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: 3QY3L

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 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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2834038.496431
FMO2-HF: Nuclear repulsion 2745391.580095
FMO2-HF: Total energy -88646.916335
FMO2-MP2: Total energy -88910.731374


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.
1.462.57-0.007-0.418-0.6860.001
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 : 0.024 / q_NPA : 0.000
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-4HIS00.020-0.0063.8020.8912.001-0.007-0.418-0.6860.001
4A-3HIS00.0700.0406.1790.5080.5080.0000.0000.0000.000
5A-2HIS0-0.004-0.0076.0320.0300.0300.0000.0000.0000.000
6A-1HIS00.0300.0077.8900.1470.1470.0000.0000.0000.000
7A0HIS00.0260.06110.2750.0490.0490.0000.0000.0000.000
8A1MET00.0120.00010.646-0.055-0.0550.0000.0000.0000.000
9A2MET0-0.031-0.02110.8440.0510.0510.0000.0000.0000.000
10A3LEU00.0030.02013.4790.0270.0270.0000.0000.0000.000
11A4ILE00.0220.01715.9510.0150.0150.0000.0000.0000.000
12A5LYS10.9510.97415.5720.0750.0750.0000.0000.0000.000
13A6LYS10.9790.99417.532-0.060-0.0600.0000.0000.0000.000
14A7ILE00.011-0.00719.3170.0080.0080.0000.0000.0000.000
15A8GLU-1-0.837-0.92721.211-0.063-0.0630.0000.0000.0000.000
16A9GLU-1-0.981-0.98920.4220.0260.0260.0000.0000.0000.000
17A10LEU0-0.073-0.03223.3620.0060.0060.0000.0000.0000.000
18A11LYS10.8350.93625.3880.0500.0500.0000.0000.0000.000
19A12ASN0-0.061-0.01825.288-0.003-0.0030.0000.0000.0000.000
20A13SER0-0.018-0.03027.7980.0060.0060.0000.0000.0000.000
21A14GLU-1-0.862-0.94629.7140.0200.0200.0000.0000.0000.000
22A15ILE0-0.063-0.03228.3780.0000.0000.0000.0000.0000.000
23A16LYS10.8940.95230.3900.0150.0150.0000.0000.0000.000
24A17ASP-1-0.849-0.91831.6550.0000.0000.0000.0000.0000.000
25A18ILE0-0.086-0.04133.6910.0010.0010.0000.0000.0000.000
26A19ILE0-0.036-0.02729.3130.0010.0010.0000.0000.0000.000
27A20ASP-1-0.795-0.89133.633-0.008-0.0080.0000.0000.0000.000
28A21LYS10.8720.94535.730-0.011-0.0110.0000.0000.0000.000
29A22ARG10.8230.91335.905-0.023-0.0230.0000.0000.0000.000
30A23ILE00.0360.02033.7010.0000.0000.0000.0000.0000.000
31A24GLN00.003-0.01237.410-0.002-0.0020.0000.0000.0000.000
32A25GLU-1-0.906-0.94940.7050.0150.0150.0000.0000.0000.000
33A26PHE00.0070.01935.6730.0010.0010.0000.0000.0000.000
34A27LYS10.9010.94238.9260.0110.0110.0000.0000.0000.000
35A28SER0-0.059-0.03942.697-0.001-0.0010.0000.0000.0000.000
36A29PHE00.002-0.00744.0230.0000.0000.0000.0000.0000.000
37A30LYS10.9170.97646.3900.0050.0050.0000.0000.0000.000
38A31ASN0-0.031-0.02147.990-0.001-0.0010.0000.0000.0000.000
39A32LYS10.8650.96447.090-0.006-0.0060.0000.0000.0000.000
40A33SER00.039-0.00551.277-0.001-0.0010.0000.0000.0000.000
41A34ASN00.049-0.00351.9240.0010.0010.0000.0000.0000.000
42A35GLU-1-0.850-0.91952.1470.0070.0070.0000.0000.0000.000
43A36GLU-1-0.948-0.97649.8110.0120.0120.0000.0000.0000.000
44A37TRP00.043-0.00146.0860.0020.0020.0000.0000.0000.000
45A38PHE0-0.004-0.01347.5140.0010.0010.0000.0000.0000.000
46A39LYS10.9300.97848.748-0.011-0.0110.0000.0000.0000.000
47A40GLU-1-0.776-0.86342.9750.0200.0200.0000.0000.0000.000
48A41LEU0-0.0090.00643.7560.0020.0020.0000.0000.0000.000
49A42CYS0-0.043-0.01944.5870.0020.0020.0000.0000.0000.000
50A43PHE0-0.0080.00538.8150.0030.0030.0000.0000.0000.000
51A44CYS0-0.052-0.00639.2420.0030.0030.0000.0000.0000.000
52A45ILE0-0.0090.00940.6870.0030.0030.0000.0000.0000.000
53A46LEU0-0.032-0.02642.7600.0030.0030.0000.0000.0000.000
54A47THR0-0.0120.00236.4520.0030.0030.0000.0000.0000.000
55A48ALA00.0290.01937.0990.0040.0040.0000.0000.0000.000
56A49ASN0-0.089-0.05436.677-0.005-0.0050.0000.0000.0000.000
57A50PHE00.0600.03237.5950.0010.0010.0000.0000.0000.000
58A51THR00.0220.02536.6940.0050.0050.0000.0000.0000.000
59A52ALA00.0510.04236.250-0.003-0.0030.0000.0000.0000.000
60A53GLU-1-0.747-0.89236.4850.0510.0510.0000.0000.0000.000
61A54GLY0-0.003-0.02739.876-0.002-0.0020.0000.0000.0000.000
62A55GLY0-0.001-0.01141.071-0.002-0.0020.0000.0000.0000.000
63A56ILE00.015-0.00739.866-0.003-0.0030.0000.0000.0000.000
64A57ARG10.9240.98942.743-0.042-0.0420.0000.0000.0000.000
65A58ILE00.0220.02045.409-0.001-0.0010.0000.0000.0000.000
66A59GLN0-0.046-0.03644.7080.0000.0000.0000.0000.0000.000
67A60LYS10.9270.96045.409-0.027-0.0270.0000.0000.0000.000
68A61GLU-1-0.947-0.95349.9120.0250.0250.0000.0000.0000.000
69A62ILE0-0.052-0.01350.693-0.001-0.0010.0000.0000.0000.000
70A63GLY00.0450.02051.585-0.001-0.0010.0000.0000.0000.000
71A64ASP-1-0.877-0.94652.9030.0120.0120.0000.0000.0000.000
72A65GLY00.0860.03955.585-0.001-0.0010.0000.0000.0000.000
73A66PHE0-0.019-0.03948.2810.0000.0000.0000.0000.0000.000
74A67LEU0-0.086-0.05953.4720.0000.0000.0000.0000.0000.000
75A68THR0-0.012-0.01056.3140.0000.0000.0000.0000.0000.000
76A69LEU0-0.0060.03055.5520.0000.0000.0000.0000.0000.000
77A70PRO00.0320.05158.1480.0000.0000.0000.0000.0000.000
78A71ARG10.9470.96454.080-0.020-0.0200.0000.0000.0000.000
79A72GLU-1-0.839-0.93556.6720.0180.0180.0000.0000.0000.000
80A73GLU-1-0.851-0.93258.0250.0180.0180.0000.0000.0000.000
81A74LEU0-0.078-0.02852.1400.0010.0010.0000.0000.0000.000
82A75GLU-1-0.878-0.97453.0290.0260.0260.0000.0000.0000.000
83A76GLU-1-0.859-0.92353.3170.0280.0280.0000.0000.0000.000
84A77LYS10.9740.98853.536-0.019-0.0190.0000.0000.0000.000
85A78LEU0-0.024-0.01348.2960.0020.0020.0000.0000.0000.000
86A79LYS10.9430.96649.232-0.029-0.0290.0000.0000.0000.000
87A80ASN0-0.060-0.03550.3830.0030.0030.0000.0000.0000.000
88A81LEU0-0.0200.00948.5520.0010.0010.0000.0000.0000.000
89A82GLY0-0.002-0.00146.2820.0020.0020.0000.0000.0000.000
90A83HIS0-0.055-0.01742.5880.0030.0030.0000.0000.0000.000
91A84ARG10.9930.98038.283-0.059-0.0590.0000.0000.0000.000
92A85PHE0-0.096-0.04941.057-0.001-0.0010.0000.0000.0000.000
93A86TYR00.0400.02545.910-0.002-0.0020.0000.0000.0000.000
94A87ARG11.0061.01548.985-0.031-0.0310.0000.0000.0000.000
95A88LYS10.9250.95444.497-0.036-0.0360.0000.0000.0000.000
96A89ARG10.8520.93340.769-0.039-0.0390.0000.0000.0000.000
97A90ALA00.0740.04647.669-0.002-0.0020.0000.0000.0000.000
98A91GLU-1-0.955-0.98051.1350.0190.0190.0000.0000.0000.000
99A92TYR0-0.031-0.02944.7330.0000.0000.0000.0000.0000.000
100A93ILE00.0210.01348.063-0.002-0.0020.0000.0000.0000.000
101A94VAL00.0340.01550.598-0.002-0.0020.0000.0000.0000.000
102A95LEU0-0.013-0.00551.511-0.002-0.0020.0000.0000.0000.000
103A96ALA0-0.025-0.00549.610-0.002-0.0020.0000.0000.0000.000
104A97ARG10.8550.91751.604-0.016-0.0160.0000.0000.0000.000
105A98ARG10.8160.91851.243-0.010-0.0100.0000.0000.0000.000
106A99PHE0-0.018-0.01851.118-0.001-0.0010.0000.0000.0000.000
107A100LYS10.9850.98652.467-0.007-0.0070.0000.0000.0000.000
108A101ASN0-0.037-0.00153.6430.0010.0010.0000.0000.0000.000
109A102ILE00.038-0.00147.944-0.001-0.0010.0000.0000.0000.000
110A103LYS10.8320.92749.3200.0000.0000.0000.0000.0000.000
111A104ASP-1-0.804-0.89450.349-0.001-0.0010.0000.0000.0000.000
112A105ILE0-0.065-0.01849.629-0.001-0.0010.0000.0000.0000.000
113A106VAL0-0.044-0.01745.101-0.001-0.0010.0000.0000.0000.000
114A107GLU-1-0.876-0.94847.269-0.006-0.0060.0000.0000.0000.000
115A108SER0-0.073-0.02948.964-0.001-0.0010.0000.0000.0000.000
116A109PHE0-0.032-0.02446.350-0.001-0.0010.0000.0000.0000.000
117A110GLU-1-0.855-0.91945.446-0.018-0.0180.0000.0000.0000.000
118A111ASN0-0.004-0.01141.5150.0000.0000.0000.0000.0000.000
119A112GLU-1-0.777-0.91937.413-0.013-0.0130.0000.0000.0000.000
120A113LYS10.8280.92334.4980.0280.0280.0000.0000.0000.000
121A114VAL00.0480.02739.5740.0020.0020.0000.0000.0000.000
122A115ALA00.0250.02643.0040.0020.0020.0000.0000.0000.000
123A116ARG10.7600.83933.8750.0080.0080.0000.0000.0000.000
124A117GLU-1-0.937-0.97141.007-0.008-0.0080.0000.0000.0000.000
125A118PHE00.0240.01742.4770.0020.0020.0000.0000.0000.000
126A119LEU0-0.028-0.01542.2790.0020.0020.0000.0000.0000.000
127A120VAL0-0.059-0.03039.5380.0020.0020.0000.0000.0000.000
128A121ARG10.9110.96242.691-0.002-0.0020.0000.0000.0000.000
129A122ASN00.0000.01045.5130.0000.0000.0000.0000.0000.000
130A123ILE0-0.024-0.00445.9470.0010.0010.0000.0000.0000.000
131A124LYS10.9670.97945.496-0.012-0.0120.0000.0000.0000.000
132A125GLY00.005-0.01043.8340.0000.0000.0000.0000.0000.000
133A126ILE0-0.036-0.01041.2330.0020.0020.0000.0000.0000.000
134A127GLY00.0620.03838.595-0.002-0.0020.0000.0000.0000.000
135A128TYR00.0670.02135.034-0.003-0.0030.0000.0000.0000.000
136A129LYS10.9441.02232.851-0.038-0.0380.0000.0000.0000.000
137A130GLU-1-0.888-0.96034.8480.0290.0290.0000.0000.0000.000
138A131ALA00.0240.01438.127-0.001-0.0010.0000.0000.0000.000
139A132SER00.018-0.01534.513-0.004-0.0040.0000.0000.0000.000
140A133HIS0-0.015-0.00835.8060.0000.0000.0000.0000.0000.000
141A134PHE00.018-0.01436.641-0.001-0.0010.0000.0000.0000.000
142A135LEU00.000-0.00138.699-0.001-0.0010.0000.0000.0000.000
143A136ARG10.8270.92132.491-0.019-0.0190.0000.0000.0000.000
144A137ASN0-0.023-0.03637.422-0.001-0.0010.0000.0000.0000.000
145A138VAL0-0.051-0.00539.6740.0000.0000.0000.0000.0000.000
146A139GLY0-0.0050.00440.476-0.002-0.0020.0000.0000.0000.000
147A140TYR0-0.035-0.01638.886-0.003-0.0030.0000.0000.0000.000
148A141ASP-1-0.762-0.88634.744-0.010-0.0100.0000.0000.0000.000
149A142ASP-1-0.806-0.88632.517-0.033-0.0330.0000.0000.0000.000
150A143VAL0-0.038-0.01633.390-0.001-0.0010.0000.0000.0000.000
151A144ALA00.0500.02728.7410.0030.0030.0000.0000.0000.000
152A145ILE0-0.041-0.00330.3220.0020.0020.0000.0000.0000.000
153A146ILE00.0160.00226.9500.0050.0050.0000.0000.0000.000
154A147ASP-1-0.858-0.92027.6390.0650.0650.0000.0000.0000.000
155A148ARG10.9340.93427.403-0.079-0.0790.0000.0000.0000.000
156A149HIS0-0.043-0.02225.2140.0160.0160.0000.0000.0000.000
157A150ILE00.0940.04721.9080.0130.0130.0000.0000.0000.000
158A151LEU0-0.037-0.01622.2680.0030.0030.0000.0000.0000.000
159A152ARG10.8690.93820.812-0.188-0.1880.0000.0000.0000.000
160A153GLU-1-0.753-0.84318.7680.1350.1350.0000.0000.0000.000
161A154LEU0-0.007-0.00817.5050.0150.0150.0000.0000.0000.000
162A155TYR0-0.031-0.01617.6470.0070.0070.0000.0000.0000.000
163A156GLU-1-0.843-0.92215.8200.2710.2710.0000.0000.0000.000
164A157ASN0-0.109-0.04913.0360.1140.1140.0000.0000.0000.000
165A158ASN0-0.036-0.01511.370-0.054-0.0540.0000.0000.0000.000
166A159TYR0-0.019-0.04914.878-0.037-0.0370.0000.0000.0000.000
167A160ILE0-0.115-0.06417.490-0.025-0.0250.0000.0000.0000.000
168A161ASP-1-0.833-0.92418.2600.0610.0610.0000.0000.0000.000
169A162GLU-1-0.939-0.96419.7810.1550.1550.0000.0000.0000.000
170A163ILE0-0.075-0.02822.329-0.018-0.0180.0000.0000.0000.000
171A164PRO00.0080.00624.567-0.003-0.0030.0000.0000.0000.000
172A165LYS10.9350.98227.726-0.092-0.0920.0000.0000.0000.000
173A166THR0-0.041-0.03830.423-0.003-0.0030.0000.0000.0000.000
174A167LEU00.0140.01128.749-0.002-0.0020.0000.0000.0000.000
175A168SER00.0210.02032.565-0.003-0.0030.0000.0000.0000.000
176A169ARG10.9630.95633.5710.0100.0100.0000.0000.0000.000
177A170ARG10.9870.98429.3090.0030.0030.0000.0000.0000.000
178A171LYS10.9130.96324.575-0.015-0.0150.0000.0000.0000.000
179A172TYR0-0.024-0.03529.1060.0030.0030.0000.0000.0000.000
180A173LEU00.024-0.00729.973-0.001-0.0010.0000.0000.0000.000
181A174GLU-1-0.894-0.93025.609-0.023-0.0230.0000.0000.0000.000
182A175ILE00.025-0.00124.426-0.004-0.0040.0000.0000.0000.000
183A176GLU-1-0.776-0.85625.564-0.012-0.0120.0000.0000.0000.000
184A177ASN0-0.010-0.02526.964-0.005-0.0050.0000.0000.0000.000
185A178ILE00.0740.07720.631-0.004-0.0040.0000.0000.0000.000
186A179LEU0-0.039-0.02722.648-0.004-0.0040.0000.0000.0000.000
187A180ARG10.8100.88824.2810.0370.0370.0000.0000.0000.000
188A181ASP-1-0.826-0.91022.624-0.095-0.0950.0000.0000.0000.000
189A182ILE0-0.034-0.02119.266-0.005-0.0050.0000.0000.0000.000
190A183GLY0-0.016-0.01521.847-0.001-0.0010.0000.0000.0000.000
191A184GLU-1-0.940-0.95424.738-0.091-0.0910.0000.0000.0000.000
192A185GLU-1-0.892-0.92717.713-0.196-0.1960.0000.0000.0000.000
193A186VAL0-0.014-0.00421.329-0.002-0.0020.0000.0000.0000.000
194A187ASN0-0.081-0.04123.7670.0060.0060.0000.0000.0000.000
195A188LEU0-0.057-0.01825.5500.0100.0100.0000.0000.0000.000
196A189LYS10.9370.97528.4060.0240.0240.0000.0000.0000.000
197A190LEU00.0120.00027.5780.0050.0050.0000.0000.0000.000
198A191SER0-0.096-0.06830.0440.0060.0060.0000.0000.0000.000
199A192GLU-1-0.839-0.93630.406-0.013-0.0130.0000.0000.0000.000
200A193LEU00.0420.02623.3160.0070.0070.0000.0000.0000.000
201A194ASP-1-0.837-0.91426.4900.0380.0380.0000.0000.0000.000
202A195LEU0-0.013-0.01328.1640.0100.0100.0000.0000.0000.000
203A196TYR00.0500.01925.0010.0070.0070.0000.0000.0000.000
204A197ILE00.0110.00722.6910.0100.0100.0000.0000.0000.000
205A198TRP0-0.037-0.02524.5130.0210.0210.0000.0000.0000.000
206A199TYR00.0010.00825.8540.0110.0110.0000.0000.0000.000
207A200LEU00.0040.00320.3860.0070.0070.0000.0000.0000.000
208A201ARG10.7760.88223.029-0.078-0.0780.0000.0000.0000.000
209A202THR0-0.099-0.07124.3720.0040.0040.0000.0000.0000.000
210A203GLY00.0240.02927.2490.0000.0000.0000.0000.0000.000
211A204LYS10.7910.88328.672-0.067-0.0670.0000.0000.0000.000
212A205VAL00.0890.04230.8210.0000.0000.0000.0000.0000.000
213A206LEU0-0.056-0.02233.257-0.002-0.0020.0000.0000.0000.000
214A207LYS10.8430.92335.720-0.023-0.0230.0000.0000.0000.000