FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: G6691

Calculation Name: 5KOU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5KOU

Chain ID: A

ChEMBL ID:

UniProt ID: Q82446

Base Structure: X-ray

Registration Date: 2023-06-21

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2708274.999786
FMO2-HF: Nuclear repulsion 2620938.419669
FMO2-HF: Total energy -87336.580117
FMO2-MP2: Total energy -87589.913879


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:429:GLY)


Summations of interaction energy for fragment #1(A:429: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.
-1.0423.1162.487-2.917-3.729-0.016
Interaction energy analysis for fragmet #1(A:429:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.067 / q_NPA : 0.035
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].
3A431LEU00.0090.0013.8520.4791.904-0.008-0.683-0.7340.003
4A432ARG10.7960.8886.3630.9740.9740.0000.0000.0000.000
5A433VAL0-0.017-0.00910.0740.0200.0200.0000.0000.0000.000
6A434LEU0-0.0140.00711.9430.0350.0350.0000.0000.0000.000
7A435LEU0-0.020-0.01414.4200.0290.0290.0000.0000.0000.000
8A436THR00.0460.02917.8340.0390.0390.0000.0000.0000.000
9A437VAL00.0280.00921.4040.0000.0000.0000.0000.0000.000
10A438GLY00.0420.00823.6220.0220.0220.0000.0000.0000.000
11A439SER0-0.024-0.01225.6320.0000.0000.0000.0000.0000.000
12A440ILE00.0340.01527.979-0.009-0.0090.0000.0000.0000.000
13A441MET0-0.0530.00424.9000.0030.0030.0000.0000.0000.000
14A442SER00.0750.04029.3250.0020.0020.0000.0000.0000.000
15A443PRO0-0.023-0.01231.204-0.007-0.0070.0000.0000.0000.000
16A444ASN0-0.023-0.00228.3200.0150.0150.0000.0000.0000.000
17A445SER0-0.018-0.05032.0710.0020.0020.0000.0000.0000.000
18A446ALA00.029-0.00233.003-0.001-0.0010.0000.0000.0000.000
19A447ASP-1-0.813-0.85633.921-0.133-0.1330.0000.0000.0000.000
20A448ARG10.8040.90435.2270.1410.1410.0000.0000.0000.000
21A449GLN00.0290.01333.601-0.008-0.0080.0000.0000.0000.000
22A450VAL0-0.051-0.02027.1010.0020.0020.0000.0000.0000.000
23A451TRP0-0.008-0.01930.5790.0040.0040.0000.0000.0000.000
24A452LEU0-0.021-0.01425.035-0.018-0.0180.0000.0000.0000.000
25A453ASN0-0.057-0.04926.1530.0320.0320.0000.0000.0000.000
26A454LYS10.8120.89927.5460.1290.1290.0000.0000.0000.000
27A455THR00.0160.00529.013-0.004-0.0040.0000.0000.0000.000
28A456LEU0-0.032-0.01625.472-0.009-0.0090.0000.0000.0000.000
29A457THR00.0290.00928.3520.0070.0070.0000.0000.0000.000
30A458ALA0-0.025-0.01030.340-0.009-0.0090.0000.0000.0000.000
31A459PRO00.0160.02132.3990.0080.0080.0000.0000.0000.000
32A460GLY00.0300.01134.570-0.004-0.0040.0000.0000.0000.000
33A461THR0-0.009-0.01336.9850.0010.0010.0000.0000.0000.000
34A462ASN00.0520.02533.9340.0000.0000.0000.0000.0000.000
35A463SER00.0670.04231.595-0.006-0.0060.0000.0000.0000.000
36A464ASN0-0.052-0.03228.308-0.017-0.0170.0000.0000.0000.000
37A465ASP-1-0.905-0.94628.943-0.094-0.0940.0000.0000.0000.000
38A466ASN00.0180.00029.735-0.009-0.0090.0000.0000.0000.000
39A467LEU0-0.041-0.01326.221-0.013-0.0130.0000.0000.0000.000
40A468VAL00.0140.01121.5280.0040.0040.0000.0000.0000.000
41A469LYS10.8840.95521.2280.1110.1110.0000.0000.0000.000
42A470ILE0-0.0190.00114.8280.0080.0080.0000.0000.0000.000
43A471ALA0-0.007-0.02416.677-0.004-0.0040.0000.0000.0000.000
44A472HIS00.0570.02012.055-0.049-0.0490.0000.0000.0000.000
45A473ASP-1-0.882-0.95015.1210.0690.0690.0000.0000.0000.000
46A474LEU0-0.033-0.00715.4420.0150.0150.0000.0000.0000.000
47A475GLY0-0.009-0.00118.3200.0040.0040.0000.0000.0000.000
48A476HIS0-0.027-0.00516.544-0.034-0.0340.0000.0000.0000.000
49A477TYR00.006-0.00717.467-0.018-0.0180.0000.0000.0000.000
50A478LEU0-0.0120.00916.5490.0130.0130.0000.0000.0000.000
51A479ILE0-0.017-0.00819.5490.0100.0100.0000.0000.0000.000
52A480MET00.0030.02721.213-0.017-0.0170.0000.0000.0000.000
53A481GLN00.0230.03222.1430.0120.0120.0000.0000.0000.000
54A482GLY00.0660.02922.6370.0240.0240.0000.0000.0000.000
55A483PHE0-0.015-0.03921.897-0.026-0.0260.0000.0000.0000.000
56A484MET00.0210.01221.5890.0120.0120.0000.0000.0000.000
57A485HIS10.8010.89121.4410.2120.2120.0000.0000.0000.000
58A486ILE0-0.054-0.01818.1470.0040.0040.0000.0000.0000.000
59A487LYS10.8460.92021.3010.2450.2450.0000.0000.0000.000
60A488THR0-0.031-0.02919.7070.0270.0270.0000.0000.0000.000
61A489VAL0-0.0060.00613.708-0.024-0.0240.0000.0000.0000.000
62A490GLU-1-0.835-0.88214.947-0.339-0.3390.0000.0000.0000.000
63A491TRP0-0.019-0.0298.752-0.239-0.2390.0000.0000.0000.000
64A492TYR0-0.043-0.03910.4220.1600.1600.0000.0000.0000.000
65A493THR0-0.004-0.0318.219-0.349-0.3490.0000.0000.0000.000
66A494PRO00.0170.0047.0840.0840.0840.0000.0000.0000.000
67A495ASP-1-0.849-0.88410.014-0.226-0.2260.0000.0000.0000.000
68A496PHE0-0.019-0.02012.4330.0540.0540.0000.0000.0000.000
69A497GLN00.0040.00812.2750.0690.0690.0000.0000.0000.000
70A498PRO00.008-0.00412.429-0.108-0.1080.0000.0000.0000.000
71A499SER0-0.030-0.0128.3770.0740.0740.0000.0000.0000.000
72A500ARG10.9130.9549.432-0.226-0.2260.0000.0000.0000.000
73A501ASP-1-0.814-0.9089.368-0.585-0.5850.0000.0000.0000.000
74A502PRO0-0.0420.0056.2110.1870.1870.0000.0000.0000.000
75A503THR00.003-0.0118.1000.1320.1320.0000.0000.0000.000
76A504PRO0-0.041-0.0218.944-0.202-0.2020.0000.0000.0000.000
77A505ILE0-0.0090.0016.1720.1490.1490.0000.0000.0000.000
78A506ALA00.0220.0027.9630.0690.0690.0000.0000.0000.000
79A507GLY00.0410.0269.895-0.050-0.0500.0000.0000.0000.000
80A508MET0-0.053-0.0049.819-0.019-0.0190.0000.0000.0000.000
81A509SER0-0.044-0.03312.6120.0500.0500.0000.0000.0000.000
82A510VAL00.0220.01215.726-0.038-0.0380.0000.0000.0000.000
83A511MET0-0.0190.00618.3860.0300.0300.0000.0000.0000.000
84A512VAL00.0260.00821.613-0.013-0.0130.0000.0000.0000.000
85A513ASN0-0.019-0.02425.2900.0160.0160.0000.0000.0000.000
86A514ILE0-0.0050.00425.8680.0000.0000.0000.0000.0000.000
87A515THR0-0.021-0.00724.8140.0130.0130.0000.0000.0000.000
88A516LYS10.8770.91915.1660.1490.1490.0000.0000.0000.000
89A517LYS10.8250.92521.3880.1400.1400.0000.0000.0000.000
90A518ALA00.0010.00218.3380.0010.0010.0000.0000.0000.000
91A519ASP-1-0.769-0.88014.038-0.188-0.1880.0000.0000.0000.000
92A520VAL0-0.025-0.02410.577-0.017-0.0170.0000.0000.0000.000
93A521TYR00.0230.0059.5420.0670.0670.0000.0000.0000.000
94A522PHE00.0160.0217.594-0.283-0.2830.0000.0000.0000.000
95A523MET0-0.041-0.0057.3280.5050.5050.0000.0000.0000.000
96A524LYS10.8450.9228.0421.4241.4240.0000.0000.0000.000
97A525GLN00.013-0.01110.5680.1920.1920.0000.0000.0000.000
98A526PHE0-0.0220.00113.414-0.031-0.0310.0000.0000.0000.000
99A527LYS10.8240.90714.3300.4590.4590.0000.0000.0000.000
100A528ASN0-0.0020.00517.6730.0120.0120.0000.0000.0000.000
101A529SER00.015-0.00421.0900.0200.0200.0000.0000.0000.000
102A530TYR00.0170.01224.054-0.003-0.0030.0000.0000.0000.000
103A531THR00.0470.01527.8520.0040.0040.0000.0000.0000.000
104A532ASN00.010-0.00131.1590.0010.0010.0000.0000.0000.000
105A533ASN00.0250.01728.308-0.003-0.0030.0000.0000.0000.000
106A534ARG10.9450.98127.4690.1490.1490.0000.0000.0000.000
107A535HIS10.8380.89422.1910.1890.1890.0000.0000.0000.000
108A536GLN0-0.005-0.00822.3230.0410.0410.0000.0000.0000.000
109A537ILE0-0.011-0.00317.165-0.020-0.0200.0000.0000.0000.000
110A538THR0-0.010-0.02318.2340.0250.0250.0000.0000.0000.000
111A539SER0-0.0010.00415.040-0.080-0.0800.0000.0000.0000.000
112A540ILE0-0.039-0.01512.9650.0800.0800.0000.0000.0000.000
113A541PHE00.032-0.00212.086-0.129-0.1290.0000.0000.0000.000
114A542LEU00.0220.03112.1970.1030.1030.0000.0000.0000.000
115A543ILE0-0.022-0.02512.903-0.039-0.0390.0000.0000.0000.000
116A544LYS10.9100.96615.1570.3690.3690.0000.0000.0000.000
117A545PRO0-0.032-0.01418.0020.0180.0180.0000.0000.0000.000
118A546LEU00.0010.00718.4460.0080.0080.0000.0000.0000.000
119A547ALA00.017-0.00322.0710.0200.0200.0000.0000.0000.000
120A548ASP-1-0.819-0.89425.409-0.143-0.1430.0000.0000.0000.000
121A549PHE0-0.056-0.03722.8240.0140.0140.0000.0000.0000.000
122A550LYS10.9510.97628.4110.0890.0890.0000.0000.0000.000
123A551VAL00.0200.01927.4140.0040.0040.0000.0000.0000.000
124A552GLN0-0.027-0.01130.2490.0000.0000.0000.0000.0000.000
125A553CYS0-0.012-0.01129.045-0.002-0.0020.0000.0000.0000.000
126A554TYR00.0500.01331.6440.0060.0060.0000.0000.0000.000
127A555MET0-0.0290.00728.912-0.009-0.0090.0000.0000.0000.000
128A556SER00.010-0.02831.7410.0140.0140.0000.0000.0000.000
129A557TYR00.0300.02731.467-0.008-0.0080.0000.0000.0000.000
130A558PHE00.0340.01526.3680.0090.0090.0000.0000.0000.000
131A559LYS10.8150.89232.1700.1230.1230.0000.0000.0000.000
132A560ARG10.9330.96134.0120.1490.1490.0000.0000.0000.000
133A561GLU-1-0.793-0.85537.174-0.109-0.1090.0000.0000.0000.000
134A562SER00.0160.00440.315-0.004-0.0040.0000.0000.0000.000
135A563HIS0-0.068-0.05141.9180.0010.0010.0000.0000.0000.000
136A564ASP-1-0.895-0.92644.803-0.083-0.0830.0000.0000.0000.000
137A565ASN0-0.064-0.05645.3800.0010.0010.0000.0000.0000.000
138A566ASP-1-0.905-0.94243.298-0.088-0.0880.0000.0000.0000.000
139A567GLY00.0210.02542.004-0.003-0.0030.0000.0000.0000.000
140A568VAL0-0.051-0.04436.199-0.005-0.0050.0000.0000.0000.000
141A569ALA00.0580.04238.4430.0000.0000.0000.0000.0000.000
142A570ASN0-0.032-0.03335.058-0.015-0.0150.0000.0000.0000.000
143A571LEU0-0.035-0.00129.3200.0040.0040.0000.0000.0000.000
144A572THR0-0.013-0.00832.5750.0010.0010.0000.0000.0000.000
145A573VAL00.0390.01229.674-0.007-0.0070.0000.0000.0000.000
146A574ARG10.8060.91033.0030.1350.1350.0000.0000.0000.000
147A575SER00.017-0.01235.484-0.005-0.0050.0000.0000.0000.000
148A576MET0-0.0140.01137.2950.0010.0010.0000.0000.0000.000
149A577THR00.0000.00134.520-0.006-0.0060.0000.0000.0000.000
150A578SER00.010-0.01435.9440.0060.0060.0000.0000.0000.000
151A579PRO0-0.0290.00835.553-0.008-0.0080.0000.0000.0000.000
152A580GLU-1-0.842-0.92433.473-0.126-0.1260.0000.0000.0000.000
153A581THR0-0.074-0.04532.938-0.002-0.0020.0000.0000.0000.000
154A582ILE00.0220.02926.3530.0030.0030.0000.0000.0000.000
155A583ARG10.8920.92129.0690.1370.1370.0000.0000.0000.000
156A584PHE00.0060.01122.543-0.015-0.0150.0000.0000.0000.000
157A585GLN00.0140.00125.9420.0080.0080.0000.0000.0000.000
158A586VAL00.004-0.01024.240-0.021-0.0210.0000.0000.0000.000
159A587GLY0-0.023-0.00421.3670.0040.0040.0000.0000.0000.000
160A588GLU-1-0.852-0.92020.806-0.257-0.2570.0000.0000.0000.000
161A589TRP00.0690.03613.025-0.035-0.0350.0000.0000.0000.000
162A590TYR00.031-0.01018.2240.0370.0370.0000.0000.0000.000
163A591LEU00.0170.03015.866-0.061-0.0610.0000.0000.0000.000
164A592LEU0-0.050-0.02817.0460.0700.0700.0000.0000.0000.000
165A593THR00.0170.00217.186-0.062-0.0620.0000.0000.0000.000
166A594SER0-0.031-0.03718.6210.0490.0490.0000.0000.0000.000
167A595THR00.0290.00019.238-0.041-0.0410.0000.0000.0000.000
168A596THR0-0.018-0.01121.0630.0360.0360.0000.0000.0000.000
169A597LEU0-0.015-0.00122.547-0.017-0.0170.0000.0000.0000.000
170A598LYS10.8670.90922.6410.1710.1710.0000.0000.0000.000
171A599GLU-1-0.845-0.93125.060-0.162-0.1620.0000.0000.0000.000
172A600ASN0-0.027-0.01727.3060.0120.0120.0000.0000.0000.000
173A601ASN00.0190.00324.501-0.019-0.0190.0000.0000.0000.000
174A602LEU0-0.0100.00319.0230.0010.0010.0000.0000.0000.000
175A603PRO00.007-0.00217.6880.0090.0090.0000.0000.0000.000
176A604GLU-1-0.885-0.93114.100-0.076-0.0760.0000.0000.0000.000
177A605GLY00.0390.02012.200-0.066-0.0660.0000.0000.0000.000
178A606TRP00.0050.00810.035-0.078-0.0780.0000.0000.0000.000
179A607VAL0-0.035-0.01412.7310.0930.0930.0000.0000.0000.000
180A608TRP00.0610.02412.758-0.050-0.0500.0000.0000.0000.000
181A609ASP-1-0.820-0.89418.264-0.150-0.1500.0000.0000.0000.000
182A610ARG10.8950.96121.3540.1350.1350.0000.0000.0000.000
183A611VAL0-0.022-0.01323.4910.0230.0230.0000.0000.0000.000
184A612GLU-1-0.831-0.91625.545-0.155-0.1550.0000.0000.0000.000
185A613LEU00.0190.00325.824-0.006-0.0060.0000.0000.0000.000
186A614LYS10.8210.92728.2960.1670.1670.0000.0000.0000.000
187A615SER00.0690.02331.237-0.006-0.0060.0000.0000.0000.000
188A616ASP-1-0.864-0.88734.758-0.109-0.1090.0000.0000.0000.000
189A617THR0-0.031-0.01831.1750.0050.0050.0000.0000.0000.000
190A618PRO0-0.053-0.03331.753-0.008-0.0080.0000.0000.0000.000
191A619TYR00.0190.01525.697-0.003-0.0030.0000.0000.0000.000
192A620TYR0-0.029-0.01425.6830.0140.0140.0000.0000.0000.000
193A621ALA00.0600.03225.353-0.019-0.0190.0000.0000.0000.000
194A622ASP-1-0.776-0.83720.856-0.405-0.4050.0000.0000.0000.000
195A623GLN00.0670.01517.8670.0080.0080.0000.0000.0000.000
196A624ALA00.0120.01117.681-0.037-0.0370.0000.0000.0000.000
197A625LEU0-0.006-0.01819.7580.0260.0260.0000.0000.0000.000
198A626THR0-0.043-0.01222.4260.0350.0350.0000.0000.0000.000
199A627TYR0-0.025-0.00319.7150.0320.0320.0000.0000.0000.000
200A628PHE0-0.042-0.03420.9400.0070.0070.0000.0000.0000.000
201A629ILE00.0300.01726.1730.0160.0160.0000.0000.0000.000
202A630THR00.0380.00329.7870.0180.0180.0000.0000.0000.000
203A631PRO0-0.048-0.01628.334-0.015-0.0150.0000.0000.0000.000
204A632PRO00.0060.02524.6550.0120.0120.0000.0000.0000.000
205A633PRO00.0260.00227.7560.0050.0050.0000.0000.0000.000
206A634VAL00.0000.00727.388-0.019-0.0190.0000.0000.0000.000
207A635ASP-1-0.834-0.91925.811-0.208-0.2080.0000.0000.0000.000
208A636SER0-0.063-0.01925.862-0.007-0.0070.0000.0000.0000.000
209A637GLN0-0.027-0.04020.485-0.011-0.0110.0000.0000.0000.000
210A638ILE0-0.0140.00018.0570.0170.0170.0000.0000.0000.000
211A639LEU00.0050.01314.533-0.037-0.0370.0000.0000.0000.000
212A640PHE0-0.047-0.03012.9910.0320.0320.0000.0000.0000.000
213A641GLU-1-0.806-0.9109.016-1.186-1.1860.0000.0000.0000.000
214A642GLY0-0.041-0.0457.8240.4020.4020.0000.0000.0000.000
215A643ASN0-0.0320.0012.265-5.384-4.9402.311-1.283-1.473-0.014
216A644THR0-0.020-0.0172.7662.0884.3770.184-0.951-1.522-0.005