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: KRN63

Calculation Name: 2I88-A-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1908337.723773
FMO2-HF: Nuclear repulsion 1840508.136906
FMO2-HF: Total energy -67829.586867
FMO2-MP2: Total energy -68032.374194


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:344:ACE )


Summations of interaction energy for fragment #1(A:344:ACE )
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.
0.457-0.9797.582-3.8-2.3450.001
Interaction energy analysis for fragmet #1(A:344:ACE )
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 : -0.013
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].
3A346LYS 10.9180.9722.091-0.463-2.1277.582-3.785-2.1330.001
4A347ASP -1-0.777-0.8874.661-0.754-0.5260.000-0.015-0.2120.000
5A348ALA 0-0.0260.0095.4350.2860.2860.0000.0000.0000.000
6A349VAL 00.0070.0017.4650.3500.3500.0000.0000.0000.000
7A350ASP -1-0.841-0.9178.992-0.240-0.2400.0000.0000.0000.000
8A351ALA 0-0.044-0.0319.7430.1090.1090.0000.0000.0000.000
9A352THR 0-0.019-0.02311.3890.1080.1080.0000.0000.0000.000
10A353VAL 0-0.0010.00013.4200.0750.0750.0000.0000.0000.000
11A354SER 0-0.012-0.00314.0430.0660.0660.0000.0000.0000.000
12A355PHE 0-0.023-0.01015.7210.0400.0400.0000.0000.0000.000
13A356TYR 00.022-0.00216.6720.0340.0340.0000.0000.0000.000
14A357GLN 00.0570.02419.2970.0200.0200.0000.0000.0000.000
15A358THR 00.0240.01620.2890.0210.0210.0000.0000.0000.000
16A359LEU 0-0.066-0.02721.3740.0180.0180.0000.0000.0000.000
17A360THR 0-0.041-0.02923.6560.0100.0100.0000.0000.0000.000
18A361GLU -1-0.984-0.97224.111-0.098-0.0980.0000.0000.0000.000
19A362LYS 10.8600.93923.3710.1510.1510.0000.0000.0000.000
20A363TYR 0-0.035-0.02625.8390.0040.0040.0000.0000.0000.000
21A364GLY 00.0340.01929.3130.0020.0020.0000.0000.0000.000
22A365GLU -1-0.857-0.94227.456-0.115-0.1150.0000.0000.0000.000
23A366LYS 10.8950.93727.6410.0680.0680.0000.0000.0000.000
24A367TYR 0-0.015-0.02425.365-0.007-0.0070.0000.0000.0000.000
25A368SER 00.0490.02523.130-0.015-0.0150.0000.0000.0000.000
26A369LYS 11.0051.00123.5420.0980.0980.0000.0000.0000.000
27A370MET 0-0.0150.01825.030-0.004-0.0040.0000.0000.0000.000
28A371ALA 00.0210.00722.478-0.005-0.0050.0000.0000.0000.000
29A372GLN 00.0330.00920.430-0.004-0.0040.0000.0000.0000.000
30A373GLU -1-0.938-0.95621.487-0.130-0.1300.0000.0000.0000.000
31A374LEU 0-0.082-0.04723.6750.0000.0000.0000.0000.0000.000
32A375ALA 00.0400.02118.111-0.006-0.0060.0000.0000.0000.000
33A376ASP -1-0.956-0.97119.316-0.257-0.2570.0000.0000.0000.000
34A377LYS 10.8840.91920.4270.1300.1300.0000.0000.0000.000
35A378SER 0-0.023-0.02820.3880.0040.0040.0000.0000.0000.000
36A379LYS 10.9821.00215.0800.3730.3730.0000.0000.0000.000
37A380GLY 0-0.0150.00619.4070.0230.0230.0000.0000.0000.000
38A381LYS 10.8020.91521.1140.1590.1590.0000.0000.0000.000
39A382LYS 10.9600.97822.3490.1380.1380.0000.0000.0000.000
40A383ILE 0-0.012-0.01324.9220.0000.0000.0000.0000.0000.000
41A384GLY 00.0140.01527.3890.0060.0060.0000.0000.0000.000
42A385ASN 00.0260.01531.0080.0010.0010.0000.0000.0000.000
43A386VAL 00.0430.01131.284-0.001-0.0010.0000.0000.0000.000
44A387ASN 0-0.028-0.02533.387-0.001-0.0010.0000.0000.0000.000
45A388GLU -1-0.874-0.92035.737-0.071-0.0710.0000.0000.0000.000
46A389ALA 00.0340.02032.1160.0010.0010.0000.0000.0000.000
47A390LEU 0-0.011-0.00834.1460.0000.0000.0000.0000.0000.000
48A391ALA 0-0.0080.00535.9970.0020.0020.0000.0000.0000.000
49A392ALA 0-0.014-0.00535.6990.0020.0020.0000.0000.0000.000
50A393PHE 0-0.005-0.00533.3220.0010.0010.0000.0000.0000.000
51A394GLU -1-0.897-0.97736.033-0.065-0.0650.0000.0000.0000.000
52A395LYS 10.9621.00339.2400.0650.0650.0000.0000.0000.000
53A396TYR 0-0.028-0.03034.7480.0010.0010.0000.0000.0000.000
54A397LYS 10.9530.98737.6630.0660.0660.0000.0000.0000.000
55A398ASP -1-0.905-0.94938.969-0.055-0.0550.0000.0000.0000.000
56A399VAL 0-0.104-0.04941.0830.0030.0030.0000.0000.0000.000
57A400LEU 00.0300.02336.0620.0020.0020.0000.0000.0000.000
58A401ASN 00.013-0.01640.0750.0000.0000.0000.0000.0000.000
59A402LYS 10.8950.95242.1350.0520.0520.0000.0000.0000.000
60A403LYS 10.9020.96141.8030.0560.0560.0000.0000.0000.000
61A404PHE 00.0420.03138.255-0.001-0.0010.0000.0000.0000.000
62A405SER 0-0.0170.00142.9300.0010.0010.0000.0000.0000.000
63A406LYS 10.8880.91243.0440.0460.0460.0000.0000.0000.000
64A407ALA 00.0250.01842.701-0.002-0.0020.0000.0000.0000.000
65A408ASP -1-0.788-0.89340.717-0.055-0.0550.0000.0000.0000.000
66A409ARG 10.8530.93438.4310.0540.0540.0000.0000.0000.000
67A410ASP -1-0.823-0.91837.793-0.056-0.0560.0000.0000.0000.000
68A411ALA 0-0.0010.00638.345-0.001-0.0010.0000.0000.0000.000
69A412ILE 0-0.023-0.00832.759-0.003-0.0030.0000.0000.0000.000
70A413PHE 0-0.006-0.00933.681-0.003-0.0030.0000.0000.0000.000
71A414ASN 00.016-0.00934.499-0.001-0.0010.0000.0000.0000.000
72A415ALA 0-0.0020.00932.1810.0010.0010.0000.0000.0000.000
73A416LEU 0-0.004-0.01828.592-0.003-0.0030.0000.0000.0000.000
74A417ALA 0-0.0290.00230.363-0.003-0.0030.0000.0000.0000.000
75A418SER 0-0.056-0.02631.4300.0050.0050.0000.0000.0000.000
76A419VAL 0-0.0290.00725.151-0.001-0.0010.0000.0000.0000.000
77A420LYS 10.9340.98024.4610.0770.0770.0000.0000.0000.000
78A421TYR 00.003-0.02219.228-0.009-0.0090.0000.0000.0000.000
79A422ASP -1-0.883-0.94719.930-0.129-0.1290.0000.0000.0000.000
80A423ASP -1-0.917-0.96019.148-0.129-0.1290.0000.0000.0000.000
81A424TRP 0-0.046-0.03619.202-0.023-0.0230.0000.0000.0000.000
82A425ALA 00.0270.01617.605-0.040-0.0400.0000.0000.0000.000
83A426LYS 10.9360.97714.8200.1580.1580.0000.0000.0000.000
84A427HIS 0-0.023-0.02012.950-0.095-0.0950.0000.0000.0000.000
85A428LEU 00.0210.01612.774-0.087-0.0870.0000.0000.0000.000
86A429ASP -1-0.833-0.9237.088-1.223-1.2230.0000.0000.0000.000
87A430GLN 00.0130.0168.393-0.162-0.1620.0000.0000.0000.000
88A431PHE 00.0450.0219.446-0.120-0.1200.0000.0000.0000.000
89A432ALA 00.0240.01510.6870.0260.0260.0000.0000.0000.000
90A433LYS 10.8280.9084.8111.4531.4530.0000.0000.0000.000
91A434TYR 0-0.0070.0008.7420.0940.0940.0000.0000.0000.000
92A435LEU 0-0.061-0.02710.7290.1230.1230.0000.0000.0000.000
93A436LYS 10.8670.94110.9050.4870.4870.0000.0000.0000.000
94A437ILE 00.0000.00512.3780.0940.0940.0000.0000.0000.000
95A438THR 0-0.060-0.03612.592-0.046-0.0460.0000.0000.0000.000
96A439GLY 00.0090.01814.4070.0230.0230.0000.0000.0000.000
97A440HIS 00.0150.01415.698-0.036-0.0360.0000.0000.0000.000
98A441VAL 00.0290.00413.416-0.011-0.0110.0000.0000.0000.000
99A442SER 0-0.050-0.01616.7970.0220.0220.0000.0000.0000.000
100A443PHE 00.018-0.01711.9460.0020.0020.0000.0000.0000.000
101A444GLY 00.0070.01517.513-0.001-0.0010.0000.0000.0000.000
102A445TYR 0-0.107-0.07720.6160.0140.0140.0000.0000.0000.000
103A446ASP -1-0.793-0.91822.242-0.133-0.1330.0000.0000.0000.000
104A447VAL 00.0210.00623.5510.0110.0110.0000.0000.0000.000
105A448VAL 00.0260.01025.3710.0090.0090.0000.0000.0000.000
106A449SER 00.0000.01027.8820.0100.0100.0000.0000.0000.000
107A450ASP -1-0.830-0.90729.299-0.089-0.0890.0000.0000.0000.000
108A451ILE 0-0.028-0.02128.1850.0050.0050.0000.0000.0000.000
109A452LEU 0-0.0070.00331.5540.0060.0060.0000.0000.0000.000
110A453LYS 10.9220.96833.0570.0790.0790.0000.0000.0000.000
111A454ILE 0-0.039-0.01033.4400.0040.0040.0000.0000.0000.000
112A455LYS 10.8770.96037.0690.0580.0580.0000.0000.0000.000
113A456ASP -1-0.940-0.97038.828-0.049-0.0490.0000.0000.0000.000
114A457THR 0-0.026-0.00939.3800.0010.0010.0000.0000.0000.000
115A458GLY 0-0.020-0.00240.1760.0020.0020.0000.0000.0000.000
116A459ASP -1-0.920-0.98039.581-0.063-0.0630.0000.0000.0000.000
117A460TRP 00.0560.00532.054-0.005-0.0050.0000.0000.0000.000
118A461LYS 10.9801.00434.7400.0540.0540.0000.0000.0000.000
119A462PRO 0-0.016-0.01134.843-0.004-0.0040.0000.0000.0000.000
120A463LEU 00.0640.03428.770-0.003-0.0030.0000.0000.0000.000
121A464PHE 00.0470.02930.139-0.008-0.0080.0000.0000.0000.000
122A465LEU 0-0.039-0.01830.524-0.004-0.0040.0000.0000.0000.000
123A466THR 0-0.072-0.03828.830-0.005-0.0050.0000.0000.0000.000
124A467LEU 00.0490.01624.817-0.008-0.0080.0000.0000.0000.000
125A468GLU -1-0.940-0.97625.778-0.105-0.1050.0000.0000.0000.000
126A469LYS 10.8990.93526.5870.0800.0800.0000.0000.0000.000
127A470LYS 10.9160.96723.2610.1120.1120.0000.0000.0000.000
128A471ALA 00.0080.02721.838-0.013-0.0130.0000.0000.0000.000
129A472ALA 00.0150.02121.816-0.010-0.0100.0000.0000.0000.000
130A473ASP -1-0.900-0.96520.571-0.158-0.1580.0000.0000.0000.000
131A474ALA 00.0300.00518.142-0.006-0.0060.0000.0000.0000.000
132A475GLY 0-0.093-0.02919.850-0.015-0.0150.0000.0000.0000.000
133A476VAL 00.033-0.00922.199-0.004-0.0040.0000.0000.0000.000
134A477SER 00.0490.01817.2600.0040.0040.0000.0000.0000.000
135A478TYR 00.0110.01217.942-0.026-0.0260.0000.0000.0000.000
136A479VAL 00.0140.00318.995-0.007-0.0070.0000.0000.0000.000
137A480VAL 00.0000.00518.3380.0050.0050.0000.0000.0000.000
138A481ALA 00.0350.01815.318-0.009-0.0090.0000.0000.0000.000
139A482LEU 0-0.0150.02316.982-0.002-0.0020.0000.0000.0000.000
140A483LEU 00.021-0.00819.4880.0060.0060.0000.0000.0000.000
141A484PHE 0-0.0010.00017.5210.0210.0210.0000.0000.0000.000
142A485SER 00.006-0.02216.469-0.019-0.0190.0000.0000.0000.000
143A486LEU 0-0.025-0.00118.1690.0180.0180.0000.0000.0000.000
144A487LEU 0-0.032-0.02321.6110.0150.0150.0000.0000.0000.000
145A488ALA 0-0.037-0.01517.7210.0120.0120.0000.0000.0000.000
146A489GLY 0-0.045-0.00919.7690.0090.0090.0000.0000.0000.000
147A490THR 0-0.060-0.01721.4180.0220.0220.0000.0000.0000.000
148A491THR 00.0310.00224.944-0.010-0.0100.0000.0000.0000.000
149A492LEU 0-0.0230.00527.5930.0100.0100.0000.0000.0000.000
150A493GLY 00.0670.02530.1860.0010.0010.0000.0000.0000.000
151A494ILE 00.0750.01932.702-0.005-0.0050.0000.0000.0000.000
152A495TRP 00.0190.01333.501-0.005-0.0050.0000.0000.0000.000
153A496GLY 00.0530.01331.854-0.002-0.0020.0000.0000.0000.000
154A497ILE 00.0100.03027.492-0.007-0.0070.0000.0000.0000.000
155A498ALA 00.0150.02029.813-0.007-0.0070.0000.0000.0000.000
156A499ILE 0-0.023-0.00631.638-0.002-0.0020.0000.0000.0000.000
157A500VAL 00.0360.01325.547-0.002-0.0020.0000.0000.0000.000
158A501THR 0-0.024-0.03727.631-0.011-0.0110.0000.0000.0000.000
159A502GLY 00.0110.00728.673-0.002-0.0020.0000.0000.0000.000
160A503ILE 0-0.013-0.00527.8790.0010.0010.0000.0000.0000.000
161A504LEU 00.0250.01823.331-0.003-0.0030.0000.0000.0000.000
162A505CYS 0-0.072-0.04227.0370.0010.0010.0000.0000.0000.000
163A506SER 0-0.071-0.02329.6820.0040.0040.0000.0000.0000.000
164A507TYR 00.0450.02227.0790.0040.0040.0000.0000.0000.000
165A508ILE 0-0.073-0.03323.337-0.001-0.0010.0000.0000.0000.000
166A509ASP -1-0.784-0.89527.494-0.109-0.1090.0000.0000.0000.000
167A510LYS 10.8320.93827.1800.1350.1350.0000.0000.0000.000
168A511ASN 00.0920.04231.076-0.008-0.0080.0000.0000.0000.000
169A512LYS 10.9100.96029.0880.1140.1140.0000.0000.0000.000
170A513LEU 00.0390.00433.185-0.001-0.0010.0000.0000.0000.000
171A514ASN 0-0.050-0.04134.897-0.002-0.0020.0000.0000.0000.000
172A515THR 00.0320.01833.6550.0020.0020.0000.0000.0000.000
173A516ILE 0-0.0050.01132.039-0.001-0.0010.0000.0000.0000.000
174A517ASN 00.020-0.00433.913-0.003-0.0030.0000.0000.0000.000
175A518GLU -1-0.903-0.93036.455-0.067-0.0670.0000.0000.0000.000
176A519VAL 0-0.092-0.04430.3540.0010.0010.0000.0000.0000.000
177A520LEU 0-0.054-0.04430.928-0.002-0.0020.0000.0000.0000.000
178A521GLY 0-0.0520.00134.3470.0020.0020.0000.0000.0000.000
179A522ILE -1-0.929-0.96736.352-0.060-0.0600.0000.0000.0000.000