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: QV5VY

Calculation Name: 4ERN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ERN

Chain ID: A

ChEMBL ID:

UniProt ID: P19447

Base Structure: X-ray

Registration Date: 2023-09-23

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3088549.004517
FMO2-HF: Nuclear repulsion 2995391.236469
FMO2-HF: Total energy -93157.768048
FMO2-MP2: Total energy -93429.131636


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:502:ILE)


Summations of interaction energy for fragment #1(A:502:ILE)
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.
-2.9891.7160.228-2.097-2.8340.001
Interaction energy analysis for fragmet #1(A:502:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.065 / q_NPA : 0.030
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].
3A504LYS10.8790.9392.934-2.3301.5060.221-1.902-2.1540.001
4A505VAL00.023-0.0025.5240.4680.4680.0000.0000.0000.000
5A506GLN00.0050.0377.9960.1430.1430.0000.0000.0000.000
6A507CYS0-0.033-0.01011.2110.0600.0600.0000.0000.0000.000
7A508ALA00.007-0.00313.6910.0150.0150.0000.0000.0000.000
8A509GLU-1-0.761-0.83617.413-0.173-0.1730.0000.0000.0000.000
9A510VAL0-0.021-0.01420.632-0.002-0.0020.0000.0000.0000.000
10A511TRP0-0.024-0.01823.2950.0140.0140.0000.0000.0000.000
11A512CYS00.0030.00526.6940.0010.0010.0000.0000.0000.000
12A513PRO00.0700.03329.4810.0040.0040.0000.0000.0000.000
13A514MET0-0.0130.03333.187-0.001-0.0010.0000.0000.0000.000
14A515SER00.0020.00735.3310.0000.0000.0000.0000.0000.000
15A516PRO00.0520.02338.0120.0010.0010.0000.0000.0000.000
16A517GLU-1-0.789-0.88741.240-0.056-0.0560.0000.0000.0000.000
17A518PHE00.0320.00036.7790.0010.0010.0000.0000.0000.000
18A519TYR0-0.048-0.02737.7450.0020.0020.0000.0000.0000.000
19A520ARG10.8840.92339.7040.0480.0480.0000.0000.0000.000
20A521GLU-1-0.795-0.87941.661-0.044-0.0440.0000.0000.0000.000
21A522TYR0-0.0100.00335.7910.0000.0000.0000.0000.0000.000
22A523VAL0-0.0040.01739.9530.0000.0000.0000.0000.0000.000
23A524ALA00.0210.01742.2410.0010.0010.0000.0000.0000.000
24A525ILE00.0140.02141.5270.0020.0020.0000.0000.0000.000
25A526LYS10.8760.92241.8420.0470.0470.0000.0000.0000.000
26A527THR0-0.023-0.01241.354-0.002-0.0020.0000.0000.0000.000
27A528LYS10.8690.91235.8660.0460.0460.0000.0000.0000.000
28A529LYS10.9230.95036.3490.0390.0390.0000.0000.0000.000
29A530ARG10.7910.88736.9360.0590.0590.0000.0000.0000.000
30A531ILE00.008-0.01031.398-0.003-0.0030.0000.0000.0000.000
31A532LEU00.0200.02432.796-0.006-0.0060.0000.0000.0000.000
32A533LEU0-0.0270.00134.336-0.002-0.0020.0000.0000.0000.000
33A534TYR0-0.019-0.02629.275-0.002-0.0020.0000.0000.0000.000
34A535THR0-0.034-0.01328.483-0.009-0.0090.0000.0000.0000.000
35A536MET0-0.0170.00030.113-0.005-0.0050.0000.0000.0000.000
36A537ASN0-0.017-0.00231.7880.0050.0050.0000.0000.0000.000
37A538PRO00.0810.02832.038-0.005-0.0050.0000.0000.0000.000
38A539ASN0-0.037-0.02932.062-0.002-0.0020.0000.0000.0000.000
39A540LYS10.7770.88326.6170.1070.1070.0000.0000.0000.000
40A541PHE00.0200.00327.658-0.007-0.0070.0000.0000.0000.000
41A542ARG10.9270.96228.4660.0800.0800.0000.0000.0000.000
42A543ALA00.0430.02725.661-0.005-0.0050.0000.0000.0000.000
43A544CYS0-0.038-0.01723.845-0.013-0.0130.0000.0000.0000.000
44A545GLN00.0710.04024.160-0.005-0.0050.0000.0000.0000.000
45A546PHE00.0220.01624.222-0.003-0.0030.0000.0000.0000.000
46A547LEU0-0.020-0.01519.984-0.011-0.0110.0000.0000.0000.000
47A548ILE0-0.012-0.00520.887-0.014-0.0140.0000.0000.0000.000
48A549LYS10.8500.92821.6700.0860.0860.0000.0000.0000.000
49A550PHE0-0.017-0.00418.654-0.002-0.0020.0000.0000.0000.000
50A551HIS10.8160.87415.8160.2900.2900.0000.0000.0000.000
51A552GLU-1-0.749-0.83518.256-0.091-0.0910.0000.0000.0000.000
52A553ARG10.8660.93420.3750.1400.1400.0000.0000.0000.000
53A554ARG10.8260.90713.6200.3480.3480.0000.0000.0000.000
54A555ASN0-0.013-0.00816.473-0.004-0.0040.0000.0000.0000.000
55A556ASP-1-0.804-0.84713.969-0.314-0.3140.0000.0000.0000.000
56A557LYS10.8450.93312.9330.0370.0370.0000.0000.0000.000
57A558ILE0-0.017-0.02113.906-0.039-0.0390.0000.0000.0000.000
58A559ILE00.0280.01514.1690.0260.0260.0000.0000.0000.000
59A560VAL0-0.009-0.00617.244-0.025-0.0250.0000.0000.0000.000
60A561PHE0-0.011-0.00318.6100.0140.0140.0000.0000.0000.000
61A562ALA00.013-0.00520.526-0.006-0.0060.0000.0000.0000.000
62A563ASP-1-0.805-0.89724.155-0.094-0.0940.0000.0000.0000.000
63A564ASN00.005-0.00825.4280.0070.0070.0000.0000.0000.000
64A565VAL00.0580.01828.890-0.002-0.0020.0000.0000.0000.000
65A566PHE00.0190.01830.4210.0010.0010.0000.0000.0000.000
66A567ALA00.048-0.00128.9420.0000.0000.0000.0000.0000.000
67A568LEU0-0.057-0.02024.873-0.002-0.0020.0000.0000.0000.000
68A569LYS10.9240.96128.0910.0370.0370.0000.0000.0000.000
69A570GLU-1-0.752-0.84231.020-0.051-0.0510.0000.0000.0000.000
70A571TYR0-0.021-0.05126.870-0.003-0.0030.0000.0000.0000.000
71A572ALA00.0020.01827.0140.0000.0000.0000.0000.0000.000
72A573ILE0-0.005-0.00328.2900.0020.0020.0000.0000.0000.000
73A574ARG10.8060.90431.7210.0600.0600.0000.0000.0000.000
74A575LEU0-0.045-0.01626.466-0.001-0.0010.0000.0000.0000.000
75A576ASN0-0.027-0.00428.4200.0010.0010.0000.0000.0000.000
76A577LYS10.7840.88323.6930.0780.0780.0000.0000.0000.000
77A578PRO00.0270.01424.0360.0020.0020.0000.0000.0000.000
78A579TYR00.008-0.00624.491-0.007-0.0070.0000.0000.0000.000
79A580ILE0-0.030-0.00621.2180.0070.0070.0000.0000.0000.000
80A581TYR00.051-0.00324.593-0.007-0.0070.0000.0000.0000.000
81A582GLY00.014-0.00326.5520.0050.0050.0000.0000.0000.000
82A583PRO0-0.016-0.02028.4340.0040.0040.0000.0000.0000.000
83A584THR0-0.0160.03326.3950.0010.0010.0000.0000.0000.000
84A585SER00.0650.04328.4660.0030.0030.0000.0000.0000.000
85A586GLN00.0640.00125.3620.0000.0000.0000.0000.0000.000
86A587GLY00.0250.02226.2920.0020.0020.0000.0000.0000.000
87A588GLU-1-0.881-0.94927.250-0.017-0.0170.0000.0000.0000.000
88A589ARG10.8740.92822.6410.0170.0170.0000.0000.0000.000
89A590MET00.0350.03120.4200.0020.0020.0000.0000.0000.000
90A591GLN00.0250.01922.7770.0050.0050.0000.0000.0000.000
91A592ILE00.0350.02421.8480.0010.0010.0000.0000.0000.000
92A593LEU0-0.015-0.00417.668-0.003-0.0030.0000.0000.0000.000
93A594GLN00.002-0.02318.6120.0100.0100.0000.0000.0000.000
94A595ASN0-0.016-0.01820.1230.0030.0030.0000.0000.0000.000
95A596PHE00.0080.01414.3990.0020.0020.0000.0000.0000.000
96A597LYS10.8710.94914.193-0.054-0.0540.0000.0000.0000.000
97A598HIS00.000-0.00316.2470.0100.0100.0000.0000.0000.000
98A599ASN0-0.0070.00018.9480.0010.0010.0000.0000.0000.000
99A600PRO00.0280.00519.948-0.009-0.0090.0000.0000.0000.000
100A601LYS10.9060.95721.000-0.006-0.0060.0000.0000.0000.000
101A602ILE0-0.048-0.01521.791-0.006-0.0060.0000.0000.0000.000
102A603ASN00.0260.00917.8910.0140.0140.0000.0000.0000.000
103A604THR00.029-0.01718.016-0.023-0.0230.0000.0000.0000.000
104A605ILE0-0.043-0.01317.9850.0130.0130.0000.0000.0000.000
105A606PHE00.0150.00520.330-0.015-0.0150.0000.0000.0000.000
106A607ILE0-0.023-0.01617.7900.0110.0110.0000.0000.0000.000
107A608SER00.015-0.04021.862-0.008-0.0080.0000.0000.0000.000
108A609LYS10.8720.91721.9550.0800.0800.0000.0000.0000.000
109A610VAL0-0.0210.00422.6790.0020.0020.0000.0000.0000.000
110A611GLY0-0.021-0.00119.1930.0070.0070.0000.0000.0000.000
111A612ASP-1-0.910-0.94416.993-0.102-0.1020.0000.0000.0000.000
112A613THR0-0.001-0.00417.234-0.003-0.0030.0000.0000.0000.000
113A614SER00.0420.00518.8570.0000.0000.0000.0000.0000.000
114A615PHE00.0290.03118.2070.0050.0050.0000.0000.0000.000
115A616ASP-1-0.875-0.95914.9610.0250.0250.0000.0000.0000.000
116A617LEU0-0.059-0.02013.383-0.001-0.0010.0000.0000.0000.000
117A618PRO0-0.0080.01212.9440.0170.0170.0000.0000.0000.000
118A619GLU-1-0.823-0.9147.1100.2210.2210.0000.0000.0000.000
119A620ALA0-0.027-0.0199.8870.0010.0010.0000.0000.0000.000
120A621ASN0-0.010-0.0058.4870.0190.0190.0000.0000.0000.000
121A622VAL00.005-0.00210.559-0.096-0.0960.0000.0000.0000.000
122A623LEU0-0.0070.01113.0270.0450.0450.0000.0000.0000.000
123A624ILE0-0.012-0.00914.668-0.026-0.0260.0000.0000.0000.000
124A625GLN0-0.001-0.00917.5890.0240.0240.0000.0000.0000.000
125A626ILE00.0340.02120.104-0.005-0.0050.0000.0000.0000.000
126A627SER00.016-0.00523.5190.0030.0030.0000.0000.0000.000
127A628SER0-0.0340.01022.998-0.014-0.0140.0000.0000.0000.000
128A629HIS10.8710.92524.6070.1030.1030.0000.0000.0000.000
129A630GLY00.0240.04825.440-0.008-0.0080.0000.0000.0000.000
130A631GLY00.1240.01425.7810.0060.0060.0000.0000.0000.000
131A632SER0-0.103-0.03521.525-0.009-0.0090.0000.0000.0000.000
132A633ARG10.9040.93719.2290.1390.1390.0000.0000.0000.000
133A634ARG10.9390.96315.6890.1500.1500.0000.0000.0000.000
134A635GLN0-0.015-0.00916.556-0.009-0.0090.0000.0000.0000.000
135A636GLU-1-0.771-0.84116.344-0.184-0.1840.0000.0000.0000.000
136A637ALA00.0140.01312.813-0.015-0.0150.0000.0000.0000.000
137A638GLN0-0.0010.00911.642-0.029-0.0290.0000.0000.0000.000
138A639ARG10.8290.90311.7590.1450.1450.0000.0000.0000.000
139A640LEU00.002-0.0018.9030.0120.0120.0000.0000.0000.000
140A641GLY00.0130.0057.565-0.019-0.0190.0000.0000.0000.000
141A642ARG10.8810.9427.1440.1000.1000.0000.0000.0000.000
142A643VAL0-0.0140.0068.9160.0510.0510.0000.0000.0000.000
143A644LEU0-0.028-0.0047.5770.0390.0390.0000.0000.0000.000
144A645ARG10.7880.8873.748-0.334-0.0310.003-0.035-0.2710.000
145A646ALA0-0.001-0.0043.791-0.602-0.2200.006-0.130-0.2580.000
146A647LYS10.8230.9105.3110.4770.591-0.001-0.004-0.1090.000
147A648LYS10.9020.9848.110-0.512-0.5120.0000.0000.0000.000
148A649GLY00.059-0.0059.4260.0380.0380.0000.0000.0000.000
149A650MET0-0.030-0.0118.9420.0850.0850.0000.0000.0000.000
150A651VAL00.009-0.0065.437-0.261-0.2610.0000.0000.0000.000
151A652ALA00.0040.0067.390-0.097-0.0970.0000.0000.0000.000
152A653GLU-1-0.904-0.9429.919-0.483-0.4830.0000.0000.0000.000
153A654GLU-1-0.898-0.9468.632-0.814-0.8140.0000.0000.0000.000
154A655TYR0-0.010-0.0098.835-0.289-0.2890.0000.0000.0000.000
155A656ASN00.0060.0024.3430.2910.361-0.001-0.026-0.0420.000
156A657ALA00.0360.0167.6140.1680.1680.0000.0000.0000.000
157A658PHE0-0.031-0.0159.605-0.057-0.0570.0000.0000.0000.000
158A659PHE00.0450.02812.2180.0560.0560.0000.0000.0000.000
159A660TYR00.0480.02713.799-0.018-0.0180.0000.0000.0000.000
160A661SER00.0110.01017.5460.0190.0190.0000.0000.0000.000
161A662LEU0-0.019-0.00720.047-0.003-0.0030.0000.0000.0000.000
162A663VAL0-0.026-0.01223.5890.0080.0080.0000.0000.0000.000
163A664SER0-0.004-0.02126.1910.0000.0000.0000.0000.0000.000
164A665GLN0-0.004-0.02029.949-0.003-0.0030.0000.0000.0000.000
165A666ASP-1-0.892-0.94531.721-0.082-0.0820.0000.0000.0000.000
166A667THR0-0.008-0.02331.7080.0060.0060.0000.0000.0000.000
167A668GLN00.0150.00131.871-0.005-0.0050.0000.0000.0000.000
168A669GLU-1-0.784-0.88326.723-0.118-0.1180.0000.0000.0000.000
169A670MET00.0700.04627.200-0.009-0.0090.0000.0000.0000.000
170A671ALA00.0050.02127.507-0.007-0.0070.0000.0000.0000.000
171A672TYR0-0.105-0.04824.661-0.002-0.0020.0000.0000.0000.000
172A673SER00.031-0.01323.172-0.006-0.0060.0000.0000.0000.000
173A674THR00.0130.00922.624-0.012-0.0120.0000.0000.0000.000
174A675LYS10.8920.94323.0020.1050.1050.0000.0000.0000.000
175A676ARG10.8120.85817.9330.1800.1800.0000.0000.0000.000
176A677GLN00.0110.02518.220-0.006-0.0060.0000.0000.0000.000
177A678ARG10.9580.97518.0590.1260.1260.0000.0000.0000.000
178A679PHE00.0030.00216.038-0.008-0.0080.0000.0000.0000.000
179A680LEU00.008-0.00812.931-0.013-0.0130.0000.0000.0000.000
180A681VAL00.0070.01613.206-0.048-0.0480.0000.0000.0000.000
181A682ASP-1-0.888-0.93214.261-0.225-0.2250.0000.0000.0000.000
182A683GLN0-0.096-0.05611.8090.0420.0420.0000.0000.0000.000
183A684GLY0-0.0010.00510.391-0.048-0.0480.0000.0000.0000.000
184A685TYR0-0.058-0.0327.049-0.087-0.0870.0000.0000.0000.000
185A686SER00.0180.00310.5520.1190.1190.0000.0000.0000.000
186A687PHE00.022-0.01012.579-0.008-0.0080.0000.0000.0000.000
187A688LYS10.8880.94015.5440.3890.3890.0000.0000.0000.000
188A689VAL00.0240.01518.783-0.002-0.0020.0000.0000.0000.000
189A690ILE0-0.022-0.01219.4310.0000.0000.0000.0000.0000.000
190A691THR00.0230.00123.3790.0060.0060.0000.0000.0000.000
191A692LYS10.9860.98126.6560.1190.1190.0000.0000.0000.000
192A693LEU0-0.042-0.00822.604-0.011-0.0110.0000.0000.0000.000
193A694ALA00.001-0.00925.1620.0110.0110.0000.0000.0000.000
194A695GLY00.1290.06326.667-0.005-0.0050.0000.0000.0000.000
195A696MET0-0.073-0.03827.9730.0000.0000.0000.0000.0000.000
196A697GLU-1-0.962-0.98729.910-0.095-0.0950.0000.0000.0000.000
197A698GLU-1-0.949-0.95930.151-0.106-0.1060.0000.0000.0000.000
198A699GLU-1-0.853-0.91727.750-0.101-0.1010.0000.0000.0000.000
199A700ASP-1-0.915-0.94031.612-0.062-0.0620.0000.0000.0000.000
200A701LEU0-0.063-0.03429.186-0.002-0.0020.0000.0000.0000.000
201A702ALA00.0410.00732.6660.0040.0040.0000.0000.0000.000
202A703PHE0-0.035-0.02633.566-0.004-0.0040.0000.0000.0000.000
203A704SER00.0050.02237.067-0.001-0.0010.0000.0000.0000.000
204A705THR00.005-0.02338.6570.0010.0010.0000.0000.0000.000
205A706LYS10.8450.88340.7160.0580.0580.0000.0000.0000.000
206A707GLU-1-0.846-0.92043.296-0.039-0.0390.0000.0000.0000.000
207A708GLU-1-0.731-0.84138.862-0.056-0.0560.0000.0000.0000.000
208A709GLN0-0.042-0.03938.0290.0000.0000.0000.0000.0000.000
209A710GLN0-0.008-0.00840.147-0.002-0.0020.0000.0000.0000.000
210A711GLN0-0.024-0.01341.9180.0000.0000.0000.0000.0000.000
211A712LEU0-0.052-0.01234.9490.0010.0010.0000.0000.0000.000
212A713LEU0-0.019-0.01439.4900.0000.0000.0000.0000.0000.000
213A714GLN00.0190.01540.9820.0000.0000.0000.0000.0000.000
214A715LYS10.8840.93437.7650.0470.0470.0000.0000.0000.000
215A716VAL0-0.033-0.02436.6890.0000.0000.0000.0000.0000.000
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