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: 527YZ

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 OptHSide
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 -2879006.898921
FMO2-HF: Nuclear repulsion 2787916.290719
FMO2-HF: Total energy -91090.608202
FMO2-MP2: Total energy -91350.073605


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.
0.272.131-0.029-0.86-0.973-0.001
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 : -0.025 / q_NPA : -0.025
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].
3B210TYR00.0170.0113.820-0.1691.692-0.029-0.860-0.973-0.001
4B211ILE00.000-0.0105.657-0.113-0.1130.0000.0000.0000.000
5B212PHE0-0.045-0.0158.6770.1350.1350.0000.0000.0000.000
6B213HIS0-0.017-0.0088.525-0.105-0.1050.0000.0000.0000.000
7B214GLU-1-0.923-0.97513.4310.2240.2240.0000.0000.0000.000
8B215GLU-1-0.895-0.96814.7970.4530.4530.0000.0000.0000.000
9B216ASP-1-0.913-0.95211.6760.6280.6280.0000.0000.0000.000
10B217MET0-0.082-0.01714.814-0.046-0.0460.0000.0000.0000.000
11B218ASN0-0.042-0.01318.116-0.007-0.0070.0000.0000.0000.000
12B219PHE0-0.011-0.01220.569-0.024-0.0240.0000.0000.0000.000
13B220VAL0-0.041-0.01224.096-0.002-0.0020.0000.0000.0000.000
14B221ASP-1-0.820-0.89327.4820.1120.1120.0000.0000.0000.000
15B222ALA00.0820.01430.777-0.006-0.0060.0000.0000.0000.000
16B223PRO00.0040.00833.915-0.007-0.0070.0000.0000.0000.000
17B224THR0-0.012-0.03130.111-0.008-0.0080.0000.0000.0000.000
18B225ILE00.0140.02230.625-0.006-0.0060.0000.0000.0000.000
19B226SER0-0.073-0.04833.776-0.007-0.0070.0000.0000.0000.000
20B227ARG10.8570.93432.502-0.088-0.0880.0000.0000.0000.000
21B228VAL0-0.046-0.02531.919-0.003-0.0030.0000.0000.0000.000
22B229PHE0-0.020-0.01135.182-0.005-0.0050.0000.0000.0000.000
23B230ASP-1-0.740-0.89436.5460.0290.0290.0000.0000.0000.000
24B231GLU-1-0.812-0.89838.5220.0320.0320.0000.0000.0000.000
25B232LYS10.8470.92740.164-0.025-0.0250.0000.0000.0000.000
26B233THR00.0500.02936.146-0.004-0.0040.0000.0000.0000.000
27B234MET0-0.0450.00133.8770.0000.0000.0000.0000.0000.000
28B235TYR0-0.077-0.06533.362-0.001-0.0010.0000.0000.0000.000
29B236ARG10.8440.92334.681-0.032-0.0320.0000.0000.0000.000
30B237ASN0-0.001-0.01829.074-0.005-0.0050.0000.0000.0000.000
31B238PHE00.008-0.00332.2570.0060.0060.0000.0000.0000.000
32B239SER0-0.019-0.01234.2930.0020.0020.0000.0000.0000.000
33B240SER0-0.028-0.02233.0320.0040.0040.0000.0000.0000.000
34B241PRO00.0140.02830.8890.0070.0070.0000.0000.0000.000
35B242ARG10.8740.91028.083-0.085-0.0850.0000.0000.0000.000
36B243GLY00.0500.00330.351-0.007-0.0070.0000.0000.0000.000
37B244MET0-0.081-0.01129.9790.0040.0040.0000.0000.0000.000
38B245CYS00.0120.00024.573-0.005-0.0050.0000.0000.0000.000
39B246LEU0-0.0290.01826.7660.0040.0040.0000.0000.0000.000
40B247ILE00.0330.00020.823-0.007-0.0070.0000.0000.0000.000
41B248ILE0-0.018-0.02724.4380.0050.0050.0000.0000.0000.000
42B249ASN00.0170.01120.194-0.033-0.0330.0000.0000.0000.000
43B250ASN00.0240.01722.9320.0200.0200.0000.0000.0000.000
44B251GLU-1-0.773-0.87718.636-0.227-0.2270.0000.0000.0000.000
45B252HIS0-0.006-0.02122.036-0.027-0.0270.0000.0000.0000.000
46B253PHE0-0.035-0.02123.5190.0110.0110.0000.0000.0000.000
47B254GLU-1-0.949-0.95427.997-0.089-0.0890.0000.0000.0000.000
48B255GLN0-0.078-0.04831.027-0.003-0.0030.0000.0000.0000.000
49B256MET0-0.040-0.00325.884-0.005-0.0050.0000.0000.0000.000
50B257PRO00.0070.00022.9020.0010.0010.0000.0000.0000.000
51B258THR00.0100.01120.3520.0020.0020.0000.0000.0000.000
52B259ARG10.8020.90318.6480.2030.2030.0000.0000.0000.000
53B260ASN00.041-0.00915.5480.0360.0360.0000.0000.0000.000
54B261GLY0-0.0010.00713.139-0.037-0.0370.0000.0000.0000.000
55B262THR00.0460.03113.7220.0010.0010.0000.0000.0000.000
56B263LYS10.8100.88415.2740.2490.2490.0000.0000.0000.000
57B264ALA00.0510.02711.2170.0510.0510.0000.0000.0000.000
58B265ASP-1-0.795-0.88112.368-0.359-0.3590.0000.0000.0000.000
59B266LYS10.8750.92514.3220.0780.0780.0000.0000.0000.000
60B267ASP-1-0.892-0.92914.9220.0670.0670.0000.0000.0000.000
61B268ASN00.0430.03210.2540.1500.1500.0000.0000.0000.000
62B269LEU00.0150.00014.4130.0300.0300.0000.0000.0000.000
63B270THR0-0.065-0.05217.3900.0140.0140.0000.0000.0000.000
64B271ASN00.001-0.00814.858-0.016-0.0160.0000.0000.0000.000
65B272LEU00.0290.03815.9960.0080.0080.0000.0000.0000.000
66B273PHE00.014-0.02918.2640.0040.0040.0000.0000.0000.000
67B274ARG10.9150.96521.317-0.094-0.0940.0000.0000.0000.000
68B275CYS0-0.0340.00719.4200.0050.0050.0000.0000.0000.000
69B276MET0-0.059-0.03220.999-0.002-0.0020.0000.0000.0000.000
70B277GLY0-0.0050.00523.618-0.011-0.0110.0000.0000.0000.000
71B278TYR0-0.049-0.04525.425-0.011-0.0110.0000.0000.0000.000
72B279THR0-0.003-0.00226.1340.0090.0090.0000.0000.0000.000
73B280VAL0-0.032-0.01122.802-0.010-0.0100.0000.0000.0000.000
74B281ILE0-0.037-0.01826.0220.0040.0040.0000.0000.0000.000
75B282CYS00.0100.01423.351-0.004-0.0040.0000.0000.0000.000
76B283LYS10.9260.94225.9790.0150.0150.0000.0000.0000.000
77B284ASP-1-0.799-0.88923.079-0.058-0.0580.0000.0000.0000.000
78B285ASN0-0.006-0.00524.816-0.008-0.0080.0000.0000.0000.000
79B286LEU0-0.0090.01327.4850.0100.0100.0000.0000.0000.000
80B287THR00.0170.00830.258-0.006-0.0060.0000.0000.0000.000
81B288GLY00.0700.01632.5120.0010.0010.0000.0000.0000.000
82B289ARG10.9450.95533.9810.0420.0420.0000.0000.0000.000
83B290GLY00.0400.02233.9450.0050.0050.0000.0000.0000.000
84B291MET00.0280.02828.3550.0050.0050.0000.0000.0000.000
85B292LEU00.0410.03332.3630.0070.0070.0000.0000.0000.000
86B293LEU0-0.018-0.01135.4010.0050.0050.0000.0000.0000.000
87B294THR00.0120.00930.8320.0060.0060.0000.0000.0000.000
88B295ILE00.006-0.00530.3670.0060.0060.0000.0000.0000.000
89B296ARG10.9290.96733.5240.0260.0260.0000.0000.0000.000
90B297ASP-1-0.814-0.90236.619-0.004-0.0040.0000.0000.0000.000
91B298PHE0-0.020-0.00830.1390.0050.0050.0000.0000.0000.000
92B299ALA00.0090.00634.5420.0050.0050.0000.0000.0000.000
93B300LYS10.7740.86736.7590.0070.0070.0000.0000.0000.000
94B301HIS00.019-0.00433.9600.0000.0000.0000.0000.0000.000
95B302GLU-1-0.811-0.85437.8720.0120.0120.0000.0000.0000.000
96B303SER0-0.081-0.03836.3800.0030.0030.0000.0000.0000.000
97B304HIS0-0.059-0.05633.4140.0070.0070.0000.0000.0000.000
98B305GLY00.0450.02534.2280.0010.0010.0000.0000.0000.000
99B306ASP-1-0.836-0.88433.9550.0350.0350.0000.0000.0000.000
100B307SER00.0040.00430.563-0.003-0.0030.0000.0000.0000.000
101B308ALA0-0.0140.00130.4780.0030.0030.0000.0000.0000.000
102B309ILE0-0.034-0.01123.932-0.003-0.0030.0000.0000.0000.000
103B310LEU0-0.0100.00326.9340.0030.0030.0000.0000.0000.000
104B311VAL00.0120.00920.509-0.005-0.0050.0000.0000.0000.000
105B312ILE0-0.019-0.00123.6410.0050.0050.0000.0000.0000.000
106B313LEU0-0.0030.00317.934-0.012-0.0120.0000.0000.0000.000
107B314SER00.0130.00521.3920.0060.0060.0000.0000.0000.000
108B315HIS00.0500.02822.162-0.020-0.0200.0000.0000.0000.000
109B316GLY0-0.025-0.01924.5120.0190.0190.0000.0000.0000.000
110B317GLU-1-0.835-0.91725.492-0.153-0.1530.0000.0000.0000.000
111B318GLU-1-0.827-0.92526.907-0.128-0.1280.0000.0000.0000.000
112B319ASN0-0.071-0.01628.5590.0090.0090.0000.0000.0000.000
113B320VAL0-0.018-0.01929.9510.0080.0080.0000.0000.0000.000
114B321ILE0-0.029-0.02026.411-0.009-0.0090.0000.0000.0000.000
115B322ILE0-0.0200.00027.9850.0110.0110.0000.0000.0000.000
116B323GLY00.0380.02028.056-0.006-0.0060.0000.0000.0000.000
117B324VAL00.012-0.00228.077-0.005-0.0050.0000.0000.0000.000
118B325ASP-1-0.780-0.90329.825-0.079-0.0790.0000.0000.0000.000
119B326ASP-1-0.791-0.91529.915-0.128-0.1280.0000.0000.0000.000
120B327ILE0-0.055-0.01132.2160.0030.0030.0000.0000.0000.000
121B328PRO0-0.029-0.01332.334-0.002-0.0020.0000.0000.0000.000
122B329ILE0-0.0060.00131.9150.0090.0090.0000.0000.0000.000
123B330SER00.0460.03532.396-0.007-0.0070.0000.0000.0000.000
124B331THR00.0350.00829.2180.0070.0070.0000.0000.0000.000
125B332HIS0-0.006-0.02731.9770.0100.0100.0000.0000.0000.000
126B333GLU-1-0.916-0.95335.067-0.045-0.0450.0000.0000.0000.000
127B334ILE00.002-0.00629.5070.0050.0050.0000.0000.0000.000
128B335TYR0-0.009-0.00829.1660.0050.0050.0000.0000.0000.000
129B336ASP-1-0.807-0.89934.109-0.028-0.0280.0000.0000.0000.000
130B337LEU0-0.080-0.01935.2260.0050.0050.0000.0000.0000.000
131B338LEU00.000-0.00531.2210.0050.0050.0000.0000.0000.000
132B339ASN00.0030.01235.8820.0070.0070.0000.0000.0000.000
133B340ALA0-0.017-0.02238.6840.0020.0020.0000.0000.0000.000
134B341ALA0-0.059-0.03341.2720.0020.0020.0000.0000.0000.000
135B342ASN0-0.065-0.03540.0780.0020.0020.0000.0000.0000.000
136B343ALA00.0220.01837.8190.0010.0010.0000.0000.0000.000
137B344PRO00.0320.00339.7740.0020.0020.0000.0000.0000.000
138B345ARG10.7780.87939.644-0.001-0.0010.0000.0000.0000.000
139B346LEU00.002-0.01134.3380.0030.0030.0000.0000.0000.000
140B347ALA00.0130.01637.854-0.001-0.0010.0000.0000.0000.000
141B348ASN0-0.089-0.03639.8430.0020.0020.0000.0000.0000.000
142B349LYS10.8760.96735.488-0.018-0.0180.0000.0000.0000.000
143B350PRO0-0.0020.00631.637-0.005-0.0050.0000.0000.0000.000
144B351LYS10.8210.93030.9440.0080.0080.0000.0000.0000.000
145B352ILE00.0090.01224.862-0.004-0.0040.0000.0000.0000.000
146B353VAL0-0.014-0.02326.4730.0020.0020.0000.0000.0000.000
147B354PHE00.0150.01220.183-0.003-0.0030.0000.0000.0000.000
148B355VAL0-0.003-0.01122.8650.0030.0030.0000.0000.0000.000
149B356GLN00.0140.00615.2610.0190.0190.0000.0000.0000.000
150B357ALA00.0160.00620.053-0.005-0.0050.0000.0000.0000.000
151B358SER0-0.021-0.01319.470-0.017-0.0170.0000.0000.0000.000
152B359ARG10.9020.95321.3970.1590.1590.0000.0000.0000.000
153B407ARG10.9920.99546.428-0.002-0.0020.0000.0000.0000.000
154B408LYS10.9600.96348.0010.0060.0060.0000.0000.0000.000
155B409LYS10.8190.89039.460-0.005-0.0050.0000.0000.0000.000
156B410PRO00.0360.01741.8960.0000.0000.0000.0000.0000.000
157B411SER00.0310.01141.9250.0010.0010.0000.0000.0000.000
158B412GLN00.013-0.00437.8720.0000.0000.0000.0000.0000.000
159B413ALA0-0.0010.00537.057-0.002-0.0020.0000.0000.0000.000
160B414ASP-1-0.769-0.84135.1940.0020.0020.0000.0000.0000.000
161B415ILE00.0020.00631.5830.0030.0030.0000.0000.0000.000
162B416LEU0-0.0050.00125.8520.0000.0000.0000.0000.0000.000
163B417ILE0-0.0080.00426.2240.0020.0020.0000.0000.0000.000
164B418ALA0-0.0030.00221.7270.0000.0000.0000.0000.0000.000
165B419TYR00.002-0.01122.884-0.009-0.0090.0000.0000.0000.000
166B420ALA00.0030.01118.148-0.003-0.0030.0000.0000.0000.000
167B421THR00.0190.00620.308-0.007-0.0070.0000.0000.0000.000
168B422THR0-0.0320.00116.587-0.039-0.0390.0000.0000.0000.000
169B434GLY00.0310.0208.8020.0510.0510.0000.0000.0000.000
170B435SER0-0.094-0.07710.163-0.102-0.1020.0000.0000.0000.000
171B436TRP00.0550.0207.887-0.035-0.0350.0000.0000.0000.000
172B437PHE00.0370.01310.1900.0900.0900.0000.0000.0000.000
173B438ILE00.0030.01412.6080.0520.0520.0000.0000.0000.000
174B439GLN00.0110.0114.953-0.270-0.2700.0000.0000.0000.000
175B440ALA00.0270.01310.0980.1190.1190.0000.0000.0000.000
176B441VAL0-0.028-0.02011.8770.0750.0750.0000.0000.0000.000
177B442CYS0-0.022-0.01111.8980.0410.0410.0000.0000.0000.000
178B443GLU-1-0.835-0.8758.0540.0980.0980.0000.0000.0000.000
179B444VAL0-0.029-0.02512.3320.0430.0430.0000.0000.0000.000
180B445PHE00.000-0.02015.5510.0120.0120.0000.0000.0000.000
181B446SER00.032-0.00314.5180.0130.0130.0000.0000.0000.000
182B447THR0-0.023-0.00414.7900.0280.0280.0000.0000.0000.000
183B448HIS00.023-0.01217.390-0.007-0.0070.0000.0000.0000.000
184B449ALA0-0.019-0.00120.070-0.017-0.0170.0000.0000.0000.000
185B450LYS10.7690.88721.347-0.181-0.1810.0000.0000.0000.000
186B451ASP-1-0.856-0.94823.1910.1230.1230.0000.0000.0000.000
187B452MET0-0.0390.00621.389-0.011-0.0110.0000.0000.0000.000
188B453ASP-1-0.826-0.91925.0460.0190.0190.0000.0000.0000.000
189B454VAL00.021-0.01323.687-0.003-0.0030.0000.0000.0000.000
190B455VAL00.0060.00223.733-0.009-0.0090.0000.0000.0000.000
191B456GLU-1-0.805-0.87824.4060.0300.0300.0000.0000.0000.000
192B457LEU0-0.0020.01319.978-0.005-0.0050.0000.0000.0000.000
193B458LEU00.010-0.01719.560-0.010-0.0100.0000.0000.0000.000
194B459THR0-0.033-0.02020.308-0.021-0.0210.0000.0000.0000.000
195B460GLU-1-0.880-0.95517.6410.0270.0270.0000.0000.0000.000
196B461VAL0-0.056-0.00715.321-0.015-0.0150.0000.0000.0000.000
197B462ASN0-0.019-0.03815.877-0.034-0.0340.0000.0000.0000.000
198B463LYS10.9280.97617.218-0.027-0.0270.0000.0000.0000.000
199B464LYS10.8530.90610.815-0.141-0.1410.0000.0000.0000.000
200B465VAL0-0.023-0.02012.714-0.041-0.0410.0000.0000.0000.000
201B466ALA0-0.0160.01213.782-0.037-0.0370.0000.0000.0000.000
202B467CYS0-0.084-0.04015.423-0.007-0.0070.0000.0000.0000.000
203B468GLY0-0.043-0.00210.149-0.105-0.1050.0000.0000.0000.000
204B481MET0-0.0020.00319.737-0.006-0.0060.0000.0000.0000.000
205B482PRO0-0.054-0.03317.3550.0120.0120.0000.0000.0000.000
206B483GLU-1-0.892-0.92620.599-0.084-0.0840.0000.0000.0000.000
207B484MET0-0.022-0.00523.2070.0050.0050.0000.0000.0000.000
208B485THR00.0110.01825.6620.0060.0060.0000.0000.0000.000
209B486SER00.017-0.00829.2700.0040.0040.0000.0000.0000.000
210B487ARG10.8770.93031.0350.0330.0330.0000.0000.0000.000
211B488LEU0-0.036-0.00429.8380.0040.0040.0000.0000.0000.000
212B489LEU0-0.050-0.04234.223-0.001-0.0010.0000.0000.0000.000
213B490LYS10.7720.89835.402-0.016-0.0160.0000.0000.0000.000
214B491LYS10.8490.91129.796-0.034-0.0340.0000.0000.0000.000
215B492PHE0-0.010-0.01927.0820.0020.0020.0000.0000.0000.000
216B493TYR00.0650.05527.298-0.006-0.0060.0000.0000.0000.000
217B494PHE00.0460.00723.842-0.004-0.0040.0000.0000.0000.000
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