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: 669ZZ

Calculation Name: 3R8C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R8C

Chain ID: A

ChEMBL ID:

UniProt ID: B1MB31

Base Structure: X-ray

Registration Date: 2023-06-20

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2010220.566315
FMO2-HF: Nuclear repulsion 1936834.075475
FMO2-HF: Total energy -73386.490841
FMO2-MP2: Total energy -73601.751246


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:SER)


Summations of interaction energy for fragment #1(A:-1:SER)
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.
-5.291-2.1112.058-1.564-3.675-0.006
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.047
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].
3A1VAL00.0330.0213.8421.1412.360-0.011-0.529-0.679-0.001
4A2VAL0-0.028-0.0146.7520.0630.0630.0000.0000.0000.000
5A3ALA00.0210.0369.8970.1760.1760.0000.0000.0000.000
6A4VAL00.010-0.01213.093-0.003-0.0030.0000.0000.0000.000
7A5ASP-1-0.766-0.87716.012-0.218-0.2180.0000.0000.0000.000
8A6GLY00.0730.02319.337-0.005-0.0050.0000.0000.0000.000
9A7PRO0-0.096-0.04122.9120.0160.0160.0000.0000.0000.000
10A8SER00.0170.00925.120-0.005-0.0050.0000.0000.0000.000
11A9GLY00.013-0.01527.0640.0000.0000.0000.0000.0000.000
12A10THR00.015-0.00424.1730.0060.0060.0000.0000.0000.000
13A11GLY0-0.0120.00224.944-0.005-0.0050.0000.0000.0000.000
14A12LYS10.8460.93619.4380.1500.1500.0000.0000.0000.000
15A13SER0-0.020-0.06919.438-0.007-0.0070.0000.0000.0000.000
16A14SER0-0.091-0.04819.0530.0050.0050.0000.0000.0000.000
17A15VAL00.0350.02118.179-0.002-0.0020.0000.0000.0000.000
18A16ALA00.0200.01414.924-0.026-0.0260.0000.0000.0000.000
19A17LYS10.9410.98314.3480.0490.0490.0000.0000.0000.000
20A18GLU-1-0.803-0.88215.012-0.160-0.1600.0000.0000.0000.000
21A19LEU0-0.021-0.01412.261-0.011-0.0110.0000.0000.0000.000
22A20ALA0-0.0010.00110.792-0.069-0.0690.0000.0000.0000.000
23A21ARG10.8370.89811.0310.0590.0590.0000.0000.0000.000
24A22GLN0-0.099-0.05713.149-0.026-0.0260.0000.0000.0000.000
25A23LEU0-0.071-0.0408.510-0.013-0.0130.0000.0000.0000.000
26A24GLY0-0.0410.0028.549-0.146-0.1460.0000.0000.0000.000
27A25ALA0-0.073-0.0326.729-0.072-0.0720.0000.0000.0000.000
28A26SER00.0460.0197.0750.0400.0400.0000.0000.0000.000
29A27TYR0-0.105-0.0948.997-0.133-0.1330.0000.0000.0000.000
30A28LEU00.0310.01911.8000.0610.0610.0000.0000.0000.000
31A29ASP-1-0.787-0.88313.724-0.096-0.0960.0000.0000.0000.000
32A30THR00.012-0.05515.8660.0210.0210.0000.0000.0000.000
33A31GLY0-0.024-0.00918.4840.0080.0080.0000.0000.0000.000
34A32ALA0-0.026-0.01720.7560.0060.0060.0000.0000.0000.000
35A33MET00.0210.02417.1840.0030.0030.0000.0000.0000.000
36A34TYR00.0440.01020.5390.0070.0070.0000.0000.0000.000
37A35ARG10.8160.88724.3990.0280.0280.0000.0000.0000.000
38A36ILE00.0270.02522.868-0.001-0.0010.0000.0000.0000.000
39A37VAL00.0140.00924.7750.0020.0020.0000.0000.0000.000
40A38THR0-0.019-0.01227.567-0.003-0.0030.0000.0000.0000.000
41A39LEU00.0030.00730.038-0.001-0.0010.0000.0000.0000.000
42A40TRP0-0.013-0.00730.1450.0010.0010.0000.0000.0000.000
43A41VAL00.0350.01031.237-0.001-0.0010.0000.0000.0000.000
44A42LEU0-0.040-0.03433.688-0.002-0.0020.0000.0000.0000.000
45A43ARG10.8140.90033.487-0.027-0.0270.0000.0000.0000.000
46A44ALA0-0.0090.01235.9320.0010.0010.0000.0000.0000.000
47A45GLY0-0.037-0.00737.6920.0000.0000.0000.0000.0000.000
48A46VAL0-0.029-0.01435.923-0.001-0.0010.0000.0000.0000.000
49A47ASP-1-0.833-0.90738.719-0.006-0.0060.0000.0000.0000.000
50A48LEU0-0.013-0.03235.190-0.001-0.0010.0000.0000.0000.000
51A49THR0-0.094-0.04737.367-0.003-0.0030.0000.0000.0000.000
52A50ASP-1-0.842-0.92439.108-0.001-0.0010.0000.0000.0000.000
53A51PRO0-0.002-0.01234.5670.0020.0020.0000.0000.0000.000
54A52ALA00.0090.00634.3460.0020.0020.0000.0000.0000.000
55A53ALA00.0180.02835.7720.0040.0040.0000.0000.0000.000
56A54ILE0-0.010-0.00931.5040.0040.0040.0000.0000.0000.000
57A55ALA0-0.035-0.02330.9730.0040.0040.0000.0000.0000.000
58A56ALA00.0410.02431.2610.0050.0050.0000.0000.0000.000
59A57ALA0-0.0010.01533.5150.0050.0050.0000.0000.0000.000
60A58THR0-0.076-0.05628.1790.0030.0030.0000.0000.0000.000
61A59ASP-1-0.859-0.92327.7810.0430.0430.0000.0000.0000.000
62A60GLN0-0.065-0.03127.2960.0140.0140.0000.0000.0000.000
63A61VAL0-0.0080.00225.745-0.002-0.0020.0000.0000.0000.000
64A62PRO00.0030.02725.3410.0120.0120.0000.0000.0000.000
65A63MET0-0.032-0.02121.534-0.001-0.0010.0000.0000.0000.000
66A64SER0-0.039-0.01120.8780.0190.0190.0000.0000.0000.000
67A65VAL00.0360.00616.730-0.026-0.0260.0000.0000.0000.000
68A66SER00.0210.02416.4660.0450.0450.0000.0000.0000.000
69A67SER00.0310.01811.025-0.070-0.0700.0000.0000.0000.000
70A68ASP-1-0.785-0.89111.7950.0610.0610.0000.0000.0000.000
71A69PRO0-0.018-0.01012.439-0.012-0.0120.0000.0000.0000.000
72A70ASP-1-0.907-0.93815.412-0.067-0.0670.0000.0000.0000.000
73A71ALA0-0.055-0.02817.6110.0020.0020.0000.0000.0000.000
74A72GLN0-0.093-0.06515.9920.0040.0040.0000.0000.0000.000
75A73THR00.0180.01719.881-0.011-0.0110.0000.0000.0000.000
76A74ALA0-0.040-0.01521.4790.0140.0140.0000.0000.0000.000
77A75LEU0-0.010-0.00223.149-0.008-0.0080.0000.0000.0000.000
78A76LEU0-0.007-0.01425.0770.0040.0040.0000.0000.0000.000
79A77ALA00.012-0.00527.882-0.004-0.0040.0000.0000.0000.000
80A78GLY0-0.042-0.01527.704-0.003-0.0030.0000.0000.0000.000
81A79GLU-1-0.874-0.92728.6820.0340.0340.0000.0000.0000.000
82A80ASP-1-0.818-0.89127.3740.0420.0420.0000.0000.0000.000
83A81VAL0-0.002-0.01027.301-0.008-0.0080.0000.0000.0000.000
84A82SER0-0.007-0.04425.608-0.006-0.0060.0000.0000.0000.000
85A83VAL0-0.022-0.01226.940-0.008-0.0080.0000.0000.0000.000
86A84PRO00.0450.01730.387-0.005-0.0050.0000.0000.0000.000
87A85ILE00.0060.01824.823-0.006-0.0060.0000.0000.0000.000
88A86ARG10.8440.92122.3300.0130.0130.0000.0000.0000.000
89A87GLY00.0320.03529.575-0.005-0.0050.0000.0000.0000.000
90A88ASN00.018-0.01832.862-0.004-0.0040.0000.0000.0000.000
91A89GLU-1-0.889-0.93935.442-0.010-0.0100.0000.0000.0000.000
92A90VAL00.0380.01229.907-0.001-0.0010.0000.0000.0000.000
93A91THR0-0.066-0.02631.286-0.004-0.0040.0000.0000.0000.000
94A92GLY0-0.040-0.01432.319-0.004-0.0040.0000.0000.0000.000
95A93ALA00.0360.03134.138-0.002-0.0020.0000.0000.0000.000
96A94VAL0-0.0080.00327.4830.0000.0000.0000.0000.0000.000
97A95SER0-0.053-0.02329.5520.0010.0010.0000.0000.0000.000
98A96ALA00.0500.02930.787-0.002-0.0020.0000.0000.0000.000
99A97VAL00.0400.02128.6140.0020.0020.0000.0000.0000.000
100A98SER0-0.019-0.03326.2470.0030.0030.0000.0000.0000.000
101A99ALA0-0.054-0.01127.160-0.005-0.0050.0000.0000.0000.000
102A100VAL00.0150.00629.681-0.002-0.0020.0000.0000.0000.000
103A101PRO0-0.016-0.01427.1890.0020.0020.0000.0000.0000.000
104A102ALA00.0630.03726.0350.0000.0000.0000.0000.0000.000
105A103VAL00.0080.00725.6460.0070.0070.0000.0000.0000.000
106A104ARG10.9160.95222.3920.0580.0580.0000.0000.0000.000
107A105GLU-1-0.955-0.96721.4680.0050.0050.0000.0000.0000.000
108A106ARG10.8160.88820.700-0.028-0.0280.0000.0000.0000.000
109A107LEU00.0170.01019.8040.0170.0170.0000.0000.0000.000
110A108VAL00.0100.00916.7800.0100.0100.0000.0000.0000.000
111A109ARG10.9610.98015.668-0.074-0.0740.0000.0000.0000.000
112A110GLN00.0100.00115.0900.0160.0160.0000.0000.0000.000
113A111GLN0-0.020-0.01914.1620.0290.0290.0000.0000.0000.000
114A112ARG10.8620.92511.1900.1360.1360.0000.0000.0000.000
115A113GLU-1-0.884-0.9239.9900.2970.2970.0000.0000.0000.000
116A114LEU0-0.043-0.03310.4560.1550.1550.0000.0000.0000.000
117A115ALA0-0.043-0.0158.0700.1500.1500.0000.0000.0000.000
118A116GLU-1-0.944-0.9786.0151.0921.0920.0000.0000.0000.000
119A117SER0-0.067-0.0275.8270.8590.8590.0000.0000.0000.000
120A118SER0-0.023-0.0197.265-0.095-0.0950.0000.0000.0000.000
121A119GLY0-0.0160.0063.153-2.028-0.9730.311-0.587-0.7800.006
122A120ALA0-0.007-0.0102.634-3.306-2.0961.668-0.928-1.950-0.010
123A121VAL00.0020.0143.1230.6400.3360.0900.480-0.266-0.001
124A122VAL0-0.0010.0016.581-0.370-0.3700.0000.0000.0000.000
125A123VAL00.009-0.0119.8640.1460.1460.0000.0000.0000.000
126A124GLU-1-0.716-0.77312.316-0.173-0.1730.0000.0000.0000.000
127A125GLY00.0190.01215.9630.0450.0450.0000.0000.0000.000
128A126ARG10.8540.91718.8150.0980.0980.0000.0000.0000.000
129A127ASP-1-0.860-0.93019.671-0.128-0.1280.0000.0000.0000.000
130A128ILE0-0.0080.01313.2790.0000.0000.0000.0000.0000.000
131A129GLY00.0580.02914.774-0.030-0.0300.0000.0000.0000.000
132A130THR0-0.046-0.03615.827-0.018-0.0180.0000.0000.0000.000
133A131VAL0-0.038-0.02718.0850.0090.0090.0000.0000.0000.000
134A132VAL0-0.042-0.01513.6940.0040.0040.0000.0000.0000.000
135A133LEU00.019-0.0129.2330.0350.0350.0000.0000.0000.000
136A134PRO00.0090.02112.212-0.094-0.0940.0000.0000.0000.000
137A135ASP-1-0.897-0.94110.036-0.493-0.4930.0000.0000.0000.000
138A136ALA0-0.053-0.0268.798-0.216-0.2160.0000.0000.0000.000
139A137ASP-1-0.810-0.8855.923-3.363-3.3630.0000.0000.0000.000
140A138VAL0-0.022-0.0069.2430.3130.3130.0000.0000.0000.000
141A139LYS10.7980.90111.8560.5270.5270.0000.0000.0000.000
142A140ILE00.0060.01514.6690.0480.0480.0000.0000.0000.000
143A141TYR00.0000.00317.1320.0310.0310.0000.0000.0000.000
144A142LEU0-0.007-0.00919.5720.0150.0150.0000.0000.0000.000
145A143THR00.015-0.01122.3450.0220.0220.0000.0000.0000.000
146A144ALA00.0060.00126.0530.0000.0000.0000.0000.0000.000
147A145SER00.0630.03829.3200.0080.0080.0000.0000.0000.000
148A146ALA00.004-0.00632.9010.0010.0010.0000.0000.0000.000
149A147GLN00.005-0.01334.9040.0020.0020.0000.0000.0000.000
150A148ALA00.0790.04931.8220.0040.0040.0000.0000.0000.000
151A149ARG10.7490.83628.9660.1000.1000.0000.0000.0000.000
152A150ALA0-0.061-0.03432.1290.0050.0050.0000.0000.0000.000
153A151GLN0-0.025-0.01235.0090.0070.0070.0000.0000.0000.000
154A152ARG10.8820.96128.1840.1100.1100.0000.0000.0000.000
155A153ARG10.8150.88132.2370.0580.0580.0000.0000.0000.000
156A154ASN00.0200.02834.5360.0050.0050.0000.0000.0000.000
157A170LEU00.0750.02538.3160.0010.0010.0000.0000.0000.000
158A171ALA00.0990.03838.806-0.003-0.0030.0000.0000.0000.000
159A172ASP-1-0.824-0.86836.281-0.052-0.0520.0000.0000.0000.000
160A173VAL0-0.032-0.00733.101-0.001-0.0010.0000.0000.0000.000
161A174GLN00.0670.02735.135-0.001-0.0010.0000.0000.0000.000
162A175ARG10.9120.94237.7530.0430.0430.0000.0000.0000.000
163A176ARG10.8780.93631.8250.0600.0600.0000.0000.0000.000
164A177ASP-1-0.794-0.83532.105-0.093-0.0930.0000.0000.0000.000
165A178HIS0-0.045-0.01533.642-0.006-0.0060.0000.0000.0000.000
166A179LEU0-0.067-0.03833.380-0.001-0.0010.0000.0000.0000.000
167A187PRO00.0200.00523.0880.0020.0020.0000.0000.0000.000
168A188LEU00.0070.00422.485-0.013-0.0130.0000.0000.0000.000
169A189ARG10.9160.96124.6070.1150.1150.0000.0000.0000.000
170A190PRO00.0290.03221.789-0.005-0.0050.0000.0000.0000.000
171A191ALA00.015-0.00518.3570.0150.0150.0000.0000.0000.000
172A192GLU-1-0.922-0.96020.409-0.208-0.2080.0000.0000.0000.000
173A193ASP-1-0.857-0.92615.814-0.454-0.4540.0000.0000.0000.000
174A194ALA0-0.085-0.04317.519-0.054-0.0540.0000.0000.0000.000
175A195LEU0-0.016-0.00916.1880.0310.0310.0000.0000.0000.000
176A196GLU-1-0.933-0.97619.758-0.190-0.1900.0000.0000.0000.000
177A197VAL0-0.015-0.00920.4920.0030.0030.0000.0000.0000.000
178A198ASP-1-0.812-0.86623.415-0.123-0.1230.0000.0000.0000.000
179A199THR00.006-0.02123.8940.0070.0070.0000.0000.0000.000
180A200SER0-0.121-0.11626.8640.0110.0110.0000.0000.0000.000
181A201ASP-1-0.917-0.94430.417-0.088-0.0880.0000.0000.0000.000
182A202MET0-0.069-0.01223.820-0.003-0.0030.0000.0000.0000.000
183A203THR00.0220.00327.6640.0010.0010.0000.0000.0000.000
184A204GLN00.024-0.00622.172-0.018-0.0180.0000.0000.0000.000
185A205GLU-1-0.900-0.96122.629-0.129-0.1290.0000.0000.0000.000
186A206GLN00.0410.03722.492-0.014-0.0140.0000.0000.0000.000
187A207VAL00.0060.00220.493-0.017-0.0170.0000.0000.0000.000
188A208VAL00.0140.00517.329-0.025-0.0250.0000.0000.0000.000
189A209ALA0-0.016-0.00517.801-0.035-0.0350.0000.0000.0000.000
190A210HIS00.002-0.00118.742-0.016-0.0160.0000.0000.0000.000
191A211LEU00.011-0.01015.643-0.021-0.0210.0000.0000.0000.000
192A212LEU00.0040.00712.964-0.065-0.0650.0000.0000.0000.000
193A213ASP-1-0.935-0.94914.192-0.343-0.3430.0000.0000.0000.000
194A214LEU0-0.007-0.00415.805-0.023-0.0230.0000.0000.0000.000
195A215VAL0-0.028-0.0259.522-0.048-0.0480.0000.0000.0000.000
196A216ARG10.8760.93111.0960.3400.3400.0000.0000.0000.000
197A217THR0-0.059-0.01712.562-0.007-0.0070.0000.0000.0000.000
198A218ARG10.8860.94910.3000.6210.6210.0000.0000.0000.000