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

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FMODB ID: Q1Q4Y

Calculation Name: 4AXZ-A-Xray372

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: 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646945.541906
FMO2-HF: Nuclear repulsion 2558176.858788
FMO2-HF: Total energy -88768.683118
FMO2-MP2: Total energy -89030.328407


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:72:ASN)


Summations of interaction energy for fragment #1(A:72: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.
-27.273-22.824.686-3.64-5.501-0.012
Interaction energy analysis for fragmet #1(A:72:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.020
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].
3A74LYS10.9470.9682.757-9.698-7.7230.611-0.845-1.7410.001
4A75GLU-1-0.899-0.9442.087-16.344-14.3004.070-2.716-3.399-0.013
5A76LYS10.9770.9903.508-1.658-1.2240.005-0.079-0.3610.000
6A77ILE00.002-0.0085.417-0.101-0.1010.0000.0000.0000.000
7A78ILE00.0190.0056.737-0.202-0.2020.0000.0000.0000.000
8A79LYS10.9110.9546.7371.4601.4600.0000.0000.0000.000
9A80LYS10.9670.9819.382-0.482-0.4820.0000.0000.0000.000
10A81ILE00.0260.03211.1340.0200.0200.0000.0000.0000.000
11A82ALA0-0.011-0.00512.519-0.012-0.0120.0000.0000.0000.000
12A83GLN0-0.040-0.02113.678-0.018-0.0180.0000.0000.0000.000
13A84GLU-1-0.852-0.93215.5190.3130.3130.0000.0000.0000.000
14A85PHE0-0.052-0.02116.5730.0080.0080.0000.0000.0000.000
15A86ASP-1-0.868-0.93117.972-0.279-0.2790.0000.0000.0000.000
16A87GLU-1-0.933-0.98219.038-0.072-0.0720.0000.0000.0000.000
17A88ASN0-0.025-0.02820.9520.0060.0060.0000.0000.0000.000
18A89GLU-1-0.878-0.93222.927-0.106-0.1060.0000.0000.0000.000
19A90LYS10.9200.96722.7850.1730.1730.0000.0000.0000.000
20A91LEU0-0.035-0.02124.6850.0030.0030.0000.0000.0000.000
21A92ILE00.0270.02127.2410.0050.0050.0000.0000.0000.000
22A93ASN0-0.037-0.03427.9940.0130.0130.0000.0000.0000.000
23A94LYS10.8720.95429.6510.0230.0230.0000.0000.0000.000
24A95ILE00.0170.01332.3960.0030.0030.0000.0000.0000.000
25A96GLY00.0140.01333.3330.0030.0030.0000.0000.0000.000
26A97PRO00.014-0.00433.9980.0030.0030.0000.0000.0000.000
27A98ASN0-0.014-0.00837.2290.0000.0000.0000.0000.0000.000
28A99ILE00.0360.02635.1880.0020.0020.0000.0000.0000.000
29A100GLU-1-0.935-0.95538.068-0.011-0.0110.0000.0000.0000.000
30A101MET00.0260.02039.8740.0000.0000.0000.0000.0000.000
31A102PHE0-0.012-0.02841.0750.0010.0010.0000.0000.0000.000
32A103ALA00.0520.02641.4570.0020.0020.0000.0000.0000.000
33A104GLN0-0.0110.00043.4750.0000.0000.0000.0000.0000.000
34A105THR0-0.026-0.01245.859-0.001-0.0010.0000.0000.0000.000
35A106ILE00.0070.00544.6130.0010.0010.0000.0000.0000.000
36A107ASN0-0.045-0.02447.339-0.002-0.0020.0000.0000.0000.000
37A108THR00.008-0.01449.107-0.001-0.0010.0000.0000.0000.000
38A109ASP-1-0.808-0.89451.5710.0150.0150.0000.0000.0000.000
39A110ILE0-0.117-0.05649.4810.0010.0010.0000.0000.0000.000
40A111GLN0-0.050-0.01651.7370.0010.0010.0000.0000.0000.000
41A112LYS10.8760.96655.173-0.011-0.0110.0000.0000.0000.000
42A113ILE0-0.016-0.00358.0420.0020.0020.0000.0000.0000.000
43A114GLU-1-0.764-0.81761.4730.0240.0240.0000.0000.0000.000
44A115PRO00.0280.02662.6680.0000.0000.0000.0000.0000.000
45A116ASN00.031-0.01066.1920.0020.0020.0000.0000.0000.000
46A117ASP-1-0.900-0.94568.4180.0150.0150.0000.0000.0000.000
47A118GLN0-0.062-0.03364.9760.0010.0010.0000.0000.0000.000
48A119PHE00.0340.01061.5390.0010.0010.0000.0000.0000.000
49A120GLY0-0.004-0.01666.1400.0000.0000.0000.0000.0000.000
50A121ILE00.0050.01362.4410.0010.0010.0000.0000.0000.000
51A122ASN00.0130.02166.3950.0010.0010.0000.0000.0000.000
52A123LYS11.0260.99269.054-0.026-0.0260.0000.0000.0000.000
53A124THR0-0.122-0.08071.6800.0000.0000.0000.0000.0000.000
54A125LEU0-0.0230.00671.122-0.001-0.0010.0000.0000.0000.000
55A126PHE0-0.0080.00967.3840.0000.0000.0000.0000.0000.000
56A127THR0-0.044-0.02670.8310.0000.0000.0000.0000.0000.000
57A128GLU-1-0.908-0.96970.1470.0300.0300.0000.0000.0000.000
58A129LYS10.8810.92969.501-0.035-0.0350.0000.0000.0000.000
59A130LYS10.9010.97269.845-0.029-0.0290.0000.0000.0000.000
60A131ASP-1-0.729-0.88363.8760.0410.0410.0000.0000.0000.000
61A132ASN00.0100.00462.381-0.002-0.0020.0000.0000.0000.000
62A133ASN00.0010.01159.3450.0020.0020.0000.0000.0000.000
63A134ILE0-0.014-0.00861.505-0.001-0.0010.0000.0000.0000.000
64A135ASP-1-0.806-0.90164.3700.0360.0360.0000.0000.0000.000
65A136PHE0-0.095-0.05058.9180.0000.0000.0000.0000.0000.000
66A137MET0-0.0140.01659.5220.0000.0000.0000.0000.0000.000
67A138LEU0-0.032-0.00761.873-0.002-0.0020.0000.0000.0000.000
68A139LYS10.8910.95362.005-0.045-0.0450.0000.0000.0000.000
69A140ASP-1-0.883-0.94757.7060.0440.0440.0000.0000.0000.000
70A141ASN00.0590.01659.5820.0020.0020.0000.0000.0000.000
71A142ARG10.9510.98454.257-0.047-0.0470.0000.0000.0000.000
72A143LEU0-0.0080.01254.4560.0000.0000.0000.0000.0000.000
73A144ARG10.8290.88556.512-0.029-0.0290.0000.0000.0000.000
74A145ARG10.8030.88550.123-0.035-0.0350.0000.0000.0000.000
75A146LEU0-0.023-0.00550.057-0.002-0.0020.0000.0000.0000.000
76A147PHE00.0350.01553.410-0.001-0.0010.0000.0000.0000.000
77A148TYR0-0.038-0.04955.853-0.002-0.0020.0000.0000.0000.000
78A149SER00.025-0.01751.145-0.002-0.0020.0000.0000.0000.000
79A150SER0-0.065-0.03051.425-0.002-0.0020.0000.0000.0000.000
80A151LEU0-0.026-0.01652.507-0.001-0.0010.0000.0000.0000.000
81A152ASN0-0.027-0.00750.631-0.001-0.0010.0000.0000.0000.000
82A153TYR0-0.001-0.00753.212-0.003-0.0030.0000.0000.0000.000
83A154ASP-1-0.854-0.91556.1820.0030.0030.0000.0000.0000.000
84A155GLU-1-0.886-0.95958.3380.0090.0090.0000.0000.0000.000
85A156ASN0-0.010-0.00761.7130.0020.0020.0000.0000.0000.000
86A157LYS10.8240.90656.376-0.008-0.0080.0000.0000.0000.000
87A158ILE0-0.0090.01458.1530.0020.0020.0000.0000.0000.000
88A159LYS10.9620.99261.962-0.010-0.0100.0000.0000.0000.000
89A160LYS10.8450.91164.788-0.006-0.0060.0000.0000.0000.000
90A161LEU00.0380.01360.4910.0010.0010.0000.0000.0000.000
91A162ALA00.0000.00564.4930.0010.0010.0000.0000.0000.000
92A163THR0-0.045-0.03066.2260.0000.0000.0000.0000.0000.000
93A164ILE0-0.021-0.01166.1240.0000.0000.0000.0000.0000.000
94A165LEU00.014-0.00463.1830.0010.0010.0000.0000.0000.000
95A166ALA0-0.0010.02067.8890.0010.0010.0000.0000.0000.000
96A167GLN0-0.021-0.00270.884-0.001-0.0010.0000.0000.0000.000
97A168THR0-0.070-0.03668.4730.0000.0000.0000.0000.0000.000
98A169SER0-0.014-0.01471.8680.0000.0000.0000.0000.0000.000
99A170SER0-0.014-0.04172.3990.0010.0010.0000.0000.0000.000
100A171SER0-0.026-0.02374.496-0.001-0.0010.0000.0000.0000.000
101A172ASN00.0240.01271.345-0.001-0.0010.0000.0000.0000.000
102A173ASP-1-0.831-0.92072.1740.0310.0310.0000.0000.0000.000
103A174TYR0-0.089-0.07663.3790.0010.0010.0000.0000.0000.000
104A175HIS00.0490.05367.5870.0010.0010.0000.0000.0000.000
105A176TYR00.0270.00667.4190.0000.0000.0000.0000.0000.000
106A177THR00.0290.02163.5120.0010.0010.0000.0000.0000.000
107A178LEU0-0.020-0.00262.3130.0010.0010.0000.0000.0000.000
108A179ILE0-0.020-0.01062.5940.0000.0000.0000.0000.0000.000
109A180GLY00.0380.01162.2630.0000.0000.0000.0000.0000.000
110A181LEU0-0.020-0.01658.0460.0020.0020.0000.0000.0000.000
111A182ILE00.0140.04257.7950.0010.0010.0000.0000.0000.000
112A183PHE00.0290.00057.7550.0000.0000.0000.0000.0000.000
113A184TRP00.019-0.00553.1970.0010.0010.0000.0000.0000.000
114A185THR0-0.044-0.05753.0460.0030.0030.0000.0000.0000.000
115A186GLY00.0520.02552.6430.0010.0010.0000.0000.0000.000
116A187PHE0-0.019-0.02952.4820.0010.0010.0000.0000.0000.000
117A188LYS10.8400.93550.435-0.061-0.0610.0000.0000.0000.000
118A189ILE00.0060.01047.5250.0030.0030.0000.0000.0000.000
119A190GLN0-0.016-0.01147.2500.0010.0010.0000.0000.0000.000
120A191GLU-1-0.853-0.92747.3870.0620.0620.0000.0000.0000.000
121A192ALA00.0070.00744.1080.0030.0030.0000.0000.0000.000
122A193PHE0-0.022-0.02042.6950.0030.0030.0000.0000.0000.000
123A194GLU-1-0.709-0.84042.6400.0370.0370.0000.0000.0000.000
124A195SER0-0.0220.00042.1040.0010.0010.0000.0000.0000.000
125A196ALA00.0280.01438.7150.0040.0040.0000.0000.0000.000
126A197VAL0-0.036-0.01938.1370.0010.0010.0000.0000.0000.000
127A198ASN0-0.075-0.04938.909-0.005-0.0050.0000.0000.0000.000
128A199ILE0-0.0050.01135.1860.0030.0030.0000.0000.0000.000
129A200LEU0-0.0230.00332.6700.0070.0070.0000.0000.0000.000
130A201THR00.0500.04534.313-0.012-0.0120.0000.0000.0000.000
131A202LYS10.9750.96632.7460.0000.0000.0000.0000.0000.000
132A203ASP-1-0.911-0.94830.5730.0590.0590.0000.0000.0000.000
133A204GLU-1-0.824-0.91429.3880.1460.1460.0000.0000.0000.000
134A205GLN0-0.069-0.05328.9840.0010.0010.0000.0000.0000.000
135A206LYS10.9500.96326.297-0.037-0.0370.0000.0000.0000.000
136A207ARG10.8640.93524.874-0.173-0.1730.0000.0000.0000.000
137A208LEU0-0.049-0.01724.3190.0230.0230.0000.0000.0000.000
138A209ILE0-0.017-0.01422.1260.0170.0170.0000.0000.0000.000
139A210PHE0-0.032-0.01919.5410.0000.0000.0000.0000.0000.000
140A211ASN0-0.048-0.01619.4460.0100.0100.0000.0000.0000.000
141A212PHE0-0.0360.00421.0790.0460.0460.0000.0000.0000.000
142A213ARG10.9890.99719.676-0.348-0.3480.0000.0000.0000.000
143A214THR00.0690.01620.251-0.019-0.0190.0000.0000.0000.000
144A215LYS10.7920.89422.071-0.233-0.2330.0000.0000.0000.000
145A216THR00.0100.00524.2080.0020.0020.0000.0000.0000.000
146A217VAL00.0240.02824.101-0.013-0.0130.0000.0000.0000.000
147A218LYS10.9380.97626.167-0.076-0.0760.0000.0000.0000.000
148A219GLU-1-0.896-0.94927.9560.1720.1720.0000.0000.0000.000
149A220ILE00.0190.01228.691-0.009-0.0090.0000.0000.0000.000
150A221GLN0-0.0070.00030.294-0.005-0.0050.0000.0000.0000.000
151A222GLU-1-0.908-0.96331.5480.0450.0450.0000.0000.0000.000
152A223ASN0-0.043-0.03333.893-0.009-0.0090.0000.0000.0000.000
153A224PHE00.0290.00735.224-0.004-0.0040.0000.0000.0000.000
154A225GLU-1-0.885-0.95935.1530.0040.0040.0000.0000.0000.000
155A226LYS10.9190.95237.451-0.070-0.0700.0000.0000.0000.000
156A227LEU0-0.0030.01639.826-0.002-0.0020.0000.0000.0000.000
157A228MET0-0.029-0.00739.895-0.004-0.0040.0000.0000.0000.000
158A229GLN0-0.032-0.01142.369-0.007-0.0070.0000.0000.0000.000
159A230GLU-1-0.899-0.96044.0740.0450.0450.0000.0000.0000.000
160A231ARG10.8450.90845.856-0.025-0.0250.0000.0000.0000.000
161A232ASN00.001-0.01345.952-0.001-0.0010.0000.0000.0000.000
162A233SER0-0.075-0.04047.622-0.004-0.0040.0000.0000.0000.000
163A234TRP00.0310.02050.1320.0000.0000.0000.0000.0000.000
164A235ILE0-0.009-0.00750.713-0.002-0.0020.0000.0000.0000.000
165A236LYS10.9290.96649.603-0.011-0.0110.0000.0000.0000.000
166A237ILE00.0180.03053.542-0.002-0.0020.0000.0000.0000.000
167A238VAL00.0130.01156.441-0.001-0.0010.0000.0000.0000.000
168A239ASP-1-0.836-0.90756.4230.0080.0080.0000.0000.0000.000
169A240ASN0-0.052-0.02956.789-0.003-0.0030.0000.0000.0000.000
170A241ILE00.0120.01560.206-0.001-0.0010.0000.0000.0000.000
171A242ILE0-0.034-0.02461.335-0.001-0.0010.0000.0000.0000.000
172A243GLY00.0320.02062.932-0.001-0.0010.0000.0000.0000.000
173A244GLU-1-0.848-0.86463.8850.0130.0130.0000.0000.0000.000
174A245TYR0-0.013-0.00166.557-0.001-0.0010.0000.0000.0000.000
175A246ASP-1-0.867-0.94166.4210.0050.0050.0000.0000.0000.000
176A247LYS10.8890.93764.407-0.010-0.0100.0000.0000.0000.000
177A248ASN0-0.0070.00469.6700.0000.0000.0000.0000.0000.000
178A249THR00.006-0.01367.654-0.001-0.0010.0000.0000.0000.000
179A250GLY0-0.003-0.00770.9150.0010.0010.0000.0000.0000.000
180A251GLY0-0.013-0.01073.9060.0000.0000.0000.0000.0000.000
181A252CYS0-0.042-0.00670.0580.0000.0000.0000.0000.0000.000
182A253LYS10.9190.96172.248-0.006-0.0060.0000.0000.0000.000
183A254ALA0-0.042-0.00774.9160.0000.0000.0000.0000.0000.000
184A255ASP-1-0.846-0.92976.5260.0170.0170.0000.0000.0000.000
185A256GLY00.0960.04774.2480.0000.0000.0000.0000.0000.000
186A257LYS10.8810.92173.331-0.021-0.0210.0000.0000.0000.000
187A258ILE0-0.0300.00573.0630.0010.0010.0000.0000.0000.000
188A259LEU00.0060.00169.0120.0000.0000.0000.0000.0000.000
189A260GLY00.0330.00869.0870.0010.0010.0000.0000.0000.000
190A261GLU-1-0.841-0.87768.1290.0280.0280.0000.0000.0000.000
191A262VAL0-0.024-0.01066.8600.0010.0010.0000.0000.0000.000
192A263ILE0-0.017-0.00863.4660.0000.0000.0000.0000.0000.000
193A264ARG10.8420.88463.574-0.029-0.0290.0000.0000.0000.000
194A265VAL0-0.018-0.00663.3760.0020.0020.0000.0000.0000.000
195A266GLY00.0080.02962.7590.0010.0010.0000.0000.0000.000
196A267TYR0-0.044-0.09758.7250.0000.0000.0000.0000.0000.000
197A268GLU-1-0.810-0.86058.7210.0400.0400.0000.0000.0000.000
198A269HIS10.7780.86057.226-0.030-0.0300.0000.0000.0000.000
199A270GLU-1-0.939-0.97154.2970.0320.0320.0000.0000.0000.000
200A271LEU0-0.094-0.02553.7900.0000.0000.0000.0000.0000.000
201A272ASP-1-0.816-0.93249.4640.0610.0610.0000.0000.0000.000
202A273SER0-0.0010.00149.6380.0010.0010.0000.0000.0000.000
203A274ASN0-0.011-0.00748.1150.0050.0050.0000.0000.0000.000
204A275LYS10.9891.00343.666-0.051-0.0510.0000.0000.0000.000
205A276SER0-0.0080.00243.8130.0030.0030.0000.0000.0000.000
206A277MET00.0400.00943.2900.0030.0030.0000.0000.0000.000
207A278GLN0-0.055-0.02839.5340.0040.0040.0000.0000.0000.000
208A279ILE0-0.038-0.02238.5630.0080.0080.0000.0000.0000.000
209A280LEU00.0050.01838.3510.0030.0030.0000.0000.0000.000
210A281ASN00.0540.03538.1930.0130.0130.0000.0000.0000.000
211A282ASN0-0.023-0.01935.4580.0170.0170.0000.0000.0000.000
212A283ILE0-0.028-0.00434.0440.0080.0080.0000.0000.0000.000
213A284GLU-1-0.867-0.95533.6320.1150.1150.0000.0000.0000.000
214A285THR0-0.123-0.06134.0010.0170.0170.0000.0000.0000.000
215A286PRO0-0.002-0.00429.2120.0190.0190.0000.0000.0000.000
216A287LEU00.0370.01329.0470.0190.0190.0000.0000.0000.000
217A288LYS10.9040.97130.636-0.177-0.1770.0000.0000.0000.000
218A289THR0-0.040-0.00325.3680.0190.0190.0000.0000.0000.000