Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: N23ZQ

Calculation Name: 1IXV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1IXV

Chain ID: A

ChEMBL ID:

UniProt ID: P50086

Base Structure: X-ray

Registration Date: 2023-09-26

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2685431.878427
FMO2-HF: Nuclear repulsion 2595958.20542
FMO2-HF: Total energy -89473.673007
FMO2-MP2: Total energy -89737.161446


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:3:ASN)


Summations of interaction energy for fragment #1(A:3: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.
-10.566-7.4760.01-1.149-1.950.003
Interaction energy analysis for fragmet #1(A:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.007
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].
3A5PRO0-0.030-0.0203.428-1.6041.0440.013-1.128-1.5320.003
4A6LEU00.0270.0145.008-0.951-0.869-0.001-0.006-0.0750.000
5A7HIS00.0710.0277.1350.1790.1790.0000.0000.0000.000
6A8GLN00.0430.0144.7750.5280.659-0.001-0.005-0.1250.000
7A9ALA00.0020.0077.447-0.412-0.4120.0000.0000.0000.000
8A10CYS0-0.087-0.04410.222-0.331-0.3310.0000.0000.0000.000
9A11MET0-0.052-0.0096.903-0.221-0.2210.0000.0000.0000.000
10A12GLU-1-0.932-0.9549.8460.7590.7590.0000.0000.0000.000
11A13ASN0-0.057-0.02512.829-0.064-0.0640.0000.0000.0000.000
12A14GLU-1-0.870-0.94411.9541.4941.4940.0000.0000.0000.000
13A15PHE00.032-0.01014.3420.1580.1580.0000.0000.0000.000
14A16PHE00.0240.01216.0700.0250.0250.0000.0000.0000.000
15A17LYS10.9500.97210.536-2.002-2.0020.0000.0000.0000.000
16A18VAL00.0020.01112.5220.1780.1780.0000.0000.0000.000
17A19GLN0-0.042-0.02113.535-0.002-0.0020.0000.0000.0000.000
18A20GLU-1-0.923-0.95413.3921.2591.2590.0000.0000.0000.000
19A21LEU0-0.048-0.0388.5330.1120.1120.0000.0000.0000.000
20A22LEU0-0.029-0.01012.047-0.058-0.0580.0000.0000.0000.000
21A23HIS0-0.0210.00514.602-0.133-0.1330.0000.0000.0000.000
22A24SER0-0.035-0.01012.7760.0440.0440.0000.0000.0000.000
23A25LYS10.9040.9417.628-3.784-3.7840.0000.0000.0000.000
24A26PRO00.1100.05112.748-0.013-0.0130.0000.0000.0000.000
25A27SER0-0.069-0.03012.750-0.031-0.0310.0000.0000.0000.000
26A28LEU00.007-0.0067.668-0.093-0.0930.0000.0000.0000.000
27A29LEU0-0.0150.00011.367-0.111-0.1110.0000.0000.0000.000
28A30LEU0-0.018-0.00814.233-0.081-0.0810.0000.0000.0000.000
29A31GLN0-0.0030.0026.558-0.033-0.0330.0000.0000.0000.000
30A32LYS10.9330.95610.5590.5670.5670.0000.0000.0000.000
31A33ASP-1-0.780-0.8677.032-2.182-2.1820.0000.0000.0000.000
32A34GLN0-0.068-0.0314.688-1.969-1.740-0.001-0.010-0.2180.000
33A35ASP-1-0.873-0.9348.032-1.889-1.8890.0000.0000.0000.000
34A36GLY00.008-0.00610.5900.3110.3110.0000.0000.0000.000
35A37ARG10.7820.88011.0921.0311.0310.0000.0000.0000.000
36A38ILE0-0.0100.00110.736-0.100-0.1000.0000.0000.0000.000
37A39PRO00.009-0.01710.896-0.032-0.0320.0000.0000.0000.000
38A40LEU00.0470.01912.8460.0110.0110.0000.0000.0000.000
39A41HIS00.0110.00014.1390.0200.0200.0000.0000.0000.000
40A42TRP0-0.013-0.0369.8530.1880.1880.0000.0000.0000.000
41A43SER00.0370.01713.9410.0240.0240.0000.0000.0000.000
42A44VAL0-0.0210.00316.220-0.001-0.0010.0000.0000.0000.000
43A45SER0-0.047-0.02715.420-0.042-0.0420.0000.0000.0000.000
44A46PHE0-0.049-0.02612.654-0.034-0.0340.0000.0000.0000.000
45A47GLN0-0.015-0.00917.3320.0650.0650.0000.0000.0000.000
46A48ALA00.0660.04917.3400.0260.0260.0000.0000.0000.000
47A49HIS0-0.021-0.03719.3770.0120.0120.0000.0000.0000.000
48A50GLU-1-0.880-0.93521.6600.3070.3070.0000.0000.0000.000
49A51ILE0-0.007-0.00215.2170.0240.0240.0000.0000.0000.000
50A52THR0-0.008-0.00819.009-0.006-0.0060.0000.0000.0000.000
51A53SER00.0450.02120.352-0.026-0.0260.0000.0000.0000.000
52A54PHE0-0.0090.00517.4360.0060.0060.0000.0000.0000.000
53A55LEU0-0.0060.00215.2380.0090.0090.0000.0000.0000.000
54A56LEU00.0340.00519.302-0.023-0.0230.0000.0000.0000.000
55A57SER0-0.057-0.02322.529-0.009-0.0090.0000.0000.0000.000
56A58LYS10.9060.95319.119-0.481-0.4810.0000.0000.0000.000
57A59MET0-0.060-0.03518.9000.0000.0000.0000.0000.0000.000
58A60GLU-1-0.890-0.94222.6220.1100.1100.0000.0000.0000.000
59A61ASN0-0.075-0.03425.581-0.028-0.0280.0000.0000.0000.000
60A62VAL0-0.0200.00420.790-0.020-0.0200.0000.0000.0000.000
61A63ASN00.0670.03124.1370.0020.0020.0000.0000.0000.000
62A64LEU00.034-0.00621.722-0.020-0.0200.0000.0000.0000.000
63A65ASP-1-0.848-0.92322.321-0.190-0.1900.0000.0000.0000.000
64A66ASP-1-0.902-0.95922.362-0.180-0.1800.0000.0000.0000.000
65A67TYR0-0.078-0.04616.732-0.035-0.0350.0000.0000.0000.000
66A68PRO0-0.060-0.04318.714-0.006-0.0060.0000.0000.0000.000
67A69ASP-1-0.781-0.86215.836-0.782-0.7820.0000.0000.0000.000
68A70ASP-1-0.819-0.90213.566-1.139-1.1390.0000.0000.0000.000
69A71SER0-0.112-0.07316.6360.0340.0340.0000.0000.0000.000
70A72GLY00.007-0.02019.3140.0700.0700.0000.0000.0000.000
71A73TRP0-0.040-0.02519.1950.0690.0690.0000.0000.0000.000
72A74THR00.0760.05119.044-0.038-0.0380.0000.0000.0000.000
73A75PRO00.0430.00018.116-0.005-0.0050.0000.0000.0000.000
74A76PHE00.0530.02120.3560.0200.0200.0000.0000.0000.000
75A77HIS0-0.0010.00722.461-0.011-0.0110.0000.0000.0000.000
76A78ILE0-0.0190.00117.2150.0030.0030.0000.0000.0000.000
77A79ALA00.0260.02021.4010.0130.0130.0000.0000.0000.000
78A80CYS0-0.031-0.00623.6920.0170.0170.0000.0000.0000.000
79A81SER0-0.050-0.02322.8000.0070.0070.0000.0000.0000.000
80A82VAL0-0.023-0.01720.837-0.002-0.0020.0000.0000.0000.000
81A83GLY00.0070.00823.7980.0140.0140.0000.0000.0000.000
82A84ASN00.0370.02825.5700.0170.0170.0000.0000.0000.000
83A85LEU00.034-0.00927.3660.0010.0010.0000.0000.0000.000
84A86GLU-1-0.937-0.95528.2680.1040.1040.0000.0000.0000.000
85A87VAL00.012-0.00123.1030.0080.0080.0000.0000.0000.000
86A88VAL0-0.028-0.01226.374-0.003-0.0030.0000.0000.0000.000
87A89LYS10.9530.96428.149-0.015-0.0150.0000.0000.0000.000
88A90SER00.0000.01826.4790.0030.0030.0000.0000.0000.000
89A91LEU0-0.041-0.02122.8880.0040.0040.0000.0000.0000.000
90A92TYR00.004-0.00626.868-0.007-0.0070.0000.0000.0000.000
91A93ASP-1-0.927-0.95830.2680.0210.0210.0000.0000.0000.000
92A94ARG10.8630.94825.355-0.020-0.0200.0000.0000.0000.000
93A95PRO00.001-0.00530.322-0.015-0.0150.0000.0000.0000.000
94A96LEU0-0.013-0.00827.935-0.012-0.0120.0000.0000.0000.000
95A97LYS10.8610.94229.022-0.002-0.0020.0000.0000.0000.000
96A98PRO0-0.0010.00526.963-0.008-0.0080.0000.0000.0000.000
97A99ASP-1-0.868-0.94328.907-0.132-0.1320.0000.0000.0000.000
98A100LEU0-0.036-0.02330.003-0.019-0.0190.0000.0000.0000.000
99A101ASN0-0.036-0.01931.807-0.012-0.0120.0000.0000.0000.000
100A102LYS10.9431.00024.7990.2460.2460.0000.0000.0000.000
101A103ILE0-0.038-0.01628.478-0.005-0.0050.0000.0000.0000.000
102A104THR0-0.0160.00523.746-0.015-0.0150.0000.0000.0000.000
103A105ASN00.0360.01120.9950.0590.0590.0000.0000.0000.000
104A106GLN0-0.087-0.04923.4310.0450.0450.0000.0000.0000.000
105A107GLY00.0410.00827.1120.0220.0220.0000.0000.0000.000
106A108VAL0-0.062-0.00726.8360.0210.0210.0000.0000.0000.000
107A109THR00.0860.02028.438-0.006-0.0060.0000.0000.0000.000
108A110CYS00.0530.00727.892-0.012-0.0120.0000.0000.0000.000
109A111LEU00.0470.03229.1390.0020.0020.0000.0000.0000.000
110A112HIS0-0.0140.00630.3100.0020.0020.0000.0000.0000.000
111A113LEU0-0.067-0.03824.729-0.003-0.0030.0000.0000.0000.000
112A114ALA00.0290.02328.366-0.001-0.0010.0000.0000.0000.000
113A115VAL00.0160.00830.0760.0070.0070.0000.0000.0000.000
114A116GLY0-0.033-0.01630.7230.0050.0050.0000.0000.0000.000
115A117LYS10.9090.96823.7250.2720.2720.0000.0000.0000.000
116A118LYS10.9100.95329.7190.1380.1380.0000.0000.0000.000
117A119TRP00.0080.02326.5930.0230.0230.0000.0000.0000.000
118A120PHE0-0.012-0.01932.217-0.003-0.0030.0000.0000.0000.000
119A121GLU-1-0.848-0.93233.953-0.051-0.0510.0000.0000.0000.000
120A122VAL00.0230.01729.4170.0030.0030.0000.0000.0000.000
121A123SER0-0.024-0.02332.707-0.007-0.0070.0000.0000.0000.000
122A124GLN0-0.0190.00034.738-0.001-0.0010.0000.0000.0000.000
123A125PHE00.0300.02032.6030.0030.0030.0000.0000.0000.000
124A126LEU0-0.017-0.00830.9150.0000.0000.0000.0000.0000.000
125A127ILE0-0.004-0.01035.122-0.001-0.0010.0000.0000.0000.000
126A128GLU-1-0.956-0.99238.632-0.033-0.0330.0000.0000.0000.000
127A129ASN0-0.086-0.04336.2360.0110.0110.0000.0000.0000.000
128A130GLY00.0060.00237.612-0.001-0.0010.0000.0000.0000.000
129A131ALA0-0.044-0.00634.995-0.007-0.0070.0000.0000.0000.000
130A132SER0-0.022-0.00936.6670.0050.0050.0000.0000.0000.000
131A133VAL00.0420.00737.114-0.009-0.0090.0000.0000.0000.000
132A134ARG10.8690.93139.2150.0970.0970.0000.0000.0000.000
133A135ILE00.0470.03334.0230.0000.0000.0000.0000.0000.000
134A136LYS10.9230.96635.9800.1520.1520.0000.0000.0000.000
135A137ASP-1-0.780-0.87331.224-0.253-0.2530.0000.0000.0000.000
136A138LYS10.9370.97027.7330.3910.3910.0000.0000.0000.000
137A139PHE0-0.053-0.03929.532-0.002-0.0020.0000.0000.0000.000
138A140ASN0-0.038-0.03134.6640.0090.0090.0000.0000.0000.000
139A141GLN0-0.033-0.00334.5580.0070.0070.0000.0000.0000.000
140A142ILE0-0.0100.01035.727-0.007-0.0070.0000.0000.0000.000
141A143PRO00.004-0.01134.750-0.004-0.0040.0000.0000.0000.000
142A144LEU00.0440.01836.292-0.001-0.0010.0000.0000.0000.000
143A145HIS00.0440.01837.3070.0020.0020.0000.0000.0000.000
144A146ARG10.9420.97328.2970.2570.2570.0000.0000.0000.000
145A147ALA0-0.005-0.00635.5510.0010.0010.0000.0000.0000.000
146A148ALA00.0020.00137.6780.0050.0050.0000.0000.0000.000
147A149SER0-0.0160.00935.799-0.002-0.0020.0000.0000.0000.000
148A150VAL0-0.030-0.01833.2530.0000.0000.0000.0000.0000.000
149A151GLY00.0530.03036.4170.0070.0070.0000.0000.0000.000
150A152SER0-0.084-0.03237.6720.0120.0120.0000.0000.0000.000
151A153LEU00.1080.03339.7310.0000.0000.0000.0000.0000.000
152A154LYS10.9700.98440.5130.0540.0540.0000.0000.0000.000
153A155LEU00.0360.01935.3830.0030.0030.0000.0000.0000.000
154A156ILE00.0370.02939.767-0.001-0.0010.0000.0000.0000.000
155A157GLU-1-0.807-0.89142.460-0.062-0.0620.0000.0000.0000.000
156A158LEU0-0.059-0.00938.4470.0030.0030.0000.0000.0000.000
157A159LEU0-0.013-0.01637.8770.0010.0010.0000.0000.0000.000
158A160CYS0-0.018-0.00141.945-0.001-0.0010.0000.0000.0000.000
159A161GLY00.0440.03145.5520.0030.0030.0000.0000.0000.000
160A162LEU0-0.043-0.02342.4340.0010.0010.0000.0000.0000.000
161A163GLY00.0250.00542.7280.0010.0010.0000.0000.0000.000
162A164LYS10.8240.92943.5790.0580.0580.0000.0000.0000.000
163A165SER0-0.013-0.02142.553-0.005-0.0050.0000.0000.0000.000
164A166ALA0-0.062-0.02044.1820.0050.0050.0000.0000.0000.000
165A167VAL00.0650.01544.631-0.006-0.0060.0000.0000.0000.000
166A168ASN00.0590.03846.274-0.007-0.0070.0000.0000.0000.000
167A169TRP0-0.039-0.01841.501-0.003-0.0030.0000.0000.0000.000
168A170GLN0-0.014-0.01443.5160.0010.0010.0000.0000.0000.000
169A171ASP-1-0.768-0.87738.232-0.192-0.1920.0000.0000.0000.000
170A172LYS10.8950.92435.2950.2460.2460.0000.0000.0000.000
171A173GLN0-0.061-0.01537.049-0.009-0.0090.0000.0000.0000.000
172A174GLY00.0390.02541.3540.0070.0070.0000.0000.0000.000
173A175TRP0-0.023-0.01740.2460.0060.0060.0000.0000.0000.000
174A176THR00.0140.01542.320-0.006-0.0060.0000.0000.0000.000
175A177PRO0-0.005-0.02641.595-0.004-0.0040.0000.0000.0000.000
176A178LEU00.0130.02442.728-0.002-0.0020.0000.0000.0000.000
177A179PHE00.0280.01643.7240.0010.0010.0000.0000.0000.000
178A180HIS0-0.038-0.02237.752-0.003-0.0030.0000.0000.0000.000
179A181ALA0-0.0100.01240.915-0.002-0.0020.0000.0000.0000.000
180A182LEU00.0130.00542.7230.0010.0010.0000.0000.0000.000
181A183ALA00.0040.01441.2590.0010.0010.0000.0000.0000.000
182A184GLU-1-0.974-0.99136.974-0.190-0.1900.0000.0000.0000.000
183A185GLY0-0.024-0.00840.5130.0030.0030.0000.0000.0000.000
184A186HIS0-0.034-0.01438.3710.0160.0160.0000.0000.0000.000
185A187GLY00.0310.00243.8330.0020.0020.0000.0000.0000.000
186A188ASP-1-0.885-0.95446.582-0.076-0.0760.0000.0000.0000.000
187A189ALA0-0.041-0.02043.5350.0020.0020.0000.0000.0000.000
188A190ALA00.002-0.00545.5140.0000.0000.0000.0000.0000.000
189A191VAL00.0530.02447.5030.0010.0010.0000.0000.0000.000
190A192LEU0-0.045-0.00545.8660.0030.0030.0000.0000.0000.000
191A193LEU0-0.044-0.04044.2030.0020.0020.0000.0000.0000.000
192A194VAL00.0040.00548.5240.0000.0000.0000.0000.0000.000
193A195GLU-1-0.839-0.91751.942-0.064-0.0640.0000.0000.0000.000
194A196LYS10.7700.88850.0660.0620.0620.0000.0000.0000.000
195A197TYR0-0.106-0.08647.8080.0030.0030.0000.0000.0000.000
196A198GLY00.0430.03351.081-0.003-0.0030.0000.0000.0000.000
197A199ALA0-0.061-0.02849.042-0.002-0.0020.0000.0000.0000.000
198A200GLU-1-0.914-0.96650.809-0.089-0.0890.0000.0000.0000.000
199A201TYR0-0.042-0.05451.107-0.007-0.0070.0000.0000.0000.000
200A202ASP-1-0.931-0.97352.652-0.089-0.0890.0000.0000.0000.000
201A203LEU0-0.048-0.01348.999-0.002-0.0020.0000.0000.0000.000
202A204VAL0-0.040-0.02550.741-0.001-0.0010.0000.0000.0000.000
203A205ASP-1-0.837-0.90545.088-0.159-0.1590.0000.0000.0000.000
204A206ASN0-0.070-0.02643.3290.0090.0090.0000.0000.0000.000
205A207LYS10.8870.91242.9810.1780.1780.0000.0000.0000.000
206A208GLY00.0050.00748.2250.0030.0030.0000.0000.0000.000
207A209ALA0-0.0080.01348.0990.0050.0050.0000.0000.0000.000
208A210LYS10.9991.01149.6520.0950.0950.0000.0000.0000.000
209A211ALA00.0460.01548.042-0.004-0.0040.0000.0000.0000.000
210A212GLU-1-0.963-0.99348.474-0.096-0.0960.0000.0000.0000.000
211A213ASP-1-0.908-0.95750.335-0.109-0.1090.0000.0000.0000.000
212A214VAL0-0.062-0.02344.767-0.004-0.0040.0000.0000.0000.000
213A215ALA0-0.046-0.01845.240-0.005-0.0050.0000.0000.0000.000
214A216LEU0-0.0050.02441.8570.0000.0000.0000.0000.0000.000
215A217ASN0-0.053-0.02645.1660.0010.0010.0000.0000.0000.000
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