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: 2NY3R

Calculation Name: 3APQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3APQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9DC23

Base Structure: X-ray

Registration Date: 2023-09-24

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2413251.466299
FMO2-HF: Nuclear repulsion 2328888.400437
FMO2-HF: Total energy -84363.065862
FMO2-MP2: Total energy -84608.33806


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:33:ILE)


Summations of interaction energy for fragment #1(A:33: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.
-2.1340.7080.448-1.476-1.813-0.007
Interaction energy analysis for fragmet #1(A:33:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / 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].
3A35ASN00.0290.0232.767-2.943-0.1480.449-1.472-1.771-0.007
4A36PHE00.053-0.0055.1390.4330.480-0.001-0.004-0.0420.000
5A37TYR0-0.033-0.0178.6420.2420.2420.0000.0000.0000.000
6A38SER0-0.005-0.0256.095-0.110-0.1100.0000.0000.0000.000
7A39LEU0-0.091-0.0328.3240.3590.3590.0000.0000.0000.000
8A40LEU0-0.006-0.01210.1190.1660.1660.0000.0000.0000.000
9A41GLY0-0.0280.00711.3600.0830.0830.0000.0000.0000.000
10A42VAL0-0.021-0.01012.1680.0500.0500.0000.0000.0000.000
11A43SER00.0390.00411.619-0.145-0.1450.0000.0000.0000.000
12A44LYS10.9590.97710.2410.9550.9550.0000.0000.0000.000
13A45THR0-0.022-0.02113.0710.0190.0190.0000.0000.0000.000
14A46ALA0-0.0270.02115.9450.0460.0460.0000.0000.0000.000
15A47SER00.0560.00917.802-0.017-0.0170.0000.0000.0000.000
16A48SER00.0610.01419.949-0.021-0.0210.0000.0000.0000.000
17A49ARG10.9110.94921.3500.1100.1100.0000.0000.0000.000
18A50GLU-1-0.876-0.93319.190-0.198-0.1980.0000.0000.0000.000
19A51ILE00.009-0.00116.0640.0100.0100.0000.0000.0000.000
20A52ARG10.7900.88318.5160.1570.1570.0000.0000.0000.000
21A53GLN00.014-0.00921.4350.0290.0290.0000.0000.0000.000
22A54ALA0-0.051-0.01316.7980.0260.0260.0000.0000.0000.000
23A55PHE00.0260.00417.6340.0280.0280.0000.0000.0000.000
24A56LYS10.9881.00318.9700.0820.0820.0000.0000.0000.000
25A57LYS10.9400.98117.954-0.002-0.0020.0000.0000.0000.000
26A58LEU0-0.079-0.04515.1560.0350.0350.0000.0000.0000.000
27A59ALA00.0600.03219.8610.0230.0230.0000.0000.0000.000
28A60LEU0-0.041-0.02622.4330.0140.0140.0000.0000.0000.000
29A61LYS10.9210.97521.194-0.123-0.1230.0000.0000.0000.000
30A62LEU0-0.017-0.03517.8100.0160.0160.0000.0000.0000.000
31A63HIS0-0.035-0.00422.2330.0120.0120.0000.0000.0000.000
32A64PRO00.0640.02322.7160.0130.0130.0000.0000.0000.000
33A65ASP-1-0.884-0.93525.0480.0070.0070.0000.0000.0000.000
34A66LYS10.8320.91927.332-0.011-0.0110.0000.0000.0000.000
35A67ASN0-0.094-0.05324.8960.0190.0190.0000.0000.0000.000
36A68PRO00.0490.03126.2960.0090.0090.0000.0000.0000.000
37A69ASN0-0.019-0.02428.6330.0010.0010.0000.0000.0000.000
38A70ASN0-0.040-0.00720.7200.0190.0190.0000.0000.0000.000
39A71PRO00.0460.02023.192-0.010-0.0100.0000.0000.0000.000
40A72ASN00.0090.00417.980-0.031-0.0310.0000.0000.0000.000
41A73ALA00.0080.02219.298-0.006-0.0060.0000.0000.0000.000
42A74HIS00.0830.05620.418-0.012-0.0120.0000.0000.0000.000
43A75GLY00.0200.00618.234-0.021-0.0210.0000.0000.0000.000
44A76ASP-1-0.902-0.96815.4280.1600.1600.0000.0000.0000.000
45A77PHE0-0.019-0.01615.916-0.041-0.0410.0000.0000.0000.000
46A78LEU00.0130.02617.617-0.038-0.0380.0000.0000.0000.000
47A79LYS10.9140.97010.485-0.090-0.0900.0000.0000.0000.000
48A80ILE0-0.022-0.00813.195-0.076-0.0760.0000.0000.0000.000
49A81ASN00.001-0.00914.766-0.045-0.0450.0000.0000.0000.000
50A82ARG10.8450.93110.3220.3890.3890.0000.0000.0000.000
51A83ALA0-0.037-0.02011.522-0.042-0.0420.0000.0000.0000.000
52A84TYR00.0380.00913.061-0.032-0.0320.0000.0000.0000.000
53A85GLU-1-0.927-0.98716.354-0.175-0.1750.0000.0000.0000.000
54A86VAL0-0.036-0.00613.248-0.003-0.0030.0000.0000.0000.000
55A87LEU0-0.064-0.04811.9250.0000.0000.0000.0000.0000.000
56A88LYS10.9190.97715.7070.2020.2020.0000.0000.0000.000
57A89ASP-1-0.820-0.89718.759-0.221-0.2210.0000.0000.0000.000
58A90GLU-1-0.828-0.92319.052-0.267-0.2670.0000.0000.0000.000
59A91ASP-1-0.945-0.97319.573-0.264-0.2640.0000.0000.0000.000
60A92LEU0-0.054-0.03317.002-0.038-0.0380.0000.0000.0000.000
61A93ARG10.8550.92314.6590.3730.3730.0000.0000.0000.000
62A94LYS10.9270.98514.6450.2180.2180.0000.0000.0000.000
63A95LYS10.8990.94115.6670.3120.3120.0000.0000.0000.000
64A96TYR00.0530.0466.681-0.170-0.1700.0000.0000.0000.000
65A97ASP-1-0.858-0.91910.673-0.836-0.8360.0000.0000.0000.000
66A98LYS10.8700.93611.7370.3010.3010.0000.0000.0000.000
67A99TYR0-0.084-0.05211.9660.0250.0250.0000.0000.0000.000
68A100GLY00.0410.0388.486-0.027-0.0270.0000.0000.0000.000
69A101GLU-1-0.839-0.9297.860-0.653-0.6530.0000.0000.0000.000
70A102LYS10.9720.98810.5050.4690.4690.0000.0000.0000.000
71A103GLY0-0.103-0.06813.4500.0120.0120.0000.0000.0000.000
72A104LEU0-0.0300.01311.6300.0270.0270.0000.0000.0000.000
73A105GLU-1-0.884-0.93715.172-0.174-0.1740.0000.0000.0000.000
74A106ASP-1-0.917-0.97512.519-0.263-0.2630.0000.0000.0000.000
75A107ASN0-0.066-0.03714.661-0.003-0.0030.0000.0000.0000.000
76A108GLN00.0580.05116.1790.0200.0200.0000.0000.0000.000
77A109GLY00.001-0.00917.253-0.012-0.0120.0000.0000.0000.000
78A110GLY0-0.004-0.01918.7860.0100.0100.0000.0000.0000.000
79A111GLN0-0.044-0.01921.0550.0230.0230.0000.0000.0000.000
80A112TYR0-0.018-0.02621.867-0.008-0.0080.0000.0000.0000.000
81A113GLU-1-0.863-0.92124.172-0.060-0.0600.0000.0000.0000.000
82A114SER00.0720.03526.7350.0090.0090.0000.0000.0000.000
83A115TRP0-0.006-0.02527.196-0.008-0.0080.0000.0000.0000.000
84A116SER0-0.014-0.02028.810-0.002-0.0020.0000.0000.0000.000
85A117TYR00.0790.05026.349-0.004-0.0040.0000.0000.0000.000
86A118TYR00.0560.01923.4480.0000.0000.0000.0000.0000.000
87A119ARG10.8150.92227.5060.0130.0130.0000.0000.0000.000
88A120TYR0-0.026-0.04830.0590.0030.0030.0000.0000.0000.000
89A121ASP-1-0.763-0.83931.012-0.058-0.0580.0000.0000.0000.000
90A122PHE0-0.0170.00922.329-0.007-0.0070.0000.0000.0000.000
91A123GLY0-0.014-0.01227.0490.0030.0030.0000.0000.0000.000
92A124ILE00.0020.01627.8410.0040.0040.0000.0000.0000.000
93A125TYR00.007-0.01031.1310.0080.0080.0000.0000.0000.000
94A126ASP-1-0.766-0.84726.082-0.119-0.1190.0000.0000.0000.000
95A127ASP-1-0.958-0.96628.658-0.060-0.0600.0000.0000.0000.000
96A128ASP-1-0.820-0.91030.764-0.047-0.0470.0000.0000.0000.000
97A129PRO0-0.044-0.02032.209-0.006-0.0060.0000.0000.0000.000
98A130GLU-1-0.860-0.94133.234-0.056-0.0560.0000.0000.0000.000
99A131ILE0-0.059-0.01833.9120.0000.0000.0000.0000.0000.000
100A132ILE0-0.029-0.00830.889-0.006-0.0060.0000.0000.0000.000
101A133THR0-0.029-0.02728.7300.0050.0050.0000.0000.0000.000
102A134LEU0-0.071-0.02429.077-0.010-0.0100.0000.0000.0000.000
103A135GLU-1-0.806-0.91125.128-0.165-0.1650.0000.0000.0000.000
104A136ARG10.9160.93628.2060.1350.1350.0000.0000.0000.000
105A137ARG10.8610.93125.5890.2020.2020.0000.0000.0000.000
106A138GLU-1-0.869-0.95126.386-0.174-0.1740.0000.0000.0000.000
107A139PHE00.0110.00830.2870.0110.0110.0000.0000.0000.000
108A140ASP-1-0.831-0.91932.660-0.113-0.1130.0000.0000.0000.000
109A141ALA0-0.021-0.01032.4090.0060.0060.0000.0000.0000.000
110A142ALA0-0.0030.00534.3030.0060.0060.0000.0000.0000.000
111A143VAL0-0.035-0.02436.1830.0070.0070.0000.0000.0000.000
112A144ASN0-0.034-0.01937.4730.0070.0070.0000.0000.0000.000
113A145SER0-0.059-0.02037.5150.0050.0050.0000.0000.0000.000
114A146GLY00.011-0.00239.3830.0020.0020.0000.0000.0000.000
115A147GLU-1-0.912-0.95038.429-0.078-0.0780.0000.0000.0000.000
116A148LEU0-0.043-0.01442.106-0.001-0.0010.0000.0000.0000.000
117A149TRP00.0500.01734.608-0.001-0.0010.0000.0000.0000.000
118A150PHE0-0.002-0.00440.9620.0020.0020.0000.0000.0000.000
119A151VAL0-0.0100.00036.477-0.002-0.0020.0000.0000.0000.000
120A152ASN00.0130.01737.8720.0020.0020.0000.0000.0000.000
121A153PHE0-0.030-0.02736.130-0.006-0.0060.0000.0000.0000.000
122A154TYR00.1190.02830.9590.0040.0040.0000.0000.0000.000
123A155SER0-0.029-0.03133.956-0.009-0.0090.0000.0000.0000.000
124A156PRO0-0.0230.01030.5660.0040.0040.0000.0000.0000.000
125A157GLY0-0.035-0.03833.2540.0010.0010.0000.0000.0000.000
126A158CYS-1-0.878-0.90035.856-0.048-0.0480.0000.0000.0000.000
127A159SER00.020-0.01638.7150.0010.0010.0000.0000.0000.000
128A160HIS00.018-0.00241.4080.0010.0010.0000.0000.0000.000
129A161CYS-1-0.841-0.92537.924-0.055-0.0550.0000.0000.0000.000
130A162HIS0-0.169-0.10334.7710.0030.0030.0000.0000.0000.000
131A163ASP-1-0.965-0.96939.520-0.028-0.0280.0000.0000.0000.000
132A164LEU0-0.049-0.02541.3860.0010.0010.0000.0000.0000.000
133A165ALA00.0050.00737.7140.0000.0000.0000.0000.0000.000
134A166PRO0-0.026-0.02239.619-0.001-0.0010.0000.0000.0000.000
135A167THR00.0640.03741.3980.0010.0010.0000.0000.0000.000
136A168TRP0-0.016-0.00537.7970.0010.0010.0000.0000.0000.000
137A169ARG10.8410.91334.6560.0460.0460.0000.0000.0000.000
138A170GLU-1-0.943-0.97339.991-0.028-0.0280.0000.0000.0000.000
139A171PHE00.017-0.01242.7670.0000.0000.0000.0000.0000.000
140A172ALA0-0.018-0.00739.4650.0000.0000.0000.0000.0000.000
141A173LYS10.9330.96738.9290.0370.0370.0000.0000.0000.000
142A174GLU-1-0.933-0.94942.103-0.030-0.0300.0000.0000.0000.000
143A175VAL0-0.050-0.04143.6030.0010.0010.0000.0000.0000.000
144A176ASP-1-0.879-0.93439.628-0.058-0.0580.0000.0000.0000.000
145A177GLY0-0.023-0.00741.4160.0020.0020.0000.0000.0000.000
146A178LEU0-0.094-0.04542.4580.0000.0000.0000.0000.0000.000
147A179LEU0-0.027-0.02143.2290.0000.0000.0000.0000.0000.000
148A180ARG10.8650.95134.5360.0850.0850.0000.0000.0000.000
149A181ILE00.0500.03538.2600.0010.0010.0000.0000.0000.000
150A182GLY00.018-0.00335.415-0.005-0.0050.0000.0000.0000.000
151A183ALA0-0.016-0.00433.3040.0070.0070.0000.0000.0000.000
152A184VAL00.009-0.00532.071-0.008-0.0080.0000.0000.0000.000
153A185ASN00.0740.04928.0670.0140.0140.0000.0000.0000.000
154A186CYS00.019-0.00830.483-0.003-0.0030.0000.0000.0000.000
155A187GLY0-0.050-0.03630.4770.0000.0000.0000.0000.0000.000
156A188ASP-1-0.934-0.96825.610-0.149-0.1490.0000.0000.0000.000
157A189ASP-1-0.870-0.93827.115-0.147-0.1470.0000.0000.0000.000
158A190ARG10.9380.97429.7270.0940.0940.0000.0000.0000.000
159A191MET0-0.002-0.00731.9860.0090.0090.0000.0000.0000.000
160A192LEU00.0460.04331.3670.0060.0060.0000.0000.0000.000
161A194ARG10.9560.98136.2230.0800.0800.0000.0000.0000.000
162A195MET0-0.091-0.04934.9060.0020.0020.0000.0000.0000.000
163A196LYS10.8720.95337.1310.0940.0940.0000.0000.0000.000
164A197GLY00.0030.01240.0900.0030.0030.0000.0000.0000.000
165A198VAL0-0.026-0.00338.9100.0040.0040.0000.0000.0000.000
166A199ASN0-0.078-0.05639.695-0.001-0.0010.0000.0000.0000.000
167A200SER0-0.051-0.01541.6950.0030.0030.0000.0000.0000.000
168A201TYR00.0010.01337.321-0.006-0.0060.0000.0000.0000.000
169A202PRO00.1550.06640.2330.0030.0030.0000.0000.0000.000
170A203SER0-0.114-0.06440.5500.0040.0040.0000.0000.0000.000
171A204LEU0-0.027-0.00540.958-0.004-0.0040.0000.0000.0000.000
172A205PHE00.0110.00241.8490.0030.0030.0000.0000.0000.000
173A206ILE0-0.0100.00142.418-0.003-0.0030.0000.0000.0000.000
174A207PHE00.005-0.01740.1620.0000.0000.0000.0000.0000.000
175A208ARG10.9950.98443.3670.0550.0550.0000.0000.0000.000
176A209SER00.0180.03442.1960.0030.0030.0000.0000.0000.000
177A210GLY0-0.003-0.00243.8370.0030.0030.0000.0000.0000.000
178A211MET0-0.061-0.02546.5090.0040.0040.0000.0000.0000.000
179A212ALA0-0.0090.00346.479-0.003-0.0030.0000.0000.0000.000
180A213ALA00.0040.00144.0710.0010.0010.0000.0000.0000.000
181A214VAL00.0090.01446.0180.0020.0020.0000.0000.0000.000
182A215LYS10.9200.96846.2570.0470.0470.0000.0000.0000.000
183A216TYR0-0.017-0.03846.6540.0020.0020.0000.0000.0000.000
184A217ASN0-0.065-0.05648.220-0.001-0.0010.0000.0000.0000.000
185A218GLY00.0190.02050.5160.0020.0020.0000.0000.0000.000
186A219ASP-1-0.837-0.91950.965-0.030-0.0300.0000.0000.0000.000
187A220ARG10.9320.95245.4250.0410.0410.0000.0000.0000.000
188A221SER00.0100.01847.9130.0000.0000.0000.0000.0000.000
189A222LYS10.9610.97647.1800.0270.0270.0000.0000.0000.000
190A223GLU-1-0.918-0.96948.876-0.027-0.0270.0000.0000.0000.000
191A224SER0-0.0170.05051.391-0.002-0.0020.0000.0000.0000.000
192A225LEU00.0090.00044.994-0.002-0.0020.0000.0000.0000.000
193A226VAL00.0500.02448.348-0.002-0.0020.0000.0000.0000.000
194A227ALA0-0.018-0.00549.747-0.001-0.0010.0000.0000.0000.000
195A228PHE0-0.0080.00047.0520.0000.0000.0000.0000.0000.000
196A229ALA00.0290.00446.897-0.001-0.0010.0000.0000.0000.000
197A230MET00.0230.00548.583-0.002-0.0020.0000.0000.0000.000
198A231GLN0-0.046-0.02051.2640.0010.0010.0000.0000.0000.000
199A232HIS0-0.040-0.02548.895-0.001-0.0010.0000.0000.0000.000
200A233VAL0-0.004-0.00247.474-0.001-0.0010.0000.0000.0000.000
201A234ARG10.8800.94349.9150.0340.0340.0000.0000.0000.000
202A235SER0-0.0380.00452.6030.0010.0010.0000.0000.0000.000
203A236THR00.0300.02651.081-0.003-0.0030.0000.0000.0000.000
204A237VAL0-0.025-0.02551.079-0.001-0.0010.0000.0000.0000.000
205A238THR0-0.031-0.02552.9900.0000.0000.0000.0000.0000.000
206A239GLU-1-0.940-0.96756.413-0.036-0.0360.0000.0000.0000.000
207A240LEU0-0.033-0.01059.2770.0010.0010.0000.0000.0000.000