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: N182Q

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 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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2032314.203305
FMO2-HF: Nuclear repulsion 1953897.508427
FMO2-HF: Total energy -78416.694878
FMO2-MP2: Total energy -78650.665966


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.
-0.3234.0551.022-2.137-3.262-0.01
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 : 0.046 / q_NPA : 0.010
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].
3A3MET0-0.017-0.0203.758-1.2070.1390.007-0.627-0.7260.002
4A4GLY00.0280.0273.2290.4041.1830.051-0.355-0.4740.001
5A5ILE0-0.060-0.0263.0830.5091.4880.224-0.314-0.889-0.003
6A6GLN00.0200.0162.708-1.460-0.1860.740-0.841-1.173-0.010
7A7ARG10.9070.9385.4521.0571.0570.0000.0000.0000.000
8A8PRO0-0.001-0.0048.1650.0370.0370.0000.0000.0000.000
9A9THR00.0960.0618.7090.0500.0500.0000.0000.0000.000
10A10SER00.1100.04110.948-0.039-0.0390.0000.0000.0000.000
11A11THR00.0310.01813.823-0.023-0.0230.0000.0000.0000.000
12A12THR0-0.028-0.02512.768-0.007-0.0070.0000.0000.0000.000
13A13THR0-0.002-0.00714.222-0.034-0.0340.0000.0000.0000.000
14A14ASP-1-0.743-0.86916.6790.0610.0610.0000.0000.0000.000
15A15LYS10.9740.98816.6890.0480.0480.0000.0000.0000.000
16A16LYS10.8480.92618.6380.0630.0630.0000.0000.0000.000
17A17GLU-1-0.819-0.89920.747-0.026-0.0260.0000.0000.0000.000
18A18ILE00.0710.02422.3600.0010.0010.0000.0000.0000.000
19A19LYS10.9170.96219.8950.1000.1000.0000.0000.0000.000
20A20ALA0-0.030-0.01225.205-0.002-0.0020.0000.0000.0000.000
21A21TYR0-0.028-0.04827.0700.0010.0010.0000.0000.0000.000
22A22LEU00.0290.00027.7090.0010.0010.0000.0000.0000.000
23A23LYS10.9490.98829.1870.0710.0710.0000.0000.0000.000
24A24GLN0-0.027-0.03230.1360.0050.0050.0000.0000.0000.000
25A25VAL00.0010.00033.1680.0010.0010.0000.0000.0000.000
26A26ASP-1-0.880-0.95433.982-0.028-0.0280.0000.0000.0000.000
27A27LYS10.8500.94335.4410.0370.0370.0000.0000.0000.000
28A28ILE00.0150.01337.2190.0010.0010.0000.0000.0000.000
29A29LYS10.9100.95938.8120.0230.0230.0000.0000.0000.000
30A30ASP-1-0.933-0.96938.212-0.036-0.0360.0000.0000.0000.000
31A31ASP-1-0.903-0.94741.285-0.030-0.0300.0000.0000.0000.000
32A32GLU-1-0.821-0.85643.489-0.010-0.0100.0000.0000.0000.000
33A33GLU-1-0.964-0.96845.323-0.023-0.0230.0000.0000.0000.000
34A34PRO00.021-0.00746.9190.0010.0010.0000.0000.0000.000
35A35ILE00.0310.01947.8920.0010.0010.0000.0000.0000.000
36A36LYS10.9240.95747.7740.0170.0170.0000.0000.0000.000
37A37THR0-0.028-0.00951.3490.0000.0000.0000.0000.0000.000
38A38VAL00.0240.02053.8020.0000.0000.0000.0000.0000.000
39A39GLY00.0130.01154.4470.0010.0010.0000.0000.0000.000
40A40LYS10.9410.96352.8550.0210.0210.0000.0000.0000.000
41A41LYS10.9310.97757.5230.0170.0170.0000.0000.0000.000
42A42ILE00.0310.00758.2220.0010.0010.0000.0000.0000.000
43A43ALA00.0390.02859.5390.0010.0010.0000.0000.0000.000
44A44GLU-1-0.945-0.97961.394-0.013-0.0130.0000.0000.0000.000
45A45LEU0-0.078-0.03463.1550.0000.0000.0000.0000.0000.000
46A46ASP-1-0.873-0.94062.766-0.006-0.0060.0000.0000.0000.000
47A47GLU-1-0.863-0.92164.896-0.008-0.0080.0000.0000.0000.000
48A48LYS10.9060.94366.8140.0120.0120.0000.0000.0000.000
49A49LYS10.9450.99168.7900.0050.0050.0000.0000.0000.000
50A50LYS10.8470.90665.7730.0070.0070.0000.0000.0000.000
51A51LYS10.9460.97470.8350.0100.0100.0000.0000.0000.000
52A52LEU00.0200.02173.7430.0000.0000.0000.0000.0000.000
53A53THR0-0.073-0.04374.3850.0010.0010.0000.0000.0000.000
54A54GLU-1-0.940-0.96377.036-0.005-0.0050.0000.0000.0000.000
55A55ASP-1-0.849-0.93879.730-0.006-0.0060.0000.0000.0000.000
56A56VAL0-0.073-0.03078.3700.0000.0000.0000.0000.0000.000
57A57ASN0-0.009-0.00880.7840.0010.0010.0000.0000.0000.000
58A58SER00.0260.01783.8370.0000.0000.0000.0000.0000.000
59A59LYS10.9590.96085.9110.0040.0040.0000.0000.0000.000
60A60ASP-1-0.819-0.88688.067-0.005-0.0050.0000.0000.0000.000
61A61THR00.044-0.00787.6650.0000.0000.0000.0000.0000.000
62A62ALA0-0.021-0.00287.2600.0000.0000.0000.0000.0000.000
63A63VAL0-0.0220.00983.3240.0000.0000.0000.0000.0000.000
64A64ARG10.9010.94782.9550.0030.0030.0000.0000.0000.000
65A65GLY00.0040.00382.4600.0000.0000.0000.0000.0000.000
66A66LYS10.8540.89877.9410.0080.0080.0000.0000.0000.000
67A67ALA00.0590.04478.6110.0000.0000.0000.0000.0000.000
68A68VAL0-0.003-0.00577.5620.0000.0000.0000.0000.0000.000
69A69LYS10.8840.92477.3640.0050.0050.0000.0000.0000.000
70A70ASP-1-0.813-0.88475.215-0.007-0.0070.0000.0000.0000.000
71A71LEU0-0.040-0.02173.1620.0000.0000.0000.0000.0000.000
72A72ILE0-0.077-0.03172.3950.0000.0000.0000.0000.0000.000
73A73LYS10.9170.96370.4450.0090.0090.0000.0000.0000.000
74A74ASN00.0080.00568.3410.0000.0000.0000.0000.0000.000
75A75ALA0-0.020-0.01167.7290.0000.0000.0000.0000.0000.000
76A76ASP-1-0.807-0.89266.786-0.005-0.0050.0000.0000.0000.000
77A77ASP-1-0.876-0.93665.986-0.009-0.0090.0000.0000.0000.000
78A78ARG10.8160.90863.3080.0050.0050.0000.0000.0000.000
79A79LEU0-0.033-0.01561.9310.0000.0000.0000.0000.0000.000
80A80LYS10.8420.90861.4160.0080.0080.0000.0000.0000.000
81A81GLU-1-0.832-0.92358.091-0.014-0.0140.0000.0000.0000.000
82A82PHE0-0.018-0.02055.5430.0000.0000.0000.0000.0000.000
83A83GLU-1-0.776-0.85756.535-0.007-0.0070.0000.0000.0000.000
84A84LYS10.8710.93554.6810.0140.0140.0000.0000.0000.000
85A85GLU-1-0.857-0.91751.715-0.008-0.0080.0000.0000.0000.000
86A86GLU-1-0.844-0.92651.598-0.003-0.0030.0000.0000.0000.000
87A87ASP-1-0.909-0.95951.768-0.008-0.0080.0000.0000.0000.000
88A88ALA0-0.047-0.01848.616-0.001-0.0010.0000.0000.0000.000
89A89ILE00.012-0.00146.857-0.001-0.0010.0000.0000.0000.000
90A90LYS10.9650.99346.8920.0050.0050.0000.0000.0000.000
91A91LYS10.9410.96744.6920.0210.0210.0000.0000.0000.000
92A92SER0-0.009-0.05743.1700.0000.0000.0000.0000.0000.000
93A93GLU-1-0.901-0.95842.1330.0030.0030.0000.0000.0000.000
94A94GLN0-0.084-0.05742.4500.0020.0020.0000.0000.0000.000
95A95ASP-1-0.906-0.95139.769-0.018-0.0180.0000.0000.0000.000
96A96PHE0-0.035-0.01636.8910.0000.0000.0000.0000.0000.000
97A97LYS10.8930.94837.288-0.004-0.0040.0000.0000.0000.000
98A98LYS10.8960.95936.8630.0160.0160.0000.0000.0000.000
99A99ALA00.0140.03233.383-0.002-0.0020.0000.0000.0000.000
100A100LYS10.8780.90930.703-0.015-0.0150.0000.0000.0000.000
101A101SER00.0240.02529.5630.0060.0060.0000.0000.0000.000
102A102HIS0-0.072-0.04025.9900.0040.0040.0000.0000.0000.000
103A103VAL0-0.027-0.01526.9200.0020.0020.0000.0000.0000.000
104A104ASP-1-0.921-0.95326.9400.0390.0390.0000.0000.0000.000
105A105ASN0-0.036-0.01923.1710.0140.0140.0000.0000.0000.000
106A106ILE0-0.070-0.01221.824-0.002-0.0020.0000.0000.0000.000
107A107ASP-1-0.921-0.95718.3430.1750.1750.0000.0000.0000.000
108A108ASN00.0400.02119.5060.0090.0090.0000.0000.0000.000
109A109ASP-1-0.780-0.89021.1390.1150.1150.0000.0000.0000.000
110A110VAL0-0.030-0.01423.888-0.011-0.0110.0000.0000.0000.000
111A111LYS10.7990.87222.146-0.042-0.0420.0000.0000.0000.000
112A112ARG10.7970.87723.925-0.102-0.1020.0000.0000.0000.000
113A113LYS10.8910.93826.597-0.085-0.0850.0000.0000.0000.000
114A114GLU-1-0.789-0.88627.1850.0390.0390.0000.0000.0000.000
115A115VAL00.0070.00427.168-0.006-0.0060.0000.0000.0000.000
116A116LYS10.9190.95530.193-0.057-0.0570.0000.0000.0000.000
117A117GLN00.0170.02732.798-0.001-0.0010.0000.0000.0000.000
118A118LEU00.011-0.00132.018-0.004-0.0040.0000.0000.0000.000
119A119ASP-1-0.820-0.90633.7100.0080.0080.0000.0000.0000.000
120A120ASP-1-0.949-0.97236.0060.0270.0270.0000.0000.0000.000
121A121VAL0-0.066-0.02938.093-0.002-0.0020.0000.0000.0000.000
122A122LEU0-0.019-0.00836.242-0.003-0.0030.0000.0000.0000.000
123A123LYS10.9250.96637.530-0.020-0.0200.0000.0000.0000.000
124A124GLU-1-0.911-0.95642.0900.0130.0130.0000.0000.0000.000
125A125LYS10.8380.91742.5680.0060.0060.0000.0000.0000.000
126A126TYR0-0.001-0.01641.158-0.001-0.0010.0000.0000.0000.000
127A127LYS10.9560.99346.239-0.015-0.0150.0000.0000.0000.000
128A128LEU0-0.012-0.02047.297-0.001-0.0010.0000.0000.0000.000
129A129HIS0-0.066-0.03948.7960.0000.0000.0000.0000.0000.000
130A130SER00.0410.03150.528-0.001-0.0010.0000.0000.0000.000
131A131ASP-1-0.957-0.97252.6450.0080.0080.0000.0000.0000.000
132A132TYR0-0.025-0.02653.0230.0000.0000.0000.0000.0000.000
133A133ALA00.0470.02354.497-0.001-0.0010.0000.0000.0000.000
134A134LYS10.9020.95656.264-0.005-0.0050.0000.0000.0000.000
135A135ALA0-0.044-0.03058.1690.0000.0000.0000.0000.0000.000
136A136TYR00.0490.02558.4830.0000.0000.0000.0000.0000.000
137A137LYS10.9040.93158.6310.0020.0020.0000.0000.0000.000
138A138LYS10.8540.94462.269-0.003-0.0030.0000.0000.0000.000
139A139ALA00.0460.02463.6110.0000.0000.0000.0000.0000.000
140A140VAL00.0490.05763.5410.0000.0000.0000.0000.0000.000
141A141ASN0-0.009-0.02065.2030.0000.0000.0000.0000.0000.000
142A142SER0-0.089-0.05868.0570.0000.0000.0000.0000.0000.000
143A143GLU-1-0.758-0.88067.846-0.003-0.0030.0000.0000.0000.000
144A144LYS10.8810.92770.3890.0040.0040.0000.0000.0000.000
145A145THR0-0.086-0.04372.1150.0000.0000.0000.0000.0000.000
146A146LEU00.0010.00774.0970.0000.0000.0000.0000.0000.000
147A147PHE00.0530.00671.6340.0000.0000.0000.0000.0000.000
148A148LYS10.9490.96175.2950.0020.0020.0000.0000.0000.000
149A149TYR0-0.0150.00878.1350.0000.0000.0000.0000.0000.000
150A150LEU00.0230.00678.7860.0000.0000.0000.0000.0000.000
151A151ASN0-0.0400.00280.3200.0000.0000.0000.0000.0000.000
152A152GLN0-0.044-0.01682.3330.0000.0000.0000.0000.0000.000
153A153ASN00.009-0.00285.1930.0000.0000.0000.0000.0000.000
154A154ASP-1-0.888-0.94188.091-0.001-0.0010.0000.0000.0000.000
155A155ALA0-0.051-0.00684.2220.0000.0000.0000.0000.0000.000
156A156THR00.0650.01885.5900.0000.0000.0000.0000.0000.000
157A157GLN00.029-0.00882.1370.0000.0000.0000.0000.0000.000
158A158GLN00.0180.01583.1770.0000.0000.0000.0000.0000.000
159A159GLY00.0470.02282.3830.0000.0000.0000.0000.0000.000
160A160VAL00.0210.00179.2060.0000.0000.0000.0000.0000.000
161A161ASN00.0240.01278.4950.0000.0000.0000.0000.0000.000
162A162GLU-1-0.979-0.99277.7550.0030.0030.0000.0000.0000.000
163A163LYS10.9240.94875.911-0.001-0.0010.0000.0000.0000.000
164A164SER00.0160.01174.1460.0000.0000.0000.0000.0000.000
165A165LYS10.9681.01272.968-0.003-0.0030.0000.0000.0000.000
166A166ALA0-0.027-0.01171.4540.0000.0000.0000.0000.0000.000
167A167ILE00.0030.01569.0700.0000.0000.0000.0000.0000.000
168A168GLU-1-0.904-0.95468.1390.0020.0020.0000.0000.0000.000
169A169GLN0-0.046-0.02666.2710.0000.0000.0000.0000.0000.000
170A170ASN0-0.037-0.04565.2900.0010.0010.0000.0000.0000.000
171A171TYR00.016-0.00863.2330.0000.0000.0000.0000.0000.000
172A172LYS10.9190.97462.662-0.004-0.0040.0000.0000.0000.000
173A173LYS10.9670.98261.361-0.005-0.0050.0000.0000.0000.000
174A174LEU00.0040.00857.9870.0000.0000.0000.0000.0000.000
175A175LYS10.8880.94457.784-0.003-0.0030.0000.0000.0000.000
176A176GLU-1-0.957-0.97056.9250.0080.0080.0000.0000.0000.000
177A177VAL0-0.017-0.01454.0000.0010.0010.0000.0000.0000.000
178A178SER00.0250.01453.2740.0000.0000.0000.0000.0000.000
179A179ASP-1-0.837-0.91752.4530.0030.0030.0000.0000.0000.000
180A180LYS10.8790.93450.683-0.010-0.0100.0000.0000.0000.000
181A181TYR00.0570.02847.4240.0010.0010.0000.0000.0000.000
182A182THR00.0260.00247.639-0.001-0.0010.0000.0000.0000.000
183A183LYS10.9120.95046.740-0.012-0.0120.0000.0000.0000.000
184A184VAL00.0090.02443.4790.0010.0010.0000.0000.0000.000
185A185LEU0-0.013-0.00142.8280.0000.0000.0000.0000.0000.000
186A186ASN0-0.011-0.00741.973-0.003-0.0030.0000.0000.0000.000
187A187LYS10.8980.96339.862-0.020-0.0200.0000.0000.0000.000
188A188VAL00.0420.00937.9430.0010.0010.0000.0000.0000.000
189A189GLN0-0.014-0.01335.3960.0000.0000.0000.0000.0000.000
190A190LYS10.9630.98335.795-0.023-0.0230.0000.0000.0000.000
191A191GLU-1-0.803-0.91434.3120.0260.0260.0000.0000.0000.000
192A192LYS10.8780.95132.3300.0150.0150.0000.0000.0000.000
193A193GLN0-0.042-0.01730.9250.0000.0000.0000.0000.0000.000
194A194ASP-1-0.921-0.93529.9850.0260.0260.0000.0000.0000.000
195A195VAL0-0.036-0.01827.7260.0030.0030.0000.0000.0000.000
196A196ASP-1-1.005-0.97626.254-0.035-0.0350.0000.0000.0000.000