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: YV6M2

Calculation Name: 2IU5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2IU5

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CIV9

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2078630.690746
FMO2-HF: Nuclear repulsion 2003563.448659
FMO2-HF: Total energy -75067.242087
FMO2-MP2: Total energy -75288.558082


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-59.316-56.00924.814-13.656-14.463-0.094
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.003
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].
3A3LYS10.9090.9303.875-5.111-3.605-0.016-0.732-0.7580.003
4A4SER0-0.028-0.0132.702-6.013-5.5193.325-1.620-2.1990.023
5A5ILE0-0.002-0.0022.478-1.666-0.0961.254-0.543-2.2800.000
6A6ILE00.0430.0385.271-0.918-0.859-0.001-0.003-0.0540.000
7A7THR0-0.018-0.0197.763-0.265-0.2650.0000.0000.0000.000
8A8GLN00.0410.0277.415-0.127-0.1270.0000.0000.0000.000
9A9LYS10.8500.9032.8645.6766.7170.042-0.496-0.5880.001
10A10ILE0-0.033-0.0068.8860.0470.0470.0000.0000.0000.000
11A11ILE0-0.027-0.02112.3090.0020.0020.0000.0000.0000.000
12A12ALA00.0360.01610.4760.0320.0320.0000.0000.0000.000
13A13LYS10.8210.90311.9040.5910.5910.0000.0000.0000.000
14A14ALA00.0140.00313.5510.0620.0620.0000.0000.0000.000
15A15PHE00.013-0.01315.6230.0610.0610.0000.0000.0000.000
16A16LYS10.8970.93310.1391.7331.7330.0000.0000.0000.000
17A17ASP-1-0.813-0.88516.748-0.467-0.4670.0000.0000.0000.000
18A18LEU0-0.065-0.02819.0350.0480.0480.0000.0000.0000.000
19A19MET00.0180.00719.2530.0610.0610.0000.0000.0000.000
20A20GLN0-0.0290.00419.8470.0310.0310.0000.0000.0000.000
21A21SER0-0.044-0.02922.1800.0330.0330.0000.0000.0000.000
22A22ASN0-0.053-0.01524.7550.0530.0530.0000.0000.0000.000
23A23ALA00.0240.01825.566-0.032-0.0320.0000.0000.0000.000
24A24TYR00.1130.03320.1260.0050.0050.0000.0000.0000.000
25A25HIS0-0.0020.00024.147-0.009-0.0090.0000.0000.0000.000
26A26GLN0-0.071-0.03926.5790.0180.0180.0000.0000.0000.000
27A27ILE00.0040.03121.2010.0130.0130.0000.0000.0000.000
28A28SER0-0.028-0.04022.892-0.010-0.0100.0000.0000.0000.000
29A29VAL00.0480.00719.690-0.010-0.0100.0000.0000.0000.000
30A30SER0-0.003-0.00521.4160.0180.0180.0000.0000.0000.000
31A31ASP-1-0.817-0.85823.892-0.160-0.1600.0000.0000.0000.000
32A32ILE00.0530.04117.0020.0060.0060.0000.0000.0000.000
33A33MET0-0.051-0.00217.619-0.009-0.0090.0000.0000.0000.000
34A34GLN0-0.041-0.03020.4490.0370.0370.0000.0000.0000.000
35A35THR0-0.035-0.01919.9040.0260.0260.0000.0000.0000.000
36A36ALA00.0190.00016.6920.0090.0090.0000.0000.0000.000
37A37LYS10.8220.92618.1690.1300.1300.0000.0000.0000.000
38A38ILE00.0200.02114.9810.0540.0540.0000.0000.0000.000
39A39ARG10.9630.96719.497-0.187-0.1870.0000.0000.0000.000
40A40ARG10.9790.96220.7530.0990.0990.0000.0000.0000.000
41A41GLN00.0490.01820.795-0.034-0.0340.0000.0000.0000.000
42A42THR0-0.033-0.02416.0250.0170.0170.0000.0000.0000.000
43A43PHE00.0690.02916.0520.0390.0390.0000.0000.0000.000
44A44TYR00.0220.01315.636-0.013-0.0130.0000.0000.0000.000
45A45ASN0-0.109-0.03814.9150.0390.0390.0000.0000.0000.000
46A46TYR0-0.059-0.02110.4060.1360.1360.0000.0000.0000.000
47A47PHE00.0510.0269.455-0.049-0.0490.0000.0000.0000.000
48A48GLN0-0.062-0.03914.7260.0750.0750.0000.0000.0000.000
49A49ASN0-0.013-0.02517.496-0.017-0.0170.0000.0000.0000.000
50A50GLN00.040-0.01316.906-0.026-0.0260.0000.0000.0000.000
51A51GLU-1-0.917-0.93517.061-0.409-0.4090.0000.0000.0000.000
52A52GLU-1-0.794-0.87814.001-0.323-0.3230.0000.0000.0000.000
53A53LEU0-0.045-0.01411.754-0.109-0.1090.0000.0000.0000.000
54A54LEU0-0.018-0.01212.391-0.187-0.1870.0000.0000.0000.000
55A55SER0-0.011-0.01513.358-0.125-0.1250.0000.0000.0000.000
56A56TRP00.0430.0124.486-0.129-0.003-0.001-0.006-0.1190.000
57A57ILE0-0.049-0.0238.465-0.484-0.4840.0000.0000.0000.000
58A58PHE0-0.020-0.01710.373-0.239-0.2390.0000.0000.0000.000
59A59GLU-1-0.935-0.9707.683-1.533-1.5330.0000.0000.0000.000
60A60ASN0-0.081-0.0554.396-1.894-1.771-0.001-0.019-0.1030.000
61A61ASP-1-0.737-0.8206.457-3.198-3.1980.0000.0000.0000.000
62A62PHE00.013-0.0108.4260.0520.0520.0000.0000.0000.000
63A63ALA00.0560.0405.8030.1690.1690.0000.0000.0000.000
64A64GLU-1-0.792-0.8931.874-19.750-21.7569.273-4.142-3.125-0.047
65A65LEU0-0.070-0.0275.5401.0881.0880.0000.0000.0000.000
66A66ILE0-0.048-0.0188.9990.5460.5460.0000.0000.0000.000
67A67ASN0-0.057-0.0417.8170.3560.3560.0000.0000.0000.000
68A68ASP-1-0.885-0.9241.854-26.739-26.41810.940-6.092-5.169-0.074
69A69ASN0-0.023-0.0234.9160.7720.845-0.001-0.003-0.0680.000
70A70SER0-0.045-0.0337.3550.2540.2540.0000.0000.0000.000
71A71ASP-1-0.886-0.93010.433-0.412-0.4120.0000.0000.0000.000
72A72TYR0-0.072-0.05013.191-0.054-0.0540.0000.0000.0000.000
73A73TYR0-0.094-0.08316.2970.0020.0020.0000.0000.0000.000
74A74GLY00.0670.03614.1940.0530.0530.0000.0000.0000.000
75A75TRP0-0.0040.00815.124-0.054-0.0540.0000.0000.0000.000
76A76GLN0-0.016-0.01116.579-0.017-0.0170.0000.0000.0000.000
77A77ASN0-0.024-0.00114.3820.0550.0550.0000.0000.0000.000
78A78GLU-1-0.732-0.84711.301-1.097-1.0970.0000.0000.0000.000
79A79LEU00.0060.01213.624-0.052-0.0520.0000.0000.0000.000
80A80LEU0-0.039-0.01216.7830.0040.0040.0000.0000.0000.000
81A81LEU0-0.009-0.01110.7370.0480.0480.0000.0000.0000.000
82A82LEU00.0430.03113.083-0.029-0.0290.0000.0000.0000.000
83A83LEU0-0.040-0.02714.3840.0500.0500.0000.0000.0000.000
84A84ARG10.8250.87315.8040.5240.5240.0000.0000.0000.000
85A85TYR0-0.008-0.00612.0670.0960.0960.0000.0000.0000.000
86A86LEU00.003-0.00414.7140.0500.0500.0000.0000.0000.000
87A87ASP-1-0.745-0.83617.587-0.438-0.4380.0000.0000.0000.000
88A88GLU-1-0.960-0.96714.314-0.796-0.7960.0000.0000.0000.000
89A89ASN0-0.106-0.06714.5220.0370.0370.0000.0000.0000.000
90A90GLN00.0070.01618.0240.0110.0110.0000.0000.0000.000
91A91ILE00.014-0.00321.4590.0090.0090.0000.0000.0000.000
92A92PHE0-0.006-0.00215.7080.0290.0290.0000.0000.0000.000
93A93TYR00.048-0.01514.0610.0420.0420.0000.0000.0000.000
94A94GLN0-0.056-0.02020.7970.0230.0230.0000.0000.0000.000
95A95LYS10.8080.90723.1900.4240.4240.0000.0000.0000.000
96A96ILE00.0100.00518.4920.0330.0330.0000.0000.0000.000
97A97PHE00.000-0.01521.8800.0170.0170.0000.0000.0000.000
98A98VAL0-0.068-0.02124.4520.0370.0370.0000.0000.0000.000
99A99ILE0-0.068-0.02622.4560.0280.0280.0000.0000.0000.000
100A100ASP-1-0.782-0.89720.386-0.516-0.5160.0000.0000.0000.000
101A101LYS10.8580.92323.3210.3420.3420.0000.0000.0000.000
102A102ASN0-0.049-0.03421.3800.0480.0480.0000.0000.0000.000
103A103PHE00.0760.05215.956-0.025-0.0250.0000.0000.0000.000
104A104GLU-1-0.822-0.88619.665-0.467-0.4670.0000.0000.0000.000
105A105HIS0-0.046-0.03821.417-0.024-0.0240.0000.0000.0000.000
106A106PHE00.0330.02311.6500.0390.0390.0000.0000.0000.000
107A107PHE00.0010.00216.595-0.089-0.0890.0000.0000.0000.000
108A108LEU0-0.002-0.01918.254-0.033-0.0330.0000.0000.0000.000
109A109ILE00.0450.02615.189-0.012-0.0120.0000.0000.0000.000
110A110GLN0-0.0260.00312.474-0.239-0.2390.0000.0000.0000.000
111A111TRP00.027-0.00515.367-0.065-0.0650.0000.0000.0000.000
112A112GLU-1-0.922-0.97918.491-0.537-0.5370.0000.0000.0000.000
113A113ASN0-0.016-0.01012.7730.1410.1410.0000.0000.0000.000
114A114LEU0-0.024-0.00914.802-0.009-0.0090.0000.0000.0000.000
115A115LEU0-0.036-0.02416.4190.0730.0730.0000.0000.0000.000
116A116ASP-1-0.804-0.90317.389-0.530-0.5300.0000.0000.0000.000
117A117LYS10.7540.86812.2291.0961.0960.0000.0000.0000.000
118A118VAL0-0.016-0.01816.6020.0660.0660.0000.0000.0000.000
119A119ILE0-0.003-0.00319.4840.0630.0630.0000.0000.0000.000
120A120PHE00.0140.00514.8510.0550.0550.0000.0000.0000.000
121A121ASP-1-0.758-0.87316.382-0.626-0.6260.0000.0000.0000.000
122A122GLN0-0.0050.00919.2260.0300.0300.0000.0000.0000.000
123A123GLU-1-0.749-0.85722.953-0.247-0.2470.0000.0000.0000.000
124A124LYS10.7780.91715.7840.5330.5330.0000.0000.0000.000
125A125LYS10.8390.93022.2200.2780.2780.0000.0000.0000.000
126A126SER0-0.065-0.04324.5250.0280.0280.0000.0000.0000.000
127A127ASP-1-0.883-0.92827.498-0.154-0.1540.0000.0000.0000.000
128A128TYR0-0.075-0.07626.745-0.018-0.0180.0000.0000.0000.000
129A129HIS0-0.074-0.04130.8500.0060.0060.0000.0000.0000.000
130A130TRP0-0.061-0.02625.950-0.002-0.0020.0000.0000.0000.000
131A131SER0-0.014-0.05530.817-0.002-0.0020.0000.0000.0000.000
132A132ASP-1-0.846-0.94826.995-0.250-0.2500.0000.0000.0000.000
133A133LEU0-0.058-0.02027.678-0.024-0.0240.0000.0000.0000.000
134A134GLU-1-0.811-0.87529.689-0.214-0.2140.0000.0000.0000.000
135A135LYS10.8590.93324.9740.2560.2560.0000.0000.0000.000
136A136SER00.0360.02324.962-0.028-0.0280.0000.0000.0000.000
137A137PHE0-0.069-0.03326.049-0.021-0.0210.0000.0000.0000.000
138A138ILE00.0130.00326.060-0.017-0.0170.0000.0000.0000.000
139A139CYS0-0.013-0.00221.757-0.013-0.0130.0000.0000.0000.000
140A140ARG10.9530.96723.8600.3280.3280.0000.0000.0000.000
141A141TYR0-0.056-0.01325.048-0.002-0.0020.0000.0000.0000.000
142A142ASN0-0.016-0.02825.0090.0060.0060.0000.0000.0000.000
143A143ALA00.0240.02821.477-0.016-0.0160.0000.0000.0000.000
144A144ALA00.015-0.00123.021-0.018-0.0180.0000.0000.0000.000
145A145ALA0-0.0120.00125.6650.0050.0050.0000.0000.0000.000
146A146ILE00.0180.00221.5680.0120.0120.0000.0000.0000.000
147A147CYS0-0.0400.03722.351-0.016-0.0160.0000.0000.0000.000
148A148ALA00.0030.00123.5240.0050.0050.0000.0000.0000.000
149A149ILE00.0310.01326.4280.0110.0110.0000.0000.0000.000
150A150THR0-0.013-0.02221.3570.0000.0000.0000.0000.0000.000
151A151ARG10.8650.92823.8810.4120.4120.0000.0000.0000.000
152A152GLU-1-0.908-0.94624.814-0.293-0.2930.0000.0000.0000.000
153A153SER0-0.050-0.03925.2950.0280.0280.0000.0000.0000.000
154A154ILE00.0200.00720.4050.0200.0200.0000.0000.0000.000
155A155ILE0-0.021-0.01124.4980.0260.0260.0000.0000.0000.000
156A156ARG10.7930.88827.3980.3150.3150.0000.0000.0000.000
157A157GLY00.0010.02826.7960.0230.0230.0000.0000.0000.000
158A158ASN0-0.130-0.07727.1350.0400.0400.0000.0000.0000.000
159A159SER0-0.036-0.03923.703-0.010-0.0100.0000.0000.0000.000
160A160LEU00.039-0.01520.5710.0280.0280.0000.0000.0000.000
161A161GLU-1-0.764-0.84320.885-0.434-0.4340.0000.0000.0000.000
162A162LYS10.8740.94022.5390.3430.3430.0000.0000.0000.000
163A163LEU0-0.0060.00324.8260.0290.0290.0000.0000.0000.000
164A164TYR0-0.032-0.02719.5710.0280.0280.0000.0000.0000.000
165A165SER00.0190.00423.628-0.006-0.0060.0000.0000.0000.000
166A166GLN0-0.015-0.01126.4760.0030.0030.0000.0000.0000.000
167A167ILE00.0440.02122.6460.0110.0110.0000.0000.0000.000
168A168VAL00.0320.02022.291-0.001-0.0010.0000.0000.0000.000
169A169ASN0-0.002-0.01124.8300.0100.0100.0000.0000.0000.000
170A170LEU0-0.022-0.00828.3130.0180.0180.0000.0000.0000.000
171A171LEU00.0160.02822.3690.0120.0120.0000.0000.0000.000
172A172LEU00.008-0.00225.1630.0180.0180.0000.0000.0000.000
173A173ALA0-0.043-0.02027.7600.0200.0200.0000.0000.0000.000
174A174GLN0-0.061-0.04528.7920.0180.0180.0000.0000.0000.000
175A175ILE00.0160.00724.4700.0090.0090.0000.0000.0000.000
176A176LYS10.8270.90628.7970.2130.2130.0000.0000.0000.000
177A177ILE0-0.031-0.01831.3860.0160.0160.0000.0000.0000.000
178A178PHE00.0130.01730.7070.0100.0100.0000.0000.0000.000
179A179GLU-1-0.788-0.82629.691-0.198-0.1980.0000.0000.0000.000