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

tag_button

FMODB ID: 6NLYZ

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 OptHSide
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 -2011468.729209
FMO2-HF: Nuclear repulsion 1935287.999359
FMO2-HF: Total energy -76180.729851
FMO2-MP2: Total energy -76404.116429


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.
-9.643-4.9190.237-1.839-3.1230.001
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 : -0.006 / q_NPA : -0.017
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].
3A4THR00.0640.0313.601-2.0390.226-0.007-1.028-1.2310.000
4A5SER0-0.091-0.0352.803-0.974-0.0560.146-0.330-0.734-0.001
5A6ILE00.0120.0033.249-0.7620.4870.100-0.437-0.9120.002
6A7ALA00.0820.0336.074-0.143-0.1430.0000.0000.0000.000
7A8LEU00.0520.0337.493-0.027-0.0270.0000.0000.0000.000
8A9ARG10.8770.9427.168-2.355-2.3550.0000.0000.0000.000
9A10ALA00.0290.01210.152-0.086-0.0860.0000.0000.0000.000
10A11GLU-1-0.916-0.95111.9050.2540.2540.0000.0000.0000.000
11A12THR0-0.053-0.04112.744-0.062-0.0620.0000.0000.0000.000
12A13TRP0-0.019-0.01614.427-0.042-0.0420.0000.0000.0000.000
13A14LEU00.0300.02015.983-0.048-0.0480.0000.0000.0000.000
14A15LEU00.0270.03117.879-0.041-0.0410.0000.0000.0000.000
15A16ALA0-0.052-0.03618.930-0.031-0.0310.0000.0000.0000.000
16A17ALA0-0.064-0.02720.000-0.024-0.0240.0000.0000.0000.000
17A18TRP0-0.028-0.02620.170-0.042-0.0420.0000.0000.0000.000
18A19HIS10.7910.90222.725-0.218-0.2180.0000.0000.0000.000
19A20VAL00.0290.02920.057-0.014-0.0140.0000.0000.0000.000
20A21LYS10.9330.96619.713-0.126-0.1260.0000.0000.0000.000
21A22VAL00.0290.01215.984-0.019-0.0190.0000.0000.0000.000
22A23PRO00.0410.04517.3170.0280.0280.0000.0000.0000.000
23A24PRO00.0550.00812.960-0.014-0.0140.0000.0000.0000.000
24A25MET00.0070.00213.1590.0000.0000.0000.0000.0000.000
25A26TRP00.0740.03415.230-0.034-0.0340.0000.0000.0000.000
26A27LEU00.0040.00211.762-0.038-0.0380.0000.0000.0000.000
27A28GLU-1-0.856-0.9427.7770.5090.5090.0000.0000.0000.000
28A29ALA00.0000.02110.926-0.191-0.1910.0000.0000.0000.000
29A30CYS0-0.037-0.00513.534-0.084-0.0840.0000.0000.0000.000
30A31ILE0-0.016-0.0217.7920.0120.0120.0000.0000.0000.000
31A32ASN0-0.065-0.0478.636-0.465-0.4650.0000.0000.0000.000
32A33TRP00.0380.02410.131-0.091-0.0910.0000.0000.0000.000
33A34ILE00.010-0.00311.4490.0090.0090.0000.0000.0000.000
34A35GLN0-0.093-0.0504.2010.0960.166-0.001-0.010-0.0590.000
35A36GLU-1-0.966-0.9879.716-0.858-0.8580.0000.0000.0000.000
36A37GLU-1-0.887-0.92412.486-0.288-0.2880.0000.0000.0000.000
37A38ASN0-0.075-0.04411.7640.0950.0950.0000.0000.0000.000
38A39ASN0-0.058-0.01812.6430.0020.0020.0000.0000.0000.000
39A40ASN0-0.019-0.0029.044-0.267-0.2670.0000.0000.0000.000
40A41VAL00.0470.0193.776-0.096-0.0160.000-0.017-0.0630.000
41A42ASN0-0.066-0.0424.382-1.857-1.715-0.001-0.017-0.1240.000
42A43LEU00.0340.0406.1440.4570.4570.0000.0000.0000.000
43A44SER0-0.040-0.0387.5480.5090.5090.0000.0000.0000.000
44A45GLN00.026-0.0157.7310.5520.5520.0000.0000.0000.000
45A46ALA0-0.013-0.0079.660-0.212-0.2120.0000.0000.0000.000
46A47GLN00.0300.02212.147-0.047-0.0470.0000.0000.0000.000
47A48MET00.0380.0498.424-0.055-0.0550.0000.0000.0000.000
48A49ASN00.0220.00111.445-0.008-0.0080.0000.0000.0000.000
49A50LYS10.9220.96913.780-0.243-0.2430.0000.0000.0000.000
50A51GLN00.0300.01013.383-0.067-0.0670.0000.0000.0000.000
51A52VAL00.0330.02512.665-0.036-0.0360.0000.0000.0000.000
52A53PHE0-0.043-0.02815.697-0.021-0.0210.0000.0000.0000.000
53A54GLU-1-0.917-0.97018.8900.0560.0560.0000.0000.0000.000
54A55GLN00.0610.03016.969-0.011-0.0110.0000.0000.0000.000
55A56TRP00.0150.01119.663-0.002-0.0020.0000.0000.0000.000
56A57LEU0-0.053-0.03321.337-0.006-0.0060.0000.0000.0000.000
57A58LEU0-0.0040.01222.796-0.001-0.0010.0000.0000.0000.000
58A59THR0-0.037-0.02422.019-0.019-0.0190.0000.0000.0000.000
59A60ASP-1-0.698-0.79924.4780.0110.0110.0000.0000.0000.000
60A61LEU0-0.021-0.02824.921-0.001-0.0010.0000.0000.0000.000
61A62ARG10.7950.86326.2740.0080.0080.0000.0000.0000.000
62A63ASP-1-0.905-0.94423.919-0.046-0.0460.0000.0000.0000.000
63A64LEU0-0.118-0.06120.8530.0020.0020.0000.0000.0000.000
64A65GLU-1-0.925-0.95622.5960.0020.0020.0000.0000.0000.000
65A66HIS0-0.025-0.02519.9610.0020.0020.0000.0000.0000.000
66A67PRO0-0.0200.00223.9990.0020.0020.0000.0000.0000.000
67A68LEU0-0.079-0.04623.8740.0150.0150.0000.0000.0000.000
68A69LEU0-0.066-0.04427.2970.0070.0070.0000.0000.0000.000
69A70PRO0-0.039-0.02130.892-0.001-0.0010.0000.0000.0000.000
70A71ASP-1-0.895-0.94832.3880.0480.0480.0000.0000.0000.000
71A72GLY00.0820.04333.9360.0010.0010.0000.0000.0000.000
72A73ILE0-0.072-0.04335.630-0.002-0.0020.0000.0000.0000.000
73A74LEU0-0.022-0.02337.690-0.002-0.0020.0000.0000.0000.000
74A75GLU-1-0.949-0.95840.1770.0340.0340.0000.0000.0000.000
75A76ILE0-0.0310.00140.013-0.002-0.0020.0000.0000.0000.000
76A77PRO00.001-0.00643.4730.0000.0000.0000.0000.0000.000
77A78LYS10.9170.93645.791-0.043-0.0430.0000.0000.0000.000
78A79GLY00.0080.01742.9450.0000.0000.0000.0000.0000.000
79A80GLU-1-0.902-0.93040.5920.0630.0630.0000.0000.0000.000
80A81LEU00.0000.01333.7160.0010.0010.0000.0000.0000.000
81A82ASN00.0320.01135.0050.0020.0020.0000.0000.0000.000
82A83GLY00.0090.02331.0630.0020.0020.0000.0000.0000.000
83A84PHE0-0.048-0.03327.451-0.002-0.0020.0000.0000.0000.000
84A85TYR0-0.015-0.02727.7170.0070.0070.0000.0000.0000.000
85A86ALA0-0.0010.01125.233-0.006-0.0060.0000.0000.0000.000
86A87LEU00.000-0.00426.888-0.002-0.0020.0000.0000.0000.000
87A88GLN00.0460.01929.0110.0040.0040.0000.0000.0000.000
88A89ILE0-0.048-0.02731.0230.0000.0000.0000.0000.0000.000
89A90ASN00.0470.03633.689-0.004-0.0040.0000.0000.0000.000
90A91SER00.0650.03335.620-0.003-0.0030.0000.0000.0000.000
91A92LEU0-0.025-0.01038.8990.0050.0050.0000.0000.0000.000
92A93VAL00.0710.04241.468-0.003-0.0030.0000.0000.0000.000
93A94ASP-1-0.757-0.88345.1530.0240.0240.0000.0000.0000.000
94A95VAL00.0140.00147.662-0.002-0.0020.0000.0000.0000.000
95A96SER0-0.057-0.02650.147-0.002-0.0020.0000.0000.0000.000
96A97GLN00.006-0.02152.4000.0000.0000.0000.0000.0000.000
97A98PRO00.0140.00651.698-0.001-0.0010.0000.0000.0000.000
98A99ALA00.0510.03454.611-0.001-0.0010.0000.0000.0000.000
99A100TYR00.018-0.00156.440-0.001-0.0010.0000.0000.0000.000
100A101SER0-0.007-0.00457.945-0.001-0.0010.0000.0000.0000.000
101A102GLN0-0.027-0.01758.4350.0000.0000.0000.0000.0000.000
102A103ILE00.0560.01959.510-0.001-0.0010.0000.0000.0000.000
103A104GLN00.0220.01562.3770.0000.0000.0000.0000.0000.000
104A105LYS10.8450.92161.371-0.007-0.0070.0000.0000.0000.000
105A106LEU0-0.023-0.01863.539-0.001-0.0010.0000.0000.0000.000
106A107ARG10.8180.91166.514-0.014-0.0140.0000.0000.0000.000
107A108GLY0-0.041-0.00868.2360.0000.0000.0000.0000.0000.000
108A109LYS10.9630.99167.468-0.005-0.0050.0000.0000.0000.000
109A120ALA00.0280.01387.7280.0000.0000.0000.0000.0000.000
110A121GLN0-0.019-0.02384.2370.0000.0000.0000.0000.0000.000
111A122VAL00.0140.01480.2780.0000.0000.0000.0000.0000.000
112A123THR0-0.013-0.01678.3920.0000.0000.0000.0000.0000.000
113A124PRO00.0250.01475.2990.0000.0000.0000.0000.0000.000
114A125LYS10.9240.96672.756-0.012-0.0120.0000.0000.0000.000
115A126PRO0-0.017-0.01469.5850.0000.0000.0000.0000.0000.000
116A127TRP00.0400.01561.9340.0000.0000.0000.0000.0000.000
117A128GLU-1-0.815-0.88864.1450.0170.0170.0000.0000.0000.000
118A129ALA0-0.069-0.01659.683-0.001-0.0010.0000.0000.0000.000
119A130LYS10.9290.97554.666-0.018-0.0180.0000.0000.0000.000
120A131PRO00.0060.00555.9810.0010.0010.0000.0000.0000.000
121A132SER00.0210.00651.485-0.001-0.0010.0000.0000.0000.000
122A133ARG10.7760.86343.418-0.036-0.0360.0000.0000.0000.000
123A134MET0-0.051-0.03247.9010.0010.0010.0000.0000.0000.000
124A135LEU00.0000.01442.225-0.003-0.0030.0000.0000.0000.000
125A136MET0-0.034-0.01743.9100.0040.0040.0000.0000.0000.000
126A137LEU0-0.002-0.01237.306-0.003-0.0030.0000.0000.0000.000
127A138GLN0-0.028-0.00739.0240.0020.0020.0000.0000.0000.000
128A139LEU0-0.010-0.01834.4260.0000.0000.0000.0000.0000.000
129A140THR00.034-0.00131.292-0.004-0.0040.0000.0000.0000.000
130A141ASP-1-0.731-0.85828.3060.0600.0600.0000.0000.0000.000
131A142GLY0-0.006-0.00427.6480.0030.0030.0000.0000.0000.000
132A143ILE0-0.0320.00327.349-0.007-0.0070.0000.0000.0000.000
133A144VAL0-0.006-0.00530.696-0.005-0.0050.0000.0000.0000.000
134A145GLN0-0.020-0.00933.5940.0000.0000.0000.0000.0000.000
135A146ILE0-0.011-0.00635.7840.0010.0010.0000.0000.0000.000
136A147GLN00.0530.03538.251-0.002-0.0020.0000.0000.0000.000
137A148GLY00.0280.01939.5260.0040.0040.0000.0000.0000.000
138A149MET0-0.0060.00640.435-0.003-0.0030.0000.0000.0000.000
139A150GLU-1-0.752-0.83743.1510.0400.0400.0000.0000.0000.000
140A151TYR0-0.040-0.02444.393-0.002-0.0020.0000.0000.0000.000
141A152GLN0-0.014-0.00445.4840.0020.0020.0000.0000.0000.000
142A153PRO00.001-0.00545.3750.0010.0010.0000.0000.0000.000
143A154ILE00.0230.01039.7820.0040.0040.0000.0000.0000.000
144A155PRO0-0.007-0.01642.325-0.002-0.0020.0000.0000.0000.000
145A156ILE0-0.036-0.00935.971-0.002-0.0020.0000.0000.0000.000
146A157LEU00.0160.02537.048-0.001-0.0010.0000.0000.0000.000
147A158HIS00.010-0.02437.984-0.003-0.0030.0000.0000.0000.000
148A159SER0-0.023-0.04640.7530.0010.0010.0000.0000.0000.000
149A160ASP-1-0.855-0.90340.8520.0100.0100.0000.0000.0000.000
150A161LEU0-0.120-0.03935.287-0.001-0.0010.0000.0000.0000.000
151A162PRO00.0670.04933.182-0.001-0.0010.0000.0000.0000.000
152A163PRO00.0350.03534.5190.0060.0060.0000.0000.0000.000
153A164GLY00.0610.00931.216-0.005-0.0050.0000.0000.0000.000
154A165THR0-0.053-0.03330.0500.0070.0070.0000.0000.0000.000
155A166LYS10.7810.90025.860-0.024-0.0240.0000.0000.0000.000
156A167ILE0-0.038-0.03229.6090.0040.0040.0000.0000.0000.000
157A168LEU0-0.037-0.02527.6320.0060.0060.0000.0000.0000.000
158A169ILE00.0150.00530.571-0.004-0.0040.0000.0000.0000.000
159A170TYR0-0.051-0.04731.3380.0110.0110.0000.0000.0000.000
160A171GLY00.0340.03233.204-0.006-0.0060.0000.0000.0000.000
161A172ASN0-0.091-0.06435.473-0.002-0.0020.0000.0000.0000.000
162A173ILE00.0210.00635.920-0.003-0.0030.0000.0000.0000.000
163A174SER00.0300.02439.596-0.001-0.0010.0000.0000.0000.000
164A175PHE00.0030.00939.571-0.001-0.0010.0000.0000.0000.000
165A176ARG10.9050.93042.906-0.034-0.0340.0000.0000.0000.000
166A177LEU0-0.037-0.02645.533-0.001-0.0010.0000.0000.0000.000
167A178GLY00.0860.05541.693-0.002-0.0020.0000.0000.0000.000
168A179VAL0-0.031-0.00941.703-0.001-0.0010.0000.0000.0000.000
169A180LEU00.014-0.00236.3480.0020.0020.0000.0000.0000.000
170A181LEU0-0.056-0.03641.031-0.003-0.0030.0000.0000.0000.000
171A182LEU00.0060.00737.9090.0040.0040.0000.0000.0000.000
172A183LYS10.8560.91440.887-0.064-0.0640.0000.0000.0000.000
173A184PRO00.0350.01140.2520.0030.0030.0000.0000.0000.000
174A185GLU-1-0.842-0.91738.7370.0700.0700.0000.0000.0000.000
175A186ASN0-0.073-0.04136.5280.0020.0020.0000.0000.0000.000
176A187VAL00.0170.00735.0960.0010.0010.0000.0000.0000.000
177A188LYS10.9640.98927.954-0.137-0.1370.0000.0000.0000.000
178A189VAL00.0000.00532.0560.0020.0020.0000.0000.0000.000
179A190LEU0-0.070-0.04226.0200.0080.0080.0000.0000.0000.000
180A191GLY00.0030.01727.8530.0030.0030.0000.0000.0000.000
181A192GLY00.0430.02127.4640.0030.0030.0000.0000.0000.000
182A193GLU-1-0.943-0.97927.930-0.008-0.0080.0000.0000.0000.000
183A194VAL0-0.0120.00327.880-0.003-0.0030.0000.0000.0000.000
184A195ASP-1-0.882-0.94028.971-0.058-0.0580.0000.0000.0000.000
185A196ALA00.0560.01429.9890.0020.0020.0000.0000.0000.000
186A197LEU0-0.025-0.01731.7580.0040.0040.0000.0000.0000.000
187A198LEU0-0.047-0.02032.5120.0040.0040.0000.0000.0000.000
188A199GLU-1-0.940-0.96633.919-0.055-0.0550.0000.0000.0000.000
189A200GLU-1-0.937-0.95736.592-0.018-0.0180.0000.0000.0000.000
190A201TYR0-0.045-0.05436.5760.0040.0040.0000.0000.0000.000
191A202ALA0-0.069-0.00539.5850.0020.0020.0000.0000.0000.000
192A203GLN0-0.105-0.04141.381-0.004-0.0040.0000.0000.0000.000
193A204GLU-1-0.992-1.00343.384-0.003-0.0030.0000.0000.0000.000