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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: 3QZ7L

Calculation Name: 2AP3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2AP3

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-03-13

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2042848.572946
FMO2-HF: Nuclear repulsion 1964429.673755
FMO2-HF: Total energy -78418.899191
FMO2-MP2: Total energy -78652.788797


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-0.9933.3561.183-2.234-3.298-0.005
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / 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].
3A3MET0-0.020-0.0193.866-1.2590.551-0.001-0.938-0.8710.005
4A4GLY00.0500.0413.1750.4461.0210.051-0.231-0.3950.000
5A5ILE0-0.061-0.0223.4780.7581.5210.099-0.182-0.680-0.001
6A6GLN00.0000.0002.789-0.5990.5881.035-0.882-1.340-0.009
7A7ARG10.9020.9325.2750.0490.063-0.001-0.001-0.0120.000
8A8PRO00.0170.0068.2500.1680.1680.0000.0000.0000.000
9A9THR00.0860.0678.8200.0010.0010.0000.0000.0000.000
10A10SER00.0410.00010.991-0.083-0.0830.0000.0000.0000.000
11A11THR00.0610.02214.131-0.039-0.0390.0000.0000.0000.000
12A12THR0-0.048-0.03512.461-0.068-0.0680.0000.0000.0000.000
13A13THR0-0.026-0.02414.525-0.076-0.0760.0000.0000.0000.000
14A14ASP-1-0.749-0.87316.8490.2660.2660.0000.0000.0000.000
15A15LYS10.9850.99316.654-0.329-0.3290.0000.0000.0000.000
16A16LYS10.8340.94018.658-0.204-0.2040.0000.0000.0000.000
17A17GLU-1-0.796-0.86620.6120.1290.1290.0000.0000.0000.000
18A18ILE00.0730.02522.301-0.016-0.0160.0000.0000.0000.000
19A19LYS10.9060.93820.470-0.152-0.1520.0000.0000.0000.000
20A20ALA0-0.039-0.00725.101-0.014-0.0140.0000.0000.0000.000
21A21TYR0-0.005-0.04726.949-0.010-0.0100.0000.0000.0000.000
22A22LEU00.0150.00827.504-0.010-0.0100.0000.0000.0000.000
23A23LYS10.9640.98629.409-0.056-0.0560.0000.0000.0000.000
24A24GLN0-0.019-0.01330.047-0.006-0.0060.0000.0000.0000.000
25A25VAL00.0410.02133.018-0.006-0.0060.0000.0000.0000.000
26A26ASP-1-0.800-0.89233.8210.0610.0610.0000.0000.0000.000
27A27LYS10.8640.92735.066-0.043-0.0430.0000.0000.0000.000
28A28ILE0-0.0210.00036.679-0.005-0.0050.0000.0000.0000.000
29A29LYS10.7780.87537.629-0.053-0.0530.0000.0000.0000.000
30A30ASP-1-0.880-0.94137.8910.0400.0400.0000.0000.0000.000
31A31ASP-1-0.870-0.91141.0660.0330.0330.0000.0000.0000.000
32A32GLU-1-0.762-0.84243.4050.0470.0470.0000.0000.0000.000
33A33GLU-1-0.811-0.87145.3530.0240.0240.0000.0000.0000.000
34A34PRO00.028-0.00147.102-0.001-0.0010.0000.0000.0000.000
35A35ILE00.0420.03547.506-0.001-0.0010.0000.0000.0000.000
36A36LYS10.9410.97747.020-0.037-0.0370.0000.0000.0000.000
37A37THR0-0.042-0.03751.020-0.002-0.0020.0000.0000.0000.000
38A38VAL00.0140.01753.411-0.001-0.0010.0000.0000.0000.000
39A39GLY00.0230.00954.099-0.001-0.0010.0000.0000.0000.000
40A40LYS10.7780.86451.044-0.024-0.0240.0000.0000.0000.000
41A41LYS10.9030.95156.943-0.020-0.0200.0000.0000.0000.000
42A42ILE00.0230.00957.612-0.001-0.0010.0000.0000.0000.000
43A43ALA00.0120.01159.271-0.001-0.0010.0000.0000.0000.000
44A44GLU-1-0.801-0.89761.1290.0150.0150.0000.0000.0000.000
45A45LEU0-0.0270.00662.816-0.001-0.0010.0000.0000.0000.000
46A46ASP-1-0.759-0.87663.7510.0220.0220.0000.0000.0000.000
47A47GLU-1-0.833-0.90164.5310.0180.0180.0000.0000.0000.000
48A48LYS10.7800.88666.013-0.017-0.0170.0000.0000.0000.000
49A49LYS10.8290.90867.147-0.022-0.0220.0000.0000.0000.000
50A50LYS10.8530.90764.729-0.021-0.0210.0000.0000.0000.000
51A51LYS10.8560.92868.679-0.016-0.0160.0000.0000.0000.000
52A52LEU00.0190.02673.384-0.001-0.0010.0000.0000.0000.000
53A53THR0-0.047-0.04174.1150.0000.0000.0000.0000.0000.000
54A54GLU-1-0.921-0.94576.7920.0120.0120.0000.0000.0000.000
55A55ASP-1-0.834-0.93279.4780.0120.0120.0000.0000.0000.000
56A56VAL0-0.074-0.04277.8270.0000.0000.0000.0000.0000.000
57A57ASN0-0.066-0.04479.9050.0000.0000.0000.0000.0000.000
58A58SER00.0360.03383.2530.0000.0000.0000.0000.0000.000
59A59LYS10.9570.96685.589-0.010-0.0100.0000.0000.0000.000
60A60ASP-1-0.831-0.88487.6520.0100.0100.0000.0000.0000.000
61A61THR00.0610.00487.1240.0000.0000.0000.0000.0000.000
62A62ALA0-0.030-0.00486.9060.0000.0000.0000.0000.0000.000
63A63VAL0-0.017-0.00682.9480.0000.0000.0000.0000.0000.000
64A64ARG10.8920.94982.517-0.013-0.0130.0000.0000.0000.000
65A65GLY0-0.003-0.00382.0920.0010.0010.0000.0000.0000.000
66A66LYS10.8300.89677.308-0.012-0.0120.0000.0000.0000.000
67A67ALA00.0690.03578.0590.0000.0000.0000.0000.0000.000
68A68VAL00.0050.00177.0530.0010.0010.0000.0000.0000.000
69A69LYS10.8760.93076.846-0.013-0.0130.0000.0000.0000.000
70A70ASP-1-0.813-0.89074.6410.0140.0140.0000.0000.0000.000
71A71LEU0-0.012-0.00572.5040.0010.0010.0000.0000.0000.000
72A72ILE0-0.064-0.03471.9310.0010.0010.0000.0000.0000.000
73A73LYS10.8590.91869.512-0.015-0.0150.0000.0000.0000.000
74A74ASN00.004-0.01468.0280.0010.0010.0000.0000.0000.000
75A75ALA0-0.018-0.00967.2560.0010.0010.0000.0000.0000.000
76A76ASP-1-0.779-0.87066.2300.0200.0200.0000.0000.0000.000
77A77ASP-1-0.838-0.90365.4640.0170.0170.0000.0000.0000.000
78A78ARG10.7660.86562.676-0.021-0.0210.0000.0000.0000.000
79A79LEU0-0.033-0.01261.3950.0010.0010.0000.0000.0000.000
80A80LYS10.8490.89760.906-0.021-0.0210.0000.0000.0000.000
81A81GLU-1-0.822-0.89358.0980.0210.0210.0000.0000.0000.000
82A82PHE00.0140.00055.4310.0010.0010.0000.0000.0000.000
83A83GLU-1-0.794-0.87156.1110.0250.0250.0000.0000.0000.000
84A84LYS10.8590.92054.605-0.020-0.0200.0000.0000.0000.000
85A85GLU-1-0.848-0.91251.5340.0350.0350.0000.0000.0000.000
86A86GLU-1-0.800-0.89651.1570.0340.0340.0000.0000.0000.000
87A87ASP-1-0.867-0.94151.2180.0320.0320.0000.0000.0000.000
88A88ALA0-0.055-0.01648.4000.0010.0010.0000.0000.0000.000
89A89ILE0-0.003-0.00846.4920.0030.0030.0000.0000.0000.000
90A90LYS10.9340.96946.465-0.034-0.0340.0000.0000.0000.000
91A91LYS10.8340.90642.421-0.037-0.0370.0000.0000.0000.000
92A92SER0-0.022-0.03142.7830.0030.0030.0000.0000.0000.000
93A93GLU-1-0.844-0.91541.8610.0550.0550.0000.0000.0000.000
94A94GLN0-0.035-0.02142.3380.0020.0020.0000.0000.0000.000
95A95ASP-1-0.832-0.90739.5850.0460.0460.0000.0000.0000.000
96A96PHE0-0.026-0.00736.2530.0030.0030.0000.0000.0000.000
97A97LYS10.8430.90237.323-0.051-0.0510.0000.0000.0000.000
98A98LYS10.8310.91637.060-0.050-0.0500.0000.0000.0000.000
99A99ALA00.0200.02733.5410.0010.0010.0000.0000.0000.000
100A100LYS10.8380.89731.160-0.106-0.1060.0000.0000.0000.000
101A101SER00.0520.04229.3770.0070.0070.0000.0000.0000.000
102A102HIS0-0.064-0.05125.6790.0000.0000.0000.0000.0000.000
103A103VAL0-0.031-0.02326.7410.0070.0070.0000.0000.0000.000
104A104ASP-1-0.824-0.90326.8430.1360.1360.0000.0000.0000.000
105A105ASN0-0.051-0.02723.1650.0080.0080.0000.0000.0000.000
106A106ILE0-0.073-0.00821.9380.0160.0160.0000.0000.0000.000
107A107ASP-1-0.831-0.89517.2050.4260.4260.0000.0000.0000.000
108A108ASN00.0240.00619.364-0.033-0.0330.0000.0000.0000.000
109A109ASP-1-0.818-0.91321.0820.2400.2400.0000.0000.0000.000
110A110VAL0-0.046-0.01323.961-0.023-0.0230.0000.0000.0000.000
111A111LYS10.8400.90522.076-0.210-0.2100.0000.0000.0000.000
112A112ARG10.8020.88923.244-0.249-0.2490.0000.0000.0000.000
113A113LYS10.9050.95526.545-0.185-0.1850.0000.0000.0000.000
114A114GLU-1-0.807-0.89326.9040.1740.1740.0000.0000.0000.000
115A115VAL00.0250.00026.944-0.012-0.0120.0000.0000.0000.000
116A116LYS10.8660.93829.973-0.146-0.1460.0000.0000.0000.000
117A117GLN0-0.013-0.00732.664-0.009-0.0090.0000.0000.0000.000
118A118LEU0-0.018-0.01231.583-0.009-0.0090.0000.0000.0000.000
119A119ASP-1-0.775-0.88233.4560.0960.0960.0000.0000.0000.000
120A120ASP-1-0.862-0.93135.7700.0850.0850.0000.0000.0000.000
121A121VAL0-0.044-0.02237.883-0.006-0.0060.0000.0000.0000.000
122A122LEU0-0.020-0.00435.853-0.006-0.0060.0000.0000.0000.000
123A123LYS10.7990.88037.277-0.094-0.0940.0000.0000.0000.000
124A124GLU-1-0.813-0.89441.8610.0550.0550.0000.0000.0000.000
125A125LYS10.8220.90642.514-0.056-0.0560.0000.0000.0000.000
126A126TYR0-0.015-0.02541.069-0.002-0.0020.0000.0000.0000.000
127A127LYS10.8550.92646.278-0.059-0.0590.0000.0000.0000.000
128A128LEU00.017-0.01147.204-0.003-0.0030.0000.0000.0000.000
129A129HIS0-0.068-0.03448.678-0.001-0.0010.0000.0000.0000.000
130A130SER00.0310.02150.398-0.003-0.0030.0000.0000.0000.000
131A131ASP-1-0.942-0.97552.3250.0440.0440.0000.0000.0000.000
132A132TYR0-0.039-0.03252.900-0.002-0.0020.0000.0000.0000.000
133A133ALA00.0160.01154.383-0.002-0.0020.0000.0000.0000.000
134A134LYS10.9150.96156.098-0.037-0.0370.0000.0000.0000.000
135A135ALA0-0.023-0.01258.071-0.002-0.0020.0000.0000.0000.000
136A136TYR00.0270.01158.266-0.002-0.0020.0000.0000.0000.000
137A137LYS10.8660.91057.996-0.032-0.0320.0000.0000.0000.000
138A138LYS10.9050.97261.997-0.029-0.0290.0000.0000.0000.000
139A139ALA00.0260.01163.357-0.001-0.0010.0000.0000.0000.000
140A140VAL00.0550.05263.453-0.001-0.0010.0000.0000.0000.000
141A141ASN0-0.025-0.02465.200-0.002-0.0020.0000.0000.0000.000
142A142SER0-0.061-0.02367.9690.0000.0000.0000.0000.0000.000
143A143GLU-1-0.739-0.83967.6260.0220.0220.0000.0000.0000.000
144A144LYS10.8570.90470.071-0.020-0.0200.0000.0000.0000.000
145A145THR0-0.078-0.04871.808-0.001-0.0010.0000.0000.0000.000
146A146LEU0-0.0060.00273.878-0.001-0.0010.0000.0000.0000.000
147A147PHE00.0390.00470.998-0.001-0.0010.0000.0000.0000.000
148A148LYS10.9610.96774.921-0.019-0.0190.0000.0000.0000.000
149A149TYR0-0.0110.01877.7620.0000.0000.0000.0000.0000.000
150A150LEU00.0280.00878.1920.0000.0000.0000.0000.0000.000
151A151ASN0-0.0410.00079.690-0.001-0.0010.0000.0000.0000.000
152A152GLN0-0.085-0.03381.7560.0000.0000.0000.0000.0000.000
153A153ASN00.0400.01084.7550.0000.0000.0000.0000.0000.000
154A154ASP-1-0.879-0.93987.5220.0130.0130.0000.0000.0000.000
155A155ALA0-0.044-0.00883.8660.0000.0000.0000.0000.0000.000
156A156THR00.0500.01985.5520.0000.0000.0000.0000.0000.000
157A157GLN00.045-0.00581.8540.0000.0000.0000.0000.0000.000
158A158GLN00.0200.01682.8430.0000.0000.0000.0000.0000.000
159A159GLY00.0380.01781.7980.0010.0010.0000.0000.0000.000
160A160VAL00.0440.00879.0920.0010.0010.0000.0000.0000.000
161A161ASN00.0380.03278.1440.0010.0010.0000.0000.0000.000
162A162GLU-1-0.935-0.95977.4030.0200.0200.0000.0000.0000.000
163A163LYS10.8580.92275.460-0.018-0.0180.0000.0000.0000.000
164A164SER00.025-0.00473.7550.0010.0010.0000.0000.0000.000
165A165LYS10.9510.98872.628-0.021-0.0210.0000.0000.0000.000
166A166ALA0-0.029-0.01271.1470.0010.0010.0000.0000.0000.000
167A167ILE00.0110.01468.8230.0010.0010.0000.0000.0000.000
168A168GLU-1-0.822-0.89667.7980.0250.0250.0000.0000.0000.000
169A169GLN0-0.028-0.01466.2900.0020.0020.0000.0000.0000.000
170A170ASN0-0.009-0.03764.9150.0020.0020.0000.0000.0000.000
171A171TYR00.018-0.01863.1110.0020.0020.0000.0000.0000.000
172A172LYS10.8300.91362.352-0.026-0.0260.0000.0000.0000.000
173A173LYS10.9160.96460.907-0.029-0.0290.0000.0000.0000.000
174A174LEU00.0070.01657.8670.0010.0010.0000.0000.0000.000
175A175LYS10.8490.90856.763-0.035-0.0350.0000.0000.0000.000
176A176GLU-1-0.843-0.90556.5420.0410.0410.0000.0000.0000.000
177A177VAL0-0.0190.00253.7570.0020.0020.0000.0000.0000.000
178A178SER00.0660.03253.0310.0020.0020.0000.0000.0000.000
179A179ASP-1-0.854-0.89352.1120.0400.0400.0000.0000.0000.000
180A180LYS10.7820.87150.170-0.042-0.0420.0000.0000.0000.000
181A181TYR00.0620.02747.0610.0030.0030.0000.0000.0000.000
182A182THR00.002-0.01747.3960.0010.0010.0000.0000.0000.000
183A183LYS10.9350.97146.415-0.049-0.0490.0000.0000.0000.000
184A184VAL00.0140.01643.0990.0030.0030.0000.0000.0000.000
185A185LEU0-0.0020.00042.4930.0030.0030.0000.0000.0000.000
186A186ASN0-0.058-0.03841.7410.0020.0020.0000.0000.0000.000
187A187LYS10.8870.96139.363-0.079-0.0790.0000.0000.0000.000
188A188VAL00.0290.00737.4340.0050.0050.0000.0000.0000.000
189A189GLN00.0150.01535.6580.0050.0050.0000.0000.0000.000
190A190LYS10.8280.89534.549-0.104-0.1040.0000.0000.0000.000
191A191GLU-1-0.751-0.88033.9960.1080.1080.0000.0000.0000.000
192A192LYS10.8410.90932.007-0.064-0.0640.0000.0000.0000.000
193A193GLN0-0.031-0.00530.5220.0020.0020.0000.0000.0000.000
194A194ASP-1-0.849-0.89629.4060.1270.1270.0000.0000.0000.000
195A195VAL0-0.010-0.00427.5210.0140.0140.0000.0000.0000.000
196A196ASP-1-1.051-1.02224.7860.1550.1550.0000.0000.0000.000