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: 6N62Z

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1616666.272428
FMO2-HF: Nuclear repulsion 1536443.919587
FMO2-HF: Total energy -80222.352841
FMO2-MP2: Total energy -80455.191483


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.
-1.0290.9360.032-1.026-0.9710
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 : 0.028 / q_NPA : 0.011
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].
3A3LEU0-0.043-0.0063.849-0.9330.108-0.001-0.657-0.3830.002
4A4LYS10.8770.9145.3483.1153.1150.0000.0000.0000.000
5A5PRO00.006-0.0138.5680.0500.0500.0000.0000.0000.000
6A6GLU-1-0.901-0.95712.061-0.568-0.5680.0000.0000.0000.000
7A7GLU-1-0.810-0.8767.341-2.538-2.5380.0000.0000.0000.000
8A8HIS0-0.015-0.01910.815-0.076-0.0760.0000.0000.0000.000
9A9GLU-1-0.876-0.94912.295-0.471-0.4710.0000.0000.0000.000
10A10ASP-1-0.892-0.93114.473-0.552-0.5520.0000.0000.0000.000
11A11ILE0-0.058-0.02711.4050.0900.0900.0000.0000.0000.000
12A12LEU0-0.030-0.01615.8500.0890.0890.0000.0000.0000.000
13A13ASN0-0.066-0.04318.3940.1180.1180.0000.0000.0000.000
14A14LYS10.9530.97616.2610.6590.6590.0000.0000.0000.000
15A15LEU0-0.043-0.02817.9790.0490.0490.0000.0000.0000.000
16A16LEU0-0.0330.00921.5300.0430.0430.0000.0000.0000.000
17A17ASP-1-0.872-0.93324.011-0.255-0.2550.0000.0000.0000.000
18A18PRO0-0.026-0.01525.806-0.003-0.0030.0000.0000.0000.000
19A19GLU-1-0.977-0.99228.621-0.179-0.1790.0000.0000.0000.000
20A20LEU0-0.0540.00921.392-0.001-0.0010.0000.0000.0000.000
21A21ALA00.0460.01525.4050.0150.0150.0000.0000.0000.000
22A22GLN00.020-0.01224.555-0.032-0.0320.0000.0000.0000.000
23A23SER0-0.016-0.01123.344-0.018-0.0180.0000.0000.0000.000
24A24GLU-1-0.837-0.92220.705-0.352-0.3520.0000.0000.0000.000
25A25ARG10.8800.93819.8570.2710.2710.0000.0000.0000.000
26A26THR0-0.083-0.05520.063-0.037-0.0370.0000.0000.0000.000
27A27GLU-1-0.933-0.96215.873-0.536-0.5360.0000.0000.0000.000
28A28ALA00.0500.03215.529-0.097-0.0970.0000.0000.0000.000
29A29LEU00.005-0.00715.234-0.103-0.1030.0000.0000.0000.000
30A30GLN0-0.0010.01114.131-0.047-0.0470.0000.0000.0000.000
31A31GLN0-0.004-0.00810.926-0.009-0.0090.0000.0000.0000.000
32A32LEU00.0130.01110.688-0.288-0.2880.0000.0000.0000.000
33A33ARG10.8900.94511.9500.4380.4380.0000.0000.0000.000
34A34VAL0-0.022-0.0228.2320.0140.0140.0000.0000.0000.000
35A35ASN00.0370.0266.717-0.912-0.9120.0000.0000.0000.000
36A36TYR00.0090.0147.362-0.211-0.2110.0000.0000.0000.000
37A37GLY00.0130.0069.9450.1470.1470.0000.0000.0000.000
38A38SER00.0260.0084.0100.1060.210-0.001-0.020-0.0830.000
39A39PHE0-0.035-0.0096.2390.2900.2900.0000.0000.0000.000
40A40VAL00.0280.0087.1300.3850.3850.0000.0000.0000.000
41A41SER0-0.020-0.0087.8410.1640.1640.0000.0000.0000.000
42A42GLU-1-0.909-0.9603.6050.9271.7470.034-0.349-0.505-0.002
43A43TYR00.0110.0097.4490.1310.1310.0000.0000.0000.000
44A44ASN0-0.013-0.02010.5620.0780.0780.0000.0000.0000.000
45A45ASP-1-0.878-0.93610.0100.5160.5160.0000.0000.0000.000
46A46LEU0-0.0030.00010.6140.0520.0520.0000.0000.0000.000
47A47THR0-0.011-0.01012.483-0.020-0.0200.0000.0000.0000.000
48A48LYS10.9210.97315.201-0.322-0.3220.0000.0000.0000.000
49A49SER0-0.055-0.00914.580-0.017-0.0170.0000.0000.0000.000
50A50HIS00.0470.01816.3370.0050.0050.0000.0000.0000.000
51A429ASN0-0.023-0.01918.045-0.022-0.0220.0000.0000.0000.000
52A430THR0-0.080-0.05719.835-0.010-0.0100.0000.0000.0000.000
53A431LEU00.0500.03619.105-0.011-0.0110.0000.0000.0000.000
54A432SER00.007-0.00321.807-0.020-0.0200.0000.0000.0000.000
55A433LYS10.9530.97724.197-0.151-0.1510.0000.0000.0000.000
56A434GLU-1-0.947-0.97123.6910.2260.2260.0000.0000.0000.000
57A435LEU00.0110.00425.504-0.009-0.0090.0000.0000.0000.000
58A436ASP-1-0.806-0.89927.5590.0710.0710.0000.0000.0000.000
59A437ASN0-0.130-0.07329.491-0.010-0.0100.0000.0000.0000.000
60A438LEU0-0.019-0.01129.116-0.006-0.0060.0000.0000.0000.000
61A439ARG10.9530.96728.414-0.087-0.0870.0000.0000.0000.000
62A440SER0-0.0050.01033.638-0.009-0.0090.0000.0000.0000.000
63A441ARG10.9210.96033.340-0.115-0.1150.0000.0000.0000.000
64A442PHE0-0.0150.00035.211-0.002-0.0020.0000.0000.0000.000
65A443GLY00.0520.02537.085-0.004-0.0040.0000.0000.0000.000
66A444ASN0-0.094-0.07139.364-0.007-0.0070.0000.0000.0000.000
67A445LEU0-0.067-0.01539.720-0.002-0.0020.0000.0000.0000.000
68A446GLU-1-0.857-0.91441.0840.0630.0630.0000.0000.0000.000
69A447GLY0-0.0180.00542.894-0.003-0.0030.0000.0000.0000.000
70A448ASN0-0.024-0.03244.6710.0000.0000.0000.0000.0000.000
71A449THR00.0590.02043.994-0.001-0.0010.0000.0000.0000.000
72A450SER0-0.053-0.03946.645-0.002-0.0020.0000.0000.0000.000
73A451GLU-1-0.949-0.95749.4410.0350.0350.0000.0000.0000.000
74A452ARG10.8280.92144.341-0.053-0.0530.0000.0000.0000.000
75A453ILE0-0.054-0.02351.655-0.002-0.0020.0000.0000.0000.000
76A454THR00.0290.01253.4620.0000.0000.0000.0000.0000.000
77A455ILE00.0970.03555.234-0.001-0.0010.0000.0000.0000.000
78A456LYS10.9630.98354.405-0.028-0.0280.0000.0000.0000.000
79A457ASN00.0490.01055.9950.0000.0000.0000.0000.0000.000
80A458ILE00.0210.03358.398-0.001-0.0010.0000.0000.0000.000
81A459LEU0-0.012-0.00261.382-0.001-0.0010.0000.0000.0000.000
82A460GLN0-0.045-0.02261.740-0.001-0.0010.0000.0000.0000.000
83A461SER0-0.060-0.03962.478-0.001-0.0010.0000.0000.0000.000
84A462ARG10.7880.88464.888-0.027-0.0270.0000.0000.0000.000
85A463PRO00.0370.02166.8760.0000.0000.0000.0000.0000.000
86A464ASP-1-0.886-0.93169.4490.0240.0240.0000.0000.0000.000
87A465ILE0-0.0140.01164.1780.0010.0010.0000.0000.0000.000
88A466SER0-0.013-0.01966.5490.0000.0000.0000.0000.0000.000
89A467ALA00.0660.01162.4320.0010.0010.0000.0000.0000.000
90A468GLU-1-0.843-0.91962.6230.0260.0260.0000.0000.0000.000
91A469GLU-1-0.920-0.95764.2490.0300.0300.0000.0000.0000.000
92A470CYS0-0.051-0.03259.9740.0010.0010.0000.0000.0000.000
93A471ASN0-0.018-0.01259.3990.0030.0030.0000.0000.0000.000
94A472PHE0-0.021-0.00459.9860.0020.0020.0000.0000.0000.000
95A473LEU0-0.053-0.02061.2740.0010.0010.0000.0000.0000.000
96A474MET0-0.024-0.00355.5500.0020.0020.0000.0000.0000.000
97A475VAL00.008-0.00255.8910.0020.0020.0000.0000.0000.000
98A476GLU-1-0.898-0.95952.7330.0400.0400.0000.0000.0000.000
99A477GLN0-0.0030.00551.4640.0010.0010.0000.0000.0000.000
100A478ILE0-0.062-0.03950.7040.0040.0040.0000.0000.0000.000
101A479ASP-1-0.895-0.94948.2090.0500.0500.0000.0000.0000.000
102A480SER0-0.081-0.03546.3330.0030.0030.0000.0000.0000.000
103A481ALA0-0.051-0.00845.8090.0040.0040.0000.0000.0000.000
104A482ASN00.0620.04743.1880.0000.0000.0000.0000.0000.000
105A483LEU00.0750.02143.511-0.003-0.0030.0000.0000.0000.000
106A484THR00.003-0.00743.656-0.003-0.0030.0000.0000.0000.000
107A485THR00.010-0.01246.300-0.003-0.0030.0000.0000.0000.000
108A486LEU00.0500.04248.236-0.003-0.0030.0000.0000.0000.000
109A487GLN00.000-0.00446.048-0.003-0.0030.0000.0000.0000.000
110A488ASN00.000-0.01449.385-0.003-0.0030.0000.0000.0000.000
111A489THR00.0730.03752.318-0.002-0.0020.0000.0000.0000.000
112A490VAL0-0.032-0.01754.024-0.003-0.0030.0000.0000.0000.000
113A491LYS10.8370.91449.469-0.070-0.0700.0000.0000.0000.000
114A492GLU-1-0.896-0.94356.1370.0540.0540.0000.0000.0000.000
115A493ILE00.0040.00857.990-0.002-0.0020.0000.0000.0000.000
116A494VAL0-0.065-0.03658.432-0.002-0.0020.0000.0000.0000.000
117A495LEU0-0.029-0.01858.492-0.001-0.0010.0000.0000.0000.000
118A496ALA0-0.0160.00562.100-0.001-0.0010.0000.0000.0000.000
119A497VAL0-0.052-0.03563.790-0.002-0.0020.0000.0000.0000.000
120A498GLY00.0440.04365.080-0.001-0.0010.0000.0000.0000.000
121A499ILE0-0.074-0.04463.834-0.002-0.0020.0000.0000.0000.000
122A500PRO00.002-0.00561.9830.0010.0010.0000.0000.0000.000
123A501TYR00.1110.04753.309-0.001-0.0010.0000.0000.0000.000
124A502PRO00.0080.00357.815-0.001-0.0010.0000.0000.0000.000
125A503LYS10.8880.93359.329-0.034-0.0340.0000.0000.0000.000
126A504LEU00.0560.04658.973-0.001-0.0010.0000.0000.0000.000
127A505ARG11.0210.99155.765-0.039-0.0390.0000.0000.0000.000
128A506ARG10.9450.97661.498-0.032-0.0320.0000.0000.0000.000
129A507LYS10.9810.98564.525-0.033-0.0330.0000.0000.0000.000
130A508ILE00.0360.03860.9250.0000.0000.0000.0000.0000.000
131A509PRO00.0310.00665.4990.0000.0000.0000.0000.0000.000
132A510LEU00.002-0.01068.584-0.001-0.0010.0000.0000.0000.000
133A511LEU00.0160.01765.5100.0000.0000.0000.0000.0000.000
134A512ALA00.0240.01368.3770.0000.0000.0000.0000.0000.000
135A513ILE0-0.0140.00370.0520.0000.0000.0000.0000.0000.000
136A514LYS10.8450.89772.492-0.027-0.0270.0000.0000.0000.000
137A515LEU0-0.0170.00068.7580.0000.0000.0000.0000.0000.000
138A516LYS10.9640.96869.687-0.028-0.0280.0000.0000.0000.000
139A517TYR0-0.0030.00274.150-0.001-0.0010.0000.0000.0000.000
140A518GLU-1-0.780-0.86776.7700.0250.0250.0000.0000.0000.000
141A519ASN00.0640.04175.739-0.001-0.0010.0000.0000.0000.000
142A520ILE00.0360.04175.7370.0000.0000.0000.0000.0000.000
143A521MET0-0.022-0.01579.619-0.001-0.0010.0000.0000.0000.000
144A522LEU00.0070.00381.140-0.001-0.0010.0000.0000.0000.000
145A523SER0-0.016-0.02580.5790.0000.0000.0000.0000.0000.000
146A524ASN0-0.074-0.04782.742-0.001-0.0010.0000.0000.0000.000
147A525PHE00.0020.01385.2930.0000.0000.0000.0000.0000.000
148A526ALA00.0760.04485.8220.0000.0000.0000.0000.0000.000
149A527GLN0-0.009-0.01884.298-0.001-0.0010.0000.0000.0000.000
150A528ARG10.8950.92587.747-0.020-0.0200.0000.0000.0000.000
151A529LEU00.0150.01290.7590.0000.0000.0000.0000.0000.000
152A530HIS00.0650.03189.7430.0000.0000.0000.0000.0000.000
153A531ARG10.7960.88486.599-0.021-0.0210.0000.0000.0000.000
154A532GLN0-0.032-0.01992.9430.0000.0000.0000.0000.0000.000
155A533VAL00.0000.02294.9190.0000.0000.0000.0000.0000.000
156A534TYR00.0330.02492.9220.0000.0000.0000.0000.0000.000
157A535SER0-0.046-0.00594.7410.0000.0000.0000.0000.0000.000
158A536GLN0-0.070-0.04491.3910.0000.0000.0000.0000.0000.000
159A537GLU-1-0.819-0.91187.1220.0210.0210.0000.0000.0000.000
160A538MET00.0030.02185.2580.0010.0010.0000.0000.0000.000
161A539ASN00.000-0.00681.2040.0010.0010.0000.0000.0000.000
162A540LEU00.0600.01080.2130.0010.0010.0000.0000.0000.000
163A541LYS10.8380.90673.163-0.032-0.0320.0000.0000.0000.000
164A542LYS10.9820.99176.784-0.027-0.0270.0000.0000.0000.000
165A543PHE0-0.024-0.01378.0750.0010.0010.0000.0000.0000.000
166A544THR00.001-0.00873.0270.0010.0010.0000.0000.0000.000
167A545ASP-1-0.801-0.87272.9910.0340.0340.0000.0000.0000.000
168A546GLN0-0.069-0.03173.2990.0010.0010.0000.0000.0000.000
169A547ALA00.0440.02974.0160.0010.0010.0000.0000.0000.000
170A548TYR00.004-0.00864.4070.0010.0010.0000.0000.0000.000
171A549TYR0-0.011-0.00869.4860.0020.0020.0000.0000.0000.000
172A550ASP-1-0.775-0.89270.4970.0360.0360.0000.0000.0000.000
173A551PHE00.0030.01764.2100.0010.0010.0000.0000.0000.000
174A552MET0-0.035-0.01562.8290.0020.0020.0000.0000.0000.000
175A553SER0-0.061-0.01666.2860.0020.0020.0000.0000.0000.000
176A554THR0-0.043-0.02967.9880.0010.0010.0000.0000.0000.000
177A555ARG10.8360.90360.721-0.049-0.0490.0000.0000.0000.000
178A556ARG10.8240.89765.677-0.040-0.0400.0000.0000.0000.000
179A557MET00.0340.01367.281-0.001-0.0010.0000.0000.0000.000
180A558ASP-1-0.900-0.93469.6400.0380.0380.0000.0000.0000.000
181A559SER00.0020.00572.211-0.001-0.0010.0000.0000.0000.000
182A560ILE0-0.0240.00270.8570.0010.0010.0000.0000.0000.000
183A561ASP-1-0.820-0.89374.8370.0290.0290.0000.0000.0000.000
184A562HIS00.0510.00876.2180.0000.0000.0000.0000.0000.000
185A563HIS00.022-0.00278.960-0.002-0.0020.0000.0000.0000.000
186A564LEU0-0.048-0.01780.311-0.001-0.0010.0000.0000.0000.000
187A565GLU-1-0.917-0.96082.2560.0270.0270.0000.0000.0000.000
188A566ARG10.9000.93783.050-0.028-0.0280.0000.0000.0000.000
189A567CYS0-0.052-0.03786.036-0.001-0.0010.0000.0000.0000.000
190A568LEU0-0.017-0.01884.117-0.001-0.0010.0000.0000.0000.000
191A569ASP-1-0.884-0.92988.0840.0230.0230.0000.0000.0000.000
192A570HIS0-0.071-0.04389.992-0.001-0.0010.0000.0000.0000.000
193A571LEU0-0.070-0.02589.9990.0000.0000.0000.0000.0000.000
194A572TYR0-0.068-0.02091.7190.0000.0000.0000.0000.0000.000
195A573ASP-1-0.993-0.98193.7090.0190.0190.0000.0000.0000.000