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: KGGK3

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2138572.671983
FMO2-HF: Nuclear repulsion 2057172.526572
FMO2-HF: Total energy -81400.145411
FMO2-MP2: Total energy -81635.929044


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.
-1.741.4090.009-1.692-1.4650.003
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 : 0.002
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].
3A390LEU0-0.010-0.0133.426-1.3721.7770.009-1.692-1.4650.003
4A391LEU00.0050.0105.928-0.350-0.3500.0000.0000.0000.000
5A392LEU0-0.015-0.0099.2500.1910.1910.0000.0000.0000.000
6A393ASP-1-0.870-0.92311.7000.0070.0070.0000.0000.0000.000
7A394VAL0-0.039-0.03014.6810.0240.0240.0000.0000.0000.000
8A395THR0-0.008-0.00117.412-0.016-0.0160.0000.0000.0000.000
9A396PRO00.0210.01620.650-0.018-0.0180.0000.0000.0000.000
10A397LEU0-0.029-0.03121.991-0.016-0.0160.0000.0000.0000.000
11A398SER0-0.060-0.05725.1460.0140.0140.0000.0000.0000.000
12A399LEU0-0.007-0.00425.8280.0030.0030.0000.0000.0000.000
13A400GLY00.0330.00729.0520.0020.0020.0000.0000.0000.000
14A401ILE0-0.0130.00132.3500.0030.0030.0000.0000.0000.000
15A402GLU-1-0.843-0.91236.103-0.034-0.0340.0000.0000.0000.000
16A403THR0-0.054-0.03038.6420.0030.0030.0000.0000.0000.000
17A404MET00.0250.00141.189-0.002-0.0020.0000.0000.0000.000
18A405GLY00.0470.01944.123-0.001-0.0010.0000.0000.0000.000
19A406GLY00.0000.01842.948-0.002-0.0020.0000.0000.0000.000
20A407VAL00.0010.00238.187-0.004-0.0040.0000.0000.0000.000
21A408MET0-0.0310.00631.0680.0040.0040.0000.0000.0000.000
22A409THR0-0.039-0.01634.806-0.003-0.0030.0000.0000.0000.000
23A410THR0-0.018-0.01928.3210.0040.0040.0000.0000.0000.000
24A411LEU0-0.046-0.02730.3120.0030.0030.0000.0000.0000.000
25A412ILE0-0.027-0.01024.1380.0060.0060.0000.0000.0000.000
26A413ALA00.0380.01423.655-0.007-0.0070.0000.0000.0000.000
27A414LYS10.9240.98721.4760.1890.1890.0000.0000.0000.000
28A415ASN0-0.037-0.02117.3370.0050.0050.0000.0000.0000.000
29A416THR0-0.038-0.02318.0360.0010.0010.0000.0000.0000.000
30A417THR0-0.011-0.01414.696-0.019-0.0190.0000.0000.0000.000
31A418ILE0-0.0180.02717.256-0.004-0.0040.0000.0000.0000.000
32A419PRO00.014-0.00417.3530.0320.0320.0000.0000.0000.000
33A420THR0-0.012-0.01220.4130.0010.0010.0000.0000.0000.000
34A421LYS10.8350.89022.846-0.058-0.0580.0000.0000.0000.000
35A422HIS00.0120.01723.476-0.004-0.0040.0000.0000.0000.000
36A423SER0-0.022-0.01228.5880.0000.0000.0000.0000.0000.000
37A424GLN00.0150.01432.330-0.002-0.0020.0000.0000.0000.000
38A425VAL0-0.043-0.02435.0230.0020.0020.0000.0000.0000.000
39A426PHE00.0330.02035.799-0.003-0.0030.0000.0000.0000.000
40A427SER00.0420.00741.0730.0030.0030.0000.0000.0000.000
41A428MET0-0.041-0.00344.600-0.001-0.0010.0000.0000.0000.000
42A429GLY00.0440.01647.0110.0000.0000.0000.0000.0000.000
43A430GLY0-0.0160.00249.109-0.001-0.0010.0000.0000.0000.000
44A435ALA0-0.002-0.00649.4820.0010.0010.0000.0000.0000.000
45A436VAL00.0190.01043.972-0.001-0.0010.0000.0000.0000.000
46A437THR0-0.014-0.01343.3820.0020.0020.0000.0000.0000.000
47A438ILE0-0.036-0.01337.962-0.002-0.0020.0000.0000.0000.000
48A439HIS0-0.0030.00339.1650.0010.0010.0000.0000.0000.000
49A440VAL00.007-0.00533.095-0.002-0.0020.0000.0000.0000.000
50A441LEU00.0020.00934.054-0.002-0.0020.0000.0000.0000.000
51A442GLN00.0400.00826.5540.0030.0030.0000.0000.0000.000
52A443GLY00.005-0.00729.593-0.002-0.0020.0000.0000.0000.000
53A444GLU-1-0.782-0.89126.661-0.104-0.1040.0000.0000.0000.000
54A445ARG10.7770.86830.1310.0760.0760.0000.0000.0000.000
55A446LYS10.8730.91532.9500.0690.0690.0000.0000.0000.000
56A447ARG10.9320.98736.1980.0610.0610.0000.0000.0000.000
57A448ALA00.0320.00537.793-0.003-0.0030.0000.0000.0000.000
58A449ALA0-0.030-0.02138.318-0.001-0.0010.0000.0000.0000.000
59A450ASP-1-0.861-0.92336.996-0.064-0.0640.0000.0000.0000.000
60A451ASN0-0.046-0.03133.298-0.012-0.0120.0000.0000.0000.000
61A452LYS10.8720.93632.5910.0460.0460.0000.0000.0000.000
62A453SER0-0.005-0.02634.3280.0030.0030.0000.0000.0000.000
63A454LEU0-0.028-0.03130.3230.0000.0000.0000.0000.0000.000
64A455GLY00.005-0.00334.8380.0040.0040.0000.0000.0000.000
65A456GLN0-0.022-0.01337.863-0.001-0.0010.0000.0000.0000.000
66A457PHE0-0.024-0.00737.5440.0020.0020.0000.0000.0000.000
67A458ASN00.0770.05442.463-0.003-0.0030.0000.0000.0000.000
68A459LEU0-0.041-0.01943.4290.0020.0020.0000.0000.0000.000
69A460ASP-1-0.880-0.94545.902-0.002-0.0020.0000.0000.0000.000
70A461GLY0-0.019-0.01049.6760.0010.0010.0000.0000.0000.000
71A462ILE0-0.031-0.01247.3790.0020.0020.0000.0000.0000.000
72A463ASN00.0150.01050.815-0.002-0.0020.0000.0000.0000.000
73A464PRO00.0310.00450.9610.0010.0010.0000.0000.0000.000
74A465ALA00.0000.01548.8730.0010.0010.0000.0000.0000.000
75A466PRO00.0350.01250.931-0.001-0.0010.0000.0000.0000.000
76A467ARG10.9050.93151.6530.0000.0000.0000.0000.0000.000
77A468GLY00.0340.03251.390-0.001-0.0010.0000.0000.0000.000
78A469MET0-0.0290.00046.155-0.002-0.0020.0000.0000.0000.000
79A470PRO00.016-0.00942.9650.0010.0010.0000.0000.0000.000
80A471GLN0-0.020-0.03244.4600.0010.0010.0000.0000.0000.000
81A472ILE0-0.0100.00840.9410.0020.0020.0000.0000.0000.000
82A473GLU-1-0.819-0.89237.0040.0180.0180.0000.0000.0000.000
83A474VAL00.0080.00434.8870.0020.0020.0000.0000.0000.000
84A475THR0-0.002-0.01031.5460.0010.0010.0000.0000.0000.000
85A476PHE0-0.002-0.00829.006-0.001-0.0010.0000.0000.0000.000
86A477ASP-1-0.836-0.91127.5220.0620.0620.0000.0000.0000.000
87A478ILE00.0070.00923.369-0.007-0.0070.0000.0000.0000.000
88A479ASP-1-0.720-0.84823.8300.0740.0740.0000.0000.0000.000
89A480ALA00.013-0.01520.082-0.004-0.0040.0000.0000.0000.000
90A481ASP-1-0.931-0.94720.2960.1030.1030.0000.0000.0000.000
91A482GLY0-0.015-0.00722.691-0.016-0.0160.0000.0000.0000.000
92A483ILE0-0.084-0.04223.144-0.018-0.0180.0000.0000.0000.000
93A484LEU0-0.0090.00726.9070.0060.0060.0000.0000.0000.000
94A485HIS10.7480.84328.414-0.044-0.0440.0000.0000.0000.000
95A486VAL00.0280.02231.3300.0010.0010.0000.0000.0000.000
96A487SER0-0.066-0.04133.8490.0010.0010.0000.0000.0000.000
97A488ALA00.0310.01636.641-0.002-0.0020.0000.0000.0000.000
98A489LYS10.9030.94838.557-0.021-0.0210.0000.0000.0000.000
99A490ASP-1-0.707-0.82341.5990.0050.0050.0000.0000.0000.000
100A491LYS10.8120.89139.212-0.012-0.0120.0000.0000.0000.000
101A492ASN0-0.046-0.01044.6290.0020.0020.0000.0000.0000.000
102A493SER0-0.057-0.05948.0800.0010.0010.0000.0000.0000.000
103A494GLY0-0.0020.00645.2430.0010.0010.0000.0000.0000.000
104A495LYS10.8360.91745.030-0.006-0.0060.0000.0000.0000.000
105A496GLU-1-0.866-0.94438.5460.0230.0230.0000.0000.0000.000
106A497GLN0-0.0180.01341.5580.0020.0020.0000.0000.0000.000
107A498LYS10.9660.96536.844-0.030-0.0300.0000.0000.0000.000
108A499ILE0-0.0110.01235.658-0.001-0.0010.0000.0000.0000.000
109A500THR0-0.009-0.01132.0720.0030.0030.0000.0000.0000.000
110A501ILE0-0.0150.00031.131-0.003-0.0030.0000.0000.0000.000
111A502LYS10.9700.98631.2720.0080.0080.0000.0000.0000.000
112A503ALA00.1100.04427.444-0.005-0.0050.0000.0000.0000.000
113A504SER0-0.015-0.01329.212-0.005-0.0050.0000.0000.0000.000
114A505SER0-0.063-0.02131.721-0.003-0.0030.0000.0000.0000.000
115A506GLY00.0140.01929.034-0.002-0.0020.0000.0000.0000.000
116A507LEU0-0.025-0.00628.6830.0000.0000.0000.0000.0000.000
117A508ASN0-0.009-0.02127.184-0.010-0.0100.0000.0000.0000.000
118A509GLU-1-0.884-0.95320.969-0.175-0.1750.0000.0000.0000.000
119A510ASP-1-0.887-0.95125.164-0.150-0.1500.0000.0000.0000.000
120A511GLU-1-0.928-0.95627.897-0.076-0.0760.0000.0000.0000.000
121A512ILE0-0.011-0.00423.5940.0000.0000.0000.0000.0000.000
122A513GLN00.0150.00021.918-0.014-0.0140.0000.0000.0000.000
123A514LYS10.7730.86926.3540.0940.0940.0000.0000.0000.000
124A515MET00.0400.07128.8320.0020.0020.0000.0000.0000.000
125A516VAL00.003-0.00924.2110.0020.0020.0000.0000.0000.000
126A517ARG10.9790.99127.3220.1590.1590.0000.0000.0000.000
127A518ASP-1-0.825-0.89729.465-0.097-0.0970.0000.0000.0000.000
128A519ALA00.012-0.00529.5420.0070.0070.0000.0000.0000.000
129A520GLU-1-0.974-0.98025.901-0.185-0.1850.0000.0000.0000.000
130A521ALA0-0.056-0.02330.6590.0040.0040.0000.0000.0000.000
131A522ASN0-0.069-0.04333.9280.0110.0110.0000.0000.0000.000
132A523ALA00.0690.04832.3160.0070.0070.0000.0000.0000.000
133A524GLU-1-0.892-0.95234.310-0.076-0.0760.0000.0000.0000.000
134A525ALA0-0.032-0.01737.4440.0060.0060.0000.0000.0000.000
135A526ASP-1-0.743-0.84935.631-0.070-0.0700.0000.0000.0000.000
136A527ARG10.8940.93735.8420.0760.0760.0000.0000.0000.000
137A528LYS10.8530.91537.7890.0740.0740.0000.0000.0000.000
138A529PHE0-0.030-0.00639.8810.0040.0040.0000.0000.0000.000
139A530GLU-1-0.787-0.88336.296-0.053-0.0530.0000.0000.0000.000
140A531GLU-1-0.805-0.88639.553-0.055-0.0550.0000.0000.0000.000
141A532LEU0-0.0230.01241.9590.0040.0040.0000.0000.0000.000
142A533VAL00.0080.01443.0560.0030.0030.0000.0000.0000.000
143A534GLN0-0.013-0.00738.0760.0030.0030.0000.0000.0000.000
144A535THR0-0.011-0.02043.7990.0030.0030.0000.0000.0000.000
145A536ARG10.8200.88146.8300.0360.0360.0000.0000.0000.000
146A537ASN0-0.023-0.01244.3080.0020.0020.0000.0000.0000.000
147A538GLN0-0.021-0.00245.9360.0030.0030.0000.0000.0000.000
148A539GLY00.0670.00848.6570.0020.0020.0000.0000.0000.000
149A540ASP-1-0.887-0.94151.204-0.017-0.0170.0000.0000.0000.000
150A541HIS00.0080.00650.0240.0020.0020.0000.0000.0000.000
151A542LEU0-0.010-0.00452.0940.0020.0020.0000.0000.0000.000
152A543LEU0-0.0060.01354.3280.0010.0010.0000.0000.0000.000
153A544HIS0-0.047-0.04054.2510.0020.0020.0000.0000.0000.000
154A545SER0-0.029-0.00454.6120.0020.0020.0000.0000.0000.000
155A546THR0-0.028-0.02856.7140.0010.0010.0000.0000.0000.000
156A547ARG10.8930.92659.4730.0150.0150.0000.0000.0000.000
157A548LYS10.8590.95258.0060.0050.0050.0000.0000.0000.000
158A549GLN00.007-0.01158.2990.0000.0000.0000.0000.0000.000
159A550VAL0-0.030-0.01062.0210.0010.0010.0000.0000.0000.000
160A551GLU-1-0.929-0.96464.637-0.007-0.0070.0000.0000.0000.000
161A552GLU-1-0.917-0.96861.344-0.003-0.0030.0000.0000.0000.000
162A553ALA0-0.036-0.01265.5920.0010.0010.0000.0000.0000.000
163A554GLY00.0320.01967.4220.0010.0010.0000.0000.0000.000
164A555ASP-1-0.917-0.96770.508-0.005-0.0050.0000.0000.0000.000
165A556LYS10.7940.90168.5250.0040.0040.0000.0000.0000.000
166A557LEU0-0.039-0.01667.1910.0000.0000.0000.0000.0000.000
167A558PRO00.0080.01870.3710.0000.0000.0000.0000.0000.000
168A559ALA00.0410.00772.0200.0000.0000.0000.0000.0000.000
169A560ASP-1-0.903-0.94973.213-0.009-0.0090.0000.0000.0000.000
170A561ASP-1-0.820-0.92368.282-0.010-0.0100.0000.0000.0000.000
171A562LYS10.8690.92668.2890.0090.0090.0000.0000.0000.000
172A563THR0-0.022-0.01768.945-0.001-0.0010.0000.0000.0000.000
173A564ALA00.0010.00567.283-0.001-0.0010.0000.0000.0000.000
174A565ILE00.0280.00363.398-0.001-0.0010.0000.0000.0000.000
175A566GLU-1-0.831-0.90764.430-0.012-0.0120.0000.0000.0000.000
176A567SER0-0.059-0.03165.754-0.001-0.0010.0000.0000.0000.000
177A568ALA00.0030.00461.794-0.001-0.0010.0000.0000.0000.000
178A569LEU0-0.0040.00160.162-0.001-0.0010.0000.0000.0000.000
179A570THR0-0.030-0.01461.113-0.001-0.0010.0000.0000.0000.000
180A571ALA0-0.016-0.00661.549-0.001-0.0010.0000.0000.0000.000
181A572LEU00.0250.01354.597-0.001-0.0010.0000.0000.0000.000
182A573GLU-1-0.771-0.87257.159-0.019-0.0190.0000.0000.0000.000
183A574THR0-0.082-0.05158.226-0.001-0.0010.0000.0000.0000.000
184A575ALA00.0090.00455.587-0.001-0.0010.0000.0000.0000.000
185A576LEU0-0.0300.00152.321-0.002-0.0020.0000.0000.0000.000
186A577LYS10.8020.89753.5610.0200.0200.0000.0000.0000.000
187A578GLY0-0.0140.01154.847-0.001-0.0010.0000.0000.0000.000
188A579GLU-1-0.866-0.94050.187-0.039-0.0390.0000.0000.0000.000
189A580ASP-1-0.882-0.93150.021-0.038-0.0380.0000.0000.0000.000
190A581LYS10.9040.93843.4560.0490.0490.0000.0000.0000.000
191A582ALA00.0480.02749.2610.0020.0020.0000.0000.0000.000
192A583ALA0-0.020-0.00350.8460.0020.0020.0000.0000.0000.000
193A584ILE0-0.015-0.01050.5380.0020.0020.0000.0000.0000.000
194A585GLU-1-0.897-0.96047.023-0.035-0.0350.0000.0000.0000.000
195A586ALA0-0.007-0.00251.7080.0020.0020.0000.0000.0000.000
196A587LYS10.7930.87654.9720.0240.0240.0000.0000.0000.000
197A588MET0-0.0290.00350.3190.0010.0010.0000.0000.0000.000
198A589GLN0-0.028-0.01451.5530.0010.0010.0000.0000.0000.000
199A590GLU-1-0.801-0.88055.716-0.021-0.0210.0000.0000.0000.000
200A591LEU00.0090.00357.7350.0010.0010.0000.0000.0000.000
201A592ALA0-0.009-0.00156.1400.0010.0010.0000.0000.0000.000
202A593GLN0-0.038-0.02258.2870.0010.0010.0000.0000.0000.000
203A594VAL0-0.044-0.00460.6640.0010.0010.0000.0000.0000.000
204A595SER0-0.007-0.01460.2820.0010.0010.0000.0000.0000.000
205A596GLN0-0.047-0.02360.9400.0000.0000.0000.0000.0000.000
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207A598LEU00.004-0.00461.6450.0010.0010.0000.0000.0000.000
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