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: KGQG3

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 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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3095520.728123
FMO2-HF: Nuclear repulsion 3002362.335083
FMO2-HF: Total energy -93158.39304
FMO2-MP2: Total energy -93429.656186


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.
-1.82.0960.06-1.469-2.4870.002
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 : 0.073 / q_NPA : 0.034
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].
3A504LYS10.8460.9403.319-0.7362.0900.051-1.231-1.6470.002
4A505VAL00.016-0.0075.2730.4560.581-0.001-0.007-0.1170.000
5A506GLN0-0.0110.0287.5650.1430.1430.0000.0000.0000.000
6A507CYS0-0.045-0.02011.1780.0700.0700.0000.0000.0000.000
7A508ALA00.001-0.00413.5800.0160.0160.0000.0000.0000.000
8A509GLU-1-0.765-0.84517.343-0.184-0.1840.0000.0000.0000.000
9A510VAL0-0.022-0.02320.534-0.002-0.0020.0000.0000.0000.000
10A511TRP0-0.012-0.00523.2910.0150.0150.0000.0000.0000.000
11A512CYS00.0050.00026.6810.0010.0010.0000.0000.0000.000
12A513PRO00.0650.02329.3600.0040.0040.0000.0000.0000.000
13A514MET0-0.0120.02433.132-0.001-0.0010.0000.0000.0000.000
14A515SER0-0.009-0.00135.2360.0000.0000.0000.0000.0000.000
15A516PRO00.0340.00637.9450.0010.0010.0000.0000.0000.000
16A517GLU-1-0.804-0.88241.248-0.060-0.0600.0000.0000.0000.000
17A518PHE00.0510.00836.6360.0010.0010.0000.0000.0000.000
18A519TYR0-0.036-0.01537.5650.0010.0010.0000.0000.0000.000
19A520ARG10.8840.92739.8410.0520.0520.0000.0000.0000.000
20A521GLU-1-0.770-0.87341.446-0.048-0.0480.0000.0000.0000.000
21A522TYR0-0.0080.00835.831-0.001-0.0010.0000.0000.0000.000
22A523VAL0-0.0090.00939.9870.0000.0000.0000.0000.0000.000
23A524ALA00.0090.01242.5500.0020.0020.0000.0000.0000.000
24A525ILE00.0070.00841.2870.0020.0020.0000.0000.0000.000
25A526LYS10.8740.92541.8310.0510.0510.0000.0000.0000.000
26A527THR0-0.028-0.01841.217-0.002-0.0020.0000.0000.0000.000
27A528LYS10.8460.90336.0910.0500.0500.0000.0000.0000.000
28A529LYS10.8890.92236.3260.0430.0430.0000.0000.0000.000
29A530ARG10.7850.88836.8440.0650.0650.0000.0000.0000.000
30A531ILE00.007-0.00731.195-0.004-0.0040.0000.0000.0000.000
31A532LEU00.0080.02132.733-0.006-0.0060.0000.0000.0000.000
32A533LEU0-0.0260.00034.193-0.002-0.0020.0000.0000.0000.000
33A534TYR00.005-0.00629.150-0.002-0.0020.0000.0000.0000.000
34A535THR0-0.037-0.01628.236-0.009-0.0090.0000.0000.0000.000
35A536MET0-0.0190.00429.971-0.006-0.0060.0000.0000.0000.000
36A537ASN00.009-0.00731.5520.0080.0080.0000.0000.0000.000
37A538PRO00.0430.01831.919-0.006-0.0060.0000.0000.0000.000
38A539ASN0-0.030-0.01631.921-0.002-0.0020.0000.0000.0000.000
39A540LYS10.7940.88926.5560.1170.1170.0000.0000.0000.000
40A541PHE00.0220.00927.468-0.008-0.0080.0000.0000.0000.000
41A542ARG10.8780.93828.4180.0850.0850.0000.0000.0000.000
42A543ALA00.0370.01425.481-0.005-0.0050.0000.0000.0000.000
43A544CYS0-0.045-0.01923.792-0.014-0.0140.0000.0000.0000.000
44A545GLN00.0690.04024.069-0.006-0.0060.0000.0000.0000.000
45A546PHE00.0370.02724.260-0.003-0.0030.0000.0000.0000.000
46A547LEU0-0.018-0.01019.596-0.011-0.0110.0000.0000.0000.000
47A548ILE0-0.020-0.01420.659-0.014-0.0140.0000.0000.0000.000
48A549LYS10.8580.92121.4310.0860.0860.0000.0000.0000.000
49A550PHE0-0.034-0.00818.553-0.001-0.0010.0000.0000.0000.000
50A551HIS10.8190.88615.6900.3070.3070.0000.0000.0000.000
51A552GLU-1-0.760-0.84418.134-0.091-0.0910.0000.0000.0000.000
52A553ARG10.8550.91420.4610.1430.1430.0000.0000.0000.000
53A554ARG10.8460.89513.0180.3590.3590.0000.0000.0000.000
54A555ASN0-0.035-0.02316.6230.0040.0040.0000.0000.0000.000
55A556ASP-1-0.796-0.83713.827-0.325-0.3250.0000.0000.0000.000
56A557LYS10.8490.93312.5200.0320.0320.0000.0000.0000.000
57A558ILE0-0.010-0.01513.488-0.048-0.0480.0000.0000.0000.000
58A559ILE00.0260.01314.1570.0280.0280.0000.0000.0000.000
59A560VAL0-0.006-0.00817.026-0.027-0.0270.0000.0000.0000.000
60A561PHE0-0.025-0.01118.6120.0130.0130.0000.0000.0000.000
61A562ALA00.0320.00220.577-0.006-0.0060.0000.0000.0000.000
62A563ASP-1-0.785-0.87724.196-0.102-0.1020.0000.0000.0000.000
63A564ASN0-0.008-0.01325.3100.0080.0080.0000.0000.0000.000
64A565VAL00.0480.01128.804-0.002-0.0020.0000.0000.0000.000
65A566PHE00.0070.01130.2810.0010.0010.0000.0000.0000.000
66A567ALA00.0570.00228.9290.0000.0000.0000.0000.0000.000
67A568LEU0-0.049-0.01224.551-0.002-0.0020.0000.0000.0000.000
68A569LYS10.8980.95527.8820.0420.0420.0000.0000.0000.000
69A570GLU-1-0.751-0.85330.824-0.054-0.0540.0000.0000.0000.000
70A571TYR0-0.032-0.04326.952-0.003-0.0030.0000.0000.0000.000
71A572ALA00.0080.00726.7680.0010.0010.0000.0000.0000.000
72A573ILE0-0.002-0.00127.9170.0030.0030.0000.0000.0000.000
73A574ARG10.8030.89831.3430.0650.0650.0000.0000.0000.000
74A575LEU0-0.028-0.01026.231-0.002-0.0020.0000.0000.0000.000
75A576ASN0-0.039-0.01428.0180.0010.0010.0000.0000.0000.000
76A577LYS10.7970.89423.6720.0820.0820.0000.0000.0000.000
77A578PRO00.0310.01024.1770.0010.0010.0000.0000.0000.000
78A579TYR0-0.002-0.00724.304-0.008-0.0080.0000.0000.0000.000
79A580ILE0-0.037-0.00820.9680.0080.0080.0000.0000.0000.000
80A581TYR00.0740.01524.317-0.008-0.0080.0000.0000.0000.000
81A582GLY00.024-0.00126.6600.0050.0050.0000.0000.0000.000
82A583PRO0-0.019-0.02528.6720.0040.0040.0000.0000.0000.000
83A584THR0-0.0160.03226.0730.0010.0010.0000.0000.0000.000
84A585SER00.0440.01628.2250.0030.0030.0000.0000.0000.000
85A586GLN00.0570.00025.5690.0000.0000.0000.0000.0000.000
86A587GLY00.0160.01926.3330.0030.0030.0000.0000.0000.000
87A588GLU-1-0.811-0.89027.268-0.018-0.0180.0000.0000.0000.000
88A589ARG10.8620.92122.8170.0230.0230.0000.0000.0000.000
89A590MET00.0260.03520.2870.0020.0020.0000.0000.0000.000
90A591GLN00.0240.01522.6940.0060.0060.0000.0000.0000.000
91A592ILE00.0230.01821.9120.0010.0010.0000.0000.0000.000
92A593LEU0-0.014-0.00617.753-0.003-0.0030.0000.0000.0000.000
93A594GLN0-0.002-0.03018.6160.0130.0130.0000.0000.0000.000
94A595ASN0-0.022-0.01020.2210.0050.0050.0000.0000.0000.000
95A596PHE00.0090.01414.2710.0030.0030.0000.0000.0000.000
96A597LYS10.8410.93614.774-0.051-0.0510.0000.0000.0000.000
97A598HIS00.012-0.00916.3100.0100.0100.0000.0000.0000.000
98A599ASN00.0140.00218.9920.0020.0020.0000.0000.0000.000
99A600PRO00.001-0.01119.938-0.011-0.0110.0000.0000.0000.000
100A601LYS10.8930.95521.078-0.011-0.0110.0000.0000.0000.000
101A602ILE0-0.024-0.01021.902-0.006-0.0060.0000.0000.0000.000
102A603ASN00.0180.00517.8500.0140.0140.0000.0000.0000.000
103A604THR00.018-0.02017.632-0.025-0.0250.0000.0000.0000.000
104A605ILE0-0.037-0.00618.1030.0140.0140.0000.0000.0000.000
105A606PHE00.0300.00620.197-0.017-0.0170.0000.0000.0000.000
106A607ILE0-0.025-0.01917.6630.0120.0120.0000.0000.0000.000
107A608SER00.020-0.01121.722-0.010-0.0100.0000.0000.0000.000
108A609LYS10.8440.90121.9660.0920.0920.0000.0000.0000.000
109A610VAL0-0.026-0.00522.1840.0000.0000.0000.0000.0000.000
110A611GLY0-0.0100.00618.9660.0070.0070.0000.0000.0000.000
111A612ASP-1-0.899-0.94617.056-0.122-0.1220.0000.0000.0000.000
112A613THR0-0.009-0.00517.321-0.002-0.0020.0000.0000.0000.000
113A614SER00.0390.00919.2290.0010.0010.0000.0000.0000.000
114A615PHE00.0510.03518.3860.0060.0060.0000.0000.0000.000
115A616ASP-1-0.824-0.91115.3020.0180.0180.0000.0000.0000.000
116A617LEU0-0.076-0.03313.9570.0030.0030.0000.0000.0000.000
117A618PRO0-0.0140.00612.9740.0080.0080.0000.0000.0000.000
118A619GLU-1-0.815-0.8997.1210.2410.2410.0000.0000.0000.000
119A620ALA0-0.033-0.0209.7000.0090.0090.0000.0000.0000.000
120A621ASN0-0.018-0.0188.2360.0250.0250.0000.0000.0000.000
121A622VAL00.003-0.00110.268-0.107-0.1070.0000.0000.0000.000
122A623LEU00.0010.01713.1040.0500.0500.0000.0000.0000.000
123A624ILE00.003-0.00414.694-0.028-0.0280.0000.0000.0000.000
124A625GLN0-0.001-0.01517.5480.0270.0270.0000.0000.0000.000
125A626ILE00.0350.02120.111-0.004-0.0040.0000.0000.0000.000
126A627SER0-0.013-0.01923.5230.0050.0050.0000.0000.0000.000
127A628SER0-0.0110.00823.098-0.017-0.0170.0000.0000.0000.000
128A629HIS10.8770.92724.8450.1150.1150.0000.0000.0000.000
129A630GLY00.0520.03425.697-0.009-0.0090.0000.0000.0000.000
130A631GLY00.0570.00925.7680.0050.0050.0000.0000.0000.000
131A632SER0-0.0350.00521.629-0.011-0.0110.0000.0000.0000.000
132A633ARG10.8820.91619.0820.1540.1540.0000.0000.0000.000
133A634ARG10.9070.94715.6340.1770.1770.0000.0000.0000.000
134A635GLN0-0.0030.00316.350-0.010-0.0100.0000.0000.0000.000
135A636GLU-1-0.771-0.83716.368-0.200-0.2000.0000.0000.0000.000
136A637ALA00.0260.01312.964-0.018-0.0180.0000.0000.0000.000
137A638GLN0-0.0160.00211.635-0.029-0.0290.0000.0000.0000.000
138A639ARG10.8200.89212.1750.1660.1660.0000.0000.0000.000
139A640LEU0-0.017-0.0048.5730.0080.0080.0000.0000.0000.000
140A641GLY00.0220.0137.516-0.024-0.0240.0000.0000.0000.000
141A642ARG10.8510.9197.5560.1080.1080.0000.0000.0000.000
142A643VAL00.0060.0239.0070.0480.0480.0000.0000.0000.000
143A644LEU0-0.026-0.0027.4250.0420.0420.0000.0000.0000.000
144A645ARG10.7610.8513.836-0.3090.0180.003-0.041-0.2890.000
145A646ALA00.0070.0133.648-0.599-0.1390.009-0.165-0.3030.000
146A647LYS10.8290.9025.3420.5720.694-0.001-0.005-0.1160.000
147A648LYS10.9490.9928.269-0.546-0.5460.0000.0000.0000.000
148A649GLY00.0290.0099.2970.0130.0130.0000.0000.0000.000
149A650MET0-0.046-0.0088.9770.0650.0650.0000.0000.0000.000
150A651VAL00.018-0.0025.221-0.414-0.4140.0000.0000.0000.000
151A652ALA00.0050.0006.804-0.241-0.2410.0000.0000.0000.000
152A653GLU-1-0.873-0.9359.640-0.506-0.5060.0000.0000.0000.000
153A654GLU-1-0.894-0.9428.632-0.837-0.8370.0000.0000.0000.000
154A655TYR0-0.011-0.0088.522-0.283-0.2830.0000.0000.0000.000
155A656ASN0-0.013-0.0084.1180.0350.071-0.001-0.020-0.0150.000
156A657ALA00.0320.0237.2130.1680.1680.0000.0000.0000.000
157A658PHE0-0.013-0.0089.200-0.049-0.0490.0000.0000.0000.000
158A659PHE00.0290.00611.9660.0620.0620.0000.0000.0000.000
159A660TYR00.0580.03313.624-0.011-0.0110.0000.0000.0000.000
160A661SER00.0080.00817.4090.0170.0170.0000.0000.0000.000
161A662LEU0-0.014-0.00120.122-0.002-0.0020.0000.0000.0000.000
162A663VAL0-0.027-0.01123.6520.0090.0090.0000.0000.0000.000
163A664SER0-0.012-0.02926.3050.0000.0000.0000.0000.0000.000
164A665GLN0-0.019-0.02730.080-0.003-0.0030.0000.0000.0000.000
165A666ASP-1-0.874-0.93831.629-0.089-0.0890.0000.0000.0000.000
166A667THR0-0.019-0.01631.9910.0060.0060.0000.0000.0000.000
167A668GLN00.0250.00632.131-0.007-0.0070.0000.0000.0000.000
168A669GLU-1-0.781-0.87026.980-0.128-0.1280.0000.0000.0000.000
169A670MET00.0650.03927.374-0.010-0.0100.0000.0000.0000.000
170A671ALA0-0.029-0.00227.936-0.006-0.0060.0000.0000.0000.000
171A672TYR0-0.104-0.04924.764-0.001-0.0010.0000.0000.0000.000
172A673SER00.0270.00323.361-0.007-0.0070.0000.0000.0000.000
173A674THR00.0150.00422.546-0.013-0.0130.0000.0000.0000.000
174A675LYS10.9040.95422.9620.1170.1170.0000.0000.0000.000
175A676ARG10.7940.84518.1450.1920.1920.0000.0000.0000.000
176A677GLN00.0240.01818.226-0.008-0.0080.0000.0000.0000.000
177A678ARG10.8580.91018.0140.1520.1520.0000.0000.0000.000
178A679PHE00.0080.01216.079-0.010-0.0100.0000.0000.0000.000
179A680LEU0-0.008-0.00512.948-0.014-0.0140.0000.0000.0000.000
180A681VAL00.0140.01713.357-0.045-0.0450.0000.0000.0000.000
181A682ASP-1-0.833-0.90014.738-0.220-0.2200.0000.0000.0000.000
182A683GLN0-0.041-0.02912.1190.0410.0410.0000.0000.0000.000
183A684GLY00.0120.02110.695-0.045-0.0450.0000.0000.0000.000
184A685TYR0-0.043-0.0277.175-0.067-0.0670.0000.0000.0000.000
185A686SER00.0140.00410.0720.1210.1210.0000.0000.0000.000
186A687PHE00.028-0.00612.063-0.015-0.0150.0000.0000.0000.000
187A688LYS10.9040.94915.1440.4200.4200.0000.0000.0000.000
188A689VAL00.0100.00418.561-0.002-0.0020.0000.0000.0000.000
189A690ILE0-0.024-0.00719.535-0.003-0.0030.0000.0000.0000.000
190A691THR00.0320.01123.4860.0040.0040.0000.0000.0000.000
191A692LYS10.9750.97926.5570.1260.1260.0000.0000.0000.000
192A693LEU0-0.0280.00022.178-0.013-0.0130.0000.0000.0000.000
193A694ALA0-0.005-0.01224.6800.0130.0130.0000.0000.0000.000
194A695GLY00.1350.06226.036-0.007-0.0070.0000.0000.0000.000
195A696MET0-0.111-0.04327.7490.0020.0020.0000.0000.0000.000
196A697GLU-1-0.866-0.95029.658-0.098-0.0980.0000.0000.0000.000
197A698GLU-1-0.948-0.95929.838-0.111-0.1110.0000.0000.0000.000
198A699GLU-1-0.841-0.90327.657-0.102-0.1020.0000.0000.0000.000
199A700ASP-1-0.923-0.94231.510-0.065-0.0650.0000.0000.0000.000
200A701LEU0-0.055-0.02628.855-0.006-0.0060.0000.0000.0000.000
201A702ALA00.0370.01132.7270.0040.0040.0000.0000.0000.000
202A703PHE0-0.060-0.04733.436-0.005-0.0050.0000.0000.0000.000
203A704SER0-0.0110.00537.012-0.001-0.0010.0000.0000.0000.000
204A705THR00.000-0.01538.7650.0020.0020.0000.0000.0000.000
205A706LYS10.8340.86940.4640.0620.0620.0000.0000.0000.000
206A707GLU-1-0.834-0.89943.305-0.042-0.0420.0000.0000.0000.000
207A708GLU-1-0.722-0.82638.549-0.060-0.0600.0000.0000.0000.000
208A709GLN0-0.013-0.01037.963-0.001-0.0010.0000.0000.0000.000
209A710GLN00.0290.00240.009-0.002-0.0020.0000.0000.0000.000
210A711GLN0-0.050-0.03641.8720.0000.0000.0000.0000.0000.000
211A712LEU0-0.055-0.01434.9140.0010.0010.0000.0000.0000.000
212A713LEU0-0.024-0.01139.4280.0000.0000.0000.0000.0000.000
213A714GLN00.0350.01941.0160.0000.0000.0000.0000.0000.000
214A715LYS10.8820.93837.6860.0510.0510.0000.0000.0000.000
215A716VAL0-0.037-0.02736.8030.0000.0000.0000.0000.0000.000
216A717LEU0-0.007-0.01139.5140.0000.0000.0000.0000.0000.000
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