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

tag_button

FMODB ID: 9GJN2

Calculation Name: 3FHF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FHF

Chain ID: A

ChEMBL ID:

UniProt ID: Q58134

Base Structure: X-ray

Registration Date: 2023-06-20

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2842184.298771
FMO2-HF: Nuclear repulsion 2753535.722029
FMO2-HF: Total energy -88648.576741
FMO2-MP2: Total energy -88912.2939


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:-6:GLY)


Summations of interaction energy for fragment #1(A:-6:GLY)
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.
2.4413.8280.007-0.575-0.8190.001
Interaction energy analysis for fragmet #1(A:-6:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.011
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].
3A-4HIS00.016-0.0063.2802.0713.4580.007-0.575-0.8190.001
4A-3HIS00.0650.0425.9750.5270.5270.0000.0000.0000.000
5A-2HIS0-0.006-0.0056.3240.0770.0770.0000.0000.0000.000
6A-1HIS0-0.026-0.0248.3280.0500.0500.0000.0000.0000.000
7A0HIS00.0290.03111.0110.0090.0090.0000.0000.0000.000
8A1MET00.0050.00610.392-0.049-0.0490.0000.0000.0000.000
9A2MET0-0.046-0.02411.2380.0220.0220.0000.0000.0000.000
10A3LEU00.0190.02213.948-0.001-0.0010.0000.0000.0000.000
11A4ILE00.0210.01716.4450.0010.0010.0000.0000.0000.000
12A5LYS10.8920.93515.443-0.107-0.1070.0000.0000.0000.000
13A6LYS10.8430.91717.999-0.125-0.1250.0000.0000.0000.000
14A7ILE00.0370.00819.818-0.001-0.0010.0000.0000.0000.000
15A8GLU-1-0.794-0.88221.5100.0010.0010.0000.0000.0000.000
16A9GLU-1-0.854-0.90419.8770.1190.1190.0000.0000.0000.000
17A10LEU0-0.055-0.01923.7580.0000.0000.0000.0000.0000.000
18A11LYS10.7870.86625.431-0.005-0.0050.0000.0000.0000.000
19A12ASN0-0.087-0.04226.036-0.008-0.0080.0000.0000.0000.000
20A13SER0-0.011-0.01528.3400.0060.0060.0000.0000.0000.000
21A14GLU-1-0.880-0.94130.2360.0500.0500.0000.0000.0000.000
22A15ILE0-0.040-0.02529.026-0.002-0.0020.0000.0000.0000.000
23A16LYS10.8760.94230.474-0.021-0.0210.0000.0000.0000.000
24A17ASP-1-0.865-0.92931.8460.0260.0260.0000.0000.0000.000
25A18ILE0-0.048-0.02834.150-0.003-0.0030.0000.0000.0000.000
26A19ILE0-0.035-0.01229.899-0.002-0.0020.0000.0000.0000.000
27A20ASP-1-0.802-0.89534.1170.0150.0150.0000.0000.0000.000
28A21LYS10.8580.91836.269-0.026-0.0260.0000.0000.0000.000
29A22ARG10.7810.87136.435-0.035-0.0350.0000.0000.0000.000
30A23ILE00.0190.00634.261-0.002-0.0020.0000.0000.0000.000
31A24GLN00.0360.00238.056-0.003-0.0030.0000.0000.0000.000
32A25GLU-1-0.861-0.89441.3420.0240.0240.0000.0000.0000.000
33A26PHE00.0130.02936.425-0.001-0.0010.0000.0000.0000.000
34A27LYS10.8420.90838.392-0.004-0.0040.0000.0000.0000.000
35A28SER0-0.054-0.04143.534-0.001-0.0010.0000.0000.0000.000
36A29PHE0-0.015-0.01744.7460.0000.0000.0000.0000.0000.000
37A30LYS10.8790.94646.445-0.001-0.0010.0000.0000.0000.000
38A31ASN0-0.012-0.00748.274-0.002-0.0020.0000.0000.0000.000
39A32LYS10.8780.96847.818-0.013-0.0130.0000.0000.0000.000
40A33SER00.015-0.00551.909-0.001-0.0010.0000.0000.0000.000
41A34ASN00.039-0.01452.4740.0000.0000.0000.0000.0000.000
42A35GLU-1-0.835-0.89852.4680.0070.0070.0000.0000.0000.000
43A36GLU-1-0.858-0.92550.2960.0140.0140.0000.0000.0000.000
44A37TRP00.0520.00446.7490.0010.0010.0000.0000.0000.000
45A38PHE00.004-0.00247.9600.0010.0010.0000.0000.0000.000
46A39LYS10.8920.94249.126-0.011-0.0110.0000.0000.0000.000
47A40GLU-1-0.757-0.83642.9810.0220.0220.0000.0000.0000.000
48A41LEU0-0.0230.00244.2400.0010.0010.0000.0000.0000.000
49A42CYS0-0.040-0.01945.0230.0010.0010.0000.0000.0000.000
50A43PHE00.0240.01139.1840.0020.0020.0000.0000.0000.000
51A44CYS0-0.0360.01739.5850.0020.0020.0000.0000.0000.000
52A45ILE00.0030.00741.0650.0010.0010.0000.0000.0000.000
53A46LEU0-0.0030.00143.1310.0010.0010.0000.0000.0000.000
54A47THR0-0.011-0.00636.9960.0030.0030.0000.0000.0000.000
55A48ALA00.0230.02137.5320.0040.0040.0000.0000.0000.000
56A49ASN0-0.046-0.02837.079-0.003-0.0030.0000.0000.0000.000
57A50PHE00.0280.03738.2400.0010.0010.0000.0000.0000.000
58A51THR00.0170.00236.6510.0040.0040.0000.0000.0000.000
59A52ALA00.0530.04136.978-0.003-0.0030.0000.0000.0000.000
60A53GLU-1-0.742-0.87437.2310.0520.0520.0000.0000.0000.000
61A54GLY0-0.0090.00340.701-0.002-0.0020.0000.0000.0000.000
62A55GLY00.014-0.00741.884-0.002-0.0020.0000.0000.0000.000
63A56ILE00.007-0.00440.509-0.002-0.0020.0000.0000.0000.000
64A57ARG10.8960.95143.935-0.036-0.0360.0000.0000.0000.000
65A58ILE00.0280.01046.401-0.002-0.0020.0000.0000.0000.000
66A59GLN0-0.029-0.02945.4400.0000.0000.0000.0000.0000.000
67A60LYS10.9080.96546.355-0.030-0.0300.0000.0000.0000.000
68A61GLU-1-0.924-0.95750.9170.0240.0240.0000.0000.0000.000
69A62ILE0-0.044-0.00751.327-0.001-0.0010.0000.0000.0000.000
70A63GLY00.0430.02052.775-0.001-0.0010.0000.0000.0000.000
71A64ASP-1-0.876-0.93653.8310.0110.0110.0000.0000.0000.000
72A65GLY00.0560.02856.403-0.001-0.0010.0000.0000.0000.000
73A66PHE00.006-0.02249.5660.0000.0000.0000.0000.0000.000
74A67LEU0-0.044-0.01954.013-0.001-0.0010.0000.0000.0000.000
75A68THR0-0.010-0.02456.741-0.001-0.0010.0000.0000.0000.000
76A69LEU0-0.0250.02156.0130.0000.0000.0000.0000.0000.000
77A70PRO00.0370.02958.940-0.001-0.0010.0000.0000.0000.000
78A71ARG10.7830.85454.430-0.012-0.0120.0000.0000.0000.000
79A72GLU-1-0.826-0.92256.6980.0120.0120.0000.0000.0000.000
80A73GLU-1-0.774-0.89857.9900.0150.0150.0000.0000.0000.000
81A74LEU0-0.043-0.00552.3940.0010.0010.0000.0000.0000.000
82A75GLU-1-0.778-0.89553.1990.0170.0170.0000.0000.0000.000
83A76GLU-1-0.750-0.85253.4810.0210.0210.0000.0000.0000.000
84A77LYS10.8260.91354.756-0.014-0.0140.0000.0000.0000.000
85A78LEU0-0.013-0.01048.6900.0020.0020.0000.0000.0000.000
86A79LYS10.8000.86949.822-0.019-0.0190.0000.0000.0000.000
87A80ASN0-0.034-0.02350.8280.0020.0020.0000.0000.0000.000
88A81LEU00.0120.03049.4290.0010.0010.0000.0000.0000.000
89A82GLY00.0170.01347.2840.0020.0020.0000.0000.0000.000
90A83HIS0-0.058-0.03742.9610.0020.0020.0000.0000.0000.000
91A84ARG10.9480.94438.126-0.043-0.0430.0000.0000.0000.000
92A85PHE0-0.053-0.02941.138-0.001-0.0010.0000.0000.0000.000
93A86TYR00.0280.02146.054-0.002-0.0020.0000.0000.0000.000
94A87ARG10.9571.00249.303-0.017-0.0170.0000.0000.0000.000
95A88LYS10.9300.96744.080-0.018-0.0180.0000.0000.0000.000
96A89ARG10.8010.88141.102-0.026-0.0260.0000.0000.0000.000
97A90ALA00.0720.04047.974-0.001-0.0010.0000.0000.0000.000
98A91GLU-1-0.872-0.92051.0610.0090.0090.0000.0000.0000.000
99A92TYR0-0.042-0.03544.684-0.001-0.0010.0000.0000.0000.000
100A93ILE00.0190.01648.150-0.001-0.0010.0000.0000.0000.000
101A94VAL00.0290.01050.850-0.001-0.0010.0000.0000.0000.000
102A95LEU0-0.040-0.02851.557-0.001-0.0010.0000.0000.0000.000
103A96ALA00.0190.01849.751-0.001-0.0010.0000.0000.0000.000
104A97ARG10.8250.90451.747-0.011-0.0110.0000.0000.0000.000
105A98ARG10.7800.88351.182-0.002-0.0020.0000.0000.0000.000
106A99PHE0-0.022-0.01650.880-0.001-0.0010.0000.0000.0000.000
107A100LYS10.9810.98552.818-0.004-0.0040.0000.0000.0000.000
108A101ASN0-0.096-0.04153.8830.0010.0010.0000.0000.0000.000
109A102ILE00.027-0.00148.252-0.001-0.0010.0000.0000.0000.000
110A103LYS10.8180.91949.885-0.004-0.0040.0000.0000.0000.000
111A104ASP-1-0.774-0.86450.9420.0000.0000.0000.0000.0000.000
112A105ILE0-0.043-0.01349.874-0.001-0.0010.0000.0000.0000.000
113A106VAL0-0.027-0.01145.411-0.001-0.0010.0000.0000.0000.000
114A107GLU-1-0.808-0.90847.614-0.001-0.0010.0000.0000.0000.000
115A108SER0-0.067-0.02349.345-0.001-0.0010.0000.0000.0000.000
116A109PHE0-0.035-0.02146.448-0.001-0.0010.0000.0000.0000.000
117A110GLU-1-0.885-0.94045.570-0.016-0.0160.0000.0000.0000.000
118A111ASN00.0200.00141.308-0.001-0.0010.0000.0000.0000.000
119A112GLU-1-0.754-0.89637.591-0.007-0.0070.0000.0000.0000.000
120A113LYS10.7940.90234.8210.0230.0230.0000.0000.0000.000
121A114VAL00.0440.02639.6340.0010.0010.0000.0000.0000.000
122A115ALA00.0250.02043.1560.0010.0010.0000.0000.0000.000
123A116ARG10.7880.86033.8390.0110.0110.0000.0000.0000.000
124A117GLU-1-0.851-0.90539.946-0.017-0.0170.0000.0000.0000.000
125A118PHE00.0270.01642.3340.0010.0010.0000.0000.0000.000
126A119LEU0-0.016-0.01442.7680.0010.0010.0000.0000.0000.000
127A120VAL0-0.038-0.02239.2880.0010.0010.0000.0000.0000.000
128A121ARG10.8850.95942.6770.0080.0080.0000.0000.0000.000
129A122ASN00.0080.02345.3370.0000.0000.0000.0000.0000.000
130A123ILE00.0000.00545.9890.0010.0010.0000.0000.0000.000
131A124LYS10.9660.97745.400-0.004-0.0040.0000.0000.0000.000
132A125GLY00.0330.00544.1850.0010.0010.0000.0000.0000.000
133A126ILE0-0.028-0.00441.3020.0020.0020.0000.0000.0000.000
134A127GLY00.0620.03938.190-0.002-0.0020.0000.0000.0000.000
135A128TYR00.0610.01234.879-0.001-0.0010.0000.0000.0000.000
136A129LYS10.8410.95932.506-0.026-0.0260.0000.0000.0000.000
137A130GLU-1-0.854-0.93234.9800.0200.0200.0000.0000.0000.000
138A131ALA00.0290.01238.4640.0000.0000.0000.0000.0000.000
139A132SER00.0350.00434.955-0.002-0.0020.0000.0000.0000.000
140A133HIS00.0010.00435.4370.0000.0000.0000.0000.0000.000
141A134PHE00.033-0.00437.2590.0010.0010.0000.0000.0000.000
142A135LEU0-0.013-0.00539.3980.0000.0000.0000.0000.0000.000
143A136ARG10.7620.88433.351-0.023-0.0230.0000.0000.0000.000
144A137ASN0-0.029-0.03738.3200.0010.0010.0000.0000.0000.000
145A138VAL0-0.057-0.02240.5420.0010.0010.0000.0000.0000.000
146A139GLY00.0130.01541.315-0.001-0.0010.0000.0000.0000.000
147A140TYR0-0.025-0.00339.393-0.001-0.0010.0000.0000.0000.000
148A141ASP-1-0.746-0.87335.5810.0030.0030.0000.0000.0000.000
149A142ASP-1-0.791-0.87232.525-0.023-0.0230.0000.0000.0000.000
150A143VAL0-0.021-0.01533.947-0.003-0.0030.0000.0000.0000.000
151A144ALA00.0590.04229.1130.0040.0040.0000.0000.0000.000
152A145ILE0-0.0160.00030.600-0.001-0.0010.0000.0000.0000.000
153A146ILE0-0.0050.00626.9110.0070.0070.0000.0000.0000.000
154A147ASP-1-0.798-0.92428.3690.0570.0570.0000.0000.0000.000
155A148ARG10.8790.93627.463-0.057-0.0570.0000.0000.0000.000
156A149HIS0-0.029-0.01025.4270.0060.0060.0000.0000.0000.000
157A150ILE00.0790.04822.3810.0090.0090.0000.0000.0000.000
158A151LEU0-0.037-0.01722.601-0.002-0.0020.0000.0000.0000.000
159A152ARG10.8540.91920.952-0.133-0.1330.0000.0000.0000.000
160A153GLU-1-0.762-0.84919.2100.1130.1130.0000.0000.0000.000
161A154LEU00.0020.00017.8400.0120.0120.0000.0000.0000.000
162A155TYR0-0.075-0.04317.3620.0070.0070.0000.0000.0000.000
163A156GLU-1-0.852-0.92015.8600.1810.1810.0000.0000.0000.000
164A157ASN0-0.057-0.03213.0080.1240.1240.0000.0000.0000.000
165A158ASN0-0.043-0.01811.408-0.071-0.0710.0000.0000.0000.000
166A159TYR0-0.011-0.01714.449-0.032-0.0320.0000.0000.0000.000
167A160ILE0-0.099-0.05717.140-0.013-0.0130.0000.0000.0000.000
168A161ASP-1-0.878-0.93618.149-0.064-0.0640.0000.0000.0000.000
169A162GLU-1-0.834-0.92119.0840.0400.0400.0000.0000.0000.000
170A163ILE0-0.044-0.00621.565-0.005-0.0050.0000.0000.0000.000
171A164PRO00.003-0.00223.929-0.002-0.0020.0000.0000.0000.000
172A165LYS10.9190.97626.915-0.043-0.0430.0000.0000.0000.000
173A166THR0-0.042-0.03629.7770.0030.0030.0000.0000.0000.000
174A167LEU00.0160.01127.939-0.005-0.0050.0000.0000.0000.000
175A168SER00.0190.01431.7770.0000.0000.0000.0000.0000.000
176A169ARG10.8550.89232.7970.0190.0190.0000.0000.0000.000
177A170ARG10.8660.91327.9240.0450.0450.0000.0000.0000.000
178A171LYS10.9300.95523.5450.0380.0380.0000.0000.0000.000
179A172TYR0-0.016-0.04228.3640.0020.0020.0000.0000.0000.000
180A173LEU00.033-0.00129.7390.0010.0010.0000.0000.0000.000
181A174GLU-1-0.779-0.83624.797-0.055-0.0550.0000.0000.0000.000
182A175ILE00.0420.01324.160-0.004-0.0040.0000.0000.0000.000
183A176GLU-1-0.791-0.86925.651-0.014-0.0140.0000.0000.0000.000
184A177ASN0-0.024-0.01426.9960.0010.0010.0000.0000.0000.000
185A178ILE00.0620.05120.6170.0000.0000.0000.0000.0000.000
186A179LEU0-0.029-0.02722.7360.0020.0020.0000.0000.0000.000
187A180ARG10.7650.85224.7140.0370.0370.0000.0000.0000.000
188A181ASP-1-0.880-0.92522.285-0.084-0.0840.0000.0000.0000.000
189A182ILE0-0.012-0.01019.5170.0020.0020.0000.0000.0000.000
190A183GLY0-0.015-0.00522.0870.0080.0080.0000.0000.0000.000
191A184GLU-1-0.939-0.97025.284-0.058-0.0580.0000.0000.0000.000
192A185GLU-1-0.836-0.90117.952-0.102-0.1020.0000.0000.0000.000
193A186VAL0-0.010-0.00121.7080.0040.0040.0000.0000.0000.000
194A187ASN0-0.106-0.04723.9780.0120.0120.0000.0000.0000.000
195A188LEU0-0.058-0.01326.3440.0060.0060.0000.0000.0000.000
196A189LYS10.8520.91128.903-0.005-0.0050.0000.0000.0000.000
197A190LEU00.005-0.00827.9710.0060.0060.0000.0000.0000.000
198A191SER0-0.086-0.07030.6510.0060.0060.0000.0000.0000.000
199A192GLU-1-0.762-0.85830.6280.0100.0100.0000.0000.0000.000
200A193LEU00.0570.02723.8450.0080.0080.0000.0000.0000.000
201A194ASP-1-0.794-0.89427.1680.0420.0420.0000.0000.0000.000
202A195LEU0-0.032-0.01228.9830.0080.0080.0000.0000.0000.000
203A196TYR00.0700.02225.6930.0070.0070.0000.0000.0000.000
204A197ILE00.0100.01423.3780.0110.0110.0000.0000.0000.000
205A198TRP0-0.058-0.03925.5160.0170.0170.0000.0000.0000.000
206A199TYR00.0230.03326.5290.0090.0090.0000.0000.0000.000
207A200LEU0-0.002-0.00621.3180.0080.0080.0000.0000.0000.000
208A201ARG10.7340.85623.820-0.070-0.0700.0000.0000.0000.000
209A202THR0-0.107-0.08625.4410.0000.0000.0000.0000.0000.000
210A203GLY00.0320.03127.994-0.002-0.0020.0000.0000.0000.000
211A204LYS10.7780.87229.520-0.070-0.0700.0000.0000.0000.000
212A205VAL00.0920.04931.4470.0010.0010.0000.0000.0000.000
213A206LEU0-0.043-0.00533.830-0.004-0.0040.0000.0000.0000.000
214A207LYS10.8220.88236.189-0.025-0.0250.0000.0000.0000.000