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: QNY3Y

Calculation Name: 1A04-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A04

Chain ID: A

ChEMBL ID:

UniProt ID: P0AF28

Base Structure: X-ray

Registration Date: 2023-09-27

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2369134.584366
FMO2-HF: Nuclear repulsion 2288913.70029
FMO2-HF: Total energy -80220.884075
FMO2-MP2: Total energy -80452.643934


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:5:GLU)


Summations of interaction energy for fragment #1(A:5:GLU)
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.
41.99244.3280.6-1.186-1.750.005
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.988 / q_NPA : -1.000
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].
3A7ALA0-0.044-0.0163.9044.2565.524-0.006-0.636-0.6250.002
4A8THR0-0.001-0.0305.723-3.470-3.4700.0000.0000.0000.000
5A9ILE00.006-0.0028.207-1.634-1.6340.0000.0000.0000.000
6A10LEU0-0.0240.01411.9140.2120.2120.0000.0000.0000.000
7A11LEU0-0.011-0.00414.828-0.631-0.6310.0000.0000.0000.000
8A12ILE00.0160.00718.071-0.168-0.1680.0000.0000.0000.000
9A13ASP-1-0.786-0.88921.45512.65512.6550.0000.0000.0000.000
10A14ASP-1-0.863-0.94124.21510.52510.5250.0000.0000.0000.000
11A15HIS00.0230.02626.207-0.318-0.3180.0000.0000.0000.000
12A16PRO00.0650.01525.6060.2310.2310.0000.0000.0000.000
13A17MET00.0060.02025.2150.3730.3730.0000.0000.0000.000
14A18LEU00.0310.02823.5530.1950.1950.0000.0000.0000.000
15A19ARG10.7720.86520.403-13.073-13.0730.0000.0000.0000.000
16A20THR0-0.037-0.03320.5300.6060.6060.0000.0000.0000.000
17A21GLY00.0140.01021.0610.3380.3380.0000.0000.0000.000
18A22VAL00.0180.00417.6480.4700.4700.0000.0000.0000.000
19A23LYS10.8430.89516.345-14.607-14.6070.0000.0000.0000.000
20A24GLN0-0.015-0.00316.1960.7560.7560.0000.0000.0000.000
21A25LEU0-0.0060.01017.2830.3400.3400.0000.0000.0000.000
22A26ILE00.0040.00311.5590.5560.5560.0000.0000.0000.000
23A27SER0-0.108-0.06112.3490.8600.8600.0000.0000.0000.000
24A28MET0-0.059-0.02713.906-0.319-0.3190.0000.0000.0000.000
25A29ALA00.0090.01012.124-0.396-0.3960.0000.0000.0000.000
26A30PRO0-0.006-0.0148.7391.2971.2970.0000.0000.0000.000
27A31ASP-1-0.866-0.8996.01228.46328.4630.0000.0000.0000.000
28A32ILE0-0.027-0.0126.7252.0422.0420.0000.0000.0000.000
29A33THR00.012-0.0076.676-1.410-1.4100.0000.0000.0000.000
30A34VAL0-0.014-0.0019.0910.3140.3140.0000.0000.0000.000
31A35VAL0-0.021-0.0207.9100.8510.8510.0000.0000.0000.000
32A36GLY00.0140.00511.027-0.447-0.4470.0000.0000.0000.000
33A37GLU-1-0.800-0.88114.81015.25915.2590.0000.0000.0000.000
34A38ALA0-0.020-0.00418.319-0.231-0.2310.0000.0000.0000.000
35A39SER0-0.012-0.00321.7070.1550.1550.0000.0000.0000.000
36A40ASN00.022-0.00325.172-0.419-0.4190.0000.0000.0000.000
37A41GLY00.0660.02925.0310.4830.4830.0000.0000.0000.000
38A42GLU-1-0.837-0.91724.70011.28711.2870.0000.0000.0000.000
39A43GLN00.0040.00221.365-0.037-0.0370.0000.0000.0000.000
40A44GLY00.031-0.00420.6180.6940.6940.0000.0000.0000.000
41A45ILE00.004-0.00420.1010.8630.8630.0000.0000.0000.000
42A46GLU-1-0.816-0.89820.80913.81013.8100.0000.0000.0000.000
43A47LEU0-0.040-0.00216.9940.7360.7360.0000.0000.0000.000
44A48ALA00.0130.00416.1371.3371.3370.0000.0000.0000.000
45A49GLU-1-0.846-0.91715.66815.81315.8130.0000.0000.0000.000
46A50SER0-0.096-0.06116.0650.8570.8570.0000.0000.0000.000
47A51LEU0-0.028-0.01412.0331.1051.1050.0000.0000.0000.000
48A52ASP-1-0.731-0.81210.83825.39125.3910.0000.0000.0000.000
49A53PRO00.0380.0409.9882.5112.5110.0000.0000.0000.000
50A54ASP-1-0.803-0.8807.10635.71235.7120.0000.0000.0000.000
51A55LEU0-0.035-0.00710.495-1.817-1.8170.0000.0000.0000.000
52A56ILE00.0020.00413.5390.4880.4880.0000.0000.0000.000
53A57LEU00.0080.00716.687-0.615-0.6150.0000.0000.0000.000
54A58LEU0-0.0050.00519.139-0.118-0.1180.0000.0000.0000.000
55A59ASP-1-0.751-0.87122.50910.70210.7020.0000.0000.0000.000
56A60LEU0-0.013-0.01025.626-0.203-0.2030.0000.0000.0000.000
57A61ASN0-0.059-0.05228.764-0.336-0.3360.0000.0000.0000.000
58A62MET0-0.0070.02925.952-0.105-0.1050.0000.0000.0000.000
59A63PRO0-0.006-0.01030.254-0.277-0.2770.0000.0000.0000.000
60A64GLY00.0340.02232.7780.1600.1600.0000.0000.0000.000
61A65MET0-0.080-0.03934.432-0.250-0.2500.0000.0000.0000.000
62A66ASN00.0170.00531.523-0.178-0.1780.0000.0000.0000.000
63A67GLY00.0510.03029.6030.2440.2440.0000.0000.0000.000
64A68LEU00.004-0.01028.9730.3550.3550.0000.0000.0000.000
65A69GLU-1-0.786-0.87630.0579.9669.9660.0000.0000.0000.000
66A70THR0-0.021-0.00425.8780.2330.2330.0000.0000.0000.000
67A71LEU0-0.024-0.01824.1990.4760.4760.0000.0000.0000.000
68A72ASP-1-0.796-0.85625.70710.54010.5400.0000.0000.0000.000
69A73LYS10.8370.91426.742-9.945-9.9450.0000.0000.0000.000
70A74LEU0-0.049-0.02219.9690.4190.4190.0000.0000.0000.000
71A75ARG10.8000.89418.593-14.417-14.4170.0000.0000.0000.000
72A76GLU-1-0.944-0.96923.63010.98910.9890.0000.0000.0000.000
73A77LYS10.7190.86420.255-13.560-13.5600.0000.0000.0000.000
74A78SER0-0.049-0.03518.9400.2200.2200.0000.0000.0000.000
75A79LEU0-0.024-0.01216.1901.1311.1310.0000.0000.0000.000
76A80SER0-0.099-0.09112.454-0.027-0.0270.0000.0000.0000.000
77A81GLY00.0200.02713.2730.3070.3070.0000.0000.0000.000
78A82ARG10.7460.85113.767-21.137-21.1370.0000.0000.0000.000
79A83ILE00.0020.00116.2380.4420.4420.0000.0000.0000.000
80A84VAL0-0.011-0.00518.227-0.597-0.5970.0000.0000.0000.000
81A85VAL0-0.0060.00420.4140.1130.1130.0000.0000.0000.000
82A86PHE00.0400.00920.618-0.033-0.0330.0000.0000.0000.000
83A87SER0-0.006-0.00725.394-0.322-0.3220.0000.0000.0000.000
84A88VAL00.0240.00429.2110.0650.0650.0000.0000.0000.000
85A89SER0-0.091-0.06232.339-0.335-0.3350.0000.0000.0000.000
86A90ASN00.0210.00232.7040.2340.2340.0000.0000.0000.000
87A91HIS0-0.0350.00634.853-0.164-0.1640.0000.0000.0000.000
88A92GLU-1-0.895-0.95034.3838.6248.6240.0000.0000.0000.000
89A93GLU-1-0.792-0.89033.8749.0589.0580.0000.0000.0000.000
90A94ASP-1-0.797-0.87632.7009.0169.0160.0000.0000.0000.000
91A95VAL0-0.021-0.00628.4420.3560.3560.0000.0000.0000.000
92A96VAL0-0.001-0.00329.3490.3670.3670.0000.0000.0000.000
93A97THR0-0.028-0.03030.9630.1400.1400.0000.0000.0000.000
94A98ALA00.0110.00427.1890.1600.1600.0000.0000.0000.000
95A99LEU0-0.031-0.01024.9450.3650.3650.0000.0000.0000.000
96A100LYS10.8430.90927.313-8.739-8.7390.0000.0000.0000.000
97A101ARG10.7710.84529.221-9.693-9.6930.0000.0000.0000.000
98A102GLY00.0210.01025.3640.1110.1110.0000.0000.0000.000
99A103ALA0-0.0150.00422.8010.7080.7080.0000.0000.0000.000
100A104ASP-1-0.771-0.90819.23515.37715.3770.0000.0000.0000.000
101A105GLY00.005-0.00421.286-0.010-0.0100.0000.0000.0000.000
102A106TYR0-0.009-0.02122.4930.0830.0830.0000.0000.0000.000
103A107LEU0-0.0020.00220.512-0.006-0.0060.0000.0000.0000.000
104A108LEU00.0380.02625.125-0.064-0.0640.0000.0000.0000.000
105A109LYS10.7480.83926.938-10.487-10.4870.0000.0000.0000.000
106A110ASP-1-0.928-0.96528.1099.7869.7860.0000.0000.0000.000
107A111MET0-0.043-0.00923.970-0.045-0.0450.0000.0000.0000.000
108A112GLU-1-0.841-0.92526.62810.40310.4030.0000.0000.0000.000
109A113PRO0-0.007-0.00523.4640.5220.5220.0000.0000.0000.000
110A114GLU-1-0.826-0.91222.07812.32312.3230.0000.0000.0000.000
111A115ASP-1-0.856-0.91122.10811.94311.9430.0000.0000.0000.000
112A116LEU0-0.022-0.00921.0060.5060.5060.0000.0000.0000.000
113A117LEU00.0170.01115.9520.7070.7070.0000.0000.0000.000
114A118LYS10.7600.85517.437-11.479-11.4790.0000.0000.0000.000
115A119ALA00.0060.01118.1740.6680.6680.0000.0000.0000.000
116A120LEU00.001-0.01415.8440.6200.6200.0000.0000.0000.000
117A121HIS0-0.055-0.03510.8980.0660.0660.0000.0000.0000.000
118A122GLN0-0.022-0.02213.3290.8960.8960.0000.0000.0000.000
119A123ALA0-0.009-0.01214.6860.6670.6670.0000.0000.0000.000
120A124ALA0-0.0250.00010.5720.5820.5820.0000.0000.0000.000
121A125ALA0-0.004-0.0119.0052.1932.1930.0000.0000.0000.000
122A126GLY00.0060.02110.2840.3510.3510.0000.0000.0000.000
123A127GLU-1-0.942-0.98113.57717.65317.6530.0000.0000.0000.000
124A128MET0-0.033-0.01115.968-0.513-0.5130.0000.0000.0000.000
125A129VAL00.0070.01118.4250.1520.1520.0000.0000.0000.000
126A130LEU0-0.0030.00721.875-0.068-0.0680.0000.0000.0000.000
127A131SER00.0200.01525.104-0.139-0.1390.0000.0000.0000.000
128A132GLU-1-0.818-0.92228.02110.13210.1320.0000.0000.0000.000
129A133ALA0-0.042-0.01431.148-0.256-0.2560.0000.0000.0000.000
130A134LEU00.006-0.01229.473-0.204-0.2040.0000.0000.0000.000
131A135THR00.0110.00029.4110.1030.1030.0000.0000.0000.000
132A136PRO0-0.007-0.00330.655-0.019-0.0190.0000.0000.0000.000
133A137VAL0-0.003-0.00133.139-0.160-0.1600.0000.0000.0000.000
134A138LEU00.0160.00327.516-0.051-0.0510.0000.0000.0000.000
135A139ALA0-0.022-0.00831.4890.0050.0050.0000.0000.0000.000
136A140ALA0-0.048-0.02433.006-0.108-0.1080.0000.0000.0000.000
137A141SER0-0.055-0.02232.540-0.202-0.2020.0000.0000.0000.000
138A142LEU0-0.0530.00029.150-0.006-0.0060.0000.0000.0000.000
139A150GLU-1-0.810-0.88832.9899.6449.6440.0000.0000.0000.000
140A151ARG10.7900.86029.140-10.219-10.2190.0000.0000.0000.000
141A152ASP-1-0.836-0.92731.5849.9999.9990.0000.0000.0000.000
142A153VAL00.0340.00728.1790.3630.3630.0000.0000.0000.000
143A154ASN0-0.084-0.04728.8430.3690.3690.0000.0000.0000.000
144A155GLN00.0010.01628.1800.0320.0320.0000.0000.0000.000
145A156LEU0-0.042-0.00723.7100.5090.5090.0000.0000.0000.000
146A157THR00.007-0.02522.477-0.136-0.1360.0000.0000.0000.000
147A158PRO00.030-0.00923.5550.2620.2620.0000.0000.0000.000
148A159ARG10.8420.91516.223-18.000-18.0000.0000.0000.0000.000
149A160GLU-1-0.725-0.83019.14714.89214.8920.0000.0000.0000.000
150A161ARG10.9030.95320.778-11.615-11.6150.0000.0000.0000.000
151A162ASP-1-0.847-0.91118.89015.45815.4580.0000.0000.0000.000
152A163ILE0-0.001-0.00314.6240.3240.3240.0000.0000.0000.000
153A164LEU00.0200.00618.1140.1660.1660.0000.0000.0000.000
154A165LYS10.9380.97620.968-13.260-13.2600.0000.0000.0000.000
155A166LEU0-0.041-0.01215.730-0.316-0.3160.0000.0000.0000.000
156A167ILE00.0140.00115.1990.2330.2330.0000.0000.0000.000
157A168ALA00.003-0.00318.172-0.232-0.2320.0000.0000.0000.000
158A169GLN0-0.065-0.03219.220-0.316-0.3160.0000.0000.0000.000
159A170GLY00.0760.03818.402-0.017-0.0170.0000.0000.0000.000
160A171LEU0-0.049-0.02014.1020.7060.7060.0000.0000.0000.000
161A172PRO00.0450.0409.8830.2050.2050.0000.0000.0000.000
162A173ASN00.0340.0018.185-2.487-2.4870.0000.0000.0000.000
163A174LYS10.9260.9602.284-57.550-56.6440.605-0.495-1.0170.003
164A175MET0-0.057-0.0087.351-0.742-0.7420.0000.0000.0000.000
165A176ILE0-0.019-0.01610.995-1.128-1.1280.0000.0000.0000.000
166A177ALA00.0270.0088.106-1.235-1.2350.0000.0000.0000.000
167A178ARG10.9660.9819.773-24.214-24.2140.0000.0000.0000.000
168A179ARG10.8490.92111.202-19.177-19.1770.0000.0000.0000.000
169A180LEU0-0.043-0.01813.519-1.741-1.7410.0000.0000.0000.000
170A181ASP-1-0.934-0.94212.26322.17522.1750.0000.0000.0000.000
171A182ILE0-0.020-0.00611.176-0.944-0.9440.0000.0000.0000.000
172A183THR00.0660.0336.5600.7620.7620.0000.0000.0000.000
173A184GLU-1-0.723-0.8774.01748.46748.6290.001-0.055-0.1080.000
174A185SER00.0110.0076.630-2.354-2.3540.0000.0000.0000.000
175A186THR0-0.032-0.0188.287-4.677-4.6770.0000.0000.0000.000
176A187VAL0-0.014-0.00710.087-2.820-2.8200.0000.0000.0000.000
177A188LYS10.8320.8997.683-34.336-34.3360.0000.0000.0000.000
178A189VAL0-0.015-0.00411.786-2.150-2.1500.0000.0000.0000.000
179A190HIS00.0230.00114.392-2.137-2.1370.0000.0000.0000.000
180A191VAL00.0090.00514.268-1.344-1.3440.0000.0000.0000.000
181A192LYS10.8460.93313.568-22.743-22.7430.0000.0000.0000.000
182A193HIS0-0.023-0.01218.015-1.329-1.3290.0000.0000.0000.000
183A194MET0-0.0210.00519.592-1.192-1.1920.0000.0000.0000.000
184A195LEU00.0390.01418.896-0.747-0.7470.0000.0000.0000.000
185A196LYS10.9740.99522.030-13.889-13.8890.0000.0000.0000.000
186A197LYS10.7600.86023.582-13.863-13.8630.0000.0000.0000.000
187A198MET0-0.042-0.01724.989-0.586-0.5860.0000.0000.0000.000
188A199LYS10.8440.93826.755-10.892-10.8920.0000.0000.0000.000
189A200LEU0-0.0380.00224.416-0.322-0.3220.0000.0000.0000.000
190A201LYS10.8490.89623.888-10.492-10.4920.0000.0000.0000.000
191A202SER00.0150.00621.2410.3850.3850.0000.0000.0000.000
192A203ARG10.8060.87612.690-21.416-21.4160.0000.0000.0000.000
193A204VAL00.0130.01219.935-0.268-0.2680.0000.0000.0000.000
194A205GLU-1-0.787-0.86122.56011.05911.0590.0000.0000.0000.000
195A206ALA00.008-0.00521.857-0.417-0.4170.0000.0000.0000.000
196A207ALA0-0.0120.00122.033-0.331-0.3310.0000.0000.0000.000
197A208VAL00.0020.00823.946-0.418-0.4180.0000.0000.0000.000
198A209TRP00.0580.01127.028-0.213-0.2130.0000.0000.0000.000
199A210VAL0-0.035-0.03024.738-0.315-0.3150.0000.0000.0000.000
200A211HIS0-0.067-0.02527.669-0.335-0.3350.0000.0000.0000.000
201A212GLN0-0.022-0.00429.394-0.224-0.2240.0000.0000.0000.000
202A213GLU-1-0.884-0.95631.3118.9498.9490.0000.0000.0000.000
203A214ARG10.8610.94330.866-9.219-9.2190.0000.0000.0000.000
204A215ILE0-0.0010.01026.8180.0040.0040.0000.0000.0000.000
205A216PHE0-0.023-0.00524.6620.1520.1520.0000.0000.0000.000