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: 8231Y

Calculation Name: 4M64-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4M64

Chain ID: B

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 426
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7375006.784286
FMO2-HF: Nuclear repulsion 7208319.555657
FMO2-HF: Total energy -166687.22863
FMO2-MP2: Total energy -167169.350987


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(B:1:MET)


Summations of interaction energy for fragment #1(B: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.
-6.432-0.231.994-2.444-5.753-0.003
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.042 / q_NPA : 0.003
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].
3B3ILE00.0980.0552.739-3.098-0.0110.461-1.222-2.3260.001
4B4SER00.0690.0243.009-0.6800.1210.072-0.191-0.6820.000
5B5MET0-0.0030.0274.6700.1640.358-0.001-0.022-0.1720.000
6B6THR00.022-0.0036.7180.1800.1800.0000.0000.0000.000
7B7THR0-0.032-0.0387.358-0.037-0.0370.0000.0000.0000.000
8B8LYS10.9351.0048.8850.2500.2500.0000.0000.0000.000
9B9LEU00.0590.01810.6710.0140.0140.0000.0000.0000.000
10B10SER0-0.038-0.02112.0900.0090.0090.0000.0000.0000.000
11B11TYR0-0.043-0.03012.643-0.016-0.0160.0000.0000.0000.000
12B12GLY00.013-0.00514.264-0.016-0.0160.0000.0000.0000.000
13B13PHE00.0610.00916.4310.0000.0000.0000.0000.0000.000
14B14GLY0-0.0040.04917.046-0.006-0.0060.0000.0000.0000.000
15B15ALA0-0.042-0.02418.517-0.010-0.0100.0000.0000.0000.000
16B16PHE00.0440.03020.318-0.003-0.0030.0000.0000.0000.000
17B17GLY00.010-0.03521.9820.0020.0020.0000.0000.0000.000
18B18LYS10.8390.92420.5420.0540.0540.0000.0000.0000.000
19B19ASP-1-0.817-0.93924.1690.0090.0090.0000.0000.0000.000
20B20PHE00.0490.04326.151-0.001-0.0010.0000.0000.0000.000
21B21ALA0-0.045-0.02627.496-0.001-0.0010.0000.0000.0000.000
22B22ILE0-0.0340.00427.113-0.005-0.0050.0000.0000.0000.000
23B23GLY0-0.016-0.02029.702-0.001-0.0010.0000.0000.0000.000
24B24ILE0-0.016-0.00831.308-0.001-0.0010.0000.0000.0000.000
25B25VAL00.0070.00032.432-0.001-0.0010.0000.0000.0000.000
26B26TYR0-0.018-0.00433.068-0.004-0.0040.0000.0000.0000.000
27B27MET0-0.009-0.00835.3530.0000.0000.0000.0000.0000.000
28B28TYR0-0.009-0.02137.7170.0010.0010.0000.0000.0000.000
29B29LEU0-0.018-0.00237.7790.0000.0000.0000.0000.0000.000
30B30MET00.0190.01140.8270.0000.0000.0000.0000.0000.000
31B31TYR0-0.032-0.00743.3980.0010.0010.0000.0000.0000.000
32B32TYR0-0.0490.02539.9590.0020.0020.0000.0000.0000.000
33B33TYR00.0540.04538.3990.0000.0000.0000.0000.0000.000
34B34THR00.014-0.00245.2470.0000.0000.0000.0000.0000.000
35B35ASP-1-0.884-0.95848.141-0.004-0.0040.0000.0000.0000.000
36B36VAL00.0900.08149.9980.0000.0000.0000.0000.0000.000
37B37VAL0-0.046-0.01751.1070.0000.0000.0000.0000.0000.000
38B38GLY00.0060.00751.9510.0000.0000.0000.0000.0000.000
39B39LEU0-0.009-0.03452.277-0.001-0.0010.0000.0000.0000.000
40B40SER0-0.007-0.04448.4360.0000.0000.0000.0000.0000.000
41B41VAL0-0.0080.04649.156-0.001-0.0010.0000.0000.0000.000
42B42GLY0-0.001-0.01248.901-0.001-0.0010.0000.0000.0000.000
43B43LEU0-0.010-0.00342.774-0.001-0.0010.0000.0000.0000.000
44B44VAL0-0.0040.00842.763-0.001-0.0010.0000.0000.0000.000
45B45GLY00.0150.00543.867-0.002-0.0020.0000.0000.0000.000
46B46THR00.002-0.00245.259-0.002-0.0020.0000.0000.0000.000
47B47LEU00.0340.03537.969-0.002-0.0020.0000.0000.0000.000
48B48PHE00.0670.00637.525-0.003-0.0030.0000.0000.0000.000
49B49LEU0-0.038-0.00240.443-0.003-0.0030.0000.0000.0000.000
50B50VAL00.0650.01538.363-0.003-0.0030.0000.0000.0000.000
51B51ALA00.054-0.01336.627-0.003-0.0030.0000.0000.0000.000
52B52ARG10.8960.96537.1590.0370.0370.0000.0000.0000.000
53B53ILE0-0.046-0.01639.329-0.003-0.0030.0000.0000.0000.000
54B54TRP0-0.040-0.00333.109-0.002-0.0020.0000.0000.0000.000
55B55ASP-1-0.925-0.96934.558-0.065-0.0650.0000.0000.0000.000
56B56ALA0-0.064-0.01835.673-0.004-0.0040.0000.0000.0000.000
57B57ILE0-0.055-0.01934.809-0.004-0.0040.0000.0000.0000.000
58B58ASN0-0.011-0.02028.564-0.008-0.0080.0000.0000.0000.000
59B59ASP-1-0.781-0.93330.274-0.095-0.0950.0000.0000.0000.000
60B60PRO0-0.012-0.01728.996-0.010-0.0100.0000.0000.0000.000
61B61ILE0-0.0170.00528.318-0.011-0.0110.0000.0000.0000.000
62B62MET00.0230.03323.901-0.004-0.0040.0000.0000.0000.000
63B63GLY0-0.039-0.04222.779-0.009-0.0090.0000.0000.0000.000
64B64TRP00.005-0.00422.953-0.019-0.0190.0000.0000.0000.000
65B65ILE00.0130.01323.347-0.011-0.0110.0000.0000.0000.000
66B66VAL0-0.036-0.02717.5470.0060.0060.0000.0000.0000.000
67B67ASN00.0230.01518.495-0.043-0.0430.0000.0000.0000.000
68B68ALA0-0.014-0.01019.758-0.004-0.0040.0000.0000.0000.000
69B69THR0-0.028-0.00423.0050.0100.0100.0000.0000.0000.000
70B70ARG10.9460.97219.1880.1340.1340.0000.0000.0000.000
71B71SER00.0080.00416.025-0.015-0.0150.0000.0000.0000.000
72B72ARG11.0411.01615.1700.3360.3360.0000.0000.0000.000
73B73TRP0-0.041-0.0118.5620.1310.1310.0000.0000.0000.000
74B74GLY00.0080.01112.1860.0190.0190.0000.0000.0000.000
75B75LYS10.9200.9669.0230.2370.2370.0000.0000.0000.000
76B76PHE00.051-0.00813.4650.0460.0460.0000.0000.0000.000
77B77LYS10.9670.95312.986-0.015-0.0150.0000.0000.0000.000
78B78PRO0-0.042-0.05414.7810.0220.0220.0000.0000.0000.000
79B79TRP00.0760.05717.4900.0060.0060.0000.0000.0000.000
80B80ILE00.0050.00514.9530.0000.0000.0000.0000.0000.000
81B81LEU0-0.0050.01117.4170.0110.0110.0000.0000.0000.000
82B82ILE0-0.044-0.00119.1440.0050.0050.0000.0000.0000.000
83B83GLY00.0870.05721.9250.0030.0030.0000.0000.0000.000
84B84THR00.0240.03020.3900.0070.0070.0000.0000.0000.000
85B85LEU00.018-0.00622.6600.0060.0060.0000.0000.0000.000
86B86THR00.0690.00825.1010.0020.0020.0000.0000.0000.000
87B87ASN00.0300.00526.594-0.004-0.0040.0000.0000.0000.000
88B88SER0-0.022-0.00527.2510.0020.0020.0000.0000.0000.000
89B89LEU00.027-0.00828.3940.0000.0000.0000.0000.0000.000
90B90VAL0-0.033-0.00430.7990.0000.0000.0000.0000.0000.000
91B91LEU00.0310.02131.1350.0000.0000.0000.0000.0000.000
92B92PHE00.0020.00031.7940.0030.0030.0000.0000.0000.000
93B93LEU0-0.047-0.02634.9060.0000.0000.0000.0000.0000.000
94B94LEU0-0.039-0.02835.9750.0000.0000.0000.0000.0000.000
95B95PHE00.0220.01137.4820.0010.0010.0000.0000.0000.000
96B96SER0-0.0170.00639.3920.0020.0020.0000.0000.0000.000
97B97ALA0-0.016-0.01841.4100.0000.0000.0000.0000.0000.000
98B98HIS00.0170.01241.078-0.001-0.0010.0000.0000.0000.000
99B99LEU0-0.0370.02144.3090.0010.0010.0000.0000.0000.000
100B100PHE0-0.046-0.01845.9290.0010.0010.0000.0000.0000.000
101B101GLU-1-0.912-0.97748.178-0.010-0.0100.0000.0000.0000.000
102B102GLY0-0.0160.00650.2580.0000.0000.0000.0000.0000.000
103B103THR0-0.056-0.02553.5990.0000.0000.0000.0000.0000.000
104B104ALA00.015-0.00553.8660.0000.0000.0000.0000.0000.000
105B105GLN00.0080.00451.513-0.001-0.0010.0000.0000.0000.000
106B106VAL00.0350.03746.000-0.001-0.0010.0000.0000.0000.000
107B107VAL0-0.033-0.01246.514-0.001-0.0010.0000.0000.0000.000
108B108PHE00.0230.00642.1680.0000.0000.0000.0000.0000.000
109B109VAL0-0.0200.00039.641-0.002-0.0020.0000.0000.0000.000
110B110CYS00.031-0.01539.423-0.001-0.0010.0000.0000.0000.000
111B111VAL00.0210.01236.794-0.002-0.0020.0000.0000.0000.000
112B112THR00.0360.01634.638-0.003-0.0030.0000.0000.0000.000
113B113TYR00.0650.04034.3040.0010.0010.0000.0000.0000.000
114B114ILE00.0410.00833.7010.0000.0000.0000.0000.0000.000
115B115LEU00.015-0.00229.578-0.005-0.0050.0000.0000.0000.000
116B116TRP0-0.0030.01430.2370.0000.0000.0000.0000.0000.000
117B117GLY00.0540.00830.246-0.002-0.0020.0000.0000.0000.000
118B118MET0-0.0200.02826.668-0.005-0.0050.0000.0000.0000.000
119B119THR0-0.193-0.13524.916-0.007-0.0070.0000.0000.0000.000
120B120TYR00.0300.00325.710-0.002-0.0020.0000.0000.0000.000
121B121THR00.0580.02127.181-0.003-0.0030.0000.0000.0000.000
122B122ILE0-0.053-0.02322.020-0.013-0.0130.0000.0000.0000.000
123B123MET0-0.096-0.05322.200-0.004-0.0040.0000.0000.0000.000
124B124ASP-1-0.857-0.92822.656-0.083-0.0830.0000.0000.0000.000
125B125ILE0-0.010-0.02719.678-0.009-0.0090.0000.0000.0000.000
126B126PRO0-0.0100.02118.052-0.023-0.0230.0000.0000.0000.000
127B127PHE0-0.001-0.02416.284-0.021-0.0210.0000.0000.0000.000
128B128TRP00.0260.02415.667-0.007-0.0070.0000.0000.0000.000
129B129SER00.0320.02414.975-0.011-0.0110.0000.0000.0000.000
130B130LEU0-0.0480.00011.097-0.076-0.0760.0000.0000.0000.000
131B131VAL00.0640.0098.107-0.041-0.0410.0000.0000.0000.000
132B132PRO0-0.077-0.0378.808-0.169-0.1690.0000.0000.0000.000
133B133THR0-0.004-0.01810.216-0.063-0.0630.0000.0000.0000.000
134B134ILE0-0.0380.0043.680-0.254-0.0230.002-0.035-0.1990.000
135B135THR0-0.022-0.0054.610-0.832-0.739-0.001-0.005-0.0870.000
136B136LEU00.0750.0405.4580.2190.2190.0000.0000.0000.000
137B137ASP-1-0.857-0.9167.3360.3430.3430.0000.0000.0000.000
138B138LYS10.8670.9429.7700.4790.4790.0000.0000.0000.000
139B139ARG10.9640.98213.1720.0460.0460.0000.0000.0000.000
140B140GLU-1-0.893-0.96011.2640.1870.1870.0000.0000.0000.000
141B141ARG10.8640.96810.4640.4090.4090.0000.0000.0000.000
142B142GLU-1-0.826-0.96811.453-0.155-0.1550.0000.0000.0000.000
143B143GLN00.0020.00113.2840.0180.0180.0000.0000.0000.000
144B144LEU0-0.005-0.0179.9420.0230.0230.0000.0000.0000.000
145B145VAL0-0.070-0.01513.101-0.021-0.0210.0000.0000.0000.000
146B146PRO0-0.029-0.02714.3790.0030.0030.0000.0000.0000.000
147B147PHE00.0010.02114.3750.0100.0100.0000.0000.0000.000
148B148PRO00.0130.00413.9540.0140.0140.0000.0000.0000.000
149B149ARG10.8710.94116.9360.0750.0750.0000.0000.0000.000
150B150PHE00.0450.03319.7990.0010.0010.0000.0000.0000.000
151B151PHE0-0.053-0.02219.8210.0020.0020.0000.0000.0000.000
152B152ALA00.0180.01321.0820.0000.0000.0000.0000.0000.000
153B153SER0-0.067-0.02722.906-0.005-0.0050.0000.0000.0000.000
154B154LEU00.0290.00626.175-0.001-0.0010.0000.0000.0000.000
155B155ALA00.0420.04027.9570.0000.0000.0000.0000.0000.000
156B156GLY00.0060.01829.7830.0000.0000.0000.0000.0000.000
157B157PHE00.0530.01832.4040.0000.0000.0000.0000.0000.000
158B158VAL0-0.0060.00132.1830.0010.0010.0000.0000.0000.000
159B159THR0-0.036-0.04432.4330.0030.0030.0000.0000.0000.000
160B160ALA00.011-0.01035.226-0.001-0.0010.0000.0000.0000.000
161B161GLY0-0.0380.00037.594-0.001-0.0010.0000.0000.0000.000
162B162ILE00.003-0.00538.4550.0000.0000.0000.0000.0000.000
163B163THR0-0.018-0.01436.1610.0010.0010.0000.0000.0000.000
164B164LEU00.0410.03239.3270.0000.0000.0000.0000.0000.000
165B165PRO00.011-0.00241.513-0.001-0.0010.0000.0000.0000.000
166B166PHE0-0.021-0.00341.3650.0000.0000.0000.0000.0000.000
167B167VAL00.0220.01041.8170.0000.0000.0000.0000.0000.000
168B168SER0-0.040-0.01843.802-0.001-0.0010.0000.0000.0000.000
169B169TYR0-0.027-0.00246.841-0.001-0.0010.0000.0000.0000.000
170B170VAL0-0.039-0.01644.6910.0000.0000.0000.0000.0000.000
171B171GLY0-0.041-0.01247.3050.0000.0000.0000.0000.0000.000
172B172GLY00.0120.00847.9530.0000.0000.0000.0000.0000.000
173B173ALA0-0.016-0.00750.9720.0000.0000.0000.0000.0000.000
174B174ASP-1-0.876-0.92849.4320.0010.0010.0000.0000.0000.000
175B175ARG10.8740.92246.3350.0010.0010.0000.0000.0000.000
176B176GLY00.002-0.04844.4030.0010.0010.0000.0000.0000.000
177B177PHE00.032-0.00743.5130.0000.0000.0000.0000.0000.000
178B178GLY00.0280.01443.6290.0020.0020.0000.0000.0000.000
179B179PHE00.0210.00437.0030.0030.0030.0000.0000.0000.000
180B180GLN00.004-0.02539.1690.0020.0020.0000.0000.0000.000
181B181MET00.0170.01638.1990.0010.0010.0000.0000.0000.000
182B182PHE00.026-0.00436.0760.0030.0030.0000.0000.0000.000
183B183THR00.0050.00334.8000.0000.0000.0000.0000.0000.000
184B184LEU00.0020.01033.9680.0000.0000.0000.0000.0000.000
185B185VAL0-0.011-0.01431.8730.0030.0030.0000.0000.0000.000
186B186LEU0-0.0130.01029.9500.0040.0040.0000.0000.0000.000
187B187ILE00.0320.02128.7200.0010.0010.0000.0000.0000.000
188B188ALA00.0460.03427.8180.0050.0050.0000.0000.0000.000
189B189PHE0-0.054-0.04326.8920.0090.0090.0000.0000.0000.000
190B190PHE0-0.0520.02522.734-0.001-0.0010.0000.0000.0000.000
191B191ILE0-0.087-0.04623.6640.0020.0020.0000.0000.0000.000
192B192ALA0-0.027-0.00323.4080.0090.0090.0000.0000.0000.000
193B193SER0-0.076-0.10020.3190.0140.0140.0000.0000.0000.000
194B194THR00.0400.00918.9050.0070.0070.0000.0000.0000.000
195B195ILE00.0090.00218.5360.0140.0140.0000.0000.0000.000
196B196VAL0-0.015-0.00114.7190.0260.0260.0000.0000.0000.000
197B197THR0-0.028-0.01514.0910.0330.0330.0000.0000.0000.000
198B198LEU0-0.060-0.02614.0820.0180.0180.0000.0000.0000.000
199B199ARG10.9460.96612.664-0.333-0.3330.0000.0000.0000.000
200B200ASN00.0280.0048.0430.0600.0600.0000.0000.0000.000
201B201VAL0-0.0140.0609.1020.1080.1080.0000.0000.0000.000
202B202HIS0-0.026-0.0259.533-0.120-0.1200.0000.0000.0000.000
203B203GLU-1-0.861-0.9456.2250.9040.9040.0000.0000.0000.000
204B204VAL0-0.033-0.0033.826-0.756-0.2400.017-0.102-0.4310.000
205B205TYR00.049-0.0044.1810.1500.7440.086-0.200-0.479-0.001
206B206SER0-0.0320.0056.669-0.312-0.3120.0000.0000.0000.000
207B207SER0-0.038-0.0252.290-0.833-0.3021.359-0.648-1.242-0.003
208B208ASP-1-0.864-0.9154.279-2.849-2.694-0.001-0.019-0.1350.000
209B209ASN0-0.041-0.0016.4660.4590.4590.0000.0000.0000.000
210B233LEU00.0160.01922.692-0.004-0.0040.0000.0000.0000.000
211B234SER00.053-0.01025.5440.0020.0020.0000.0000.0000.000
212B235CYS0-0.0400.00027.9400.0020.0020.0000.0000.0000.000
213B236LEU00.042-0.01423.5220.0070.0070.0000.0000.0000.000
214B237LEU00.0110.03426.5650.0070.0070.0000.0000.0000.000
215B238GLY00.0480.01629.1530.0060.0060.0000.0000.0000.000
216B239MET0-0.054-0.01428.6310.0050.0050.0000.0000.0000.000
217B240ALA0-0.026-0.01827.2750.0060.0060.0000.0000.0000.000
218B241LEU00.0050.02129.1160.0070.0070.0000.0000.0000.000
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