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: 2J7NR

Calculation Name: 3NBI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NBI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H9A7

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2011426.582082
FMO2-HF: Nuclear repulsion 1935247.183564
FMO2-HF: Total energy -76179.398518
FMO2-MP2: Total energy -76402.947859


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:2:ASN)


Summations of interaction energy for fragment #1(A:2:ASN)
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.
-12.541-7.8330.204-1.9-3.0120.002
Interaction energy analysis for fragmet #1(A:2:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.014
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].
3A4THR00.0870.0443.640-1.9170.312-0.001-1.022-1.2060.000
4A5SER0-0.082-0.0322.838-1.269-0.4060.136-0.296-0.703-0.001
5A6ILE00.0160.0103.284-1.595-0.1980.072-0.559-0.9100.003
6A7ALA00.0710.0226.096-0.491-0.4910.0000.0000.0000.000
7A8LEU00.0460.0317.523-0.152-0.1520.0000.0000.0000.000
8A9ARG10.8880.9447.361-3.154-3.1540.0000.0000.0000.000
9A10ALA00.0360.01310.179-0.189-0.1890.0000.0000.0000.000
10A11GLU-1-0.920-0.95411.9310.5160.5160.0000.0000.0000.000
11A12THR0-0.046-0.03012.881-0.132-0.1320.0000.0000.0000.000
12A13TRP0-0.033-0.02314.458-0.086-0.0860.0000.0000.0000.000
13A14LEU00.0300.01616.085-0.090-0.0900.0000.0000.0000.000
14A15LEU00.0000.01917.901-0.078-0.0780.0000.0000.0000.000
15A16ALA0-0.061-0.04018.948-0.053-0.0530.0000.0000.0000.000
16A17ALA0-0.060-0.02020.030-0.043-0.0430.0000.0000.0000.000
17A18TRP0-0.034-0.03020.280-0.074-0.0740.0000.0000.0000.000
18A19HIS10.8500.93222.782-0.354-0.3540.0000.0000.0000.000
19A20VAL00.0200.02420.091-0.026-0.0260.0000.0000.0000.000
20A21LYS10.9310.96019.735-0.260-0.2600.0000.0000.0000.000
21A22VAL00.0220.01116.046-0.033-0.0330.0000.0000.0000.000
22A23PRO00.0550.04317.3560.0450.0450.0000.0000.0000.000
23A24PRO00.0530.01613.008-0.001-0.0010.0000.0000.0000.000
24A25MET00.0260.00513.2050.0200.0200.0000.0000.0000.000
25A26TRP00.0710.03715.091-0.016-0.0160.0000.0000.0000.000
26A27LEU0-0.004-0.00111.703-0.029-0.0290.0000.0000.0000.000
27A28GLU-1-0.929-0.9818.6050.8250.8250.0000.0000.0000.000
28A29ALA0-0.0010.01010.727-0.187-0.1870.0000.0000.0000.000
29A30CYS0-0.0370.00013.335-0.099-0.0990.0000.0000.0000.000
30A31ILE0-0.020-0.0287.7850.0430.0430.0000.0000.0000.000
31A32ASN0-0.027-0.0208.816-0.524-0.5240.0000.0000.0000.000
32A33TRP00.0340.02610.598-0.122-0.1220.0000.0000.0000.000
33A34ILE00.003-0.00611.891-0.002-0.0020.0000.0000.0000.000
34A35GLN0-0.073-0.0374.762-0.235-0.176-0.001-0.002-0.0560.000
35A36GLU-1-0.974-0.99510.199-0.983-0.9830.0000.0000.0000.000
36A37GLU-1-0.920-0.93712.920-0.294-0.2940.0000.0000.0000.000
37A38ASN0-0.094-0.05912.1500.0880.0880.0000.0000.0000.000
38A39ASN0-0.030-0.00613.036-0.036-0.0360.0000.0000.0000.000
39A40ASN0-0.0220.0058.976-0.520-0.5200.0000.0000.0000.000
40A41VAL00.0480.0223.9390.0060.054-0.001-0.012-0.0350.000
41A42ASN0-0.080-0.0554.482-1.966-1.854-0.001-0.009-0.1020.000
42A43LEU00.0300.0296.3270.4110.4110.0000.0000.0000.000
43A44SER0-0.018-0.0077.8230.6610.6610.0000.0000.0000.000
44A45GLN00.031-0.0117.6380.7370.7370.0000.0000.0000.000
45A46ALA0-0.029-0.0169.623-0.258-0.2580.0000.0000.0000.000
46A47GLN0-0.027-0.02612.539-0.178-0.1780.0000.0000.0000.000
47A48MET00.0560.0608.5850.0100.0100.0000.0000.0000.000
48A49ASN00.0420.01311.4490.0030.0030.0000.0000.0000.000
49A50LYS10.9170.96013.712-0.482-0.4820.0000.0000.0000.000
50A51GLN00.0650.03214.426-0.099-0.0990.0000.0000.0000.000
51A52VAL00.0510.03612.645-0.055-0.0550.0000.0000.0000.000
52A53PHE0-0.051-0.03215.706-0.048-0.0480.0000.0000.0000.000
53A54GLU-1-0.921-0.97018.8250.1650.1650.0000.0000.0000.000
54A55GLN00.0560.02717.401-0.035-0.0350.0000.0000.0000.000
55A56TRP00.0200.02419.709-0.019-0.0190.0000.0000.0000.000
56A57LEU0-0.046-0.03321.319-0.021-0.0210.0000.0000.0000.000
57A58LEU0-0.0060.01723.044-0.013-0.0130.0000.0000.0000.000
58A59THR0-0.037-0.03722.276-0.023-0.0230.0000.0000.0000.000
59A60ASP-1-0.788-0.89324.6970.0770.0770.0000.0000.0000.000
60A61LEU0-0.028-0.04025.0180.0030.0030.0000.0000.0000.000
61A62ARG10.8480.92326.317-0.050-0.0500.0000.0000.0000.000
62A63ASP-1-0.910-0.94223.6750.0300.0300.0000.0000.0000.000
63A64LEU0-0.126-0.06520.9530.0100.0100.0000.0000.0000.000
64A65GLU-1-0.925-0.95622.6410.0790.0790.0000.0000.0000.000
65A66HIS0-0.028-0.02320.5910.0030.0030.0000.0000.0000.000
66A67PRO0-0.036-0.00424.0410.0020.0020.0000.0000.0000.000
67A68LEU0-0.072-0.03924.0710.0230.0230.0000.0000.0000.000
68A69LEU0-0.065-0.04227.3330.0070.0070.0000.0000.0000.000
69A70PRO0-0.041-0.01430.9280.0000.0000.0000.0000.0000.000
70A71ASP-1-0.900-0.95332.4230.1060.1060.0000.0000.0000.000
71A72GLY00.0990.04833.9720.0000.0000.0000.0000.0000.000
72A73ILE0-0.080-0.04835.868-0.004-0.0040.0000.0000.0000.000
73A74LEU0-0.029-0.02737.824-0.004-0.0040.0000.0000.0000.000
74A75GLU-1-0.946-0.95840.1690.0770.0770.0000.0000.0000.000
75A76ILE0-0.0310.00340.043-0.004-0.0040.0000.0000.0000.000
76A77PRO00.004-0.00343.5070.0000.0000.0000.0000.0000.000
77A78LYS10.9240.93745.823-0.080-0.0800.0000.0000.0000.000
78A79GLY00.0090.01942.977-0.001-0.0010.0000.0000.0000.000
79A80GLU-1-0.899-0.93540.5660.1130.1130.0000.0000.0000.000
80A81LEU00.0050.01733.7960.0020.0020.0000.0000.0000.000
81A82ASN00.0450.01734.8970.0010.0010.0000.0000.0000.000
82A83GLY00.0040.02731.0890.0040.0040.0000.0000.0000.000
83A84PHE0-0.057-0.03727.478-0.004-0.0040.0000.0000.0000.000
84A85TYR0-0.002-0.02927.7440.0140.0140.0000.0000.0000.000
85A86ALA0-0.0050.00925.274-0.012-0.0120.0000.0000.0000.000
86A87LEU0-0.002-0.00626.9210.0020.0020.0000.0000.0000.000
87A88GLN00.0520.03229.0670.0130.0130.0000.0000.0000.000
88A89ILE0-0.040-0.02431.023-0.005-0.0050.0000.0000.0000.000
89A90ASN00.0470.04533.790-0.001-0.0010.0000.0000.0000.000
90A91SER00.0580.02935.620-0.005-0.0050.0000.0000.0000.000
91A92LEU0-0.0090.00238.8990.0070.0070.0000.0000.0000.000
92A93VAL00.0660.04041.468-0.004-0.0040.0000.0000.0000.000
93A94ASP-1-0.772-0.89945.1060.0570.0570.0000.0000.0000.000
94A95VAL00.0150.00147.758-0.004-0.0040.0000.0000.0000.000
95A96SER0-0.054-0.01850.147-0.004-0.0040.0000.0000.0000.000
96A97GLN0-0.017-0.01652.322-0.003-0.0030.0000.0000.0000.000
97A98PRO00.006-0.00751.715-0.003-0.0030.0000.0000.0000.000
98A99ALA00.0510.03654.616-0.003-0.0030.0000.0000.0000.000
99A100TYR00.0160.00156.440-0.002-0.0020.0000.0000.0000.000
100A101SER0-0.029-0.01657.886-0.003-0.0030.0000.0000.0000.000
101A102GLN0-0.015-0.01558.180-0.002-0.0020.0000.0000.0000.000
102A103ILE00.0610.02359.566-0.002-0.0020.0000.0000.0000.000
103A104GLN00.0160.01262.2130.0000.0000.0000.0000.0000.000
104A105LYS10.8690.93161.710-0.027-0.0270.0000.0000.0000.000
105A106LEU0-0.015-0.01463.629-0.001-0.0010.0000.0000.0000.000
106A107ARG10.9180.98066.505-0.033-0.0330.0000.0000.0000.000
107A108GLY0-0.043-0.01068.2360.0000.0000.0000.0000.0000.000
108A109LYS10.9590.99166.848-0.023-0.0230.0000.0000.0000.000
109A120ALA00.0380.01487.6260.0000.0000.0000.0000.0000.000
110A121GLN0-0.021-0.02584.2040.0000.0000.0000.0000.0000.000
111A122VAL00.0110.01780.2770.0000.0000.0000.0000.0000.000
112A123THR0-0.032-0.02478.3070.0000.0000.0000.0000.0000.000
113A124PRO00.0200.01475.2530.0000.0000.0000.0000.0000.000
114A125LYS10.9330.97072.676-0.028-0.0280.0000.0000.0000.000
115A126PRO0-0.038-0.04669.7720.0000.0000.0000.0000.0000.000
116A127TRP00.0560.03361.9930.0000.0000.0000.0000.0000.000
117A128GLU-1-0.906-0.94364.1450.0390.0390.0000.0000.0000.000
118A129ALA0-0.063-0.02259.537-0.001-0.0010.0000.0000.0000.000
119A130LYS10.9550.98355.010-0.044-0.0440.0000.0000.0000.000
120A131PRO0-0.0060.00356.0640.0020.0020.0000.0000.0000.000
121A132SER00.0270.00851.388-0.001-0.0010.0000.0000.0000.000
122A133ARG10.7920.88243.647-0.078-0.0780.0000.0000.0000.000
123A134MET0-0.037-0.02347.8990.0010.0010.0000.0000.0000.000
124A135LEU0-0.0070.01042.143-0.004-0.0040.0000.0000.0000.000
125A136MET0-0.034-0.01343.9580.0050.0050.0000.0000.0000.000
126A137LEU0-0.003-0.01737.321-0.003-0.0030.0000.0000.0000.000
127A138GLN0-0.018-0.00539.0080.0030.0030.0000.0000.0000.000
128A139LEU0-0.014-0.02134.6060.0020.0020.0000.0000.0000.000
129A140THR00.0390.01931.216-0.007-0.0070.0000.0000.0000.000
130A141ASP-1-0.728-0.86428.3060.1470.1470.0000.0000.0000.000
131A142GLY0-0.005-0.00527.6890.0100.0100.0000.0000.0000.000
132A143ILE0-0.0280.00327.414-0.011-0.0110.0000.0000.0000.000
133A144VAL0-0.016-0.00930.739-0.012-0.0120.0000.0000.0000.000
134A145GLN0-0.023-0.01733.6350.0040.0040.0000.0000.0000.000
135A146ILE0-0.013-0.01035.965-0.002-0.0020.0000.0000.0000.000
136A147GLN00.0490.03738.289-0.003-0.0030.0000.0000.0000.000
137A148GLY00.0330.02139.5600.0060.0060.0000.0000.0000.000
138A149MET0-0.0080.00640.469-0.004-0.0040.0000.0000.0000.000
139A150GLU-1-0.735-0.83143.2010.0860.0860.0000.0000.0000.000
140A151TYR0-0.039-0.02444.422-0.004-0.0040.0000.0000.0000.000
141A152GLN0-0.026-0.01345.5240.0000.0000.0000.0000.0000.000
142A153PRO00.001-0.00345.4000.0020.0020.0000.0000.0000.000
143A154ILE00.0340.00939.8310.0050.0050.0000.0000.0000.000
144A155PRO0-0.014-0.01842.242-0.002-0.0020.0000.0000.0000.000
145A156ILE0-0.030-0.00735.891-0.003-0.0030.0000.0000.0000.000
146A157LEU00.0060.02037.0070.0010.0010.0000.0000.0000.000
147A158HIS00.012-0.02338.147-0.007-0.0070.0000.0000.0000.000
148A159SER00.012-0.03040.6890.0020.0020.0000.0000.0000.000
149A160ASP-1-0.885-0.92540.8190.0450.0450.0000.0000.0000.000
150A161LEU0-0.143-0.05035.2620.0010.0010.0000.0000.0000.000
151A162PRO00.0670.05033.497-0.003-0.0030.0000.0000.0000.000
152A163PRO00.0400.04434.6710.0110.0110.0000.0000.0000.000
153A164GLY00.0640.00831.442-0.004-0.0040.0000.0000.0000.000
154A165THR0-0.063-0.04930.0870.0150.0150.0000.0000.0000.000
155A166LYS10.7810.89925.786-0.126-0.1260.0000.0000.0000.000
156A167ILE0-0.025-0.02929.5190.0020.0020.0000.0000.0000.000
157A168LEU0-0.049-0.02327.7500.0110.0110.0000.0000.0000.000
158A169ILE00.0210.00830.598-0.010-0.0100.0000.0000.0000.000
159A170TYR0-0.031-0.03531.3760.0160.0160.0000.0000.0000.000
160A171GLY00.0170.01833.228-0.010-0.0100.0000.0000.0000.000
161A172ASN0-0.097-0.06035.494-0.003-0.0030.0000.0000.0000.000
162A173ILE00.0150.00336.083-0.005-0.0050.0000.0000.0000.000
163A174SER00.0290.02639.623-0.001-0.0010.0000.0000.0000.000
164A175PHE00.0040.01039.790-0.001-0.0010.0000.0000.0000.000
165A176ARG10.8860.92142.938-0.072-0.0720.0000.0000.0000.000
166A177LEU0-0.030-0.02445.568-0.001-0.0010.0000.0000.0000.000
167A178GLY00.0850.05441.730-0.003-0.0030.0000.0000.0000.000
168A179VAL0-0.030-0.00941.7400.0010.0010.0000.0000.0000.000
169A180LEU00.015-0.00436.4210.0010.0010.0000.0000.0000.000
170A181LEU0-0.063-0.04041.064-0.005-0.0050.0000.0000.0000.000
171A182LEU00.0120.00937.9700.0050.0050.0000.0000.0000.000
172A183LYS10.9120.95640.924-0.109-0.1090.0000.0000.0000.000
173A184PRO00.0170.00040.2800.0060.0060.0000.0000.0000.000
174A185GLU-1-0.912-0.95738.7660.1270.1270.0000.0000.0000.000
175A186ASN0-0.066-0.03336.543-0.001-0.0010.0000.0000.0000.000
176A187VAL00.0140.00735.1080.0050.0050.0000.0000.0000.000
177A188LYS10.9680.99028.075-0.245-0.2450.0000.0000.0000.000
178A189VAL00.0040.00531.9950.0060.0060.0000.0000.0000.000
179A190LEU0-0.072-0.04325.9650.0110.0110.0000.0000.0000.000
180A191GLY00.0020.01627.7790.0060.0060.0000.0000.0000.000
181A192GLY00.0390.01927.5800.0070.0070.0000.0000.0000.000
182A193GLU-1-0.947-0.98028.2270.0430.0430.0000.0000.0000.000
183A194VAL0-0.0020.01028.2680.0030.0030.0000.0000.0000.000
184A195ASP-1-0.879-0.93729.538-0.015-0.0150.0000.0000.0000.000
185A196ALA00.0590.01230.330-0.002-0.0020.0000.0000.0000.000
186A197LEU0-0.009-0.01032.1470.0020.0020.0000.0000.0000.000
187A198LEU0-0.048-0.02332.9930.0010.0010.0000.0000.0000.000
188A199GLU-1-0.938-0.96634.447-0.027-0.0270.0000.0000.0000.000
189A200GLU-1-0.966-0.97236.4380.0180.0180.0000.0000.0000.000
190A201TYR0-0.010-0.02936.6140.0020.0020.0000.0000.0000.000
191A202ALA0-0.061-0.00140.1440.0010.0010.0000.0000.0000.000
192A203GLN0-0.097-0.04241.463-0.008-0.0080.0000.0000.0000.000
193A204GLU-1-1.015-1.00943.9320.0280.0280.0000.0000.0000.000