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: JLGG9

Calculation Name: 1DOV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DOV

Chain ID: A

ChEMBL ID:

UniProt ID: P26231

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 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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1603275.423454
FMO2-HF: Nuclear repulsion 1533308.69357
FMO2-HF: Total energy -69966.729884
FMO2-MP2: Total energy -70169.345672


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:82:GLU)


Summations of interaction energy for fragment #1(A:82:GLU)
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.
-150.079-152.68124.19-11.134-10.4530.104
Interaction energy analysis for fragmet #1(A:82:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.805 / q_NPA : -0.894
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].
3A84GLN00.0100.0201.870-38.681-43.39522.859-9.793-8.3530.105
4A85PHE00.0990.0575.243-3.911-3.783-0.001-0.008-0.1190.000
5A86LEU00.0300.0236.738-2.578-2.5780.0000.0000.0000.000
6A87LYS10.8730.9213.962-68.567-68.1920.000-0.173-0.2010.001
7A88GLU-1-0.908-0.9648.67229.94529.9450.0000.0000.0000.000
8A89GLU-1-0.823-0.89511.15118.34418.3440.0000.0000.0000.000
9A90LEU0-0.011-0.00911.128-1.932-1.9320.0000.0000.0000.000
10A91VAL0-0.0050.00212.196-1.763-1.7630.0000.0000.0000.000
11A92VAL0-0.0050.00214.666-1.631-1.6310.0000.0000.0000.000
12A93ALA00.0070.00416.440-1.286-1.2860.0000.0000.0000.000
13A94VAL0-0.011-0.01116.209-1.132-1.1320.0000.0000.0000.000
14A95GLU-1-0.794-0.87318.71813.08013.0800.0000.0000.0000.000
15A96ASP-1-0.873-0.92020.93813.57213.5720.0000.0000.0000.000
16A97VAL0-0.031-0.02021.627-0.832-0.8320.0000.0000.0000.000
17A98ARG10.7510.83822.873-13.642-13.6420.0000.0000.0000.000
18A99LYS10.8570.92322.560-14.607-14.6070.0000.0000.0000.000
19A100GLN0-0.003-0.00926.642-0.916-0.9160.0000.0000.0000.000
20A101GLY00.0020.01027.342-0.461-0.4610.0000.0000.0000.000
21A102ASP-1-0.860-0.91528.83510.95310.9530.0000.0000.0000.000
22A103LEU0-0.0070.00130.904-0.461-0.4610.0000.0000.0000.000
23A104MET0-0.0190.00731.768-0.452-0.4520.0000.0000.0000.000
24A105LYS10.9550.97632.345-10.169-10.1690.0000.0000.0000.000
25A106SER0-0.046-0.02634.475-0.322-0.3220.0000.0000.0000.000
26A107ALA00.0400.01736.817-0.267-0.2670.0000.0000.0000.000
27A108ALA0-0.024-0.02736.981-0.256-0.2560.0000.0000.0000.000
28A109GLY00.0010.01238.647-0.181-0.1810.0000.0000.0000.000
29A110GLU-1-0.856-0.94640.4547.3497.3490.0000.0000.0000.000
30A111PHE0-0.046-0.03741.878-0.217-0.2170.0000.0000.0000.000
31A112ALA0-0.034-0.01742.148-0.152-0.1520.0000.0000.0000.000
32A113ASP-1-0.900-0.94144.0977.0697.0690.0000.0000.0000.000
33A114ASP-1-0.886-0.94246.5486.3736.3730.0000.0000.0000.000
34A115PRO00.0310.02146.7760.0200.0200.0000.0000.0000.000
35A116CYS0-0.045-0.02847.805-0.055-0.0550.0000.0000.0000.000
36A117SER00.0050.01948.059-0.049-0.0490.0000.0000.0000.000
37A118SER0-0.014-0.01847.4600.2230.2230.0000.0000.0000.000
38A119VAL00.0270.00945.7250.1550.1550.0000.0000.0000.000
39A120LYS10.8540.93043.919-6.753-6.7530.0000.0000.0000.000
40A121ARG10.9891.00842.575-6.811-6.8110.0000.0000.0000.000
41A122GLY00.0110.00341.8500.1970.1970.0000.0000.0000.000
42A123ASN0-0.015-0.00540.0930.1920.1920.0000.0000.0000.000
43A124MET00.0440.03237.9240.2620.2620.0000.0000.0000.000
44A125VAL0-0.021-0.01636.9610.2820.2820.0000.0000.0000.000
45A126ARG10.8440.90736.434-7.700-7.7000.0000.0000.0000.000
46A127ALA00.0590.03633.7820.2750.2750.0000.0000.0000.000
47A128ALA00.0410.01032.2840.3810.3810.0000.0000.0000.000
48A129ARG10.9160.96431.605-8.265-8.2650.0000.0000.0000.000
49A130ALA00.0390.04029.9440.3280.3280.0000.0000.0000.000
50A131LEU00.0370.01226.7660.4780.4780.0000.0000.0000.000
51A132LEU00.0010.00326.7040.5050.5050.0000.0000.0000.000
52A133SER0-0.024-0.01626.2340.3450.3450.0000.0000.0000.000
53A134ALA00.0100.01023.4810.5070.5070.0000.0000.0000.000
54A135VAL00.012-0.00622.0100.7740.7740.0000.0000.0000.000
55A136THR0-0.037-0.03421.7070.6430.6430.0000.0000.0000.000
56A137ARG10.8460.91016.309-16.974-16.9740.0000.0000.0000.000
57A138LEU00.002-0.00116.4870.9230.9230.0000.0000.0000.000
58A139LEU0-0.028-0.02216.8221.0761.0760.0000.0000.0000.000
59A140ILE00.0070.00517.2860.6450.6450.0000.0000.0000.000
60A141LEU00.0120.01611.6970.7130.7130.0000.0000.0000.000
61A142ALA0-0.001-0.00212.6061.9361.9360.0000.0000.0000.000
62A143ASP-1-0.781-0.85212.66119.69819.6980.0000.0000.0000.000
63A144MET0-0.004-0.00311.9980.5170.5170.0000.0000.0000.000
64A145ALA00.0020.0078.6351.8691.8690.0000.0000.0000.000
65A146ASP-1-0.855-0.9278.10130.65930.6590.0000.0000.0000.000
66A147VAL00.0710.0339.8351.4801.4800.0000.0000.0000.000
67A148TYR0-0.020-0.0243.656-0.791-0.5090.004-0.050-0.2360.000
68A149LYS10.7870.8865.095-29.743-29.7430.0000.0000.0000.000
69A150LEU0-0.044-0.0196.1511.0651.0650.0000.0000.0000.000
70A151LEU00.020-0.0038.358-0.355-0.3550.0000.0000.0000.000
71A152VAL00.0150.0162.381-2.618-1.2911.328-1.110-1.544-0.002
72A153GLN0-0.028-0.0165.4180.4480.4480.0000.0000.0000.000
73A154LEU0-0.020-0.0127.759-2.599-2.5990.0000.0000.0000.000
74A155LYS10.9000.9217.658-21.933-21.9330.0000.0000.0000.000
75A156VAL0-0.0190.0076.467-1.642-1.6420.0000.0000.0000.000
76A157VAL0-0.019-0.0059.108-2.048-2.0480.0000.0000.0000.000
77A158GLU-1-0.810-0.88012.25217.06417.0640.0000.0000.0000.000
78A159ASP-1-0.814-0.90211.41317.48917.4890.0000.0000.0000.000
79A160GLY00.0190.01213.114-0.924-0.9240.0000.0000.0000.000
80A161ILE0-0.022-0.02514.892-1.190-1.1900.0000.0000.0000.000
81A162LEU0-0.041-0.01816.680-0.991-0.9910.0000.0000.0000.000
82A163LYS10.8660.91912.710-19.292-19.2920.0000.0000.0000.000
83A164LEU0-0.045-0.01818.624-0.593-0.5930.0000.0000.0000.000
84A165ARG10.7690.85820.948-11.645-11.6450.0000.0000.0000.000
85A166ASN0-0.014-0.01420.612-0.896-0.8960.0000.0000.0000.000
86A167ALA00.0000.02022.912-0.136-0.1360.0000.0000.0000.000
87A168GLY00.0320.01824.073-0.329-0.3290.0000.0000.0000.000
88A169ASN0-0.024-0.01726.991-0.717-0.7170.0000.0000.0000.000
89A170GLU-1-0.781-0.89127.2729.6439.6430.0000.0000.0000.000
90A171GLN0-0.0140.00027.7490.3760.3760.0000.0000.0000.000
91A172ASP-1-0.821-0.90923.26211.94211.9420.0000.0000.0000.000
92A173LEU0-0.0100.00922.8450.6990.6990.0000.0000.0000.000
93A174GLY00.0210.01223.5200.4340.4340.0000.0000.0000.000
94A175ILE0-0.030-0.00419.8500.2860.2860.0000.0000.0000.000
95A176GLN00.010-0.00817.8101.3541.3540.0000.0000.0000.000
96A177TYR00.0180.00718.7770.8830.8830.0000.0000.0000.000
97A178LYS10.8650.92019.978-12.121-12.1210.0000.0000.0000.000
98A179ALA00.0130.01215.3620.5680.5680.0000.0000.0000.000
99A180LEU0-0.0040.00814.9621.2251.2250.0000.0000.0000.000
100A181LYS10.8190.90015.896-14.325-14.3250.0000.0000.0000.000
101A182PRO00.0530.02314.1830.1190.1190.0000.0000.0000.000
102A183GLU-1-0.793-0.8699.72729.84129.8410.0000.0000.0000.000
103A184VAL00.007-0.00412.6390.6440.6440.0000.0000.0000.000
104A185ASP-1-0.789-0.87715.46816.04916.0490.0000.0000.0000.000
105A186LYS10.8100.8798.742-30.753-30.7530.0000.0000.0000.000
106A187LEU00.0410.02211.3940.4660.4660.0000.0000.0000.000
107A188ASN00.0060.01612.666-0.524-0.5240.0000.0000.0000.000
108A189ILE0-0.005-0.00713.921-0.474-0.4740.0000.0000.0000.000
109A190MET0-0.074-0.0377.006-0.226-0.2260.0000.0000.0000.000
110A191ALA00.0380.01012.691-0.407-0.4070.0000.0000.0000.000
111A192ALA0-0.044-0.02815.285-0.874-0.8740.0000.0000.0000.000
112A193LYS10.9570.98912.916-23.275-23.2750.0000.0000.0000.000
113A194ARG10.8370.90913.558-20.263-20.2630.0000.0000.0000.000
114A195GLN00.0140.02616.657-0.424-0.4240.0000.0000.0000.000
115A196GLN0-0.029-0.02519.704-0.199-0.1990.0000.0000.0000.000
116A197GLU-1-0.862-0.91516.44618.18818.1880.0000.0000.0000.000
117A198LEU0-0.053-0.02518.892-0.503-0.5030.0000.0000.0000.000
118A199LYS10.9580.97921.985-13.287-13.2870.0000.0000.0000.000
119A200ASP-1-0.812-0.91025.39610.36510.3650.0000.0000.0000.000
120A201VAL00.002-0.00726.1930.4360.4360.0000.0000.0000.000
121A202GLY00.0930.06127.6330.1560.1560.0000.0000.0000.000
122A203ASN0-0.024-0.03423.0500.1400.1400.0000.0000.0000.000
123A204ARG10.8310.91923.273-12.000-12.0000.0000.0000.0000.000
124A205ASP-1-0.875-0.93924.13411.11811.1180.0000.0000.0000.000
125A206GLN0-0.046-0.01923.3500.2980.2980.0000.0000.0000.000
126A207MET0-0.0240.00716.4790.2900.2900.0000.0000.0000.000
127A208ALA0-0.027-0.00621.5850.3280.3280.0000.0000.0000.000
128A209ALA00.0120.00524.0410.0290.0290.0000.0000.0000.000
129A210ALA0-0.018-0.00120.705-0.058-0.0580.0000.0000.0000.000
130A211ARG10.8730.91018.457-15.044-15.0440.0000.0000.0000.000
131A212GLY00.0010.01120.9110.0600.0600.0000.0000.0000.000
132A213ILE0-0.030-0.02524.349-0.181-0.1810.0000.0000.0000.000
133A214LEU00.0050.00416.968-0.152-0.1520.0000.0000.0000.000
134A215GLN0-0.027-0.01620.0980.2070.2070.0000.0000.0000.000
135A216LYS10.9150.96822.124-10.829-10.8290.0000.0000.0000.000
136A217ASN00.010-0.01524.443-0.576-0.5760.0000.0000.0000.000
137A218VAL00.0100.02019.848-0.225-0.2250.0000.0000.0000.000
138A219PRO00.009-0.00223.022-0.130-0.1300.0000.0000.0000.000
139A220ILE00.0250.02325.936-0.319-0.3190.0000.0000.0000.000
140A221LEU00.0280.02222.303-0.331-0.3310.0000.0000.0000.000
141A222TYR00.0020.02024.585-0.093-0.0930.0000.0000.0000.000
142A223THR0-0.015-0.01326.153-0.375-0.3750.0000.0000.0000.000
143A224ALA00.0070.00428.938-0.306-0.3060.0000.0000.0000.000
144A225SER0-0.013-0.05026.358-0.174-0.1740.0000.0000.0000.000
145A226GLN0-0.001-0.00128.4090.0290.0290.0000.0000.0000.000
146A227ALA00.0230.01330.428-0.241-0.2410.0000.0000.0000.000
147A228CYS0-0.127-0.06230.469-0.233-0.2330.0000.0000.0000.000
148A229LEU0-0.044-0.00628.161-0.154-0.1540.0000.0000.0000.000
149A230GLN0-0.042-0.02932.669-0.358-0.3580.0000.0000.0000.000
150A231HIS0-0.012-0.00735.833-0.189-0.1890.0000.0000.0000.000
151A232PRO00.0520.03735.364-0.011-0.0110.0000.0000.0000.000
152A233ASP-1-0.887-0.94536.3457.5267.5260.0000.0000.0000.000
153A234VAL0-0.0190.00037.834-0.122-0.1220.0000.0000.0000.000
154A235ALA0-0.016-0.02136.0670.2440.2440.0000.0000.0000.000
155A236ALA00.0180.00535.4940.1970.1970.0000.0000.0000.000
156A237TYR00.0320.00733.9900.1480.1480.0000.0000.0000.000
157A238LYS10.9390.96531.305-8.099-8.0990.0000.0000.0000.000
158A239ALA00.0070.01230.6540.3020.3020.0000.0000.0000.000
159A240ASN00.0150.00431.4020.2200.2200.0000.0000.0000.000
160A241ARG10.8670.92226.484-10.119-10.1190.0000.0000.0000.000
161A242ASP-1-0.763-0.85226.75110.71610.7160.0000.0000.0000.000
162A243LEU0-0.009-0.00226.9660.2870.2870.0000.0000.0000.000
163A244ILE0-0.0020.00425.7510.2870.2870.0000.0000.0000.000
164A245TYR00.0280.00319.2180.1860.1860.0000.0000.0000.000
165A246LYS10.9360.96922.717-9.926-9.9260.0000.0000.0000.000
166A247GLN00.0210.01023.7900.4330.4330.0000.0000.0000.000
167A248LEU0-0.0170.01420.0700.2630.2630.0000.0000.0000.000
168A249GLN00.011-0.01016.1410.7200.7200.0000.0000.0000.000
169A250GLN0-0.0240.00319.4140.3690.3690.0000.0000.0000.000
170A251ALA0-0.016-0.00621.4830.1740.1740.0000.0000.0000.000
171A252VAL00.012-0.00214.9550.4170.4170.0000.0000.0000.000
172A253THR0-0.017-0.03416.6420.7900.7900.0000.0000.0000.000
173A254GLY00.0010.00618.1790.0650.0650.0000.0000.0000.000
174A255ILE00.001-0.00815.1090.0150.0150.0000.0000.0000.000
175A256SER0-0.014-0.00714.4310.6150.6150.0000.0000.0000.000
176A257ASN0-0.0130.00515.3560.1390.1390.0000.0000.0000.000
177A258ALA00.0140.00518.526-0.028-0.0280.0000.0000.0000.000
178A259ALA00.021-0.00214.888-0.128-0.1280.0000.0000.0000.000
179A260GLN0-0.053-0.04714.7590.8530.8530.0000.0000.0000.000
180A261ALA0-0.0150.00617.204-0.428-0.4280.0000.0000.0000.000
181A262THR0-0.110-0.06018.359-1.103-1.1030.0000.0000.0000.000