0000.0000.0000.000
110A170ALA00.0070.0125.461-0.008-0.0080.0000.0000.0000.000
111A171TYR0-0.059-0.0482.691-5.754-2.3954.042-2.255-5.147-0.024
112A172GLY00.0460.0374.8020.1150.110-0.001-0.0100.0160.000
113A173VAL00.017-0.0127.6660.6790.6790.0000.0000.0000.000
114A174GLU-1-0.809-0.9029.523-0.777-0.7770.0000.0000.0000.000
115A175ALA00.0250.0006.1820.4170.4170.0000.0000.0000.000
116A176ALA00.0020.0008.1850.4530.4530.0000.0000.0000.000
117A177ALA00.0140.01310.6470.2870.2870.0000.0000.0000.000
118A178GLN0-0.038-0.00410.6240.3620.3620.0000.0000.0000.000
119A179VAL0-0.060-0.0348.8970.1620.1620.0000.0000.0000.000
120A180TYR0-0.089-0.06412.1200.1900.1900.0000.0000.0000.000
121A181PHE00.003-0.00315.0840.0530.0530.0000.0000.0000.000
122A182GLY0-0.0020.01815.8640.0500.0500.0000.0000.0000.000
123A183LYS10.8610.92916.2740.5620.5620.0000.0000.0000.000
124A184HIS10.8550.93614.4440.4750.4750.0000.0000.0000.000
125A185VAL00.040-0.00213.7010.0400.0400.0000.0000.0000.000
126A186TRP0-0.021-0.03815.266-0.009-0.0090.0000.0000.0000.000
127A187GLU-1-0.916-0.96018.666-0.405-0.4050.0000.0000.0000.000
128A188LEU0-0.082-0.02515.9160.0270.0270.0000.0000.0000.000
129A189SER00.0240.00020.2940.0210.0210.0000.0000.0000.000
130A190LEU00.015-0.00522.275-0.067-0.0670.0000.0000.0000.000
131A191ASP-1-0.858-0.94723.285-0.546-0.5460.0000.0000.0000.000
132A192GLU-1-0.769-0.84719.461-0.600-0.6000.0000.0000.0000.000
133A193ALA0-0.021-0.01318.655-0.117-0.1170.0000.0000.0000.000
134A194ALA0-0.005-0.01618.672-0.111-0.1110.0000.0000.0000.000
135A195LEU0-0.024-0.00317.898-0.019-0.0190.0000.0000.0000.000
136A196LEU00.0290.01113.560-0.089-0.0890.0000.0000.0000.000
137A197ALA00.0390.02715.162-0.146-0.1460.0000.0000.0000.000
138A198ALA0-0.033-0.01217.0450.0200.0200.0000.0000.0000.000
139A199LEU0-0.059-0.02613.5220.0750.0750.0000.0000.0000.000
140A200PRO00.0140.01912.1230.0400.0400.0000.0000.0000.000
141A201LYS10.8970.95812.9590.6440.6440.0000.0000.0000.000
142A202ALA0-0.093-0.06714.7890.1520.1520.0000.0000.0000.000
143A203PRO00.0580.03810.9400.1620.1620.0000.0000.0000.000
144A204ALA00.0390.02513.7770.0740.0740.0000.0000.0000.000
145A205LYS10.9080.95915.7210.4390.4390.0000.0000.0000.000
146A206TYR00.026-0.01717.6700.0870.0870.0000.0000.0000.000
147A207ASN00.0410.03513.9410.0080.0080.0000.0000.0000.000
148A208PRO00.0680.01216.2570.0990.0990.0000.0000.0000.000
149A209PHE00.004-0.00714.1710.0470.0470.0000.0000.0000.000
150A210TYR0-0.055-0.02814.8140.0410.0410.0000.0000.0000.000
151A211HIS0-0.0020.00919.5970.0780.0780.0000.0000.0000.000
152A212PRO00.0310.01922.387-0.051-0.0510.0000.0000.0000.000
153A213GLU-1-0.814-0.89823.455-0.285-0.2850.0000.0000.0000.000
154A214ARG10.8260.90122.0140.2830.2830.0000.0000.0000.000
155A215ALA0-0.0380.00120.487-0.034-0.0340.0000.0000.0000.000
156A216LEU00.0580.03221.885-0.046-0.0460.0000.0000.0000.000
157A217GLN00.0020.00224.686-0.028-0.0280.0000.0000.0000.000
158A218ARG10.8650.92918.7380.7570.7570.0000.0000.0000.000
159A219ARG10.9030.94522.0250.4270.4270.0000.0000.0000.000
160A220ASN00.0830.04023.122-0.042-0.0420.0000.0000.0000.000
161A221LEU0-0.066-0.01324.5870.0170.0170.0000.0000.0000.000
162A222VAL0-0.014-0.00520.6500.0110.0110.0000.0000.0000.000
163A223LEU00.0460.01323.757-0.004-0.0040.0000.0000.0000.000
164A224LYS10.9270.97826.3850.3640.3640.0000.0000.0000.000
165A225ARG10.6850.82324.5860.5500.5500.0000.0000.0000.000
166A226MET00.0030.00923.707-0.009-0.0090.0000.0000.0000.000
167A227LEU00.0150.02026.6430.0140.0140.0000.0000.0000.000
168A228GLU-1-0.913-0.95029.818-0.385-0.3850.0000.0000.0000.000
169A229GLU-1-0.905-0.94326.104-0.492-0.4920.0000.0000.0000.000
170A230GLY00.0060.01629.336-0.001-0.0010.0000.0000.0000.000
171A231TYR0-0.068-0.04024.866-0.014-0.0140.0000.0000.0000.000
172A232ILE0-0.044-0.01227.317-0.014-0.0140.0000.0000.0000.000
173A233THR00.0390.00430.0170.0070.0070.0000.0000.0000.000
174A234PRO00.024-0.00633.181-0.014-0.0140.0000.0000.0000.000
175A235GLU-1-0.864-0.93035.250-0.285-0.2850.0000.0000.0000.000
176A236GLN00.0470.02630.413-0.009-0.0090.0000.0000.0000.000
177A237TYR0-0.016-0.00730.097-0.013-0.0130.0000.0000.0000.000
178A238GLU-1-0.919-0.97031.489-0.276-0.2760.0000.0000.0000.000
179A239GLU-1-0.892-0.93830.864-0.307-0.3070.0000.0000.0000.000
180A240ALA0-0.004-0.01227.344-0.003-0.0030.0000.0000.0000.000
181A241VAL0-0.091-0.04028.556-0.013-0.0130.0000.0000.0000.000
182A242ASN0-0.048-0.03529.9290.0220.0220.0000.0000.0000.000
183A243LYS10.8390.96227.2440.3420.3420.0000.0000.0000.000