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: 6Y3MZ

Calculation Name: 4K2O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4K2O

Chain ID: A

ChEMBL ID:

UniProt ID: Q13009

Base Structure: X-ray

Registration Date: 2023-09-20

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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2856271.648971
FMO2-HF: Nuclear repulsion 2763759.998524
FMO2-HF: Total energy -92511.650447
FMO2-MP2: Total energy -92780.231408


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:432:GLY)


Summations of interaction energy for fragment #1(A:432: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.
-2.81-1.0550.077-0.657-1.1760
Interaction energy analysis for fragmet #1(A:432:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.001
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].
3A434VAL00.006-0.0163.7991.8252.581-0.008-0.320-0.4280.000
4A435ARG10.8870.9676.715-1.716-1.7160.0000.0000.0000.000
5A436LYS10.8910.9308.731-0.376-0.3760.0000.0000.0000.000
6A437ALA0-0.023-0.01410.561-0.016-0.0160.0000.0000.0000.000
7A438GLY00.0340.02412.8960.0010.0010.0000.0000.0000.000
8A439ALA00.0010.01416.393-0.005-0.0050.0000.0000.0000.000
9A440LEU0-0.006-0.00316.1240.0200.0200.0000.0000.0000.000
10A441ALA0-0.0270.00219.805-0.017-0.0170.0000.0000.0000.000
11A442VAL00.005-0.00818.5230.0180.0180.0000.0000.0000.000
12A443LYS10.8480.92621.676-0.084-0.0840.0000.0000.0000.000
13A444ASN0-0.007-0.00122.0830.0070.0070.0000.0000.0000.000
14A445PHE0-0.014-0.01324.052-0.008-0.0080.0000.0000.0000.000
15A446LEU00.0170.01824.830-0.008-0.0080.0000.0000.0000.000
16A447VAL0-0.053-0.03324.4180.0060.0060.0000.0000.0000.000
17A448HIS00.0500.02824.635-0.017-0.0170.0000.0000.0000.000
18A449LYS10.9310.97224.631-0.069-0.0690.0000.0000.0000.000
19A450LYS11.0190.99627.196-0.050-0.0500.0000.0000.0000.000
20A451ASN00.0170.01429.3840.0020.0020.0000.0000.0000.000
21A452LYS10.8140.94027.374-0.105-0.1050.0000.0000.0000.000
22A453LYS10.8510.89030.544-0.065-0.0650.0000.0000.0000.000
23A454VAL00.0350.02527.419-0.001-0.0010.0000.0000.0000.000
24A455GLU-1-0.871-0.91329.2470.0550.0550.0000.0000.0000.000
25A456SER00.0570.01329.1850.0090.0090.0000.0000.0000.000
26A457ALA0-0.0360.00526.899-0.005-0.0050.0000.0000.0000.000
27A458THR00.0260.01628.977-0.005-0.0050.0000.0000.0000.000
28A459ARG11.0150.99929.889-0.038-0.0380.0000.0000.0000.000
29A460ARG10.9530.97027.173-0.046-0.0460.0000.0000.0000.000
30A461LYS10.9710.98529.302-0.018-0.0180.0000.0000.0000.000
31A462TRP0-0.001-0.00824.084-0.003-0.0030.0000.0000.0000.000
32A463LYS10.8170.89322.234-0.008-0.0080.0000.0000.0000.000
33A464HIS00.0270.01522.2870.0110.0110.0000.0000.0000.000
34A465TYR00.0340.01617.351-0.012-0.0120.0000.0000.0000.000
35A466TRP00.0680.04513.5820.0400.0400.0000.0000.0000.000
36A467VAL0-0.001-0.01712.851-0.015-0.0150.0000.0000.0000.000
37A468SER00.0050.0058.835-0.044-0.0440.0000.0000.0000.000
38A469LEU00.0130.0087.868-0.024-0.0240.0000.0000.0000.000
39A470LYS10.9360.9753.2470.6580.8500.028-0.058-0.1620.000
40A471GLY0-0.0040.0023.5090.2200.8090.049-0.197-0.4420.000
41A472CYS0-0.0020.0104.028-1.342-1.1920.009-0.072-0.0870.000
42A473THR0-0.0010.0016.391-0.333-0.3330.0000.0000.0000.000
43A474LEU00.0080.0197.5900.0420.0420.0000.0000.0000.000
44A475PHE0-0.006-0.0195.673-0.122-0.1220.0000.0000.0000.000
45A476PHE0-0.007-0.00810.7650.0020.0020.0000.0000.0000.000
46A477TYR00.0370.00210.327-0.052-0.0520.0000.0000.0000.000
47A478GLU-1-0.761-0.87415.9760.0030.0030.0000.0000.0000.000
48A479SER0-0.029-0.01819.733-0.011-0.0110.0000.0000.0000.000
49A480ASP-1-0.922-0.95121.155-0.035-0.0350.0000.0000.0000.000
50A481GLY0-0.0160.00418.958-0.011-0.0110.0000.0000.0000.000
51A490ILE00.031-0.00413.465-0.019-0.0190.0000.0000.0000.000
52A491PRO0-0.074-0.01910.7470.0300.0300.0000.0000.0000.000
53A492LYS10.9190.97713.7930.0240.0240.0000.0000.0000.000
54A493HIS0-0.012-0.01215.3970.0050.0050.0000.0000.0000.000
55A494ALA00.0330.00810.784-0.019-0.0190.0000.0000.0000.000
56A495VAL0-0.0130.00411.945-0.006-0.0060.0000.0000.0000.000
57A496TRP00.0070.0189.7240.0430.0430.0000.0000.0000.000
58A497VAL00.004-0.01710.566-0.054-0.0540.0000.0000.0000.000
59A498GLU-1-0.884-0.95010.6730.5950.5950.0000.0000.0000.000
60A499ASN0-0.027-0.01212.477-0.096-0.0960.0000.0000.0000.000
61A500SER00.0310.01014.786-0.081-0.0810.0000.0000.0000.000
62A501ILE0-0.0070.01816.9250.0220.0220.0000.0000.0000.000
63A502VAL0-0.011-0.00816.632-0.017-0.0170.0000.0000.0000.000
64A503GLN0-0.006-0.01919.853-0.021-0.0210.0000.0000.0000.000
65A504ALA00.0410.01923.425-0.005-0.0050.0000.0000.0000.000
66A505VAL0-0.043-0.03325.280-0.004-0.0040.0000.0000.0000.000
67A506PRO00.030-0.00127.947-0.006-0.0060.0000.0000.0000.000
68A507GLU-1-0.893-0.92730.3380.0840.0840.0000.0000.0000.000
69A508HIS0-0.056-0.03229.151-0.008-0.0080.0000.0000.0000.000
70A509PRO00.0390.02031.733-0.003-0.0030.0000.0000.0000.000
71A510LYS10.9000.93733.196-0.046-0.0460.0000.0000.0000.000
72A511LYS10.8190.91327.362-0.070-0.0700.0000.0000.0000.000
73A512ASP-1-0.756-0.84729.8220.0780.0780.0000.0000.0000.000
74A513PHE00.006-0.01525.0160.0030.0030.0000.0000.0000.000
75A514VAL0-0.0010.00724.3640.0070.0070.0000.0000.0000.000
76A515PHE00.0130.00417.6370.0070.0070.0000.0000.0000.000
77A516CYS0-0.068-0.02922.294-0.010-0.0100.0000.0000.0000.000
78A517LEU00.0100.02114.8510.0140.0140.0000.0000.0000.000
79A518SER00.0420.01319.493-0.024-0.0240.0000.0000.0000.000
80A519ASN00.005-0.01316.8610.0220.0220.0000.0000.0000.000
81A520SER00.0420.01516.279-0.030-0.0300.0000.0000.0000.000
82A521LEU00.0020.00417.812-0.019-0.0190.0000.0000.0000.000
83A522GLY00.0540.04121.075-0.021-0.0210.0000.0000.0000.000
84A523ASP-1-0.881-0.93520.5040.1240.1240.0000.0000.0000.000
85A524ALA00.003-0.01321.3850.0220.0220.0000.0000.0000.000
86A525PHE0-0.039-0.01818.426-0.024-0.0240.0000.0000.0000.000
87A526LEU0-0.021-0.00421.4400.0130.0130.0000.0000.0000.000
88A527PHE00.014-0.00616.263-0.008-0.0080.0000.0000.0000.000
89A528GLN00.0010.00621.421-0.005-0.0050.0000.0000.0000.000
90A529THR0-0.0060.00720.381-0.013-0.0130.0000.0000.0000.000
91A530THR00.0270.00122.257-0.005-0.0050.0000.0000.0000.000
92A531SER00.0430.01124.067-0.006-0.0060.0000.0000.0000.000
93A532GLN00.017-0.01624.3180.0080.0080.0000.0000.0000.000
94A533THR00.0600.03123.0340.0090.0090.0000.0000.0000.000
95A534GLU-1-0.775-0.86318.6960.1970.1970.0000.0000.0000.000
96A535LEU0-0.065-0.03019.6680.0320.0320.0000.0000.0000.000
97A536GLU-1-0.839-0.91120.2440.1970.1970.0000.0000.0000.000
98A537ASN00.0040.00417.5930.0490.0490.0000.0000.0000.000
99A538TRP0-0.050-0.03512.2290.0950.0950.0000.0000.0000.000
100A539ILE0-0.024-0.00915.6510.0720.0720.0000.0000.0000.000
101A540THR00.0110.00416.0810.0500.0500.0000.0000.0000.000
102A541ALA0-0.0030.00512.0810.0930.0930.0000.0000.0000.000
103A542ILE00.013-0.00611.6660.2150.2150.0000.0000.0000.000
104A543HIS00.0440.02212.7280.0850.0850.0000.0000.0000.000
105A544SER00.0510.02712.0180.0000.0000.0000.0000.0000.000
106A545ALA0-0.056-0.0188.5350.1700.1700.0000.0000.0000.000
107A546CYS0-0.049-0.0229.3740.0640.0640.0000.0000.0000.000
108A547ALA00.0180.02011.917-0.057-0.0570.0000.0000.0000.000
109A548THR0-0.047-0.0457.4360.0450.0450.0000.0000.0000.000
110A549ALA00.000-0.0048.619-0.078-0.0780.0000.0000.0000.000
111A550VAL00.0160.0149.570-0.157-0.1570.0000.0000.0000.000
112A551ALA00.002-0.01112.157-0.088-0.0880.0000.0000.0000.000
113A552ARG10.9650.9734.021-1.691-1.623-0.001-0.010-0.0570.000
114A553HIS00.0130.03511.053-0.079-0.0790.0000.0000.0000.000
115A554HIS10.8010.88313.450-0.328-0.3280.0000.0000.0000.000
116A555HIS00.0210.02213.702-0.024-0.0240.0000.0000.0000.000
117A556LYS10.8220.90014.317-0.225-0.2250.0000.0000.0000.000
118A557GLU-1-0.818-0.90613.2110.2580.2580.0000.0000.0000.000
119A558ASP-1-0.864-0.93713.9830.3240.3240.0000.0000.0000.000
120A559THR00.021-0.00812.9790.0260.0260.0000.0000.0000.000
121A560LEU00.0210.01515.360-0.017-0.0170.0000.0000.0000.000
122A561ARG10.9620.98518.610-0.182-0.1820.0000.0000.0000.000
123A562LEU0-0.0050.01616.213-0.024-0.0240.0000.0000.0000.000
124A563LEU00.004-0.00116.411-0.019-0.0190.0000.0000.0000.000
125A564LYS10.9490.98519.589-0.238-0.2380.0000.0000.0000.000
126A565SER0-0.0010.00622.406-0.023-0.0230.0000.0000.0000.000
127A566GLU-1-0.847-0.90419.6590.1940.1940.0000.0000.0000.000
128A567ILE0-0.014-0.00622.246-0.011-0.0110.0000.0000.0000.000
129A568LYS10.9921.01224.813-0.128-0.1280.0000.0000.0000.000
130A569LYS10.8240.89023.455-0.185-0.1850.0000.0000.0000.000
131A570LEU0-0.020-0.00523.599-0.010-0.0100.0000.0000.0000.000
132A571GLU-1-0.834-0.91027.7060.1420.1420.0000.0000.0000.000
133A572GLN0-0.001-0.00530.541-0.007-0.0070.0000.0000.0000.000
134A573LYS10.9390.98426.004-0.150-0.1500.0000.0000.0000.000
135A574ILE00.002-0.00229.305-0.006-0.0060.0000.0000.0000.000
136A575ASP-1-0.827-0.89133.0990.0770.0770.0000.0000.0000.000
137A576MET0-0.002-0.00535.508-0.007-0.0070.0000.0000.0000.000
138A577ASP-1-0.820-0.94234.3090.0850.0850.0000.0000.0000.000
139A578GLU-1-0.928-0.95936.5910.0840.0840.0000.0000.0000.000
140A579LYS10.7910.88038.758-0.080-0.0800.0000.0000.0000.000
141A580MET00.0150.00939.993-0.005-0.0050.0000.0000.0000.000
142A581LYS10.8150.91039.065-0.072-0.0720.0000.0000.0000.000
143A582LYS10.8900.94740.905-0.076-0.0760.0000.0000.0000.000
144A583MET0-0.033-0.00944.647-0.003-0.0030.0000.0000.0000.000
145A584GLY00.0280.01345.015-0.003-0.0030.0000.0000.0000.000
146A585GLU-1-0.847-0.94543.7990.0600.0600.0000.0000.0000.000
147A586MET0-0.019-0.00347.620-0.002-0.0020.0000.0000.0000.000
148A587GLN0-0.054-0.02849.317-0.002-0.0020.0000.0000.0000.000
149A588LEU0-0.014-0.00948.013-0.002-0.0020.0000.0000.0000.000
150A589SER0-0.048-0.00751.778-0.002-0.0020.0000.0000.0000.000
151A590SER0-0.002-0.00754.839-0.001-0.0010.0000.0000.0000.000
152A591VAL0-0.048-0.01152.199-0.001-0.0010.0000.0000.0000.000
153A592THR00.0180.00355.4350.0000.0000.0000.0000.0000.000
154A593ASP-1-0.804-0.89755.0000.0310.0310.0000.0000.0000.000
155A594SER00.0250.00954.7160.0010.0010.0000.0000.0000.000
156A595LYS10.9460.97647.913-0.036-0.0360.0000.0000.0000.000
157A596ALA00.0260.00650.5850.0020.0020.0000.0000.0000.000
158A597ALA00.0060.00549.9830.0020.0020.0000.0000.0000.000
159A598ALA0-0.020-0.01749.0420.0020.0020.0000.0000.0000.000
160A599THR0-0.037-0.02445.4580.0020.0020.0000.0000.0000.000
161A600ILE00.0110.00844.8900.0030.0030.0000.0000.0000.000
162A601LEU0-0.017-0.00744.7310.0030.0030.0000.0000.0000.000
163A602ASP-1-0.893-0.94942.2390.0510.0510.0000.0000.0000.000
164A603GLN0-0.0050.00037.6260.0020.0020.0000.0000.0000.000
165A604ILE0-0.0170.00339.8940.0050.0050.0000.0000.0000.000
166A605PHE00.009-0.01039.9170.0040.0040.0000.0000.0000.000
167A606VAL0-0.028-0.00435.3310.0050.0050.0000.0000.0000.000
168A607TRP00.013-0.00235.3910.0040.0040.0000.0000.0000.000
169A608GLU-1-0.930-0.95835.5730.0770.0770.0000.0000.0000.000
170A609GLN0-0.027-0.02133.0850.0070.0070.0000.0000.0000.000
171A610ASN00.0240.00831.0770.0090.0090.0000.0000.0000.000
172A611LEU00.0260.02030.6150.0110.0110.0000.0000.0000.000
173A612GLU-1-0.745-0.79631.1620.1090.1090.0000.0000.0000.000
174A613GLN0-0.009-0.00524.9540.0000.0000.0000.0000.0000.000
175A614PHE0-0.011-0.01026.4610.0170.0170.0000.0000.0000.000
176A615GLN00.0450.02227.1460.0200.0200.0000.0000.0000.000
177A616MET0-0.0370.00824.2810.0160.0160.0000.0000.0000.000
178A617ASP-1-0.839-0.92022.2990.2380.2380.0000.0000.0000.000
179A618LEU0-0.040-0.00622.6500.0250.0250.0000.0000.0000.000
180A619PHE00.002-0.01023.9680.0120.0120.0000.0000.0000.000
181A620ARG10.8350.91017.265-0.303-0.3030.0000.0000.0000.000
182A621PHE00.021-0.00218.0220.0360.0360.0000.0000.0000.000
183A622ARG10.8980.92920.576-0.151-0.1510.0000.0000.0000.000
184A623CYS0-0.038-0.01020.240-0.006-0.0060.0000.0000.0000.000
185A624TYR0-0.055-0.04616.2750.0370.0370.0000.0000.0000.000
186A625LEU0-0.0070.00817.6010.0330.0330.0000.0000.0000.000
187A626ALA0-0.0080.00520.030-0.003-0.0030.0000.0000.0000.000
188A627SER0-0.072-0.05116.3870.0240.0240.0000.0000.0000.000
189A628LEU0-0.001-0.01614.0390.0170.0170.0000.0000.0000.000
190A629GLN0-0.024-0.02217.745-0.028-0.0280.0000.0000.0000.000
191A630GLY00.0230.03120.697-0.025-0.0250.0000.0000.0000.000
192A631GLY0-0.0310.00022.403-0.024-0.0240.0000.0000.0000.000
193A632GLU-1-0.927-0.96324.1350.1560.1560.0000.0000.0000.000
194A633LEU0-0.031-0.03321.5640.0110.0110.0000.0000.0000.000
195A634PRO00.0030.01224.217-0.019-0.0190.0000.0000.0000.000
196A635ASN00.024-0.00727.319-0.002-0.0020.0000.0000.0000.000
197A636PRO00.0670.02328.163-0.003-0.0030.0000.0000.0000.000
198A637LYS10.9820.98230.114-0.097-0.0970.0000.0000.0000.000
199A638ARG10.9560.97532.562-0.111-0.1110.0000.0000.0000.000
200A639LEU00.0440.03527.138-0.004-0.0040.0000.0000.0000.000
201A640LEU00.006-0.00531.363-0.004-0.0040.0000.0000.0000.000
202A641ALA0-0.051-0.01433.470-0.006-0.0060.0000.0000.0000.000
203A642PHE00.0010.00132.906-0.004-0.0040.0000.0000.0000.000
204A643ALA0-0.047-0.00433.9130.0000.0000.0000.0000.0000.000
205A644SER00.0270.00034.999-0.008-0.0080.0000.0000.0000.000
206A645ARG11.0130.99037.442-0.055-0.0550.0000.0000.0000.000
207A646PRO00.0390.00337.523-0.001-0.0010.0000.0000.0000.000
208A647THR0-0.036-0.03732.846-0.001-0.0010.0000.0000.0000.000
209A648LYS10.9130.94235.573-0.082-0.0820.0000.0000.0000.000
210A649VAL0-0.0020.00437.735-0.002-0.0020.0000.0000.0000.000
211A650ALA0-0.029-0.01034.477-0.002-0.0020.0000.0000.0000.000
212A651MET0-0.0130.00231.590-0.001-0.0010.0000.0000.0000.000
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