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: 7GJ3K

Calculation Name: 4AXZ-A-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4AXZ

Chain ID: A

ChEMBL ID:

UniProt ID: O50962

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 220
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2653648.166955
FMO2-HF: Nuclear repulsion 2564708.625391
FMO2-HF: Total energy -88939.541565
FMO2-MP2: Total energy -89201.714477


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:71:ACE )


Summations of interaction energy for fragment #1(A:71:ACE )
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.
0.872.629-0.005-0.811-0.944-0.002
Interaction energy analysis for fragmet #1(A:71:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.002
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].
3A73GLU -1-0.822-0.9143.849-0.1641.471-0.005-0.790-0.841-0.002
4A74LYS 10.9490.9704.4480.3370.4610.000-0.021-0.1030.000
5A75GLU -1-0.891-0.9396.166-1.128-1.1280.0000.0000.0000.000
6A76LYS 10.9740.9887.8380.7190.7190.0000.0000.0000.000
7A77ILE 00.000-0.0099.5140.1470.1470.0000.0000.0000.000
8A78ILE 00.0220.00610.6970.0840.0840.0000.0000.0000.000
9A79LYS 10.9110.95411.8980.6270.6270.0000.0000.0000.000
10A80LYS 10.9640.98013.7150.3720.3720.0000.0000.0000.000
11A81ILE 00.0280.03314.5380.0340.0340.0000.0000.0000.000
12A82ALA 0-0.012-0.00516.7020.0290.0290.0000.0000.0000.000
13A83GLN 0-0.039-0.02118.3430.0000.0000.0000.0000.0000.000
14A84GLU -1-0.854-0.93219.901-0.125-0.1250.0000.0000.0000.000
15A85PHE 0-0.045-0.01920.2130.0150.0150.0000.0000.0000.000
16A86ASP -1-0.870-0.93222.779-0.166-0.1660.0000.0000.0000.000
17A87GLU -1-0.932-0.98224.084-0.135-0.1350.0000.0000.0000.000
18A88ASN 0-0.027-0.02924.6770.0160.0160.0000.0000.0000.000
19A89GLU -1-0.878-0.93227.280-0.097-0.0970.0000.0000.0000.000
20A90LYS 10.9210.96827.8880.1260.1260.0000.0000.0000.000
21A91LEU 0-0.039-0.02229.0050.0080.0080.0000.0000.0000.000
22A92ILE 00.0280.02131.1710.0070.0070.0000.0000.0000.000
23A93ASN 0-0.036-0.03332.4440.0090.0090.0000.0000.0000.000
24A94LYS 10.8690.95334.4770.0720.0720.0000.0000.0000.000
25A95ILE 00.0180.01336.2360.0040.0040.0000.0000.0000.000
26A96GLY 00.0120.01337.5330.0030.0030.0000.0000.0000.000
27A97PRO 00.014-0.00538.2940.0030.0030.0000.0000.0000.000
28A98ASN 0-0.011-0.00741.4640.0000.0000.0000.0000.0000.000
29A99ILE 00.0340.02539.0250.0030.0030.0000.0000.0000.000
30A100GLU -1-0.934-0.95441.963-0.045-0.0450.0000.0000.0000.000
31A101MET 00.0260.02043.7370.0020.0020.0000.0000.0000.000
32A102PHE 0-0.011-0.02845.1210.0020.0020.0000.0000.0000.000
33A103ALA 00.0500.02645.0970.0020.0020.0000.0000.0000.000
34A104GLN 0-0.0090.00147.1560.0010.0010.0000.0000.0000.000
35A105THR 0-0.028-0.01349.6080.0020.0020.0000.0000.0000.000
36A106ILE 00.0080.00548.2450.0010.0010.0000.0000.0000.000
37A107ASN 0-0.047-0.02450.8510.0020.0020.0000.0000.0000.000
38A108THR 00.010-0.01352.6530.0010.0010.0000.0000.0000.000
39A109ASP -1-0.810-0.89555.251-0.023-0.0230.0000.0000.0000.000
40A110ILE 0-0.117-0.05652.8770.0010.0010.0000.0000.0000.000
41A111GLN 0-0.050-0.01555.1370.0020.0020.0000.0000.0000.000
42A112LYS 10.8750.96658.8100.0230.0230.0000.0000.0000.000
43A113ILE 0-0.015-0.00361.6260.0000.0000.0000.0000.0000.000
44A114GLU -1-0.767-0.81864.922-0.016-0.0160.0000.0000.0000.000
45A115PRO 00.0300.02666.1820.0010.0010.0000.0000.0000.000
46A116ASN 00.031-0.01069.7620.0000.0000.0000.0000.0000.000
47A117ASP -1-0.900-0.94572.036-0.014-0.0140.0000.0000.0000.000
48A118GLN 0-0.063-0.03368.4130.0000.0000.0000.0000.0000.000
49A119PHE 00.0370.01165.1740.0000.0000.0000.0000.0000.000
50A120GLY 0-0.004-0.01669.7820.0000.0000.0000.0000.0000.000
51A121ILE 00.0000.01165.9470.0000.0000.0000.0000.0000.000
52A122ASN 00.0150.02169.7760.0000.0000.0000.0000.0000.000
53A123LYS 11.0260.99272.4070.0100.0100.0000.0000.0000.000
54A124THR 0-0.123-0.08074.9290.0000.0000.0000.0000.0000.000
55A125LEU 0-0.0210.00774.5900.0000.0000.0000.0000.0000.000
56A126PHE 0-0.0100.00770.9050.0000.0000.0000.0000.0000.000
57A127THR 0-0.045-0.02774.1490.0000.0000.0000.0000.0000.000
58A128GLU -1-0.904-0.96873.197-0.010-0.0100.0000.0000.0000.000
59A129LYS 10.8810.92972.4660.0090.0090.0000.0000.0000.000
60A130LYS 10.9020.97372.8470.0090.0090.0000.0000.0000.000
61A131ASP -1-0.732-0.88466.942-0.012-0.0120.0000.0000.0000.000
62A132ASN 00.0130.00465.1870.0000.0000.0000.0000.0000.000
63A133ASN 0-0.0010.01062.3240.0000.0000.0000.0000.0000.000
64A134ILE 0-0.012-0.00764.5490.0000.0000.0000.0000.0000.000
65A135ASP -1-0.806-0.90167.517-0.011-0.0110.0000.0000.0000.000
66A136PHE 0-0.095-0.05061.7500.0000.0000.0000.0000.0000.000
67A137MET 0-0.0170.01662.8340.0000.0000.0000.0000.0000.000
68A138LEU 0-0.029-0.00565.0610.0000.0000.0000.0000.0000.000
69A139LYS 10.8890.95364.8250.0120.0120.0000.0000.0000.000
70A140ASP -1-0.884-0.94860.667-0.015-0.0150.0000.0000.0000.000
71A141ASN 00.0600.01562.6890.0000.0000.0000.0000.0000.000
72A142ARG 10.9540.98557.2800.0160.0160.0000.0000.0000.000
73A143LEU 0-0.0100.01257.570-0.001-0.0010.0000.0000.0000.000
74A144ARG 10.8280.88459.7240.0140.0140.0000.0000.0000.000
75A145ARG 10.8040.88653.5070.0220.0220.0000.0000.0000.000
76A146LEU 0-0.021-0.00553.378-0.001-0.0010.0000.0000.0000.000
77A147PHE 00.0330.01456.937-0.001-0.0010.0000.0000.0000.000
78A148TYR 0-0.037-0.04859.3820.0000.0000.0000.0000.0000.000
79A149SER 00.028-0.01654.8050.0000.0000.0000.0000.0000.000
80A150SER 0-0.071-0.03355.106-0.001-0.0010.0000.0000.0000.000
81A151LEU 0-0.028-0.01656.1820.0000.0000.0000.0000.0000.000
82A152ASN 0-0.019-0.00454.6400.0000.0000.0000.0000.0000.000
83A153TYR 0-0.003-0.00857.1290.0000.0000.0000.0000.0000.000
84A154ASP -1-0.857-0.91560.002-0.020-0.0200.0000.0000.0000.000
85A155GLU -1-0.884-0.95862.336-0.018-0.0180.0000.0000.0000.000
86A156ASN 0-0.008-0.00765.5830.0010.0010.0000.0000.0000.000
87A157LYS 10.8220.90660.5890.0220.0220.0000.0000.0000.000
88A158ILE 0-0.0120.01361.9100.0010.0010.0000.0000.0000.000
89A159LYS 10.9610.99265.7390.0150.0150.0000.0000.0000.000
90A160LYS 10.8520.91368.8260.0170.0170.0000.0000.0000.000
91A161LEU 00.0310.01164.2180.0010.0010.0000.0000.0000.000
92A162ALA 00.0050.00768.2940.0010.0010.0000.0000.0000.000
93A163THR 0-0.045-0.03069.8700.0010.0010.0000.0000.0000.000
94A164ILE 0-0.023-0.01270.1110.0000.0000.0000.0000.0000.000
95A165LEU 00.012-0.00566.7420.0000.0000.0000.0000.0000.000
96A166ALA 00.0010.02271.4620.0000.0000.0000.0000.0000.000
97A167GLN 0-0.022-0.00374.4100.0010.0010.0000.0000.0000.000
98A168THR 0-0.071-0.03772.0060.0000.0000.0000.0000.0000.000
99A169SER 0-0.011-0.01375.3720.0000.0000.0000.0000.0000.000
100A170SER 0-0.016-0.04175.6970.0000.0000.0000.0000.0000.000
101A171SER 0-0.029-0.02477.7820.0000.0000.0000.0000.0000.000
102A172ASN 00.0260.01374.4330.0000.0000.0000.0000.0000.000
103A173ASP -1-0.832-0.92175.222-0.009-0.0090.0000.0000.0000.000
104A174TYR 0-0.089-0.07566.4990.0000.0000.0000.0000.0000.000
105A175HIS 00.0500.05270.7660.0000.0000.0000.0000.0000.000
106A176TYR 00.0290.00870.712-0.001-0.0010.0000.0000.0000.000
107A177THR 00.0280.02066.5810.0000.0000.0000.0000.0000.000
108A178LEU 0-0.020-0.00265.652-0.001-0.0010.0000.0000.0000.000
109A179ILE 0-0.018-0.00965.923-0.001-0.0010.0000.0000.0000.000
110A180GLY 00.0380.01165.604-0.001-0.0010.0000.0000.0000.000
111A181LEU 0-0.018-0.01561.142-0.001-0.0010.0000.0000.0000.000
112A182ILE 00.0160.04361.101-0.001-0.0010.0000.0000.0000.000
113A183PHE 00.026-0.00161.188-0.001-0.0010.0000.0000.0000.000
114A184TRP 00.016-0.00756.103-0.001-0.0010.0000.0000.0000.000
115A185THR 0-0.043-0.05656.436-0.001-0.0010.0000.0000.0000.000
116A186GLY 00.0530.02556.048-0.001-0.0010.0000.0000.0000.000
117A187PHE 0-0.022-0.03055.949-0.001-0.0010.0000.0000.0000.000
118A188LYS 10.8350.93353.4170.0180.0180.0000.0000.0000.000
119A189ILE 00.0120.01151.063-0.001-0.0010.0000.0000.0000.000
120A190GLN 0-0.018-0.01150.705-0.002-0.0020.0000.0000.0000.000
121A191GLU -1-0.845-0.92450.524-0.021-0.0210.0000.0000.0000.000
122A192ALA 00.0040.00647.394-0.001-0.0010.0000.0000.0000.000
123A193PHE 0-0.017-0.01946.347-0.002-0.0020.0000.0000.0000.000
124A194GLU -1-0.715-0.84246.158-0.027-0.0270.0000.0000.0000.000
125A195SER 0-0.0200.00045.209-0.001-0.0010.0000.0000.0000.000
126A196ALA 00.0240.01242.119-0.002-0.0020.0000.0000.0000.000
127A197VAL 0-0.044-0.02141.582-0.003-0.0030.0000.0000.0000.000
128A198ASN 0-0.065-0.04542.399-0.002-0.0020.0000.0000.0000.000
129A199ILE 0-0.0070.01038.321-0.001-0.0010.0000.0000.0000.000
130A200LEU 0-0.0230.00336.205-0.003-0.0030.0000.0000.0000.000
131A201THR 00.0530.04637.563-0.003-0.0030.0000.0000.0000.000
132A202LYS 10.9740.96536.3690.0460.0460.0000.0000.0000.000
133A203ASP -1-0.912-0.94833.850-0.057-0.0570.0000.0000.0000.000
134A204GLU -1-0.824-0.91532.630-0.056-0.0560.0000.0000.0000.000
135A205GLN 0-0.069-0.05432.348-0.007-0.0070.0000.0000.0000.000
136A206LYS 10.9490.96229.7240.0730.0730.0000.0000.0000.000
137A207ARG 10.8590.93728.3370.0470.0470.0000.0000.0000.000
138A208LEU 0-0.048-0.01727.567-0.006-0.0060.0000.0000.0000.000
139A209ILE 0-0.023-0.01525.966-0.007-0.0070.0000.0000.0000.000
140A210PHE 0-0.032-0.01823.178-0.010-0.0100.0000.0000.0000.000
141A211ASN 0-0.045-0.01422.729-0.006-0.0060.0000.0000.0000.000
142A212PHE 0-0.0400.00124.0320.0060.0060.0000.0000.0000.000
143A213ARG 10.9910.99822.8960.0680.0680.0000.0000.0000.000
144A214THR 00.0700.01723.9030.0070.0070.0000.0000.0000.000
145A215LYS 10.7920.89525.8780.0690.0690.0000.0000.0000.000
146A216THR 00.0090.00427.5840.0040.0040.0000.0000.0000.000
147A217VAL 00.0270.02927.7290.0060.0060.0000.0000.0000.000
148A218LYS 10.9340.97429.9980.0740.0740.0000.0000.0000.000
149A219GLU -1-0.896-0.94831.938-0.050-0.0500.0000.0000.0000.000
150A220ILE 00.0190.01132.0660.0040.0040.0000.0000.0000.000
151A221GLN 0-0.0070.00134.3120.0000.0000.0000.0000.0000.000
152A222GLU -1-0.909-0.96335.792-0.055-0.0550.0000.0000.0000.000
153A223ASN 0-0.043-0.03337.3870.0060.0060.0000.0000.0000.000
154A224PHE 00.0280.00738.9340.0030.0030.0000.0000.0000.000
155A225GLU -1-0.884-0.95939.692-0.050-0.0500.0000.0000.0000.000
156A226LYS 10.9200.95341.2380.0400.0400.0000.0000.0000.000
157A227LEU 00.0020.01843.5900.0020.0020.0000.0000.0000.000
158A228MET 0-0.034-0.00944.0810.0010.0010.0000.0000.0000.000
159A229GLN 0-0.032-0.01146.4540.0010.0010.0000.0000.0000.000
160A230GLU -1-0.899-0.96047.797-0.026-0.0260.0000.0000.0000.000
161A231ARG 10.8430.90749.7070.0300.0300.0000.0000.0000.000
162A232ASN 00.002-0.01250.3580.0020.0020.0000.0000.0000.000
163A233SER 0-0.074-0.04051.7320.0010.0010.0000.0000.0000.000
164A234TRP 00.0310.02054.1030.0010.0010.0000.0000.0000.000
165A235ILE 0-0.013-0.00854.8270.0010.0010.0000.0000.0000.000
166A236LYS 10.9330.96854.0690.0280.0280.0000.0000.0000.000
167A237ILE 00.0190.03057.3640.0010.0010.0000.0000.0000.000
168A238VAL 00.0130.01160.4340.0010.0010.0000.0000.0000.000
169A239ASP -1-0.839-0.90760.804-0.021-0.0210.0000.0000.0000.000
170A240ASN 0-0.048-0.02761.1540.0010.0010.0000.0000.0000.000
171A241ILE 00.0080.01464.0100.0010.0010.0000.0000.0000.000
172A242ILE 0-0.037-0.02565.4640.0010.0010.0000.0000.0000.000
173A243GLY 00.0350.02167.2100.0000.0000.0000.0000.0000.000
174A244GLU -1-0.849-0.86468.124-0.015-0.0150.0000.0000.0000.000
175A245TYR 0-0.013-0.00170.8030.0010.0010.0000.0000.0000.000
176A246ASP -1-0.868-0.94070.835-0.015-0.0150.0000.0000.0000.000
177A247LYS 10.8920.93868.8740.0160.0160.0000.0000.0000.000
178A248ASN 0-0.0100.00374.1520.0000.0000.0000.0000.0000.000
179A249THR 00.008-0.01271.9370.0000.0000.0000.0000.0000.000
180A250GLY 0-0.003-0.00675.1810.0000.0000.0000.0000.0000.000
181A251GLY 0-0.016-0.01278.0700.0000.0000.0000.0000.0000.000
182A252CYS 0-0.041-0.00574.1250.0000.0000.0000.0000.0000.000
183A253LYS 10.9180.96176.5490.0130.0130.0000.0000.0000.000
184A254ALA 0-0.044-0.00778.9860.0000.0000.0000.0000.0000.000
185A255ASP -1-0.845-0.93080.442-0.010-0.0100.0000.0000.0000.000
186A256GLY 00.0990.04877.9290.0000.0000.0000.0000.0000.000
187A257LYS 10.8740.91976.9100.0090.0090.0000.0000.0000.000
188A258ILE 0-0.0240.00776.7780.0000.0000.0000.0000.0000.000
189A259LEU 00.0070.00272.9120.0000.0000.0000.0000.0000.000
190A260GLY 00.0300.00872.6410.0000.0000.0000.0000.0000.000
191A261GLU -1-0.837-0.87671.677-0.012-0.0120.0000.0000.0000.000
192A262VAL 0-0.028-0.01270.8410.0000.0000.0000.0000.0000.000
193A263ILE 0-0.016-0.00867.184-0.001-0.0010.0000.0000.0000.000
194A264ARG 10.8430.88467.2520.0110.0110.0000.0000.0000.000
195A265VAL 0-0.020-0.00666.9200.0000.0000.0000.0000.0000.000
196A266GLY 00.0090.03066.6600.0000.0000.0000.0000.0000.000
197A267TYR 0-0.044-0.09862.666-0.001-0.0010.0000.0000.0000.000
198A268GLU -1-0.808-0.86062.329-0.014-0.0140.0000.0000.0000.000
199A269HIS 10.7770.85960.7130.0160.0160.0000.0000.0000.000
200A270GLU -1-0.940-0.97158.136-0.020-0.0200.0000.0000.0000.000
201A271LEU 0-0.093-0.02457.404-0.001-0.0010.0000.0000.0000.000
202A272ASP -1-0.817-0.93352.791-0.021-0.0210.0000.0000.0000.000
203A273SER 00.0000.00052.967-0.001-0.0010.0000.0000.0000.000
204A274ASN 0-0.011-0.00751.320-0.001-0.0010.0000.0000.0000.000
205A275LYS 10.9901.00347.1730.0260.0260.0000.0000.0000.000
206A276SER 0-0.0050.00347.070-0.002-0.0020.0000.0000.0000.000
207A277MET 00.0360.00746.547-0.002-0.0020.0000.0000.0000.000
208A278GLN 0-0.056-0.02842.4100.0010.0010.0000.0000.0000.000
209A279ILE 0-0.036-0.02141.982-0.001-0.0010.0000.0000.0000.000
210A280LEU 00.0070.01841.596-0.002-0.0020.0000.0000.0000.000
211A281ASN 00.0520.03441.271-0.002-0.0020.0000.0000.0000.000
212A282ASN 0-0.022-0.01838.5380.0010.0010.0000.0000.0000.000
213A283ILE 0-0.026-0.00437.126-0.003-0.0030.0000.0000.0000.000
214A284GLU -1-0.872-0.95736.709-0.031-0.0310.0000.0000.0000.000
215A285THR 0-0.122-0.06136.617-0.001-0.0010.0000.0000.0000.000
216A286PRO 00.0050.00032.1930.0000.0000.0000.0000.0000.000
217A287LEU 00.0540.02331.760-0.003-0.0030.0000.0000.0000.000
218A288LYS 10.9390.97733.2670.0260.0260.0000.0000.0000.000
219A289THR 0-0.058-0.01627.8390.0040.0040.0000.0000.0000.000
220A290NME 0-0.034-0.00729.494-0.002-0.0020.0000.0000.0000.000