Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: V5361

Calculation Name: 3E20-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E20

Chain ID: A

ChEMBL ID:

UniProt ID: P79063

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2099551.131914
FMO2-HF: Nuclear repulsion 2022244.856252
FMO2-HF: Total energy -77306.275663
FMO2-MP2: Total energy -77528.33676


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:467:ALA)


Summations of interaction energy for fragment #1(A:467:ALA)
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.
0.1911.9870.035-0.651-1.180.003
Interaction energy analysis for fragmet #1(A:467:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.026
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].
3A469PHE0-0.005-0.0183.811-0.5090.594-0.016-0.472-0.6150.003
4A470ILE00.0230.0096.0110.3950.3950.0000.0000.0000.000
5A471MET0-0.0020.0158.441-0.011-0.0110.0000.0000.0000.000
6A472PRO00.005-0.00311.9380.0100.0100.0000.0000.0000.000
7A473ILE0-0.018-0.00414.777-0.017-0.0170.0000.0000.0000.000
8A474ALA00.0500.03217.8990.0200.0200.0000.0000.0000.000
9A475SER0-0.051-0.01420.3830.0110.0110.0000.0000.0000.000
10A476LYS10.8980.95222.1030.0100.0100.0000.0000.0000.000
11A477TYR0-0.032-0.00324.4250.0070.0070.0000.0000.0000.000
12A478LYS10.9000.94526.7490.0330.0330.0000.0000.0000.000
13A479ASP-1-0.884-0.95629.237-0.048-0.0480.0000.0000.0000.000
14A480LEU0-0.0200.00829.960-0.004-0.0040.0000.0000.0000.000
15A481GLY0-0.001-0.00127.554-0.006-0.0060.0000.0000.0000.000
16A482THR0-0.079-0.06424.2250.0060.0060.0000.0000.0000.000
17A483ILE00.0000.01322.360-0.013-0.0130.0000.0000.0000.000
18A484LEU0-0.022-0.00918.8950.0140.0140.0000.0000.0000.000
19A485GLU-1-0.854-0.94018.980-0.073-0.0730.0000.0000.0000.000
20A486GLY00.0770.02816.5610.0200.0200.0000.0000.0000.000
21A487LYS10.9320.98813.786-0.010-0.0100.0000.0000.0000.000
22A488ILE0-0.067-0.0098.3200.0190.0190.0000.0000.0000.000
23A489GLU-1-0.890-0.9559.6690.0720.0720.0000.0000.0000.000
24A490ALA0-0.019-0.0184.2630.0590.147-0.001-0.007-0.0790.000
25A491GLY00.0100.0203.084-0.607-0.4220.048-0.084-0.1490.000
26A492SER0-0.017-0.0193.9270.3620.4980.002-0.015-0.1230.000
27A493ILE00.0000.0097.013-0.146-0.1460.0000.0000.0000.000
28A494LYS10.9900.98010.2200.4350.4350.0000.0000.0000.000
29A495LYS10.9200.97313.0460.1980.1980.0000.0000.0000.000
30A496ASN0-0.051-0.02316.707-0.006-0.0060.0000.0000.0000.000
31A497SER00.001-0.00113.098-0.041-0.0410.0000.0000.0000.000
32A498ASN00.000-0.00714.5170.0460.0460.0000.0000.0000.000
33A499VAL0-0.042-0.00912.255-0.065-0.0650.0000.0000.0000.000
34A500LEU0-0.028-0.03013.2380.0340.0340.0000.0000.0000.000
35A501VAL0-0.001-0.00714.2250.0000.0000.0000.0000.0000.000
36A502MET0-0.0300.03313.4410.0040.0040.0000.0000.0000.000
37A503PRO00.062-0.02516.244-0.010-0.0100.0000.0000.0000.000
38A504ILE0-0.034-0.02418.1560.0030.0030.0000.0000.0000.000
39A505ASN00.0170.00717.6670.0070.0070.0000.0000.0000.000
40A506GLN00.0360.03918.997-0.014-0.0140.0000.0000.0000.000
41A507THR0-0.051-0.02217.225-0.012-0.0120.0000.0000.0000.000
42A508LEU0-0.027-0.00417.9640.0090.0090.0000.0000.0000.000
43A509GLU-1-0.863-0.93517.800-0.181-0.1810.0000.0000.0000.000
44A510VAL0-0.003-0.00114.9220.0200.0200.0000.0000.0000.000
45A511THR0-0.113-0.07217.935-0.012-0.0120.0000.0000.0000.000
46A512ALA00.0360.01119.3240.0080.0080.0000.0000.0000.000
47A513ILE0-0.0060.00514.868-0.005-0.0050.0000.0000.0000.000
48A514TYR00.0070.00918.2340.0060.0060.0000.0000.0000.000
49A515ASP-1-0.776-0.88218.770-0.125-0.1250.0000.0000.0000.000
50A516GLU-1-0.925-0.99619.774-0.060-0.0600.0000.0000.0000.000
51A517ALA0-0.082-0.02922.0520.0100.0100.0000.0000.0000.000
52A518ASP-1-0.886-0.91923.597-0.067-0.0670.0000.0000.0000.000
53A519GLU-1-0.930-0.95723.222-0.091-0.0910.0000.0000.0000.000
54A520GLU-1-0.978-1.00120.929-0.166-0.1660.0000.0000.0000.000
55A521ILE0-0.019-0.00315.789-0.006-0.0060.0000.0000.0000.000
56A522SER0-0.050-0.03616.858-0.022-0.0220.0000.0000.0000.000
57A523SER0-0.055-0.05211.919-0.047-0.0470.0000.0000.0000.000
58A524SER00.0380.05112.0780.0400.0400.0000.0000.0000.000
59A525ILE0-0.016-0.0138.406-0.128-0.1280.0000.0000.0000.000
60A526CYS00.005-0.0246.6650.0580.0580.0000.0000.0000.000
61A527GLY0-0.072-0.0428.7280.0290.0290.0000.0000.0000.000
62A528ASP-1-0.827-0.90411.769-0.200-0.2000.0000.0000.0000.000
63A529GLN0-0.009-0.00813.7780.0030.0030.0000.0000.0000.000
64A530VAL0-0.019-0.00814.341-0.007-0.0070.0000.0000.0000.000
65A531ARG10.8480.90517.0920.1010.1010.0000.0000.0000.000
66A532LEU0-0.038-0.02614.291-0.018-0.0180.0000.0000.0000.000
67A533ARG11.0191.01818.7460.1140.1140.0000.0000.0000.000
68A534VAL0-0.049-0.02618.743-0.019-0.0190.0000.0000.0000.000
69A535ARG10.9130.95621.2300.1200.1200.0000.0000.0000.000
70A536GLY00.014-0.00722.481-0.009-0.0090.0000.0000.0000.000
71A537ASP-1-0.874-0.92824.742-0.022-0.0220.0000.0000.0000.000
72A538ASP-1-0.793-0.90123.757-0.051-0.0510.0000.0000.0000.000
73A539SER0-0.113-0.04925.0040.0070.0070.0000.0000.0000.000
74A540ASP-1-0.841-0.92425.0820.0160.0160.0000.0000.0000.000
75A541VAL0-0.093-0.04820.7930.0090.0090.0000.0000.0000.000
76A542GLN00.005-0.00522.401-0.012-0.0120.0000.0000.0000.000
77A543THR0-0.073-0.03321.5040.0030.0030.0000.0000.0000.000
78A544GLY00.0510.00920.0250.0080.0080.0000.0000.0000.000
79A545TYR0-0.032-0.01618.1290.0250.0250.0000.0000.0000.000
80A546VAL0-0.025-0.02711.799-0.003-0.0030.0000.0000.0000.000
81A547LEU0-0.0030.02513.3410.0020.0020.0000.0000.0000.000
82A548THR00.0060.0138.3600.0240.0240.0000.0000.0000.000
83A549SER00.0240.0147.573-0.120-0.1200.0000.0000.0000.000
84A550THR00.004-0.0109.5350.1190.1190.0000.0000.0000.000
85A551LYS10.8850.9507.9540.3130.3130.0000.0000.0000.000
86A552ASN0-0.004-0.0115.996-0.313-0.3130.0000.0000.0000.000
87A553PRO00.0220.0207.6880.0690.0690.0000.0000.0000.000
88A554VAL00.013-0.0079.2070.1730.1730.0000.0000.0000.000
89A555HIS0-0.053-0.0379.985-0.199-0.1990.0000.0000.0000.000
90A556ALA00.009-0.00912.812-0.054-0.0540.0000.0000.0000.000
91A557THR0-0.020-0.00316.316-0.008-0.0080.0000.0000.0000.000
92A558THR00.0430.03019.548-0.005-0.0050.0000.0000.0000.000
93A559ARG10.9400.99722.302-0.155-0.1550.0000.0000.0000.000
94A560PHE00.003-0.00219.7650.0320.0320.0000.0000.0000.000
95A561ILE00.0070.01721.186-0.026-0.0260.0000.0000.0000.000
96A562ALA00.0590.00620.8600.0320.0320.0000.0000.0000.000
97A563GLN0-0.070-0.02722.195-0.020-0.0200.0000.0000.0000.000
98A564ILE00.0280.00423.7450.0040.0040.0000.0000.0000.000
99A565ALA0-0.059-0.02326.379-0.007-0.0070.0000.0000.0000.000
100A566ILE0-0.0050.01728.476-0.001-0.0010.0000.0000.0000.000
101A567LEU0-0.063-0.03729.002-0.003-0.0030.0000.0000.0000.000
102A568GLU-1-0.855-0.95032.8620.0500.0500.0000.0000.0000.000
103A569LEU00.012-0.01834.1310.0000.0000.0000.0000.0000.000
104A570PRO0-0.0450.01936.7200.0000.0000.0000.0000.0000.000
105A571SER0-0.014-0.02139.848-0.002-0.0020.0000.0000.0000.000
106A572ILE0-0.0010.02139.2840.0020.0020.0000.0000.0000.000
107A573LEU0-0.0010.01232.4970.0000.0000.0000.0000.0000.000
108A574THR00.002-0.03536.1970.0020.0020.0000.0000.0000.000
109A575THR0-0.004-0.01533.909-0.002-0.0020.0000.0000.0000.000
110A576GLY00.0530.05133.9440.0030.0030.0000.0000.0000.000
111A577TYR0-0.091-0.05332.2970.0000.0000.0000.0000.0000.000
112A578SER00.1030.04032.0260.0080.0080.0000.0000.0000.000
113A579CYS0-0.138-0.05730.075-0.002-0.0020.0000.0000.0000.000
114A580VAL00.0730.05427.5070.0030.0030.0000.0000.0000.000
115A581MET0-0.012-0.00321.4340.0020.0020.0000.0000.0000.000
116A582HIS0-0.026-0.00223.026-0.004-0.0040.0000.0000.0000.000
117A583ILE0-0.009-0.02416.7500.0050.0050.0000.0000.0000.000
118A584HIS00.012-0.00714.639-0.020-0.0200.0000.0000.0000.000
119A585THR0-0.046-0.00617.301-0.011-0.0110.0000.0000.0000.000
120A586ALA0-0.0040.00819.023-0.009-0.0090.0000.0000.0000.000
121A587VAL0-0.047-0.04320.7890.0060.0060.0000.0000.0000.000
122A588GLU-1-0.901-0.94723.4130.0770.0770.0000.0000.0000.000
123A589GLU-1-0.913-0.94425.4520.0820.0820.0000.0000.0000.000
124A590VAL0-0.038-0.02825.2380.0100.0100.0000.0000.0000.000
125A591SER00.0440.03427.798-0.008-0.0080.0000.0000.0000.000
126A592PHE0-0.058-0.05528.9780.0120.0120.0000.0000.0000.000
127A593ALA00.0500.03628.969-0.005-0.0050.0000.0000.0000.000
128A594LYS10.8390.89329.705-0.136-0.1360.0000.0000.0000.000
129A595LEU00.0120.01530.1420.0090.0090.0000.0000.0000.000
130A596LEU0-0.012-0.00226.989-0.005-0.0050.0000.0000.0000.000
131A597HIS0-0.072-0.05228.4670.0030.0030.0000.0000.0000.000
132A598LYS11.0221.00431.357-0.077-0.0770.0000.0000.0000.000
133A599LEU0-0.041-0.01027.5510.0050.0050.0000.0000.0000.000
134A600ASP-1-0.876-0.93531.8410.0730.0730.0000.0000.0000.000
135A601LYS10.9390.96032.499-0.057-0.0570.0000.0000.0000.000
136A602THR00.044-0.00530.6300.0030.0030.0000.0000.0000.000
137A603ASN00.0150.02225.621-0.005-0.0050.0000.0000.0000.000
138A604ARG10.9580.98928.652-0.080-0.0800.0000.0000.0000.000
139A605LYS11.0211.00425.567-0.170-0.1700.0000.0000.0000.000
140A606SER00.0200.01831.085-0.004-0.0040.0000.0000.0000.000
141A607LYS10.9710.97733.892-0.087-0.0870.0000.0000.0000.000
142A608LYS10.9380.97235.512-0.073-0.0730.0000.0000.0000.000
143A609PRO00.0410.04034.4540.0010.0010.0000.0000.0000.000
144A610PRO0-0.040-0.02233.867-0.006-0.0060.0000.0000.0000.000
145A611MET00.0060.00836.8170.0010.0010.0000.0000.0000.000
146A612PHE0-0.018-0.01137.664-0.001-0.0010.0000.0000.0000.000
147A613ALA00.010-0.02234.3700.0030.0030.0000.0000.0000.000
148A614THR00.036-0.00736.150-0.004-0.0040.0000.0000.0000.000
149A615LYS11.0010.98735.652-0.047-0.0470.0000.0000.0000.000
150A616GLY00.0050.01434.004-0.001-0.0010.0000.0000.0000.000
151A617MET0-0.0830.01133.867-0.002-0.0020.0000.0000.0000.000
152A618LYS10.8620.93428.578-0.092-0.0920.0000.0000.0000.000
153A619ILE0-0.016-0.01829.091-0.005-0.0050.0000.0000.0000.000
154A620ILE0-0.022-0.01024.9650.0080.0080.0000.0000.0000.000
155A621ALA00.0280.01026.713-0.008-0.0080.0000.0000.0000.000
156A622GLU-1-0.832-0.90825.6770.1640.1640.0000.0000.0000.000
157A623LEU0-0.026-0.00924.359-0.015-0.0150.0000.0000.0000.000
158A624GLU-1-0.900-0.96424.9530.1310.1310.0000.0000.0000.000
159A625THR00.000-0.00323.267-0.003-0.0030.0000.0000.0000.000
160A626GLN00.0090.00626.1510.0040.0040.0000.0000.0000.000
161A627THR00.0150.00824.9600.0010.0010.0000.0000.0000.000
162A628PRO0-0.001-0.00520.6840.0080.0080.0000.0000.0000.000
163A629VAL00.0790.04118.332-0.015-0.0150.0000.0000.0000.000
164A630CYS0-0.064-0.03013.7930.0260.0260.0000.0000.0000.000
165A631MET0-0.034-0.00814.055-0.026-0.0260.0000.0000.0000.000
166A632GLU-1-0.775-0.8919.0241.0991.0990.0000.0000.0000.000
167A633ARG10.8340.90511.505-0.847-0.8470.0000.0000.0000.000
168A634PHE0-0.053-0.02212.2030.0420.0420.0000.0000.0000.000
169A635GLU-1-1.030-1.02613.2270.4480.4480.0000.0000.0000.000
170A636ASP-1-0.826-0.8748.5200.9870.9870.0000.0000.0000.000
171A637TYR00.0440.0053.9210.0270.3110.002-0.073-0.2140.000
172A638GLN00.020-0.0059.636-0.125-0.1250.0000.0000.0000.000
173A639TYR00.004-0.01112.117-0.024-0.0240.0000.0000.0000.000
174A640MET00.0200.0339.781-0.062-0.0620.0000.0000.0000.000
175A641GLY00.0610.02112.8070.0150.0150.0000.0000.0000.000
176A642ARG10.8590.92015.075-0.198-0.1980.0000.0000.0000.000
177A643PHE00.0790.05518.0370.0000.0000.0000.0000.0000.000
178A644THR0-0.096-0.03820.881-0.006-0.0060.0000.0000.0000.000
179A645LEU00.0430.00224.5580.0010.0010.0000.0000.0000.000
180A646ARG10.9290.95427.494-0.064-0.0640.0000.0000.0000.000
181A647ASP-1-0.819-0.87930.5200.0590.0590.0000.0000.0000.000
182A648GLN00.039-0.02630.101-0.002-0.0020.0000.0000.0000.000
183A649GLY0-0.0200.02733.735-0.003-0.0030.0000.0000.0000.000
184A650THR0-0.048-0.04434.257-0.001-0.0010.0000.0000.0000.000
185A651THR00.006-0.00128.5320.0020.0020.0000.0000.0000.000
186A652VAL00.0240.02930.9160.0000.0000.0000.0000.0000.000
187A653ALA0-0.008-0.01028.4830.0010.0010.0000.0000.0000.000
188A654VAL00.0240.03424.2690.0000.0000.0000.0000.0000.000
189A655GLY0-0.010-0.01823.101-0.004-0.0040.0000.0000.0000.000
190A656LYS10.9280.96818.516-0.176-0.1760.0000.0000.0000.000
191A657VAL00.0330.05516.085-0.013-0.0130.0000.0000.0000.000
192A658VAL0-0.085-0.04117.0190.0330.0330.0000.0000.0000.000
193A659LYS10.9320.94817.524-0.270-0.2700.0000.0000.0000.000
194A660ILE00.0740.05214.568-0.045-0.0450.0000.0000.0000.000
195A661LEU0-0.129-0.06117.7130.0120.0120.0000.0000.0000.000
196A662ASP-1-0.861-0.92718.4720.2200.2200.0000.0000.0000.000