FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: ZNY7N

Calculation Name: 3BG1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BG1

Chain ID: A

ChEMBL ID:

UniProt ID: P49687

Base Structure: X-ray

Registration Date: 2023-09-26

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 291
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4099001.277954
FMO2-HF: Nuclear repulsion 3984486.218441
FMO2-HF: Total energy -114515.059512
FMO2-MP2: Total energy -114846.364088


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:14:ASP)


Summations of interaction energy for fragment #1(A:14:ASP)
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.
13.10711.48521.43-11.353-8.4530.102
Interaction energy analysis for fragmet #1(A:14:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.911 / q_NPA : -0.942
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].
3A16ILE0-0.021-0.0183.8315.2377.126-0.014-0.801-1.0740.002
4A17HIS0-0.046-0.0046.6931.7081.7080.0000.0000.0000.000
5A18ASP-1-0.830-0.9298.99918.70818.7080.0000.0000.0000.000
6A19ALA0-0.022-0.02311.2612.0822.0820.0000.0000.0000.000
7A20GLN00.0620.05513.211-1.351-1.3510.0000.0000.0000.000
8A21MET00.008-0.00116.9620.3020.3020.0000.0000.0000.000
9A22ASP-1-0.855-0.92419.15913.51613.5160.0000.0000.0000.000
10A23TYR00.034-0.00521.632-0.428-0.4280.0000.0000.0000.000
11A24TYR0-0.049-0.04225.251-0.009-0.0090.0000.0000.0000.000
12A25GLY0-0.0050.01223.384-0.168-0.1680.0000.0000.0000.000
13A26THR0-0.061-0.02223.496-0.061-0.0610.0000.0000.0000.000
14A27ARG10.8060.87219.143-13.626-13.6260.0000.0000.0000.000
15A28LEU0-0.0030.00414.197-0.532-0.5320.0000.0000.0000.000
16A29ALA00.0240.03414.3730.7930.7930.0000.0000.0000.000
17A30THR0-0.036-0.0328.1970.5550.5550.0000.0000.0000.000
18A31CYS0-0.086-0.0198.634-0.065-0.0650.0000.0000.0000.000
19A32SER00.049-0.0083.676-2.988-2.6330.007-0.172-0.1900.001
20A33SER00.009-0.0351.622-37.014-43.56021.131-9.124-5.4600.087
21A34ASP-1-0.785-0.8332.92337.07939.6500.304-1.192-1.6820.012
22A35ARG10.8730.9544.351-39.553-39.4440.002-0.064-0.0470.000
23A36SER0-0.069-0.0436.711-6.721-6.7210.0000.0000.0000.000
24A37VAL00.0060.0028.6881.6371.6370.0000.0000.0000.000
25A38LYS10.8180.9294.812-49.473-49.4730.0000.0000.0000.000
26A39ILE00.0120.00811.039-0.431-0.4310.0000.0000.0000.000
27A40PHE00.0230.0019.648-0.380-0.3800.0000.0000.0000.000
28A41ASP-1-0.795-0.88015.61212.96012.9600.0000.0000.0000.000
29A42VAL00.0530.01517.3690.6340.6340.0000.0000.0000.000
30A43ARG10.8910.92320.034-13.048-13.0480.0000.0000.0000.000
31A44ASN0-0.065-0.04023.145-0.040-0.0400.0000.0000.0000.000
32A45GLY00.0230.02321.179-0.192-0.1920.0000.0000.0000.000
33A46GLY0-0.038-0.02019.4950.6780.6780.0000.0000.0000.000
34A47GLN0-0.021-0.01113.1830.4600.4600.0000.0000.0000.000
35A48ILE0-0.023-0.00716.3260.1910.1910.0000.0000.0000.000
36A49LEU0-0.042-0.01411.4850.0060.0060.0000.0000.0000.000
37A50ILE0-0.033-0.01414.958-1.011-1.0110.0000.0000.0000.000
38A51ALA00.0100.00415.495-0.641-0.6410.0000.0000.0000.000
39A52ASP-1-0.792-0.9269.32732.00432.0040.0000.0000.0000.000
40A53LEU0-0.0100.01512.680-0.623-0.6230.0000.0000.0000.000
41A54ARG10.8400.8907.903-31.829-31.8290.0000.0000.0000.000
42A55GLY00.0110.00312.644-1.749-1.7490.0000.0000.0000.000
43A56HIS10.8200.90811.607-23.320-23.3200.0000.0000.0000.000
44A57GLU-1-0.851-0.92412.15319.34919.3490.0000.0000.0000.000
45A58GLY0-0.048-0.03310.5000.1020.1020.0000.0000.0000.000
46A59PRO00.0190.0236.9470.2060.2060.0000.0000.0000.000
47A60VAL0-0.0280.0028.164-4.964-4.9640.0000.0000.0000.000
48A61TRP0-0.031-0.0048.5813.0973.0970.0000.0000.0000.000
49A62GLN00.0860.02411.818-0.436-0.4360.0000.0000.0000.000
50A63VAL0-0.014-0.02513.148-0.157-0.1570.0000.0000.0000.000
51A64ALA0-0.0120.00815.992-0.307-0.3070.0000.0000.0000.000
52A65TRP00.0100.00517.761-0.259-0.2590.0000.0000.0000.000
53A66ALA0-0.0150.00921.584-0.343-0.3430.0000.0000.0000.000
54A67HIS00.0540.01625.1770.1040.1040.0000.0000.0000.000
55A68PRO00.0390.01127.323-0.141-0.1410.0000.0000.0000.000
56A69MET0-0.055-0.01029.043-0.338-0.3380.0000.0000.0000.000
57A70TYR0-0.040-0.03029.590-0.350-0.3500.0000.0000.0000.000
58A71GLY00.0130.01129.4470.0730.0730.0000.0000.0000.000
59A72ASN0-0.054-0.04124.3420.0570.0570.0000.0000.0000.000
60A73ILE0-0.010-0.01323.5250.0760.0760.0000.0000.0000.000
61A74LEU0-0.0110.00415.8390.1530.1530.0000.0000.0000.000
62A75ALA00.0030.00919.679-0.045-0.0450.0000.0000.0000.000
63A76SER00.0100.00414.3181.2881.2880.0000.0000.0000.000
64A77CYS0-0.0240.00715.311-0.948-0.9480.0000.0000.0000.000
65A78SER00.027-0.01011.7141.7461.7460.0000.0000.0000.000
66A79TYR00.005-0.01312.060-1.945-1.9450.0000.0000.0000.000
67A80ASP-1-0.795-0.87413.93419.89819.8980.0000.0000.0000.000
68A81ARG10.8600.94615.737-17.956-17.9560.0000.0000.0000.000
69A82LYS10.8130.90017.467-17.919-17.9190.0000.0000.0000.000
70A83VAL0-0.007-0.01417.3751.1681.1680.0000.0000.0000.000
71A84ILE0-0.054-0.02116.343-0.806-0.8060.0000.0000.0000.000
72A85ILE00.0070.00019.3790.5520.5520.0000.0000.0000.000
73A86TRP00.0360.00715.505-0.943-0.9430.0000.0000.0000.000
74A87ARG10.8890.94521.111-11.139-11.1390.0000.0000.0000.000
75A88GLU-1-0.725-0.82623.19913.49413.4940.0000.0000.0000.000
76A89GLU-1-0.907-0.95124.92410.26210.2620.0000.0000.0000.000
77A90ASN0-0.075-0.04528.116-0.050-0.0500.0000.0000.0000.000
78A91GLY00.0290.02124.416-0.086-0.0860.0000.0000.0000.000
79A92THR0-0.044-0.03123.3780.6110.6110.0000.0000.0000.000
80A93TRP0-0.046-0.02619.7090.1830.1830.0000.0000.0000.000
81A94GLU-1-0.898-0.94320.89413.10413.1040.0000.0000.0000.000
82A95LYS10.7600.86420.049-15.510-15.5100.0000.0000.0000.000
83A96SER0-0.022-0.00322.481-0.533-0.5330.0000.0000.0000.000
84A97HIS00.0190.01124.343-0.558-0.5580.0000.0000.0000.000
85A98GLU-1-0.819-0.89919.99516.53316.5330.0000.0000.0000.000
86A99HIS0-0.0180.00222.345-0.687-0.6870.0000.0000.0000.000
87A100ALA00.0560.01221.9730.8280.8280.0000.0000.0000.000
88A101GLY0-0.0070.01223.362-0.259-0.2590.0000.0000.0000.000
89A102HIS0-0.024-0.01122.542-0.169-0.1690.0000.0000.0000.000
90A103ASP-1-0.846-0.92623.41912.52412.5240.0000.0000.0000.000
91A104SER0-0.094-0.06319.9200.2840.2840.0000.0000.0000.000
92A105SER0-0.034-0.01615.461-0.246-0.2460.0000.0000.0000.000
93A106VAL00.0260.01417.136-0.817-0.8170.0000.0000.0000.000
94A107ASN00.0230.02115.5961.8231.8230.0000.0000.0000.000
95A108SER00.0140.00215.9170.5540.5540.0000.0000.0000.000
96A109VAL00.006-0.01618.406-0.724-0.7240.0000.0000.0000.000
97A110CYS0-0.0320.00020.5630.0600.0600.0000.0000.0000.000
98A111TRP00.016-0.00622.113-0.739-0.7390.0000.0000.0000.000
99A112ALA0-0.0080.00225.861-0.073-0.0730.0000.0000.0000.000
100A113PRO0-0.015-0.01229.5320.0730.0730.0000.0000.0000.000
101A114HIS00.0130.00331.384-0.051-0.0510.0000.0000.0000.000
102A115ASP-1-0.843-0.90532.6048.9578.9570.0000.0000.0000.000
103A116TYR0-0.062-0.02733.560-0.416-0.4160.0000.0000.0000.000
104A117GLY00.014-0.00234.101-0.325-0.3250.0000.0000.0000.000
105A118LEU0-0.0250.01727.6330.2600.2600.0000.0000.0000.000
106A119ILE00.004-0.00729.7640.0150.0150.0000.0000.0000.000
107A120LEU0-0.003-0.00322.0110.2660.2660.0000.0000.0000.000
108A121ALA00.0020.01325.974-0.185-0.1850.0000.0000.0000.000
109A122CYS0-0.0100.00022.0960.8530.8530.0000.0000.0000.000
110A123GLY00.0310.01021.530-0.776-0.7760.0000.0000.0000.000
111A124SER0-0.034-0.04620.3730.9060.9060.0000.0000.0000.000
112A125SER00.014-0.00318.636-0.361-0.3610.0000.0000.0000.000
113A126ASP-1-0.783-0.86820.77713.46013.4600.0000.0000.0000.000
114A127GLY00.0290.02323.885-0.569-0.5690.0000.0000.0000.000
115A128ALA0-0.073-0.02925.540-0.530-0.5300.0000.0000.0000.000
116A129ILE00.0160.00225.2260.5120.5120.0000.0000.0000.000
117A130SER0-0.050-0.02025.379-0.415-0.4150.0000.0000.0000.000
118A131LEU00.0140.00926.6890.3670.3670.0000.0000.0000.000
119A132LEU00.0080.00724.144-0.425-0.4250.0000.0000.0000.000
120A133THR0-0.027-0.02128.6470.0460.0460.0000.0000.0000.000
121A134TYR00.0060.01730.595-0.020-0.0200.0000.0000.0000.000
122A135THR0-0.036-0.03732.153-0.183-0.1830.0000.0000.0000.000
123A136GLY0-0.036-0.02035.1890.0660.0660.0000.0000.0000.000
124A137GLU-1-0.888-0.94735.7319.0209.0200.0000.0000.0000.000
125A138GLY0-0.0100.00531.8080.2930.2930.0000.0000.0000.000
126A139GLN0-0.080-0.04732.5470.0020.0020.0000.0000.0000.000
127A140TRP00.0690.01427.4940.1890.1890.0000.0000.0000.000
128A141GLU-1-0.879-0.90131.3779.0049.0040.0000.0000.0000.000
129A142VAL0-0.045-0.03728.4290.3380.3380.0000.0000.0000.000
130A143LYS10.8460.93531.359-9.257-9.2570.0000.0000.0000.000
131A144LYS10.8280.91627.239-11.571-11.5710.0000.0000.0000.000
132A145ILE0-0.0020.00329.998-0.429-0.4290.0000.0000.0000.000
133A146ASN00.031-0.00729.7040.7180.7180.0000.0000.0000.000
134A147ASN0-0.028-0.02629.663-0.368-0.3680.0000.0000.0000.000
135A148ALA00.0630.05328.214-0.247-0.2470.0000.0000.0000.000
136A149HIS10.7730.85826.101-12.026-12.0260.0000.0000.0000.000
137A150THR0-0.025-0.01827.6650.1540.1540.0000.0000.0000.000
138A151ILE0-0.013-0.00923.529-0.153-0.1530.0000.0000.0000.000
139A152GLY00.0360.03422.3870.6030.6030.0000.0000.0000.000
140A153CYS0-0.122-0.07222.457-0.433-0.4330.0000.0000.0000.000
141A154ASN0-0.069-0.05418.7341.4131.4130.0000.0000.0000.000
142A155ALA00.0310.03218.7770.8320.8320.0000.0000.0000.000
143A156VAL00.009-0.00421.267-0.868-0.8680.0000.0000.0000.000
144A157SER00.0220.02723.4320.2080.2080.0000.0000.0000.000
145A158TRP0-0.002-0.02425.922-0.750-0.7500.0000.0000.0000.000
146A159ALA00.0140.01829.2140.0830.0830.0000.0000.0000.000
147A160PRO0-0.002-0.00732.3110.0400.0400.0000.0000.0000.000
148A161ALA00.0200.01133.607-0.211-0.2110.0000.0000.0000.000
149A162VAL0-0.041-0.02336.371-0.213-0.2130.0000.0000.0000.000
150A163VAL00.0380.01539.414-0.042-0.0420.0000.0000.0000.000
151A164PRO0-0.0370.00042.457-0.056-0.0560.0000.0000.0000.000
152A165GLY00.010-0.00245.112-0.182-0.1820.0000.0000.0000.000
153A166SER0-0.042-0.02346.8690.0060.0060.0000.0000.0000.000
154A167LEU0-0.005-0.01248.182-0.170-0.1700.0000.0000.0000.000
155A168ILE0-0.014-0.00246.330-0.106-0.1060.0000.0000.0000.000
156A169ASP-1-0.885-0.94446.3027.0857.0850.0000.0000.0000.000
157A170HIS0-0.001-0.01148.719-0.175-0.1750.0000.0000.0000.000
158A171PRO0-0.0270.01652.0250.0520.0520.0000.0000.0000.000
159A172SER0-0.073-0.04552.194-0.057-0.0570.0000.0000.0000.000
160A173GLY00.0430.01951.5490.0310.0310.0000.0000.0000.000
161A174GLN0-0.041-0.03147.7600.1420.1420.0000.0000.0000.000
162A175LYS10.9070.96038.714-8.416-8.4160.0000.0000.0000.000
163A176PRO00.0260.01142.791-0.026-0.0260.0000.0000.0000.000
164A177ASN0-0.011-0.00642.5380.3390.3390.0000.0000.0000.000
165A178TYR00.0270.00238.855-0.097-0.0970.0000.0000.0000.000
166A179ILE00.0230.00738.9800.0210.0210.0000.0000.0000.000
167A180LYS10.8720.93535.765-8.454-8.4540.0000.0000.0000.000
168A181ARG10.9220.95934.811-8.339-8.3390.0000.0000.0000.000
169A182PHE0-0.014-0.00328.6090.2380.2380.0000.0000.0000.000
170A183ALA00.0020.01428.818-0.324-0.3240.0000.0000.0000.000
171A184SER00.0400.02125.8090.4130.4130.0000.0000.0000.000
172A185GLY00.0610.02924.467-0.544-0.5440.0000.0000.0000.000
173A186GLY00.0470.01722.9490.4640.4640.0000.0000.0000.000
174A187CYS0-0.035-0.00621.2210.0730.0730.0000.0000.0000.000
175A188ASP-1-0.775-0.87023.54911.43311.4330.0000.0000.0000.000
176A189ASN0-0.037-0.01426.186-0.090-0.0900.0000.0000.0000.000
177A190LEU0-0.0210.00527.614-0.219-0.2190.0000.0000.0000.000
178A191ILE0-0.017-0.01327.1740.5570.5570.0000.0000.0000.000
179A192LYS10.7420.85129.293-10.595-10.5950.0000.0000.0000.000
180A193LEU00.0160.00530.4480.4050.4050.0000.0000.0000.000
181A194TRP0-0.043-0.02129.763-0.314-0.3140.0000.0000.0000.000
182A195LYS10.8670.91134.029-7.770-7.7700.0000.0000.0000.000
183A196GLU-1-0.849-0.91536.4608.8788.8780.0000.0000.0000.000
184A197GLU-1-0.873-0.92637.7567.6017.6010.0000.0000.0000.000
185A198GLU-1-0.850-0.92241.2707.5987.5980.0000.0000.0000.000
186A199ASP-1-0.844-0.91342.5557.6867.6860.0000.0000.0000.000
187A200GLY00.0210.01940.783-0.018-0.0180.0000.0000.0000.000
188A201GLN0-0.066-0.03937.1510.2290.2290.0000.0000.0000.000
189A202TRP00.0510.01433.692-0.145-0.1450.0000.0000.0000.000
190A203LYS10.7830.89936.320-8.008-8.0080.0000.0000.0000.000
191A204GLU-1-0.815-0.90234.2649.6189.6180.0000.0000.0000.000
192A205GLU-1-0.881-0.94135.8398.4768.4760.0000.0000.0000.000
193A206GLN0-0.013-0.02136.146-0.218-0.2180.0000.0000.0000.000
194A207LYS10.9240.97934.071-8.668-8.6680.0000.0000.0000.000
195A208LEU0-0.0020.00732.312-0.281-0.2810.0000.0000.0000.000
196A209GLU-1-0.940-0.97331.8219.4469.4460.0000.0000.0000.000
197A210ALA00.013-0.00531.370-0.298-0.2980.0000.0000.0000.000
198A211HIS0-0.0330.01826.335-0.107-0.1070.0000.0000.0000.000
199A212SER0-0.016-0.03428.020-0.302-0.3020.0000.0000.0000.000
200A213ASP-1-0.886-0.94123.05313.57513.5750.0000.0000.0000.000
201A214TRP0-0.016-0.02017.9330.4280.4280.0000.0000.0000.000
202A215VAL0-0.0190.00022.2960.3030.3030.0000.0000.0000.000
203A216ARG10.7910.89916.424-17.983-17.9830.0000.0000.0000.000
204A217ASP-1-0.722-0.87119.13916.90616.9060.0000.0000.0000.000
205A218VAL0-0.037-0.03621.051-0.776-0.7760.0000.0000.0000.000
206A219ALA00.0050.01423.6020.1870.1870.0000.0000.0000.000
207A220TRP00.0360.00825.516-0.581-0.5810.0000.0000.0000.000
208A221ALA00.0100.02028.4900.3170.3170.0000.0000.0000.000
209A222PRO0-0.031-0.01329.307-0.209-0.2090.0000.0000.0000.000
210A223SER00.0570.01332.025-0.155-0.1550.0000.0000.0000.000
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