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: NNV7Q

Calculation Name: 2IAI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IAI

Chain ID: A

ChEMBL ID:

UniProt ID: Q9XA31

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2140814.323971
FMO2-HF: Nuclear repulsion 2060414.691197
FMO2-HF: Total energy -80399.632774
FMO2-MP2: Total energy -80636.008299


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:-8:GLY)


Summations of interaction energy for fragment #1(A:-8: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.
-4.654-2.090.802-1.254-2.1110.001
Interaction energy analysis for fragmet #1(A:-8:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / 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].
3A-6GLU-1-0.819-0.9003.790-4.170-3.020-0.002-0.430-0.7170.001
4A-5ASN00.0220.0075.9930.7090.7090.0000.0000.0000.000
5A-4LEU00.020-0.0039.483-0.009-0.0090.0000.0000.0000.000
6A-3TYR0-0.069-0.02911.4980.1520.1520.0000.0000.0000.000
7A-2PHE00.0500.01214.9650.0850.0850.0000.0000.0000.000
8A-1GLN0-0.004-0.00416.323-0.018-0.0180.0000.0000.0000.000
9A0GLY00.0150.01214.5950.0250.0250.0000.0000.0000.000
10A1MET0-0.0380.00713.135-0.040-0.0400.0000.0000.0000.000
11A2THR00.002-0.0177.666-0.027-0.0270.0000.0000.0000.000
12A3THR00.0330.0335.709-0.052-0.0520.0000.0000.0000.000
13A4ALA00.0020.0056.649-0.308-0.3080.0000.0000.0000.000
14A5LYS10.8330.8912.581-4.100-3.5520.723-0.554-0.7170.001
15A6ARG10.8300.9013.196-0.952-0.2070.082-0.268-0.559-0.001
16A7ASP-1-0.810-0.8875.5394.3524.473-0.001-0.002-0.1180.000
17A8THR0-0.001-0.0068.182-0.298-0.2980.0000.0000.0000.000
18A9TYR0-0.026-0.0139.1000.0290.0290.0000.0000.0000.000
19A10THR0-0.013-0.01613.7520.0470.0470.0000.0000.0000.000
20A11PRO0-0.0060.00215.689-0.036-0.0360.0000.0000.0000.000
21A12GLU-1-0.895-0.92518.0910.2350.2350.0000.0000.0000.000
22A13THR0-0.005-0.00821.0450.0080.0080.0000.0000.0000.000
23A14LEU00.0460.00623.5440.0010.0010.0000.0000.0000.000
24A15LEU0-0.003-0.00724.732-0.004-0.0040.0000.0000.0000.000
25A16SER00.0560.04123.252-0.009-0.0090.0000.0000.0000.000
26A17VAL00.0360.01419.969-0.007-0.0070.0000.0000.0000.000
27A18ALA0-0.018-0.02222.493-0.009-0.0090.0000.0000.0000.000
28A19VAL0-0.001-0.00625.347-0.012-0.0120.0000.0000.0000.000
29A20GLN00.0150.01419.379-0.010-0.0100.0000.0000.0000.000
30A21VAL00.0270.01521.353-0.009-0.0090.0000.0000.0000.000
31A22PHE0-0.053-0.03623.760-0.012-0.0120.0000.0000.0000.000
32A23ILE0-0.023-0.00226.105-0.011-0.0110.0000.0000.0000.000
33A24GLU-1-0.958-0.96820.6500.1080.1080.0000.0000.0000.000
34A25ARG10.8980.95120.214-0.119-0.1190.0000.0000.0000.000
35A26GLY00.0450.03726.579-0.007-0.0070.0000.0000.0000.000
36A27TYR00.0410.00729.4070.0110.0110.0000.0000.0000.000
37A28ASP-1-0.881-0.93531.0920.0580.0580.0000.0000.0000.000
38A29GLY0-0.008-0.00429.6850.0030.0030.0000.0000.0000.000
39A30THR0-0.025-0.00225.6370.0090.0090.0000.0000.0000.000
40A31SER0-0.003-0.01125.3310.0010.0010.0000.0000.0000.000
41A32MET00.0630.01225.7210.0060.0060.0000.0000.0000.000
42A33GLU-1-0.837-0.89321.4430.2190.2190.0000.0000.0000.000
43A34HIS00.0280.01321.3120.0230.0230.0000.0000.0000.000
44A35LEU00.0550.03720.8280.0190.0190.0000.0000.0000.000
45A36SER0-0.064-0.04021.1230.0210.0210.0000.0000.0000.000
46A37LYS10.8090.87715.996-0.252-0.2520.0000.0000.0000.000
47A38ALA00.0320.02216.4570.0470.0470.0000.0000.0000.000
48A39ALA00.0020.00917.4360.0270.0270.0000.0000.0000.000
49A40GLY00.0160.01716.3230.0330.0330.0000.0000.0000.000
50A41ILE00.0070.01517.0300.0150.0150.0000.0000.0000.000
51A42SER00.0200.02020.210-0.024-0.0240.0000.0000.0000.000
52A43LYS10.9500.93822.603-0.169-0.1690.0000.0000.0000.000
53A44SER0-0.0110.00525.684-0.007-0.0070.0000.0000.0000.000
54A45SER00.0350.00923.830-0.018-0.0180.0000.0000.0000.000
55A46ILE00.0310.00923.689-0.006-0.0060.0000.0000.0000.000
56A47TYR0-0.017-0.00427.108-0.010-0.0100.0000.0000.0000.000
57A48HIS0-0.0410.00127.519-0.017-0.0170.0000.0000.0000.000
58A49HIS0-0.049-0.01326.365-0.013-0.0130.0000.0000.0000.000
59A50VAL0-0.027-0.02929.514-0.012-0.0120.0000.0000.0000.000
60A51THR00.0460.02031.8340.0060.0060.0000.0000.0000.000
61A52GLY00.031-0.00230.9960.0010.0010.0000.0000.0000.000
62A53LYS10.8490.90929.680-0.081-0.0810.0000.0000.0000.000
63A54GLU-1-0.789-0.86731.1390.0630.0630.0000.0000.0000.000
64A55GLU-1-0.754-0.83333.8970.0840.0840.0000.0000.0000.000
65A56LEU0-0.021-0.01027.686-0.001-0.0010.0000.0000.0000.000
66A57LEU00.0200.00931.716-0.002-0.0020.0000.0000.0000.000
67A58ARG10.8950.91133.441-0.079-0.0790.0000.0000.0000.000
68A59ARG10.8160.89031.850-0.111-0.1110.0000.0000.0000.000
69A60ALA00.0140.01731.511-0.002-0.0020.0000.0000.0000.000
70A61VAL0-0.014-0.02133.408-0.005-0.0050.0000.0000.0000.000
71A62SER0-0.019-0.01136.651-0.005-0.0050.0000.0000.0000.000
72A63ARG10.7470.87232.890-0.065-0.0650.0000.0000.0000.000
73A64ALA00.0160.00735.899-0.003-0.0030.0000.0000.0000.000
74A65LEU0-0.043-0.03237.474-0.004-0.0040.0000.0000.0000.000
75A66ASP-1-0.883-0.95040.0170.0500.0500.0000.0000.0000.000
76A67GLU-1-0.850-0.91537.3450.0470.0470.0000.0000.0000.000
77A68LEU0-0.022-0.00940.382-0.003-0.0030.0000.0000.0000.000
78A69PHE0-0.051-0.05642.889-0.003-0.0030.0000.0000.0000.000
79A70GLY00.0260.03244.298-0.002-0.0020.0000.0000.0000.000
80A71ILE0-0.0040.00142.901-0.002-0.0020.0000.0000.0000.000
81A72LEU0-0.068-0.04046.461-0.002-0.0020.0000.0000.0000.000
82A73ASP-1-0.846-0.90149.3410.0250.0250.0000.0000.0000.000
83A74GLU-1-0.739-0.79745.3000.0260.0260.0000.0000.0000.000
84A75GLU-1-0.898-0.95350.0480.0170.0170.0000.0000.0000.000
85A76HIS00.004-0.01551.369-0.001-0.0010.0000.0000.0000.000
86A77ALA0-0.0010.01150.587-0.001-0.0010.0000.0000.0000.000
87A78ARG10.7690.86852.718-0.022-0.0220.0000.0000.0000.000
88A79VAL0-0.040-0.01155.8570.0000.0000.0000.0000.0000.000
89A80GLY00.0530.03657.4240.0000.0000.0000.0000.0000.000
90A81THR00.006-0.00559.9100.0010.0010.0000.0000.0000.000
91A82ALA00.0070.00258.5840.0010.0010.0000.0000.0000.000
92A83ALA0-0.003-0.00657.0460.0010.0010.0000.0000.0000.000
93A84GLU-1-0.855-0.91055.7250.0090.0090.0000.0000.0000.000
94A85ARG10.8320.92854.112-0.013-0.0130.0000.0000.0000.000
95A86LEU0-0.045-0.02552.5360.0010.0010.0000.0000.0000.000
96A87GLU-1-0.816-0.89850.8840.0060.0060.0000.0000.0000.000
97A88TYR0-0.049-0.04947.4660.0000.0000.0000.0000.0000.000
98A89VAL00.016-0.00447.9870.0010.0010.0000.0000.0000.000
99A90VAL0-0.016-0.01246.6520.0010.0010.0000.0000.0000.000
100A91ARG10.8030.86845.197-0.005-0.0050.0000.0000.0000.000
101A92ARG10.8340.86941.290-0.025-0.0250.0000.0000.0000.000
102A93MET0-0.060-0.02342.1880.0020.0020.0000.0000.0000.000
103A94VAL0-0.017-0.00440.0030.0010.0010.0000.0000.0000.000
104A95GLU-1-0.870-0.92338.7950.0190.0190.0000.0000.0000.000
105A96VAL0-0.016-0.01137.5660.0030.0030.0000.0000.0000.000
106A97LEU0-0.067-0.01635.5310.0040.0040.0000.0000.0000.000
107A98MET0-0.044-0.01434.2080.0000.0000.0000.0000.0000.000
108A99ALA0-0.0240.00232.7510.0020.0020.0000.0000.0000.000
109A100GLU-1-0.805-0.89132.3030.0670.0670.0000.0000.0000.000
110A101LEU00.0440.05029.2700.0040.0040.0000.0000.0000.000
111A102PRO0-0.015-0.00827.7940.0000.0000.0000.0000.0000.000
112A103TYR00.0260.00529.2070.0060.0060.0000.0000.0000.000
113A104VAL00.0590.01632.669-0.001-0.0010.0000.0000.0000.000
114A105THR00.000-0.01130.955-0.005-0.0050.0000.0000.0000.000
115A106LEU0-0.057-0.03829.560-0.001-0.0010.0000.0000.0000.000
116A107LEU0-0.0070.00833.474-0.002-0.0020.0000.0000.0000.000
117A108LEU0-0.040-0.03636.682-0.002-0.0020.0000.0000.0000.000
118A109ARG10.8830.93729.185-0.041-0.0410.0000.0000.0000.000
119A110VAL0-0.0610.00136.4410.0000.0000.0000.0000.0000.000
120A111ARG10.8940.94438.222-0.033-0.0330.0000.0000.0000.000
121A112GLY00.0940.05439.554-0.001-0.0010.0000.0000.0000.000
122A113ASN0-0.017-0.01340.485-0.002-0.0020.0000.0000.0000.000
123A114THR0-0.022-0.02137.7840.0000.0000.0000.0000.0000.000
124A115GLY00.002-0.00541.154-0.003-0.0030.0000.0000.0000.000
125A116THR0-0.002-0.02037.487-0.002-0.0020.0000.0000.0000.000
126A117GLU-1-0.818-0.88837.8220.0500.0500.0000.0000.0000.000
127A118ARG10.8970.93540.794-0.044-0.0440.0000.0000.0000.000
128A119TRP00.0180.02240.506-0.002-0.0020.0000.0000.0000.000
129A120ALA00.0630.02640.459-0.002-0.0020.0000.0000.0000.000
130A121LEU0-0.052-0.04442.396-0.003-0.0030.0000.0000.0000.000
131A122GLU-1-0.946-0.98944.5770.0330.0330.0000.0000.0000.000
132A123ARG10.9160.97444.378-0.039-0.0390.0000.0000.0000.000
133A124ARG10.9530.98940.851-0.031-0.0310.0000.0000.0000.000
134A125ARG10.8820.95845.449-0.030-0.0300.0000.0000.0000.000
135A126GLU-1-0.932-0.96548.9110.0240.0240.0000.0000.0000.000
136A127PHE00.0190.00745.954-0.001-0.0010.0000.0000.0000.000
137A128ASP-1-0.809-0.87948.4790.0160.0160.0000.0000.0000.000
138A129HIS00.0280.01949.753-0.003-0.0030.0000.0000.0000.000
139A130ARG10.8440.92551.082-0.026-0.0260.0000.0000.0000.000
140A131VAL00.0490.02648.736-0.001-0.0010.0000.0000.0000.000
141A132ALA0-0.018-0.01452.143-0.001-0.0010.0000.0000.0000.000
142A133ALA0-0.064-0.03254.647-0.001-0.0010.0000.0000.0000.000
143A134LEU00.0560.03552.646-0.001-0.0010.0000.0000.0000.000
144A135LEU00.0160.02053.922-0.001-0.0010.0000.0000.0000.000
145A136LYS10.9130.94456.897-0.013-0.0130.0000.0000.0000.000
146A137ASP-1-0.927-0.96059.7880.0120.0120.0000.0000.0000.000
147A138ALA00.0270.00458.580-0.001-0.0010.0000.0000.0000.000
148A139ALA0-0.046-0.02160.600-0.001-0.0010.0000.0000.0000.000
149A140ALA0-0.083-0.03862.509-0.001-0.0010.0000.0000.0000.000
150A141GLU-1-0.871-0.93762.6710.0100.0100.0000.0000.0000.000
151A142GLY0-0.051-0.00964.9980.0000.0000.0000.0000.0000.000
152A143ASP-1-0.870-0.93560.7280.0050.0050.0000.0000.0000.000
153A144VAL0-0.074-0.03957.708-0.001-0.0010.0000.0000.0000.000
154A145ARG10.7740.84858.389-0.001-0.0010.0000.0000.0000.000
155A146ALA00.0630.01161.5510.0010.0010.0000.0000.0000.000
156A147ASP-1-0.842-0.87062.5390.0010.0010.0000.0000.0000.000
157A148VAL0-0.044-0.02656.743-0.001-0.0010.0000.0000.0000.000
158A149GLU-1-0.873-0.93159.1980.0080.0080.0000.0000.0000.000
159A150VAL00.0840.04657.2630.0000.0000.0000.0000.0000.000
160A151ARG10.9120.93654.988-0.015-0.0150.0000.0000.0000.000
161A152LEU0-0.0170.01153.4420.0010.0010.0000.0000.0000.000
162A153ALA00.0440.00853.0310.0000.0000.0000.0000.0000.000
163A154THR00.0340.00350.6870.0000.0000.0000.0000.0000.000
164A155ARG10.7260.83148.195-0.015-0.0150.0000.0000.0000.000
165A156LEU0-0.003-0.01348.1320.0000.0000.0000.0000.0000.000
166A157VAL00.0460.04247.734-0.001-0.0010.0000.0000.0000.000
167A158PHE00.015-0.00945.5280.0010.0010.0000.0000.0000.000
168A159GLY0-0.033-0.00343.8570.0010.0010.0000.0000.0000.000
169A160MET0-0.008-0.00542.836-0.001-0.0010.0000.0000.0000.000
170A161ILE00.0470.02441.655-0.001-0.0010.0000.0000.0000.000
171A162ASN0-0.020-0.04039.7820.0030.0030.0000.0000.0000.000
172A163SER0-0.008-0.00138.2440.0010.0010.0000.0000.0000.000
173A164ILE00.0280.01835.963-0.002-0.0020.0000.0000.0000.000
174A165VAL0-0.043-0.02933.4620.0000.0000.0000.0000.0000.000
175A166GLU-1-1.021-1.01332.3210.0050.0050.0000.0000.0000.000
176A167TRP0-0.050-0.02332.128-0.004-0.0040.0000.0000.0000.000
177A168TYR0-0.068-0.04832.169-0.003-0.0030.0000.0000.0000.000
178A169ARG10.8410.89225.1150.0360.0360.0000.0000.0000.000
179A170PRO0-0.0170.01127.401-0.004-0.0040.0000.0000.0000.000
180A171GLU-1-0.869-0.91527.286-0.033-0.0330.0000.0000.0000.000
181A183SER00.0190.00040.7180.0010.0010.0000.0000.0000.000
182A184GLY0-0.023-0.00440.4780.0010.0010.0000.0000.0000.000
183A185VAL00.003-0.00736.358-0.002-0.0020.0000.0000.0000.000
184A186SER00.0340.01534.165-0.002-0.0020.0000.0000.0000.000
185A187GLY00.0730.03534.9060.0010.0010.0000.0000.0000.000
186A188ALA0-0.026-0.00936.5700.0010.0010.0000.0000.0000.000
187A189GLY00.0800.04235.7170.0000.0000.0000.0000.0000.000
188A190GLU-1-0.781-0.88633.5710.0040.0040.0000.0000.0000.000
189A191ARG10.8590.91337.487-0.002-0.0020.0000.0000.0000.000
190A192GLU-1-0.956-0.95439.301-0.015-0.0150.0000.0000.0000.000
191A193VAL00.0100.00037.3700.0000.0000.0000.0000.0000.000
192A194VAL00.0190.00940.6840.0000.0000.0000.0000.0000.000
193A195ASP-1-0.795-0.87642.9380.0000.0000.0000.0000.0000.000
194A196ALA0-0.059-0.01643.4540.0000.0000.0000.0000.0000.000
195A197VAL00.0170.00442.6160.0000.0000.0000.0000.0000.000
196A198ALA00.0160.01745.6280.0000.0000.0000.0000.0000.000
197A199ARG10.8400.89247.5420.0030.0030.0000.0000.0000.000
198A200LEU0-0.034-0.01446.1090.0000.0000.0000.0000.0000.000
199A201VAL0-0.043-0.02448.0710.0000.0000.0000.0000.0000.000
200A202PHE00.0020.00250.7340.0000.0000.0000.0000.0000.000
201A203GLY00.0000.01253.2990.0000.0000.0000.0000.0000.000
202A204GLY0-0.066-0.02052.462-0.001-0.0010.0000.0000.0000.000
203A205LEU00.010-0.01948.904-0.001-0.0010.0000.0000.0000.000
204A206ARG10.8940.95652.8180.0060.0060.0000.0000.0000.000
205A207LYS11.0331.02555.3190.0140.0140.0000.0000.0000.000