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: X6ZLZ

Calculation Name: 1A62-A-Xray41

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A62

Chain ID: A

ChEMBL ID:

UniProt ID: P0AG30

Base Structure: X-ray

Registration Date: 2019-02-15

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1233118.114675
FMO2-HF: Nuclear repulsion 1178743.828287
FMO2-HF: Total energy -54374.286389
FMO2-MP2: Total energy -54532.098009


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-15.87-4.0438.422-5.388-14.861-0.015
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.021
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].
3A3LEU00.0480.0183.822-1.2080.989-0.019-1.102-1.0750.000
4A4THR0-0.085-0.0205.6910.3280.3280.0000.0000.0000.000
5A5GLU-1-0.861-0.9164.7520.6530.871-0.001-0.008-0.2080.000
6A6LEU00.0130.0052.544-1.197-0.5732.405-0.542-2.4870.002
7A7LYS10.9110.9525.862-0.326-0.3260.0000.0000.0000.000
8A8ASN0-0.0280.0048.949-0.049-0.0490.0000.0000.0000.000
9A9THR0-0.015-0.0087.432-0.073-0.0730.0000.0000.0000.000
10A10PRO0-0.011-0.0029.7330.0710.0710.0000.0000.0000.000
11A11VAL00.0540.00311.5220.0450.0450.0000.0000.0000.000
12A12SER00.0020.00112.3670.0480.0480.0000.0000.0000.000
13A13GLU-1-0.857-0.9219.6430.0270.0270.0000.0000.0000.000
14A14LEU0-0.0130.0146.730-0.032-0.0320.0000.0000.0000.000
15A15ILE0-0.030-0.0128.1320.0440.0440.0000.0000.0000.000
16A16THR00.0180.0369.795-0.027-0.0270.0000.0000.0000.000
17A17LEU00.0220.0182.775-0.939-0.1250.677-0.206-1.2860.000
18A18GLY00.031-0.0095.721-0.311-0.3110.0000.0000.0000.000
19A19GLU-1-0.901-0.9467.086-0.164-0.1640.0000.0000.0000.000
20A20ASN0-0.0090.0067.4330.0810.0810.0000.0000.0000.000
21A21MET0-0.0400.0202.2270.0700.1611.184-0.214-1.062-0.002
22A22GLY00.0380.0297.3650.1340.1340.0000.0000.0000.000
23A23LEU0-0.0420.0117.5720.1170.1170.0000.0000.0000.000
24A24GLU-1-0.887-0.96511.084-0.051-0.0510.0000.0000.0000.000
25A25ASN0-0.093-0.06514.1520.0420.0420.0000.0000.0000.000
26A26LEU00.0960.0429.4580.0360.0360.0000.0000.0000.000
27A27ALA00.0140.00613.8530.0280.0280.0000.0000.0000.000
28A28ARG10.8870.96316.426-0.125-0.1250.0000.0000.0000.000
29A29MET0-0.036-0.00114.153-0.001-0.0010.0000.0000.0000.000
30A30ARG10.9810.98416.229-0.211-0.2110.0000.0000.0000.000
31A31LYS10.8950.94010.769-0.424-0.4240.0000.0000.0000.000
32A32GLN00.011-0.00111.4560.1070.1070.0000.0000.0000.000
33A33ASP-1-0.813-0.86811.6130.4560.4560.0000.0000.0000.000
34A34ILE0-0.0200.0048.9020.0710.0710.0000.0000.0000.000
35A35ILE00.0090.0106.2770.2420.2420.0000.0000.0000.000
36A36PHE00.006-0.0066.8080.5270.5270.0000.0000.0000.000
37A37ALA0-0.0220.0008.5740.0740.0740.0000.0000.0000.000
38A38ILE00.0820.0332.994-0.693-0.6341.699-0.380-1.3780.001
39A39LEU00.0230.0123.099-1.1430.0710.401-0.349-1.2660.000
40A40LYS10.8250.9045.132-1.359-1.327-0.001-0.002-0.0300.000
41A41GLN0-0.011-0.0066.398-0.188-0.1880.0000.0000.0000.000
42A42HIS00.0510.0232.760-3.687-0.6551.748-1.143-3.637-0.011
43A43ALA00.0210.0045.472-0.579-0.5790.0000.0000.0000.000
44A44LYS10.8210.9077.494-0.220-0.2200.0000.0000.0000.000
45A45SER0-0.066-0.0287.479-0.009-0.0090.0000.0000.0000.000
46A46GLY0-0.038-0.0129.554-0.055-0.0550.0000.0000.0000.000
47A47GLU-1-0.932-0.9585.293-2.043-2.0430.0000.0000.0000.000
48A48ASP-1-0.895-0.9504.903-0.244-0.2440.0000.0000.0000.000
49A49ILE0-0.050-0.0132.707-4.507-2.2580.250-0.985-1.513-0.007
50A50PHE0-0.034-0.0352.9570.2071.5040.079-0.457-0.9190.002
51A51GLY00.0180.0045.725-0.337-0.3370.0000.0000.0000.000
52A52ASP-1-0.835-0.9258.7840.2860.2860.0000.0000.0000.000
53A53GLY00.0540.03011.9620.0040.0040.0000.0000.0000.000
54A54VAL00.0110.01415.107-0.005-0.0050.0000.0000.0000.000
55A55LEU0-0.0090.00018.876-0.002-0.0020.0000.0000.0000.000
56A56GLU-1-0.822-0.88420.5730.0890.0890.0000.0000.0000.000
57A57ILE0-0.068-0.03223.1910.0000.0000.0000.0000.0000.000
58A58LEU00.008-0.00624.6360.0000.0000.0000.0000.0000.000
59A59GLN00.020-0.01327.316-0.006-0.0060.0000.0000.0000.000
60A60ASP-1-0.915-0.94828.3400.0470.0470.0000.0000.0000.000
61A61GLY0-0.0220.00128.535-0.004-0.0040.0000.0000.0000.000
62A62PHE0-0.071-0.03122.859-0.003-0.0030.0000.0000.0000.000
63A63GLY00.0520.00822.3780.0030.0030.0000.0000.0000.000
64A64PHE0-0.018-0.01617.769-0.002-0.0020.0000.0000.0000.000
65A65LEU0-0.0330.00414.026-0.003-0.0030.0000.0000.0000.000
66A66ARG10.8440.92715.798-0.108-0.1080.0000.0000.0000.000
67A67SER00.0820.03814.8280.0010.0010.0000.0000.0000.000
68A68ALA00.0410.03415.934-0.011-0.0110.0000.0000.0000.000
69A69ASP-1-0.959-0.97116.7310.1830.1830.0000.0000.0000.000
70A70SER0-0.019-0.02218.322-0.008-0.0080.0000.0000.0000.000
71A71SER0-0.040-0.01420.252-0.010-0.0100.0000.0000.0000.000
72A72TYR00.0090.01221.801-0.009-0.0090.0000.0000.0000.000
73A73LEU00.0050.02321.814-0.007-0.0070.0000.0000.0000.000
74A74ALA0-0.016-0.02020.5350.0100.0100.0000.0000.0000.000
75A75GLY00.0280.01017.8750.0030.0030.0000.0000.0000.000
76A76PRO00.0030.00315.907-0.006-0.0060.0000.0000.0000.000
77A77ASP-1-0.796-0.88611.4800.3420.3420.0000.0000.0000.000
78A78ASP-1-0.710-0.81912.7070.1410.1410.0000.0000.0000.000
79A79ILE0-0.0220.00910.5070.0020.0020.0000.0000.0000.000
80A80TYR00.006-0.01014.430-0.011-0.0110.0000.0000.0000.000
81A81VAL00.0220.01416.874-0.019-0.0190.0000.0000.0000.000
82A82SER00.0060.02719.0350.0020.0020.0000.0000.0000.000
83A83PRO00.0830.01821.6480.0000.0000.0000.0000.0000.000
84A84SER0-0.036-0.00922.4160.0020.0020.0000.0000.0000.000
85A85GLN0-0.027-0.03216.2950.0110.0110.0000.0000.0000.000
86A86ILE00.0610.03221.2240.0030.0030.0000.0000.0000.000
87A87ARG10.9030.94923.385-0.023-0.0230.0000.0000.0000.000
88A88ARG10.8720.95021.534-0.021-0.0210.0000.0000.0000.000
89A89PHE0-0.022-0.03118.731-0.002-0.0020.0000.0000.0000.000
90A90ASN0-0.0140.01423.2600.0080.0080.0000.0000.0000.000
91A91LEU0-0.0190.00519.8260.0030.0030.0000.0000.0000.000
92A92ARG10.8920.94323.933-0.064-0.0640.0000.0000.0000.000
93A93THR0-0.003-0.01024.1420.0050.0050.0000.0000.0000.000
94A94GLY00.0050.00123.791-0.003-0.0030.0000.0000.0000.000
95A95ASP-1-0.793-0.88921.2170.0870.0870.0000.0000.0000.000
96A96THR0-0.019-0.00116.7660.0020.0020.0000.0000.0000.000
97A97ILE0-0.057-0.02814.801-0.002-0.0020.0000.0000.0000.000
98A98SER00.0740.03511.182-0.003-0.0030.0000.0000.0000.000
99A99GLY00.014-0.00510.2160.0190.0190.0000.0000.0000.000
100A100LYS10.9090.9917.6120.2440.2440.0000.0000.0000.000
101A101ILE00.0180.0156.9820.1600.1600.0000.0000.0000.000
102A102ARG10.8660.9268.739-0.146-0.1460.0000.0000.0000.000
103A103PRO00.0320.0179.1480.0710.0710.0000.0000.0000.000
104A104PRO00.0050.04111.232-0.079-0.0790.0000.0000.0000.000
105A105LYS10.9540.97214.9570.0170.0170.0000.0000.0000.000
106A106GLU-1-0.864-0.92917.2770.0860.0860.0000.0000.0000.000
107A107GLY00.0100.02720.000-0.018-0.0180.0000.0000.0000.000
108A108GLU-1-0.796-0.86117.6250.0560.0560.0000.0000.0000.000
109A109ARG10.9670.97718.362-0.107-0.1070.0000.0000.0000.000
110A110TYR0-0.034-0.01915.3670.0260.0260.0000.0000.0000.000
111A111PHE00.0250.0368.379-0.030-0.0300.0000.0000.0000.000
112A112ALA0-0.039-0.01412.790-0.009-0.0090.0000.0000.0000.000
113A113LEU00.0410.02512.206-0.048-0.0480.0000.0000.0000.000
114A114LEU0-0.034-0.01110.5650.0160.0160.0000.0000.0000.000
115A115LYS10.8590.93511.801-0.026-0.0260.0000.0000.0000.000
116A116VAL00.0330.02912.3970.0040.0040.0000.0000.0000.000
117A117ASN0-0.009-0.0299.699-0.083-0.0830.0000.0000.0000.000
118A118GLU-1-0.854-0.92613.5980.2930.2930.0000.0000.0000.000
119A119VAL0-0.026-0.02015.775-0.010-0.0100.0000.0000.0000.000
120A120ASN0-0.050-0.05118.7840.0030.0030.0000.0000.0000.000
121A121PHE0-0.031-0.03416.681-0.008-0.0080.0000.0000.0000.000
122A122ASP-1-0.723-0.83218.1950.1210.1210.0000.0000.0000.000
123A123LYS10.9150.98018.186-0.084-0.0840.0000.0000.0000.000
124A124PRO0-0.051-0.02717.407-0.011-0.0110.0000.0000.0000.000
125A125GLU-1-1.040-1.03120.2040.0650.0650.0000.0000.0000.000
126A0NME00.001-0.00223.083-0.004-0.0040.0000.0000.0000.000
127A1001HOH00.0120.0017.295-0.103-0.1030.0000.0000.0000.000
128A1002HOH00.0310.02116.9500.0030.0030.0000.0000.0000.000
129A1003HOH0-0.038-0.02212.000-0.005-0.0050.0000.0000.0000.000
130A1004HOH00.0360.03025.3470.0000.0000.0000.0000.0000.000
131A1005HOH0-0.022-0.0227.471-0.137-0.1370.0000.0000.0000.000
132A1006HOH0-0.021-0.04613.7190.0120.0120.0000.0000.0000.000
133A1007HOH00.005-0.0059.406-0.031-0.0310.0000.0000.0000.000
134A1008HOH0-0.076-0.06824.910-0.002-0.0020.0000.0000.0000.000
135A1009HOH00.0140.01415.8180.0000.0000.0000.0000.0000.000
136A1011HOH00.0250.00814.7920.0220.0220.0000.0000.0000.000
137A1012HOH0-0.049-0.04317.268-0.002-0.0020.0000.0000.0000.000
138A1013HOH0-0.033-0.03512.243-0.011-0.0110.0000.0000.0000.000
139A1014HOH0-0.0030.0117.5710.1460.1460.0000.0000.0000.000
140A1015HOH0-0.042-0.03319.585-0.002-0.0020.0000.0000.0000.000
141A1016HOH0-0.050-0.02913.5360.0100.0100.0000.0000.0000.000
142A1017HOH0-0.026-0.02522.0280.0030.0030.0000.0000.0000.000
143A1018HOH00.0400.00924.0700.0020.0020.0000.0000.0000.000
144A1019HOH0-0.016-0.01919.429-0.003-0.0030.0000.0000.0000.000
145A1021HOH0-0.010-0.00314.5790.0000.0000.0000.0000.0000.000
146A1023HOH0-0.025-0.02212.594-0.021-0.0210.0000.0000.0000.000
147A1024HOH0-0.0040.0019.717-0.070-0.0700.0000.0000.0000.000
148A1026HOH0-0.067-0.05415.979-0.007-0.0070.0000.0000.0000.000
149A1032HOH00.0330.02313.9130.0200.0200.0000.0000.0000.000
150A1035HOH0-0.006-0.02210.793-0.026-0.0260.0000.0000.0000.000
151A1037HOH0-0.015-0.02819.464-0.001-0.0010.0000.0000.0000.000
152A1042HOH0-0.0050.00522.2180.0040.0040.0000.0000.0000.000
153A1043HOH0-0.013-0.00612.206-0.005-0.0050.0000.0000.0000.000
154A1048HOH00.0040.0016.729-0.187-0.1870.0000.0000.0000.000
155A1050HOH00.0080.00516.890-0.002-0.0020.0000.0000.0000.000
156A1052HOH0-0.046-0.03422.451-0.003-0.0030.0000.0000.0000.000
157A1061HOH0-0.034-0.0275.235-0.133-0.1330.0000.0000.0000.000
158A1075HOH0-0.033-0.01627.169-0.002-0.0020.0000.0000.0000.000
159A1077HOH0-0.039-0.03213.957-0.009-0.0090.0000.0000.0000.000
160A1079HOH0-0.026-0.01925.757-0.002-0.0020.0000.0000.0000.000
161A1089HOH0-0.013-0.01216.380-0.007-0.0070.0000.0000.0000.000
162A1107HOH0-0.025-0.02018.3480.0010.0010.0000.0000.0000.000
163A1120HOH00.0170.0295.879-0.066-0.0660.0000.0000.0000.000
164A1133HOH0-0.027-0.02516.2150.0080.0080.0000.0000.0000.000
165A1134HOH0-0.011-0.01426.217-0.001-0.0010.0000.0000.0000.000
166A1152HOH0-0.018-0.01410.2530.0180.0180.0000.0000.0000.000
167A2006HOH0-0.025-0.01818.675-0.008-0.0080.0000.0000.0000.000
168A2008HOH00.0230.01624.9920.0030.0030.0000.0000.0000.000
169A2059HOH0-0.041-0.0359.607-0.035-0.0350.0000.0000.0000.000
170A2096HOH0-0.0060.00428.1050.0010.0010.0000.0000.0000.000
171A3002HOH00.0060.00620.4620.0030.0030.0000.0000.0000.000
172A3011HOH0-0.036-0.0408.466-0.067-0.0670.0000.0000.0000.000
173A3012HOH0-0.072-0.04223.629-0.002-0.0020.0000.0000.0000.000
174A3016HOH00.004-0.00912.1340.0170.0170.0000.0000.0000.000
175A3022HOH0-0.041-0.02515.224-0.006-0.0060.0000.0000.0000.000
176A3037HOH0-0.054-0.03817.6600.0060.0060.0000.0000.0000.000
177A3053HOH00.001-0.00914.0270.0150.0150.0000.0000.0000.000
178A3203HOH0-0.022-0.01225.986-0.002-0.0020.0000.0000.0000.000
179A4001HOH00.000-0.01118.6450.0090.0090.0000.0000.0000.000
180A4015HOH00.0230.00915.001-0.003-0.0030.0000.0000.0000.000
181A4025HOH0-0.039-0.04917.1330.0050.0050.0000.0000.0000.000
182A4034HOH00.0160.00522.0610.0020.0020.0000.0000.0000.000
183A4035HOH00.0380.0229.033-0.025-0.0250.0000.0000.0000.000
184A4039HOH0-0.012-0.00913.7420.0010.0010.0000.0000.0000.000
185A4061HOH0-0.031-0.02527.095-0.001-0.0010.0000.0000.0000.000
186A4102HOH00.0370.02321.783-0.003-0.0030.0000.0000.0000.000
187A4111HOH00.0250.01520.7170.0040.0040.0000.0000.0000.000
188A4119HOH0-0.048-0.0408.6720.0940.0940.0000.0000.0000.000
189A4124HOH0-0.032-0.05213.142-0.017-0.0170.0000.0000.0000.000
190A5012HOH00.0080.01123.8230.0000.0000.0000.0000.0000.000
191A5013HOH00.0000.00728.6450.0010.0010.0000.0000.0000.000
192A5020HOH0-0.006-0.0108.4860.0420.0420.0000.0000.0000.000
193A5034HOH0-0.0090.0019.9850.0270.0270.0000.0000.0000.000
194A5058HOH0-0.048-0.05112.2090.0070.0070.0000.0000.0000.000
195A5061HOH0-0.028-0.01622.820-0.004-0.0040.0000.0000.0000.000
196A5084HOH00.0170.01926.5250.0010.0010.0000.0000.0000.000
197A5094HOH0-0.033-0.0169.6750.0280.0280.0000.0000.0000.000