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: 66ZKZ

Calculation Name: 1CMX-A-Xray372

Preferred Name:

Target Type:

Ligand Name: amino-acetaldehyde

ligand 3-letter code: GLZ

PDB ID: 1CMX

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG48

Base Structure: X-ray

Registration Date: 2023-03-13

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2551874.058027
FMO2-HF: Nuclear repulsion 2468980.321941
FMO2-HF: Total energy -82893.736086
FMO2-MP2: Total energy -83139.12873


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:6:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
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.
-160.876-158.2880.663-1.075-2.175-0.002
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.949 / q_NPA : 0.953
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].
3A8VAL00.0110.0153.8631.4743.161-0.018-0.820-0.849-0.001
4A9VAL00.0400.0267.007-0.294-0.2940.0000.0000.0000.000
5A10PRO0-0.032-0.01110.711-0.270-0.2700.0000.0000.0000.000
6A11ILE00.0210.01712.4760.6470.6470.0000.0000.0000.000
7A12GLU-1-0.668-0.77714.939-11.480-11.4800.0000.0000.0000.000
8A13SER00.0030.00818.710-0.079-0.0790.0000.0000.0000.000
9A14ASN0-0.026-0.03120.8850.7300.7300.0000.0000.0000.000
10A15PRO00.0660.02822.271-0.382-0.3820.0000.0000.0000.000
11A16GLU-1-0.877-0.91223.219-11.510-11.5100.0000.0000.0000.000
12A17VAL00.0390.02317.867-0.206-0.2060.0000.0000.0000.000
13A18PHE0-0.020-0.01917.400-0.582-0.5820.0000.0000.0000.000
14A19THR00.018-0.00620.141-0.161-0.1610.0000.0000.0000.000
15A20ASN0-0.109-0.04820.083-0.343-0.3430.0000.0000.0000.000
16A21PHE00.011-0.01513.311-0.250-0.2500.0000.0000.0000.000
17A22ALA0-0.0040.00818.045-0.212-0.2120.0000.0000.0000.000
18A23HIS0-0.029-0.02620.3910.2560.2560.0000.0000.0000.000
19A24LYS10.7980.89316.73914.93614.9360.0000.0000.0000.000
20A25LEU0-0.021-0.01215.201-0.309-0.3090.0000.0000.0000.000
21A26GLY00.015-0.01619.012-0.037-0.0370.0000.0000.0000.000
22A27LEU0-0.064-0.01022.7480.4050.4050.0000.0000.0000.000
23A28LYS10.8940.92624.7329.3169.3160.0000.0000.0000.000
24A29ASN0-0.044-0.03427.6490.0320.0320.0000.0000.0000.000
25A30GLU-1-0.950-0.96529.643-8.165-8.1650.0000.0000.0000.000
26A31TRP0-0.037-0.02228.5440.2060.2060.0000.0000.0000.000
27A32ALA00.0210.02126.378-0.269-0.2690.0000.0000.0000.000
28A33TYR0-0.003-0.01821.391-0.090-0.0900.0000.0000.0000.000
29A34PHE0-0.002-0.00126.0420.1780.1780.0000.0000.0000.000
30A35ASP-1-0.868-0.94127.885-9.811-9.8110.0000.0000.0000.000
31A36ILE0-0.046-0.02528.1920.3280.3280.0000.0000.0000.000
32A37TYR00.012-0.00730.072-0.049-0.0490.0000.0000.0000.000
33A38SER0-0.034-0.04232.0650.0870.0870.0000.0000.0000.000
34A39LEU00.0060.00330.835-0.039-0.0390.0000.0000.0000.000
35A40THR0-0.041-0.03034.5930.0450.0450.0000.0000.0000.000
36A41GLU-1-0.853-0.90138.173-7.135-7.1350.0000.0000.0000.000
37A42PRO0-0.038-0.01539.893-0.053-0.0530.0000.0000.0000.000
38A43GLU-1-0.901-0.95941.869-6.500-6.5000.0000.0000.0000.000
39A44LEU0-0.006-0.01237.159-0.042-0.0420.0000.0000.0000.000
40A45LEU0-0.0120.00034.900-0.182-0.1820.0000.0000.0000.000
41A46ALA0-0.0080.00537.818-0.017-0.0170.0000.0000.0000.000
42A47PHE0-0.116-0.05337.7220.0490.0490.0000.0000.0000.000
43A48LEU00.0150.01131.388-0.208-0.2080.0000.0000.0000.000
44A49PRO0-0.024-0.00333.0790.1730.1730.0000.0000.0000.000
45A50ARG10.8100.87833.8637.5987.5980.0000.0000.0000.000
46A51PRO0-0.040-0.03434.0020.1250.1250.0000.0000.0000.000
47A52VAL0-0.008-0.01529.320-0.177-0.1770.0000.0000.0000.000
48A53LYS10.7780.88229.0539.4879.4870.0000.0000.0000.000
49A54ALA00.0210.01824.391-0.233-0.2330.0000.0000.0000.000
50A55ILE00.0010.01225.6480.1740.1740.0000.0000.0000.000
51A56VAL0-0.023-0.00819.693-0.353-0.3530.0000.0000.0000.000
52A57LEU0-0.010-0.00221.7390.4630.4630.0000.0000.0000.000
53A58LEU0-0.025-0.00918.243-0.667-0.6670.0000.0000.0000.000
54A59PHE00.0370.01420.3770.4880.4880.0000.0000.0000.000
55A60PRO00.0430.02420.531-0.769-0.7690.0000.0000.0000.000
56A61ILE0-0.077-0.02417.1930.1310.1310.0000.0000.0000.000
57A62ASN0-0.108-0.05820.519-0.436-0.4360.0000.0000.0000.000
58A78ASP-1-0.947-0.98827.824-9.748-9.7480.0000.0000.0000.000
59A79VAL00.0500.03024.2030.1890.1890.0000.0000.0000.000
60A80ILE0-0.034-0.00119.967-0.367-0.3670.0000.0000.0000.000
61A81TRP0-0.036-0.03216.431-0.259-0.2590.0000.0000.0000.000
62A82PHE0-0.007-0.01113.831-0.414-0.4140.0000.0000.0000.000
63A83LYS10.8430.91611.69719.74219.7420.0000.0000.0000.000
64A84GLN0-0.023-0.0208.5150.5970.5970.0000.0000.0000.000
65A85SER0-0.048-0.0457.0480.6380.6380.0000.0000.0000.000
66A86VAL0-0.052-0.0202.464-7.246-6.8900.677-0.130-0.902-0.001
67A87LYS10.8220.8934.30229.66129.910-0.001-0.071-0.1770.000
68A88ASN00.002-0.0216.3400.2650.2650.0000.0000.0000.000
69A89ALA00.0070.0086.8531.6381.6380.0000.0000.0000.000
70A90CYS0-0.055-0.0108.8450.6180.6180.0000.0000.0000.000
71A91GLY00.0980.05012.0390.7650.7650.0000.0000.0000.000
72A92LEU00.0300.01610.2450.5770.5770.0000.0000.0000.000
73A93TYR00.0250.0018.077-0.464-0.4640.0000.0000.0000.000
74A94ALA00.0260.03413.4680.6530.6530.0000.0000.0000.000
75A95ILE00.0390.04316.2390.7060.7060.0000.0000.0000.000
76A96LEU0-0.005-0.00512.9340.5130.5130.0000.0000.0000.000
77A97HIS0-0.0070.01015.8680.6440.6440.0000.0000.0000.000
78A98SER00.000-0.00119.1810.7080.7080.0000.0000.0000.000
79A99LEU00.0140.01419.4830.5090.5090.0000.0000.0000.000
80A100SER0-0.006-0.02619.3550.2770.2770.0000.0000.0000.000
81A101ASN0-0.073-0.04122.0730.4680.4680.0000.0000.0000.000
82A102ASN00.017-0.00524.8490.7650.7650.0000.0000.0000.000
83A103GLN00.0540.01924.4780.1030.1030.0000.0000.0000.000
84A104SER0-0.044-0.01526.6270.1470.1470.0000.0000.0000.000
85A105LEU0-0.0100.00226.9230.2460.2460.0000.0000.0000.000
86A106LEU0-0.0070.00422.670-0.141-0.1410.0000.0000.0000.000
87A107GLU-1-0.843-0.90126.229-8.882-8.8820.0000.0000.0000.000
88A108PRO0-0.048-0.02826.603-0.388-0.3880.0000.0000.0000.000
89A109GLY0-0.0120.00326.3020.1590.1590.0000.0000.0000.000
90A110SER0-0.0170.00222.949-0.348-0.3480.0000.0000.0000.000
91A111ASP-1-0.865-0.94718.294-13.799-13.7990.0000.0000.0000.000
92A112LEU0-0.018-0.00717.544-0.559-0.5590.0000.0000.0000.000
93A113ASP-1-0.773-0.86219.801-10.819-10.8190.0000.0000.0000.000
94A114ASN0-0.051-0.03321.3820.4720.4720.0000.0000.0000.000
95A115PHE0-0.043-0.01615.731-0.138-0.1380.0000.0000.0000.000
96A116LEU0-0.003-0.01119.716-0.064-0.0640.0000.0000.0000.000
97A117LYS10.8790.91921.76610.66910.6690.0000.0000.0000.000
98A118SER0-0.0040.01221.1860.1360.1360.0000.0000.0000.000
99A119GLN0-0.0320.01817.3870.2200.2200.0000.0000.0000.000
100A120SER0-0.044-0.03622.2660.1490.1490.0000.0000.0000.000
101A121ASP-1-0.935-0.95125.830-10.462-10.4620.0000.0000.0000.000
102A122THR0-0.075-0.05623.4010.1240.1240.0000.0000.0000.000
103A123SER0-0.102-0.04925.8430.1160.1160.0000.0000.0000.000
104A124SER0-0.038-0.02020.4960.1820.1820.0000.0000.0000.000
105A125SER00.002-0.02918.5170.1410.1410.0000.0000.0000.000
106A126LYS10.9570.96621.65210.31810.3180.0000.0000.0000.000
107A127ASN0-0.040-0.01622.7570.2550.2550.0000.0000.0000.000
108A128ARG10.8720.94219.09414.96814.9680.0000.0000.0000.000
109A129PHE00.0750.03415.701-0.355-0.3550.0000.0000.0000.000
110A130ASP-1-0.802-0.89413.991-18.531-18.5310.0000.0000.0000.000
111A131ASP-1-0.778-0.84613.872-19.399-19.3990.0000.0000.0000.000
112A132VAL00.039-0.0099.705-0.746-0.7460.0000.0000.0000.000
113A133THR0-0.014-0.00711.278-1.608-1.6080.0000.0000.0000.000
114A134THR00.0230.00012.1720.3920.3920.0000.0000.0000.000
115A135ASP-1-0.859-0.8977.554-30.783-30.7830.0000.0000.0000.000
116A136GLN0-0.027-0.0208.547-2.528-2.5280.0000.0000.0000.000
117A137PHE00.0180.02210.1720.1830.1830.0000.0000.0000.000
118A138VAL00.0520.0217.8220.2630.2630.0000.0000.0000.000
119A139LEU0-0.005-0.0153.586-1.097-0.8010.005-0.054-0.2470.000
120A140ASN0-0.083-0.0527.4190.1620.1620.0000.0000.0000.000
121A141VAL00.0820.05610.8210.7360.7360.0000.0000.0000.000
122A142ILE0-0.0070.0025.6940.6020.6020.0000.0000.0000.000
123A143LYS10.8220.9007.28327.33427.3340.0000.0000.0000.000
124A144GLU-1-0.890-0.9339.468-15.434-15.4340.0000.0000.0000.000
125A145ASN0-0.019-0.00712.1261.7771.7770.0000.0000.0000.000
126A146VAL00.000-0.0039.0360.2830.2830.0000.0000.0000.000
127A147GLN0-0.004-0.01211.4890.1290.1290.0000.0000.0000.000
128A148THR00.0590.03814.9480.1950.1950.0000.0000.0000.000
129A149PHE0-0.047-0.01910.373-0.110-0.1100.0000.0000.0000.000
130A150SER0-0.041-0.02013.297-0.295-0.2950.0000.0000.0000.000
131A151THR0-0.0190.00415.3760.5090.5090.0000.0000.0000.000
132A152GLY00.017-0.00218.775-0.332-0.3320.0000.0000.0000.000
133A153GLN0-0.083-0.04521.3350.4620.4620.0000.0000.0000.000
134A154SER0-0.092-0.06221.5340.1950.1950.0000.0000.0000.000
135A155GLU-1-0.954-0.98119.658-12.089-12.0890.0000.0000.0000.000
136A156ALA00.0000.00314.987-0.281-0.2810.0000.0000.0000.000
137A157PRO00.0080.00314.032-0.167-0.1670.0000.0000.0000.000
138A158GLU-1-0.864-0.91411.002-19.938-19.9380.0000.0000.0000.000
139A159ALA0-0.015-0.0136.918-0.358-0.3580.0000.0000.0000.000
140A160THR0-0.087-0.0647.797-1.996-1.9960.0000.0000.0000.000
141A161ALA00.0260.0308.768-0.743-0.7430.0000.0000.0000.000
142A162ASP-1-0.858-0.92511.206-23.358-23.3580.0000.0000.0000.000
143A163THR0-0.001-0.00712.9231.2041.2040.0000.0000.0000.000
144A164ASN0-0.045-0.02315.3720.7800.7800.0000.0000.0000.000
145A165LEU00.0130.02317.6920.4860.4860.0000.0000.0000.000
146A166HIS0-0.027-0.03413.841-1.516-1.5160.0000.0000.0000.000
147A167TYR00.011-0.03314.9730.9230.9230.0000.0000.0000.000
148A168ILE0-0.050-0.01116.702-0.698-0.6980.0000.0000.0000.000
149A169THR0-0.013-0.02019.3240.2410.2410.0000.0000.0000.000
150A170TYR0-0.041-0.03721.5880.0530.0530.0000.0000.0000.000
151A171VAL00.003-0.01524.320-0.014-0.0140.0000.0000.0000.000
152A172GLU-1-0.818-0.90327.060-9.225-9.2250.0000.0000.0000.000
153A173GLU-1-0.886-0.94227.257-10.102-10.1020.0000.0000.0000.000
154A174ASN0-0.078-0.02530.1260.5530.5530.0000.0000.0000.000
155A175GLY0-0.027-0.02033.0230.1950.1950.0000.0000.0000.000
156A176GLY0-0.061-0.02032.0600.1680.1680.0000.0000.0000.000
157A177ILE00.0330.02129.670-0.100-0.1000.0000.0000.0000.000
158A178PHE00.002-0.01325.376-0.001-0.0010.0000.0000.0000.000
159A179GLU-1-0.699-0.79222.973-11.336-11.3360.0000.0000.0000.000
160A180LEU0-0.055-0.03320.029-0.305-0.3050.0000.0000.0000.000
161A181ASP-1-0.691-0.84416.217-16.563-16.5630.0000.0000.0000.000
162A182GLY00.0330.03713.7610.0240.0240.0000.0000.0000.000
163A183ARG10.8200.89910.18821.25621.2560.0000.0000.0000.000
164A184ASN00.0180.00314.233-0.034-0.0340.0000.0000.0000.000
165A185LEU0-0.049-0.03213.521-0.066-0.0660.0000.0000.0000.000
166A186SER0-0.043-0.02417.038-0.259-0.2590.0000.0000.0000.000
167A187GLY00.0080.01919.3990.4830.4830.0000.0000.0000.000
168A188PRO0-0.0250.00720.458-0.067-0.0670.0000.0000.0000.000
169A189LEU0-0.0080.00122.4670.3080.3080.0000.0000.0000.000
170A190TYR0-0.033-0.01825.2010.3180.3180.0000.0000.0000.000
171A191LEU00.004-0.00527.9030.0380.0380.0000.0000.0000.000
172A192GLY00.0010.00330.9100.2990.2990.0000.0000.0000.000
173A193LYS10.8900.93533.4407.5657.5650.0000.0000.0000.000
174A194SER00.027-0.00634.490-0.027-0.0270.0000.0000.0000.000
175A195ASP-1-0.849-0.90536.245-6.938-6.9380.0000.0000.0000.000
176A196PRO0-0.052-0.03439.024-0.099-0.0990.0000.0000.0000.000
177A197THR0-0.084-0.06141.1210.1530.1530.0000.0000.0000.000
178A198ALA0-0.0370.00337.7090.0780.0780.0000.0000.0000.000
179A199THR0-0.065-0.06839.103-0.064-0.0640.0000.0000.0000.000
180A200ASP-1-0.744-0.84033.697-8.328-8.3280.0000.0000.0000.000
181A201LEU00.0350.01828.0570.1240.1240.0000.0000.0000.000
182A202ILE00.0230.01331.540-0.071-0.0710.0000.0000.0000.000
183A203GLU-1-0.845-0.88733.835-7.221-7.2210.0000.0000.0000.000
184A204GLN00.0070.01933.4420.1870.1870.0000.0000.0000.000
185A205GLU-1-0.847-0.92434.386-7.771-7.7710.0000.0000.0000.000
186A206LEU0-0.037-0.00933.123-0.088-0.0880.0000.0000.0000.000
187A207VAL00.0230.01028.824-0.224-0.2240.0000.0000.0000.000
188A208ARG10.8350.91531.0187.5797.5790.0000.0000.0000.000
189A209VAL00.0160.00433.159-0.072-0.0720.0000.0000.0000.000
190A210ARG10.8160.89725.37710.69210.6920.0000.0000.0000.000
191A211VAL00.0500.01027.500-0.202-0.2020.0000.0000.0000.000
192A212ALA00.014-0.00229.400-0.102-0.1020.0000.0000.0000.000
193A213SER0-0.062-0.03030.4930.0840.0840.0000.0000.0000.000
194A214TYR0-0.064-0.04024.473-0.157-0.1570.0000.0000.0000.000
195A215MET0-0.027-0.01428.595-0.023-0.0230.0000.0000.0000.000
196A216GLU-1-0.871-0.91630.693-7.966-7.9660.0000.0000.0000.000
197A217ASN0-0.065-0.04528.884-0.215-0.2150.0000.0000.0000.000
198A218ALA00.014-0.00228.555-0.065-0.0650.0000.0000.0000.000
199A219ASN0-0.074-0.05129.946-0.013-0.0130.0000.0000.0000.000
200A220GLU-1-0.947-0.95532.831-8.510-8.5100.0000.0000.0000.000
201A221GLU-1-0.914-0.95426.815-10.794-10.7940.0000.0000.0000.000
202A222ASP-1-0.947-0.95730.808-8.484-8.4840.0000.0000.0000.000
203A223VAL0-0.069-0.02526.732-0.103-0.1030.0000.0000.0000.000
204A224LEU00.012-0.00828.714-0.080-0.0800.0000.0000.0000.000
205A225ASN0-0.060-0.02023.5950.2400.2400.0000.0000.0000.000
206A226PHE00.048-0.00424.375-0.461-0.4610.0000.0000.0000.000
207A227ALA0-0.0080.00623.4280.2580.2580.0000.0000.0000.000
208A228MET0-0.014-0.00524.247-0.244-0.2440.0000.0000.0000.000
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