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: 59M7Z

Calculation Name: 1CMX-A-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 218
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2568578.312635
FMO2-HF: Nuclear repulsion 2485345.533429
FMO2-HF: Total energy -83232.779206
FMO2-MP2: Total energy -83479.515877


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:5:ACE )


Summations of interaction energy for fragment #1(A:5:ACE )
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.
-0.3471.1760.007-0.712-0.817-0.001
Interaction energy analysis for fragmet #1(A:5:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.002
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].
3A7ALA 00.0020.0083.4550.0061.4060.007-0.701-0.705-0.001
4A8VAL 00.0220.0234.5730.1930.3160.000-0.011-0.1120.000
5A9VAL 00.0080.0046.9810.0480.0480.0000.0000.0000.000
6A10PRO 0-0.027-0.01510.210-0.046-0.0460.0000.0000.0000.000
7A11ILE 00.0680.03513.1480.0280.0280.0000.0000.0000.000
8A12GLU -1-0.647-0.71415.253-0.001-0.0010.0000.0000.0000.000
9A13SER 0-0.020-0.00818.903-0.005-0.0050.0000.0000.0000.000
10A14ASN 0-0.042-0.04421.3880.0050.0050.0000.0000.0000.000
11A15PRO 00.0520.01622.444-0.005-0.0050.0000.0000.0000.000
12A16GLU -1-0.923-0.96222.6590.0070.0070.0000.0000.0000.000
13A17VAL 00.0740.04117.546-0.003-0.0030.0000.0000.0000.000
14A18PHE 0-0.035-0.02219.179-0.011-0.0110.0000.0000.0000.000
15A19THR 00.0290.01220.614-0.010-0.0100.0000.0000.0000.000
16A20ASN 0-0.058-0.00919.0210.0030.0030.0000.0000.0000.000
17A21PHE 00.012-0.01212.933-0.004-0.0040.0000.0000.0000.000
18A22ALA 0-0.019-0.00118.077-0.009-0.0090.0000.0000.0000.000
19A23HIS 0-0.050-0.03620.8960.0010.0010.0000.0000.0000.000
20A24LYS 10.8710.95615.431-0.007-0.0070.0000.0000.0000.000
21A25LEU 0-0.032-0.01616.110-0.008-0.0080.0000.0000.0000.000
22A26GLY 00.043-0.00119.568-0.004-0.0040.0000.0000.0000.000
23A27LEU 0-0.066-0.00523.1590.0020.0020.0000.0000.0000.000
24A28LYS 10.8910.95525.2110.0500.0500.0000.0000.0000.000
25A29ASN 00.015-0.01728.247-0.003-0.0030.0000.0000.0000.000
26A30GLU -1-0.977-0.97229.505-0.023-0.0230.0000.0000.0000.000
27A31TRP 0-0.037-0.01329.069-0.001-0.0010.0000.0000.0000.000
28A32ALA 00.1220.07527.590-0.001-0.0010.0000.0000.0000.000
29A33TYR 0-0.086-0.07322.979-0.005-0.0050.0000.0000.0000.000
30A34PHE 0-0.066-0.04526.7720.0070.0070.0000.0000.0000.000
31A35ASP -1-0.844-0.92828.190-0.028-0.0280.0000.0000.0000.000
32A36ILE 0-0.061-0.02129.7850.0010.0010.0000.0000.0000.000
33A37TYR 00.0300.00131.363-0.001-0.0010.0000.0000.0000.000
34A38SER 0-0.001-0.00933.5790.0010.0010.0000.0000.0000.000
35A39LEU 0-0.0200.00033.3210.0000.0000.0000.0000.0000.000
36A40THR 0-0.052-0.04336.589-0.001-0.0010.0000.0000.0000.000
37A41GLU -1-0.880-0.94639.972-0.018-0.0180.0000.0000.0000.000
38A42PRO 0-0.0180.00241.4400.0000.0000.0000.0000.0000.000
39A43GLU -1-0.904-0.97943.160-0.014-0.0140.0000.0000.0000.000
40A44LEU 00.0130.01838.5400.0000.0000.0000.0000.0000.000
41A45LEU 0-0.057-0.01637.170-0.001-0.0010.0000.0000.0000.000
42A46ALA 00.0120.00639.542-0.001-0.0010.0000.0000.0000.000
43A47PHE 0-0.089-0.03538.0770.0020.0020.0000.0000.0000.000
44A48LEU 0-0.008-0.00133.3120.0000.0000.0000.0000.0000.000
45A49PRO 0-0.0070.00033.7090.0000.0000.0000.0000.0000.000
46A50ARG 10.8550.94735.5270.0280.0280.0000.0000.0000.000
47A51PRO 0-0.035-0.03635.9370.0020.0020.0000.0000.0000.000
48A52VAL 0-0.004-0.00731.521-0.001-0.0010.0000.0000.0000.000
49A53LYS 10.9620.95630.8110.0490.0490.0000.0000.0000.000
50A54ALA 00.0250.02126.743-0.005-0.0050.0000.0000.0000.000
51A55ILE 0-0.0090.00528.1660.0060.0060.0000.0000.0000.000
52A56VAL 0-0.031-0.01121.777-0.009-0.0090.0000.0000.0000.000
53A57LEU 00.005-0.00324.5570.0110.0110.0000.0000.0000.000
54A58LEU 0-0.034-0.01920.188-0.013-0.0130.0000.0000.0000.000
55A59PHE 00.0200.00523.1500.0100.0100.0000.0000.0000.000
56A60PRO 00.0440.01723.200-0.011-0.0110.0000.0000.0000.000
57A61ILE 0-0.077-0.02720.823-0.004-0.0040.0000.0000.0000.000
58A62ASN 0-0.029-0.02323.926-0.005-0.0050.0000.0000.0000.000
59A63NME 00.0210.02927.683-0.003-0.0030.0000.0000.0000.000
60A77ACE 0-0.032-0.03431.236-0.001-0.0010.0000.0000.0000.000
61A78ASP -1-0.945-0.97631.439-0.069-0.0690.0000.0000.0000.000
62A79VAL 00.0640.05327.9220.0030.0030.0000.0000.0000.000
63A80ILE 0-0.030-0.01223.202-0.008-0.0080.0000.0000.0000.000
64A81TRP 0-0.043-0.01621.097-0.007-0.0070.0000.0000.0000.000
65A82PHE 00.020-0.00217.389-0.008-0.0080.0000.0000.0000.000
66A83LYS 10.8590.95316.4170.2810.2810.0000.0000.0000.000
67A84GLN 0-0.049-0.03312.6820.0100.0100.0000.0000.0000.000
68A85SER 0-0.052-0.04411.2030.0480.0480.0000.0000.0000.000
69A86VAL 0-0.031-0.0056.422-0.210-0.2100.0000.0000.0000.000
70A87LYS 10.8430.9078.3100.4130.4130.0000.0000.0000.000
71A88ASN 00.021-0.0048.651-0.082-0.0820.0000.0000.0000.000
72A89ALA 00.0130.0169.4500.0590.0590.0000.0000.0000.000
73A90CYS 0-0.0450.01411.3930.0310.0310.0000.0000.0000.000
74A91GLY 00.1040.03814.9160.0160.0160.0000.0000.0000.000
75A92LEU 00.0150.01111.5110.0140.0140.0000.0000.0000.000
76A93TYR 00.0410.00411.849-0.042-0.0420.0000.0000.0000.000
77A94ALA 00.0170.04216.4550.0210.0210.0000.0000.0000.000
78A95ILE 00.0260.02317.1490.0170.0170.0000.0000.0000.000
79A96LEU 0-0.006-0.00215.2500.0110.0110.0000.0000.0000.000
80A97HIS 0-0.017-0.00719.4140.0060.0060.0000.0000.0000.000
81A98SER 00.031-0.00422.1970.0150.0150.0000.0000.0000.000
82A99LEU 00.0060.00421.2070.0110.0110.0000.0000.0000.000
83A100SER 00.003-0.01421.7520.0060.0060.0000.0000.0000.000
84A101ASN 0-0.065-0.01924.3970.0070.0070.0000.0000.0000.000
85A102ASN 00.0320.01327.1390.0120.0120.0000.0000.0000.000
86A103GLN 00.0650.02627.114-0.001-0.0010.0000.0000.0000.000
87A104SER 0-0.025-0.00828.6540.0050.0050.0000.0000.0000.000
88A105LEU 0-0.043-0.02528.5400.0050.0050.0000.0000.0000.000
89A106LEU 00.0070.01424.0130.0020.0020.0000.0000.0000.000
90A107GLU -1-0.891-0.95726.629-0.030-0.0300.0000.0000.0000.000
91A108PRO 0-0.058-0.03127.093-0.006-0.0060.0000.0000.0000.000
92A109GLY 0-0.0160.00626.9130.0050.0050.0000.0000.0000.000
93A110SER 0-0.0300.00623.2380.0000.0000.0000.0000.0000.000
94A111ASP -1-0.858-0.94318.089-0.084-0.0840.0000.0000.0000.000
95A112LEU 0-0.038-0.02619.411-0.017-0.0170.0000.0000.0000.000
96A113ASP -1-0.836-0.92221.085-0.075-0.0750.0000.0000.0000.000
97A114ASN 0-0.029-0.02622.3670.0020.0020.0000.0000.0000.000
98A115PHE 0-0.060-0.02017.717-0.006-0.0060.0000.0000.0000.000
99A116LEU 0-0.014-0.01121.469-0.005-0.0050.0000.0000.0000.000
100A117LYS 10.9170.96024.1240.0680.0680.0000.0000.0000.000
101A118SER 0-0.0050.01222.7720.0040.0040.0000.0000.0000.000
102A119GLN 00.0200.02521.1980.0020.0020.0000.0000.0000.000
103A120SER 0-0.034-0.01024.9070.0030.0030.0000.0000.0000.000
104A121ASP -1-0.989-0.97628.457-0.067-0.0670.0000.0000.0000.000
105A122THR 0-0.081-0.05425.8340.0010.0010.0000.0000.0000.000
106A123SER 0-0.092-0.04128.4500.0020.0020.0000.0000.0000.000
107A124SER 00.017-0.00823.3980.0040.0040.0000.0000.0000.000
108A125SER 00.003-0.00622.1890.0050.0050.0000.0000.0000.000
109A126LYS 10.9310.94225.2570.0810.0810.0000.0000.0000.000
110A127ASN 0-0.044-0.01926.0020.0010.0010.0000.0000.0000.000
111A128ARG 10.9641.00023.6180.1390.1390.0000.0000.0000.000
112A129PHE 00.0540.02519.159-0.001-0.0010.0000.0000.0000.000
113A130ASP -1-0.881-0.96617.949-0.244-0.2440.0000.0000.0000.000
114A131ASP -1-0.886-0.93017.533-0.246-0.2460.0000.0000.0000.000
115A132VAL 00.0210.00513.413-0.035-0.0350.0000.0000.0000.000
116A133THR 0-0.011-0.01714.232-0.039-0.0390.0000.0000.0000.000
117A134THR 00.0270.01715.5040.0100.0100.0000.0000.0000.000
118A135ASP -1-0.842-0.91810.918-0.592-0.5920.0000.0000.0000.000
119A136GLN 0-0.041-0.02510.291-0.170-0.1700.0000.0000.0000.000
120A137PHE 00.0340.02411.5200.0140.0140.0000.0000.0000.000
121A138VAL 00.0130.01110.1450.0160.0160.0000.0000.0000.000
122A139LEU 0-0.021-0.0305.581-0.116-0.1160.0000.0000.0000.000
123A140ASN 0-0.047-0.0247.7500.0860.0860.0000.0000.0000.000
124A141VAL 00.1080.07910.3180.0800.0800.0000.0000.0000.000
125A142ILE 0-0.041-0.0075.9220.0480.0480.0000.0000.0000.000
126A143LYS 10.8630.9215.2460.1760.1760.0000.0000.0000.000
127A144GLU -1-0.942-0.9588.1390.0680.0680.0000.0000.0000.000
128A145ASN 0-0.058-0.06210.6020.0280.0280.0000.0000.0000.000
129A146VAL 00.008-0.0027.187-0.003-0.0030.0000.0000.0000.000
130A147GLN 0-0.028-0.0169.692-0.008-0.0080.0000.0000.0000.000
131A148THR 00.0730.03812.8880.0000.0000.0000.0000.0000.000
132A149PHE 0-0.058-0.03510.111-0.036-0.0360.0000.0000.0000.000
133A150SER 0-0.029-0.02011.9320.0090.0090.0000.0000.0000.000
134A151THR 0-0.0490.00414.235-0.003-0.0030.0000.0000.0000.000
135A152GLY 00.0360.01817.651-0.012-0.0120.0000.0000.0000.000
136A153GLN 0-0.105-0.06620.6510.0090.0090.0000.0000.0000.000
137A154SER 0-0.085-0.08820.6120.0040.0040.0000.0000.0000.000
138A155GLU -1-0.942-0.97819.2630.0920.0920.0000.0000.0000.000
139A156ALA 0-0.024-0.00614.067-0.010-0.0100.0000.0000.0000.000
140A157PRO 00.0190.01214.3050.0180.0180.0000.0000.0000.000
141A158GLU -1-0.910-0.96011.4760.3110.3110.0000.0000.0000.000
142A159ALA 0-0.031-0.0067.079-0.037-0.0370.0000.0000.0000.000
143A160THR 0-0.044-0.0338.038-0.131-0.1310.0000.0000.0000.000
144A161ALA 00.0050.0009.924-0.067-0.0670.0000.0000.0000.000
145A162ASP -1-0.879-0.93613.389-0.152-0.1520.0000.0000.0000.000
146A163THR 00.0400.01115.2950.0260.0260.0000.0000.0000.000
147A164ASN 0-0.035-0.01817.6600.0020.0020.0000.0000.0000.000
148A165LEU 00.0120.02519.4740.0030.0030.0000.0000.0000.000
149A166HIS 0-0.061-0.06018.063-0.027-0.0270.0000.0000.0000.000
150A167TYR 00.003-0.04217.2490.0170.0170.0000.0000.0000.000
151A168ILE 0-0.0330.00020.357-0.018-0.0180.0000.0000.0000.000
152A169THR 0-0.012-0.00822.6420.0040.0040.0000.0000.0000.000
153A170TYR 0-0.038-0.03724.800-0.002-0.0020.0000.0000.0000.000
154A171VAL 00.027-0.00427.3270.0010.0010.0000.0000.0000.000
155A172GLU -1-0.925-0.96430.130-0.059-0.0590.0000.0000.0000.000
156A173GLU -1-0.922-0.96530.233-0.080-0.0800.0000.0000.0000.000
157A174ASN 0-0.075-0.03233.2940.0100.0100.0000.0000.0000.000
158A175GLY 0-0.006-0.00636.4140.0000.0000.0000.0000.0000.000
159A176GLY 0-0.0650.01835.9340.0030.0030.0000.0000.0000.000
160A177ILE 00.0590.03433.265-0.002-0.0020.0000.0000.0000.000
161A178PHE 00.0190.00229.231-0.001-0.0010.0000.0000.0000.000
162A179GLU -1-0.710-0.79826.728-0.092-0.0920.0000.0000.0000.000
163A180LEU 0-0.057-0.04423.536-0.006-0.0060.0000.0000.0000.000
164A181ASP -1-0.694-0.84020.426-0.188-0.1880.0000.0000.0000.000
165A182GLY 00.0430.03017.811-0.004-0.0040.0000.0000.0000.000
166A183ARG 10.8530.91015.4800.2910.2910.0000.0000.0000.000
167A184ASN 00.0440.04019.2070.0100.0100.0000.0000.0000.000
168A185LEU 00.004-0.02520.041-0.009-0.0090.0000.0000.0000.000
169A186SER 0-0.039-0.00922.776-0.003-0.0030.0000.0000.0000.000
170A187GLY 00.0000.00924.2240.0090.0090.0000.0000.0000.000
171A188PRO 0-0.029-0.01625.2140.0020.0020.0000.0000.0000.000
172A189LEU 0-0.0170.00626.8190.0050.0050.0000.0000.0000.000
173A190TYR 0-0.034-0.01329.6580.0050.0050.0000.0000.0000.000
174A191LEU 0-0.013-0.02632.1380.0010.0010.0000.0000.0000.000
175A192GLY 00.0060.00534.8770.0050.0050.0000.0000.0000.000
176A193LYS 10.8700.91637.3060.0460.0460.0000.0000.0000.000
177A194SER 00.009-0.03238.3500.0000.0000.0000.0000.0000.000
178A195ASP -1-0.886-0.94439.716-0.037-0.0370.0000.0000.0000.000
179A196PRO 0-0.075-0.05042.3060.0000.0000.0000.0000.0000.000
180A197THR 0-0.068-0.01844.0950.0010.0010.0000.0000.0000.000
181A198ALA 00.0210.02740.1770.0010.0010.0000.0000.0000.000
182A199THR 0-0.056-0.02741.374-0.001-0.0010.0000.0000.0000.000
183A200ASP -1-0.795-0.90936.123-0.039-0.0390.0000.0000.0000.000
184A201LEU 00.0350.01830.9000.0010.0010.0000.0000.0000.000
185A202ILE 0-0.020-0.00634.075-0.001-0.0010.0000.0000.0000.000
186A203GLU -1-0.989-0.99736.462-0.029-0.0290.0000.0000.0000.000
187A204GLN 00.0520.03036.5010.0000.0000.0000.0000.0000.000
188A205GLU -1-0.890-0.95837.643-0.038-0.0380.0000.0000.0000.000
189A206LEU 0-0.026-0.00936.716-0.001-0.0010.0000.0000.0000.000
190A207VAL 00.0150.01532.142-0.003-0.0030.0000.0000.0000.000
191A208ARG 10.9670.98434.2540.0350.0350.0000.0000.0000.000
192A209VAL 00.0170.01236.3020.0000.0000.0000.0000.0000.000
193A210ARG 10.8210.91529.7140.0790.0790.0000.0000.0000.000
194A211VAL 00.036-0.00130.540-0.002-0.0020.0000.0000.0000.000
195A212ALA 0-0.019-0.01732.6650.0000.0000.0000.0000.0000.000
196A213SER 0-0.048-0.02334.6740.0010.0010.0000.0000.0000.000
197A214TYR 0-0.037-0.02628.553-0.001-0.0010.0000.0000.0000.000
198A215MET 0-0.021-0.02231.8890.0020.0020.0000.0000.0000.000
199A216GLU -1-0.950-0.95533.377-0.031-0.0310.0000.0000.0000.000
200A217ASN 00.0240.00632.122-0.001-0.0010.0000.0000.0000.000
201A218ALA 00.002-0.00331.4410.0010.0010.0000.0000.0000.000
202A219ASN 0-0.040-0.04132.7000.0040.0040.0000.0000.0000.000
203A220GLU -1-0.994-0.97836.251-0.033-0.0330.0000.0000.0000.000
204A221GLU -1-1.008-0.99430.821-0.045-0.0450.0000.0000.0000.000
205A222ASP -1-0.955-0.95334.135-0.018-0.0180.0000.0000.0000.000
206A223VAL 0-0.087-0.04129.1430.0020.0020.0000.0000.0000.000
207A224LEU 00.015-0.01530.963-0.001-0.0010.0000.0000.0000.000
208A225ASN 0-0.069-0.03325.3380.0030.0030.0000.0000.0000.000
209A226PHE 00.0550.01326.550-0.009-0.0090.0000.0000.0000.000
210A227ALA 0-0.0060.00924.9070.0060.0060.0000.0000.0000.000
211A228MET 0-0.007-0.00326.419-0.008-0.0080.0000.0000.0000.000
212A229LEU 0-0.0040.01223.0020.0060.0060.0000.0000.0000.000
213A230GLY 00.0030.00427.036-0.007-0.0070.0000.0000.0000.000
214A231LEU 0-0.0190.01125.7940.0040.0040.0000.0000.0000.000
215A232GLY 00.0470.00628.5300.0000.0000.0000.0000.0000.000
216A233PRO 0-0.025-0.01531.1450.0000.0000.0000.0000.0000.000
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