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: 2J2QR

Calculation Name: 3OA7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OA7

Chain ID: A

ChEMBL ID:

UniProt ID: P53865

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1617557.228583
FMO2-HF: Nuclear repulsion 1537336.936149
FMO2-HF: Total energy -80220.292434
FMO2-MP2: Total energy -80453.395936


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-0.0871.430.029-0.71-0.835-0.002
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.013
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].
3A3LEU0-0.023-0.0013.8490.7301.3390.000-0.373-0.2350.000
4A4LYS10.9000.9396.539-0.255-0.2550.0000.0000.0000.000
5A5PRO0-0.017-0.0238.699-0.094-0.0940.0000.0000.0000.000
6A6GLU-1-0.904-0.96612.063-0.114-0.1140.0000.0000.0000.000
7A7GLU-1-0.795-0.8717.348-0.921-0.9210.0000.0000.0000.000
8A8HIS0-0.033-0.03110.872-0.156-0.1560.0000.0000.0000.000
9A9GLU-1-0.913-0.96912.153-0.273-0.2730.0000.0000.0000.000
10A10ASP-1-0.863-0.91514.140-0.288-0.2880.0000.0000.0000.000
11A11ILE0-0.081-0.04111.1140.0350.0350.0000.0000.0000.000
12A12LEU0-0.019-0.01715.4740.0460.0460.0000.0000.0000.000
13A13ASN0-0.048-0.02118.1310.0430.0430.0000.0000.0000.000
14A14LYS10.9510.97416.4260.3990.3990.0000.0000.0000.000
15A15LEU0-0.030-0.02817.9170.0270.0270.0000.0000.0000.000
16A16LEU0-0.038-0.01021.2250.0240.0240.0000.0000.0000.000
17A17ASP-1-0.912-0.94723.643-0.165-0.1650.0000.0000.0000.000
18A18PRO0-0.051-0.02725.453-0.008-0.0080.0000.0000.0000.000
19A19GLU-1-0.959-0.99128.411-0.126-0.1260.0000.0000.0000.000
20A20LEU0-0.0430.01020.868-0.004-0.0040.0000.0000.0000.000
21A21ALA00.0400.01725.1760.0080.0080.0000.0000.0000.000
22A22GLN00.007-0.01624.393-0.019-0.0190.0000.0000.0000.000
23A23SER0-0.021-0.01623.418-0.018-0.0180.0000.0000.0000.000
24A24GLU-1-0.812-0.90820.561-0.309-0.3090.0000.0000.0000.000
25A25ARG10.9220.97819.7000.2070.2070.0000.0000.0000.000
26A26THR0-0.080-0.05319.937-0.033-0.0330.0000.0000.0000.000
27A27GLU-1-0.937-0.96416.015-0.446-0.4460.0000.0000.0000.000
28A28ALA00.0640.03615.356-0.094-0.0940.0000.0000.0000.000
29A29LEU0-0.002-0.00815.079-0.088-0.0880.0000.0000.0000.000
30A30GLN0-0.0210.00314.050-0.019-0.0190.0000.0000.0000.000
31A31GLN00.003-0.01210.333-0.002-0.0020.0000.0000.0000.000
32A32LEU00.0120.01610.621-0.271-0.2710.0000.0000.0000.000
33A33ARG10.8940.95311.9440.4500.4500.0000.0000.0000.000
34A34VAL0-0.034-0.0328.242-0.008-0.0080.0000.0000.0000.000
35A35ASN00.0480.0356.555-0.973-0.9730.0000.0000.0000.000
36A36TYR00.0030.0127.356-0.207-0.2070.0000.0000.0000.000
37A37GLY00.0070.0039.9390.1330.1330.0000.0000.0000.000
38A38SER0-0.006-0.0053.4990.5000.6390.003-0.041-0.1010.000
39A39PHE00.0230.0156.2350.2550.2550.0000.0000.0000.000
40A40VAL00.0190.0047.1250.3650.3650.0000.0000.0000.000
41A41SER0-0.014-0.0097.8730.1720.1720.0000.0000.0000.000
42A42GLU-1-0.915-0.9563.7091.1191.8880.026-0.296-0.499-0.002
43A43TYR0-0.0060.0017.4470.1870.1870.0000.0000.0000.000
44A44ASN0-0.001-0.02010.5590.1120.1120.0000.0000.0000.000
45A45ASP-1-0.899-0.94110.0080.0750.0750.0000.0000.0000.000
46A46LEU00.004-0.00210.1790.0670.0670.0000.0000.0000.000
47A47THR0-0.012-0.00812.4850.0110.0110.0000.0000.0000.000
48A48LYS10.9020.95315.140-0.107-0.1070.0000.0000.0000.000
49A49SER0-0.064-0.01614.583-0.004-0.0040.0000.0000.0000.000
50A50HIS00.0400.01816.3350.0210.0210.0000.0000.0000.000
51A429ASN0-0.016-0.01818.046-0.003-0.0030.0000.0000.0000.000
52A430THR0-0.069-0.04720.054-0.007-0.0070.0000.0000.0000.000
53A431LEU00.0610.03818.748-0.004-0.0040.0000.0000.0000.000
54A432SER00.0090.00321.808-0.007-0.0070.0000.0000.0000.000
55A433LYS10.9490.98424.198-0.062-0.0620.0000.0000.0000.000
56A434GLU-1-0.974-0.99323.4170.1370.1370.0000.0000.0000.000
57A435LEU0-0.004-0.00825.532-0.004-0.0040.0000.0000.0000.000
58A436ASP-1-0.866-0.93027.5590.0510.0510.0000.0000.0000.000
59A437ASN0-0.072-0.04229.946-0.009-0.0090.0000.0000.0000.000
60A438LEU0-0.038-0.01429.124-0.004-0.0040.0000.0000.0000.000
61A439ARG11.0291.00328.508-0.079-0.0790.0000.0000.0000.000
62A440SER0-0.0050.01433.638-0.005-0.0050.0000.0000.0000.000
63A441ARG10.8940.94333.267-0.068-0.0680.0000.0000.0000.000
64A442PHE0-0.021-0.00435.167-0.001-0.0010.0000.0000.0000.000
65A443GLY00.0720.03137.085-0.002-0.0020.0000.0000.0000.000
66A444ASN0-0.041-0.03639.364-0.005-0.0050.0000.0000.0000.000
67A445LEU0-0.091-0.02639.749-0.002-0.0020.0000.0000.0000.000
68A446GLU-1-0.953-0.96840.5690.0590.0590.0000.0000.0000.000
69A447GLY0-0.023-0.00142.895-0.002-0.0020.0000.0000.0000.000
70A448ASN00.0380.01444.6710.0020.0020.0000.0000.0000.000
71A449THR00.0470.01844.024-0.001-0.0010.0000.0000.0000.000
72A450SER0-0.074-0.05646.6460.0000.0000.0000.0000.0000.000
73A451GLU-1-0.978-0.98549.4420.0290.0290.0000.0000.0000.000
74A452ARG10.9280.98044.290-0.049-0.0490.0000.0000.0000.000
75A453ILE0-0.032-0.01251.656-0.001-0.0010.0000.0000.0000.000
76A454THR0-0.0120.01053.7630.0010.0010.0000.0000.0000.000
77A455ILE00.1330.04055.235-0.002-0.0020.0000.0000.0000.000
78A456LYS10.9880.98454.684-0.034-0.0340.0000.0000.0000.000
79A457ASN00.0160.00155.9970.0000.0000.0000.0000.0000.000
80A458ILE00.0190.02258.384-0.001-0.0010.0000.0000.0000.000
81A459LEU0-0.018-0.00761.383-0.001-0.0010.0000.0000.0000.000
82A460GLN0-0.042-0.02061.633-0.001-0.0010.0000.0000.0000.000
83A461SER0-0.056-0.03362.570-0.001-0.0010.0000.0000.0000.000
84A462ARG10.8250.90464.974-0.025-0.0250.0000.0000.0000.000
85A463PRO00.0240.02066.8770.0010.0010.0000.0000.0000.000
86A464ASP-1-0.884-0.93669.4500.0230.0230.0000.0000.0000.000
87A465ILE0-0.0190.01364.1200.0000.0000.0000.0000.0000.000
88A466SER00.0280.02466.5490.0000.0000.0000.0000.0000.000
89A467ALA00.057-0.00362.4330.0010.0010.0000.0000.0000.000
90A468GLU-1-0.911-0.96762.6230.0280.0280.0000.0000.0000.000
91A469GLU-1-0.918-0.95364.2490.0280.0280.0000.0000.0000.000
92A470CYS0-0.039-0.02759.9290.0010.0010.0000.0000.0000.000
93A471ASN0-0.008-0.00559.2240.0020.0020.0000.0000.0000.000
94A472PHE0-0.019-0.00459.9860.0010.0010.0000.0000.0000.000
95A473LEU0-0.055-0.02661.3360.0010.0010.0000.0000.0000.000
96A474MET0-0.023-0.00255.5850.0010.0010.0000.0000.0000.000
97A475VAL00.008-0.00155.9300.0010.0010.0000.0000.0000.000
98A476GLU-1-0.905-0.95952.7590.0420.0420.0000.0000.0000.000
99A477GLN00.0000.01051.5550.0020.0020.0000.0000.0000.000
100A478ILE0-0.073-0.04550.7030.0020.0020.0000.0000.0000.000
101A479ASP-1-0.913-0.95048.3010.0460.0460.0000.0000.0000.000
102A480SER0-0.084-0.04546.3220.0030.0030.0000.0000.0000.000
103A481ALA0-0.047-0.00345.8090.0030.0030.0000.0000.0000.000
104A482ASN00.0560.03543.136-0.002-0.0020.0000.0000.0000.000
105A483LEU00.0710.01343.531-0.003-0.0030.0000.0000.0000.000
106A484THR00.0150.00744.262-0.002-0.0020.0000.0000.0000.000
107A485THR00.012-0.00146.299-0.003-0.0030.0000.0000.0000.000
108A486LEU00.0510.03248.655-0.003-0.0030.0000.0000.0000.000
109A487GLN0-0.048-0.02846.057-0.002-0.0020.0000.0000.0000.000
110A488ASN0-0.014-0.01849.408-0.003-0.0030.0000.0000.0000.000
111A489THR00.0610.03852.318-0.002-0.0020.0000.0000.0000.000
112A490VAL0-0.037-0.02354.040-0.002-0.0020.0000.0000.0000.000
113A491LYS10.9170.95050.147-0.046-0.0460.0000.0000.0000.000
114A492GLU-1-0.899-0.94356.1360.0400.0400.0000.0000.0000.000
115A493ILE00.0040.01457.763-0.002-0.0020.0000.0000.0000.000
116A494VAL0-0.070-0.04358.515-0.002-0.0020.0000.0000.0000.000
117A495LEU0-0.025-0.01558.496-0.001-0.0010.0000.0000.0000.000
118A496ALA0-0.0130.00562.099-0.001-0.0010.0000.0000.0000.000
119A497VAL0-0.054-0.03763.824-0.001-0.0010.0000.0000.0000.000
120A498GLY00.0500.04565.082-0.001-0.0010.0000.0000.0000.000
121A499ILE0-0.080-0.04263.787-0.001-0.0010.0000.0000.0000.000
122A500PRO0-0.004-0.01161.9810.0010.0010.0000.0000.0000.000
123A501TYR00.1180.05154.025-0.001-0.0010.0000.0000.0000.000
124A502PRO00.0280.01058.4020.0000.0000.0000.0000.0000.000
125A503LYS10.8720.93159.329-0.021-0.0210.0000.0000.0000.000
126A504LEU00.0530.04058.861-0.001-0.0010.0000.0000.0000.000
127A505ARG11.0240.99255.808-0.030-0.0300.0000.0000.0000.000
128A506ARG10.9500.98561.498-0.022-0.0220.0000.0000.0000.000
129A507LYS10.9660.97264.525-0.022-0.0220.0000.0000.0000.000
130A508ILE00.0450.03660.8710.0000.0000.0000.0000.0000.000
131A509PRO00.0320.01065.4990.0000.0000.0000.0000.0000.000
132A510LEU00.011-0.00568.5840.0000.0000.0000.0000.0000.000
133A511LEU00.0150.02165.3880.0000.0000.0000.0000.0000.000
134A512ALA00.006-0.00168.3710.0000.0000.0000.0000.0000.000
135A513ILE0-0.0080.00770.0520.0000.0000.0000.0000.0000.000
136A514LYS10.9450.98072.462-0.020-0.0200.0000.0000.0000.000
137A515LEU0-0.0130.00068.6750.0000.0000.0000.0000.0000.000
138A516LYS10.9550.96369.102-0.024-0.0240.0000.0000.0000.000
139A517TYR00.0070.00874.1500.0000.0000.0000.0000.0000.000
140A518GLU-1-0.874-0.94377.4350.0190.0190.0000.0000.0000.000
141A519ASN00.0600.03976.133-0.001-0.0010.0000.0000.0000.000
142A520ILE00.0090.01175.9450.0000.0000.0000.0000.0000.000
143A521MET0-0.030-0.02579.6190.0000.0000.0000.0000.0000.000
144A522LEU00.0140.00180.7110.0000.0000.0000.0000.0000.000
145A523SER0-0.026-0.01180.7780.0000.0000.0000.0000.0000.000
146A524ASN0-0.044-0.02882.934-0.001-0.0010.0000.0000.0000.000
147A525PHE00.0070.01885.2920.0000.0000.0000.0000.0000.000
148A526ALA00.0770.04785.8590.0000.0000.0000.0000.0000.000
149A527GLN00.008-0.01083.924-0.001-0.0010.0000.0000.0000.000
150A528ARG10.8890.91987.746-0.017-0.0170.0000.0000.0000.000
151A529LEU00.0070.00990.7580.0000.0000.0000.0000.0000.000
152A530HIS00.0580.03389.7380.0000.0000.0000.0000.0000.000
153A531ARG10.8730.94586.692-0.018-0.0180.0000.0000.0000.000
154A532GLN0-0.038-0.02192.9420.0000.0000.0000.0000.0000.000
155A533VAL00.0040.02495.0080.0000.0000.0000.0000.0000.000
156A534TYR00.0260.02792.7400.0000.0000.0000.0000.0000.000
157A535SER0-0.0730.00494.7060.0000.0000.0000.0000.0000.000
158A536GLN0-0.063-0.06691.8130.0000.0000.0000.0000.0000.000
159A537GLU-1-0.857-0.97287.2450.0180.0180.0000.0000.0000.000
160A538MET00.0040.03585.3230.0000.0000.0000.0000.0000.000
161A539ASN0-0.008-0.01681.3820.0010.0010.0000.0000.0000.000
162A540LEU00.0510.01180.1120.0000.0000.0000.0000.0000.000
163A541LYS10.9130.96073.607-0.026-0.0260.0000.0000.0000.000
164A542LYS10.9730.99076.782-0.021-0.0210.0000.0000.0000.000
165A543PHE0-0.017-0.01078.0740.0000.0000.0000.0000.0000.000
166A544THR0-0.0040.00073.0490.0000.0000.0000.0000.0000.000
167A545ASP-1-0.862-0.92972.9880.0280.0280.0000.0000.0000.000
168A546GLN0-0.058-0.01873.2980.0000.0000.0000.0000.0000.000
169A547ALA00.0520.03174.0580.0000.0000.0000.0000.0000.000
170A548TYR00.008-0.00364.3920.0010.0010.0000.0000.0000.000
171A549TYR0-0.020-0.01269.4840.0010.0010.0000.0000.0000.000
172A550ASP-1-0.808-0.91170.4960.0260.0260.0000.0000.0000.000
173A551PHE00.0100.00364.1690.0010.0010.0000.0000.0000.000
174A552MET0-0.053-0.03262.6390.0010.0010.0000.0000.0000.000
175A553SER0-0.049-0.02966.5160.0010.0010.0000.0000.0000.000
176A554THR0-0.0450.00167.9860.0000.0000.0000.0000.0000.000
177A555ARG10.8480.92160.897-0.035-0.0350.0000.0000.0000.000
178A556ARG10.8270.87465.676-0.026-0.0260.0000.0000.0000.000
179A557MET00.0160.00467.3540.0000.0000.0000.0000.0000.000
180A558ASP-1-0.883-0.90769.8930.0240.0240.0000.0000.0000.000
181A559SER0-0.0030.00972.210-0.001-0.0010.0000.0000.0000.000
182A560ILE0-0.0140.00071.1590.0010.0010.0000.0000.0000.000
183A561ASP-1-0.866-0.92774.8360.0200.0200.0000.0000.0000.000
184A562HIS00.0400.00575.8510.0000.0000.0000.0000.0000.000
185A563HIS00.036-0.00478.959-0.001-0.0010.0000.0000.0000.000
186A564LEU0-0.043-0.01880.3780.0000.0000.0000.0000.0000.000
187A565GLU-1-0.919-0.95681.9140.0190.0190.0000.0000.0000.000
188A566ARG10.9350.97683.219-0.020-0.0200.0000.0000.0000.000
189A567CYS0-0.074-0.05686.032-0.001-0.0010.0000.0000.0000.000
190A568LEU0-0.027-0.01884.2630.0000.0000.0000.0000.0000.000
191A569ASP-1-0.872-0.93388.0830.0160.0160.0000.0000.0000.000
192A570HIS0-0.046-0.02489.757-0.001-0.0010.0000.0000.0000.000
193A571LEU0-0.086-0.03390.3580.0000.0000.0000.0000.0000.000
194A572TYR0-0.078-0.01991.4860.0000.0000.0000.0000.0000.000
195A573ASP-1-0.978-0.97893.7090.0140.0140.0000.0000.0000.000