FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 3QY2L

Calculation Name: 4M64-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M64

Chain ID: A

ChEMBL ID:

UniProt ID: P30878

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 448
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7998265.66223
FMO2-HF: Nuclear repulsion 7823675.161674
FMO2-HF: Total energy -174590.500555
FMO2-MP2: Total energy -175097.006273


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.
7.834-37.12973.229-8.776-19.4910.002
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 : 0.021 / q_NPA : 0.058
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].
3A3ILE00.0110.0052.1059.872-11.70138.290-6.197-10.520-0.009
4A4SER00.025-0.0112.0244.919-18.31632.909-3.694-5.9800.013
5A5MET00.0320.0213.746-1.554-2.8270.0051.889-0.6210.003
6A6THR0-0.033-0.0366.063-1.284-1.2840.0000.0000.0000.000
7A7THR0-0.044-0.0307.006-0.461-0.4610.0000.0000.0000.000
8A8LYS10.9710.9808.857-0.988-0.9880.0000.0000.0000.000
9A9LEU00.0340.01910.481-0.226-0.2260.0000.0000.0000.000
10A10SER00.0560.01812.030-0.164-0.1640.0000.0000.0000.000
11A11TYR0-0.044-0.00612.602-0.115-0.1150.0000.0000.0000.000
12A12GLY0-0.040-0.01014.409-0.112-0.1120.0000.0000.0000.000
13A13PHE00.0240.01216.310-0.065-0.0650.0000.0000.0000.000
14A14GLY00.0340.01517.138-0.057-0.0570.0000.0000.0000.000
15A15ALA0-0.076-0.04218.291-0.054-0.0540.0000.0000.0000.000
16A16PHE0-0.014-0.01320.104-0.035-0.0350.0000.0000.0000.000
17A17GLY00.0500.03121.685-0.027-0.0270.0000.0000.0000.000
18A18LYS10.9040.93418.497-0.303-0.3030.0000.0000.0000.000
19A19ASP-1-0.866-0.94123.2280.1840.1840.0000.0000.0000.000
20A20PHE00.0070.01125.426-0.021-0.0210.0000.0000.0000.000
21A21ALA0-0.025-0.04026.499-0.015-0.0150.0000.0000.0000.000
22A22ILE0-0.042-0.01726.429-0.014-0.0140.0000.0000.0000.000
23A23GLY00.0350.00929.103-0.013-0.0130.0000.0000.0000.000
24A24ILE0-0.015-0.01131.094-0.012-0.0120.0000.0000.0000.000
25A25VAL00.0100.01831.581-0.009-0.0090.0000.0000.0000.000
26A26TYR0-0.036-0.00132.802-0.009-0.0090.0000.0000.0000.000
27A27MET0-0.0290.00134.761-0.009-0.0090.0000.0000.0000.000
28A28TYR0-0.046-0.05036.788-0.006-0.0060.0000.0000.0000.000
29A29LEU00.022-0.00237.039-0.006-0.0060.0000.0000.0000.000
30A30MET0-0.0220.01739.531-0.004-0.0040.0000.0000.0000.000
31A31TYR00.0320.00141.799-0.004-0.0040.0000.0000.0000.000
32A32TYR00.006-0.03342.318-0.001-0.0010.0000.0000.0000.000
33A33TYR0-0.071-0.02543.835-0.004-0.0040.0000.0000.0000.000
34A34THR0-0.056-0.02445.350-0.004-0.0040.0000.0000.0000.000
35A35ASP-1-0.856-0.90346.2020.0580.0580.0000.0000.0000.000
36A36VAL0-0.0390.00945.206-0.001-0.0010.0000.0000.0000.000
37A37VAL00.0190.00847.774-0.002-0.0020.0000.0000.0000.000
38A38GLY0-0.031-0.01248.525-0.001-0.0010.0000.0000.0000.000
39A39LEU00.0020.00249.371-0.002-0.0020.0000.0000.0000.000
40A40SER0-0.0090.00651.118-0.001-0.0010.0000.0000.0000.000
41A41VAL0-0.022-0.02446.060-0.002-0.0020.0000.0000.0000.000
42A42GLY00.0490.00846.1260.0030.0030.0000.0000.0000.000
43A43LEU0-0.0030.02547.1970.0010.0010.0000.0000.0000.000
44A44VAL00.0770.03145.2050.0010.0010.0000.0000.0000.000
45A45GLY00.011-0.00244.7540.0000.0000.0000.0000.0000.000
46A46THR00.0470.00445.117-0.001-0.0010.0000.0000.0000.000
47A47LEU00.0360.02239.9170.0000.0000.0000.0000.0000.000
48A48PHE00.0140.01240.6610.0010.0010.0000.0000.0000.000
49A49LEU0-0.060-0.02540.292-0.001-0.0010.0000.0000.0000.000
50A50VAL0-0.007-0.00437.459-0.002-0.0020.0000.0000.0000.000
51A51ALA00.051-0.00436.4100.0010.0010.0000.0000.0000.000
52A52ARG10.8860.95536.055-0.016-0.0160.0000.0000.0000.000
53A53ILE0-0.056-0.03434.387-0.004-0.0040.0000.0000.0000.000
54A54TRP0-0.0430.00833.0740.0020.0020.0000.0000.0000.000
55A55ASP-1-0.893-0.93630.2800.0410.0410.0000.0000.0000.000
56A56ALA0-0.014-0.01529.559-0.002-0.0020.0000.0000.0000.000
57A57ILE00.028-0.00829.430-0.004-0.0040.0000.0000.0000.000
58A58ASN00.0700.02625.491-0.001-0.0010.0000.0000.0000.000
59A59ASP-1-0.781-0.93422.9090.0440.0440.0000.0000.0000.000
60A60PRO0-0.087-0.03323.562-0.010-0.0100.0000.0000.0000.000
61A61ILE00.018-0.00923.831-0.012-0.0120.0000.0000.0000.000
62A62MET00.0080.03721.204-0.008-0.0080.0000.0000.0000.000
63A63GLY0-0.016-0.01519.0240.0000.0000.0000.0000.0000.000
64A64TRP0-0.087-0.03119.027-0.028-0.0280.0000.0000.0000.000
65A65ILE0-0.078-0.02218.805-0.010-0.0100.0000.0000.0000.000
66A66VAL0-0.0180.00313.852-0.014-0.0140.0000.0000.0000.000
67A67ASN0-0.038-0.01813.7910.0010.0010.0000.0000.0000.000
68A68ALA00.0190.00816.1980.0110.0110.0000.0000.0000.000
69A69THR00.0030.00318.533-0.016-0.0160.0000.0000.0000.000
70A70ARG10.9390.96721.1600.0810.0810.0000.0000.0000.000
71A71SER0-0.0050.01019.1080.0060.0060.0000.0000.0000.000
72A72ARG11.0291.01216.1400.1990.1990.0000.0000.0000.000
73A73TRP00.036-0.02013.469-0.071-0.0710.0000.0000.0000.000
74A74GLY00.0040.00512.5250.0440.0440.0000.0000.0000.000
75A75LYS10.8620.9606.588-0.646-0.6460.0000.0000.0000.000
76A76PHE00.0870.03610.5310.0680.0680.0000.0000.0000.000
77A77LYS10.8410.95711.021-0.492-0.4920.0000.0000.0000.000
78A78PRO00.031-0.00512.783-0.001-0.0010.0000.0000.0000.000
79A79TRP00.1270.04714.686-0.013-0.0130.0000.0000.0000.000
80A80ILE00.014-0.00713.660-0.001-0.0010.0000.0000.0000.000
81A81LEU0-0.087-0.01216.6750.0130.0130.0000.0000.0000.000
82A82ILE0-0.021-0.00418.286-0.015-0.0150.0000.0000.0000.000
83A83GLY00.0730.05119.958-0.025-0.0250.0000.0000.0000.000
84A84THR0-0.019-0.02219.357-0.020-0.0200.0000.0000.0000.000
85A85LEU00.017-0.01721.672-0.012-0.0120.0000.0000.0000.000
86A86THR0-0.063-0.04023.904-0.020-0.0200.0000.0000.0000.000
87A87ASN00.0250.01225.497-0.020-0.0200.0000.0000.0000.000
88A88SER00.014-0.01026.484-0.006-0.0060.0000.0000.0000.000
89A89LEU0-0.0290.00727.929-0.006-0.0060.0000.0000.0000.000
90A90VAL00.0250.03330.024-0.006-0.0060.0000.0000.0000.000
91A91LEU0-0.030-0.00431.283-0.004-0.0040.0000.0000.0000.000
92A92PHE00.024-0.00731.860-0.001-0.0010.0000.0000.0000.000
93A93LEU0-0.056-0.01333.695-0.006-0.0060.0000.0000.0000.000
94A94LEU0-0.041-0.02035.824-0.005-0.0050.0000.0000.0000.000
95A95PHE0-0.036-0.02435.852-0.002-0.0020.0000.0000.0000.000
96A96SER00.008-0.00337.769-0.005-0.0050.0000.0000.0000.000
97A97ALA0-0.016-0.00439.548-0.003-0.0030.0000.0000.0000.000
98A98HIS00.0390.02042.739-0.001-0.0010.0000.0000.0000.000
99A99LEU0-0.003-0.00446.1730.0000.0000.0000.0000.0000.000
100A100PHE00.013-0.01141.986-0.003-0.0030.0000.0000.0000.000
101A101GLU-1-0.880-0.94345.8360.0570.0570.0000.0000.0000.000
102A102GLY0-0.033-0.00647.459-0.002-0.0020.0000.0000.0000.000
103A103THR0-0.077-0.03447.302-0.003-0.0030.0000.0000.0000.000
104A104ALA00.0320.01948.0860.0010.0010.0000.0000.0000.000
105A105GLN00.0680.00444.5760.0000.0000.0000.0000.0000.000
106A106VAL0-0.061-0.02244.4280.0010.0010.0000.0000.0000.000
107A107VAL00.0300.01944.1190.0000.0000.0000.0000.0000.000
108A108PHE00.0030.00240.4870.0000.0000.0000.0000.0000.000
109A109VAL00.0240.01139.4600.0030.0030.0000.0000.0000.000
110A110CYS00.0130.00938.9690.0020.0020.0000.0000.0000.000
111A111VAL00.0280.00735.6450.0020.0020.0000.0000.0000.000
112A112THR0-0.0210.00434.6650.0060.0060.0000.0000.0000.000
113A113TYR00.0000.00433.6870.0060.0060.0000.0000.0000.000
114A114ILE00.026-0.00431.2790.0020.0020.0000.0000.0000.000
115A115LEU00.0010.01029.2400.0030.0030.0000.0000.0000.000
116A116TRP00.0740.00528.8760.0100.0100.0000.0000.0000.000
117A117GLY00.0140.01629.1550.0050.0050.0000.0000.0000.000
118A118MET00.0150.00725.9420.0000.0000.0000.0000.0000.000
119A119THR0-0.018-0.01924.1830.0070.0070.0000.0000.0000.000
120A120TYR0-0.0180.00324.4010.0080.0080.0000.0000.0000.000
121A121THR00.0610.04224.396-0.004-0.0040.0000.0000.0000.000
122A122ILE0-0.092-0.03719.742-0.002-0.0020.0000.0000.0000.000
123A123MET0-0.043-0.05320.0080.0410.0410.0000.0000.0000.000
124A124ASP-1-0.849-0.92220.1760.1240.1240.0000.0000.0000.000
125A125ILE0-0.033-0.00717.6610.0050.0050.0000.0000.0000.000
126A126PRO0-0.0120.01215.6560.0070.0070.0000.0000.0000.000
127A127PHE00.043-0.00114.7480.0450.0450.0000.0000.0000.000
128A128TRP00.0130.01115.3490.0580.0580.0000.0000.0000.000
129A129SER00.0530.08714.819-0.048-0.0480.0000.0000.0000.000
130A130LEU0-0.0140.0028.575-0.021-0.0210.0000.0000.0000.000
131A131VAL0-0.031-0.00410.1810.1730.1730.0000.0000.0000.000
132A132PRO0-0.004-0.01711.1130.0790.0790.0000.0000.0000.000
133A133THR0-0.047-0.0247.344-0.013-0.0130.0000.0000.0000.000
134A134ILE0-0.026-0.0166.784-0.091-0.0910.0000.0000.0000.000
135A135THR00.0210.0013.413-0.368-0.0280.005-0.083-0.2620.000
136A136LEU00.0450.0024.430-0.0840.116-0.001-0.009-0.1900.000
137A137ASP-1-0.925-0.9427.489-0.632-0.6320.0000.0000.0000.000
138A138LYS10.9500.9669.5690.5770.5770.0000.0000.0000.000
139A139ARG10.8710.93213.1170.3440.3440.0000.0000.0000.000
140A140GLU-1-0.863-0.93312.934-0.039-0.0390.0000.0000.0000.000
141A141ARG10.8390.90713.3570.2340.2340.0000.0000.0000.000
142A142GLU-1-0.901-0.97214.2330.0310.0310.0000.0000.0000.000
143A143GLN0-0.011-0.02516.9670.0510.0510.0000.0000.0000.000
144A144LEU00.0290.01912.6800.0340.0340.0000.0000.0000.000
145A145VAL0-0.0290.00215.1120.0770.0770.0000.0000.0000.000
146A146PRO0-0.010-0.01316.5070.0330.0330.0000.0000.0000.000
147A147PHE00.0210.00117.7540.0030.0030.0000.0000.0000.000
148A148PRO0-0.024-0.00416.3860.0140.0140.0000.0000.0000.000
149A149ARG10.8840.95618.886-0.198-0.1980.0000.0000.0000.000
150A150PHE00.0150.01121.519-0.005-0.0050.0000.0000.0000.000
151A151PHE00.0750.03622.194-0.013-0.0130.0000.0000.0000.000
152A152ALA0-0.010-0.01123.073-0.008-0.0080.0000.0000.0000.000
153A153SER0-0.044-0.03024.817-0.020-0.0200.0000.0000.0000.000
154A154LEU00.0120.00826.804-0.013-0.0130.0000.0000.0000.000
155A155ALA00.0410.02328.010-0.011-0.0110.0000.0000.0000.000
156A156GLY00.0290.01429.872-0.008-0.0080.0000.0000.0000.000
157A157PHE0-0.063-0.02431.908-0.010-0.0100.0000.0000.0000.000
158A158VAL0-0.0070.00032.896-0.007-0.0070.0000.0000.0000.000
159A159THR0-0.010-0.00632.873-0.006-0.0060.0000.0000.0000.000
160A160ALA00.013-0.01135.601-0.005-0.0050.0000.0000.0000.000
161A161GLY0-0.0020.01438.484-0.006-0.0060.0000.0000.0000.000
162A162ILE00.025-0.00237.678-0.004-0.0040.0000.0000.0000.000
163A163THR00.016-0.00137.0210.0000.0000.0000.0000.0000.000
164A164LEU00.0290.01939.644-0.002-0.0020.0000.0000.0000.000
165A165PRO00.0240.00042.461-0.003-0.0030.0000.0000.0000.000
166A166PHE0-0.037-0.00841.001-0.002-0.0020.0000.0000.0000.000
167A167VAL0-0.036-0.01641.0760.0000.0000.0000.0000.0000.000
168A168SER0-0.065-0.02943.424-0.003-0.0030.0000.0000.0000.000
169A169TYR0-0.0210.00546.864-0.004-0.0040.0000.0000.0000.000
170A170VAL0-0.034-0.02044.752-0.002-0.0020.0000.0000.0000.000
171A171GLY00.0520.02647.968-0.002-0.0020.0000.0000.0000.000
172A172GLY0-0.033-0.01649.0010.0010.0010.0000.0000.0000.000
173A173ALA0-0.015-0.00550.561-0.002-0.0020.0000.0000.0000.000
174A174ASP-1-0.817-0.90047.9960.0620.0620.0000.0000.0000.000
175A175ARG10.8840.90644.371-0.058-0.0580.0000.0000.0000.000
176A176GLY00.0120.03243.2110.0050.0050.0000.0000.0000.000
177A177PHE00.0480.01342.4590.0040.0040.0000.0000.0000.000
178A178GLY0-0.025-0.00943.5750.0040.0040.0000.0000.0000.000
179A179PHE0-0.021-0.02834.5760.0070.0070.0000.0000.0000.000
180A180GLN00.0190.06038.3450.0080.0080.0000.0000.0000.000
181A181MET00.0000.01938.8730.0070.0070.0000.0000.0000.000
182A182PHE00.014-0.01637.3540.0080.0080.0000.0000.0000.000
183A183THR0-0.003-0.03133.2860.0110.0110.0000.0000.0000.000
184A184LEU00.0060.00733.1590.0150.0150.0000.0000.0000.000
185A185VAL0-0.026-0.00432.6210.0140.0140.0000.0000.0000.000
186A186LEU0-0.0070.02028.6500.0150.0150.0000.0000.0000.000
187A187ILE00.011-0.00328.8390.0210.0210.0000.0000.0000.000
188A188ALA00.0190.03727.6930.0220.0220.0000.0000.0000.000
189A189PHE00.0060.00026.1770.0250.0250.0000.0000.0000.000
190A190PHE0-0.014-0.00922.9350.0360.0360.0000.0000.0000.000
191A191ILE0-0.001-0.01523.5630.0280.0280.0000.0000.0000.000
192A192ALA00.005-0.01222.8810.0290.0290.0000.0000.0000.000
193A193SER00.001-0.00919.0820.0440.0440.0000.0000.0000.000
194A194THR0-0.0510.01018.8670.0630.0630.0000.0000.0000.000
195A195ILE00.0360.04319.5530.0260.0260.0000.0000.0000.000
196A196VAL0-0.056-0.02315.3210.0470.0470.0000.0000.0000.000
197A197THR0-0.011-0.05514.5060.0760.0760.0000.0000.0000.000
198A198LEU0-0.020-0.00314.5310.0770.0770.0000.0000.0000.000
199A199ARG10.9680.99015.152-0.543-0.5430.0000.0000.0000.000
200A200ASN0-0.0030.00311.561-0.025-0.0250.0000.0000.0000.000
201A201VAL00.0080.0059.7050.2500.2500.0000.0000.0000.000
202A202HIS0-0.078-0.0558.4750.0820.0820.0000.0000.0000.000
203A203GLU-1-0.771-0.8834.9221.7831.7830.0000.0000.0000.000
204A204VAL0-0.007-0.0272.119-0.869-0.9741.990-0.379-1.506-0.003
205A205TYR00.0100.0424.133-0.571-0.4990.000-0.008-0.0650.000
206A206SER00.0540.0166.769-0.125-0.1250.0000.0000.0000.000
207A207SER0-0.052-0.0323.420-1.222-0.6110.031-0.295-0.347-0.002
208A208ASP-1-0.887-0.9615.559-0.844-0.8440.0000.0000.0000.000
209A209ASN00.0240.0258.1450.1790.1790.0000.0000.0000.000
210A210GLY0-0.060-0.0279.6310.0780.0780.0000.0000.0000.000
211A211VAL0-0.027-0.0128.2060.0730.0730.0000.0000.0000.000
212A212THR00.003-0.00110.8230.0330.0330.0000.0000.0000.000
213A213ALA0-0.066-0.02113.1690.0750.0750.0000.0000.0000.000
214A214GLY00.0860.02312.8660.0250.0250.0000.0000.0000.000
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