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: 4926N

Calculation Name: 4M9R-B-Xray372

Preferred Name: Cell death protein 3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4M9R

Chain ID: B

ChEMBL ID: CHEMBL1250361

UniProt ID: P42573

Base Structure: X-ray

Registration Date: 2023-09-20

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

DOI:


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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2879582.239315
FMO2-HF: Nuclear repulsion 2788493.141356
FMO2-HF: Total energy -91089.097959
FMO2-MP2: Total energy -91348.623533


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:208:THR)


Summations of interaction energy for fragment #1(B:208:THR)
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.
-0.6581.256-0.028-0.862-1.023-0.001
Interaction energy analysis for fragmet #1(B:208:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / 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].
3B210TYR00.0350.0183.820-0.3401.535-0.027-0.862-0.986-0.001
4B211ILE00.005-0.0125.6490.0390.0390.0000.0000.0000.000
5B212PHE0-0.039-0.0118.6850.1000.1000.0000.0000.0000.000
6B213HIS0-0.0070.0028.8450.0020.0020.0000.0000.0000.000
7B214GLU-1-0.927-0.97113.443-0.076-0.0760.0000.0000.0000.000
8B215GLU-1-0.905-0.97614.800-0.084-0.0840.0000.0000.0000.000
9B216ASP-1-0.935-0.96211.525-0.051-0.0510.0000.0000.0000.000
10B217MET0-0.076-0.02014.8140.0060.0060.0000.0000.0000.000
11B218ASN0-0.054-0.02218.1400.0270.0270.0000.0000.0000.000
12B219PHE0-0.008-0.01820.622-0.008-0.0080.0000.0000.0000.000
13B220VAL0-0.052-0.01624.1320.0100.0100.0000.0000.0000.000
14B221ASP-1-0.816-0.88727.5150.0010.0010.0000.0000.0000.000
15B222ALA00.0660.01330.8230.0000.0000.0000.0000.0000.000
16B223PRO0-0.010-0.01033.7000.0000.0000.0000.0000.0000.000
17B224THR0-0.023-0.04330.4690.0020.0020.0000.0000.0000.000
18B225ILE00.0180.02130.4880.0000.0000.0000.0000.0000.000
19B226SER0-0.072-0.03633.779-0.001-0.0010.0000.0000.0000.000
20B227ARG10.8940.94932.747-0.009-0.0090.0000.0000.0000.000
21B228VAL0-0.043-0.02131.9210.0010.0010.0000.0000.0000.000
22B229PHE0-0.037-0.02035.189-0.002-0.0020.0000.0000.0000.000
23B230ASP-1-0.770-0.89836.519-0.009-0.0090.0000.0000.0000.000
24B231GLU-1-0.887-0.94938.457-0.018-0.0180.0000.0000.0000.000
25B232LYS10.8530.91440.0740.0130.0130.0000.0000.0000.000
26B233THR00.0350.01936.3460.0000.0000.0000.0000.0000.000
27B234MET0-0.0340.00233.305-0.002-0.0020.0000.0000.0000.000
28B235TYR0-0.075-0.08633.2670.0000.0000.0000.0000.0000.000
29B236ARG10.9410.97634.5910.0280.0280.0000.0000.0000.000
30B237ASN00.001-0.01129.019-0.005-0.0050.0000.0000.0000.000
31B238PHE00.004-0.04032.180-0.001-0.0010.0000.0000.0000.000
32B239SER0-0.0090.01833.8200.0010.0010.0000.0000.0000.000
33B240SER00.002-0.01333.003-0.001-0.0010.0000.0000.0000.000
34B241PRO00.0250.02530.893-0.001-0.0010.0000.0000.0000.000
35B242ARG10.8660.97427.9180.0530.0530.0000.0000.0000.000
36B243GLY00.0460.00230.3550.0050.0050.0000.0000.0000.000
37B244MET0-0.081-0.01629.998-0.003-0.0030.0000.0000.0000.000
38B245CYS00.0040.00023.7040.0000.0000.0000.0000.0000.000
39B246LEU0-0.0210.01826.767-0.006-0.0060.0000.0000.0000.000
40B247ILE00.0500.01020.800-0.002-0.0020.0000.0000.0000.000
41B248ILE0-0.032-0.03224.3810.0000.0000.0000.0000.0000.000
42B249ASN00.0500.03419.444-0.011-0.0110.0000.0000.0000.000
43B250ASN00.0410.03822.7860.0090.0090.0000.0000.0000.000
44B251GLU-1-0.870-0.94418.748-0.344-0.3440.0000.0000.0000.000
45B252HIS00.010-0.01422.0260.0010.0010.0000.0000.0000.000
46B253PHE0-0.053-0.02423.7170.0020.0020.0000.0000.0000.000
47B254GLU-1-0.973-0.97327.732-0.098-0.0980.0000.0000.0000.000
48B255GLN0-0.059-0.03330.8630.0040.0040.0000.0000.0000.000
49B256MET0-0.047-0.00925.9930.0020.0020.0000.0000.0000.000
50B257PRO00.006-0.00622.557-0.005-0.0050.0000.0000.0000.000
51B258THR00.0270.01420.353-0.001-0.0010.0000.0000.0000.000
52B259ARG10.7860.90518.5400.2600.2600.0000.0000.0000.000
53B260ASN00.0590.00715.229-0.017-0.0170.0000.0000.0000.000
54B261GLY0-0.047-0.04412.898-0.023-0.0230.0000.0000.0000.000
55B262THR00.0760.05813.524-0.047-0.0470.0000.0000.0000.000
56B263LYS10.8850.95814.1250.4920.4920.0000.0000.0000.000
57B264ALA00.0350.01811.1220.0170.0170.0000.0000.0000.000
58B265ASP-1-0.820-0.92012.445-0.600-0.6000.0000.0000.0000.000
59B266LYS10.9080.94914.2270.2820.2820.0000.0000.0000.000
60B267ASP-1-0.884-0.90714.860-0.336-0.3360.0000.0000.0000.000
61B268ASN00.0380.03010.2130.0840.0840.0000.0000.0000.000
62B269LEU00.008-0.00214.4120.0560.0560.0000.0000.0000.000
63B270THR0-0.063-0.07217.4120.0500.0500.0000.0000.0000.000
64B271ASN00.002-0.00414.5220.0630.0630.0000.0000.0000.000
65B272LEU00.0320.03516.2010.0360.0360.0000.0000.0000.000
66B273PHE00.005-0.03218.2590.0310.0310.0000.0000.0000.000
67B274ARG10.9380.97121.3120.1810.1810.0000.0000.0000.000
68B275CYS00.0260.04919.4110.0190.0190.0000.0000.0000.000
69B276MET0-0.074-0.03420.0580.0240.0240.0000.0000.0000.000
70B277GLY00.0120.01523.5720.0110.0110.0000.0000.0000.000
71B278TYR0-0.055-0.06425.2670.0080.0080.0000.0000.0000.000
72B279THR0-0.012-0.00726.136-0.006-0.0060.0000.0000.0000.000
73B280VAL0-0.017-0.00422.8570.0030.0030.0000.0000.0000.000
74B281ILE0-0.036-0.01726.0240.0030.0030.0000.0000.0000.000
75B282CYS0-0.0130.00923.601-0.012-0.0120.0000.0000.0000.000
76B283LYS10.9150.94125.8970.1330.1330.0000.0000.0000.000
77B284ASP-1-0.829-0.92223.136-0.220-0.2200.0000.0000.0000.000
78B285ASN00.001-0.01124.9320.0080.0080.0000.0000.0000.000
79B286LEU0-0.028-0.00227.2960.0120.0120.0000.0000.0000.000
80B287THR00.0260.00730.070-0.003-0.0030.0000.0000.0000.000
81B288GLY00.0640.01032.337-0.003-0.0030.0000.0000.0000.000
82B289ARG10.9530.96033.7970.0670.0670.0000.0000.0000.000
83B290GLY00.0460.02433.7860.0030.0030.0000.0000.0000.000
84B291MET00.0280.03727.3600.0010.0010.0000.0000.0000.000
85B292LEU00.0310.02732.2300.0020.0020.0000.0000.0000.000
86B293LEU0-0.019-0.01235.2820.0040.0040.0000.0000.0000.000
87B294THR00.0350.01030.8070.0010.0010.0000.0000.0000.000
88B295ILE00.007-0.00430.2060.0010.0010.0000.0000.0000.000
89B296ARG10.9210.96233.4520.0650.0650.0000.0000.0000.000
90B297ASP-1-0.922-0.96936.201-0.071-0.0710.0000.0000.0000.000
91B298PHE0-0.041-0.02430.3250.0020.0020.0000.0000.0000.000
92B299ALA00.0220.01034.5090.0030.0030.0000.0000.0000.000
93B300LYS10.9200.93936.7410.0640.0640.0000.0000.0000.000
94B301HIS00.024-0.00733.6470.0010.0010.0000.0000.0000.000
95B302GLU-1-0.883-0.91937.873-0.047-0.0470.0000.0000.0000.000
96B303SER0-0.074-0.03536.2040.0020.0020.0000.0000.0000.000
97B304HIS0-0.080-0.06133.623-0.003-0.0030.0000.0000.0000.000
98B305GLY00.0430.02434.2830.0040.0040.0000.0000.0000.000
99B306ASP-1-0.835-0.90933.951-0.042-0.0420.0000.0000.0000.000
100B307SER0-0.0130.00630.588-0.001-0.0010.0000.0000.0000.000
101B308ALA0-0.0140.00130.538-0.002-0.0020.0000.0000.0000.000
102B309ILE0-0.025-0.00623.9820.0020.0020.0000.0000.0000.000
103B310LEU0-0.0060.00726.917-0.002-0.0020.0000.0000.0000.000
104B311VAL00.0190.01320.523-0.002-0.0020.0000.0000.0000.000
105B312ILE0-0.031-0.00323.5480.0010.0010.0000.0000.0000.000
106B313LEU0-0.003-0.00517.960-0.007-0.0070.0000.0000.0000.000
107B314SER00.0060.00421.2510.0000.0000.0000.0000.0000.000
108B315HIS00.0640.03322.376-0.007-0.0070.0000.0000.0000.000
109B316GLY0-0.027-0.02724.2940.0100.0100.0000.0000.0000.000
110B317GLU-1-0.873-0.94325.290-0.106-0.1060.0000.0000.0000.000
111B318GLU-1-0.825-0.91526.796-0.095-0.0950.0000.0000.0000.000
112B319ASN0-0.067-0.02128.418-0.003-0.0030.0000.0000.0000.000
113B320VAL0-0.030-0.03029.8060.0040.0040.0000.0000.0000.000
114B321ILE0-0.041-0.02726.576-0.009-0.0090.0000.0000.0000.000
115B322ILE0-0.0280.00027.6550.0090.0090.0000.0000.0000.000
116B323GLY00.0260.01627.854-0.012-0.0120.0000.0000.0000.000
117B324VAL00.0230.01328.3300.0010.0010.0000.0000.0000.000
118B325ASP-1-0.801-0.92329.598-0.100-0.1000.0000.0000.0000.000
119B326ASP-1-0.773-0.90529.957-0.116-0.1160.0000.0000.0000.000
120B327ILE0-0.062-0.01831.9720.0070.0070.0000.0000.0000.000
121B328PRO0-0.040-0.02032.133-0.006-0.0060.0000.0000.0000.000
122B329ILE0-0.0080.01531.6550.0070.0070.0000.0000.0000.000
123B330SER00.0520.03232.239-0.004-0.0040.0000.0000.0000.000
124B331THR00.0380.01129.2090.0020.0020.0000.0000.0000.000
125B332HIS00.029-0.00631.8660.0000.0000.0000.0000.0000.000
126B333GLU-1-0.914-0.94734.976-0.069-0.0690.0000.0000.0000.000
127B334ILE0-0.009-0.01429.5100.0010.0010.0000.0000.0000.000
128B335TYR0-0.028-0.01528.1660.0020.0020.0000.0000.0000.000
129B336ASP-1-0.853-0.92234.057-0.056-0.0560.0000.0000.0000.000
130B337LEU0-0.109-0.04035.2280.0040.0040.0000.0000.0000.000
131B338LEU00.0040.00231.2130.0010.0010.0000.0000.0000.000
132B339ASN00.0430.03335.8630.0040.0040.0000.0000.0000.000
133B340ALA0-0.028-0.03338.6760.0000.0000.0000.0000.0000.000
134B341ALA0-0.082-0.04141.2860.0020.0020.0000.0000.0000.000
135B342ASN0-0.009-0.00439.9820.0040.0040.0000.0000.0000.000
136B343ALA00.0280.02137.884-0.002-0.0020.0000.0000.0000.000
137B344PRO00.0310.00539.7920.0010.0010.0000.0000.0000.000
138B345ARG10.7730.92439.6970.0550.0550.0000.0000.0000.000
139B346LEU00.0260.00734.324-0.001-0.0010.0000.0000.0000.000
140B347ALA00.0090.01337.9070.0010.0010.0000.0000.0000.000
141B348ASN0-0.095-0.05439.9340.0020.0020.0000.0000.0000.000
142B349LYS10.8480.95735.5870.0530.0530.0000.0000.0000.000
143B350PRO00.0040.02031.611-0.002-0.0020.0000.0000.0000.000
144B351LYS10.8300.91030.9830.0560.0560.0000.0000.0000.000
145B352ILE00.0090.01624.8750.0040.0040.0000.0000.0000.000
146B353VAL0-0.004-0.02026.415-0.007-0.0070.0000.0000.0000.000
147B354PHE00.0110.00920.5120.0030.0030.0000.0000.0000.000
148B355VAL0-0.012-0.01522.785-0.003-0.0030.0000.0000.0000.000
149B356GLN00.0300.01514.8340.0400.0400.0000.0000.0000.000
150B357ALA00.001-0.00119.934-0.011-0.0110.0000.0000.0000.000
151B358SER0-0.018-0.01619.251-0.009-0.0090.0000.0000.0000.000
152B359ARG10.9210.97421.1830.1220.1220.0000.0000.0000.000
153B407ARG10.9991.00146.3530.0240.0240.0000.0000.0000.000
154B408LYS10.9610.96048.0540.0260.0260.0000.0000.0000.000
155B409LYS10.8320.91239.3520.0380.0380.0000.0000.0000.000
156B410PRO00.0320.02041.9130.0000.0000.0000.0000.0000.000
157B411SER00.0400.01741.959-0.001-0.0010.0000.0000.0000.000
158B412GLN00.014-0.00537.743-0.004-0.0040.0000.0000.0000.000
159B413ALA0-0.012-0.00237.076-0.002-0.0020.0000.0000.0000.000
160B414ASP-1-0.762-0.83335.280-0.044-0.0440.0000.0000.0000.000
161B415ILE0-0.0050.00931.486-0.003-0.0030.0000.0000.0000.000
162B416LEU00.0060.00325.7800.0050.0050.0000.0000.0000.000
163B417ILE0-0.0060.00526.188-0.006-0.0060.0000.0000.0000.000
164B418ALA0-0.017-0.00821.7250.0070.0070.0000.0000.0000.000
165B419TYR00.0220.00022.849-0.018-0.0180.0000.0000.0000.000
166B420ALA00.0150.01618.0690.0080.0080.0000.0000.0000.000
167B421THR00.0140.00420.219-0.012-0.0120.0000.0000.0000.000
168B422THR0-0.027-0.00217.210-0.021-0.0210.0000.0000.0000.000
169B434GLY00.0350.0218.522-0.008-0.0080.0000.0000.0000.000
170B435SER0-0.086-0.0479.9730.0510.0510.0000.0000.0000.000
171B436TRP00.0750.0268.125-0.092-0.0920.0000.0000.0000.000
172B437PHE00.0260.01210.1040.0500.0500.0000.0000.0000.000
173B438ILE00.0070.01312.3560.0330.0330.0000.0000.0000.000
174B439GLN00.0080.0144.714-0.274-0.235-0.0010.000-0.0370.000
175B440ALA00.0350.01710.1370.0890.0890.0000.0000.0000.000
176B441VAL0-0.031-0.02111.9730.0620.0620.0000.0000.0000.000
177B442CYS0-0.024-0.00812.0030.0320.0320.0000.0000.0000.000
178B443GLU-1-0.909-0.9157.729-0.097-0.0970.0000.0000.0000.000
179B444VAL0-0.022-0.02112.2570.0490.0490.0000.0000.0000.000
180B445PHE0-0.024-0.02715.4820.0220.0220.0000.0000.0000.000
181B446SER00.007-0.02614.3530.0090.0090.0000.0000.0000.000
182B447THR0-0.020-0.00314.8680.0250.0250.0000.0000.0000.000
183B448HIS00.015-0.00717.4170.0030.0030.0000.0000.0000.000
184B449ALA0-0.0120.00120.036-0.001-0.0010.0000.0000.0000.000
185B450LYS10.8450.92121.837-0.032-0.0320.0000.0000.0000.000
186B451ASP-1-0.936-0.98223.6100.0220.0220.0000.0000.0000.000
187B452MET00.0130.02720.7520.0000.0000.0000.0000.0000.000
188B453ASP-1-0.877-0.95725.008-0.036-0.0360.0000.0000.0000.000
189B454VAL00.025-0.02223.679-0.001-0.0010.0000.0000.0000.000
190B455VAL0-0.0040.00023.853-0.007-0.0070.0000.0000.0000.000
191B456GLU-1-0.871-0.90324.364-0.010-0.0100.0000.0000.0000.000
192B457LEU0-0.0090.00820.0840.0000.0000.0000.0000.0000.000
193B458LEU00.016-0.01619.631-0.008-0.0080.0000.0000.0000.000
194B459THR0-0.038-0.03520.394-0.006-0.0060.0000.0000.0000.000
195B460GLU-1-0.906-0.96017.7010.0340.0340.0000.0000.0000.000
196B461VAL0-0.056-0.00615.6260.0010.0010.0000.0000.0000.000
197B462ASN00.040-0.00415.951-0.026-0.0260.0000.0000.0000.000
198B463LYS10.9400.97617.376-0.053-0.0530.0000.0000.0000.000
199B464LYS10.9250.95211.840-0.090-0.0900.0000.0000.0000.000
200B465VAL0-0.037-0.01612.743-0.005-0.0050.0000.0000.0000.000
201B466ALA0-0.0320.00013.8000.0000.0000.0000.0000.0000.000
202B467CYS0-0.086-0.04315.4050.0140.0140.0000.0000.0000.000
203B468GLY00.0020.02210.0940.0150.0150.0000.0000.0000.000
204B481MET0-0.046-0.03019.685-0.008-0.0080.0000.0000.0000.000
205B482PRO0-0.0180.00017.6350.0030.0030.0000.0000.0000.000
206B483GLU-1-0.910-0.94320.557-0.069-0.0690.0000.0000.0000.000
207B484MET0-0.040-0.01423.596-0.008-0.0080.0000.0000.0000.000
208B485THR00.0070.01125.6780.0110.0110.0000.0000.0000.000
209B486SER00.002-0.01029.278-0.004-0.0040.0000.0000.0000.000
210B487ARG10.8990.95231.0800.0650.0650.0000.0000.0000.000
211B488LEU0-0.0230.00029.9570.0020.0020.0000.0000.0000.000
212B489LEU0-0.053-0.04234.3050.0030.0030.0000.0000.0000.000
213B490LYS10.8090.93135.5080.0290.0290.0000.0000.0000.000
214B491LYS10.9390.98130.5260.0090.0090.0000.0000.0000.000
215B492PHE00.002-0.01526.8640.0020.0020.0000.0000.0000.000
216B493TYR00.0820.06527.169-0.003-0.0030.0000.0000.0000.000
217B494PHE00.0380.00523.745-0.003-0.0030.0000.0000.0000.000
218B495TRP00.002-0.00926.662-0.003-0.0030.0000.0000.0000.000
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