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: 17JGZ

Calculation Name: 2C08-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2C08

Chain ID: A

ChEMBL ID:

UniProt ID: O35179

Base Structure: X-ray

Registration Date: 2023-06-21

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2007878.62564
FMO2-HF: Nuclear repulsion 1924056.982676
FMO2-HF: Total energy -83821.642964
FMO2-MP2: Total energy -84063.373907


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:25:GLU)


Summations of interaction energy for fragment #1(A:25: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.
4.376.8722.472-2.377-2.5980.01
Interaction energy analysis for fragmet #1(A:25:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.955 / q_NPA : -0.994
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].
3A27THR00.0280.0213.8160.1752.506-0.029-1.280-1.0220.001
4A28LYS10.8560.9251.922-63.414-63.2432.501-1.097-1.5760.009
5A29LEU00.0160.0207.170-1.296-1.2960.0000.0000.0000.000
6A30ASP-1-0.833-0.92810.63518.69818.6980.0000.0000.0000.000
7A31ASP-1-0.897-0.96312.87320.21020.2100.0000.0000.0000.000
8A32ASP-1-0.909-0.93614.59414.08014.0800.0000.0000.0000.000
9A33PHE0-0.0020.00513.729-0.217-0.2170.0000.0000.0000.000
10A34LYS10.9280.9547.425-27.505-27.5050.0000.0000.0000.000
11A35GLU-1-0.774-0.85914.09914.04514.0450.0000.0000.0000.000
12A36MET0-0.018-0.00317.386-0.644-0.6440.0000.0000.0000.000
13A37GLU-1-0.892-0.96413.62318.71218.7120.0000.0000.0000.000
14A38ARG10.7840.86616.609-14.848-14.8480.0000.0000.0000.000
15A39LYS10.9310.96517.991-12.508-12.5080.0000.0000.0000.000
16A40VAL00.0530.03819.786-0.621-0.6210.0000.0000.0000.000
17A41ASP-1-0.838-0.90118.85014.14214.1420.0000.0000.0000.000
18A42VAL0-0.089-0.05320.961-0.501-0.5010.0000.0000.0000.000
19A43THR0-0.006-0.00923.246-0.571-0.5710.0000.0000.0000.000
20A44SER00.0000.00723.641-0.593-0.5930.0000.0000.0000.000
21A45ARG10.8510.90120.378-13.779-13.7790.0000.0000.0000.000
22A46ALA0-0.0250.00125.787-0.391-0.3910.0000.0000.0000.000
23A47VAL00.0410.02628.571-0.380-0.3800.0000.0000.0000.000
24A48MET00.0180.01528.458-0.447-0.4470.0000.0000.0000.000
25A49GLU-1-0.875-0.92729.4689.6229.6220.0000.0000.0000.000
26A50ILE00.0240.01331.403-0.352-0.3520.0000.0000.0000.000
27A51MET0-0.0130.04133.114-0.422-0.4220.0000.0000.0000.000
28A52THR0-0.037-0.03633.110-0.264-0.2640.0000.0000.0000.000
29A53LYS10.8810.91032.892-9.321-9.3210.0000.0000.0000.000
30A54THR0-0.009-0.01737.295-0.257-0.2570.0000.0000.0000.000
31A55ILE0-0.035-0.02037.851-0.289-0.2890.0000.0000.0000.000
32A56GLU-1-0.992-1.00837.4317.9917.9910.0000.0000.0000.000
33A57TYR0-0.029-0.00741.152-0.183-0.1830.0000.0000.0000.000
34A58LEU0-0.050-0.01843.042-0.174-0.1740.0000.0000.0000.000
35A59GLN0-0.067-0.03644.365-0.209-0.2090.0000.0000.0000.000
36A60PRO00.0520.03144.4500.1300.1300.0000.0000.0000.000
37A61ASN00.002-0.00845.3220.0930.0930.0000.0000.0000.000
38A62PRO0-0.005-0.02342.7890.0150.0150.0000.0000.0000.000
39A63ALA0-0.072-0.02544.5140.0490.0490.0000.0000.0000.000
40A64SER00.0130.01046.932-0.125-0.1250.0000.0000.0000.000
41A65ARG10.9370.98240.110-7.423-7.4230.0000.0000.0000.000
42A66ALA0-0.027-0.00943.8440.1450.1450.0000.0000.0000.000
43A67LYS10.9851.01042.731-6.941-6.9410.0000.0000.0000.000
44A87PRO00.011-0.00152.254-0.023-0.0230.0000.0000.0000.000
45A88GLN0-0.019-0.00551.4700.1180.1180.0000.0000.0000.000
46A89ALA00.0110.00753.757-0.102-0.1020.0000.0000.0000.000
47A90GLU-1-0.853-0.93554.3015.6765.6760.0000.0000.0000.000
48A91ALA00.0480.02257.551-0.117-0.1170.0000.0000.0000.000
49A92LEU0-0.004-0.00256.403-0.099-0.0990.0000.0000.0000.000
50A93LEU0-0.027-0.00959.649-0.103-0.1030.0000.0000.0000.000
51A94ALA00.0440.01461.479-0.104-0.1040.0000.0000.0000.000
52A95GLU-1-0.964-0.97463.0974.8704.8700.0000.0000.0000.000
53A96ALA0-0.021-0.01364.047-0.104-0.1040.0000.0000.0000.000
54A97MET0-0.029-0.00964.283-0.089-0.0890.0000.0000.0000.000
55A98LEU00.0230.01567.057-0.101-0.1010.0000.0000.0000.000
56A99LYS10.8870.95467.962-4.725-4.7250.0000.0000.0000.000
57A100PHE00.004-0.01567.532-0.055-0.0550.0000.0000.0000.000
58A101GLY00.0210.02671.492-0.067-0.0670.0000.0000.0000.000
59A102ARG10.8980.93970.442-4.488-4.4880.0000.0000.0000.000
60A103GLU-1-1.014-1.00473.8034.2394.2390.0000.0000.0000.000
61A104LEU0-0.057-0.02775.156-0.050-0.0500.0000.0000.0000.000
62A105GLY0-0.0070.00877.444-0.064-0.0640.0000.0000.0000.000
63A106ASP-1-0.970-1.01879.1763.9123.9120.0000.0000.0000.000
64A107ASP-1-0.928-0.94481.4763.7393.7390.0000.0000.0000.000
65A108CYS0-0.085-0.01879.3730.0110.0110.0000.0000.0000.000
66A109ASN00.0540.01178.448-0.019-0.0190.0000.0000.0000.000
67A110PHE0-0.008-0.02070.9730.0410.0410.0000.0000.0000.000
68A111GLY00.0970.05074.1660.0600.0600.0000.0000.0000.000
69A112PRO00.0180.00574.2200.0710.0710.0000.0000.0000.000
70A113ALA00.0150.01572.9160.0470.0470.0000.0000.0000.000
71A114LEU0-0.059-0.02069.1850.0810.0810.0000.0000.0000.000
72A115GLY00.0200.01069.6300.0710.0710.0000.0000.0000.000
73A116GLU-1-0.899-0.96370.1084.3264.3260.0000.0000.0000.000
74A117VAL0-0.002-0.01065.7940.0650.0650.0000.0000.0000.000
75A118GLY00.0540.01765.7970.0910.0910.0000.0000.0000.000
76A119GLU-1-0.866-0.92565.2634.6724.6720.0000.0000.0000.000
77A120ALA00.0000.01064.7910.0700.0700.0000.0000.0000.000
78A121MET0-0.045-0.01658.8340.1030.1030.0000.0000.0000.000
79A122ARG10.8270.89860.743-4.725-4.7250.0000.0000.0000.000
80A123GLU-1-0.894-0.95061.0334.9064.9060.0000.0000.0000.000
81A124LEU0-0.016-0.02157.6960.0970.0970.0000.0000.0000.000
82A125SER00.0160.00456.9180.1240.1240.0000.0000.0000.000
83A126GLU-1-0.924-0.95056.2525.1675.1670.0000.0000.0000.000
84A127VAL0-0.010-0.00255.2840.1000.1000.0000.0000.0000.000
85A128LYS10.8430.95248.483-6.182-6.1820.0000.0000.0000.000
86A129ASP-1-0.867-0.93551.8265.8545.8540.0000.0000.0000.000
87A130SER0-0.099-0.06951.7800.1190.1190.0000.0000.0000.000
88A131LEU00.0370.01948.0550.1130.1130.0000.0000.0000.000
89A132ASP-1-0.829-0.92547.5416.5716.5710.0000.0000.0000.000
90A133MET0-0.070-0.04546.9840.1970.1970.0000.0000.0000.000
91A134GLU-1-0.887-0.94747.5886.3486.3480.0000.0000.0000.000
92A135VAL00.000-0.00242.8570.1680.1680.0000.0000.0000.000
93A136LYS10.7920.86942.003-6.999-6.9990.0000.0000.0000.000
94A137GLN0-0.028-0.01242.6210.0930.0930.0000.0000.0000.000
95A138ASN00.019-0.00343.3430.1160.1160.0000.0000.0000.000
96A139PHE0-0.017-0.00637.1060.1200.1200.0000.0000.0000.000
97A140ILE0-0.034-0.02038.3760.2010.2010.0000.0000.0000.000
98A141ASP-1-0.795-0.88237.5297.5697.5690.0000.0000.0000.000
99A142PRO0-0.022-0.00137.5060.2100.2100.0000.0000.0000.000
100A143LEU00.0470.03233.2210.2540.2540.0000.0000.0000.000
101A144GLN0-0.022-0.01632.9440.2540.2540.0000.0000.0000.000
102A145ASN0-0.041-0.03433.1540.1570.1570.0000.0000.0000.000
103A146LEU0-0.0040.00430.1000.1680.1680.0000.0000.0000.000
104A147HIS0-0.022-0.02126.5940.4540.4540.0000.0000.0000.000
105A148ASP-1-0.932-0.96728.6149.4529.4520.0000.0000.0000.000
106A149LYS10.8790.93029.247-8.282-8.2820.0000.0000.0000.000
107A150ASP-1-0.779-0.89228.8409.7919.7910.0000.0000.0000.000
108A151LEU00.0350.03424.8560.4980.4980.0000.0000.0000.000
109A152ARG10.9490.98724.407-9.821-9.8210.0000.0000.0000.000
110A153GLU-1-0.985-0.99124.59011.03411.0340.0000.0000.0000.000
111A154ILE00.0590.02521.1960.5230.5230.0000.0000.0000.000
112A155GLN0-0.0070.00120.2840.3320.3320.0000.0000.0000.000
113A156HIS0-0.077-0.04119.8060.8410.8410.0000.0000.0000.000
114A157HIS0-0.002-0.00820.3700.9130.9130.0000.0000.0000.000
115A158LEU00.0460.02915.7240.6130.6130.0000.0000.0000.000
116A159LYS10.9250.97515.838-13.351-13.3510.0000.0000.0000.000
117A160LYS10.9030.94416.180-12.277-12.2770.0000.0000.0000.000
118A161LEU00.0240.01713.9020.5270.5270.0000.0000.0000.000
119A162GLU-1-0.804-0.8839.42727.09827.0980.0000.0000.0000.000
120A163GLY0-0.028-0.01912.0371.1931.1930.0000.0000.0000.000
121A164ARG10.8700.92413.518-13.717-13.7170.0000.0000.0000.000
122A165ARG10.8510.9525.700-29.609-29.6090.0000.0000.0000.000
123A166LEU0-0.024-0.0127.5691.3041.3040.0000.0000.0000.000
124A167ASP-1-0.918-0.9629.95718.41018.4100.0000.0000.0000.000
125A168PHE00.0310.0109.981-0.313-0.3130.0000.0000.0000.000
126A169ASP-1-0.796-0.9136.46032.59632.5960.0000.0000.0000.000
127A170TYR0-0.091-0.0528.3890.3140.3140.0000.0000.0000.000
128A171LYS10.8730.91610.438-16.102-16.1020.0000.0000.0000.000
129A172LYS10.9130.9709.291-21.971-21.9710.0000.0000.0000.000
130A173LYS10.9530.9576.999-29.865-29.8650.0000.0000.0000.000
131A174ARG10.8300.93110.236-18.186-18.1860.0000.0000.0000.000
132A175GLN00.1020.06413.378-0.104-0.1040.0000.0000.0000.000
133A176GLY0-0.006-0.00915.200-0.807-0.8070.0000.0000.0000.000
134A177LYS10.8930.93617.567-15.737-15.7370.0000.0000.0000.000
135A178ILE0-0.0160.01216.248-0.504-0.5040.0000.0000.0000.000
136A179PRO00.0260.02120.0530.1030.1030.0000.0000.0000.000
137A180ASP-1-0.844-0.93120.00913.62213.6220.0000.0000.0000.000
138A181GLU-1-0.836-0.90220.31711.92911.9290.0000.0000.0000.000
139A182GLU-1-0.905-0.95319.15414.19314.1930.0000.0000.0000.000
140A183LEU0-0.015-0.00413.4910.5270.5270.0000.0000.0000.000
141A184ARG10.8900.94916.883-11.700-11.7000.0000.0000.0000.000
142A185GLN0-0.053-0.05019.1720.2590.2590.0000.0000.0000.000
143A186ALA0-0.069-0.02515.242-0.009-0.0090.0000.0000.0000.000
144A187LEU00.000-0.00213.9130.5030.5030.0000.0000.0000.000
145A188GLU-1-0.870-0.93116.20612.19612.1960.0000.0000.0000.000
146A189LYS10.9230.95818.348-13.571-13.5710.0000.0000.0000.000
147A190PHE0-0.020-0.02012.2780.1740.1740.0000.0000.0000.000
148A191ASP-1-0.857-0.93216.23916.33516.3350.0000.0000.0000.000
149A192GLU-1-0.922-0.95718.14912.06012.0600.0000.0000.0000.000
150A193SER0-0.063-0.05818.008-0.247-0.2470.0000.0000.0000.000
151A194LYS10.9300.98314.530-16.622-16.6220.0000.0000.0000.000
152A195GLU-1-0.914-0.95017.75112.11512.1150.0000.0000.0000.000
153A196ILE0-0.060-0.02521.261-0.382-0.3820.0000.0000.0000.000
154A197ALA0-0.026-0.02018.417-0.370-0.3700.0000.0000.0000.000
155A198GLU-1-0.830-0.93318.26814.60714.6070.0000.0000.0000.000
156A199SER0-0.0060.01420.938-0.503-0.5030.0000.0000.0000.000
157A200SER00.0050.01723.008-0.234-0.2340.0000.0000.0000.000
158A201MET0-0.033-0.01217.533-0.184-0.1840.0000.0000.0000.000
159A202PHE00.0100.00723.257-0.195-0.1950.0000.0000.0000.000
160A203ASN0-0.053-0.06525.200-0.608-0.6080.0000.0000.0000.000
161A204LEU00.0030.01325.447-0.282-0.2820.0000.0000.0000.000
162A205LEU0-0.079-0.06622.434-0.176-0.1760.0000.0000.0000.000
163A206GLU-1-0.938-0.95026.8609.3779.3770.0000.0000.0000.000
164A207MET0-0.0370.00929.791-0.304-0.3040.0000.0000.0000.000
165A208ASP-1-0.888-0.95030.0519.6849.6840.0000.0000.0000.000
166A209ILE0-0.032-0.01832.704-0.251-0.2510.0000.0000.0000.000
167A210GLU-1-0.899-0.96735.1778.1598.1590.0000.0000.0000.000
168A211GLN00.0330.02831.487-0.229-0.2290.0000.0000.0000.000
169A212VAL0-0.029-0.02334.991-0.196-0.1960.0000.0000.0000.000
170A213SER0-0.035-0.01037.323-0.283-0.2830.0000.0000.0000.000
171A214GLN00.0490.01735.923-0.071-0.0710.0000.0000.0000.000
172A215LEU0-0.041-0.01835.654-0.170-0.1700.0000.0000.0000.000
173A216SER0-0.034-0.01639.626-0.234-0.2340.0000.0000.0000.000
174A217ALA00.0310.01342.478-0.189-0.1890.0000.0000.0000.000
175A218LEU0-0.022-0.00240.192-0.162-0.1620.0000.0000.0000.000
176A219VAL0-0.007-0.01342.711-0.161-0.1610.0000.0000.0000.000
177A220GLN0-0.058-0.02045.307-0.283-0.2830.0000.0000.0000.000
178A221ALA00.0840.05647.010-0.142-0.1420.0000.0000.0000.000
179A222GLN0-0.056-0.04144.423-0.087-0.0870.0000.0000.0000.000
180A223LEU0-0.030-0.01648.784-0.169-0.1690.0000.0000.0000.000
181A224GLU-1-0.900-0.95451.1735.4655.4650.0000.0000.0000.000
182A225TYR00.0160.00951.574-0.115-0.1150.0000.0000.0000.000
183A226HIS0-0.021-0.02549.924-0.200-0.2000.0000.0000.0000.000
184A227LYS10.9180.96954.442-5.725-5.7250.0000.0000.0000.000
185A228GLN00.0430.02956.990-0.087-0.0870.0000.0000.0000.000
186A229ALA0-0.006-0.00356.722-0.115-0.1150.0000.0000.0000.000
187A230VAL0-0.012-0.00957.791-0.106-0.1060.0000.0000.0000.000
188A231GLN00.003-0.00360.217-0.131-0.1310.0000.0000.0000.000
189A232ILE00.0130.02161.466-0.101-0.1010.0000.0000.0000.000
190A233LEU0-0.003-0.00959.550-0.093-0.0930.0000.0000.0000.000
191A234GLN00.0020.01563.749-0.065-0.0650.0000.0000.0000.000
192A235GLN00.0020.00665.987-0.057-0.0570.0000.0000.0000.000
193A236VAL0-0.007-0.01466.053-0.092-0.0920.0000.0000.0000.000
194A237THR0-0.029-0.02066.171-0.044-0.0440.0000.0000.0000.000
195A238VAL0-0.018-0.01168.777-0.068-0.0680.0000.0000.0000.000
196A239ARG10.9560.98571.683-4.347-4.3470.0000.0000.0000.000
197A240LEU0-0.003-0.00369.232-0.071-0.0710.0000.0000.0000.000
198A241GLU-1-0.943-0.97471.2424.3604.3600.0000.0000.0000.000
199A242GLU-1-0.983-0.99574.2163.9823.9820.0000.0000.0000.000
200A243ARG10.9340.97075.826-4.184-4.1840.0000.0000.0000.000
201A244ILE0-0.059-0.03173.450-0.047-0.0470.0000.0000.0000.000
202A245ARG10.8900.93977.356-4.121-4.1210.0000.0000.0000.000
203A246GLN0-0.082-0.02880.298-0.081-0.0810.0000.0000.0000.000
204A247ALA0-0.0320.00280.910-0.048-0.0480.0000.0000.0000.000