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: V5571

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2703036.972834
FMO2-HF: Nuclear repulsion 2615701.41751
FMO2-HF: Total energy -87335.555324
FMO2-MP2: Total energy -87588.814645


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.
1.1054.3820.189-1.468-1.999-0.004
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 : 0.024 / q_NPA : -0.008
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].
3A431LEU0-0.018-0.0163.8090.3001.326-0.010-0.410-0.6060.001
4A432ARG10.9010.9416.2580.6060.6060.0000.0000.0000.000
5A433VAL0-0.019-0.0099.986-0.033-0.0330.0000.0000.0000.000
6A434LEU00.0070.00511.9920.0690.0690.0000.0000.0000.000
7A435LEU0-0.014-0.01514.4550.0040.0040.0000.0000.0000.000
8A436THR00.0360.02517.6450.0460.0460.0000.0000.0000.000
9A437VAL00.0250.01021.183-0.013-0.0130.0000.0000.0000.000
10A438GLY00.0440.01223.3820.0160.0160.0000.0000.0000.000
11A439SER0-0.021-0.00625.3190.0030.0030.0000.0000.0000.000
12A440ILE00.0320.01527.629-0.011-0.0110.0000.0000.0000.000
13A441MET0-0.0360.00425.9340.0020.0020.0000.0000.0000.000
14A442SER00.0250.02729.5560.0040.0040.0000.0000.0000.000
15A443PRO00.0190.00431.062-0.009-0.0090.0000.0000.0000.000
16A444ASN00.0130.00728.5930.0160.0160.0000.0000.0000.000
17A445SER00.009-0.02132.4650.0010.0010.0000.0000.0000.000
18A446ALA00.0310.00632.752-0.001-0.0010.0000.0000.0000.000
19A447ASP-1-0.904-0.92633.748-0.096-0.0960.0000.0000.0000.000
20A448ARG10.8850.95135.1340.1050.1050.0000.0000.0000.000
21A449GLN0-0.0020.00133.817-0.006-0.0060.0000.0000.0000.000
22A450VAL0-0.029-0.00627.322-0.002-0.0020.0000.0000.0000.000
23A451TRP0-0.030-0.03330.7460.0070.0070.0000.0000.0000.000
24A452LEU0-0.030-0.02225.154-0.014-0.0140.0000.0000.0000.000
25A453ASN0-0.057-0.05026.4000.0240.0240.0000.0000.0000.000
26A454LYS10.8860.93727.6170.0860.0860.0000.0000.0000.000
27A455THR00.006-0.01029.4170.0010.0010.0000.0000.0000.000
28A456LEU0-0.010-0.01325.952-0.010-0.0100.0000.0000.0000.000
29A457THR0-0.0140.00129.042-0.001-0.0010.0000.0000.0000.000
30A458ALA00.0360.01930.893-0.006-0.0060.0000.0000.0000.000
31A459PRO0-0.0050.00532.9050.0070.0070.0000.0000.0000.000
32A460GLY00.009-0.00535.236-0.005-0.0050.0000.0000.0000.000
33A461THR00.0010.00237.7510.0020.0020.0000.0000.0000.000
34A462ASN00.0470.01634.4590.0060.0060.0000.0000.0000.000
35A463SER00.0580.03632.583-0.005-0.0050.0000.0000.0000.000
36A464ASN00.002-0.01228.647-0.008-0.0080.0000.0000.0000.000
37A465ASP-1-0.974-0.98929.806-0.120-0.1200.0000.0000.0000.000
38A466ASN00.0140.00930.461-0.012-0.0120.0000.0000.0000.000
39A467LEU0-0.029-0.00126.721-0.007-0.0070.0000.0000.0000.000
40A468VAL00.0140.00821.838-0.002-0.0020.0000.0000.0000.000
41A469LYS10.8940.95221.8920.1320.1320.0000.0000.0000.000
42A470ILE00.0010.01115.369-0.006-0.0060.0000.0000.0000.000
43A471ALA0-0.009-0.02717.5890.0080.0080.0000.0000.0000.000
44A472HIS00.0810.02712.522-0.021-0.0210.0000.0000.0000.000
45A473ASP-1-0.942-0.96315.967-0.172-0.1720.0000.0000.0000.000
46A474LEU00.0290.00316.5380.0280.0280.0000.0000.0000.000
47A475GLY0-0.037-0.01919.2090.0220.0220.0000.0000.0000.000
48A476HIS0-0.028-0.00617.141-0.007-0.0070.0000.0000.0000.000
49A477TYR00.009-0.00718.335-0.019-0.0190.0000.0000.0000.000
50A478LEU0-0.0030.01316.5430.0200.0200.0000.0000.0000.000
51A479ILE0-0.019-0.01119.984-0.008-0.0080.0000.0000.0000.000
52A480MET0-0.0020.00821.557-0.006-0.0060.0000.0000.0000.000
53A481GLN00.0280.04422.4280.0150.0150.0000.0000.0000.000
54A482GLY00.0550.03422.8490.0150.0150.0000.0000.0000.000
55A483PHE00.003-0.02722.195-0.024-0.0240.0000.0000.0000.000
56A484MET00.0290.01721.7690.0140.0140.0000.0000.0000.000
57A485HIS10.7840.87321.6510.1950.1950.0000.0000.0000.000
58A486ILE0-0.035-0.01917.9190.0070.0070.0000.0000.0000.000
59A487LYS10.9170.95721.1380.2120.2120.0000.0000.0000.000
60A488THR0-0.017-0.01418.8190.0180.0180.0000.0000.0000.000
61A489VAL00.0050.00812.983-0.010-0.0100.0000.0000.0000.000
62A490GLU-1-0.938-0.95014.752-0.274-0.2740.0000.0000.0000.000
63A491TRP00.0400.0058.357-0.153-0.1530.0000.0000.0000.000
64A492TYR0-0.013-0.00410.3140.1390.1390.0000.0000.0000.000
65A493THR0-0.002-0.0037.772-0.310-0.3100.0000.0000.0000.000
66A494PRO00.0470.0126.8130.0390.0390.0000.0000.0000.000
67A495ASP-1-0.905-0.9409.8400.0330.0330.0000.0000.0000.000
68A496PHE0-0.044-0.03012.1810.0100.0100.0000.0000.0000.000
69A497GLN00.0280.03111.8220.0130.0130.0000.0000.0000.000
70A498PRO00.0330.00812.055-0.098-0.0980.0000.0000.0000.000
71A499SER00.0010.0037.9610.0410.0410.0000.0000.0000.000
72A500ARG10.9050.9519.5800.0310.0310.0000.0000.0000.000
73A501ASP-1-0.873-0.9369.051-0.598-0.5980.0000.0000.0000.000
74A502PRO0-0.044-0.0016.0430.1020.1020.0000.0000.0000.000
75A503THR00.006-0.0127.9240.1470.1470.0000.0000.0000.000
76A504PRO0-0.045-0.0268.449-0.187-0.1870.0000.0000.0000.000
77A505ILE0-0.005-0.0036.9760.0120.0120.0000.0000.0000.000
78A506ALA00.0150.0019.0510.1520.1520.0000.0000.0000.000
79A507GLY00.0200.01510.883-0.043-0.0430.0000.0000.0000.000
80A508MET0-0.060-0.00510.7600.0650.0650.0000.0000.0000.000
81A509SER0-0.036-0.02013.5500.0140.0140.0000.0000.0000.000
82A510VAL00.0210.01716.5430.0030.0030.0000.0000.0000.000
83A511MET0-0.027-0.00519.1920.0170.0170.0000.0000.0000.000
84A512VAL00.0400.01822.417-0.001-0.0010.0000.0000.0000.000
85A513ASN0-0.020-0.01026.0070.0090.0090.0000.0000.0000.000
86A514ILE00.0150.00826.707-0.002-0.0020.0000.0000.0000.000
87A515THR0-0.054-0.02325.6630.0030.0030.0000.0000.0000.000
88A516LYS10.9830.98216.6500.3040.3040.0000.0000.0000.000
89A517LYS10.8900.94122.0570.1760.1760.0000.0000.0000.000
90A518ALA00.0220.01318.7610.0050.0050.0000.0000.0000.000
91A519ASP-1-0.835-0.90214.177-0.366-0.3660.0000.0000.0000.000
92A520VAL0-0.006-0.01511.0780.0100.0100.0000.0000.0000.000
93A521TYR00.0230.0099.753-0.012-0.0120.0000.0000.0000.000
94A522PHE00.0160.0197.991-0.235-0.2350.0000.0000.0000.000
95A523MET0-0.0210.0057.9240.3700.3700.0000.0000.0000.000
96A524LYS10.9520.9888.1990.2420.2420.0000.0000.0000.000
97A525GLN0-0.002-0.01910.5620.1330.1330.0000.0000.0000.000
98A526PHE0-0.040-0.01713.3270.0140.0140.0000.0000.0000.000
99A527LYS10.8740.92414.7640.0880.0880.0000.0000.0000.000
100A528ASN0-0.0080.00918.2840.0250.0250.0000.0000.0000.000
101A529SER00.0170.00721.7050.0000.0000.0000.0000.0000.000
102A530TYR00.0200.01824.635-0.002-0.0020.0000.0000.0000.000
103A531THR00.0360.00928.3600.0040.0040.0000.0000.0000.000
104A532ASN00.012-0.00231.429-0.002-0.0020.0000.0000.0000.000
105A533ASN00.0200.02728.6320.0000.0000.0000.0000.0000.000
106A534ARG10.9560.99228.1020.0480.0480.0000.0000.0000.000
107A535HIS10.8410.90022.5660.0410.0410.0000.0000.0000.000
108A536GLN00.020-0.00322.5300.0130.0130.0000.0000.0000.000
109A537ILE0-0.019-0.02317.3140.0000.0000.0000.0000.0000.000
110A538THR0-0.020-0.04518.2460.0060.0060.0000.0000.0000.000
111A539SER0-0.023-0.00514.730-0.028-0.0280.0000.0000.0000.000
112A540ILE0-0.016-0.00113.0270.0470.0470.0000.0000.0000.000
113A541PHE00.013-0.01212.610-0.091-0.0910.0000.0000.0000.000
114A542LEU00.0130.03012.0740.0890.0890.0000.0000.0000.000
115A543ILE0-0.025-0.02513.418-0.058-0.0580.0000.0000.0000.000
116A544LYS10.9911.00416.0590.4040.4040.0000.0000.0000.000
117A545PRO0-0.049-0.02817.9590.0000.0000.0000.0000.0000.000
118A546LEU0-0.005-0.00218.9020.0040.0040.0000.0000.0000.000
119A547ALA0-0.025-0.02622.3270.0190.0190.0000.0000.0000.000
120A548ASP-1-0.826-0.88425.616-0.171-0.1710.0000.0000.0000.000
121A549PHE0-0.080-0.04423.3900.0110.0110.0000.0000.0000.000
122A550LYS10.9390.96828.4650.1020.1020.0000.0000.0000.000
123A551VAL00.0230.02827.6650.0030.0030.0000.0000.0000.000
124A552GLN0-0.033-0.01230.6930.0040.0040.0000.0000.0000.000
125A553CYS00.002-0.00129.467-0.004-0.0040.0000.0000.0000.000
126A554TYR00.0490.01832.0290.0070.0070.0000.0000.0000.000
127A555MET0-0.0150.00729.727-0.006-0.0060.0000.0000.0000.000
128A556SER0-0.004-0.02831.9020.0110.0110.0000.0000.0000.000
129A557TYR00.0200.02031.521-0.007-0.0070.0000.0000.0000.000
130A558PHE00.0150.01026.6650.0080.0080.0000.0000.0000.000
131A559LYS10.8490.91432.3190.0700.0700.0000.0000.0000.000
132A560ARG10.9430.96033.0790.0770.0770.0000.0000.0000.000
133A561GLU-1-0.834-0.88137.214-0.059-0.0590.0000.0000.0000.000
134A562SER00.008-0.00140.209-0.002-0.0020.0000.0000.0000.000
135A563HIS0-0.043-0.03341.9020.0000.0000.0000.0000.0000.000
136A564ASP-1-0.896-0.92745.078-0.040-0.0400.0000.0000.0000.000
137A565ASN0-0.066-0.05645.4850.0020.0020.0000.0000.0000.000
138A566ASP-1-0.917-0.94543.696-0.032-0.0320.0000.0000.0000.000
139A567GLY00.0070.01242.3700.0000.0000.0000.0000.0000.000
140A568VAL0-0.055-0.03436.478-0.003-0.0030.0000.0000.0000.000
141A569ALA00.0640.04438.0190.0010.0010.0000.0000.0000.000
142A570ASN0-0.042-0.03634.949-0.005-0.0050.0000.0000.0000.000
143A571LEU0-0.0120.00029.3880.0010.0010.0000.0000.0000.000
144A572THR0-0.003-0.00532.4710.0000.0000.0000.0000.0000.000
145A573VAL00.0410.02030.040-0.005-0.0050.0000.0000.0000.000
146A574ARG10.8330.91733.2230.0930.0930.0000.0000.0000.000
147A575SER00.0630.02335.629-0.005-0.0050.0000.0000.0000.000
148A576MET0-0.0080.00837.371-0.002-0.0020.0000.0000.0000.000
149A577THR0-0.009-0.00334.650-0.004-0.0040.0000.0000.0000.000
150A578SER00.0260.01336.2430.0060.0060.0000.0000.0000.000
151A579PRO0-0.0240.00135.931-0.007-0.0070.0000.0000.0000.000
152A580GLU-1-0.866-0.92833.676-0.098-0.0980.0000.0000.0000.000
153A581THR0-0.080-0.05233.427-0.003-0.0030.0000.0000.0000.000
154A582ILE00.0040.01626.8450.0000.0000.0000.0000.0000.000
155A583ARG10.9300.93729.6200.1210.1210.0000.0000.0000.000
156A584PHE0-0.019-0.00223.204-0.007-0.0070.0000.0000.0000.000
157A585GLN00.033-0.00325.5200.0050.0050.0000.0000.0000.000
158A586VAL00.005-0.01323.885-0.022-0.0220.0000.0000.0000.000
159A587GLY0-0.020-0.00821.0960.0080.0080.0000.0000.0000.000
160A588GLU-1-0.868-0.89920.936-0.243-0.2430.0000.0000.0000.000
161A589TRP00.0260.00113.223-0.039-0.0390.0000.0000.0000.000
162A590TYR00.0380.00518.3140.0430.0430.0000.0000.0000.000
163A591LEU00.0040.01916.058-0.055-0.0550.0000.0000.0000.000
164A592LEU0-0.051-0.03017.4160.0530.0530.0000.0000.0000.000
165A593THR00.0190.00317.458-0.040-0.0400.0000.0000.0000.000
166A594SER0-0.013-0.00418.8370.0290.0290.0000.0000.0000.000
167A595THR00.0220.00519.369-0.020-0.0200.0000.0000.0000.000
168A596THR0-0.018-0.02221.1140.0110.0110.0000.0000.0000.000
169A597LEU0-0.044-0.00622.8870.0000.0000.0000.0000.0000.000
170A598LYS10.9440.97421.9990.0620.0620.0000.0000.0000.000
171A599GLU-1-0.903-0.95825.302-0.058-0.0580.0000.0000.0000.000
172A600ASN0-0.021-0.02427.4290.0050.0050.0000.0000.0000.000
173A601ASN00.003-0.00824.949-0.010-0.0100.0000.0000.0000.000
174A602LEU0-0.017-0.00519.645-0.006-0.0060.0000.0000.0000.000
175A603PRO0-0.017-0.01618.3810.0130.0130.0000.0000.0000.000
176A604GLU-1-0.874-0.93115.7610.1740.1740.0000.0000.0000.000
177A605GLY00.0140.01312.8360.0000.0000.0000.0000.0000.000
178A606TRP0-0.0090.01010.069-0.060-0.0600.0000.0000.0000.000
179A607VAL0-0.030-0.01313.2280.0330.0330.0000.0000.0000.000
180A608TRP00.0610.01913.182-0.040-0.0400.0000.0000.0000.000
181A609ASP-1-0.898-0.94718.199-0.079-0.0790.0000.0000.0000.000
182A610ARG10.8930.95721.4400.1200.1200.0000.0000.0000.000
183A611VAL0-0.041-0.02123.5610.0160.0160.0000.0000.0000.000
184A612GLU-1-0.952-0.96725.647-0.102-0.1020.0000.0000.0000.000
185A613LEU00.0200.00825.8270.0040.0040.0000.0000.0000.000
186A614LYS10.9610.97928.8060.0780.0780.0000.0000.0000.000
187A615SER00.0470.00931.733-0.005-0.0050.0000.0000.0000.000
188A616ASP-1-0.918-0.93635.100-0.058-0.0580.0000.0000.0000.000
189A617THR0-0.053-0.03731.2250.0050.0050.0000.0000.0000.000
190A618PRO0-0.063-0.03331.945-0.006-0.0060.0000.0000.0000.000
191A619TYR00.0450.04026.2000.0000.0000.0000.0000.0000.000
192A620TYR0-0.026-0.02226.0480.0100.0100.0000.0000.0000.000
193A621ALA00.0550.03425.299-0.012-0.0120.0000.0000.0000.000
194A622ASP-1-0.775-0.81220.789-0.206-0.2060.0000.0000.0000.000
195A623GLN00.0890.01417.664-0.004-0.0040.0000.0000.0000.000
196A624ALA00.0020.00817.742-0.025-0.0250.0000.0000.0000.000
197A625LEU00.012-0.01719.7070.0070.0070.0000.0000.0000.000
198A626THR0-0.042-0.01322.4690.0190.0190.0000.0000.0000.000
199A627TYR0-0.034-0.00720.0650.0170.0170.0000.0000.0000.000
200A628PHE0-0.042-0.03221.123-0.002-0.0020.0000.0000.0000.000
201A629ILE00.0080.00726.3270.0120.0120.0000.0000.0000.000
202A630THR00.017-0.00729.8130.0080.0080.0000.0000.0000.000
203A631PRO0-0.036-0.01328.275-0.010-0.0100.0000.0000.0000.000
204A632PRO00.0080.01824.4430.0090.0090.0000.0000.0000.000
205A633PRO00.0310.01027.449-0.001-0.0010.0000.0000.0000.000
206A634VAL00.0060.01427.205-0.014-0.0140.0000.0000.0000.000
207A635ASP-1-0.896-0.95625.817-0.155-0.1550.0000.0000.0000.000
208A636SER0-0.091-0.05125.557-0.004-0.0040.0000.0000.0000.000
209A637GLN00.010-0.01520.651-0.005-0.0050.0000.0000.0000.000
210A638ILE0-0.023-0.00318.1300.0180.0180.0000.0000.0000.000
211A639LEU0-0.0130.00914.311-0.037-0.0370.0000.0000.0000.000
212A640PHE0-0.067-0.03512.8830.0430.0430.0000.0000.0000.000
213A641GLU-1-0.929-0.9659.240-0.439-0.4390.0000.0000.0000.000
214A642GLY0-0.048-0.0497.8090.3400.3400.0000.0000.0000.000
215A643ASN0-0.0020.0233.534-0.963-0.5340.011-0.305-0.136-0.002
216A644THR0-0.015-0.0102.9400.8572.6790.188-0.753-1.257-0.003