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: YZ392

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 OptAll
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 -2881290.255245
FMO2-HF: Nuclear repulsion 2790198.898466
FMO2-HF: Total energy -91091.356779
FMO2-MP2: Total energy -91350.746001


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.
0.8362.13-0.016-0.552-0.7260
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 : -0.022 / 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].
3B210TYR0-0.031-0.0203.8670.6661.960-0.016-0.552-0.7260.000
4B211ILE0-0.026-0.0215.813-0.201-0.2010.0000.0000.0000.000
5B212PHE0-0.018-0.0089.0250.1420.1420.0000.0000.0000.000
6B213HIS0-0.032-0.0108.575-0.126-0.1260.0000.0000.0000.000
7B214GLU-1-0.931-0.97213.6090.2000.2000.0000.0000.0000.000
8B215GLU-1-0.913-0.97815.0340.4500.4500.0000.0000.0000.000
9B216ASP-1-0.835-0.90911.6020.6330.6330.0000.0000.0000.000
10B217MET0-0.090-0.02314.585-0.044-0.0440.0000.0000.0000.000
11B218ASN0-0.054-0.01718.044-0.009-0.0090.0000.0000.0000.000
12B219PHE0-0.007-0.01020.722-0.026-0.0260.0000.0000.0000.000
13B220VAL0-0.058-0.02424.300-0.001-0.0010.0000.0000.0000.000
14B221ASP-1-0.784-0.85727.9890.1060.1060.0000.0000.0000.000
15B222ALA00.0800.02231.273-0.006-0.0060.0000.0000.0000.000
16B223PRO0-0.0060.00034.351-0.007-0.0070.0000.0000.0000.000
17B224THR0-0.023-0.05130.414-0.007-0.0070.0000.0000.0000.000
18B225ILE0-0.0130.00630.980-0.005-0.0050.0000.0000.0000.000
19B226SER0-0.069-0.05933.999-0.007-0.0070.0000.0000.0000.000
20B227ARG10.8430.93832.742-0.090-0.0900.0000.0000.0000.000
21B228VAL0-0.024-0.00931.896-0.002-0.0020.0000.0000.0000.000
22B229PHE0-0.007-0.01635.285-0.005-0.0050.0000.0000.0000.000
23B230ASP-1-0.749-0.88136.7220.0270.0270.0000.0000.0000.000
24B231GLU-1-0.819-0.89938.8020.0280.0280.0000.0000.0000.000
25B232LYS10.8250.92541.042-0.025-0.0250.0000.0000.0000.000
26B233THR00.034-0.00136.324-0.004-0.0040.0000.0000.0000.000
27B234MET0-0.0440.01234.1600.0000.0000.0000.0000.0000.000
28B235TYR0-0.076-0.06733.558-0.002-0.0020.0000.0000.0000.000
29B236ARG10.8270.90735.004-0.027-0.0270.0000.0000.0000.000
30B237ASN0-0.004-0.03029.309-0.006-0.0060.0000.0000.0000.000
31B238PHE00.0070.00132.5240.0060.0060.0000.0000.0000.000
32B239SER0-0.0040.00134.6100.0020.0020.0000.0000.0000.000
33B240SER0-0.027-0.01633.2840.0040.0040.0000.0000.0000.000
34B241PRO00.0200.03730.9390.0070.0070.0000.0000.0000.000
35B242ARG10.8590.89828.113-0.077-0.0770.0000.0000.0000.000
36B243GLY00.023-0.00130.741-0.006-0.0060.0000.0000.0000.000
37B244MET0-0.067-0.01429.8290.0040.0040.0000.0000.0000.000
38B245CYS00.0150.00424.709-0.004-0.0040.0000.0000.0000.000
39B246LEU0-0.0090.02826.6340.0010.0010.0000.0000.0000.000
40B247ILE00.028-0.00321.215-0.006-0.0060.0000.0000.0000.000
41B248ILE0-0.002-0.00124.6180.0030.0030.0000.0000.0000.000
42B249ASN00.024-0.00420.152-0.034-0.0340.0000.0000.0000.000
43B250ASN00.0230.02922.9850.0160.0160.0000.0000.0000.000
44B251GLU-1-0.734-0.86218.264-0.315-0.3150.0000.0000.0000.000
45B252HIS0-0.010-0.01421.823-0.025-0.0250.0000.0000.0000.000
46B253PHE0-0.040-0.02423.3850.0080.0080.0000.0000.0000.000
47B254GLU-1-0.932-0.95628.132-0.107-0.1070.0000.0000.0000.000
48B255GLN0-0.072-0.03630.6610.0000.0000.0000.0000.0000.000
49B256MET0-0.063-0.01125.591-0.005-0.0050.0000.0000.0000.000
50B257PRO0-0.0030.00122.9950.0000.0000.0000.0000.0000.000
51B258THR0-0.001-0.00820.424-0.003-0.0030.0000.0000.0000.000
52B259ARG10.8120.92018.8520.2280.2280.0000.0000.0000.000
53B260ASN0-0.032-0.03616.6620.0210.0210.0000.0000.0000.000
54B261GLY00.0360.02113.787-0.089-0.0890.0000.0000.0000.000
55B262THR00.0080.00714.2170.0130.0130.0000.0000.0000.000
56B263LYS10.7870.88615.4790.3540.3540.0000.0000.0000.000
57B264ALA00.0770.03911.6150.0530.0530.0000.0000.0000.000
58B265ASP-1-0.799-0.86712.569-0.450-0.4500.0000.0000.0000.000
59B266LYS10.8350.89114.6130.1250.1250.0000.0000.0000.000
60B267ASP-1-0.885-0.93315.458-0.002-0.0020.0000.0000.0000.000
61B268ASN00.0250.01610.3840.1670.1670.0000.0000.0000.000
62B269LEU00.0140.00314.5820.0400.0400.0000.0000.0000.000
63B270THR0-0.070-0.05617.7450.0190.0190.0000.0000.0000.000
64B271ASN00.0070.00015.408-0.009-0.0090.0000.0000.0000.000
65B272LEU00.0350.03716.2240.0110.0110.0000.0000.0000.000
66B273PHE00.015-0.02318.3310.0060.0060.0000.0000.0000.000
67B274ARG10.8920.94221.725-0.057-0.0570.0000.0000.0000.000
68B275CYS0-0.0180.01519.7650.0060.0060.0000.0000.0000.000
69B276MET0-0.041-0.02421.2930.0000.0000.0000.0000.0000.000
70B277GLY00.0240.02123.749-0.008-0.0080.0000.0000.0000.000
71B278TYR0-0.072-0.04725.572-0.010-0.0100.0000.0000.0000.000
72B279THR00.006-0.01426.1940.0060.0060.0000.0000.0000.000
73B280VAL0-0.032-0.00822.748-0.011-0.0110.0000.0000.0000.000
74B281ILE0-0.053-0.01725.9880.0060.0060.0000.0000.0000.000
75B282CYS00.0240.02422.912-0.004-0.0040.0000.0000.0000.000
76B283LYS10.9060.93625.7160.0380.0380.0000.0000.0000.000
77B284ASP-1-0.760-0.86222.822-0.103-0.1030.0000.0000.0000.000
78B285ASN0-0.016-0.01124.513-0.006-0.0060.0000.0000.0000.000
79B286LEU00.0160.02927.3840.0090.0090.0000.0000.0000.000
80B287THR00.0400.02630.256-0.007-0.0070.0000.0000.0000.000
81B288GLY00.0810.02232.7870.0030.0030.0000.0000.0000.000
82B289ARG10.9630.96633.7340.0540.0540.0000.0000.0000.000
83B290GLY00.0460.02334.4950.0060.0060.0000.0000.0000.000
84B291MET00.0040.01828.3230.0050.0050.0000.0000.0000.000
85B292LEU00.0200.02232.4500.0060.0060.0000.0000.0000.000
86B293LEU0-0.046-0.02935.5230.0060.0060.0000.0000.0000.000
87B294THR0-0.010-0.01631.2610.0060.0060.0000.0000.0000.000
88B295ILE00.0150.00630.3240.0060.0060.0000.0000.0000.000
89B296ARG10.9220.97233.7040.0360.0360.0000.0000.0000.000
90B297ASP-1-0.810-0.89936.917-0.015-0.0150.0000.0000.0000.000
91B298PHE0-0.013-0.00530.3150.0050.0050.0000.0000.0000.000
92B299ALA00.0130.00834.9360.0050.0050.0000.0000.0000.000
93B300LYS10.7890.86837.2090.0190.0190.0000.0000.0000.000
94B301HIS00.008-0.00234.4270.0000.0000.0000.0000.0000.000
95B302GLU-1-0.797-0.84638.1990.0030.0030.0000.0000.0000.000
96B303SER0-0.086-0.04836.2610.0030.0030.0000.0000.0000.000
97B304HIS0-0.058-0.03933.3600.0070.0070.0000.0000.0000.000
98B305GLY00.0730.03434.5500.0000.0000.0000.0000.0000.000
99B306ASP-1-0.820-0.88434.3520.0290.0290.0000.0000.0000.000
100B307SER00.0020.00931.087-0.003-0.0030.0000.0000.0000.000
101B308ALA0-0.017-0.00730.6740.0030.0030.0000.0000.0000.000
102B309ILE0-0.031-0.00224.268-0.003-0.0030.0000.0000.0000.000
103B310LEU0-0.028-0.01426.8390.0020.0020.0000.0000.0000.000
104B311VAL00.0170.01420.563-0.004-0.0040.0000.0000.0000.000
105B312ILE0-0.016-0.00923.3030.0050.0050.0000.0000.0000.000
106B313LEU0-0.0040.01017.873-0.014-0.0140.0000.0000.0000.000
107B314SER0-0.013-0.03021.2690.0040.0040.0000.0000.0000.000
108B315HIS00.0540.02322.161-0.020-0.0200.0000.0000.0000.000
109B316GLY0-0.044-0.03724.4750.0200.0200.0000.0000.0000.000
110B317GLU-1-0.842-0.90725.517-0.163-0.1630.0000.0000.0000.000
111B318GLU-1-0.838-0.92626.875-0.138-0.1380.0000.0000.0000.000
112B319ASN0-0.036-0.00528.3800.0130.0130.0000.0000.0000.000
113B320VAL0-0.018-0.00830.0430.0090.0090.0000.0000.0000.000
114B321ILE0-0.032-0.01826.170-0.011-0.0110.0000.0000.0000.000
115B322ILE0-0.0060.01127.7430.0120.0120.0000.0000.0000.000
116B323GLY00.0250.01528.118-0.006-0.0060.0000.0000.0000.000
117B324VAL0-0.018-0.02228.400-0.007-0.0070.0000.0000.0000.000
118B325ASP-1-0.763-0.90129.890-0.099-0.0990.0000.0000.0000.000
119B326ASP-1-0.776-0.90529.545-0.152-0.1520.0000.0000.0000.000
120B327ILE0-0.047-0.00931.9490.0030.0030.0000.0000.0000.000
121B328PRO0-0.025-0.00732.323-0.003-0.0030.0000.0000.0000.000
122B329ILE0-0.037-0.01132.2990.0090.0090.0000.0000.0000.000
123B330SER00.0330.02332.475-0.007-0.0070.0000.0000.0000.000
124B331THR0-0.015-0.02428.9850.0060.0060.0000.0000.0000.000
125B332HIS00.003-0.01831.8260.0090.0090.0000.0000.0000.000
126B333GLU-1-0.892-0.94734.842-0.057-0.0570.0000.0000.0000.000
127B334ILE00.018-0.00129.4420.0060.0060.0000.0000.0000.000
128B335TYR00.0140.00628.9090.0050.0050.0000.0000.0000.000
129B336ASP-1-0.803-0.88133.957-0.033-0.0330.0000.0000.0000.000
130B337LEU0-0.108-0.04135.3900.0060.0060.0000.0000.0000.000
131B338LEU00.0210.00531.5090.0050.0050.0000.0000.0000.000
132B339ASN0-0.004-0.00836.0340.0080.0080.0000.0000.0000.000
133B340ALA0-0.005-0.02938.8440.0010.0010.0000.0000.0000.000
134B341ALA0-0.050-0.02341.3200.0020.0020.0000.0000.0000.000
135B342ASN0-0.052-0.02740.1190.0020.0020.0000.0000.0000.000
136B343ALA00.0220.02537.8770.0010.0010.0000.0000.0000.000
137B344PRO00.015-0.00239.8970.0030.0030.0000.0000.0000.000
138B345ARG10.7850.87239.4100.0080.0080.0000.0000.0000.000
139B346LEU00.0120.00334.3560.0030.0030.0000.0000.0000.000
140B347ALA00.0190.01638.033-0.001-0.0010.0000.0000.0000.000
141B348ASN0-0.095-0.04440.3080.0020.0020.0000.0000.0000.000
142B349LYS10.8520.95435.756-0.008-0.0080.0000.0000.0000.000
143B350PRO0-0.0080.00431.767-0.005-0.0050.0000.0000.0000.000
144B351LYS10.7960.91431.2880.0170.0170.0000.0000.0000.000
145B352ILE0-0.0080.00125.150-0.004-0.0040.0000.0000.0000.000
146B353VAL00.002-0.01026.6230.0010.0010.0000.0000.0000.000
147B354PHE00.0280.01420.371-0.004-0.0040.0000.0000.0000.000
148B355VAL0-0.026-0.01922.4140.0020.0020.0000.0000.0000.000
149B356GLN00.0290.01015.3920.0260.0260.0000.0000.0000.000
150B357ALA00.0270.02119.899-0.012-0.0120.0000.0000.0000.000
151B358SER0-0.043-0.02819.625-0.030-0.0300.0000.0000.0000.000
152B359ARG10.9370.97621.5670.1700.1700.0000.0000.0000.000
153B407ARG10.9941.00046.4090.0010.0010.0000.0000.0000.000
154B408LYS10.9510.95948.2520.0090.0090.0000.0000.0000.000
155B409LYS10.8110.87739.8100.0020.0020.0000.0000.0000.000
156B410PRO00.0390.02141.7980.0000.0000.0000.0000.0000.000
157B411SER00.0080.00641.9450.0010.0010.0000.0000.0000.000
158B412GLN00.019-0.00238.128-0.001-0.0010.0000.0000.0000.000
159B413ALA00.0190.02037.140-0.002-0.0020.0000.0000.0000.000
160B414ASP-1-0.725-0.82335.289-0.004-0.0040.0000.0000.0000.000
161B415ILE0-0.0190.00131.8420.0010.0010.0000.0000.0000.000
162B416LEU0-0.008-0.00525.8530.0020.0020.0000.0000.0000.000
163B417ILE0-0.017-0.00826.4560.0010.0010.0000.0000.0000.000
164B418ALA0-0.0080.01121.8610.0000.0000.0000.0000.0000.000
165B419TYR00.0280.00922.535-0.015-0.0150.0000.0000.0000.000
166B420ALA00.0130.01318.432-0.001-0.0010.0000.0000.0000.000
167B421THR00.0000.00020.279-0.002-0.0020.0000.0000.0000.000
168B422THR0-0.019-0.00516.490-0.037-0.0370.0000.0000.0000.000
169B434GLY00.0310.0198.5290.0610.0610.0000.0000.0000.000
170B435SER0-0.092-0.0859.740-0.157-0.1570.0000.0000.0000.000
171B436TRP00.0250.0067.799-0.009-0.0090.0000.0000.0000.000
172B437PHE00.0220.00710.3040.0840.0840.0000.0000.0000.000
173B438ILE00.0090.01412.7810.0630.0630.0000.0000.0000.000
174B439GLN00.0110.0055.208-0.309-0.3090.0000.0000.0000.000
175B440ALA00.0200.01310.2610.1280.1280.0000.0000.0000.000
176B441VAL0-0.025-0.01912.2170.0750.0750.0000.0000.0000.000
177B442CYS0-0.0140.00211.9490.0480.0480.0000.0000.0000.000
178B443GLU-1-0.798-0.8628.4010.0520.0520.0000.0000.0000.000
179B444VAL0-0.0210.00312.6780.0520.0520.0000.0000.0000.000
180B445PHE0-0.015-0.02416.0440.0130.0130.0000.0000.0000.000
181B446SER00.045-0.01014.8270.0120.0120.0000.0000.0000.000
182B447THR0-0.037-0.01814.9120.0360.0360.0000.0000.0000.000
183B448HIS00.017-0.01917.398-0.002-0.0020.0000.0000.0000.000
184B449ALA0-0.0080.00120.502-0.016-0.0160.0000.0000.0000.000
185B450LYS10.7660.88921.456-0.180-0.1800.0000.0000.0000.000
186B451ASP-1-0.824-0.93023.5940.1240.1240.0000.0000.0000.000
187B452MET0-0.0410.00221.487-0.010-0.0100.0000.0000.0000.000
188B453ASP-1-0.779-0.90625.2160.0160.0160.0000.0000.0000.000
189B454VAL0-0.006-0.01124.237-0.003-0.0030.0000.0000.0000.000
190B455VAL00.0150.00924.154-0.010-0.0100.0000.0000.0000.000
191B456GLU-1-0.794-0.86824.6400.0330.0330.0000.0000.0000.000
192B457LEU0-0.0060.00120.363-0.003-0.0030.0000.0000.0000.000
193B458LEU00.025-0.00119.754-0.011-0.0110.0000.0000.0000.000
194B459THR0-0.020-0.01520.383-0.019-0.0190.0000.0000.0000.000
195B460GLU-1-0.791-0.88317.8590.0310.0310.0000.0000.0000.000
196B461VAL0-0.053-0.01115.542-0.011-0.0110.0000.0000.0000.000
197B462ASN0-0.025-0.04015.861-0.032-0.0320.0000.0000.0000.000
198B463LYS10.8230.89717.051-0.060-0.0600.0000.0000.0000.000
199B464LYS10.8510.91111.096-0.130-0.1300.0000.0000.0000.000
200B465VAL0-0.007-0.00712.482-0.038-0.0380.0000.0000.0000.000
201B466ALA0-0.042-0.01013.669-0.030-0.0300.0000.0000.0000.000
202B467CYS0-0.068-0.03415.2040.0020.0020.0000.0000.0000.000
203B468GLY0-0.042-0.0069.855-0.079-0.0790.0000.0000.0000.000
204B481MET00.0070.00919.374-0.005-0.0050.0000.0000.0000.000
205B482PRO0-0.043-0.02817.4340.0090.0090.0000.0000.0000.000
206B483GLU-1-0.857-0.89420.590-0.080-0.0800.0000.0000.0000.000
207B484MET0-0.003-0.01322.8300.0040.0040.0000.0000.0000.000
208B485THR0-0.009-0.00525.7920.0140.0140.0000.0000.0000.000
209B486SER00.008-0.00329.3880.0030.0030.0000.0000.0000.000
210B487ARG10.8750.92531.1170.0400.0400.0000.0000.0000.000
211B488LEU0-0.0260.00029.8480.0040.0040.0000.0000.0000.000
212B489LEU0-0.066-0.04234.219-0.001-0.0010.0000.0000.0000.000
213B490LYS10.8000.91435.269-0.013-0.0130.0000.0000.0000.000
214B491LYS10.8250.90229.596-0.035-0.0350.0000.0000.0000.000
215B492PHE0-0.019-0.03627.6520.0020.0020.0000.0000.0000.000
216B493TYR00.0660.05327.600-0.006-0.0060.0000.0000.0000.000
217B494PHE00.0370.00324.207-0.006-0.0060.0000.0000.0000.000
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