FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 4JJQN

Calculation Name: 4JNF-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 4JNF

Chain ID: A

ChEMBL ID:
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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:


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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2142274.438223
FMO2-HF: Nuclear repulsion 2060874.070082
FMO2-HF: Total energy -81400.368141
FMO2-MP2: Total energy -81636.201145


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.
-1.0951.350.001-1.31-1.1350.002
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 : -0.006 / 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].
3A390LEU0-0.009-0.0073.614-0.7961.6490.001-1.310-1.1350.002
4A391LEU00.0030.0086.076-0.353-0.3530.0000.0000.0000.000
5A392LEU0-0.009-0.0189.2820.2100.2100.0000.0000.0000.000
6A393ASP-1-0.877-0.91712.1350.0230.0230.0000.0000.0000.000
7A394VAL0-0.018-0.02215.1590.0240.0240.0000.0000.0000.000
8A395THR0-0.012-0.00917.934-0.013-0.0130.0000.0000.0000.000
9A396PRO00.0020.00721.171-0.017-0.0170.0000.0000.0000.000
10A397LEU0-0.036-0.03122.122-0.017-0.0170.0000.0000.0000.000
11A398SER0-0.044-0.05525.2790.0140.0140.0000.0000.0000.000
12A399LEU0-0.002-0.00426.0310.0020.0020.0000.0000.0000.000
13A400GLY00.0290.00829.2210.0020.0020.0000.0000.0000.000
14A401ILE0-0.0100.00532.5660.0020.0020.0000.0000.0000.000
15A402GLU-1-0.829-0.90636.374-0.030-0.0300.0000.0000.0000.000
16A403THR0-0.062-0.03839.0210.0030.0030.0000.0000.0000.000
17A404MET00.0270.00141.599-0.002-0.0020.0000.0000.0000.000
18A405GLY00.0460.02744.468-0.001-0.0010.0000.0000.0000.000
19A406GLY0-0.0040.02343.340-0.002-0.0020.0000.0000.0000.000
20A407VAL00.000-0.00338.345-0.004-0.0040.0000.0000.0000.000
21A408MET0-0.035-0.00231.2490.0040.0040.0000.0000.0000.000
22A409THR0-0.053-0.02235.133-0.002-0.0020.0000.0000.0000.000
23A410THR0-0.025-0.02128.4590.0040.0040.0000.0000.0000.000
24A411LEU0-0.030-0.01830.6540.0020.0020.0000.0000.0000.000
25A412ILE0-0.021-0.00824.3600.0070.0070.0000.0000.0000.000
26A413ALA00.0500.02623.979-0.007-0.0070.0000.0000.0000.000
27A414LYS10.9350.99421.8280.1700.1700.0000.0000.0000.000
28A415ASN0-0.048-0.03517.1780.0050.0050.0000.0000.0000.000
29A416THR0-0.041-0.01218.0060.0060.0060.0000.0000.0000.000
30A417THR0-0.017-0.01314.650-0.021-0.0210.0000.0000.0000.000
31A418ILE0-0.0110.02617.391-0.008-0.0080.0000.0000.0000.000
32A419PRO00.011-0.00117.5030.0330.0330.0000.0000.0000.000
33A420THR0-0.027-0.01620.5410.0010.0010.0000.0000.0000.000
34A421LYS10.8290.89223.026-0.063-0.0630.0000.0000.0000.000
35A422HIS00.0220.01623.678-0.004-0.0040.0000.0000.0000.000
36A423SER0-0.030-0.02028.8390.0000.0000.0000.0000.0000.000
37A424GLN00.0180.01632.622-0.002-0.0020.0000.0000.0000.000
38A425VAL0-0.042-0.02035.4640.0020.0020.0000.0000.0000.000
39A426PHE00.0430.02536.430-0.003-0.0030.0000.0000.0000.000
40A427SER00.0470.01141.6230.0030.0030.0000.0000.0000.000
41A428MET0-0.037-0.00245.219-0.001-0.0010.0000.0000.0000.000
42A429GLY00.0290.00847.4430.0000.0000.0000.0000.0000.000
43A430GLY00.0020.00649.327-0.002-0.0020.0000.0000.0000.000
44A435ALA00.0030.00149.9180.0010.0010.0000.0000.0000.000
45A436VAL00.0120.00944.134-0.001-0.0010.0000.0000.0000.000
46A437THR0-0.023-0.02543.8060.0020.0020.0000.0000.0000.000
47A438ILE0-0.047-0.02138.363-0.001-0.0010.0000.0000.0000.000
48A439HIS0-0.015-0.00639.5820.0010.0010.0000.0000.0000.000
49A440VAL00.0130.00233.513-0.002-0.0020.0000.0000.0000.000
50A441LEU0-0.0020.00334.311-0.002-0.0020.0000.0000.0000.000
51A442GLN00.0330.00226.7980.0030.0030.0000.0000.0000.000
52A443GLY00.024-0.00229.664-0.002-0.0020.0000.0000.0000.000
53A444GLU-1-0.758-0.86826.899-0.089-0.0890.0000.0000.0000.000
54A445ARG10.7470.86130.4250.0670.0670.0000.0000.0000.000
55A446LYS10.8660.91133.2240.0610.0610.0000.0000.0000.000
56A447ARG10.9260.98836.5840.0560.0560.0000.0000.0000.000
57A448ALA00.009-0.00238.076-0.003-0.0030.0000.0000.0000.000
58A449ALA0-0.006-0.01338.6330.0000.0000.0000.0000.0000.000
59A450ASP-1-0.861-0.91437.541-0.057-0.0570.0000.0000.0000.000
60A451ASN0-0.032-0.03933.513-0.011-0.0110.0000.0000.0000.000
61A452LYS10.8740.93132.7400.0410.0410.0000.0000.0000.000
62A453SER00.001-0.02234.3480.0040.0040.0000.0000.0000.000
63A454LEU0-0.031-0.02330.7950.0000.0000.0000.0000.0000.000
64A455GLY00.0180.00335.0520.0040.0040.0000.0000.0000.000
65A456GLN0-0.025-0.01038.128-0.001-0.0010.0000.0000.0000.000
66A457PHE0-0.022-0.00537.7190.0020.0020.0000.0000.0000.000
67A458ASN00.0470.02842.630-0.003-0.0030.0000.0000.0000.000
68A459LEU0-0.040-0.02043.6360.0020.0020.0000.0000.0000.000
69A460ASP-1-0.831-0.91146.0820.0000.0000.0000.0000.0000.000
70A461GLY0-0.013-0.00449.9010.0010.0010.0000.0000.0000.000
71A462ILE0-0.044-0.01347.6720.0020.0020.0000.0000.0000.000
72A463ASN00.0350.02051.118-0.002-0.0020.0000.0000.0000.000
73A464PRO00.0320.00851.5160.0010.0010.0000.0000.0000.000
74A465ALA00.0250.02949.1380.0010.0010.0000.0000.0000.000
75A466PRO00.0170.00951.257-0.001-0.0010.0000.0000.0000.000
76A467ARG10.9110.92851.971-0.001-0.0010.0000.0000.0000.000
77A468GLY00.0290.03451.597-0.001-0.0010.0000.0000.0000.000
78A469MET0-0.032-0.00546.166-0.001-0.0010.0000.0000.0000.000
79A470PRO00.015-0.00343.0060.0000.0000.0000.0000.0000.000
80A471GLN0-0.042-0.04644.6520.0010.0010.0000.0000.0000.000
81A472ILE0-0.0040.00541.3400.0030.0030.0000.0000.0000.000
82A473GLU-1-0.833-0.91537.4650.0210.0210.0000.0000.0000.000
83A474VAL00.0050.01235.2900.0020.0020.0000.0000.0000.000
84A475THR0-0.011-0.01632.0890.0020.0020.0000.0000.0000.000
85A476PHE00.007-0.00529.374-0.002-0.0020.0000.0000.0000.000
86A477ASP-1-0.844-0.91227.7540.0640.0640.0000.0000.0000.000
87A478ILE00.0140.01323.620-0.009-0.0090.0000.0000.0000.000
88A479ASP-1-0.738-0.84924.0450.0770.0770.0000.0000.0000.000
89A480ALA00.012-0.02219.979-0.002-0.0020.0000.0000.0000.000
90A481ASP-1-0.923-0.94620.2900.1040.1040.0000.0000.0000.000
91A482GLY00.0050.00722.771-0.015-0.0150.0000.0000.0000.000
92A483ILE0-0.091-0.04723.215-0.018-0.0180.0000.0000.0000.000
93A484LEU00.0000.00927.0520.0060.0060.0000.0000.0000.000
94A485HIS10.7610.84128.413-0.047-0.0470.0000.0000.0000.000
95A486VAL00.0160.01331.2260.0000.0000.0000.0000.0000.000
96A487SER0-0.069-0.05433.9480.0010.0010.0000.0000.0000.000
97A488ALA00.0280.01536.944-0.002-0.0020.0000.0000.0000.000
98A489LYS10.8520.92438.213-0.024-0.0240.0000.0000.0000.000
99A490ASP-1-0.705-0.81941.9250.0070.0070.0000.0000.0000.000
100A491LYS10.8200.88639.301-0.016-0.0160.0000.0000.0000.000
101A492ASN0-0.045-0.01245.0060.0010.0010.0000.0000.0000.000
102A493SER0-0.070-0.05648.1360.0000.0000.0000.0000.0000.000
103A494GLY0-0.0100.00145.6350.0010.0010.0000.0000.0000.000
104A495LYS10.8470.92145.235-0.008-0.0080.0000.0000.0000.000
105A496GLU-1-0.801-0.89638.5290.0250.0250.0000.0000.0000.000
106A497GLN0-0.0090.01841.8300.0020.0020.0000.0000.0000.000
107A498LYS10.9580.95737.045-0.031-0.0310.0000.0000.0000.000
108A499ILE0-0.0080.01235.575-0.001-0.0010.0000.0000.0000.000
109A500THR0-0.016-0.00531.9710.0050.0050.0000.0000.0000.000
110A501ILE0-0.0210.00131.354-0.002-0.0020.0000.0000.0000.000
111A502LYS10.9860.98931.2490.0040.0040.0000.0000.0000.000
112A503ALA00.1080.04627.648-0.004-0.0040.0000.0000.0000.000
113A504SER0-0.018-0.01729.399-0.005-0.0050.0000.0000.0000.000
114A505SER0-0.079-0.03332.071-0.003-0.0030.0000.0000.0000.000
115A506GLY0-0.0030.01929.173-0.002-0.0020.0000.0000.0000.000
116A507LEU0-0.027-0.00528.9500.0000.0000.0000.0000.0000.000
117A508ASN0-0.015-0.03127.380-0.009-0.0090.0000.0000.0000.000
118A509GLU-1-0.879-0.94521.184-0.156-0.1560.0000.0000.0000.000
119A510ASP-1-0.826-0.91125.247-0.141-0.1410.0000.0000.0000.000
120A511GLU-1-0.849-0.91227.915-0.067-0.0670.0000.0000.0000.000
121A512ILE0-0.023-0.00623.8110.0000.0000.0000.0000.0000.000
122A513GLN00.003-0.00822.765-0.017-0.0170.0000.0000.0000.000
123A514LYS10.7230.85926.7640.0870.0870.0000.0000.0000.000
124A515MET00.0270.04929.0850.0010.0010.0000.0000.0000.000
125A516VAL0-0.012-0.00624.7780.0030.0030.0000.0000.0000.000
126A517ARG10.8810.92128.0630.1440.1440.0000.0000.0000.000
127A518ASP-1-0.798-0.88230.109-0.088-0.0880.0000.0000.0000.000
128A519ALA0-0.001-0.00830.2130.0070.0070.0000.0000.0000.000
129A520GLU-1-0.950-0.98026.209-0.169-0.1690.0000.0000.0000.000
130A521ALA0-0.054-0.02131.0420.0030.0030.0000.0000.0000.000
131A522ASN0-0.056-0.04134.3980.0100.0100.0000.0000.0000.000
132A523ALA00.0320.03032.6990.0070.0070.0000.0000.0000.000
133A524GLU-1-0.787-0.88634.810-0.067-0.0670.0000.0000.0000.000
134A525ALA0-0.020-0.01137.8830.0050.0050.0000.0000.0000.000
135A526ASP-1-0.751-0.86136.596-0.060-0.0600.0000.0000.0000.000
136A527ARG10.8540.90936.4070.0700.0700.0000.0000.0000.000
137A528LYS10.8200.90238.3430.0690.0690.0000.0000.0000.000
138A529PHE0-0.0110.00340.6090.0030.0030.0000.0000.0000.000
139A530GLU-1-0.788-0.87736.740-0.048-0.0480.0000.0000.0000.000
140A531GLU-1-0.825-0.90140.252-0.049-0.0490.0000.0000.0000.000
141A532LEU0-0.0330.02142.5480.0030.0030.0000.0000.0000.000
142A533VAL00.0050.00943.5640.0030.0030.0000.0000.0000.000
143A534GLN0-0.021-0.01438.4880.0030.0030.0000.0000.0000.000
144A535THR0-0.018-0.03044.2220.0030.0030.0000.0000.0000.000
145A536ARG10.7920.86947.3400.0320.0320.0000.0000.0000.000
146A537ASN0-0.016-0.01844.4030.0020.0020.0000.0000.0000.000
147A538GLN0-0.008-0.00446.0250.0030.0030.0000.0000.0000.000
148A539GLY00.0610.01148.7620.0020.0020.0000.0000.0000.000
149A540ASP-1-0.887-0.94151.669-0.015-0.0150.0000.0000.0000.000
150A541HIS00.0090.00550.2100.0010.0010.0000.0000.0000.000
151A542LEU0-0.0110.00152.2850.0010.0010.0000.0000.0000.000
152A543LEU0-0.0070.01554.3670.0010.0010.0000.0000.0000.000
153A544HIS0-0.043-0.03454.6370.0020.0020.0000.0000.0000.000
154A545SER0-0.046-0.01954.8020.0010.0010.0000.0000.0000.000
155A546THR0-0.013-0.02156.9110.0010.0010.0000.0000.0000.000
156A547ARG10.8990.92659.6350.0130.0130.0000.0000.0000.000
157A548LYS10.8350.92057.9360.0040.0040.0000.0000.0000.000
158A549GLN00.0260.00757.9910.0000.0000.0000.0000.0000.000
159A550VAL0-0.0130.00062.0910.0010.0010.0000.0000.0000.000
160A551GLU-1-0.872-0.93664.983-0.006-0.0060.0000.0000.0000.000
161A552GLU-1-0.895-0.94161.516-0.002-0.0020.0000.0000.0000.000
162A553ALA0-0.017-0.00165.8390.0010.0010.0000.0000.0000.000
163A554GLY00.0330.01767.5640.0010.0010.0000.0000.0000.000
164A555ASP-1-0.911-0.96770.616-0.004-0.0040.0000.0000.0000.000
165A556LYS10.7640.88068.7190.0030.0030.0000.0000.0000.000
166A557LEU0-0.036-0.02267.2010.0000.0000.0000.0000.0000.000
167A558PRO0-0.0130.00670.6220.0000.0000.0000.0000.0000.000
168A559ALA00.0390.02072.2400.0000.0000.0000.0000.0000.000
169A560ASP-1-0.900-0.93973.400-0.008-0.0080.0000.0000.0000.000
170A561ASP-1-0.802-0.91568.460-0.008-0.0080.0000.0000.0000.000
171A562LYS10.8260.90468.4950.0070.0070.0000.0000.0000.000
172A563THR0-0.031-0.02868.980-0.001-0.0010.0000.0000.0000.000
173A564ALA0-0.0090.00467.604-0.001-0.0010.0000.0000.0000.000
174A565ILE00.0290.00763.348-0.001-0.0010.0000.0000.0000.000
175A566GLU-1-0.815-0.91264.553-0.011-0.0110.0000.0000.0000.000
176A567SER0-0.059-0.02065.979-0.001-0.0010.0000.0000.0000.000
177A568ALA00.0080.00461.967-0.001-0.0010.0000.0000.0000.000
178A569LEU0-0.024-0.00360.345-0.001-0.0010.0000.0000.0000.000
179A570THR0-0.018-0.01961.393-0.001-0.0010.0000.0000.0000.000
180A571ALA0-0.027-0.00561.898-0.001-0.0010.0000.0000.0000.000
181A572LEU00.0230.00654.806-0.001-0.0010.0000.0000.0000.000
182A573GLU-1-0.763-0.86457.497-0.016-0.0160.0000.0000.0000.000
183A574THR0-0.072-0.03759.075-0.001-0.0010.0000.0000.0000.000
184A575ALA0-0.006-0.00755.994-0.001-0.0010.0000.0000.0000.000
185A576LEU0-0.0130.00652.743-0.002-0.0020.0000.0000.0000.000
186A577LYS10.7850.87954.0980.0180.0180.0000.0000.0000.000
187A578GLY0-0.0150.00355.326-0.001-0.0010.0000.0000.0000.000
188A579GLU-1-0.837-0.92449.996-0.035-0.0350.0000.0000.0000.000
189A580ASP-1-0.877-0.93550.191-0.035-0.0350.0000.0000.0000.000
190A581LYS10.8900.94444.1060.0440.0440.0000.0000.0000.000
191A582ALA00.0410.02749.6050.0020.0020.0000.0000.0000.000
192A583ALA0-0.011-0.00751.5650.0020.0020.0000.0000.0000.000
193A584ILE0-0.011-0.00350.9380.0020.0020.0000.0000.0000.000
194A585GLU-1-0.886-0.96247.314-0.031-0.0310.0000.0000.0000.000
195A586ALA0-0.010-0.00551.9950.0020.0020.0000.0000.0000.000
196A587LYS10.7750.86955.3420.0220.0220.0000.0000.0000.000
197A588MET0-0.0150.00750.4040.0010.0010.0000.0000.0000.000
198A589GLN0-0.025-0.00651.5330.0020.0020.0000.0000.0000.000
199A590GLU-1-0.801-0.88256.055-0.018-0.0180.0000.0000.0000.000
200A591LEU00.0120.00257.7440.0010.0010.0000.0000.0000.000
201A592ALA0-0.0060.00556.2270.0010.0010.0000.0000.0000.000
202A593GLN0-0.047-0.02458.3720.0010.0010.0000.0000.0000.000
203A594VAL0-0.035-0.00960.9310.0010.0010.0000.0000.0000.000
204A595SER00.003-0.00860.2180.0010.0010.0000.0000.0000.000
205A596GLN0-0.061-0.03561.3660.0000.0000.0000.0000.0000.000
206A597LYS10.9680.99662.8470.0060.0060.0000.0000.0000.000
207A598LEU00.0110.00261.7040.0010.0010.0000.0000.0000.000
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