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: 89Q7Y

Calculation Name: 2QNI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QNI

Chain ID: A

ChEMBL ID:

UniProt ID: A9CKF0

Base Structure: X-ray

Registration Date: 2023-09-23

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2189994.63893
FMO2-HF: Nuclear repulsion 2113726.253638
FMO2-HF: Total energy -76268.385292
FMO2-MP2: Total energy -76492.04663


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:21:GLY)


Summations of interaction energy for fragment #1(A:21: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.
-11.568-8.4287.16-5.066-5.229-0.042
Interaction energy analysis for fragmet #1(A:21:GLY)
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 : -0.021
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].
3A23HIS0-0.049-0.0273.172-0.6041.0840.009-0.907-0.7890.001
4A24ALA00.0200.0223.943-0.416-0.2260.003-0.073-0.1200.000
5A25LEU0-0.033-0.0156.5210.2860.2860.0000.0000.0000.000
6A26TYR00.0040.0109.396-0.146-0.1460.0000.0000.0000.000
7A27ILE0-0.002-0.01011.7700.0680.0680.0000.0000.0000.000
8A28THR0-0.028-0.03715.207-0.032-0.0320.0000.0000.0000.000
9A29HIS0-0.004-0.00418.9710.0120.0120.0000.0000.0000.000
10A30PRO0-0.0240.00920.7790.0090.0090.0000.0000.0000.000
11A31GLN00.0450.01523.397-0.011-0.0110.0000.0000.0000.000
12A32VAL00.0250.01927.114-0.002-0.0020.0000.0000.0000.000
13A33LYS10.9190.95428.9880.0210.0210.0000.0000.0000.000
14A34ILE0-0.0160.00531.938-0.004-0.0040.0000.0000.0000.000
15A35ASP-1-0.832-0.92834.942-0.025-0.0250.0000.0000.0000.000
16A36PRO0-0.061-0.02537.556-0.001-0.0010.0000.0000.0000.000
17A37ALA0-0.037-0.02340.014-0.001-0.0010.0000.0000.0000.000
18A38VAL0-0.030-0.00834.101-0.003-0.0030.0000.0000.0000.000
19A39PRO00.0390.02234.8640.0020.0020.0000.0000.0000.000
20A40VAL00.0570.01933.207-0.002-0.0020.0000.0000.0000.000
21A41PRO0-0.047-0.03030.7170.0010.0010.0000.0000.0000.000
22A42GLU-1-0.964-0.98329.348-0.074-0.0740.0000.0000.0000.000
23A43TRP0-0.057-0.02130.5360.0040.0040.0000.0000.0000.000
24A44GLY00.0750.03827.504-0.006-0.0060.0000.0000.0000.000
25A45LEU0-0.052-0.03022.4790.0060.0060.0000.0000.0000.000
26A46SER0-0.055-0.03127.1700.0020.0020.0000.0000.0000.000
27A47GLU-1-0.926-0.96628.2600.0200.0200.0000.0000.0000.000
28A48ARG10.8890.92426.492-0.061-0.0610.0000.0000.0000.000
29A49GLY00.0370.01425.2910.0080.0080.0000.0000.0000.000
30A50ALA00.026-0.00323.7900.0050.0050.0000.0000.0000.000
31A51GLU-1-0.885-0.91923.6480.0600.0600.0000.0000.0000.000
32A52ARG10.7620.86521.992-0.058-0.0580.0000.0000.0000.000
33A53ALA00.0210.00919.3960.0180.0180.0000.0000.0000.000
34A54ARG10.9860.98618.9080.0000.0000.0000.0000.0000.000
35A55GLU-1-0.973-0.97620.1060.1130.1130.0000.0000.0000.000
36A56ALA00.0360.00916.0350.0260.0260.0000.0000.0000.000
37A57SER0-0.077-0.04515.5700.0390.0390.0000.0000.0000.000
38A58ARG10.9340.97215.852-0.080-0.0800.0000.0000.0000.000
39A59LEU0-0.0240.00514.7830.0300.0300.0000.0000.0000.000
40A60PRO0-0.050-0.04412.6620.0020.0020.0000.0000.0000.000
41A61TRP0-0.0010.0029.1810.0660.0660.0000.0000.0000.000
42A62ALA00.0470.0398.9480.0340.0340.0000.0000.0000.000
43A63LYS10.8930.93811.254-0.349-0.3490.0000.0000.0000.000
44A64ALA0-0.036-0.0097.013-0.068-0.0680.0000.0000.0000.000
45A65LEU0-0.047-0.0116.572-0.071-0.0710.0000.0000.0000.000
46A66ARG10.9380.9636.0330.4110.4110.0000.0000.0000.000
47A67ARG10.8920.9617.3890.7710.7710.0000.0000.0000.000
48A68ILE00.0120.0108.6050.0090.0090.0000.0000.0000.000
49A69VAL0-0.001-0.00210.483-0.001-0.0010.0000.0000.0000.000
50A70SER00.017-0.00113.1740.0460.0460.0000.0000.0000.000
51A71SER00.0140.00316.687-0.019-0.0190.0000.0000.0000.000
52A72ALA00.0290.00119.8680.0030.0030.0000.0000.0000.000
53A73GLU-1-0.836-0.91822.745-0.086-0.0860.0000.0000.0000.000
54A74THR00.0590.02823.494-0.007-0.0070.0000.0000.0000.000
55A75LYS10.9620.98824.3760.0640.0640.0000.0000.0000.000
56A76ALA0-0.0310.00719.8580.0120.0120.0000.0000.0000.000
57A77ILE00.0430.01519.711-0.002-0.0020.0000.0000.0000.000
58A78GLU-1-0.883-0.94320.355-0.045-0.0450.0000.0000.0000.000
59A79THR0-0.011-0.02517.7740.0190.0190.0000.0000.0000.000
60A80ALA00.001-0.00316.1300.0160.0160.0000.0000.0000.000
61A81HIS00.020-0.00416.5950.0000.0000.0000.0000.0000.000
62A82MET0-0.045-0.01918.9550.0160.0160.0000.0000.0000.000
63A83LEU0-0.024-0.02314.3910.0280.0280.0000.0000.0000.000
64A84ALA0-0.026-0.00614.6940.0330.0330.0000.0000.0000.000
65A85GLU-1-0.947-0.96215.648-0.008-0.0080.0000.0000.0000.000
66A86THR0-0.071-0.02815.9140.0110.0110.0000.0000.0000.000
67A87SER00.004-0.00211.941-0.018-0.0180.0000.0000.0000.000
68A88GLY00.0000.01214.021-0.029-0.0290.0000.0000.0000.000
69A89ALA0-0.077-0.03510.684-0.054-0.0540.0000.0000.0000.000
70A90ALA0-0.014-0.00211.5430.0270.0270.0000.0000.0000.000
71A91ILE00.0280.00812.349-0.042-0.0420.0000.0000.0000.000
72A92GLU-1-0.904-0.95113.261-0.607-0.6070.0000.0000.0000.000
73A93ILE0-0.0090.00215.5090.0070.0070.0000.0000.0000.000
74A94ILE0-0.021-0.02015.780-0.014-0.0140.0000.0000.0000.000
75A95GLU-1-0.882-0.95618.947-0.145-0.1450.0000.0000.0000.000
76A96ALA00.0220.00720.4660.0140.0140.0000.0000.0000.000
77A97MET0-0.070-0.02315.116-0.018-0.0180.0000.0000.0000.000
78A98HIS0-0.010-0.00120.0790.0080.0080.0000.0000.0000.000
79A99GLU-1-0.777-0.88123.538-0.076-0.0760.0000.0000.0000.000
80A100ASN0-0.023-0.01725.114-0.012-0.0120.0000.0000.0000.000
81A101ASP-1-0.884-0.93027.483-0.076-0.0760.0000.0000.0000.000
82A102ARG10.9710.96028.5290.0560.0560.0000.0000.0000.000
83A103SER0-0.016-0.00633.4860.0070.0070.0000.0000.0000.000
84A104ALA0-0.0010.00135.5650.0040.0040.0000.0000.0000.000
85A105THR0-0.0190.00236.9900.0040.0040.0000.0000.0000.000
86A106GLY0-0.0020.01939.2260.0030.0030.0000.0000.0000.000
87A107PHE0-0.041-0.03739.1620.0000.0000.0000.0000.0000.000
88A108LEU00.0240.00937.4860.0010.0010.0000.0000.0000.000
89A109PRO0-0.0090.01339.0630.0010.0010.0000.0000.0000.000
90A110PRO00.0540.00937.478-0.001-0.0010.0000.0000.0000.000
91A111PRO0-0.0020.00738.0360.0000.0000.0000.0000.0000.000
92A112GLU-1-0.880-0.96139.867-0.011-0.0110.0000.0000.0000.000
93A113PHE0-0.0230.00131.161-0.003-0.0030.0000.0000.0000.000
94A114GLU-1-0.834-0.91833.682-0.006-0.0060.0000.0000.0000.000
95A115LYS10.9550.98235.4380.0050.0050.0000.0000.0000.000
96A116ALA00.0050.01436.714-0.001-0.0010.0000.0000.0000.000
97A117ALA0-0.024-0.00931.578-0.004-0.0040.0000.0000.0000.000
98A118ASP-1-0.847-0.91832.521-0.006-0.0060.0000.0000.0000.000
99A119TRP0-0.064-0.03434.120-0.001-0.0010.0000.0000.0000.000
100A120PHE0-0.042-0.02927.846-0.002-0.0020.0000.0000.0000.000
101A121PHE00.009-0.00625.910-0.004-0.0040.0000.0000.0000.000
102A122ALA0-0.0140.00331.048-0.001-0.0010.0000.0000.0000.000
103A123HIS10.8210.92034.0880.0280.0280.0000.0000.0000.000
104A124PRO00.1110.05930.295-0.004-0.0040.0000.0000.0000.000
105A125GLU-1-0.935-0.97232.127-0.062-0.0620.0000.0000.0000.000
106A126GLU-1-0.956-0.97634.296-0.036-0.0360.0000.0000.0000.000
107A127SER0-0.029-0.02835.1870.0000.0000.0000.0000.0000.000
108A128PHE00.0240.00235.9070.0050.0050.0000.0000.0000.000
109A129GLN0-0.027-0.01737.370-0.003-0.0030.0000.0000.0000.000
110A130GLY00.0290.01638.3600.0000.0000.0000.0000.0000.000
111A131TRP0-0.087-0.03733.481-0.003-0.0030.0000.0000.0000.000
112A132GLU-1-0.713-0.82627.626-0.116-0.1160.0000.0000.0000.000
113A133ARG10.7720.85831.8730.0840.0840.0000.0000.0000.000
114A134ALA00.0480.03128.502-0.009-0.0090.0000.0000.0000.000
115A135ILE0-0.009-0.01027.308-0.009-0.0090.0000.0000.0000.000
116A136ASP-1-0.813-0.88727.218-0.107-0.1070.0000.0000.0000.000
117A137ALA00.0160.01425.728-0.014-0.0140.0000.0000.0000.000
118A138GLN0-0.012-0.01322.534-0.009-0.0090.0000.0000.0000.000
119A139ALA0-0.017-0.00622.182-0.021-0.0210.0000.0000.0000.000
120A140ARG10.7960.87122.2860.1220.1220.0000.0000.0000.000
121A141ILE0-0.026-0.01118.067-0.034-0.0340.0000.0000.0000.000
122A142VAL00.0010.00317.871-0.047-0.0470.0000.0000.0000.000
123A143GLU-1-0.958-0.97917.380-0.288-0.2880.0000.0000.0000.000
124A144ALA0-0.025-0.01017.812-0.049-0.0490.0000.0000.0000.000
125A145VAL0-0.004-0.01012.275-0.067-0.0670.0000.0000.0000.000
126A146LYS10.8920.92112.9500.2850.2850.0000.0000.0000.000
127A147ALA0-0.026-0.00214.008-0.085-0.0850.0000.0000.0000.000
128A148VAL0-0.044-0.02910.285-0.060-0.0600.0000.0000.0000.000
129A149LEU0-0.031-0.0307.795-0.213-0.2130.0000.0000.0000.000
130A150ASP-1-0.829-0.8869.986-0.771-0.7710.0000.0000.0000.000
131A151ARG10.7910.90712.3320.5900.5900.0000.0000.0000.000
132A152HIS0-0.0380.0003.1781.1211.2950.010-0.072-0.1120.000
133A153ASP-1-0.790-0.8706.853-1.979-1.9790.0000.0000.0000.000
134A154ALA00.0640.0104.317-0.785-0.471-0.001-0.104-0.2080.000
135A155ARG10.7940.8742.072-5.361-6.3175.317-2.501-1.859-0.034
136A156GLN0-0.068-0.0353.192-0.7200.5080.141-0.548-0.820-0.004
137A157PRO0-0.004-0.0032.526-1.747-0.7051.632-1.410-1.263-0.005
138A158ILE00.0240.0233.2770.137-0.5020.0500.5830.0060.000
139A159ALA0-0.003-0.0055.9090.2550.2550.0000.0000.0000.000
140A160PHE00.0200.0069.223-0.082-0.0820.0000.0000.0000.000
141A161VAL0-0.011-0.01212.4860.0770.0770.0000.0000.0000.000
142A162GLY00.0440.00415.661-0.026-0.0260.0000.0000.0000.000
143A163HIS0-0.0200.01818.8750.0170.0170.0000.0000.0000.000
144A164GLY00.0530.01220.609-0.008-0.0080.0000.0000.0000.000
145A165GLY00.0600.04122.4360.0040.0040.0000.0000.0000.000
146A166VAL00.004-0.01520.7980.0030.0030.0000.0000.0000.000
147A167GLY0-0.011-0.00818.510-0.014-0.0140.0000.0000.0000.000
148A168THR0-0.105-0.01919.0470.0030.0030.0000.0000.0000.000
149A169LEU0-0.027-0.00421.5840.0030.0030.0000.0000.0000.000
150A170LEU0-0.0090.00314.362-0.009-0.0090.0000.0000.0000.000
151A171LYS10.8260.90617.283-0.074-0.0740.0000.0000.0000.000
152A172CYS0-0.0430.00818.4170.0100.0100.0000.0000.0000.000
153A173HIS00.0280.01617.3910.0220.0220.0000.0000.0000.000
154A174ILE0-0.037-0.02113.6740.0000.0000.0000.0000.0000.000
155A175GLU-1-0.848-0.87617.2690.0740.0740.0000.0000.0000.000
156A176GLY00.0100.01319.4970.0160.0160.0000.0000.0000.000
157A177ARG0-0.063-0.05721.6720.0040.0040.0000.0000.0000.000
158A178GLY0-0.017-0.01424.669-0.013-0.0130.0000.0000.0000.000
159A179ILE0-0.006-0.02225.8620.0040.0040.0000.0000.0000.000
160A180SER-1-0.779-0.88926.5080.0030.0030.0000.0000.0000.000
161A181ARG10.8660.90426.5280.0050.0050.0000.0000.0000.000
162A182SER00.0160.02126.7450.0090.0090.0000.0000.0000.000
163A183LYN00.0810.11122.3330.0010.0010.0000.0000.0000.000
164A184ASP-1-0.972-1.10421.285-0.016-0.0160.0000.0000.0000.000
165A185GLN00.1280.12221.4170.0080.0080.0000.0000.0000.000
166A186PRO0-0.027-0.01222.358-0.006-0.0060.0000.0000.0000.000
167A187ALA00.014-0.00125.104-0.006-0.0060.0000.0000.0000.000
168A188GLY0-0.029-0.01826.7820.0080.0080.0000.0000.0000.000
169A189GLY00.0210.02523.127-0.005-0.0050.0000.0000.0000.000
170A190GLY00.0220.00319.7960.0140.0140.0000.0000.0000.000
171A191ASN0-0.047-0.02918.9030.0430.0430.0000.0000.0000.000
172A192LEU0-0.006-0.00512.481-0.030-0.0300.0000.0000.0000.000
173A193PHE00.0520.02013.6180.0290.0290.0000.0000.0000.000
174A194ARG10.9390.9626.941-1.293-1.2930.0000.0000.0000.000
175A195PHE00.0150.0049.3120.0060.0060.0000.0000.0000.000
176A196SER00.0120.0148.232-0.112-0.1120.0000.0000.0000.000
177A197ILE00.0330.0074.648-0.191-0.092-0.001-0.034-0.0640.000
178A198ALA0-0.030-0.0318.4950.0390.0390.0000.0000.0000.000
179A199GLU-1-0.903-0.95310.4660.0210.0210.0000.0000.0000.000
180A200PHE0-0.0240.00011.9480.0030.0030.0000.0000.0000.000
181A201SER0-0.033-0.00712.3770.0130.0130.0000.0000.0000.000
182A202LEU0-0.046-0.04314.8910.0370.0370.0000.0000.0000.000
183A203ALA0-0.045-0.01117.3640.0220.0220.0000.0000.0000.000
184A204ALA0-0.0090.00917.570-0.003-0.0030.0000.0000.0000.000
185A205ALA00.0460.03114.7260.0230.0230.0000.0000.0000.000
186A206SER0-0.058-0.06316.8080.0340.0340.0000.0000.0000.000
187A207PRO0-0.051-0.00318.2080.0020.0020.0000.0000.0000.000
188A208THR0-0.053-0.03813.8440.0370.0370.0000.0000.0000.000
189A209CYS0-0.086-0.02014.4170.0170.0170.0000.0000.0000.000
190A210ASP-1-0.857-0.93216.1820.1150.1150.0000.0000.0000.000
191A211TRP0-0.123-0.08017.4370.0280.0280.0000.0000.0000.000
192A212THR0-0.040-0.01616.2860.0100.0100.0000.0000.0000.000
193A213ALA00.0460.03617.953-0.009-0.0090.0000.0000.0000.000
194A214MET0-0.001-0.00615.9160.0260.0260.0000.0000.0000.000
195A215GLU-1-0.792-0.90216.6380.1500.1500.0000.0000.0000.000
196A216THR0-0.066-0.02319.0940.0070.0070.0000.0000.0000.000
197A217TRP00.0200.0199.4430.0730.0730.0000.0000.0000.000
198A218GLN00.005-0.01515.2790.0130.0130.0000.0000.0000.000
199A219GLY0-0.045-0.01010.0160.1730.1730.0000.0000.0000.000