FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: QVVKY

Calculation Name: 4JNF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4JNF

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6Y8

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2136845.875248
FMO2-HF: Nuclear repulsion 2055446.65595
FMO2-HF: Total energy -81399.219298
FMO2-MP2: Total energy -81634.961148


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:388:SER)


Summations of interaction energy for fragment #1(A:388:SER)
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.
-1.8711.166-0.002-1.604-1.4310.004
Interaction energy analysis for fragmet #1(A:388:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / 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].
3A390LEU0-0.012-0.0163.556-1.3791.658-0.002-1.604-1.4310.004
4A391LEU00.0020.0106.094-0.292-0.2920.0000.0000.0000.000
5A392LEU0-0.023-0.0168.9250.0560.0560.0000.0000.0000.000
6A393ASP-1-0.850-0.90811.313-0.058-0.0580.0000.0000.0000.000
7A394VAL0-0.045-0.03014.388-0.004-0.0040.0000.0000.0000.000
8A395THR0-0.020-0.01317.050-0.001-0.0010.0000.0000.0000.000
9A396PRO00.0410.02620.281-0.007-0.0070.0000.0000.0000.000
10A397LEU0-0.051-0.03821.598-0.004-0.0040.0000.0000.0000.000
11A398SER0-0.074-0.06324.7710.0000.0000.0000.0000.0000.000
12A399LEU0-0.002-0.00125.5780.0040.0040.0000.0000.0000.000
13A400GLY00.0310.00528.709-0.001-0.0010.0000.0000.0000.000
14A401ILE0-0.0130.00232.0240.0020.0020.0000.0000.0000.000
15A402GLU-1-0.857-0.91735.774-0.032-0.0320.0000.0000.0000.000
16A403THR0-0.053-0.03938.4370.0010.0010.0000.0000.0000.000
17A404MET00.019-0.00240.8770.0000.0000.0000.0000.0000.000
18A405GLY00.0320.01243.815-0.001-0.0010.0000.0000.0000.000
19A406GLY00.0030.01742.6080.0000.0000.0000.0000.0000.000
20A407VAL00.0000.00337.840-0.001-0.0010.0000.0000.0000.000
21A408MET0-0.0390.00630.4690.0010.0010.0000.0000.0000.000
22A409THR0-0.032-0.00734.522-0.001-0.0010.0000.0000.0000.000
23A410THR0-0.007-0.01427.9880.0020.0020.0000.0000.0000.000
24A411LEU0-0.048-0.02930.0350.0010.0010.0000.0000.0000.000
25A412ILE0-0.019-0.00223.804-0.001-0.0010.0000.0000.0000.000
26A413ALA00.0340.01123.3440.0010.0010.0000.0000.0000.000
27A414LYS10.9681.00021.3750.1010.1010.0000.0000.0000.000
28A415ASN0-0.034-0.01717.5070.0020.0020.0000.0000.0000.000
29A416THR0-0.042-0.02817.728-0.008-0.0080.0000.0000.0000.000
30A417THR0-0.008-0.01214.5690.0030.0030.0000.0000.0000.000
31A418ILE0-0.0120.02616.9660.0000.0000.0000.0000.0000.000
32A419PRO00.009-0.00417.0720.0020.0020.0000.0000.0000.000
33A420THR0-0.019-0.02020.110-0.005-0.0050.0000.0000.0000.000
34A421LYS10.9460.96522.5660.0460.0460.0000.0000.0000.000
35A422HIS00.0100.02223.2710.0000.0000.0000.0000.0000.000
36A423SER0-0.021-0.01028.3120.0020.0020.0000.0000.0000.000
37A424GLN00.0300.02532.048-0.003-0.0030.0000.0000.0000.000
38A425VAL0-0.047-0.02434.7620.0020.0020.0000.0000.0000.000
39A426PHE00.0320.01635.6400.0000.0000.0000.0000.0000.000
40A427SER00.027-0.00240.8220.0010.0010.0000.0000.0000.000
41A428MET0-0.0340.00644.330-0.001-0.0010.0000.0000.0000.000
42A429GLY00.0380.01546.7410.0000.0000.0000.0000.0000.000
43A430GLY0-0.0140.00448.8220.0000.0000.0000.0000.0000.000
44A435ALA00.001-0.00849.1170.0000.0000.0000.0000.0000.000
45A436VAL00.0140.00943.822-0.001-0.0010.0000.0000.0000.000
46A437THR0-0.006-0.00742.9660.0010.0010.0000.0000.0000.000
47A438ILE0-0.035-0.01337.615-0.001-0.0010.0000.0000.0000.000
48A439HIS0-0.004-0.00538.7500.0000.0000.0000.0000.0000.000
49A440VAL00.006-0.00532.744-0.001-0.0010.0000.0000.0000.000
50A441LEU0-0.0050.00333.7080.0010.0010.0000.0000.0000.000
51A442GLN00.0640.02326.2720.0010.0010.0000.0000.0000.000
52A443GLY00.005-0.00529.2090.0020.0020.0000.0000.0000.000
53A444GLU-1-0.774-0.87726.623-0.073-0.0730.0000.0000.0000.000
54A445ARG10.8720.93529.9050.0460.0460.0000.0000.0000.000
55A446LYS10.9730.99232.0100.0530.0530.0000.0000.0000.000
56A447ARG10.9430.98736.0360.0350.0350.0000.0000.0000.000
57A448ALA00.0320.00637.435-0.001-0.0010.0000.0000.0000.000
58A449ALA0-0.036-0.02737.945-0.001-0.0010.0000.0000.0000.000
59A450ASP-1-0.911-0.94436.703-0.037-0.0370.0000.0000.0000.000
60A451ASN0-0.060-0.03932.925-0.005-0.0050.0000.0000.0000.000
61A452LYS10.9190.97632.1980.0390.0390.0000.0000.0000.000
62A453SER0-0.019-0.02433.9420.0000.0000.0000.0000.0000.000
63A454LEU0-0.046-0.04029.9450.0000.0000.0000.0000.0000.000
64A455GLY00.0090.00434.4530.0010.0010.0000.0000.0000.000
65A456GLN0-0.018-0.01437.4890.0000.0000.0000.0000.0000.000
66A457PHE0-0.028-0.00837.3120.0010.0010.0000.0000.0000.000
67A458ASN00.0760.05042.123-0.001-0.0010.0000.0000.0000.000
68A459LEU0-0.034-0.01443.0120.0000.0000.0000.0000.0000.000
69A460ASP-1-0.874-0.94145.601-0.020-0.0200.0000.0000.0000.000
70A461GLY0-0.029-0.01949.3740.0000.0000.0000.0000.0000.000
71A462ILE0-0.043-0.01547.1620.0000.0000.0000.0000.0000.000
72A463ASN00.0050.00150.5430.0000.0000.0000.0000.0000.000
73A464PRO00.0300.00750.715-0.001-0.0010.0000.0000.0000.000
74A465ALA00.0070.01648.5880.0010.0010.0000.0000.0000.000
75A466PRO00.0370.01650.6330.0000.0000.0000.0000.0000.000
76A467ARG10.9030.92951.3370.0170.0170.0000.0000.0000.000
77A468GLY00.0290.02851.1190.0000.0000.0000.0000.0000.000
78A469MET0-0.039-0.00546.009-0.001-0.0010.0000.0000.0000.000
79A470PRO00.031-0.00142.7730.0000.0000.0000.0000.0000.000
80A471GLN0-0.039-0.04244.1710.0000.0000.0000.0000.0000.000
81A472ILE0-0.0080.00940.6150.0000.0000.0000.0000.0000.000
82A473GLU-1-0.940-0.96736.535-0.034-0.0340.0000.0000.0000.000
83A474VAL00.0030.00534.4140.0010.0010.0000.0000.0000.000
84A475THR0-0.007-0.01331.204-0.002-0.0020.0000.0000.0000.000
85A476PHE0-0.012-0.01228.6480.0020.0020.0000.0000.0000.000
86A477ASP-1-0.907-0.96927.233-0.044-0.0440.0000.0000.0000.000
87A478ILE00.0020.00822.7610.0020.0020.0000.0000.0000.000
88A479ASP-1-0.733-0.87423.548-0.039-0.0390.0000.0000.0000.000
89A480ALA00.000-0.02419.776-0.002-0.0020.0000.0000.0000.000
90A481ASP-1-0.927-0.94220.096-0.028-0.0280.0000.0000.0000.000
91A482GLY0-0.026-0.01222.4050.0000.0000.0000.0000.0000.000
92A483ILE0-0.084-0.03722.877-0.001-0.0010.0000.0000.0000.000
93A484LEU0-0.0140.00226.622-0.001-0.0010.0000.0000.0000.000
94A485HIS10.7730.88228.2130.0370.0370.0000.0000.0000.000
95A486VAL00.0330.02531.028-0.002-0.0020.0000.0000.0000.000
96A487SER0-0.019-0.01333.5400.0010.0010.0000.0000.0000.000
97A488ALA00.0240.01536.355-0.001-0.0010.0000.0000.0000.000
98A489LYS10.9760.98938.9800.0290.0290.0000.0000.0000.000
99A490ASP-1-0.727-0.85641.315-0.023-0.0230.0000.0000.0000.000
100A491LYS10.8930.93640.2790.0300.0300.0000.0000.0000.000
101A492ASN0-0.031-0.00644.2940.0010.0010.0000.0000.0000.000
102A493SER0-0.067-0.04247.7250.0010.0010.0000.0000.0000.000
103A494GLY0-0.0010.00244.9010.0010.0010.0000.0000.0000.000
104A495LYS10.8680.93844.7050.0190.0190.0000.0000.0000.000
105A496GLU-1-0.923-0.97438.552-0.028-0.0280.0000.0000.0000.000
106A497GLN0-0.0180.01041.2730.0010.0010.0000.0000.0000.000
107A498LYS10.9580.96336.5100.0240.0240.0000.0000.0000.000
108A499ILE0-0.0070.01135.2960.0010.0010.0000.0000.0000.000
109A500THR0-0.017-0.01831.811-0.002-0.0020.0000.0000.0000.000
110A501ILE00.0010.00630.7350.0010.0010.0000.0000.0000.000
111A502LYS10.9600.97931.0500.0250.0250.0000.0000.0000.000
112A503ALA00.1200.04927.516-0.001-0.0010.0000.0000.0000.000
113A504SER0-0.047-0.02729.187-0.002-0.0020.0000.0000.0000.000
114A505SER0-0.041-0.01531.8050.0010.0010.0000.0000.0000.000
115A506GLY0-0.008-0.00428.8600.0000.0000.0000.0000.0000.000
116A507LEU0-0.031-0.01628.4110.0020.0020.0000.0000.0000.000
117A508ASN00.0080.00527.277-0.005-0.0050.0000.0000.0000.000
118A509GLU-1-0.872-0.95720.992-0.080-0.0800.0000.0000.0000.000
119A510ASP-1-0.892-0.94325.281-0.063-0.0630.0000.0000.0000.000
120A511GLU-1-0.946-0.97827.998-0.044-0.0440.0000.0000.0000.000
121A512ILE0-0.009-0.00423.393-0.001-0.0010.0000.0000.0000.000
122A513GLN00.007-0.00422.106-0.005-0.0050.0000.0000.0000.000
123A514LYS10.8210.90326.3270.0450.0450.0000.0000.0000.000
124A515MET00.0110.04428.4240.0010.0010.0000.0000.0000.000
125A516VAL0-0.011-0.01324.2090.0000.0000.0000.0000.0000.000
126A517ARG10.9680.98327.3300.0670.0670.0000.0000.0000.000
127A518ASP-1-0.837-0.91229.422-0.046-0.0460.0000.0000.0000.000
128A519ALA0-0.013-0.01329.7120.0030.0030.0000.0000.0000.000
129A520GLU-1-0.986-0.98626.003-0.083-0.0830.0000.0000.0000.000
130A521ALA0-0.047-0.02030.7110.0030.0030.0000.0000.0000.000
131A522ASN0-0.069-0.03833.8980.0060.0060.0000.0000.0000.000
132A523ALA00.0730.05132.4820.0020.0020.0000.0000.0000.000
133A524GLU-1-0.975-0.99634.488-0.040-0.0400.0000.0000.0000.000
134A525ALA0-0.020-0.01737.6220.0020.0020.0000.0000.0000.000
135A526ASP-1-0.763-0.88035.312-0.044-0.0440.0000.0000.0000.000
136A527ARG10.9400.97936.1600.0420.0420.0000.0000.0000.000
137A528LYS10.9190.95338.0000.0350.0350.0000.0000.0000.000
138A529PHE0-0.043-0.01239.7620.0020.0020.0000.0000.0000.000
139A530GLU-1-0.866-0.94636.365-0.043-0.0430.0000.0000.0000.000
140A531GLU-1-0.883-0.95039.299-0.037-0.0370.0000.0000.0000.000
141A532LEU0-0.034-0.00742.1070.0010.0010.0000.0000.0000.000
142A533VAL00.0000.00742.8800.0020.0020.0000.0000.0000.000
143A534GLN0-0.019-0.01038.2260.0020.0020.0000.0000.0000.000
144A535THR00.007-0.00143.6740.0010.0010.0000.0000.0000.000
145A536ARG10.9000.93146.8250.0260.0260.0000.0000.0000.000
146A537ASN00.001-0.00244.0880.0020.0020.0000.0000.0000.000
147A538GLN0-0.036-0.00845.3390.0000.0000.0000.0000.0000.000
148A539GLY00.0580.00948.4390.0010.0010.0000.0000.0000.000
149A540ASP-1-0.904-0.95850.849-0.021-0.0210.0000.0000.0000.000
150A541HIS00.0130.00749.7580.0010.0010.0000.0000.0000.000
151A542LEU0-0.019-0.00651.8430.0010.0010.0000.0000.0000.000
152A543LEU0-0.0030.01054.0940.0010.0010.0000.0000.0000.000
153A544HIS0-0.035-0.02454.1570.0010.0010.0000.0000.0000.000
154A545SER0-0.055-0.01454.3810.0010.0010.0000.0000.0000.000
155A546THR00.020-0.00856.4800.0010.0010.0000.0000.0000.000
156A547ARG10.9080.93159.2470.0170.0170.0000.0000.0000.000
157A548LYS10.9070.97056.8690.0180.0180.0000.0000.0000.000
158A549GLN00.012-0.00357.9590.0000.0000.0000.0000.0000.000
159A550VAL0-0.028-0.00961.7910.0010.0010.0000.0000.0000.000
160A551GLU-1-0.958-0.97864.398-0.013-0.0130.0000.0000.0000.000
161A552GLU-1-0.983-1.00061.148-0.015-0.0150.0000.0000.0000.000
162A553ALA0-0.054-0.01265.3410.0000.0000.0000.0000.0000.000
163A554GLY00.0290.01267.1680.0000.0000.0000.0000.0000.000
164A555ASP-1-0.922-0.97070.271-0.011-0.0110.0000.0000.0000.000
165A556LYS10.8480.92969.1290.0120.0120.0000.0000.0000.000
166A557LEU0-0.033-0.01267.0160.0000.0000.0000.0000.0000.000
167A558PRO00.0000.01270.1280.0000.0000.0000.0000.0000.000
168A559ALA00.0370.00471.8220.0000.0000.0000.0000.0000.000
169A560ASP-1-0.889-0.94773.119-0.012-0.0120.0000.0000.0000.000
170A561ASP-1-0.817-0.92368.077-0.013-0.0130.0000.0000.0000.000
171A562LYS10.9160.96368.1560.0120.0120.0000.0000.0000.000
172A563THR0-0.018-0.00968.7610.0000.0000.0000.0000.0000.000
173A564ALA0-0.002-0.00267.2590.0000.0000.0000.0000.0000.000
174A565ILE00.0300.00363.2050.0000.0000.0000.0000.0000.000
175A566GLU-1-0.913-0.95964.300-0.014-0.0140.0000.0000.0000.000
176A567SER0-0.032-0.01665.6310.0000.0000.0000.0000.0000.000
177A568ALA00.0000.00661.7460.0000.0000.0000.0000.0000.000
178A569LEU0-0.010-0.00759.975-0.001-0.0010.0000.0000.0000.000
179A570THR0-0.0070.00460.9910.0000.0000.0000.0000.0000.000
180A571ALA0-0.022-0.01761.6870.0000.0000.0000.0000.0000.000
181A572LEU00.0180.01254.547-0.001-0.0010.0000.0000.0000.000
182A573GLU-1-0.887-0.93657.127-0.017-0.0170.0000.0000.0000.000
183A574THR0-0.062-0.03958.1390.0000.0000.0000.0000.0000.000
184A575ALA00.001-0.00255.6860.0000.0000.0000.0000.0000.000
185A576LEU0-0.033-0.00352.232-0.001-0.0010.0000.0000.0000.000
186A577LYS10.8940.95653.5040.0170.0170.0000.0000.0000.000
187A578GLY0-0.0020.01854.9890.0000.0000.0000.0000.0000.000
188A579GLU-1-0.968-0.99650.382-0.025-0.0250.0000.0000.0000.000
189A580ASP-1-0.884-0.93250.231-0.023-0.0230.0000.0000.0000.000
190A581LYS10.9420.95644.0970.0300.0300.0000.0000.0000.000
191A582ALA00.0550.03149.4510.0000.0000.0000.0000.0000.000
192A583ALA0-0.0100.00251.0330.0010.0010.0000.0000.0000.000
193A584ILE0-0.013-0.00950.7800.0010.0010.0000.0000.0000.000
194A585GLU-1-0.909-0.96347.173-0.026-0.0260.0000.0000.0000.000
195A586ALA0-0.0050.00051.8710.0000.0000.0000.0000.0000.000
196A587LYS10.9230.96055.1380.0180.0180.0000.0000.0000.000
197A588MET0-0.032-0.00450.0140.0000.0000.0000.0000.0000.000
198A589GLN0-0.026-0.01552.0830.0010.0010.0000.0000.0000.000
199A590GLU-1-0.914-0.95355.855-0.017-0.0170.0000.0000.0000.000
200A591LEU00.001-0.00157.5680.0010.0010.0000.0000.0000.000
201A592ALA0-0.0110.00356.1330.0000.0000.0000.0000.0000.000
202A593GLN0-0.040-0.02458.2810.0000.0000.0000.0000.0000.000
203A594VAL0-0.038-0.00160.7770.0010.0010.0000.0000.0000.000
204A595SER0-0.013-0.02060.1370.0000.0000.0000.0000.0000.000
205A596GLN00.0200.01159.5360.0000.0000.0000.0000.0000.000
206A597LYS10.9831.00462.7520.0130.0130.0000.0000.0000.000
207A598LEU00.003-0.00261.4650.0000.0000.0000.0000.0000.000
208A599MET0-0.017-0.01158.2170.0000.0000.0000.0000.0000.000
209A600GLU-1-0.939-0.97860.996-0.014-0.0140.0000.0000.0000.000
210A601ILE0-0.047-0.02863.4470.0000.0000.0000.0000.0000.000
211A602ALA0-0.0140.00060.0130.0000.0000.0000.0000.0000.000
212A603GLN0-0.103-0.04556.8990.0000.0000.0000.0000.0000.000
213A604GLN0-0.074-0.01660.9640.0000.0000.0000.0000.0000.000