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: 177ZZ

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 OptHSide
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 -2704344.150371
FMO2-HF: Nuclear repulsion 2617007.868706
FMO2-HF: Total energy -87336.281664
FMO2-MP2: Total energy -87589.586208


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.
-0.7083.5780.26-2.065-2.481-0.004
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 : 0.053 / q_NPA : 0.031
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].
3A431LEU0-0.001-0.0063.8090.5072.115-0.012-0.786-0.8090.003
4A432ARG10.8030.8886.2581.1531.1530.0000.0000.0000.000
5A433VAL0-0.031-0.0199.9860.0600.0600.0000.0000.0000.000
6A434LEU00.0050.00812.0050.0290.0290.0000.0000.0000.000
7A435LEU0-0.014-0.01214.4870.0430.0430.0000.0000.0000.000
8A436THR00.0430.02917.6590.0360.0360.0000.0000.0000.000
9A437VAL00.0270.01221.1960.0030.0030.0000.0000.0000.000
10A438GLY00.0440.01123.3970.0220.0220.0000.0000.0000.000
11A439SER0-0.015-0.00325.333-0.002-0.0020.0000.0000.0000.000
12A440ILE00.0290.01827.644-0.008-0.0080.0000.0000.0000.000
13A441MET0-0.0480.00625.6660.0040.0040.0000.0000.0000.000
14A442SER00.0670.03929.5720.0010.0010.0000.0000.0000.000
15A443PRO0-0.038-0.01931.146-0.006-0.0060.0000.0000.0000.000
16A444ASN00.0120.01428.6800.0110.0110.0000.0000.0000.000
17A445SER00.014-0.03032.4790.0060.0060.0000.0000.0000.000
18A446ALA00.0200.00132.765-0.004-0.0040.0000.0000.0000.000
19A447ASP-1-0.845-0.88233.764-0.126-0.1260.0000.0000.0000.000
20A448ARG10.8380.91435.3670.1270.1270.0000.0000.0000.000
21A449GLN00.0030.00533.902-0.009-0.0090.0000.0000.0000.000
22A450VAL0-0.026-0.00227.3450.0030.0030.0000.0000.0000.000
23A451TRP0-0.029-0.03130.8200.0040.0040.0000.0000.0000.000
24A452LEU0-0.030-0.02225.242-0.014-0.0140.0000.0000.0000.000
25A453ASN0-0.060-0.05026.5280.0280.0280.0000.0000.0000.000
26A454LYS10.8450.92927.6530.1180.1180.0000.0000.0000.000
27A455THR00.0150.00329.468-0.003-0.0030.0000.0000.0000.000
28A456LEU0-0.011-0.01725.897-0.007-0.0070.0000.0000.0000.000
29A457THR00.0190.01629.0330.0060.0060.0000.0000.0000.000
30A458ALA0-0.018-0.01430.774-0.009-0.0090.0000.0000.0000.000
31A459PRO0-0.0010.01032.8440.0080.0080.0000.0000.0000.000
32A460GLY00.0200.00035.139-0.002-0.0020.0000.0000.0000.000
33A461THR0-0.002-0.00237.6420.0000.0000.0000.0000.0000.000
34A462ASN00.0480.02234.491-0.001-0.0010.0000.0000.0000.000
35A463SER00.0720.04332.456-0.005-0.0050.0000.0000.0000.000
36A464ASN0-0.017-0.02028.843-0.015-0.0150.0000.0000.0000.000
37A465ASP-1-0.902-0.94129.667-0.062-0.0620.0000.0000.0000.000
38A466ASN0-0.009-0.00730.317-0.006-0.0060.0000.0000.0000.000
39A467LEU0-0.0270.00026.615-0.011-0.0110.0000.0000.0000.000
40A468VAL00.0130.00621.7620.0080.0080.0000.0000.0000.000
41A469LYS10.8850.94621.8010.0710.0710.0000.0000.0000.000
42A470ILE0-0.0100.00815.2600.0140.0140.0000.0000.0000.000
43A471ALA0-0.004-0.02717.499-0.016-0.0160.0000.0000.0000.000
44A472HIS00.0700.02012.573-0.040-0.0400.0000.0000.0000.000
45A473ASP-1-0.933-0.96315.8020.1380.1380.0000.0000.0000.000
46A474LEU00.0110.00416.2270.0160.0160.0000.0000.0000.000
47A475GLY0-0.025-0.01519.0340.0000.0000.0000.0000.0000.000
48A476HIS0-0.038-0.01017.050-0.036-0.0360.0000.0000.0000.000
49A477TYR00.0400.01218.261-0.004-0.0040.0000.0000.0000.000
50A478LEU0-0.0100.01616.8310.0040.0040.0000.0000.0000.000
51A479ILE0-0.019-0.00719.9610.0110.0110.0000.0000.0000.000
52A480MET0-0.0040.01221.534-0.017-0.0170.0000.0000.0000.000
53A481GLN00.0320.03922.4430.0090.0090.0000.0000.0000.000
54A482GLY00.0650.03622.8980.0220.0220.0000.0000.0000.000
55A483PHE0-0.007-0.03322.204-0.018-0.0180.0000.0000.0000.000
56A484MET00.0280.01821.7620.0080.0080.0000.0000.0000.000
57A485HIS10.7990.87621.6680.1820.1820.0000.0000.0000.000
58A486ILE0-0.050-0.02317.867-0.004-0.0040.0000.0000.0000.000
59A487LYS10.8530.92321.1520.2290.2290.0000.0000.0000.000
60A488THR0-0.021-0.02218.9380.0270.0270.0000.0000.0000.000
61A489VAL0-0.0070.00213.140-0.033-0.0330.0000.0000.0000.000
62A490GLU-1-0.858-0.90014.761-0.317-0.3170.0000.0000.0000.000
63A491TRP0-0.018-0.0238.996-0.215-0.2150.0000.0000.0000.000
64A492TYR0-0.055-0.04510.3250.1600.1600.0000.0000.0000.000
65A493THR0-0.003-0.0157.763-0.381-0.3810.0000.0000.0000.000
66A494PRO00.0380.0066.8310.1120.1120.0000.0000.0000.000
67A495ASP-1-0.867-0.9039.833-0.345-0.3450.0000.0000.0000.000
68A496PHE0-0.035-0.02612.1680.0700.0700.0000.0000.0000.000
69A497GLN00.0090.01411.7630.1200.1200.0000.0000.0000.000
70A498PRO00.0220.00112.056-0.113-0.1130.0000.0000.0000.000
71A499SER0-0.0030.0047.9730.0520.0520.0000.0000.0000.000
72A500ARG10.9100.9529.545-0.425-0.4250.0000.0000.0000.000
73A501ASP-1-0.828-0.9189.052-0.435-0.4350.0000.0000.0000.000
74A502PRO0-0.0410.0056.0610.2210.2210.0000.0000.0000.000
75A503THR00.006-0.0087.9370.0510.0510.0000.0000.0000.000
76A504PRO0-0.051-0.0298.456-0.116-0.1160.0000.0000.0000.000
77A505ILE0-0.013-0.0056.8000.1770.1770.0000.0000.0000.000
78A506ALA00.0210.0048.979-0.026-0.0260.0000.0000.0000.000
79A507GLY00.0200.01610.611-0.046-0.0460.0000.0000.0000.000
80A508MET0-0.054-0.00510.458-0.054-0.0540.0000.0000.0000.000
81A509SER0-0.042-0.02313.3270.0320.0320.0000.0000.0000.000
82A510VAL00.0190.01116.320-0.028-0.0280.0000.0000.0000.000
83A511MET0-0.0210.00619.0100.0310.0310.0000.0000.0000.000
84A512VAL00.0250.00622.227-0.016-0.0160.0000.0000.0000.000
85A513ASN0-0.058-0.04025.8280.0170.0170.0000.0000.0000.000
86A514ILE00.0160.01326.482-0.001-0.0010.0000.0000.0000.000
87A515THR0-0.043-0.01525.5430.0140.0140.0000.0000.0000.000
88A516LYS10.9420.94816.191-0.004-0.0040.0000.0000.0000.000
89A517LYS10.8820.93821.8280.0800.0800.0000.0000.0000.000
90A518ALA00.0160.01218.759-0.004-0.0040.0000.0000.0000.000
91A519ASP-1-0.800-0.88014.215-0.032-0.0320.0000.0000.0000.000
92A520VAL0-0.011-0.01610.916-0.042-0.0420.0000.0000.0000.000
93A521TYR00.0270.0089.7690.0900.0900.0000.0000.0000.000
94A522PHE00.0220.0197.924-0.195-0.1950.0000.0000.0000.000
95A523MET0-0.0330.0007.7850.4480.4480.0000.0000.0000.000
96A524LYS10.9160.9718.3031.3851.3850.0000.0000.0000.000
97A525GLN0-0.001-0.01010.7210.1960.1960.0000.0000.0000.000
98A526PHE0-0.032-0.00713.523-0.070-0.0700.0000.0000.0000.000
99A527LYS10.8600.93315.2380.4840.4840.0000.0000.0000.000
100A528ASN0-0.0110.00318.552-0.005-0.0050.0000.0000.0000.000
101A529SER00.0220.01021.9480.0220.0220.0000.0000.0000.000
102A530TYR00.0220.01524.806-0.003-0.0030.0000.0000.0000.000
103A531THR00.0390.01128.5450.0040.0040.0000.0000.0000.000
104A532ASN00.008-0.00331.6570.0000.0000.0000.0000.0000.000
105A533ASN00.0150.01928.773-0.004-0.0040.0000.0000.0000.000
106A534ARG10.9530.98928.3480.1580.1580.0000.0000.0000.000
107A535HIS10.8350.89322.8140.2000.2000.0000.0000.0000.000
108A536GLN00.012-0.00622.7420.0410.0410.0000.0000.0000.000
109A537ILE0-0.020-0.01917.618-0.028-0.0280.0000.0000.0000.000
110A538THR0-0.006-0.01118.4200.0430.0430.0000.0000.0000.000
111A539SER0-0.014-0.00414.897-0.078-0.0780.0000.0000.0000.000
112A540ILE0-0.030-0.01013.1760.0810.0810.0000.0000.0000.000
113A541PHE00.026-0.00712.548-0.117-0.1170.0000.0000.0000.000
114A542LEU00.0170.02812.4280.0860.0860.0000.0000.0000.000
115A543ILE0-0.030-0.02713.434-0.006-0.0060.0000.0000.0000.000
116A544LYS10.9290.97615.4280.2350.2350.0000.0000.0000.000
117A545PRO0-0.036-0.02117.9720.0250.0250.0000.0000.0000.000
118A546LEU00.0000.00018.7720.0070.0070.0000.0000.0000.000
119A547ALA0-0.023-0.02722.3370.0170.0170.0000.0000.0000.000
120A548ASP-1-0.832-0.89425.628-0.103-0.1030.0000.0000.0000.000
121A549PHE0-0.081-0.04723.3880.0140.0140.0000.0000.0000.000
122A550LYS10.9500.97628.4800.0610.0610.0000.0000.0000.000
123A551VAL00.0170.01927.5780.0070.0070.0000.0000.0000.000
124A552GLN0-0.026-0.01230.575-0.003-0.0030.0000.0000.0000.000
125A553CYS0-0.001-0.00629.413-0.003-0.0030.0000.0000.0000.000
126A554TYR00.0480.02131.9840.0070.0070.0000.0000.0000.000
127A555MET0-0.0100.01129.446-0.010-0.0100.0000.0000.0000.000
128A556SER00.017-0.01831.9430.0120.0120.0000.0000.0000.000
129A557TYR00.0200.02231.618-0.006-0.0060.0000.0000.0000.000
130A558PHE00.0190.00926.6910.0080.0080.0000.0000.0000.000
131A559LYS10.8320.90532.4560.1190.1190.0000.0000.0000.000
132A560ARG10.9510.96733.8650.1530.1530.0000.0000.0000.000
133A561GLU-1-0.805-0.86937.402-0.105-0.1050.0000.0000.0000.000
134A562SER00.0130.00240.421-0.005-0.0050.0000.0000.0000.000
135A563HIS0-0.076-0.04942.5090.0020.0020.0000.0000.0000.000
136A564ASP-1-0.888-0.92645.311-0.086-0.0860.0000.0000.0000.000
137A565ASN0-0.065-0.05545.8540.0010.0010.0000.0000.0000.000
138A566ASP-1-0.911-0.94444.000-0.095-0.0950.0000.0000.0000.000
139A567GLY00.0080.01642.616-0.004-0.0040.0000.0000.0000.000
140A568VAL0-0.058-0.03636.707-0.005-0.0050.0000.0000.0000.000
141A569ALA00.0600.04238.2940.0040.0040.0000.0000.0000.000
142A570ASN0-0.050-0.04335.252-0.015-0.0150.0000.0000.0000.000
143A571LEU0-0.0100.00429.5670.0060.0060.0000.0000.0000.000
144A572THR0-0.001-0.00632.667-0.002-0.0020.0000.0000.0000.000
145A573VAL00.0340.01830.089-0.005-0.0050.0000.0000.0000.000
146A574ARG10.8280.91633.3540.1240.1240.0000.0000.0000.000
147A575SER00.0610.02935.723-0.004-0.0040.0000.0000.0000.000
148A576MET0-0.0210.00537.4450.0010.0010.0000.0000.0000.000
149A577THR0-0.0060.00034.601-0.006-0.0060.0000.0000.0000.000
150A578SER00.0160.00336.2620.0060.0060.0000.0000.0000.000
151A579PRO0-0.027-0.00435.928-0.007-0.0070.0000.0000.0000.000
152A580GLU-1-0.862-0.92533.661-0.107-0.1070.0000.0000.0000.000
153A581THR0-0.083-0.05433.3480.0010.0010.0000.0000.0000.000
154A582ILE0-0.0020.01126.779-0.001-0.0010.0000.0000.0000.000
155A583ARG10.9270.94029.6670.1050.1050.0000.0000.0000.000
156A584PHE0-0.0070.00523.183-0.013-0.0130.0000.0000.0000.000
157A585GLN00.008-0.00625.5870.0070.0070.0000.0000.0000.000
158A586VAL00.014-0.00823.916-0.017-0.0170.0000.0000.0000.000
159A587GLY0-0.013-0.00121.0930.0040.0040.0000.0000.0000.000
160A588GLU-1-0.878-0.91020.946-0.199-0.1990.0000.0000.0000.000
161A589TRP00.0700.02713.133-0.023-0.0230.0000.0000.0000.000
162A590TYR00.0460.00018.3280.0290.0290.0000.0000.0000.000
163A591LEU00.0020.01815.897-0.046-0.0460.0000.0000.0000.000
164A592LEU0-0.053-0.03017.4010.0560.0560.0000.0000.0000.000
165A593THR00.0170.00117.487-0.057-0.0570.0000.0000.0000.000
166A594SER0-0.015-0.01918.9130.0520.0520.0000.0000.0000.000
167A595THR00.012-0.00519.475-0.041-0.0410.0000.0000.0000.000
168A596THR0-0.030-0.03121.1760.0340.0340.0000.0000.0000.000
169A597LEU0-0.045-0.00623.059-0.018-0.0180.0000.0000.0000.000
170A598LYS10.8760.92122.8400.1790.1790.0000.0000.0000.000
171A599GLU-1-0.908-0.96225.485-0.162-0.1620.0000.0000.0000.000
172A600ASN0-0.029-0.02627.6270.0090.0090.0000.0000.0000.000
173A601ASN00.004-0.00125.065-0.021-0.0210.0000.0000.0000.000
174A602LEU0-0.0070.00119.8080.0070.0070.0000.0000.0000.000
175A603PRO00.009-0.00518.5170.0040.0040.0000.0000.0000.000
176A604GLU-1-0.889-0.93514.877-0.145-0.1450.0000.0000.0000.000
177A605GLY00.0210.01013.015-0.065-0.0650.0000.0000.0000.000
178A606TRP00.0020.00110.255-0.072-0.0720.0000.0000.0000.000
179A607VAL0-0.024-0.01213.3570.0850.0850.0000.0000.0000.000
180A608TRP00.0660.02613.247-0.047-0.0470.0000.0000.0000.000
181A609ASP-1-0.840-0.90018.246-0.148-0.1480.0000.0000.0000.000
182A610ARG10.8970.95421.5160.1070.1070.0000.0000.0000.000
183A611VAL0-0.041-0.02423.6080.0200.0200.0000.0000.0000.000
184A612GLU-1-0.875-0.93925.726-0.142-0.1420.0000.0000.0000.000
185A613LEU00.0290.01025.893-0.004-0.0040.0000.0000.0000.000
186A614LYS10.9520.99228.9050.1530.1530.0000.0000.0000.000
187A615SER00.0430.00231.852-0.007-0.0070.0000.0000.0000.000
188A616ASP-1-0.906-0.94335.226-0.105-0.1050.0000.0000.0000.000
189A617THR0-0.050-0.03031.3570.0030.0030.0000.0000.0000.000
190A618PRO0-0.051-0.02732.097-0.006-0.0060.0000.0000.0000.000
191A619TYR00.0330.02526.197-0.002-0.0020.0000.0000.0000.000
192A620TYR0-0.022-0.01826.2490.0140.0140.0000.0000.0000.000
193A621ALA00.0590.03425.516-0.017-0.0170.0000.0000.0000.000
194A622ASP-1-0.777-0.83420.975-0.409-0.4090.0000.0000.0000.000
195A623GLN00.0800.01517.8260.0230.0230.0000.0000.0000.000
196A624ALA00.0090.00617.887-0.020-0.0200.0000.0000.0000.000
197A625LEU00.001-0.01519.8860.0290.0290.0000.0000.0000.000
198A626THR0-0.040-0.00922.6880.0360.0360.0000.0000.0000.000
199A627TYR0-0.035-0.01120.0090.0340.0340.0000.0000.0000.000
200A628PHE0-0.037-0.03121.2430.0110.0110.0000.0000.0000.000
201A629ILE00.0110.00826.4470.0170.0170.0000.0000.0000.000
202A630THR00.0410.00629.9510.0160.0160.0000.0000.0000.000
203A631PRO0-0.048-0.02128.353-0.016-0.0160.0000.0000.0000.000
204A632PRO0-0.0030.01624.4380.0100.0100.0000.0000.0000.000
205A633PRO00.0300.00827.4650.0070.0070.0000.0000.0000.000
206A634VAL0-0.0050.00427.220-0.017-0.0170.0000.0000.0000.000
207A635ASP-1-0.836-0.92425.749-0.187-0.1870.0000.0000.0000.000
208A636SER0-0.070-0.02625.570-0.012-0.0120.0000.0000.0000.000
209A637GLN00.004-0.02320.621-0.010-0.0100.0000.0000.0000.000
210A638ILE0-0.030-0.00518.1230.0110.0110.0000.0000.0000.000
211A639LEU0-0.0020.01614.460-0.033-0.0330.0000.0000.0000.000
212A640PHE0-0.054-0.02913.1350.0290.0290.0000.0000.0000.000
213A641GLU-1-0.820-0.9039.241-1.341-1.3410.0000.0000.0000.000
214A642GLY0-0.083-0.0628.0290.4290.4290.0000.0000.0000.000
215A643ASN0-0.036-0.0123.337-3.323-2.7020.067-0.409-0.280-0.002
216A644THR00.0070.0003.0020.5402.5970.205-0.870-1.392-0.005