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: 941G2

Calculation Name: 2C46-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C46

Chain ID: A

ChEMBL ID:

UniProt ID: O60942

Base Structure: X-ray

Registration Date: 2023-09-20

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 205
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2532945.613571
FMO2-HF: Nuclear repulsion 2448324.962697
FMO2-HF: Total energy -84620.650874
FMO2-MP2: Total energy -84863.026011


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:-5:ASN)


Summations of interaction energy for fragment #1(A:-5:ASN)
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.
-36.998-24.3836.291-7.49-11.415-0.009
Interaction energy analysis for fragmet #1(A:-5:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.029
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].
3A-3TYR00.0130.0422.377-10.732-6.9852.206-2.280-3.6730.022
4A-2PHE0-0.048-0.0262.846-3.591-1.8320.319-0.499-1.5790.002
5A-1GLN0-0.0060.0003.902-2.696-2.4850.000-0.090-0.1200.000
6A0SER00.003-0.0097.5240.5330.5330.0000.0000.0000.000
7A1MET00.0210.0309.5080.4860.4860.0000.0000.0000.000
8A2ALA0-0.0160.00411.9350.0020.0020.0000.0000.0000.000
9A3HIS00.0360.01814.291-0.020-0.0200.0000.0000.0000.000
10A4ASN0-0.017-0.0128.9270.1550.1550.0000.0000.0000.000
11A5LYS11.0331.02713.038-0.894-0.8940.0000.0000.0000.000
12A6ILE0-0.015-0.00514.1370.2660.2660.0000.0000.0000.000
13A7PRO0-0.026-0.02213.844-0.075-0.0750.0000.0000.0000.000
14A8PRO00.0870.05316.705-0.067-0.0670.0000.0000.0000.000
15A9ARG10.9360.98420.336-0.489-0.4890.0000.0000.0000.000
16A10TRP0-0.024-0.01915.078-0.052-0.0520.0000.0000.0000.000
17A11LEU0-0.018-0.02319.506-0.026-0.0260.0000.0000.0000.000
18A12ASN00.0550.03221.081-0.031-0.0310.0000.0000.0000.000
19A13CYS0-0.0440.02920.730-0.018-0.0180.0000.0000.0000.000
20A14PRO00.0480.03521.7990.0140.0140.0000.0000.0000.000
21A15ARG10.8500.89919.080-0.332-0.3320.0000.0000.0000.000
22A16ARG10.9110.96619.281-0.162-0.1620.0000.0000.0000.000
23A17GLY00.0170.01621.378-0.020-0.0200.0000.0000.0000.000
24A18GLN0-0.040-0.02923.948-0.010-0.0100.0000.0000.0000.000
25A19PRO0-0.004-0.02224.7530.0220.0220.0000.0000.0000.000
26A20VAL00.0370.01725.536-0.014-0.0140.0000.0000.0000.000
27A21ALA00.0490.02427.351-0.006-0.0060.0000.0000.0000.000
28A22GLY0-0.031-0.01228.036-0.014-0.0140.0000.0000.0000.000
29A23ARG10.8530.92825.777-0.104-0.1040.0000.0000.0000.000
30A24PHE00.0610.01621.720-0.001-0.0010.0000.0000.0000.000
31A25LEU0-0.044-0.01118.790-0.015-0.0150.0000.0000.0000.000
32A26PRO00.0210.03219.5400.0520.0520.0000.0000.0000.000
33A27LEU0-0.008-0.02514.551-0.062-0.0620.0000.0000.0000.000
34A28LYS10.8350.93716.669-0.629-0.6290.0000.0000.0000.000
35A29THR0-0.042-0.02711.0270.0960.0960.0000.0000.0000.000
36A30MET00.0130.03010.746-0.244-0.2440.0000.0000.0000.000
37A31LEU0-0.003-0.00710.3870.4730.4730.0000.0000.0000.000
38A32GLY00.017-0.0118.901-0.392-0.3920.0000.0000.0000.000
39A33PRO0-0.001-0.0199.6240.0610.0610.0000.0000.0000.000
40A34ARG10.8820.9558.283-1.160-1.1600.0000.0000.0000.000
41A35TYR0-0.013-0.0348.422-0.232-0.2320.0000.0000.0000.000
42A36ASP-1-0.761-0.86013.3610.3730.3730.0000.0000.0000.000
43A37SER0-0.045-0.02116.316-0.024-0.0240.0000.0000.0000.000
44A38GLN0-0.016-0.01814.697-0.024-0.0240.0000.0000.0000.000
45A39VAL0-0.038-0.00816.0640.0290.0290.0000.0000.0000.000
46A40ALA00.0520.03219.054-0.039-0.0390.0000.0000.0000.000
47A41GLU-1-0.934-0.98121.0060.2090.2090.0000.0000.0000.000
48A42GLU-1-0.795-0.89921.4990.2680.2680.0000.0000.0000.000
49A43ASN0-0.030-0.01420.885-0.004-0.0040.0000.0000.0000.000
50A44ARG10.8290.93716.844-0.243-0.2430.0000.0000.0000.000
51A45PHE00.036-0.01115.899-0.095-0.0950.0000.0000.0000.000
52A46HIS10.8280.89912.180-0.235-0.2350.0000.0000.0000.000
53A47PRO00.1070.0368.246-0.055-0.0550.0000.0000.0000.000
54A48SER00.0170.01111.398-0.017-0.0170.0000.0000.0000.000
55A49MET00.0000.01013.844-0.009-0.0090.0000.0000.0000.000
56A50LEU00.0200.01513.377-0.009-0.0090.0000.0000.0000.000
57A51SER00.0350.01014.495-0.044-0.0440.0000.0000.0000.000
58A52ASN0-0.039-0.02516.258-0.070-0.0700.0000.0000.0000.000
59A53TYR00.0280.01219.171-0.005-0.0050.0000.0000.0000.000
60A54LEU00.0080.01116.667-0.006-0.0060.0000.0000.0000.000
61A55LYS10.9750.98117.3220.3410.3410.0000.0000.0000.000
62A56SER0-0.071-0.02422.2190.0040.0040.0000.0000.0000.000
63A57LEU0-0.023-0.01623.9240.0030.0030.0000.0000.0000.000
64A58LYS10.8780.94724.9740.0290.0290.0000.0000.0000.000
65A59VAL00.0380.02122.908-0.001-0.0010.0000.0000.0000.000
66A60LYS10.8340.92617.3760.3040.3040.0000.0000.0000.000
67A61MET00.0160.02616.0680.0540.0540.0000.0000.0000.000
68A62GLY00.0690.03317.477-0.078-0.0780.0000.0000.0000.000
69A63LEU0-0.061-0.03014.753-0.082-0.0820.0000.0000.0000.000
70A64LEU00.0120.01610.5590.0240.0240.0000.0000.0000.000
71A65VAL00.000-0.00813.0450.0210.0210.0000.0000.0000.000
72A66ASP-1-0.768-0.8459.1472.8262.8260.0000.0000.0000.000
73A67LEU00.0300.00112.4540.0840.0840.0000.0000.0000.000
74A68THR0-0.094-0.04810.4360.1990.1990.0000.0000.0000.000
75A69ASN00.0360.00810.9490.1150.1150.0000.0000.0000.000
76A70THR0-0.0010.0057.5460.5800.5800.0000.0000.0000.000
77A71SER00.0570.0232.835-2.701-1.2700.359-0.860-0.9300.000
78A72ARG10.9270.9693.4652.7153.3210.063-0.208-0.4610.000
79A73PHE00.0090.0185.884-0.943-0.9430.0000.0000.0000.000
80A74TYR0-0.028-0.0535.968-1.154-1.1540.0000.0000.0000.000
81A75ASP-1-0.781-0.8842.200-16.957-13.6432.942-3.069-3.187-0.037
82A76ARG10.8730.9282.814-1.450-0.0940.402-0.438-1.3200.004
83A77ASN00.0620.0323.3801.2121.4030.000-0.046-0.1450.000
84A78ASP-1-0.911-0.9695.404-0.397-0.3970.0000.0000.0000.000
85A79ILE0-0.078-0.0437.3180.4820.4820.0000.0000.0000.000
86A80GLU-1-0.810-0.9236.354-2.584-2.5840.0000.0000.0000.000
87A81LYS10.8800.9639.1401.3791.3790.0000.0000.0000.000
88A82GLU-1-0.942-0.97110.999-0.476-0.4760.0000.0000.0000.000
89A83GLY0-0.0010.00913.0760.1480.1480.0000.0000.0000.000
90A84ILE0-0.094-0.02212.6010.1440.1440.0000.0000.0000.000
91A85LYS10.9710.98712.0090.1400.1400.0000.0000.0000.000
92A86TYR0-0.026-0.0567.5570.3500.3500.0000.0000.0000.000
93A87ILE0-0.024-0.02210.755-0.133-0.1330.0000.0000.0000.000
94A88LYS10.7960.9136.650-3.394-3.3940.0000.0000.0000.000
95A89LEU0-0.011-0.00611.035-0.191-0.1910.0000.0000.0000.000
96A90GLN0-0.007-0.00410.3580.1390.1390.0000.0000.0000.000
97A91CYS0-0.022-0.00414.331-0.161-0.1610.0000.0000.0000.000
98A92LYS10.8510.92117.656-0.456-0.4560.0000.0000.0000.000
99A93GLY00.009-0.00119.5750.0240.0240.0000.0000.0000.000
100A94HIS00.0620.01920.188-0.051-0.0510.0000.0000.0000.000
101A95GLY0-0.054-0.02522.183-0.047-0.0470.0000.0000.0000.000
102A96GLU-1-0.752-0.85123.7700.5020.5020.0000.0000.0000.000
103A97CYS0-0.0070.01823.6430.0440.0440.0000.0000.0000.000
104A98PRO0-0.032-0.00621.7250.0150.0150.0000.0000.0000.000
105A99THR00.0790.03923.127-0.036-0.0360.0000.0000.0000.000
106A100THR00.0820.03224.9700.0060.0060.0000.0000.0000.000
107A101GLU-1-0.880-0.93723.1560.3620.3620.0000.0000.0000.000
108A102ASN0-0.020-0.01419.7790.0290.0290.0000.0000.0000.000
109A103THR00.0510.01121.6710.0180.0180.0000.0000.0000.000
110A104GLU-1-0.810-0.88524.2840.1950.1950.0000.0000.0000.000
111A105THR0-0.063-0.03918.509-0.018-0.0180.0000.0000.0000.000
112A106PHE0-0.021-0.02719.378-0.017-0.0170.0000.0000.0000.000
113A107ILE00.0470.02321.260-0.033-0.0330.0000.0000.0000.000
114A108ARG10.9050.95723.275-0.177-0.1770.0000.0000.0000.000
115A109LEU0-0.071-0.02116.682-0.058-0.0580.0000.0000.0000.000
116A110CYS00.0300.00920.947-0.050-0.0500.0000.0000.0000.000
117A111GLU-1-0.887-0.93922.2380.0710.0710.0000.0000.0000.000
118A112ARG10.8860.94718.784-0.043-0.0430.0000.0000.0000.000
119A113PHE0-0.078-0.04518.138-0.050-0.0500.0000.0000.0000.000
120A114ASN00.0040.00623.211-0.012-0.0120.0000.0000.0000.000
121A115GLU-1-0.829-0.93425.897-0.013-0.0130.0000.0000.0000.000
122A116ARG10.8020.92921.6330.1040.1040.0000.0000.0000.000
123A117ASN00.0220.00228.361-0.003-0.0030.0000.0000.0000.000
124A118PRO0-0.0150.00826.5280.0040.0040.0000.0000.0000.000
125A119PRO00.015-0.00426.349-0.004-0.0040.0000.0000.0000.000
126A120GLU-1-0.899-0.94421.160-0.170-0.1700.0000.0000.0000.000
127A121LEU0-0.037-0.01121.0900.0310.0310.0000.0000.0000.000
128A122ILE00.0100.00318.430-0.034-0.0340.0000.0000.0000.000
129A123GLY0-0.015-0.01716.7190.0240.0240.0000.0000.0000.000
130A124VAL00.0050.00016.8010.0220.0220.0000.0000.0000.000
131A125HIS00.0170.04211.0860.0090.0090.0000.0000.0000.000
132A126CYM-1-0.778-0.80615.0711.0101.0100.0000.0000.0000.000
133A127THR0-0.026-0.02014.8200.1650.1650.0000.0000.0000.000
134A128HIS00.019-0.02715.8610.0240.0240.0000.0000.0000.000
135A129GLY00.0420.01818.894-0.071-0.0710.0000.0000.0000.000
136A130PHE0-0.015-0.01919.922-0.058-0.0580.0000.0000.0000.000
137A131ASN00.0440.01822.823-0.064-0.0640.0000.0000.0000.000
138A132ARG10.9630.96818.560-0.899-0.8990.0000.0000.0000.000
139A133THR00.016-0.05319.159-0.023-0.0230.0000.0000.0000.000
140A134GLY00.0430.01821.173-0.046-0.0460.0000.0000.0000.000
141A135PHE00.019-0.00124.149-0.030-0.0300.0000.0000.0000.000
142A136LEU00.013-0.00219.946-0.029-0.0290.0000.0000.0000.000
143A137ILE0-0.033-0.01422.063-0.039-0.0390.0000.0000.0000.000
144A138CYS0-0.015-0.00225.318-0.041-0.0410.0000.0000.0000.000
145A139ALA00.0690.03526.667-0.024-0.0240.0000.0000.0000.000
146A140PHE0-0.038-0.01125.658-0.027-0.0270.0000.0000.0000.000
147A141LEU0-0.043-0.03227.985-0.026-0.0260.0000.0000.0000.000
148A142VAL00.0130.01830.606-0.017-0.0170.0000.0000.0000.000
149A143GLU-1-0.861-0.87630.1880.2320.2320.0000.0000.0000.000
150A144LYS10.8450.93529.044-0.122-0.1220.0000.0000.0000.000
151A145MET0-0.132-0.08130.347-0.015-0.0150.0000.0000.0000.000
152A146ASP-1-0.872-0.91333.4000.1110.1110.0000.0000.0000.000
153A147TRP0-0.066-0.03032.8630.0020.0020.0000.0000.0000.000
154A148SER00.0950.04736.1130.0060.0060.0000.0000.0000.000
155A149ILE00.0480.00732.0810.0100.0100.0000.0000.0000.000
156A150GLU-1-0.838-0.91935.1050.1880.1880.0000.0000.0000.000
157A151ALA0-0.020-0.00536.5380.0060.0060.0000.0000.0000.000
158A152ALA0-0.0200.00831.4390.0060.0060.0000.0000.0000.000
159A153VAL00.022-0.01131.5930.0180.0180.0000.0000.0000.000
160A154ALA00.0190.01432.2340.0140.0140.0000.0000.0000.000
161A155THR0-0.028-0.02130.703-0.005-0.0050.0000.0000.0000.000
162A156PHE0-0.043-0.01423.9230.0100.0100.0000.0000.0000.000
163A157ALA00.015-0.01028.9210.0160.0160.0000.0000.0000.000
164A158GLN0-0.0170.01131.1780.0030.0030.0000.0000.0000.000
165A159ALA0-0.061-0.02927.598-0.004-0.0040.0000.0000.0000.000
166A160ARG10.7810.88721.001-0.509-0.5090.0000.0000.0000.000
167A161PRO00.0620.06627.1880.0280.0280.0000.0000.0000.000
168A162PRO0-0.018-0.02427.7980.0190.0190.0000.0000.0000.000
169A163GLY00.0310.00928.059-0.017-0.0170.0000.0000.0000.000
170A164ILE0-0.073-0.04126.7090.0360.0360.0000.0000.0000.000
171A165TYR00.0570.01324.444-0.013-0.0130.0000.0000.0000.000
172A166LYS10.9200.97924.856-0.578-0.5780.0000.0000.0000.000
173A167GLY00.0640.02029.063-0.009-0.0090.0000.0000.0000.000
174A168ASP-1-0.848-0.93029.9140.3590.3590.0000.0000.0000.000
175A169TYR0-0.143-0.10923.1240.0280.0280.0000.0000.0000.000
176A170LEU00.0050.00629.198-0.007-0.0070.0000.0000.0000.000
177A171LYS10.9630.99032.214-0.269-0.2690.0000.0000.0000.000
178A172GLU-1-0.726-0.81629.5530.3050.3050.0000.0000.0000.000
179A173LEU0-0.062-0.02928.585-0.010-0.0100.0000.0000.0000.000
180A174PHE00.0400.01232.203-0.009-0.0090.0000.0000.0000.000
181A175ARG10.8350.90132.509-0.282-0.2820.0000.0000.0000.000
182A176ARG10.6980.82427.153-0.363-0.3630.0000.0000.0000.000
183A177TYR0-0.098-0.12930.0950.0030.0030.0000.0000.0000.000
184A178GLY00.0040.00935.952-0.010-0.0100.0000.0000.0000.000
185A179ASP-1-0.819-0.89039.0670.1650.1650.0000.0000.0000.000
186A180ILE0-0.057-0.04537.3630.0090.0090.0000.0000.0000.000
187A181GLU-1-0.939-0.97439.7300.1940.1940.0000.0000.0000.000
188A182GLU-1-0.966-0.97741.5900.1560.1560.0000.0000.0000.000
189A183ALA0-0.064-0.02236.7130.0060.0060.0000.0000.0000.000
190A184PRO0-0.010-0.00235.872-0.004-0.0040.0000.0000.0000.000
191A185PRO0-0.036-0.01836.7410.0150.0150.0000.0000.0000.000
192A186PRO0-0.012-0.02733.2160.0040.0040.0000.0000.0000.000
193A187PRO0-0.0130.01732.223-0.014-0.0140.0000.0000.0000.000
194A188LEU00.0330.00734.4310.0100.0100.0000.0000.0000.000
195A189LEU0-0.025-0.01430.2250.0100.0100.0000.0000.0000.000
196A190PRO0-0.020-0.01729.032-0.016-0.0160.0000.0000.0000.000
197A191ASP-1-0.863-0.93830.6760.3420.3420.0000.0000.0000.000
198A192TRP00.0120.00823.3280.0370.0370.0000.0000.0000.000
199A193CYS0-0.130-0.06226.5330.0560.0560.0000.0000.0000.000
200A194PHE00.0190.00727.440-0.023-0.0230.0000.0000.0000.000
201A195GLU-1-1.001-1.01427.5420.4700.4700.0000.0000.0000.000
202A196ASP-1-0.831-0.93128.3260.3560.3560.0000.0000.0000.000
203A197ASP-1-0.951-0.96427.9820.5270.5270.0000.0000.0000.000
204A198GLU-1-0.990-0.99328.5770.3900.3900.0000.0000.0000.000
205A199ASP-1-1.026-1.00526.5650.4780.4780.0000.0000.0000.000