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: ZV2JN

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2859850.036404
FMO2-HF: Nuclear repulsion 2767337.91656
FMO2-HF: Total energy -92512.119844
FMO2-MP2: Total energy -92780.880441


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.
-3.278-1.5540.562-0.817-1.47-0.002
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 : -0.004
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].
3A434VAL00.013-0.0123.8590.3321.045-0.002-0.348-0.3630.001
4A435ARG10.8740.9536.437-1.086-1.0860.0000.0000.0000.000
5A436LYS10.8580.9128.164-0.084-0.0840.0000.0000.0000.000
6A437ALA0-0.016-0.00510.116-0.112-0.1120.0000.0000.0000.000
7A438GLY00.0530.02112.6280.0570.0570.0000.0000.0000.000
8A439ALA00.0080.01716.211-0.022-0.0220.0000.0000.0000.000
9A440LEU0-0.013-0.00415.9070.0230.0230.0000.0000.0000.000
10A441ALA0-0.0270.00119.621-0.016-0.0160.0000.0000.0000.000
11A442VAL00.000-0.01518.3140.0140.0140.0000.0000.0000.000
12A443LYS10.8510.92021.419-0.009-0.0090.0000.0000.0000.000
13A444ASN00.0010.00521.8810.0030.0030.0000.0000.0000.000
14A445PHE0-0.012-0.01423.764-0.003-0.0030.0000.0000.0000.000
15A446LEU00.0220.01724.770-0.001-0.0010.0000.0000.0000.000
16A447VAL0-0.049-0.02624.125-0.001-0.0010.0000.0000.0000.000
17A448HIS0-0.0040.01124.388-0.006-0.0060.0000.0000.0000.000
18A449LYS10.8900.94522.883-0.017-0.0170.0000.0000.0000.000
19A450LYS11.0000.99026.774-0.009-0.0090.0000.0000.0000.000
20A451ASN00.0140.00029.967-0.002-0.0020.0000.0000.0000.000
21A452LYS10.8100.92326.624-0.067-0.0670.0000.0000.0000.000
22A453LYS10.8530.90630.125-0.031-0.0310.0000.0000.0000.000
23A454VAL00.0210.02226.967-0.002-0.0020.0000.0000.0000.000
24A455GLU-1-0.855-0.90428.9210.0220.0220.0000.0000.0000.000
25A456SER00.0380.00228.9120.0040.0040.0000.0000.0000.000
26A457ALA0-0.043-0.00826.680-0.005-0.0050.0000.0000.0000.000
27A458THR00.0200.01528.748-0.003-0.0030.0000.0000.0000.000
28A459ARG11.0221.00429.6930.0000.0000.0000.0000.0000.000
29A460ARG10.9520.97627.2630.0180.0180.0000.0000.0000.000
30A461LYS10.9780.98129.3540.0400.0400.0000.0000.0000.000
31A462TRP00.0050.00523.609-0.002-0.0020.0000.0000.0000.000
32A463LYS10.8110.88522.0940.0980.0980.0000.0000.0000.000
33A464HIS00.0510.02722.1710.0060.0060.0000.0000.0000.000
34A465TYR00.0300.01117.230-0.006-0.0060.0000.0000.0000.000
35A466TRP00.0670.04913.6790.0480.0480.0000.0000.0000.000
36A467VAL0-0.017-0.01712.591-0.033-0.0330.0000.0000.0000.000
37A468SER00.007-0.0028.782-0.086-0.0860.0000.0000.0000.000
38A469LEU00.0030.0067.442-0.059-0.0590.0000.0000.0000.000
39A470LYS10.9270.9723.2841.1961.4010.028-0.062-0.1710.000
40A471GLY00.005-0.0012.927-0.3140.5070.471-0.507-0.786-0.003
41A472CYS0-0.044-0.0033.316-0.410-0.4640.0660.104-0.1160.000
42A473THR00.0160.0155.995-0.125-0.1250.0000.0000.0000.000
43A474LEU0-0.0050.0197.175-0.119-0.1190.0000.0000.0000.000
44A475PHE00.012-0.0105.595-0.071-0.0710.0000.0000.0000.000
45A476PHE0-0.019-0.01510.5980.0050.0050.0000.0000.0000.000
46A477TYR00.0520.00910.319-0.072-0.0720.0000.0000.0000.000
47A478GLU-1-0.766-0.87915.881-0.097-0.0970.0000.0000.0000.000
48A479SER0-0.065-0.05819.704-0.014-0.0140.0000.0000.0000.000
49A480ASP-1-0.879-0.91221.550-0.105-0.1050.0000.0000.0000.000
50A481GLY0-0.038-0.00319.343-0.007-0.0070.0000.0000.0000.000
51A490ILE00.0430.00513.424-0.034-0.0340.0000.0000.0000.000
52A491PRO0-0.081-0.02210.6920.0370.0370.0000.0000.0000.000
53A492LYS10.9160.96913.8640.1400.1400.0000.0000.0000.000
54A493HIS00.004-0.00515.3890.0290.0290.0000.0000.0000.000
55A494ALA00.0190.00110.682-0.050-0.0500.0000.0000.0000.000
56A495VAL0-0.0100.00011.6430.0230.0230.0000.0000.0000.000
57A496TRP00.0050.0089.485-0.012-0.0120.0000.0000.0000.000
58A497VAL0-0.004-0.01010.108-0.025-0.0250.0000.0000.0000.000
59A498GLU-1-0.812-0.90610.5330.4870.4870.0000.0000.0000.000
60A499ASN0-0.029-0.01311.979-0.086-0.0860.0000.0000.0000.000
61A500SER00.000-0.00414.379-0.063-0.0630.0000.0000.0000.000
62A501ILE00.0020.02516.6370.0280.0280.0000.0000.0000.000
63A502VAL0-0.025-0.01516.234-0.025-0.0250.0000.0000.0000.000
64A503GLN00.007-0.01019.504-0.003-0.0030.0000.0000.0000.000
65A504ALA00.0530.02323.000-0.008-0.0080.0000.0000.0000.000
66A505VAL0-0.058-0.04224.819-0.001-0.0010.0000.0000.0000.000
67A506PRO00.0460.01427.639-0.007-0.0070.0000.0000.0000.000
68A507GLU-1-0.902-0.93930.0860.0510.0510.0000.0000.0000.000
69A508HIS0-0.030-0.01828.787-0.006-0.0060.0000.0000.0000.000
70A509PRO00.0430.01331.422-0.003-0.0030.0000.0000.0000.000
71A510LYS10.8740.93232.883-0.009-0.0090.0000.0000.0000.000
72A511LYS10.8100.91126.728-0.005-0.0050.0000.0000.0000.000
73A512ASP-1-0.764-0.85729.8240.0330.0330.0000.0000.0000.000
74A513PHE00.031-0.00124.932-0.002-0.0020.0000.0000.0000.000
75A514VAL0-0.027-0.00524.1760.0000.0000.0000.0000.0000.000
76A515PHE00.0060.00117.3520.0110.0110.0000.0000.0000.000
77A516CYS0-0.050-0.01922.022-0.013-0.0130.0000.0000.0000.000
78A517LEU00.0040.01914.6670.0150.0150.0000.0000.0000.000
79A518SER00.0340.00819.298-0.021-0.0210.0000.0000.0000.000
80A519ASN00.0490.01216.7030.0260.0260.0000.0000.0000.000
81A520SER00.0440.01215.637-0.022-0.0220.0000.0000.0000.000
82A521LEU0-0.031-0.00917.186-0.009-0.0090.0000.0000.0000.000
83A522GLY00.0670.03820.685-0.013-0.0130.0000.0000.0000.000
84A523ASP-1-0.877-0.93720.4600.0320.0320.0000.0000.0000.000
85A524ALA0-0.010-0.01821.1490.0180.0180.0000.0000.0000.000
86A525PHE0-0.035-0.01918.443-0.019-0.0190.0000.0000.0000.000
87A526LEU0-0.0060.00821.1460.0130.0130.0000.0000.0000.000
88A527PHE0-0.003-0.01216.101-0.014-0.0140.0000.0000.0000.000
89A528GLN00.0190.00921.349-0.001-0.0010.0000.0000.0000.000
90A529THR0-0.0120.00319.966-0.020-0.0200.0000.0000.0000.000
91A530THR00.0400.00922.2140.0050.0050.0000.0000.0000.000
92A531SER00.0440.02223.8240.0020.0020.0000.0000.0000.000
93A532GLN00.012-0.01423.930-0.002-0.0020.0000.0000.0000.000
94A533THR00.0760.04122.7650.0060.0060.0000.0000.0000.000
95A534GLU-1-0.797-0.86218.4320.0690.0690.0000.0000.0000.000
96A535LEU0-0.051-0.02519.2360.0120.0120.0000.0000.0000.000
97A536GLU-1-0.842-0.91219.7060.1320.1320.0000.0000.0000.000
98A537ASN0-0.020-0.00816.9970.0530.0530.0000.0000.0000.000
99A538TRP0-0.036-0.02511.8830.0610.0610.0000.0000.0000.000
100A539ILE0-0.012-0.00915.0090.0470.0470.0000.0000.0000.000
101A540THR00.0120.00316.1970.0450.0450.0000.0000.0000.000
102A541ALA0-0.0030.00711.6080.0850.0850.0000.0000.0000.000
103A542ILE00.016-0.00511.3470.1570.1570.0000.0000.0000.000
104A543HIS00.0540.02512.2820.0660.0660.0000.0000.0000.000
105A544SER00.0520.02012.3190.0330.0330.0000.0000.0000.000
106A545ALA0-0.063-0.0248.1880.2060.2060.0000.0000.0000.000
107A546CYS0-0.043-0.0219.6140.1000.1000.0000.0000.0000.000
108A547ALA00.0160.01612.147-0.010-0.0100.0000.0000.0000.000
109A548THR0-0.029-0.0217.7780.0760.0760.0000.0000.0000.000
110A549ALA00.0060.0079.1200.0340.0340.0000.0000.0000.000
111A550VAL00.0190.00910.013-0.114-0.1140.0000.0000.0000.000
112A551ALA0-0.001-0.00712.343-0.075-0.0750.0000.0000.0000.000
113A552ARG10.9630.9764.573-2.705-2.666-0.001-0.004-0.0340.000
114A553HIS00.0290.03511.170-0.079-0.0790.0000.0000.0000.000
115A554HIS10.7890.87413.432-0.379-0.3790.0000.0000.0000.000
116A555HIS00.0260.02713.827-0.012-0.0120.0000.0000.0000.000
117A556LYS10.7990.87214.236-0.358-0.3580.0000.0000.0000.000
118A557GLU-1-0.790-0.87813.2550.4570.4570.0000.0000.0000.000
119A558ASP-1-0.812-0.91414.3830.3980.3980.0000.0000.0000.000
120A559THR0-0.010-0.02713.567-0.009-0.0090.0000.0000.0000.000
121A560LEU00.0120.01015.984-0.037-0.0370.0000.0000.0000.000
122A561ARG10.9090.97119.112-0.271-0.2710.0000.0000.0000.000
123A562LEU0-0.0140.00116.613-0.030-0.0300.0000.0000.0000.000
124A563LEU00.0220.00417.043-0.028-0.0280.0000.0000.0000.000
125A564LYS10.9230.96620.270-0.282-0.2820.0000.0000.0000.000
126A565SER00.0220.01822.835-0.026-0.0260.0000.0000.0000.000
127A566GLU-1-0.844-0.89220.0480.2130.2130.0000.0000.0000.000
128A567ILE0-0.022-0.00922.843-0.016-0.0160.0000.0000.0000.000
129A568LYS11.0021.01725.313-0.146-0.1460.0000.0000.0000.000
130A569LYS10.8110.88023.801-0.212-0.2120.0000.0000.0000.000
131A570LEU0-0.030-0.00823.812-0.012-0.0120.0000.0000.0000.000
132A571GLU-1-0.802-0.90028.0720.1410.1410.0000.0000.0000.000
133A572GLN0-0.008-0.01630.985-0.005-0.0050.0000.0000.0000.000
134A573LYS10.9300.97626.392-0.149-0.1490.0000.0000.0000.000
135A574ILE0-0.016-0.00229.922-0.007-0.0070.0000.0000.0000.000
136A575ASP-1-0.811-0.89433.6130.0760.0760.0000.0000.0000.000
137A576MET00.0110.01235.751-0.007-0.0070.0000.0000.0000.000
138A577ASP-1-0.774-0.91434.6490.0790.0790.0000.0000.0000.000
139A578GLU-1-0.919-0.96236.9350.0720.0720.0000.0000.0000.000
140A579LYS10.7970.89239.035-0.080-0.0800.0000.0000.0000.000
141A580MET00.008-0.00140.110-0.005-0.0050.0000.0000.0000.000
142A581LYS10.8090.90239.283-0.061-0.0610.0000.0000.0000.000
143A582LYS10.8780.93341.022-0.069-0.0690.0000.0000.0000.000
144A583MET0-0.025-0.00744.939-0.003-0.0030.0000.0000.0000.000
145A584GLY00.0270.01445.324-0.003-0.0030.0000.0000.0000.000
146A585GLU-1-0.855-0.95243.9810.0510.0510.0000.0000.0000.000
147A586MET0-0.0110.00447.754-0.002-0.0020.0000.0000.0000.000
148A587GLN0-0.031-0.01049.676-0.002-0.0020.0000.0000.0000.000
149A588LEU0-0.023-0.01548.011-0.002-0.0020.0000.0000.0000.000
150A589SER0-0.068-0.02851.928-0.002-0.0020.0000.0000.0000.000
151A590SER0-0.014-0.01255.078-0.001-0.0010.0000.0000.0000.000
152A591VAL0-0.041-0.01052.6640.0000.0000.0000.0000.0000.000
153A592THR00.0290.00455.8300.0000.0000.0000.0000.0000.000
154A593ASP-1-0.800-0.88754.9340.0260.0260.0000.0000.0000.000
155A594SER00.0100.00754.8490.0010.0010.0000.0000.0000.000
156A595LYS10.8940.94347.155-0.032-0.0320.0000.0000.0000.000
157A596ALA00.0190.01450.5610.0020.0020.0000.0000.0000.000
158A597ALA00.0320.01650.1570.0020.0020.0000.0000.0000.000
159A598ALA0-0.010-0.01249.0280.0020.0020.0000.0000.0000.000
160A599THR0-0.022-0.02345.7380.0010.0010.0000.0000.0000.000
161A600ILE0-0.0130.00845.1870.0030.0030.0000.0000.0000.000
162A601LEU0-0.018-0.01044.9410.0030.0030.0000.0000.0000.000
163A602ASP-1-0.881-0.95042.9140.0400.0400.0000.0000.0000.000
164A603GLN00.008-0.00337.7210.0020.0020.0000.0000.0000.000
165A604ILE0-0.0090.01040.1520.0040.0040.0000.0000.0000.000
166A605PHE00.004-0.00839.8340.0030.0030.0000.0000.0000.000
167A606VAL0-0.0150.00235.5060.0040.0040.0000.0000.0000.000
168A607TRP00.0100.00035.5670.0040.0040.0000.0000.0000.000
169A608GLU-1-0.896-0.94935.9440.0620.0620.0000.0000.0000.000
170A609GLN0-0.068-0.03732.9580.0040.0040.0000.0000.0000.000
171A610ASN00.0050.00331.4740.0060.0060.0000.0000.0000.000
172A611LEU00.0010.01431.0060.0100.0100.0000.0000.0000.000
173A612GLU-1-0.726-0.79430.9160.0810.0810.0000.0000.0000.000
174A613GLN0-0.0130.00324.806-0.003-0.0030.0000.0000.0000.000
175A614PHE0-0.001-0.01526.7850.0160.0160.0000.0000.0000.000
176A615GLN00.0590.02227.6280.0190.0190.0000.0000.0000.000
177A616MET0-0.0350.01324.2020.0130.0130.0000.0000.0000.000
178A617ASP-1-0.805-0.90922.5410.1970.1970.0000.0000.0000.000
179A618LEU0-0.0500.00022.9130.0240.0240.0000.0000.0000.000
180A619PHE00.002-0.01623.9770.0130.0130.0000.0000.0000.000
181A620ARG10.8120.89517.587-0.245-0.2450.0000.0000.0000.000
182A621PHE00.014-0.00718.4440.0330.0330.0000.0000.0000.000
183A622ARG10.8870.92820.899-0.134-0.1340.0000.0000.0000.000
184A623CYS0-0.049-0.01420.267-0.004-0.0040.0000.0000.0000.000
185A624TYR0-0.049-0.03616.6250.0310.0310.0000.0000.0000.000
186A625LEU0-0.0070.00418.1650.0310.0310.0000.0000.0000.000
187A626ALA0-0.0020.01020.6230.0020.0020.0000.0000.0000.000
188A627SER0-0.052-0.04016.8470.0170.0170.0000.0000.0000.000
189A628LEU0-0.026-0.03114.5280.0230.0230.0000.0000.0000.000
190A629GLN00.002-0.00118.228-0.006-0.0060.0000.0000.0000.000
191A630GLY00.0140.02820.968-0.022-0.0220.0000.0000.0000.000
192A631GLY0-0.0120.00622.610-0.023-0.0230.0000.0000.0000.000
193A632GLU-1-0.934-0.96924.0320.1320.1320.0000.0000.0000.000
194A633LEU0-0.018-0.02221.1670.0130.0130.0000.0000.0000.000
195A634PRO0-0.0040.00324.160-0.016-0.0160.0000.0000.0000.000
196A635ASN00.0520.00527.368-0.006-0.0060.0000.0000.0000.000
197A636PRO00.0510.01127.558-0.003-0.0030.0000.0000.0000.000
198A637LYS10.9720.97929.623-0.070-0.0700.0000.0000.0000.000
199A638ARG10.9670.98332.557-0.094-0.0940.0000.0000.0000.000
200A639LEU00.0280.02926.902-0.003-0.0030.0000.0000.0000.000
201A640LEU0-0.011-0.01730.779-0.004-0.0040.0000.0000.0000.000
202A641ALA0-0.0190.00233.037-0.006-0.0060.0000.0000.0000.000
203A642PHE00.0210.00132.986-0.004-0.0040.0000.0000.0000.000
204A643ALA0-0.0450.00933.078-0.001-0.0010.0000.0000.0000.000
205A644SER00.0340.00134.436-0.006-0.0060.0000.0000.0000.000
206A645ARG11.0020.99637.010-0.039-0.0390.0000.0000.0000.000
207A646PRO00.0330.00136.853-0.002-0.0020.0000.0000.0000.000
208A647THR0-0.040-0.03732.207-0.003-0.0030.0000.0000.0000.000
209A648LYS10.8770.92634.923-0.065-0.0650.0000.0000.0000.000
210A649VAL00.0020.00436.965-0.003-0.0030.0000.0000.0000.000
211A650ALA0-0.025-0.01033.995-0.003-0.0030.0000.0000.0000.000
212A651MET0-0.056-0.02730.816-0.001-0.0010.0000.0000.0000.000
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