Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: M9N5Z

Calculation Name: 3B02-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B02

Chain ID: A

ChEMBL ID:

UniProt ID: Q53W63

Base Structure: X-ray

Registration Date: 2023-09-27

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2209831.59455
FMO2-HF: Nuclear repulsion 2132915.397391
FMO2-HF: Total energy -76916.197159
FMO2-MP2: Total energy -77143.411639


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-19.689-16.03421.662-9.062-16.253-0.039
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : 0.019
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].
3A3ARG10.8460.9043.7140.2502.662-0.011-1.157-1.2440.003
4A4PHE00.0150.0045.373-0.353-0.314-0.001-0.004-0.0340.000
5A5ALA00.0650.0458.8330.1620.1620.0000.0000.0000.000
6A6ARG10.7290.82412.0160.0420.0420.0000.0000.0000.000
7A7LYS10.7590.86414.920-0.011-0.0110.0000.0000.0000.000
8A8GLU-1-0.848-0.91111.022-0.699-0.6990.0000.0000.0000.000
9A9THR0-0.025-0.02514.2740.0820.0820.0000.0000.0000.000
10A10ILE0-0.066-0.0328.956-0.073-0.0730.0000.0000.0000.000
11A11TYR0-0.043-0.01311.517-0.033-0.0330.0000.0000.0000.000
12A12LEU0-0.010-0.00614.3160.0440.0440.0000.0000.0000.000
13A13ARG10.8620.91818.162-0.001-0.0010.0000.0000.0000.000
14A14GLY0-0.002-0.00320.927-0.012-0.0120.0000.0000.0000.000
15A15GLU-1-0.873-0.92916.395-0.205-0.2050.0000.0000.0000.000
16A16GLU-1-0.802-0.87116.542-0.059-0.0590.0000.0000.0000.000
17A17ALA0-0.0010.01415.421-0.020-0.0200.0000.0000.0000.000
18A18ARG10.7780.84312.6090.1640.1640.0000.0000.0000.000
19A19THR0-0.033-0.0157.8600.0670.0670.0000.0000.0000.000
20A20LEU00.0080.03610.999-0.040-0.0400.0000.0000.0000.000
21A21TYR00.0370.0016.5570.0220.0220.0000.0000.0000.000
22A22ARG10.7640.8414.411-1.443-1.379-0.001-0.005-0.0570.000
23A23LEU0-0.0070.0136.1920.6950.821-0.001-0.004-0.1200.000
24A24GLU-1-0.802-0.8692.364-2.065-0.8002.554-1.423-2.395-0.011
25A25GLU-1-0.821-0.8945.675-0.305-0.3050.0000.0000.0000.000
26A26GLY00.0240.0088.1510.0170.0170.0000.0000.0000.000
27A27LEU0-0.009-0.01611.3690.0400.0400.0000.0000.0000.000
28A28VAL0-0.0020.00411.103-0.050-0.0500.0000.0000.0000.000
29A29ARG10.7560.83614.150-0.042-0.0420.0000.0000.0000.000
30A30VAL00.0210.01816.373-0.021-0.0210.0000.0000.0000.000
31A31VAL0-0.025-0.02218.538-0.004-0.0040.0000.0000.0000.000
32A32GLU-1-0.745-0.84821.5870.0240.0240.0000.0000.0000.000
33A33LEU0-0.017-0.00624.547-0.002-0.0020.0000.0000.0000.000
34A34LEU0-0.026-0.00827.1060.0020.0020.0000.0000.0000.000
35A35PRO00.006-0.01530.768-0.006-0.0060.0000.0000.0000.000
36A36ASP-1-0.825-0.87033.6960.0020.0020.0000.0000.0000.000
37A37GLY00.0110.01031.809-0.003-0.0030.0000.0000.0000.000
38A38ARG10.8060.87330.607-0.017-0.0170.0000.0000.0000.000
39A39LEU00.0030.00922.7590.0000.0000.0000.0000.0000.000
40A40ILE0-0.013-0.01025.9130.0030.0030.0000.0000.0000.000
41A41THR00.0170.00921.4560.0000.0000.0000.0000.0000.000
42A42LEU0-0.0140.02022.473-0.001-0.0010.0000.0000.0000.000
43A43ARG10.7980.84916.427-0.271-0.2710.0000.0000.0000.000
44A44HIS00.0380.04118.176-0.014-0.0140.0000.0000.0000.000
45A45VAL0-0.033-0.01512.3160.0010.0010.0000.0000.0000.000
46A46LEU00.0500.00613.530-0.006-0.0060.0000.0000.0000.000
47A47PRO0-0.001-0.0059.5690.0790.0790.0000.0000.0000.000
48A48GLY0-0.0060.0018.888-0.139-0.1390.0000.0000.0000.000
49A49ASP-1-0.799-0.8539.9460.4020.4020.0000.0000.0000.000
50A50TYR00.009-0.0069.8100.1930.1930.0000.0000.0000.000
51A51PHE00.0080.0009.250-0.126-0.1260.0000.0000.0000.000
52A52GLY00.1050.05611.9790.0610.0610.0000.0000.0000.000
53A53GLU-1-0.808-0.89113.9740.2740.2740.0000.0000.0000.000
54A54GLU-1-0.728-0.87516.4910.1360.1360.0000.0000.0000.000
55A55ALA0-0.0010.01214.361-0.022-0.0220.0000.0000.0000.000
56A56LEU0-0.094-0.05716.1260.0090.0090.0000.0000.0000.000
57A57GLU-1-0.926-0.96518.3330.1110.1110.0000.0000.0000.000
58A58GLY00.0240.03420.832-0.020-0.0200.0000.0000.0000.000
59A59LYS10.8270.88920.310-0.081-0.0810.0000.0000.0000.000
60A60ALA00.0070.00919.440-0.018-0.0180.0000.0000.0000.000
61A61TYR0-0.050-0.02012.382-0.005-0.0050.0000.0000.0000.000
62A62ARG10.8280.89218.971-0.068-0.0680.0000.0000.0000.000
63A63TYR0-0.021-0.02019.454-0.016-0.0160.0000.0000.0000.000
64A64THR00.0410.02418.112-0.017-0.0170.0000.0000.0000.000
65A65ALA0-0.0100.01014.0460.0360.0360.0000.0000.0000.000
66A66GLU-1-0.762-0.87014.857-0.048-0.0480.0000.0000.0000.000
67A67ALA00.0370.02511.8110.0760.0760.0000.0000.0000.000
68A68MET0-0.0190.00113.629-0.047-0.0470.0000.0000.0000.000
69A69THR0-0.024-0.03012.190-0.016-0.0160.0000.0000.0000.000
70A70GLU-1-0.844-0.91910.664-0.261-0.2610.0000.0000.0000.000
71A71ALA0-0.0010.0208.8160.1040.1040.0000.0000.0000.000
72A72VAL0-0.019-0.0062.481-0.025-1.7115.161-1.102-2.3730.000
73A73VAL00.0240.0184.269-0.0340.6170.011-0.205-0.4570.000
74A74GLN00.0720.0252.139-14.689-13.22213.858-6.058-9.268-0.032
75A75GLY0-0.003-0.0033.452-1.402-2.0850.0920.896-0.3050.001
76A76LEU0-0.044-0.0345.3950.5710.5710.0000.0000.0000.000
77A77GLU-1-0.858-0.9338.1910.0340.0340.0000.0000.0000.000
78A78PRO0-0.035-0.02910.9730.0540.0540.0000.0000.0000.000
79A79ARG10.8980.94314.039-0.177-0.1770.0000.0000.0000.000
80A80ALA00.0310.03212.695-0.035-0.0350.0000.0000.0000.000
81A81MET0-0.069-0.01512.8170.0930.0930.0000.0000.0000.000
82A82ASP-1-0.739-0.87014.9480.3830.3830.0000.0000.0000.000
83A83HIS00.0280.01416.9440.0070.0070.0000.0000.0000.000
84A84GLU-1-0.840-0.91314.8350.3830.3830.0000.0000.0000.000
85A85ALA0-0.067-0.03112.8340.0150.0150.0000.0000.0000.000
86A86LEU00.0510.02614.0040.0110.0110.0000.0000.0000.000
87A87HIS0-0.0010.00316.941-0.013-0.0130.0000.0000.0000.000
88A88ARG10.7690.85411.846-0.497-0.4970.0000.0000.0000.000
89A89VAL00.0100.01213.2170.0000.0000.0000.0000.0000.000
90A90ALA00.0230.01715.158-0.023-0.0230.0000.0000.0000.000
91A91ARG10.9430.96617.542-0.256-0.2560.0000.0000.0000.000
92A92ASN0-0.028-0.01714.105-0.005-0.0050.0000.0000.0000.000
93A93LEU00.0640.02616.304-0.020-0.0200.0000.0000.0000.000
94A94ALA00.0080.00918.342-0.027-0.0270.0000.0000.0000.000
95A95ARG10.8930.94416.466-0.303-0.3030.0000.0000.0000.000
96A96GLN00.002-0.01614.810-0.049-0.0490.0000.0000.0000.000
97A97MET00.0070.02019.639-0.022-0.0220.0000.0000.0000.000
98A98ARG10.8430.90122.027-0.191-0.1910.0000.0000.0000.000
99A99ARG10.7930.86615.993-0.326-0.3260.0000.0000.0000.000
100A100VAL0-0.018-0.00222.576-0.012-0.0120.0000.0000.0000.000
101A101GLN00.0550.03124.212-0.010-0.0100.0000.0000.0000.000
102A102ALA00.0040.00326.449-0.012-0.0120.0000.0000.0000.000
103A103TYR0-0.054-0.04325.040-0.010-0.0100.0000.0000.0000.000
104A104GLU-1-0.881-0.96227.1010.0880.0880.0000.0000.0000.000
105A105ALA00.0110.01929.617-0.009-0.0090.0000.0000.0000.000
106A106HIS0-0.035-0.00328.349-0.008-0.0080.0000.0000.0000.000
107A107LEU0-0.059-0.03228.295-0.008-0.0080.0000.0000.0000.000
108A108GLN0-0.061-0.03731.941-0.010-0.0100.0000.0000.0000.000
109A109THR0-0.047-0.01834.363-0.004-0.0040.0000.0000.0000.000
110A110GLY00.0320.01435.9160.0010.0010.0000.0000.0000.000
111A111GLU-1-0.852-0.94137.6030.0290.0290.0000.0000.0000.000
112A112LEU0-0.030-0.00234.1320.0020.0020.0000.0000.0000.000
113A113ARG10.7020.78635.294-0.023-0.0230.0000.0000.0000.000
114A114ALA00.0690.04935.7110.0010.0010.0000.0000.0000.000
115A115ARG10.8070.90732.375-0.038-0.0380.0000.0000.0000.000
116A116ILE00.011-0.01431.1600.0050.0050.0000.0000.0000.000
117A117ALA00.0000.00830.7850.0040.0040.0000.0000.0000.000
118A118ARG10.8160.89729.617-0.062-0.0620.0000.0000.0000.000
119A119TYR0-0.016-0.02622.3990.0030.0030.0000.0000.0000.000
120A120LEU0-0.022-0.02226.0830.0070.0070.0000.0000.0000.000
121A121LEU0-0.0060.00026.7130.0040.0040.0000.0000.0000.000
122A122PHE0-0.0090.00020.6650.0090.0090.0000.0000.0000.000
123A123LEU0-0.001-0.00821.0970.0140.0140.0000.0000.0000.000
124A124ALA0-0.012-0.00621.8220.0070.0070.0000.0000.0000.000
125A125ASP-1-0.938-0.94221.8170.1240.1240.0000.0000.0000.000
126A126THR0-0.055-0.04317.7760.0320.0320.0000.0000.0000.000
127A127PRO0-0.024-0.02213.629-0.028-0.0280.0000.0000.0000.000
128A128LEU0-0.0010.01716.286-0.019-0.0190.0000.0000.0000.000
129A129SER0-0.056-0.01918.811-0.035-0.0350.0000.0000.0000.000
130A130ALA00.0130.00220.0590.0020.0020.0000.0000.0000.000
131A131ARG10.9570.97322.395-0.046-0.0460.0000.0000.0000.000
132A132ASP-1-0.796-0.87725.310-0.002-0.0020.0000.0000.0000.000
133A133ARG10.9410.95828.1170.0020.0020.0000.0000.0000.000
134A134GLN0-0.037-0.00731.4520.0030.0030.0000.0000.0000.000
135A135GLY00.0420.02330.7770.0020.0020.0000.0000.0000.000
136A136ILE0-0.004-0.00325.741-0.002-0.0020.0000.0000.0000.000
137A137TYR0-0.018-0.01522.340-0.009-0.0090.0000.0000.0000.000
138A138VAL00.0480.02923.2930.0090.0090.0000.0000.0000.000
139A139THR0-0.053-0.02820.359-0.019-0.0190.0000.0000.0000.000
140A140VAL00.0040.01121.3970.0000.0000.0000.0000.0000.000
141A141SER0-0.045-0.04923.778-0.009-0.0090.0000.0000.0000.000
142A142HIS00.003-0.04126.2510.0070.0070.0000.0000.0000.000
143A143GLU-1-0.800-0.88126.600-0.011-0.0110.0000.0000.0000.000
144A144GLU-1-0.730-0.80721.0930.0160.0160.0000.0000.0000.000
145A145ILE00.0370.01725.1970.0110.0110.0000.0000.0000.000
146A146ALA0-0.0150.02327.8010.0050.0050.0000.0000.0000.000
147A147ASP-1-0.809-0.89825.4230.0210.0210.0000.0000.0000.000
148A148ALA0-0.0140.00424.8420.0090.0090.0000.0000.0000.000
149A149THR0-0.019-0.03426.8120.0040.0040.0000.0000.0000.000
150A150ALA00.0450.03730.329-0.003-0.0030.0000.0000.0000.000
151A151SER0-0.037-0.01832.265-0.004-0.0040.0000.0000.0000.000
152A152ILE00.0440.02133.285-0.002-0.0020.0000.0000.0000.000
153A153ARG10.8860.90031.2250.0180.0180.0000.0000.0000.000
154A154GLU-1-0.830-0.87633.083-0.009-0.0090.0000.0000.0000.000
155A155SER00.012-0.00436.6690.0010.0010.0000.0000.0000.000
156A156VAL00.0230.01831.1450.0010.0010.0000.0000.0000.000
157A157SER0-0.044-0.03534.538-0.001-0.0010.0000.0000.0000.000
158A158LYS10.8410.90035.648-0.010-0.0100.0000.0000.0000.000
159A159VAL00.0440.02136.6870.0000.0000.0000.0000.0000.000
160A160LEU00.0500.02331.4130.0010.0010.0000.0000.0000.000
161A161ALA0-0.076-0.01735.878-0.001-0.0010.0000.0000.0000.000
162A162ASP-1-0.780-0.85438.9160.0100.0100.0000.0000.0000.000
163A163LEU00.0600.02235.3040.0000.0000.0000.0000.0000.000
164A164ARG10.8360.89734.214-0.002-0.0020.0000.0000.0000.000
165A165ARG10.8090.90238.529-0.008-0.0080.0000.0000.0000.000
166A166GLU-1-0.827-0.88841.4470.0180.0180.0000.0000.0000.000
167A167GLY00.0060.01339.8830.0010.0010.0000.0000.0000.000
168A168LEU00.0070.00836.8000.0010.0010.0000.0000.0000.000
169A169ILE0-0.015-0.00333.0210.0040.0040.0000.0000.0000.000
170A170ALA00.0290.01333.290-0.004-0.0040.0000.0000.0000.000
171A171THR0-0.0070.00431.0820.0030.0030.0000.0000.0000.000
172A172ALA00.0130.01030.105-0.004-0.0040.0000.0000.0000.000
173A173TYR00.006-0.01026.7760.0010.0010.0000.0000.0000.000
174A174ARG10.9390.96921.4870.0660.0660.0000.0000.0000.000
175A175ARG10.8820.97124.0710.0130.0130.0000.0000.0000.000
176A176VAL00.0160.00226.433-0.006-0.0060.0000.0000.0000.000
177A177TYR0-0.062-0.05228.0570.0050.0050.0000.0000.0000.000
178A178LEU0-0.014-0.01527.582-0.001-0.0010.0000.0000.0000.000
179A179LEU0-0.044-0.01531.6080.0010.0010.0000.0000.0000.000
180A180ASP-1-0.792-0.89134.9470.0340.0340.0000.0000.0000.000
181A181LEU00.000-0.01230.5710.0010.0010.0000.0000.0000.000
182A182ALA00.1090.05733.9530.0020.0020.0000.0000.0000.000
183A183ALA0-0.080-0.04436.7100.0000.0000.0000.0000.0000.000
184A184LEU0-0.005-0.00731.8040.0000.0000.0000.0000.0000.000
185A185GLU-1-0.897-0.95632.9250.0640.0640.0000.0000.0000.000
186A186ARG10.8190.91135.099-0.035-0.0350.0000.0000.0000.000
187A187GLU-1-0.851-0.89536.6950.0300.0300.0000.0000.0000.000
188A188ALA0-0.0070.00333.2300.0000.0000.0000.0000.0000.000
189A189GLY0-0.0100.02235.2190.0020.0020.0000.0000.0000.000
190A190SER0-0.046-0.03332.866-0.001-0.0010.0000.0000.0000.000
191A191ALA00.0440.01528.983-0.001-0.0010.0000.0000.0000.000
192A192LEU0-0.005-0.00925.546-0.002-0.0020.0000.0000.0000.000
193A193GLU-1-0.831-0.91423.9690.1500.1500.0000.0000.0000.000
194A194ALA00.0520.03621.5180.0130.0130.0000.0000.0000.000
195A195ALA0-0.0270.00118.8610.0150.0150.0000.0000.0000.000