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: K3NZ3

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 OptHSide
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 -2649325.839776
FMO2-HF: Nuclear repulsion 2560555.56089
FMO2-HF: Total energy -88770.278886
FMO2-MP2: Total energy -89031.943238


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.
-18.93-15.4323.314-2.559-4.253-0.002
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 : 0.000 / q_NPA : -0.018
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].
3A74LYS10.9390.9672.788-9.610-7.5710.510-0.842-1.7070.000
4A75GLU-1-0.822-0.8942.111-11.292-10.2352.800-1.625-2.232-0.002
5A76LYS10.8810.9233.620-1.537-1.1350.004-0.092-0.3140.000
6A77ILE0-0.003-0.0085.5140.2180.2180.0000.0000.0000.000
7A78ILE00.008-0.0016.761-0.069-0.0690.0000.0000.0000.000
8A79LYS10.8410.9126.7373.1663.1660.0000.0000.0000.000
9A80LYS10.9750.9839.5010.5230.5230.0000.0000.0000.000
10A81ILE00.0240.03110.9630.0800.0800.0000.0000.0000.000
11A82ALA0-0.0010.00112.5870.0300.0300.0000.0000.0000.000
12A83GLN0-0.062-0.03713.795-0.059-0.0590.0000.0000.0000.000
13A84GLU-1-0.837-0.91315.6380.0660.0660.0000.0000.0000.000
14A85PHE0-0.044-0.02116.5620.0330.0330.0000.0000.0000.000
15A86ASP-1-0.836-0.91818.226-0.407-0.4070.0000.0000.0000.000
16A87GLU-1-0.865-0.92519.023-0.332-0.3320.0000.0000.0000.000
17A88ASN0-0.020-0.02021.0640.0150.0150.0000.0000.0000.000
18A89GLU-1-0.832-0.91423.049-0.216-0.2160.0000.0000.0000.000
19A90LYS10.7830.88422.3500.3370.3370.0000.0000.0000.000
20A91LEU0-0.030-0.01524.8340.0150.0150.0000.0000.0000.000
21A92ILE00.0190.00827.3100.0150.0150.0000.0000.0000.000
22A93ASN0-0.032-0.02527.9810.0270.0270.0000.0000.0000.000
23A94LYS10.7630.89730.1620.1070.1070.0000.0000.0000.000
24A95ILE0-0.021-0.00932.2870.0080.0080.0000.0000.0000.000
25A96GLY00.0230.01833.4570.0090.0090.0000.0000.0000.000
26A97PRO00.014-0.00334.1720.0080.0080.0000.0000.0000.000
27A98ASN0-0.010-0.00737.3520.0010.0010.0000.0000.0000.000
28A99ILE00.0290.02135.2420.0060.0060.0000.0000.0000.000
29A100GLU-1-0.908-0.93037.777-0.052-0.0520.0000.0000.0000.000
30A101MET00.0290.01739.8940.0030.0030.0000.0000.0000.000
31A102PHE0-0.002-0.01141.0740.0040.0040.0000.0000.0000.000
32A103ALA00.0450.02341.4370.0050.0050.0000.0000.0000.000
33A104GLN0-0.0050.00343.4990.0010.0010.0000.0000.0000.000
34A105THR0-0.027-0.01945.8800.0020.0020.0000.0000.0000.000
35A106ILE0-0.005-0.00144.6150.0020.0020.0000.0000.0000.000
36A107ASN0-0.034-0.01447.3070.0010.0010.0000.0000.0000.000
37A108THR00.014-0.01349.1300.0010.0010.0000.0000.0000.000
38A109ASP-1-0.761-0.85451.588-0.014-0.0140.0000.0000.0000.000
39A110ILE0-0.115-0.05449.4830.0020.0020.0000.0000.0000.000
40A111GLN0-0.071-0.03251.7840.0030.0030.0000.0000.0000.000
41A112LYS10.8330.93855.2220.0170.0170.0000.0000.0000.000
42A113ILE0-0.017-0.00258.0660.0020.0020.0000.0000.0000.000
43A114GLU-1-0.780-0.83461.4250.0020.0020.0000.0000.0000.000
44A115PRO00.0280.02762.6930.0010.0010.0000.0000.0000.000
45A116ASN00.026-0.01266.2170.0010.0010.0000.0000.0000.000
46A117ASP-1-0.874-0.94068.369-0.004-0.0040.0000.0000.0000.000
47A118GLN0-0.070-0.04264.9640.0010.0010.0000.0000.0000.000
48A119PHE00.0250.00761.4200.0000.0000.0000.0000.0000.000
49A120GLY00.011-0.00566.167-0.001-0.0010.0000.0000.0000.000
50A121ILE0-0.0070.00962.3920.0010.0010.0000.0000.0000.000
51A122ASN00.0110.01366.4250.0020.0020.0000.0000.0000.000
52A123LYS10.9000.92269.084-0.012-0.0120.0000.0000.0000.000
53A124THR0-0.117-0.06671.7110.0000.0000.0000.0000.0000.000
54A125LEU0-0.0250.00471.215-0.001-0.0010.0000.0000.0000.000
55A126PHE0-0.0060.00867.2450.0000.0000.0000.0000.0000.000
56A127THR0-0.025-0.02070.8630.0010.0010.0000.0000.0000.000
57A128GLU-1-0.805-0.90970.1810.0140.0140.0000.0000.0000.000
58A129LYS10.8920.93569.557-0.019-0.0190.0000.0000.0000.000
59A130LYS10.8280.92569.917-0.011-0.0110.0000.0000.0000.000
60A131ASP-1-0.720-0.88063.7890.0170.0170.0000.0000.0000.000
61A132ASN0-0.011-0.00462.4760.0000.0000.0000.0000.0000.000
62A133ASN0-0.051-0.01659.3300.0020.0020.0000.0000.0000.000
63A134ILE00.0070.00661.540-0.001-0.0010.0000.0000.0000.000
64A135ASP-1-0.804-0.90264.4030.0170.0170.0000.0000.0000.000
65A136PHE0-0.068-0.04459.4340.0010.0010.0000.0000.0000.000
66A137MET0-0.0040.02159.5920.0000.0000.0000.0000.0000.000
67A138LEU0-0.041-0.00861.905-0.001-0.0010.0000.0000.0000.000
68A139LYS10.8760.95262.267-0.024-0.0240.0000.0000.0000.000
69A140ASP-1-0.806-0.89458.0560.0220.0220.0000.0000.0000.000
70A141ASN00.0620.01959.6250.0010.0010.0000.0000.0000.000
71A142ARG10.8650.93154.407-0.025-0.0250.0000.0000.0000.000
72A143LEU0-0.0160.00454.505-0.001-0.0010.0000.0000.0000.000
73A144ARG10.8230.87856.543-0.009-0.0090.0000.0000.0000.000
74A145ARG10.7890.85850.036-0.004-0.0040.0000.0000.0000.000
75A146LEU0-0.022-0.00750.066-0.003-0.0030.0000.0000.0000.000
76A147PHE00.0370.01653.438-0.003-0.0030.0000.0000.0000.000
77A148TYR0-0.025-0.02955.882-0.003-0.0030.0000.0000.0000.000
78A149SER00.028-0.02551.215-0.002-0.0020.0000.0000.0000.000
79A150SER0-0.077-0.03151.452-0.003-0.0030.0000.0000.0000.000
80A151LEU0-0.026-0.01452.535-0.002-0.0020.0000.0000.0000.000
81A152ASN0-0.035-0.02050.868-0.001-0.0010.0000.0000.0000.000
82A153TYR0-0.012-0.00953.269-0.001-0.0010.0000.0000.0000.000
83A154ASP-1-0.830-0.90356.207-0.025-0.0250.0000.0000.0000.000
84A155GLU-1-0.861-0.95358.434-0.013-0.0130.0000.0000.0000.000
85A156ASN0-0.015-0.00761.7380.0030.0030.0000.0000.0000.000
86A157LYS10.8180.89656.4680.0260.0260.0000.0000.0000.000
87A158ILE0-0.0150.00958.1040.0020.0020.0000.0000.0000.000
88A159LYS10.9610.99761.9880.0100.0100.0000.0000.0000.000
89A160LYS10.8030.89364.9380.0200.0200.0000.0000.0000.000
90A161LEU00.0390.01360.5480.0010.0010.0000.0000.0000.000
91A162ALA0-0.0010.00864.5720.0020.0020.0000.0000.0000.000
92A163THR0-0.044-0.04966.2550.0010.0010.0000.0000.0000.000
93A164ILE0-0.0130.00766.3100.0010.0010.0000.0000.0000.000
94A165LEU00.016-0.00563.1970.0010.0010.0000.0000.0000.000
95A166ALA0-0.0030.01767.9190.0010.0010.0000.0000.0000.000
96A167GLN0-0.0290.00370.9150.0000.0000.0000.0000.0000.000
97A168THR0-0.069-0.03568.5130.0000.0000.0000.0000.0000.000
98A169SER0-0.015-0.01471.8990.0010.0010.0000.0000.0000.000
99A170SER00.003-0.03172.3910.0000.0000.0000.0000.0000.000
100A171SER0-0.035-0.03274.5290.0000.0000.0000.0000.0000.000
101A172ASN00.0280.01071.1480.0000.0000.0000.0000.0000.000
102A173ASP-1-0.763-0.87572.3480.0110.0110.0000.0000.0000.000
103A174TYR0-0.048-0.04163.5130.0010.0010.0000.0000.0000.000
104A175HIS00.0570.06167.6210.0000.0000.0000.0000.0000.000
105A176TYR00.009-0.00267.452-0.001-0.0010.0000.0000.0000.000
106A177THR00.0280.01963.5360.0000.0000.0000.0000.0000.000
107A178LEU0-0.0070.00462.4100.0000.0000.0000.0000.0000.000
108A179ILE0-0.010-0.00762.627-0.001-0.0010.0000.0000.0000.000
109A180GLY00.011-0.00262.2960.0000.0000.0000.0000.0000.000
110A181LEU00.008-0.00158.1420.0010.0010.0000.0000.0000.000
111A182ILE00.0000.01657.828-0.001-0.0010.0000.0000.0000.000
112A183PHE00.029-0.00157.786-0.001-0.0010.0000.0000.0000.000
113A184TRP00.0370.00253.0340.0010.0010.0000.0000.0000.000
114A185THR0-0.042-0.03953.0210.0010.0010.0000.0000.0000.000
115A186GLY00.0510.02252.675-0.001-0.0010.0000.0000.0000.000
116A187PHE0-0.023-0.03152.5130.0000.0000.0000.0000.0000.000
117A188LYS10.8010.89450.388-0.028-0.0280.0000.0000.0000.000
118A189ILE00.0110.01547.7570.0010.0010.0000.0000.0000.000
119A190GLN0-0.024-0.01847.280-0.003-0.0030.0000.0000.0000.000
120A191GLU-1-0.804-0.88347.4170.0280.0280.0000.0000.0000.000
121A192ALA00.0220.01444.1960.0030.0030.0000.0000.0000.000
122A193PHE0-0.015-0.01943.0270.0000.0000.0000.0000.0000.000
123A194GLU-1-0.705-0.82142.6690.0010.0010.0000.0000.0000.000
124A195SER0-0.035-0.01442.2150.0020.0020.0000.0000.0000.000
125A196ALA00.0380.01838.7380.0030.0030.0000.0000.0000.000
126A197VAL0-0.041-0.02538.166-0.002-0.0020.0000.0000.0000.000
127A198ASN0-0.082-0.04938.936-0.004-0.0040.0000.0000.0000.000
128A199ILE00.0070.01635.1350.0030.0030.0000.0000.0000.000
129A200LEU0-0.0320.00132.7780.0040.0040.0000.0000.0000.000
130A201THR00.0480.03434.452-0.013-0.0130.0000.0000.0000.000
131A202LYS10.9700.95432.7820.0410.0410.0000.0000.0000.000
132A203ASP-1-0.879-0.93330.5430.0080.0080.0000.0000.0000.000
133A204GLU-1-0.775-0.87529.4130.0790.0790.0000.0000.0000.000
134A205GLN0-0.069-0.04429.012-0.009-0.0090.0000.0000.0000.000
135A206LYS10.8950.92926.475-0.001-0.0010.0000.0000.0000.000
136A207ARG10.8190.89824.898-0.107-0.1070.0000.0000.0000.000
137A208LEU0-0.037-0.02124.3480.0140.0140.0000.0000.0000.000
138A209ILE0-0.022-0.01222.0320.0030.0030.0000.0000.0000.000
139A210PHE0-0.024-0.01619.775-0.014-0.0140.0000.0000.0000.000
140A211ASN0-0.061-0.02619.4740.0240.0240.0000.0000.0000.000
141A212PHE0-0.0230.01121.1130.0450.0450.0000.0000.0000.000
142A213ARG10.9430.97019.395-0.167-0.1670.0000.0000.0000.000
143A214THR00.0690.00120.284-0.005-0.0050.0000.0000.0000.000
144A215LYS10.7750.87622.178-0.057-0.0570.0000.0000.0000.000
145A216THR00.0030.00124.2410.0110.0110.0000.0000.0000.000
146A217VAL00.0350.03824.1600.0000.0000.0000.0000.0000.000
147A218LYS10.8920.94026.2750.0740.0740.0000.0000.0000.000
148A219GLU-1-0.857-0.91728.0630.0530.0530.0000.0000.0000.000
149A220ILE00.0330.02128.695-0.001-0.0010.0000.0000.0000.000
150A221GLN00.009-0.00530.322-0.006-0.0060.0000.0000.0000.000
151A222GLU-1-0.870-0.92631.496-0.069-0.0690.0000.0000.0000.000
152A223ASN0-0.093-0.06233.6990.0020.0020.0000.0000.0000.000
153A224PHE00.0570.02235.2730.0020.0020.0000.0000.0000.000
154A225GLU-1-0.768-0.88734.568-0.081-0.0810.0000.0000.0000.000
155A226LYS10.9220.95735.9660.0210.0210.0000.0000.0000.000
156A227LEU00.0060.02339.9290.0010.0010.0000.0000.0000.000
157A228MET0-0.026-0.00639.914-0.001-0.0010.0000.0000.0000.000
158A229GLN0-0.0050.00442.484-0.003-0.0030.0000.0000.0000.000
159A230GLU-1-0.811-0.89044.213-0.004-0.0040.0000.0000.0000.000
160A231ARG10.8510.91945.9670.0200.0200.0000.0000.0000.000
161A232ASN0-0.018-0.02045.6010.0020.0020.0000.0000.0000.000
162A233SER0-0.075-0.04847.688-0.002-0.0020.0000.0000.0000.000
163A234TRP00.0320.02050.2390.0020.0020.0000.0000.0000.000
164A235ILE0-0.014-0.00650.5480.0000.0000.0000.0000.0000.000
165A236LYS10.9390.97149.6880.0360.0360.0000.0000.0000.000
166A237ILE00.0170.03053.6800.0000.0000.0000.0000.0000.000
167A238VAL00.0250.01856.5470.0010.0010.0000.0000.0000.000
168A239ASP-1-0.833-0.90256.632-0.025-0.0250.0000.0000.0000.000
169A240ASN0-0.071-0.04257.019-0.001-0.0010.0000.0000.0000.000
170A241ILE00.0060.01060.2060.0010.0010.0000.0000.0000.000
171A242ILE0-0.024-0.01661.3690.0010.0010.0000.0000.0000.000
172A243GLY00.0460.02563.0400.0000.0000.0000.0000.0000.000
173A244GLU-1-0.804-0.86164.052-0.017-0.0170.0000.0000.0000.000
174A245TYR00.0290.00966.6620.0000.0000.0000.0000.0000.000
175A246ASP-1-0.818-0.90166.548-0.019-0.0190.0000.0000.0000.000
176A247LYS10.8100.89064.4290.0190.0190.0000.0000.0000.000
177A248ASN0-0.015-0.00369.7760.0010.0010.0000.0000.0000.000
178A249THR00.013-0.02067.7880.0000.0000.0000.0000.0000.000
179A250GLY00.0210.00871.0180.0010.0010.0000.0000.0000.000
180A251GLY0-0.009-0.00474.0070.0010.0010.0000.0000.0000.000
181A252CYS0-0.069-0.03071.4560.0010.0010.0000.0000.0000.000
182A253LYS10.8500.92171.9350.0160.0160.0000.0000.0000.000
183A254ALA0-0.051-0.01175.0240.0000.0000.0000.0000.0000.000
184A255ASP-1-0.839-0.91576.629-0.002-0.0020.0000.0000.0000.000
185A256GLY00.0970.04474.3550.0000.0000.0000.0000.0000.000
186A257LYS10.8820.92173.427-0.003-0.0030.0000.0000.0000.000
187A258ILE0-0.0300.00073.1820.0000.0000.0000.0000.0000.000
188A259LEU0-0.0090.00169.131-0.001-0.0010.0000.0000.0000.000
189A260GLY00.0330.00869.1880.0000.0000.0000.0000.0000.000
190A261GLU-1-0.829-0.87068.2320.0030.0030.0000.0000.0000.000
191A262VAL0-0.035-0.01667.1180.0000.0000.0000.0000.0000.000
192A263ILE0-0.027-0.01563.602-0.001-0.0010.0000.0000.0000.000
193A264ARG10.8290.88063.676-0.005-0.0050.0000.0000.0000.000
194A265VAL0-0.025-0.00863.4740.0010.0010.0000.0000.0000.000
195A266GLY00.0010.01262.8560.0000.0000.0000.0000.0000.000
196A267TYR0-0.026-0.05558.792-0.001-0.0010.0000.0000.0000.000
197A268GLU-1-0.837-0.88358.8220.0100.0100.0000.0000.0000.000
198A269HIS10.7860.87357.2220.0050.0050.0000.0000.0000.000
199A270GLU-1-0.893-0.93954.415-0.008-0.0080.0000.0000.0000.000
200A271LEU0-0.096-0.02353.891-0.001-0.0010.0000.0000.0000.000
201A272ASP-1-0.758-0.89849.2250.0140.0140.0000.0000.0000.000
202A273SER00.0020.00949.687-0.001-0.0010.0000.0000.0000.000
203A274ASN0-0.025-0.01548.1500.0040.0040.0000.0000.0000.000
204A275LYS10.8370.89544.3530.0030.0030.0000.0000.0000.000
205A276SER0-0.027-0.00143.8470.0000.0000.0000.0000.0000.000
206A277MET00.0410.00743.3230.0010.0010.0000.0000.0000.000
207A278GLN0-0.044-0.02839.4940.0060.0060.0000.0000.0000.000
208A279ILE0-0.033-0.01838.7830.0040.0040.0000.0000.0000.000
209A280LEU0-0.0050.01538.3850.0000.0000.0000.0000.0000.000
210A281ASN00.0490.03738.2270.0100.0100.0000.0000.0000.000
211A282ASN0-0.024-0.00535.5390.0170.0170.0000.0000.0000.000
212A283ILE0-0.033-0.01034.0760.0010.0010.0000.0000.0000.000
213A284GLU-1-0.873-0.95533.6670.0630.0630.0000.0000.0000.000
214A285THR0-0.100-0.06333.9820.0130.0130.0000.0000.0000.000
215A286PRO0-0.015-0.00829.1040.0190.0190.0000.0000.0000.000
216A287LEU00.0330.02029.0840.0160.0160.0000.0000.0000.000
217A288LYS10.9210.98530.671-0.123-0.1230.0000.0000.0000.000
218A289THR0-0.058-0.01825.5320.0280.0280.0000.0000.0000.000