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

tag_button

FMODB ID: 37NKL

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2700968.754543
FMO2-HF: Nuclear repulsion 2611493.490385
FMO2-HF: Total energy -89475.264158
FMO2-MP2: Total energy -89738.846488


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.
-17.518-12.9240.485-2.309-2.771-0.014
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 : -0.018 / q_NPA : -0.011
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].
3A5PRO00.011-0.0023.459-2.2970.1930.010-1.118-1.3820.003
4A6LEU00.0060.0165.498-1.006-1.0060.0000.0000.0000.000
5A7HIS00.0330.0056.3870.2170.2170.0000.0000.0000.000
6A8GLN0-0.024-0.0155.3631.3551.3550.0000.0000.0000.000
7A9ALA0-0.011-0.0067.323-0.694-0.6940.0000.0000.0000.000
8A10CYS0-0.068-0.03310.516-0.422-0.4220.0000.0000.0000.000
9A11MET0-0.047-0.0106.579-0.311-0.3110.0000.0000.0000.000
10A12GLU-1-0.872-0.9299.8991.6441.6440.0000.0000.0000.000
11A13ASN0-0.029-0.02412.808-0.112-0.1120.0000.0000.0000.000
12A14GLU-1-0.771-0.85612.1791.8771.8770.0000.0000.0000.000
13A15PHE00.002-0.01914.7300.1510.1510.0000.0000.0000.000
14A16PHE00.0260.01316.4260.0080.0080.0000.0000.0000.000
15A17LYS10.8710.90910.711-2.254-2.2540.0000.0000.0000.000
16A18VAL00.0060.00012.9130.1420.1420.0000.0000.0000.000
17A19GLN0-0.058-0.02114.048-0.054-0.0540.0000.0000.0000.000
18A20GLU-1-0.873-0.94014.1861.1331.1330.0000.0000.0000.000
19A21LEU0-0.042-0.0138.9230.0930.0930.0000.0000.0000.000
20A22LEU0-0.043-0.01212.427-0.091-0.0910.0000.0000.0000.000
21A23HIS0-0.0080.00514.891-0.169-0.1690.0000.0000.0000.000
22A24SER0-0.048-0.04213.3720.0130.0130.0000.0000.0000.000
23A25LYS10.9020.9478.126-2.903-2.9030.0000.0000.0000.000
24A26PRO00.0670.03412.723-0.003-0.0030.0000.0000.0000.000
25A27SER0-0.028-0.01712.666-0.010-0.0100.0000.0000.0000.000
26A28LEU0-0.009-0.0127.913-0.126-0.1260.0000.0000.0000.000
27A29LEU0-0.023-0.00211.141-0.093-0.0930.0000.0000.0000.000
28A30LEU00.008-0.00513.986-0.060-0.0600.0000.0000.0000.000
29A31GLN0-0.0180.0006.5960.1710.1710.0000.0000.0000.000
30A32LYS10.9200.96610.2270.8010.8010.0000.0000.0000.000
31A33ASP-1-0.780-0.8835.466-3.576-3.5760.0000.0000.0000.000
32A34GLN0-0.057-0.0472.543-8.912-6.8080.475-1.191-1.389-0.017
33A35ASP-1-0.878-0.9236.693-2.086-2.0860.0000.0000.0000.000
34A36GLY00.0360.0119.9650.4480.4480.0000.0000.0000.000
35A37ARG10.7600.8639.9771.0761.0760.0000.0000.0000.000
36A38ILE00.0110.01110.845-0.148-0.1480.0000.0000.0000.000
37A39PRO00.015-0.01310.7930.0020.0020.0000.0000.0000.000
38A40LEU00.0610.02812.4020.0370.0370.0000.0000.0000.000
39A41HIS00.0090.00613.0830.0420.0420.0000.0000.0000.000
40A42TRP0-0.004-0.0197.9620.2210.2210.0000.0000.0000.000
41A43SER00.025-0.00712.8840.0260.0260.0000.0000.0000.000
42A44VAL0-0.0180.00015.687-0.006-0.0060.0000.0000.0000.000
43A45SER0-0.060-0.03614.329-0.048-0.0480.0000.0000.0000.000
44A46PHE0-0.013-0.00411.940-0.029-0.0290.0000.0000.0000.000
45A47GLN0-0.0020.01016.5100.0510.0510.0000.0000.0000.000
46A48ALA00.0720.06316.9490.0190.0190.0000.0000.0000.000
47A49HIS0-0.019-0.01018.962-0.021-0.0210.0000.0000.0000.000
48A50GLU-1-0.868-0.92621.4870.3770.3770.0000.0000.0000.000
49A51ILE0-0.0150.00315.2310.0000.0000.0000.0000.0000.000
50A52THR0-0.007-0.01218.688-0.020-0.0200.0000.0000.0000.000
51A53SER00.0180.01019.783-0.045-0.0450.0000.0000.0000.000
52A54PHE00.010-0.00417.712-0.018-0.0180.0000.0000.0000.000
53A55LEU0-0.0150.00115.0850.0030.0030.0000.0000.0000.000
54A56LEU00.0480.01319.170-0.038-0.0380.0000.0000.0000.000
55A57SER0-0.058-0.03222.394-0.015-0.0150.0000.0000.0000.000
56A58LYS10.8360.92619.495-0.443-0.4430.0000.0000.0000.000
57A59MET0-0.027-0.01218.763-0.003-0.0030.0000.0000.0000.000
58A60GLU-1-0.898-0.94322.4740.0730.0730.0000.0000.0000.000
59A61ASN0-0.061-0.03225.860-0.023-0.0230.0000.0000.0000.000
60A62VAL0-0.0110.00420.639-0.026-0.0260.0000.0000.0000.000
61A63ASN00.0550.01424.1010.0340.0340.0000.0000.0000.000
62A64LEU00.014-0.00121.410-0.027-0.0270.0000.0000.0000.000
63A65ASP-1-0.835-0.92221.698-0.233-0.2330.0000.0000.0000.000
64A66ASP-1-0.868-0.93422.044-0.252-0.2520.0000.0000.0000.000
65A67TYR0-0.064-0.03616.068-0.070-0.0700.0000.0000.0000.000
66A68PRO0-0.054-0.02418.2080.0240.0240.0000.0000.0000.000
67A69ASP-1-0.771-0.86414.575-0.831-0.8310.0000.0000.0000.000
68A70ASP-1-0.850-0.92512.564-1.365-1.3650.0000.0000.0000.000
69A71SER0-0.056-0.04015.5870.0760.0760.0000.0000.0000.000
70A72GLY0-0.020-0.03218.0890.0920.0920.0000.0000.0000.000
71A73TRP0-0.053-0.03617.9010.0840.0840.0000.0000.0000.000
72A74THR00.0430.01617.970-0.038-0.0380.0000.0000.0000.000
73A75PRO00.0600.01017.2650.0030.0030.0000.0000.0000.000
74A76PHE00.0770.04019.1550.0300.0300.0000.0000.0000.000
75A77HIS00.0250.02221.110-0.001-0.0010.0000.0000.0000.000
76A78ILE0-0.0280.00115.6950.0100.0100.0000.0000.0000.000
77A79ALA00.0370.02019.9960.0220.0220.0000.0000.0000.000
78A80CYS0-0.055-0.02422.4780.0200.0200.0000.0000.0000.000
79A81SER00.0080.00421.6540.0100.0100.0000.0000.0000.000
80A82VAL0-0.041-0.01719.644-0.002-0.0020.0000.0000.0000.000
81A83GLY00.0150.01022.7520.0190.0190.0000.0000.0000.000
82A84ASN0-0.030-0.02824.3870.0060.0060.0000.0000.0000.000
83A85LEU00.0390.00326.315-0.002-0.0020.0000.0000.0000.000
84A86GLU-1-0.900-0.93827.6960.1500.1500.0000.0000.0000.000
85A87VAL00.0230.00221.7790.0030.0030.0000.0000.0000.000
86A88VAL0-0.027-0.01825.190-0.011-0.0110.0000.0000.0000.000
87A89LYS10.9440.96526.764-0.034-0.0340.0000.0000.0000.000
88A90SER0-0.0230.00125.554-0.005-0.0050.0000.0000.0000.000
89A91LEU0-0.019-0.01721.454-0.002-0.0020.0000.0000.0000.000
90A92TYR0-0.002-0.02125.609-0.018-0.0180.0000.0000.0000.000
91A93ASP-1-0.915-0.95529.0710.0100.0100.0000.0000.0000.000
92A94ARG10.8610.94825.232-0.007-0.0070.0000.0000.0000.000
93A95PRO00.007-0.00930.034-0.013-0.0130.0000.0000.0000.000
94A96LEU0-0.035-0.00927.464-0.015-0.0150.0000.0000.0000.000
95A97LYS10.8290.91428.3610.0080.0080.0000.0000.0000.000
96A98PRO0-0.0070.01126.176-0.009-0.0090.0000.0000.0000.000
97A99ASP-1-0.821-0.91728.294-0.149-0.1490.0000.0000.0000.000
98A100LEU0-0.041-0.02128.965-0.019-0.0190.0000.0000.0000.000
99A101ASN0-0.067-0.04930.602-0.005-0.0050.0000.0000.0000.000
100A102LYS10.8920.97023.4370.3100.3100.0000.0000.0000.000
101A103ILE0-0.032-0.00827.273-0.005-0.0050.0000.0000.0000.000
102A104THR0-0.0210.00022.426-0.026-0.0260.0000.0000.0000.000
103A105ASN00.025-0.00219.8310.0730.0730.0000.0000.0000.000
104A106GLN0-0.009-0.00722.2530.0170.0170.0000.0000.0000.000
105A107GLY00.0110.00125.6360.0270.0270.0000.0000.0000.000
106A108VAL0-0.050-0.01825.1260.0260.0260.0000.0000.0000.000
107A109THR00.0900.02526.530-0.016-0.0160.0000.0000.0000.000
108A110CYS00.024-0.00226.254-0.015-0.0150.0000.0000.0000.000
109A111LEU00.0550.04227.3900.0090.0090.0000.0000.0000.000
110A112HIS0-0.0240.00028.8740.0040.0040.0000.0000.0000.000
111A113LEU0-0.052-0.01723.093-0.002-0.0020.0000.0000.0000.000
112A114ALA00.0200.01726.9280.0060.0060.0000.0000.0000.000
113A115VAL0-0.009-0.01028.7780.0110.0110.0000.0000.0000.000
114A116GLY0-0.028-0.01529.2760.0070.0070.0000.0000.0000.000
115A117LYS10.8620.93722.1810.1980.1980.0000.0000.0000.000
116A118LYS10.8640.92928.6410.1040.1040.0000.0000.0000.000
117A119TRP00.0120.02225.4610.0240.0240.0000.0000.0000.000
118A120PHE00.0100.00131.177-0.005-0.0050.0000.0000.0000.000
119A121GLU-1-0.789-0.91033.346-0.024-0.0240.0000.0000.0000.000
120A122VAL00.0000.01228.2540.0030.0030.0000.0000.0000.000
121A123SER0-0.016-0.03131.570-0.012-0.0120.0000.0000.0000.000
122A124GLN0-0.086-0.05333.428-0.004-0.0040.0000.0000.0000.000
123A125PHE00.0320.02631.4810.0000.0000.0000.0000.0000.000
124A126LEU0-0.002-0.00229.375-0.003-0.0030.0000.0000.0000.000
125A127ILE00.007-0.00233.585-0.004-0.0040.0000.0000.0000.000
126A128GLU-1-0.910-0.95137.136-0.019-0.0190.0000.0000.0000.000
127A129ASN0-0.044-0.01034.9370.0090.0090.0000.0000.0000.000
128A130GLY00.0080.01036.619-0.004-0.0040.0000.0000.0000.000
129A131ALA0-0.035-0.01533.347-0.009-0.0090.0000.0000.0000.000
130A132SER0-0.001-0.00835.1260.0060.0060.0000.0000.0000.000
131A133VAL00.0140.00235.687-0.012-0.0120.0000.0000.0000.000
132A134ARG10.8270.91137.6020.1000.1000.0000.0000.0000.000
133A135ILE00.0420.03432.624-0.003-0.0030.0000.0000.0000.000
134A136LYS10.8890.95534.9850.1640.1640.0000.0000.0000.000
135A137ASP-1-0.751-0.86129.869-0.262-0.2620.0000.0000.0000.000
136A138LYS10.9150.95726.0010.4330.4330.0000.0000.0000.000
137A139PHE0-0.003-0.00828.280-0.006-0.0060.0000.0000.0000.000
138A140ASN0-0.039-0.02033.4920.0060.0060.0000.0000.0000.000
139A141GLN0-0.024-0.00333.5920.0110.0110.0000.0000.0000.000
140A142ILE0-0.0010.01334.382-0.010-0.0100.0000.0000.0000.000
141A143PRO00.004-0.01333.047-0.001-0.0010.0000.0000.0000.000
142A144LEU00.0480.02834.7090.0030.0030.0000.0000.0000.000
143A145HIS00.0420.01735.8750.0040.0040.0000.0000.0000.000
144A146ARG10.8940.94627.8020.2480.2480.0000.0000.0000.000
145A147ALA00.011-0.00134.1510.0040.0040.0000.0000.0000.000
146A148ALA0-0.016-0.00236.3070.0080.0080.0000.0000.0000.000
147A149SER00.0220.02534.4700.0020.0020.0000.0000.0000.000
148A150VAL0-0.008-0.00831.7810.0040.0040.0000.0000.0000.000
149A151GLY00.0730.03934.9660.0110.0110.0000.0000.0000.000
150A152SER0-0.091-0.04936.2320.0140.0140.0000.0000.0000.000
151A153LEU00.0890.03738.364-0.002-0.0020.0000.0000.0000.000
152A154LYS10.8700.95337.7070.0260.0260.0000.0000.0000.000
153A155LEU00.011-0.00234.8520.0020.0020.0000.0000.0000.000
154A156ILE00.0290.02438.476-0.004-0.0040.0000.0000.0000.000
155A157GLU-1-0.765-0.83741.353-0.050-0.0500.0000.0000.0000.000
156A158LEU0-0.049-0.00337.1380.0010.0010.0000.0000.0000.000
157A159LEU00.003-0.00736.328-0.001-0.0010.0000.0000.0000.000
158A160CYS0-0.023-0.00540.459-0.004-0.0040.0000.0000.0000.000
159A161GLY00.0510.03944.1100.0020.0020.0000.0000.0000.000
160A162LEU0-0.024-0.00540.6700.0020.0020.0000.0000.0000.000
161A163GLY0-0.008-0.02141.0520.0010.0010.0000.0000.0000.000
162A164LYS10.8350.92441.9030.0520.0520.0000.0000.0000.000
163A165SER00.020-0.00941.224-0.007-0.0070.0000.0000.0000.000
164A166ALA0-0.063-0.01542.5130.0050.0050.0000.0000.0000.000
165A167VAL00.0450.02042.962-0.005-0.0050.0000.0000.0000.000
166A168ASN00.016-0.00344.713-0.007-0.0070.0000.0000.0000.000
167A169TRP0-0.045-0.03840.175-0.005-0.0050.0000.0000.0000.000
168A170GLN00.0090.00342.089-0.002-0.0020.0000.0000.0000.000
169A171ASP-1-0.805-0.89437.149-0.189-0.1890.0000.0000.0000.000
170A172LYS10.8500.89833.7490.2630.2630.0000.0000.0000.000
171A173GLN0-0.043-0.01136.066-0.013-0.0130.0000.0000.0000.000
172A174GLY00.0600.03940.2260.0070.0070.0000.0000.0000.000
173A175TRP0-0.028-0.02039.3590.0080.0080.0000.0000.0000.000
174A176THR00.0180.01841.017-0.006-0.0060.0000.0000.0000.000
175A177PRO0-0.017-0.02539.934-0.002-0.0020.0000.0000.0000.000
176A178LEU00.0230.03341.1710.0000.0000.0000.0000.0000.000
177A179PHE00.0300.02142.2880.0030.0030.0000.0000.0000.000
178A180HIS0-0.041-0.03136.5980.0000.0000.0000.0000.0000.000
179A181ALA0-0.022-0.00439.7230.0000.0000.0000.0000.0000.000
180A182LEU00.0090.00641.5920.0030.0030.0000.0000.0000.000
181A183ALA0-0.0180.00240.1630.0030.0030.0000.0000.0000.000
182A184GLU-1-0.957-0.98135.774-0.161-0.1610.0000.0000.0000.000
183A185GLY00.0020.00039.1720.0050.0050.0000.0000.0000.000
184A186HIS0-0.0280.00737.3660.0180.0180.0000.0000.0000.000
185A187GLY00.0390.00542.7770.0000.0000.0000.0000.0000.000
186A188ASP-1-0.882-0.94845.610-0.058-0.0580.0000.0000.0000.000
187A189ALA0-0.032-0.02042.3560.0020.0020.0000.0000.0000.000
188A190ALA00.0120.00044.353-0.002-0.0020.0000.0000.0000.000
189A191VAL00.0310.01746.3140.0000.0000.0000.0000.0000.000
190A192LEU0-0.059-0.02044.4640.0010.0010.0000.0000.0000.000
191A193LEU0-0.030-0.03342.6450.0000.0000.0000.0000.0000.000
192A194VAL0-0.0050.00747.058-0.001-0.0010.0000.0000.0000.000
193A195GLU-1-0.821-0.91450.644-0.056-0.0560.0000.0000.0000.000
194A196LYS10.7680.88048.2840.0510.0510.0000.0000.0000.000
195A197TYR0-0.092-0.09446.4970.0020.0020.0000.0000.0000.000
196A198GLY00.0510.04149.444-0.004-0.0040.0000.0000.0000.000
197A199ALA0-0.020-0.02447.555-0.004-0.0040.0000.0000.0000.000
198A200GLU-1-0.883-0.93749.334-0.087-0.0870.0000.0000.0000.000
199A201TYR0-0.050-0.05850.169-0.007-0.0070.0000.0000.0000.000
200A202ASP-1-0.837-0.92051.249-0.083-0.0830.0000.0000.0000.000
201A203LEU0-0.026-0.00147.580-0.002-0.0020.0000.0000.0000.000
202A204VAL0-0.036-0.02048.9980.0010.0010.0000.0000.0000.000
203A205ASP-1-0.839-0.90843.805-0.159-0.1590.0000.0000.0000.000
204A206ASN0-0.035-0.02641.7190.0090.0090.0000.0000.0000.000
205A207LYS10.8610.92641.1260.1710.1710.0000.0000.0000.000
206A208GLY0-0.005-0.00547.4860.0040.0040.0000.0000.0000.000
207A209ALA0-0.0180.00347.1910.0050.0050.0000.0000.0000.000
208A210LYS10.8370.89948.4690.0840.0840.0000.0000.0000.000
209A211ALA00.0360.01546.559-0.003-0.0030.0000.0000.0000.000
210A212GLU-1-0.779-0.87347.013-0.084-0.0840.0000.0000.0000.000
211A213ASP-1-0.883-0.93248.989-0.095-0.0950.0000.0000.0000.000
212A214VAL0-0.060-0.02243.369-0.002-0.0020.0000.0000.0000.000
213A215ALA0-0.010-0.00743.840-0.004-0.0040.0000.0000.0000.000
214A216LEU0-0.0260.00840.6690.0010.0010.0000.0000.0000.000
215A217ASN0-0.044-0.03343.9900.0000.0000.0000.0000.0000.000
216A218GLU-1-0.754-0.86347.385-0.078-0.0780.0000.0000.0000.000
217A219GLN0-0.104-0.07449.7380.0070.0070.0000.0000.0000.000
218A220VAL00.0190.02545.4170.0040.0040.0000.0000.0000.000
219A221LYS10.8150.87548.7510.0900.0900.0000.0000.0000.000
220A222LYS10.9390.97150.9210.0590.0590.0000.0000.0000.000
221A223PHE0-0.014-0.00349.5470.0020.0020.0000.0000.0000.000
222A224PHE00.0540.01849.7050.0020.0020.0000.0000.0000.000
223A225LEU00.005-0.00551.7420.0020.0020.0000.0000.0000.000
224A226ASN0-0.128-0.06055.1580.0050.0050.0000.0000.0000.000
225A227ASN0-0.109-0.06253.2730.0060.0060.0000.0000.0000.000
226A228VAL0-0.0090.00052.168-0.001-0.0010.0000.0000.0000.000
227A229VAL0-0.0260.00255.3840.0020.0020.0000.0000.0000.000
228A230ASP-1-0.934-0.93857.440-0.057-0.0570.0000.0000.0000.000
229A231ALA0-0.025-0.01957.9160.0010.0010.0000.0000.0000.000