Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YZ132

Calculation Name: 3NWJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NWJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8GY88

Base Structure: X-ray

Registration Date: 2023-06-22

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2144990.232499
FMO2-HF: Nuclear repulsion 2068576.048902
FMO2-HF: Total energy -76414.183598
FMO2-MP2: Total energy -76635.886688


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:82:GLN)


Summations of interaction energy for fragment #1(A:82: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.
-10.696-5.7363.404-3.229-5.132-0.005
Interaction energy analysis for fragmet #1(A:82:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.053 / 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].
3A84ILE00.0490.0263.405-3.787-0.9290.060-1.366-1.5520.006
4A85LEU00.0090.0032.115-3.288-2.3753.149-1.457-2.604-0.009
5A86LYS10.9400.9713.561-1.220-0.5820.013-0.190-0.460-0.001
6A87LYS10.9580.9815.964-0.691-0.6910.0000.0000.0000.000
7A88LYS10.9050.9596.9220.1000.1000.0000.0000.0000.000
8A89ALA0-0.017-0.0057.841-0.006-0.0060.0000.0000.0000.000
9A90GLU-1-0.983-0.9989.6590.3790.3790.0000.0000.0000.000
10A91GLU-1-0.882-0.94310.8670.0560.0560.0000.0000.0000.000
11A92VAL00.0460.02212.036-0.003-0.0030.0000.0000.0000.000
12A93LYS10.8350.93614.333-0.086-0.0860.0000.0000.0000.000
13A94PRO0-0.008-0.00916.182-0.001-0.0010.0000.0000.0000.000
14A95TYR00.0620.05117.218-0.003-0.0030.0000.0000.0000.000
15A96LEU0-0.019-0.00315.741-0.004-0.0040.0000.0000.0000.000
16A97ASN0-0.031-0.02019.2720.0080.0080.0000.0000.0000.000
17A98GLY00.0150.01020.6080.0010.0010.0000.0000.0000.000
18A99ARG10.9000.95221.4520.0330.0330.0000.0000.0000.000
19A100SER00.0140.00619.915-0.002-0.0020.0000.0000.0000.000
20A101MET0-0.026-0.00213.580-0.011-0.0110.0000.0000.0000.000
21A102TYR00.0230.00919.1140.0090.0090.0000.0000.0000.000
22A103LEU00.0100.01614.162-0.013-0.0130.0000.0000.0000.000
23A104VAL00.0060.01618.7830.0180.0180.0000.0000.0000.000
24A105GLY00.0660.02020.492-0.027-0.0270.0000.0000.0000.000
25A106MET00.0290.04622.6610.0180.0180.0000.0000.0000.000
26A107MET00.0200.01922.907-0.012-0.0120.0000.0000.0000.000
27A108GLY00.0630.03121.646-0.008-0.0080.0000.0000.0000.000
28A109SER0-0.014-0.01319.054-0.039-0.0390.0000.0000.0000.000
29A110GLY00.0650.02115.881-0.053-0.0530.0000.0000.0000.000
30A111LYS10.8090.90415.3660.1700.1700.0000.0000.0000.000
31A112THR00.0390.00015.791-0.021-0.0210.0000.0000.0000.000
32A113THR0-0.042-0.01611.7870.0700.0700.0000.0000.0000.000
33A114VAL00.0470.01610.668-0.007-0.0070.0000.0000.0000.000
34A115GLY00.0590.02311.157-0.022-0.0220.0000.0000.0000.000
35A116LYS10.8680.94412.3530.1250.1250.0000.0000.0000.000
36A117ILE0-0.0130.0046.1980.0750.0750.0000.0000.0000.000
37A118MET00.0120.0198.166-0.001-0.0010.0000.0000.0000.000
38A119ALA00.0090.00610.1880.0580.0580.0000.0000.0000.000
39A120ARG10.9550.9668.517-0.722-0.7220.0000.0000.0000.000
40A121SER0-0.072-0.0486.3930.0380.0380.0000.0000.0000.000
41A122LEU00.0080.0128.1450.0700.0700.0000.0000.0000.000
42A123GLY0-0.022-0.00411.5540.0470.0470.0000.0000.0000.000
43A124TYR0-0.060-0.03113.5310.0030.0030.0000.0000.0000.000
44A125THR0-0.017-0.00515.0960.0230.0230.0000.0000.0000.000
45A126PHE00.006-0.01015.022-0.026-0.0260.0000.0000.0000.000
46A127PHE00.006-0.00717.0230.0270.0270.0000.0000.0000.000
47A128ASP-1-0.773-0.82719.660-0.135-0.1350.0000.0000.0000.000
48A129CYS00.006-0.00421.7140.0160.0160.0000.0000.0000.000
49A130ASP-1-0.830-0.92225.100-0.088-0.0880.0000.0000.0000.000
50A131THR0-0.010-0.02723.5030.0110.0110.0000.0000.0000.000
51A132LEU0-0.060-0.03624.5310.0130.0130.0000.0000.0000.000
52A133ILE0-0.033-0.00427.2520.0080.0080.0000.0000.0000.000
53A134GLU-1-0.906-0.96328.735-0.040-0.0400.0000.0000.0000.000
54A135GLN0-0.026-0.01025.3780.0140.0140.0000.0000.0000.000
55A136ALA0-0.043-0.01430.5590.0090.0090.0000.0000.0000.000
56A137MET0-0.049-0.00533.0700.0020.0020.0000.0000.0000.000
57A138LYS10.8680.91332.841-0.018-0.0180.0000.0000.0000.000
58A139GLY0-0.004-0.00237.7460.0010.0010.0000.0000.0000.000
59A140THR0-0.0130.02338.6910.0000.0000.0000.0000.0000.000
60A141SER0-0.053-0.06535.450-0.001-0.0010.0000.0000.0000.000
61A142VAL00.024-0.01532.1770.0000.0000.0000.0000.0000.000
62A143ALA00.0040.00835.153-0.003-0.0030.0000.0000.0000.000
63A144GLU-1-0.713-0.81637.066-0.022-0.0220.0000.0000.0000.000
64A145ILE0-0.027-0.01437.4290.0000.0000.0000.0000.0000.000
65A146PHE0-0.024-0.02734.116-0.003-0.0030.0000.0000.0000.000
66A147GLU-1-0.940-0.97239.304-0.040-0.0400.0000.0000.0000.000
67A148HIS0-0.072-0.02942.3620.0020.0020.0000.0000.0000.000
68A149PHE0-0.051-0.02642.0360.0020.0020.0000.0000.0000.000
69A150GLY00.0130.02740.905-0.001-0.0010.0000.0000.0000.000
70A151GLU-1-0.819-0.90534.238-0.084-0.0840.0000.0000.0000.000
71A152SER0-0.052-0.03537.060-0.001-0.0010.0000.0000.0000.000
72A153VAL00.0770.03438.3480.0000.0000.0000.0000.0000.000
73A154PHE00.0400.02129.8490.0020.0020.0000.0000.0000.000
74A155ARG10.7700.85030.4070.0810.0810.0000.0000.0000.000
75A156GLU-1-0.780-0.86134.721-0.040-0.0400.0000.0000.0000.000
76A157LYS10.8150.89933.8770.0260.0260.0000.0000.0000.000
77A158GLU-1-0.783-0.89429.173-0.082-0.0820.0000.0000.0000.000
78A159THR0-0.040-0.03830.8590.0010.0010.0000.0000.0000.000
79A160GLU-1-0.856-0.91432.878-0.018-0.0180.0000.0000.0000.000
80A161ALA00.0200.01628.6970.0050.0050.0000.0000.0000.000
81A162LEU00.014-0.00526.0440.0030.0030.0000.0000.0000.000
82A163LYS10.9320.98229.0000.0170.0170.0000.0000.0000.000
83A164LYS10.8830.92729.703-0.014-0.0140.0000.0000.0000.000
84A165LEU0-0.002-0.01424.0260.0060.0060.0000.0000.0000.000
85A166SER0-0.020-0.01826.9150.0070.0070.0000.0000.0000.000
86A167LEU0-0.037-0.02127.9830.0020.0020.0000.0000.0000.000
87A168MET0-0.0190.01229.1720.0030.0030.0000.0000.0000.000
88A169TYR0-0.025-0.00423.9420.0090.0090.0000.0000.0000.000
89A170HIS00.0620.03423.528-0.014-0.0140.0000.0000.0000.000
90A171GLN00.0260.01118.7140.0160.0160.0000.0000.0000.000
91A172VAL0-0.0100.00318.5200.0140.0140.0000.0000.0000.000
92A173VAL0-0.014-0.00214.236-0.019-0.0190.0000.0000.0000.000
93A174VAL0-0.0020.00317.5290.0130.0130.0000.0000.0000.000
94A175SER0-0.027-0.03218.251-0.021-0.0210.0000.0000.0000.000
95A176THR0-0.010-0.03019.8590.0250.0250.0000.0000.0000.000
96A177GLY00.1520.08923.291-0.018-0.0180.0000.0000.0000.000
97A178GLY0-0.065-0.04325.900-0.005-0.0050.0000.0000.0000.000
98A179GLY00.018-0.00326.767-0.002-0.0020.0000.0000.0000.000
99A180ALA00.0020.02426.4410.0070.0070.0000.0000.0000.000
100A181VAL00.002-0.00426.1680.0080.0080.0000.0000.0000.000
101A182ILE00.0160.02828.9750.0030.0030.0000.0000.0000.000
102A183ARG10.8480.91732.5340.0550.0550.0000.0000.0000.000
103A184PRO00.0560.01732.784-0.001-0.0010.0000.0000.0000.000
104A185ILE0-0.032-0.01533.5730.0010.0010.0000.0000.0000.000
105A186ASN00.0360.01629.7200.0110.0110.0000.0000.0000.000
106A187TRP00.0180.00525.2630.0010.0010.0000.0000.0000.000
107A188LYS10.9320.98129.5560.0320.0320.0000.0000.0000.000
108A189TYR0-0.043-0.02129.2910.0100.0100.0000.0000.0000.000
109A190MET00.006-0.00124.986-0.001-0.0010.0000.0000.0000.000
110A191HIS00.0100.01025.0560.0000.0000.0000.0000.0000.000
111A192LYS10.8250.92427.0170.0350.0350.0000.0000.0000.000
112A193GLY0-0.033-0.01123.0280.0100.0100.0000.0000.0000.000
113A194ILE00.0120.01618.518-0.004-0.0040.0000.0000.0000.000
114A195SER00.0300.01419.823-0.013-0.0130.0000.0000.0000.000
115A196ILE0-0.001-0.01614.877-0.009-0.0090.0000.0000.0000.000
116A197TRP00.0540.01718.626-0.006-0.0060.0000.0000.0000.000
117A198LEU0-0.038-0.01414.473-0.023-0.0230.0000.0000.0000.000
118A199ASP-1-0.820-0.90417.957-0.231-0.2310.0000.0000.0000.000
119A200VAL0-0.010-0.02318.427-0.046-0.0460.0000.0000.0000.000
120A201PRO00.0660.04520.9220.0210.0210.0000.0000.0000.000
121A202LEU00.0630.03124.017-0.012-0.0120.0000.0000.0000.000
122A203GLU-1-0.824-0.92326.219-0.225-0.2250.0000.0000.0000.000
123A204ALA00.001-0.00621.172-0.006-0.0060.0000.0000.0000.000
124A205LEU0-0.057-0.02221.469-0.014-0.0140.0000.0000.0000.000
125A206ALA00.006-0.00223.8800.0090.0090.0000.0000.0000.000
126A207HIS0-0.028-0.01921.0510.0360.0360.0000.0000.0000.000
127A208ARG10.8070.89816.1420.4640.4640.0000.0000.0000.000
128A209ILE0-0.055-0.02322.7100.0100.0100.0000.0000.0000.000
129A210ALA0-0.036-0.01625.8760.0170.0170.0000.0000.0000.000
130A211ALA0-0.0410.00122.9480.0130.0130.0000.0000.0000.000
131A228THR00.0290.00631.3740.0040.0040.0000.0000.0000.000
132A229TYR00.0740.03127.471-0.001-0.0010.0000.0000.0000.000
133A230THR00.0490.01831.141-0.002-0.0020.0000.0000.0000.000
134A231ALA00.0040.01234.1640.0040.0040.0000.0000.0000.000
135A232ALA00.0160.00629.3470.0050.0050.0000.0000.0000.000
136A233LEU00.0350.01329.3990.0010.0010.0000.0000.0000.000
137A234ASN00.0210.00931.378-0.001-0.0010.0000.0000.0000.000
138A235ARG10.9280.98032.8660.1090.1090.0000.0000.0000.000
139A236LEU0-0.009-0.00627.0860.0040.0040.0000.0000.0000.000
140A237SER00.004-0.00330.720-0.002-0.0020.0000.0000.0000.000
141A238THR0-0.032-0.02432.9320.0070.0070.0000.0000.0000.000
142A239ILE0-0.056-0.02730.2270.0060.0060.0000.0000.0000.000
143A240TRP00.0440.01626.152-0.003-0.0030.0000.0000.0000.000
144A241ASP-1-0.831-0.91731.172-0.128-0.1280.0000.0000.0000.000
145A242ALA0-0.035-0.00734.0560.0080.0080.0000.0000.0000.000
146A243ARG10.7990.88930.0570.1130.1130.0000.0000.0000.000
147A244GLY00.017-0.00328.715-0.004-0.0040.0000.0000.0000.000
148A245GLU-1-0.807-0.88528.745-0.105-0.1050.0000.0000.0000.000
149A246ALA00.0190.02630.2550.0010.0010.0000.0000.0000.000
150A247TYR0-0.051-0.04224.600-0.002-0.0020.0000.0000.0000.000
151A248THR0-0.053-0.04825.131-0.005-0.0050.0000.0000.0000.000
152A249LYS10.7980.89826.6110.0970.0970.0000.0000.0000.000
153A250ALA0-0.027-0.01922.0720.0090.0090.0000.0000.0000.000
154A251SER00.0050.01121.1480.0020.0020.0000.0000.0000.000
155A252ALA00.0220.02017.889-0.001-0.0010.0000.0000.0000.000
156A253ARG10.8410.91019.3660.2530.2530.0000.0000.0000.000
157A254VAL0-0.014-0.00713.293-0.010-0.0100.0000.0000.0000.000
158A255SER00.006-0.01716.371-0.010-0.0100.0000.0000.0000.000
159A256LEU00.016-0.01214.583-0.034-0.0340.0000.0000.0000.000
160A257GLU-1-0.878-0.93416.444-0.354-0.3540.0000.0000.0000.000
161A258ASN00.0270.03417.912-0.007-0.0070.0000.0000.0000.000
162A259ILE00.0010.01611.463-0.010-0.0100.0000.0000.0000.000
163A260THR0-0.035-0.03614.482-0.036-0.0360.0000.0000.0000.000
164A261LEU0-0.0060.00016.065-0.014-0.0140.0000.0000.0000.000
165A262LYS10.8100.89612.2680.4450.4450.0000.0000.0000.000
166A263LEU0-0.048-0.02210.1890.0050.0050.0000.0000.0000.000
167A264GLY00.0060.01914.211-0.055-0.0550.0000.0000.0000.000
168A265TYR0-0.119-0.0849.5980.0390.0390.0000.0000.0000.000
169A266ARG10.8640.90816.6460.5980.5980.0000.0000.0000.000
170A267SER00.019-0.01418.1430.0700.0700.0000.0000.0000.000
171A268VAL00.0370.01316.487-0.067-0.0670.0000.0000.0000.000
172A269SER0-0.058-0.03216.6080.0140.0140.0000.0000.0000.000
173A270ASP-1-0.803-0.85615.066-0.637-0.6370.0000.0000.0000.000
174A271LEU0-0.0150.01311.663-0.143-0.1430.0000.0000.0000.000
175A272THR0-0.014-0.0166.6840.0630.0630.0000.0000.0000.000
176A273PRO0-0.004-0.0268.949-0.011-0.0110.0000.0000.0000.000
177A274ALA00.014-0.0053.8160.0080.1230.000-0.028-0.0870.000
178A275GLU-1-0.752-0.8365.452-2.042-2.0420.0000.0000.0000.000
179A276ILE00.0140.0107.1410.2840.2840.0000.0000.0000.000
180A277ALA0-0.010-0.0096.6110.1540.1540.0000.0000.0000.000
181A278ILE0-0.015-0.0082.663-0.2680.1680.182-0.188-0.429-0.001
182A279GLU-1-0.784-0.8736.850-0.282-0.2820.0000.0000.0000.000
183A280ALA0-0.002-0.01510.5140.1020.1020.0000.0000.0000.000
184A281PHE0-0.014-0.0167.3500.0740.0740.0000.0000.0000.000
185A282GLU-1-0.840-0.90910.384-0.196-0.1960.0000.0000.0000.000
186A283GLN0-0.052-0.03712.4290.0760.0760.0000.0000.0000.000
187A284VAL0-0.026-0.01514.0050.0350.0350.0000.0000.0000.000
188A285GLN0-0.030-0.02713.2060.0310.0310.0000.0000.0000.000
189A286SER00.0310.02115.7290.0240.0240.0000.0000.0000.000
190A287TYR0-0.0020.00318.2400.0120.0120.0000.0000.0000.000
191A288LEU0-0.029-0.02716.9800.0160.0160.0000.0000.0000.000
192A289GLU-1-0.895-0.95017.769-0.083-0.0830.0000.0000.0000.000
193A290LYS10.7730.88820.8670.1140.1140.0000.0000.0000.000
194A291GLU-1-1.010-0.99224.369-0.036-0.0360.0000.0000.0000.000