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: 16JQZ

Calculation Name: 2IAD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IAD

Chain ID: A

ChEMBL ID:

UniProt ID: P04228

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 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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1932683.852389
FMO2-HF: Nuclear repulsion 1859427.678718
FMO2-HF: Total energy -73256.173671
FMO2-MP2: Total energy -73474.661962


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:1:ILE)


Summations of interaction energy for fragment #1(A:1:ILE)
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.
-4.223-1.160.145-1.433-1.776-0.002
Interaction energy analysis for fragmet #1(A:1:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / 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].
3A2ALA0-0.012-0.0132.987-2.6190.3470.146-1.420-1.693-0.002
4A3ASP-1-0.910-0.9414.622-1.282-1.185-0.001-0.013-0.0830.000
5A4HIS10.7550.8337.3271.6401.6400.0000.0000.0000.000
6A5VAL0-0.0070.0005.792-0.406-0.4060.0000.0000.0000.000
7A6GLY00.0270.0267.9590.2550.2550.0000.0000.0000.000
8A7PHE0-0.067-0.0267.2290.0210.0210.0000.0000.0000.000
9A8TYR0-0.008-0.02911.7200.0250.0250.0000.0000.0000.000
10A9GLY00.0690.03514.0690.0310.0310.0000.0000.0000.000
11A10THR0-0.005-0.00713.4620.0390.0390.0000.0000.0000.000
12A11THR0-0.049-0.03016.033-0.026-0.0260.0000.0000.0000.000
13A12VAL00.0220.02318.5550.0340.0340.0000.0000.0000.000
14A13TYR0-0.007-0.02820.962-0.025-0.0250.0000.0000.0000.000
15A14GLN00.0150.00024.2290.0300.0300.0000.0000.0000.000
16A15SER00.0390.00526.684-0.010-0.0100.0000.0000.0000.000
17A16PRO0-0.038-0.00229.747-0.009-0.0090.0000.0000.0000.000
18A17GLY00.0460.00931.797-0.002-0.0020.0000.0000.0000.000
19A18ASP-1-0.882-0.92030.6380.0540.0540.0000.0000.0000.000
20A19ILE00.0130.02227.409-0.009-0.0090.0000.0000.0000.000
21A20GLY00.0290.00625.2130.0150.0150.0000.0000.0000.000
22A21GLN0-0.019-0.01020.081-0.017-0.0170.0000.0000.0000.000
23A22TYR0-0.028-0.03619.1740.0250.0250.0000.0000.0000.000
24A23THR00.0380.01017.653-0.001-0.0010.0000.0000.0000.000
25A24HIS00.0220.04916.2730.0500.0500.0000.0000.0000.000
26A25GLU-1-0.839-0.92813.215-0.279-0.2790.0000.0000.0000.000
27A26PHE0-0.043-0.03712.050-0.053-0.0530.0000.0000.0000.000
28A27ASP-1-0.768-0.85710.623-1.284-1.2840.0000.0000.0000.000
29A28GLY0-0.0040.00211.6890.0270.0270.0000.0000.0000.000
30A29ASP-1-0.884-0.92112.694-0.330-0.3300.0000.0000.0000.000
31A30GLU-1-0.827-0.90816.008-0.184-0.1840.0000.0000.0000.000
32A31LEU0-0.031-0.03016.7170.0120.0120.0000.0000.0000.000
33A32PHE0-0.044-0.03119.6150.0230.0230.0000.0000.0000.000
34A33TYR00.0360.02121.002-0.001-0.0010.0000.0000.0000.000
35A34VAL0-0.034-0.01823.364-0.001-0.0010.0000.0000.0000.000
36A35ASP-1-0.763-0.85725.998-0.033-0.0330.0000.0000.0000.000
37A36LEU0-0.029-0.01125.7990.0020.0020.0000.0000.0000.000
38A37ASP-1-0.888-0.92529.817-0.015-0.0150.0000.0000.0000.000
39A38LYS10.8010.86932.9390.0410.0410.0000.0000.0000.000
40A39LYS10.8920.93930.7660.0100.0100.0000.0000.0000.000
41A40LYS10.8960.93230.6530.0630.0630.0000.0000.0000.000
42A41THR00.006-0.00224.6160.0080.0080.0000.0000.0000.000
43A42VAL0-0.027-0.00226.766-0.005-0.0050.0000.0000.0000.000
44A43TRP00.0290.00521.447-0.009-0.0090.0000.0000.0000.000
45A44ARG10.9120.98521.9760.2140.2140.0000.0000.0000.000
46A45LEU00.0390.03122.4270.0090.0090.0000.0000.0000.000
47A46PRO0-0.004-0.01125.521-0.003-0.0030.0000.0000.0000.000
48A47GLU-1-0.873-0.94626.505-0.205-0.2050.0000.0000.0000.000
49A48PHE00.007-0.02020.469-0.002-0.0020.0000.0000.0000.000
50A49GLY00.0010.00625.478-0.001-0.0010.0000.0000.0000.000
51A50GLN0-0.091-0.04726.9650.0170.0170.0000.0000.0000.000
52A51LEU0-0.050-0.02326.0400.0080.0080.0000.0000.0000.000
53A52ILE0-0.052-0.00721.190-0.007-0.0070.0000.0000.0000.000
54A53LEU00.0050.00024.6700.0070.0070.0000.0000.0000.000
55A54PHE00.0250.01120.371-0.004-0.0040.0000.0000.0000.000
56A55GLU-1-0.854-0.91924.253-0.073-0.0730.0000.0000.0000.000
57A56PRO00.0090.00525.3710.0080.0080.0000.0000.0000.000
58A57GLN0-0.047-0.03425.7670.0020.0020.0000.0000.0000.000
59A58GLY00.0340.02023.3560.0130.0130.0000.0000.0000.000
60A59GLY00.0560.02522.5830.0110.0110.0000.0000.0000.000
61A60LEU0-0.026-0.02523.6280.0200.0200.0000.0000.0000.000
62A61GLN0-0.020-0.00724.8260.0040.0040.0000.0000.0000.000
63A62ASN00.0170.00918.3460.0210.0210.0000.0000.0000.000
64A63ILE0-0.037-0.00922.6830.0210.0210.0000.0000.0000.000
65A64ALA0-0.052-0.02924.8440.0140.0140.0000.0000.0000.000
66A65ALA0-0.0020.00722.6340.0090.0090.0000.0000.0000.000
67A66GLU-1-0.801-0.90819.8940.2200.2200.0000.0000.0000.000
68A67LYS10.8120.92023.437-0.045-0.0450.0000.0000.0000.000
69A68HIS0-0.050-0.02326.276-0.002-0.0020.0000.0000.0000.000
70A69ASN0-0.024-0.04021.5660.0030.0030.0000.0000.0000.000
71A70LEU00.0140.03424.5170.0160.0160.0000.0000.0000.000
72A71GLY00.0000.01125.7770.0070.0070.0000.0000.0000.000
73A72ILE0-0.046-0.03626.2280.0040.0040.0000.0000.0000.000
74A73LEU00.013-0.00721.4510.0080.0080.0000.0000.0000.000
75A74THR0-0.017-0.00925.2700.0040.0040.0000.0000.0000.000
76A75LYS10.9340.96827.832-0.124-0.1240.0000.0000.0000.000
77A76ARG10.9110.96922.097-0.267-0.2670.0000.0000.0000.000
78A77SER0-0.001-0.00124.6600.0170.0170.0000.0000.0000.000
79A78ASN0-0.078-0.02226.999-0.005-0.0050.0000.0000.0000.000
80A79PHE0-0.035-0.04729.911-0.010-0.0100.0000.0000.0000.000
81A80THR00.0290.03225.903-0.015-0.0150.0000.0000.0000.000
82A81PRO0-0.026-0.00227.1650.0060.0060.0000.0000.0000.000
83A82ALA00.0080.00124.9010.0160.0160.0000.0000.0000.000
84A83THR0-0.011-0.01424.332-0.013-0.0130.0000.0000.0000.000
85A84ASN0-0.026-0.03024.4180.0090.0090.0000.0000.0000.000
86A85GLU-1-0.854-0.91021.1740.1900.1900.0000.0000.0000.000
87A86ALA00.004-0.00124.522-0.016-0.0160.0000.0000.0000.000
88A87PRO00.0160.00823.3320.0010.0010.0000.0000.0000.000
89A88GLN0-0.033-0.01020.2080.0120.0120.0000.0000.0000.000
90A89ALA00.0060.01523.433-0.012-0.0120.0000.0000.0000.000
91A90THR0-0.050-0.03423.9760.0040.0040.0000.0000.0000.000
92A91VAL00.002-0.00225.988-0.009-0.0090.0000.0000.0000.000
93A92PHE0-0.022-0.01422.907-0.001-0.0010.0000.0000.0000.000
94A93PRO00.0280.02728.318-0.001-0.0010.0000.0000.0000.000
95A94LYS10.9630.98626.7530.1910.1910.0000.0000.0000.000
96A95SER0-0.008-0.01228.097-0.018-0.0180.0000.0000.0000.000
97A96PRO00.0030.00030.7500.0080.0080.0000.0000.0000.000
98A97VAL00.0060.00333.2430.0020.0020.0000.0000.0000.000
99A98LEU00.0140.01135.7560.0030.0030.0000.0000.0000.000
100A99LEU0-0.0020.00339.1180.0000.0000.0000.0000.0000.000
101A100GLY00.0080.00642.1650.0000.0000.0000.0000.0000.000
102A101GLN0-0.037-0.02238.046-0.002-0.0020.0000.0000.0000.000
103A102PRO0-0.051-0.03738.189-0.002-0.0020.0000.0000.0000.000
104A103ASN0-0.0040.00132.658-0.015-0.0150.0000.0000.0000.000
105A104THR0-0.045-0.03730.3310.0020.0020.0000.0000.0000.000
106A105LEU0-0.0160.01030.787-0.009-0.0090.0000.0000.0000.000
107A106ILE0-0.013-0.01524.608-0.002-0.0020.0000.0000.0000.000
108A107CYS0-0.063-0.02126.9300.0060.0060.0000.0000.0000.000
109A108PHE00.0040.01117.4950.0000.0000.0000.0000.0000.000
110A109VAL00.011-0.01822.9190.0130.0130.0000.0000.0000.000
111A110ASP-1-0.798-0.91117.448-0.033-0.0330.0000.0000.0000.000
112A111ASN0-0.066-0.03818.6030.0310.0310.0000.0000.0000.000
113A112ILE0-0.033-0.00519.7900.0090.0090.0000.0000.0000.000
114A113PHE00.0400.02519.8270.0170.0170.0000.0000.0000.000
115A114PRO00.0550.01522.4320.0020.0020.0000.0000.0000.000
116A115PRO0-0.0190.02121.482-0.015-0.0150.0000.0000.0000.000
117A116VAL0-0.048-0.02723.487-0.012-0.0120.0000.0000.0000.000
118A117ILE0-0.032-0.01725.3940.0040.0040.0000.0000.0000.000
119A118ASN0-0.032-0.01728.338-0.010-0.0100.0000.0000.0000.000
120A119ILE00.0180.01425.7190.0020.0020.0000.0000.0000.000
121A120THR0-0.011-0.00530.365-0.003-0.0030.0000.0000.0000.000
122A121TRP00.0450.02229.7200.0020.0020.0000.0000.0000.000
123A122LEU0-0.054-0.02935.3280.0040.0040.0000.0000.0000.000
124A123ARG10.9130.96538.3480.0540.0540.0000.0000.0000.000
125A124ASN0-0.065-0.05840.7050.0040.0040.0000.0000.0000.000
126A125SER0-0.024-0.01841.8150.0030.0030.0000.0000.0000.000
127A126LYS10.8930.95042.6200.0370.0370.0000.0000.0000.000
128A127SER00.0090.00639.891-0.002-0.0020.0000.0000.0000.000
129A128VAL0-0.054-0.01937.7220.0000.0000.0000.0000.0000.000
130A129THR0-0.022-0.00437.835-0.002-0.0020.0000.0000.0000.000
131A130ASP-1-0.854-0.94037.420-0.062-0.0620.0000.0000.0000.000
132A131GLY00.0520.01936.323-0.003-0.0030.0000.0000.0000.000
133A132VAL0-0.044-0.00132.312-0.005-0.0050.0000.0000.0000.000
134A133TYR0-0.057-0.03225.533-0.005-0.0050.0000.0000.0000.000
135A134GLU-1-0.807-0.91026.458-0.048-0.0480.0000.0000.0000.000
136A135THR0-0.0140.01421.902-0.002-0.0020.0000.0000.0000.000
137A136SER0-0.030-0.03121.0950.0290.0290.0000.0000.0000.000
138A137PHE0-0.063-0.04620.290-0.008-0.0080.0000.0000.0000.000
139A138LEU00.0250.02816.3790.0080.0080.0000.0000.0000.000
140A139VAL00.0170.00311.7340.0500.0500.0000.0000.0000.000
141A140ASN00.0120.02612.273-0.142-0.1420.0000.0000.0000.000
142A141ARG10.8360.8906.917-0.470-0.4700.0000.0000.0000.000
143A142ASP-1-0.860-0.9099.7800.5220.5220.0000.0000.0000.000
144A143HIS0-0.041-0.01911.093-0.090-0.0900.0000.0000.0000.000
145A144SER00.0100.02714.609-0.054-0.0540.0000.0000.0000.000
146A145PHE0-0.030-0.04315.7650.0030.0030.0000.0000.0000.000
147A146HIS00.002-0.00314.916-0.017-0.0170.0000.0000.0000.000
148A147LYS10.7480.85019.0170.0420.0420.0000.0000.0000.000
149A148LEU00.0320.01619.7560.0000.0000.0000.0000.0000.000
150A149SER00.0220.03323.7260.0030.0030.0000.0000.0000.000
151A150TYR0-0.023-0.02923.642-0.011-0.0110.0000.0000.0000.000
152A151LEU00.0610.03529.6710.0090.0090.0000.0000.0000.000
153A152THR0-0.0140.01233.304-0.007-0.0070.0000.0000.0000.000
154A153PHE0-0.009-0.01733.8080.0070.0070.0000.0000.0000.000
155A154ILE00.0020.00137.624-0.007-0.0070.0000.0000.0000.000
156A155PRO0-0.072-0.02137.2180.0050.0050.0000.0000.0000.000
157A156SER00.0780.00539.8810.0000.0000.0000.0000.0000.000
158A157ASP-1-0.865-0.92742.175-0.058-0.0580.0000.0000.0000.000
159A158ASP-1-0.977-0.94743.907-0.044-0.0440.0000.0000.0000.000
160A159ASP-1-0.835-0.90941.617-0.053-0.0530.0000.0000.0000.000
161A160ILE0-0.0130.01439.757-0.002-0.0020.0000.0000.0000.000
162A161TYR0-0.023-0.03835.7660.0010.0010.0000.0000.0000.000
163A162ASP-1-0.851-0.93135.168-0.027-0.0270.0000.0000.0000.000
164A164LYS10.8560.90232.3170.0090.0090.0000.0000.0000.000
165A165VAL00.0140.01227.519-0.003-0.0030.0000.0000.0000.000
166A166GLU-1-0.840-0.90830.7870.0090.0090.0000.0000.0000.000
167A167HIS00.0650.00725.430-0.004-0.0040.0000.0000.0000.000
168A168TRP00.0160.00929.1910.0020.0020.0000.0000.0000.000
169A169GLY0-0.060-0.01528.1380.0030.0030.0000.0000.0000.000
170A170LEU0-0.092-0.04829.206-0.002-0.0020.0000.0000.0000.000
171A171GLU-1-0.926-0.94931.5370.0500.0500.0000.0000.0000.000
172A172GLU-1-0.972-0.99234.8160.0170.0170.0000.0000.0000.000
173A173PRO0-0.066-0.04034.246-0.001-0.0010.0000.0000.0000.000
174A174VAL00.0540.04629.874-0.003-0.0030.0000.0000.0000.000
175A175LEU0-0.007-0.01633.002-0.005-0.0050.0000.0000.0000.000
176A176LYS10.8150.92028.7120.0220.0220.0000.0000.0000.000
177A177HIS00.0490.01232.334-0.002-0.0020.0000.0000.0000.000
178A178TRP00.0340.00932.345-0.005-0.0050.0000.0000.0000.000
179A179SER0-0.079-0.04535.1230.0040.0040.0000.0000.0000.000
180A180SER0-0.005-0.00637.530-0.006-0.0060.0000.0000.0000.000
181A181ALA00.0970.07139.239-0.002-0.0020.0000.0000.0000.000
182A182ASP-1-0.891-0.95137.938-0.053-0.0530.0000.0000.0000.000
183A183LEU0-0.076-0.03938.8950.0050.0050.0000.0000.0000.000
184A184VAL00.0790.04237.8300.0010.0010.0000.0000.0000.000
185A185PRO0-0.018-0.01736.8100.0010.0010.0000.0000.0000.000
186A186ARG10.8460.93539.1630.0220.0220.0000.0000.0000.000