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: 9G732

Calculation Name: 2I88-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2I88

Chain ID: A

ChEMBL ID:

UniProt ID: P02978

Base Structure: X-ray

Registration Date: 2023-03-13

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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1902777.481767
FMO2-HF: Nuclear repulsion 1835099.098244
FMO2-HF: Total energy -67678.383523
FMO2-MP2: Total energy -67880.750893


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:345:ILE)


Summations of interaction energy for fragment #1(A:345: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.
-4.3480.9912.827-2.166-5.999-0.006
Interaction energy analysis for fragmet #1(A:345:ILE)
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 : 0.000
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].
3A347ASP-1-0.784-0.8933.441-4.733-2.6140.025-0.772-1.371-0.001
4A348ALA0-0.0430.0002.506-0.6030.4411.204-0.719-1.529-0.003
5A349VAL00.0090.0022.6660.5541.3060.384-0.241-0.895-0.001
6A350ASP-1-0.839-0.9154.991-0.397-0.330-0.001-0.007-0.0590.000
7A351ALA0-0.042-0.0317.0990.3610.3610.0000.0000.0000.000
8A352THR0-0.021-0.0246.9420.3460.3460.0000.0000.0000.000
9A353VAL00.0000.0019.2170.2270.2270.0000.0000.0000.000
10A354SER0-0.012-0.00311.2510.1940.1940.0000.0000.0000.000
11A355PHE0-0.024-0.01112.3500.1130.1130.0000.0000.0000.000
12A356TYR00.026-0.00210.9810.1020.1020.0000.0000.0000.000
13A357GLN00.0550.02415.2790.0530.0530.0000.0000.0000.000
14A358THR00.0260.01717.0840.0560.0560.0000.0000.0000.000
15A359LEU0-0.066-0.02716.8990.0480.0480.0000.0000.0000.000
16A360THR0-0.042-0.03019.6090.0250.0250.0000.0000.0000.000
17A361GLU-1-0.979-0.97021.415-0.233-0.2330.0000.0000.0000.000
18A362LYS10.8580.93820.7980.3450.3450.0000.0000.0000.000
19A363TYR0-0.038-0.02822.0450.0120.0120.0000.0000.0000.000
20A364GLY00.0270.01625.0400.0040.0040.0000.0000.0000.000
21A365GLU-1-0.849-0.93822.797-0.268-0.2680.0000.0000.0000.000
22A366LYS10.8950.93722.3670.1480.1480.0000.0000.0000.000
23A367TYR0-0.020-0.02820.661-0.014-0.0140.0000.0000.0000.000
24A368SER00.0500.02518.312-0.032-0.0320.0000.0000.0000.000
25A369LYS11.0091.00418.0020.2200.2200.0000.0000.0000.000
26A370MET0-0.0230.01519.024-0.007-0.0070.0000.0000.0000.000
27A371ALA00.0230.00717.185-0.008-0.0080.0000.0000.0000.000
28A372GLN00.0360.01214.525-0.001-0.0010.0000.0000.0000.000
29A373GLU-1-0.935-0.95515.288-0.286-0.2860.0000.0000.0000.000
30A374LEU0-0.088-0.05017.4470.0070.0070.0000.0000.0000.000
31A375ALA00.0430.02312.248-0.003-0.0030.0000.0000.0000.000
32A376ASP-1-0.955-0.97012.925-0.610-0.6100.0000.0000.0000.000
33A377LYS10.8840.91814.1320.2750.2750.0000.0000.0000.000
34A378SER0-0.017-0.02514.6500.0200.0200.0000.0000.0000.000
35A379LYS10.9791.0018.5510.9460.9460.0000.0000.0000.000
36A380GLY0-0.0130.00713.5830.0490.0490.0000.0000.0000.000
37A381LYS10.8020.91615.5510.3150.3150.0000.0000.0000.000
38A382LYS10.9570.97718.0110.2190.2190.0000.0000.0000.000
39A383ILE0-0.011-0.01420.580-0.004-0.0040.0000.0000.0000.000
40A384GLY00.0170.01623.0420.0120.0120.0000.0000.0000.000
41A385ASN00.0290.01726.4790.0030.0030.0000.0000.0000.000
42A386VAL00.0400.00927.317-0.005-0.0050.0000.0000.0000.000
43A387ASN0-0.027-0.02529.250-0.004-0.0040.0000.0000.0000.000
44A388GLU-1-0.871-0.91930.907-0.133-0.1330.0000.0000.0000.000
45A389ALA00.0330.01927.4760.0000.0000.0000.0000.0000.000
46A390LEU0-0.005-0.00629.409-0.001-0.0010.0000.0000.0000.000
47A391ALA0-0.0110.00431.6660.0020.0020.0000.0000.0000.000
48A392ALA0-0.015-0.00530.5310.0040.0040.0000.0000.0000.000
49A393PHE0-0.004-0.00428.7760.0000.0000.0000.0000.0000.000
50A394GLU-1-0.893-0.97531.239-0.129-0.1290.0000.0000.0000.000
51A395LYS10.9611.00334.7120.1290.1290.0000.0000.0000.000
52A396TYR0-0.029-0.03129.8880.0020.0020.0000.0000.0000.000
53A397LYS10.9570.98833.2870.1330.1330.0000.0000.0000.000
54A398ASP-1-0.903-0.94734.347-0.111-0.1110.0000.0000.0000.000
55A399VAL0-0.104-0.04935.9420.0060.0060.0000.0000.0000.000
56A400LEU00.0160.01531.3970.0050.0050.0000.0000.0000.000
57A401ASN00.023-0.01235.410-0.002-0.0020.0000.0000.0000.000
58A402LYS10.9050.95837.7620.1060.1060.0000.0000.0000.000
59A403LYS10.8850.94837.1500.1170.1170.0000.0000.0000.000
60A404PHE00.0420.03233.850-0.003-0.0030.0000.0000.0000.000
61A405SER0-0.0120.00538.7840.0030.0030.0000.0000.0000.000
62A406LYS10.8940.91639.4930.0950.0950.0000.0000.0000.000
63A407ALA00.0300.02139.627-0.004-0.0040.0000.0000.0000.000
64A408ASP-1-0.792-0.89637.116-0.118-0.1180.0000.0000.0000.000
65A409ARG10.8540.93435.1120.1120.1120.0000.0000.0000.000
66A410ASP-1-0.821-0.91634.893-0.117-0.1170.0000.0000.0000.000
67A411ALA0-0.0010.00635.710-0.003-0.0030.0000.0000.0000.000
68A412ILE0-0.029-0.01129.866-0.007-0.0070.0000.0000.0000.000
69A413PHE0-0.001-0.00631.323-0.007-0.0070.0000.0000.0000.000
70A414ASN00.015-0.00932.522-0.001-0.0010.0000.0000.0000.000
71A415ALA0-0.0010.00929.9550.0010.0010.0000.0000.0000.000
72A416LEU0-0.006-0.01926.357-0.006-0.0060.0000.0000.0000.000
73A417ALA0-0.0260.00328.748-0.005-0.0050.0000.0000.0000.000
74A418SER0-0.053-0.02530.0920.0100.0100.0000.0000.0000.000
75A419VAL0-0.0310.00623.679-0.004-0.0040.0000.0000.0000.000
76A420LYS10.9360.98224.0140.1700.1700.0000.0000.0000.000
77A421TYR00.004-0.02118.335-0.018-0.0180.0000.0000.0000.000
78A422ASP-1-0.880-0.94619.809-0.254-0.2540.0000.0000.0000.000
79A423ASP-1-0.916-0.96018.701-0.270-0.2700.0000.0000.0000.000
80A424TRP0-0.049-0.03717.579-0.046-0.0460.0000.0000.0000.000
81A425ALA00.0260.01616.017-0.076-0.0760.0000.0000.0000.000
82A426LYS10.9410.97814.0720.3630.3630.0000.0000.0000.000
83A427HIS0-0.022-0.01911.391-0.159-0.1590.0000.0000.0000.000
84A428LEU00.0230.01710.645-0.166-0.1660.0000.0000.0000.000
85A429ASP-1-0.835-0.9226.997-1.338-1.3380.0000.0000.0000.000
86A430GLN00.0110.0145.902-0.258-0.2580.0000.0000.0000.000
87A431PHE00.0430.0206.242-0.469-0.4690.0000.0000.0000.000
88A432ALA00.0340.0197.796-0.014-0.0140.0000.0000.0000.000
89A433LYS10.8180.9022.353-0.1390.9041.216-0.396-1.864-0.001
90A434TYR0-0.0090.0004.187-0.313-0.0270.000-0.031-0.2550.000
91A435LEU0-0.058-0.0255.0560.2680.296-0.0010.000-0.0260.000
92A436LYS10.8690.9425.5640.9150.9150.0000.0000.0000.000
93A437ILE0-0.0020.0047.2060.2140.2140.0000.0000.0000.000
94A438THR0-0.057-0.0358.627-0.045-0.0450.0000.0000.0000.000
95A439GLY00.0100.01810.4640.0540.0540.0000.0000.0000.000
96A440HIS00.0200.01612.544-0.039-0.0390.0000.0000.0000.000
97A441VAL00.0250.00311.268-0.032-0.0320.0000.0000.0000.000
98A442SER0-0.050-0.01614.5400.0400.0400.0000.0000.0000.000
99A443PHE00.020-0.01610.803-0.012-0.0120.0000.0000.0000.000
100A444GLY00.0070.01516.279-0.011-0.0110.0000.0000.0000.000
101A445TYR0-0.109-0.07719.4340.0210.0210.0000.0000.0000.000
102A446ASP-1-0.794-0.91820.577-0.258-0.2580.0000.0000.0000.000
103A447VAL00.0220.00621.2060.0190.0190.0000.0000.0000.000
104A448VAL00.0240.00923.5700.0150.0150.0000.0000.0000.000
105A449SER00.0000.01025.9760.0180.0180.0000.0000.0000.000
106A450ASP-1-0.827-0.90626.977-0.167-0.1670.0000.0000.0000.000
107A451ILE0-0.034-0.02425.3600.0100.0100.0000.0000.0000.000
108A452LEU0-0.0060.00329.3730.0110.0110.0000.0000.0000.000
109A453LYS10.9280.97131.1480.1510.1510.0000.0000.0000.000
110A454ILE0-0.038-0.01030.5100.0070.0070.0000.0000.0000.000
111A455LYS10.8760.95834.4830.1210.1210.0000.0000.0000.000
112A456ASP-1-0.940-0.97036.406-0.100-0.1000.0000.0000.0000.000
113A457THR0-0.023-0.00736.6450.0030.0030.0000.0000.0000.000
114A458GLY0-0.023-0.00437.2430.0040.0040.0000.0000.0000.000
115A459ASP-1-0.919-0.98036.436-0.121-0.1210.0000.0000.0000.000
116A460TRP00.0530.00428.652-0.010-0.0100.0000.0000.0000.000
117A461LYS10.9821.00531.3450.1010.1010.0000.0000.0000.000
118A462PRO0-0.013-0.01031.483-0.007-0.0070.0000.0000.0000.000
119A463LEU00.0600.03225.848-0.005-0.0050.0000.0000.0000.000
120A464PHE00.0440.02726.925-0.014-0.0140.0000.0000.0000.000
121A465LEU0-0.034-0.01626.982-0.005-0.0050.0000.0000.0000.000
122A466THR0-0.074-0.03826.173-0.007-0.0070.0000.0000.0000.000
123A467LEU00.0490.01621.441-0.012-0.0120.0000.0000.0000.000
124A468GLU-1-0.939-0.97722.379-0.185-0.1850.0000.0000.0000.000
125A469LYS10.9020.93623.2100.1460.1460.0000.0000.0000.000
126A470LYS10.9200.97020.7140.1980.1980.0000.0000.0000.000
127A471ALA00.0060.02618.551-0.018-0.0180.0000.0000.0000.000
128A472ALA00.0160.02118.527-0.011-0.0110.0000.0000.0000.000
129A473ASP-1-0.901-0.96517.153-0.234-0.2340.0000.0000.0000.000
130A474ALA00.0310.00614.738-0.008-0.0080.0000.0000.0000.000
131A475GLY0-0.096-0.03015.724-0.035-0.0350.0000.0000.0000.000
132A476VAL00.034-0.00818.128-0.009-0.0090.0000.0000.0000.000
133A477SER00.0490.01812.7410.0010.0010.0000.0000.0000.000
134A478TYR00.0130.01313.799-0.059-0.0590.0000.0000.0000.000
135A479VAL00.0140.00415.208-0.017-0.0170.0000.0000.0000.000
136A480VAL0-0.0060.00213.4500.0080.0080.0000.0000.0000.000
137A481ALA00.0380.01911.856-0.027-0.0270.0000.0000.0000.000
138A482LEU0-0.0150.02213.378-0.008-0.0080.0000.0000.0000.000
139A483LEU00.024-0.00716.4990.0060.0060.0000.0000.0000.000
140A484PHE0-0.009-0.00212.7400.0430.0430.0000.0000.0000.000
141A485SER00.013-0.02014.056-0.041-0.0410.0000.0000.0000.000
142A486LEU0-0.026-0.00115.5940.0320.0320.0000.0000.0000.000
143A487LEU0-0.035-0.02617.9080.0270.0270.0000.0000.0000.000
144A488ALA0-0.038-0.01615.1320.0220.0220.0000.0000.0000.000
145A489GLY0-0.037-0.00617.0420.0160.0160.0000.0000.0000.000
146A490THR0-0.061-0.01619.2930.0460.0460.0000.0000.0000.000
147A491THR00.0320.00222.369-0.026-0.0260.0000.0000.0000.000
148A492LEU0-0.0200.00824.4450.0220.0220.0000.0000.0000.000
149A493GLY00.0690.02727.2060.0010.0010.0000.0000.0000.000
150A494ILE00.0670.01328.699-0.008-0.0080.0000.0000.0000.000
151A495TRP00.0130.00829.250-0.010-0.0100.0000.0000.0000.000
152A496GLY00.0630.01828.350-0.002-0.0020.0000.0000.0000.000
153A497ILE00.0170.03423.478-0.012-0.0120.0000.0000.0000.000
154A498ALA00.0010.01225.302-0.014-0.0140.0000.0000.0000.000
155A499ILE0-0.026-0.00827.547-0.002-0.0020.0000.0000.0000.000
156A500VAL00.0390.01621.604-0.002-0.0020.0000.0000.0000.000
157A501THR0-0.017-0.03522.704-0.024-0.0240.0000.0000.0000.000
158A502GLY0-0.0010.00223.778-0.003-0.0030.0000.0000.0000.000
159A503ILE0-0.007-0.00223.6710.0050.0050.0000.0000.0000.000
160A504LEU00.0310.02218.673-0.002-0.0020.0000.0000.0000.000
161A505CYS0-0.076-0.04422.0050.0020.0020.0000.0000.0000.000
162A506SER0-0.075-0.02624.2200.0100.0100.0000.0000.0000.000
163A507TYR00.0550.02722.3330.0110.0110.0000.0000.0000.000
164A508ILE0-0.072-0.03217.9980.0020.0020.0000.0000.0000.000
165A509ASP-1-0.782-0.89421.973-0.213-0.2130.0000.0000.0000.000
166A510LYS10.8320.94020.8540.2850.2850.0000.0000.0000.000
167A511ASN00.0900.04225.161-0.020-0.0200.0000.0000.0000.000
168A512LYS10.9150.96223.0400.2450.2450.0000.0000.0000.000
169A513LEU00.0350.00327.625-0.003-0.0030.0000.0000.0000.000
170A514ASN0-0.043-0.03929.267-0.005-0.0050.0000.0000.0000.000
171A515THR00.0340.01927.7720.0040.0040.0000.0000.0000.000
172A516ILE00.0080.02026.555-0.003-0.0030.0000.0000.0000.000
173A517ASN00.018-0.01028.433-0.007-0.0070.0000.0000.0000.000
174A518GLU-1-0.916-0.93930.733-0.142-0.1420.0000.0000.0000.000
175A519VAL0-0.071-0.03124.8440.0020.0020.0000.0000.0000.000
176A520LEU0-0.035-0.03226.142-0.004-0.0040.0000.0000.0000.000
177A521GLY0-0.0210.02129.3110.0040.0040.0000.0000.0000.000
178A522ILE0-0.047-0.02431.5410.0080.0080.0000.0000.0000.000