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: Z6Y8N

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1619370.140399
FMO2-HF: Nuclear repulsion 1539146.556469
FMO2-HF: Total energy -80223.58393
FMO2-MP2: Total energy -80456.26054


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.
-1.1590.8730.04-1.065-1.0080
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 : 0.032 / 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].
3A3LEU0-0.045-0.0123.887-0.6050.483-0.004-0.658-0.4260.002
4A4LYS10.8530.8985.7452.6592.6590.0000.0000.0000.000
5A5PRO00.004-0.0178.6770.0460.0460.0000.0000.0000.000
6A6GLU-1-0.901-0.95112.149-0.540-0.5400.0000.0000.0000.000
7A7GLU-1-0.778-0.8597.709-2.229-2.2290.0000.0000.0000.000
8A8HIS0-0.002-0.01010.910-0.139-0.1390.0000.0000.0000.000
9A9GLU-1-0.864-0.93912.499-0.450-0.4500.0000.0000.0000.000
10A10ASP-1-0.931-0.94614.746-0.558-0.5580.0000.0000.0000.000
11A11ILE0-0.018-0.01111.7780.0600.0600.0000.0000.0000.000
12A12LEU0-0.032-0.01816.0690.0760.0760.0000.0000.0000.000
13A13ASN0-0.074-0.05118.5380.1100.1100.0000.0000.0000.000
14A14LYS10.8710.93716.2200.7110.7110.0000.0000.0000.000
15A15LEU0-0.036-0.03318.3430.0470.0470.0000.0000.0000.000
16A16LEU0-0.0400.00521.7900.0390.0390.0000.0000.0000.000
17A17ASP-1-0.836-0.90424.315-0.253-0.2530.0000.0000.0000.000
18A18PRO0-0.032-0.01426.261-0.004-0.0040.0000.0000.0000.000
19A19GLU-1-0.970-0.98928.887-0.178-0.1780.0000.0000.0000.000
20A20LEU0-0.087-0.02322.0120.0010.0010.0000.0000.0000.000
21A21ALA00.0290.01326.3100.0070.0070.0000.0000.0000.000
22A22GLN00.039-0.00725.045-0.033-0.0330.0000.0000.0000.000
23A23SER0-0.0240.00723.423-0.017-0.0170.0000.0000.0000.000
24A24GLU-1-0.787-0.90820.693-0.362-0.3620.0000.0000.0000.000
25A25ARG10.8450.92520.1140.2750.2750.0000.0000.0000.000
26A26THR0-0.049-0.04720.618-0.033-0.0330.0000.0000.0000.000
27A27GLU-1-0.936-0.96716.026-0.634-0.6340.0000.0000.0000.000
28A28ALA00.0430.02716.001-0.102-0.1020.0000.0000.0000.000
29A29LEU00.011-0.00315.717-0.099-0.0990.0000.0000.0000.000
30A30GLN00.0010.00514.091-0.021-0.0210.0000.0000.0000.000
31A31GLN00.0120.00211.701-0.029-0.0290.0000.0000.0000.000
32A32LEU00.0280.02110.971-0.295-0.2950.0000.0000.0000.000
33A33ARG10.8890.94612.0670.4680.4680.0000.0000.0000.000
34A34VAL0-0.022-0.0158.0250.0360.0360.0000.0000.0000.000
35A35ASN00.0350.0347.065-0.935-0.9350.0000.0000.0000.000
36A36TYR00.0070.0057.641-0.142-0.1420.0000.0000.0000.000
37A37GLY00.0060.0029.9330.1280.1280.0000.0000.0000.000
38A38SER00.0160.0043.9740.0350.113-0.001-0.014-0.0640.000
39A39PHE0-0.022-0.0116.2270.3700.3700.0000.0000.0000.000
40A40VAL00.0150.0027.0330.4140.4140.0000.0000.0000.000
41A41SER0-0.040-0.0117.6880.1670.1670.0000.0000.0000.000
42A42GLU-1-0.879-0.9473.4450.6431.5090.045-0.393-0.518-0.002
43A43TYR00.0280.0187.2780.1750.1750.0000.0000.0000.000
44A44ASN0-0.036-0.01810.4410.1110.1110.0000.0000.0000.000
45A45ASP-1-0.874-0.9329.5550.4520.4520.0000.0000.0000.000
46A46LEU00.0090.00310.4320.0490.0490.0000.0000.0000.000
47A47THR0-0.006-0.01212.128-0.020-0.0200.0000.0000.0000.000
48A48LYS10.8930.95014.759-0.322-0.3220.0000.0000.0000.000
49A49SER0-0.0160.00714.1690.0170.0170.0000.0000.0000.000
50A50HIS00.0270.01616.1100.0040.0040.0000.0000.0000.000
51A429ASN0-0.020-0.02617.993-0.028-0.0280.0000.0000.0000.000
52A430THR0-0.077-0.04019.295-0.014-0.0140.0000.0000.0000.000
53A431LEU00.0690.03119.275-0.015-0.0150.0000.0000.0000.000
54A432SER0-0.013-0.01221.728-0.024-0.0240.0000.0000.0000.000
55A433LYS10.9740.99324.014-0.176-0.1760.0000.0000.0000.000
56A434GLU-1-0.949-0.97523.4770.2460.2460.0000.0000.0000.000
57A435LEU00.0150.01325.275-0.010-0.0100.0000.0000.0000.000
58A436ASP-1-0.802-0.89027.3520.0890.0890.0000.0000.0000.000
59A437ASN0-0.091-0.04629.481-0.012-0.0120.0000.0000.0000.000
60A438LEU0-0.016-0.00429.169-0.007-0.0070.0000.0000.0000.000
61A439ARG10.8930.92628.120-0.110-0.1100.0000.0000.0000.000
62A440SER00.005-0.00333.306-0.009-0.0090.0000.0000.0000.000
63A441ARG10.8910.94933.141-0.128-0.1280.0000.0000.0000.000
64A442PHE00.0090.01135.242-0.001-0.0010.0000.0000.0000.000
65A443GLY00.0380.02037.089-0.005-0.0050.0000.0000.0000.000
66A444ASN0-0.092-0.06639.185-0.008-0.0080.0000.0000.0000.000
67A445LEU0-0.067-0.01539.257-0.002-0.0020.0000.0000.0000.000
68A446GLU-1-0.863-0.92041.2440.0740.0740.0000.0000.0000.000
69A447GLY0-0.0060.00842.920-0.004-0.0040.0000.0000.0000.000
70A448ASN0-0.030-0.03344.4660.0000.0000.0000.0000.0000.000
71A449THR00.0630.02143.676-0.002-0.0020.0000.0000.0000.000
72A450SER0-0.042-0.03246.633-0.002-0.0020.0000.0000.0000.000
73A451GLU-1-0.969-0.96049.3080.0420.0420.0000.0000.0000.000
74A452ARG10.7620.85444.278-0.064-0.0640.0000.0000.0000.000
75A453ILE0-0.051-0.02151.415-0.002-0.0020.0000.0000.0000.000
76A454THR00.0510.03853.0040.0000.0000.0000.0000.0000.000
77A455ILE00.0740.01654.820-0.002-0.0020.0000.0000.0000.000
78A456LYS10.9630.97953.962-0.037-0.0370.0000.0000.0000.000
79A457ASN00.0150.00255.9580.0000.0000.0000.0000.0000.000
80A458ILE00.0130.02958.332-0.001-0.0010.0000.0000.0000.000
81A459LEU00.0170.00061.385-0.001-0.0010.0000.0000.0000.000
82A460GLN0-0.059-0.01861.399-0.002-0.0020.0000.0000.0000.000
83A461SER0-0.060-0.04062.453-0.001-0.0010.0000.0000.0000.000
84A462ARG10.7680.87364.419-0.032-0.0320.0000.0000.0000.000
85A463PRO00.0580.02266.8100.0000.0000.0000.0000.0000.000
86A464ASP-1-0.873-0.91469.2870.0290.0290.0000.0000.0000.000
87A465ILE0-0.040-0.00664.1820.0010.0010.0000.0000.0000.000
88A466SER0-0.001-0.02066.5330.0000.0000.0000.0000.0000.000
89A467ALA00.0450.01162.1710.0010.0010.0000.0000.0000.000
90A468GLU-1-0.831-0.90762.4430.0320.0320.0000.0000.0000.000
91A469GLU-1-0.916-0.95464.1480.0350.0350.0000.0000.0000.000
92A470CYS0-0.047-0.02959.9330.0020.0020.0000.0000.0000.000
93A471ASN00.000-0.00459.2510.0030.0030.0000.0000.0000.000
94A472PHE0-0.044-0.01360.0330.0020.0020.0000.0000.0000.000
95A473LEU0-0.062-0.03660.9290.0010.0010.0000.0000.0000.000
96A474MET0-0.0210.00055.2420.0020.0020.0000.0000.0000.000
97A475VAL00.0280.00755.5450.0020.0020.0000.0000.0000.000
98A476GLU-1-0.913-0.97052.2220.0480.0480.0000.0000.0000.000
99A477GLN0-0.0110.00251.0420.0020.0020.0000.0000.0000.000
100A478ILE0-0.031-0.02350.5550.0030.0030.0000.0000.0000.000
101A479ASP-1-0.845-0.90847.7490.0630.0630.0000.0000.0000.000
102A480SER0-0.039-0.00746.1520.0030.0030.0000.0000.0000.000
103A481ALA0-0.049-0.00946.0510.0040.0040.0000.0000.0000.000
104A482ASN00.0520.03743.2820.0000.0000.0000.0000.0000.000
105A483LEU00.0900.03043.362-0.003-0.0030.0000.0000.0000.000
106A484THR00.005-0.00443.679-0.003-0.0030.0000.0000.0000.000
107A485THR00.006-0.00946.388-0.003-0.0030.0000.0000.0000.000
108A486LEU00.0230.03347.721-0.004-0.0040.0000.0000.0000.000
109A487GLN00.0190.00346.162-0.004-0.0040.0000.0000.0000.000
110A488ASN00.0020.00149.449-0.003-0.0030.0000.0000.0000.000
111A489THR00.0820.03952.383-0.003-0.0030.0000.0000.0000.000
112A490VAL0-0.032-0.01653.884-0.003-0.0030.0000.0000.0000.000
113A491LYS10.8240.90349.477-0.076-0.0760.0000.0000.0000.000
114A492GLU-1-0.901-0.95255.9890.0600.0600.0000.0000.0000.000
115A493ILE00.0040.00458.075-0.003-0.0030.0000.0000.0000.000
116A494VAL0-0.058-0.04258.344-0.002-0.0020.0000.0000.0000.000
117A495LEU0-0.040-0.02658.474-0.002-0.0020.0000.0000.0000.000
118A496ALA0-0.0030.01762.088-0.001-0.0010.0000.0000.0000.000
119A497VAL0-0.048-0.02763.672-0.002-0.0020.0000.0000.0000.000
120A498GLY00.0420.03865.020-0.002-0.0020.0000.0000.0000.000
121A499ILE0-0.084-0.04363.605-0.002-0.0020.0000.0000.0000.000
122A500PRO00.016-0.00261.4500.0020.0020.0000.0000.0000.000
123A501TYR00.1190.06053.124-0.002-0.0020.0000.0000.0000.000
124A502PRO00.0230.00757.529-0.001-0.0010.0000.0000.0000.000
125A503LYS10.9010.94459.406-0.038-0.0380.0000.0000.0000.000
126A504LEU00.0540.04458.991-0.002-0.0020.0000.0000.0000.000
127A505ARG11.0090.98855.370-0.045-0.0450.0000.0000.0000.000
128A506ARG10.9130.94961.308-0.037-0.0370.0000.0000.0000.000
129A507LYS10.9670.98664.702-0.036-0.0360.0000.0000.0000.000
130A508ILE00.0490.03860.832-0.001-0.0010.0000.0000.0000.000
131A509PRO00.0390.01265.4070.0000.0000.0000.0000.0000.000
132A510LEU00.0090.00368.444-0.001-0.0010.0000.0000.0000.000
133A511LEU00.0000.00665.299-0.001-0.0010.0000.0000.0000.000
134A512ALA00.0290.01468.0030.0000.0000.0000.0000.0000.000
135A513ILE0-0.0060.00169.784-0.001-0.0010.0000.0000.0000.000
136A514LYS10.8300.88672.197-0.030-0.0300.0000.0000.0000.000
137A515LEU0-0.016-0.00768.4800.0000.0000.0000.0000.0000.000
138A516LYS10.9610.97069.411-0.032-0.0320.0000.0000.0000.000
139A517TYR0-0.0030.00973.896-0.001-0.0010.0000.0000.0000.000
140A518GLU-1-0.768-0.86676.3430.0280.0280.0000.0000.0000.000
141A519ASN00.0410.02575.307-0.001-0.0010.0000.0000.0000.000
142A520ILE00.0210.04075.4940.0000.0000.0000.0000.0000.000
143A521MET0-0.023-0.00979.367-0.001-0.0010.0000.0000.0000.000
144A522LEU00.0250.01081.269-0.001-0.0010.0000.0000.0000.000
145A523SER0-0.009-0.02080.3150.0000.0000.0000.0000.0000.000
146A524ASN0-0.043-0.03582.457-0.001-0.0010.0000.0000.0000.000
147A525PHE0-0.012-0.00685.041-0.001-0.0010.0000.0000.0000.000
148A526ALA00.0860.04085.7570.0000.0000.0000.0000.0000.000
149A527GLN00.0120.00184.400-0.001-0.0010.0000.0000.0000.000
150A528ARG10.8420.90986.526-0.023-0.0230.0000.0000.0000.000
151A529LEU00.0300.02490.655-0.001-0.0010.0000.0000.0000.000
152A530HIS00.0530.02689.7480.0000.0000.0000.0000.0000.000
153A531ARG10.8270.88186.327-0.024-0.0240.0000.0000.0000.000
154A532GLN0-0.068-0.02192.887-0.001-0.0010.0000.0000.0000.000
155A533VAL0-0.0110.01294.9110.0000.0000.0000.0000.0000.000
156A534TYR0-0.024-0.01092.9080.0000.0000.0000.0000.0000.000
157A535SER00.0080.01494.3910.0000.0000.0000.0000.0000.000
158A536GLN0-0.063-0.06490.9260.0000.0000.0000.0000.0000.000
159A537GLU-1-0.820-0.87586.7170.0240.0240.0000.0000.0000.000
160A538MET00.0100.01984.9920.0010.0010.0000.0000.0000.000
161A539ASN00.0100.00480.6980.0010.0010.0000.0000.0000.000
162A540LEU00.0580.01080.1360.0010.0010.0000.0000.0000.000
163A541LYS10.8360.91472.991-0.035-0.0350.0000.0000.0000.000
164A542LYS10.9910.99776.651-0.029-0.0290.0000.0000.0000.000
165A543PHE00.0080.00077.9620.0010.0010.0000.0000.0000.000
166A544THR0-0.006-0.00373.0490.0010.0010.0000.0000.0000.000
167A545ASP-1-0.827-0.90073.0190.0370.0370.0000.0000.0000.000
168A546GLN0-0.069-0.03373.2100.0010.0010.0000.0000.0000.000
169A547ALA00.0550.02673.9940.0010.0010.0000.0000.0000.000
170A548TYR0-0.006-0.01164.4010.0010.0010.0000.0000.0000.000
171A549TYR00.0130.00469.4040.0020.0020.0000.0000.0000.000
172A550ASP-1-0.786-0.88470.5550.0380.0380.0000.0000.0000.000
173A551PHE00.0180.01463.7430.0010.0010.0000.0000.0000.000
174A552MET0-0.067-0.03562.8480.0020.0020.0000.0000.0000.000
175A553SER0-0.036-0.01966.1390.0020.0020.0000.0000.0000.000
176A554THR0-0.049-0.03068.1580.0010.0010.0000.0000.0000.000
177A555ARG10.8230.90760.632-0.053-0.0530.0000.0000.0000.000
178A556ARG10.8270.89765.200-0.042-0.0420.0000.0000.0000.000
179A557MET00.014-0.00467.1400.0000.0000.0000.0000.0000.000
180A558ASP-1-0.851-0.90369.6960.0400.0400.0000.0000.0000.000
181A559SER0-0.031-0.01572.117-0.001-0.0010.0000.0000.0000.000
182A560ILE0-0.0100.01170.6290.0010.0010.0000.0000.0000.000
183A561ASP-1-0.777-0.83974.8450.0310.0310.0000.0000.0000.000
184A562HIS00.0360.00876.4050.0000.0000.0000.0000.0000.000
185A563HIS00.032-0.00378.781-0.002-0.0020.0000.0000.0000.000
186A564LEU0-0.027-0.00779.893-0.001-0.0010.0000.0000.0000.000
187A565GLU-1-0.938-0.96482.0080.0290.0290.0000.0000.0000.000
188A566ARG10.8570.88582.838-0.030-0.0300.0000.0000.0000.000
189A567CYS0-0.063-0.03885.521-0.001-0.0010.0000.0000.0000.000
190A568LEU0-0.030-0.01983.941-0.001-0.0010.0000.0000.0000.000
191A569ASP-1-0.872-0.92587.8850.0250.0250.0000.0000.0000.000
192A570HIS0-0.078-0.04789.735-0.001-0.0010.0000.0000.0000.000
193A571LEU0-0.081-0.02589.6150.0000.0000.0000.0000.0000.000
194A572TYR0-0.071-0.02291.8650.0000.0000.0000.0000.0000.000
195A573ASP-1-0.980-0.98393.6660.0200.0200.0000.0000.0000.000