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: 3JQNL

Calculation Name: 5CDD-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CDD

Chain ID: C

ChEMBL ID:

UniProt ID: D1FK67

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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2176216.598405
FMO2-HF: Nuclear repulsion 2098234.99076
FMO2-HF: Total energy -77981.607645
FMO2-MP2: Total energy -78210.811722


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(C:59:ASP)


Summations of interaction energy for fragment #1(C:59:ASP)
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.
-63.576-54.1940.643-4.728-5.2980.033
Interaction energy analysis for fragmet #1(C:59:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.784 / q_NPA : -0.893
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].
3C61HIS00.0150.0112.769-21.478-14.9830.218-3.392-3.3210.033
4C62SER0-0.033-0.0292.526-11.487-9.0210.425-1.204-1.6870.000
5C63ILE0-0.002-0.0044.137-6.616-6.1950.000-0.132-0.2900.000
6C64ILE00.0400.0086.390-4.451-4.4510.0000.0000.0000.000
7C65GLN00.0170.0017.230-3.731-3.7310.0000.0000.0000.000
8C66PHE0-0.053-0.0348.331-2.413-2.4130.0000.0000.0000.000
9C67LEU00.001-0.00510.216-2.310-2.3100.0000.0000.0000.000
10C68GLN0-0.030-0.00211.730-2.304-2.3040.0000.0000.0000.000
11C69ARG10.8930.96410.801-22.066-22.0660.0000.0000.0000.000
12C70PRO00.0280.02715.169-0.080-0.0800.0000.0000.0000.000
13C71VAL0-0.041-0.01417.9500.1220.1220.0000.0000.0000.000
14C72LEU00.000-0.00820.581-0.142-0.1420.0000.0000.0000.000
15C73ILE0-0.064-0.03021.7430.1460.1460.0000.0000.0000.000
16C74ASP-1-0.830-0.92725.2019.6119.6110.0000.0000.0000.000
17C75ASN0-0.004-0.00428.8950.4070.4070.0000.0000.0000.000
18C76ILE0-0.083-0.03731.704-0.197-0.1970.0000.0000.0000.000
19C77GLU-1-0.787-0.90834.9957.6077.6070.0000.0000.0000.000
20C78ILE0-0.052-0.02438.305-0.130-0.1300.0000.0000.0000.000
21C79ILE00.035-0.00441.060-0.071-0.0710.0000.0000.0000.000
22C80ALA00.019-0.00544.589-0.057-0.0570.0000.0000.0000.000
23C81GLY00.0020.02747.316-0.111-0.1110.0000.0000.0000.000
24C82THR0-0.035-0.04248.0340.0820.0820.0000.0000.0000.000
25C83THR0-0.0300.00449.209-0.091-0.0910.0000.0000.0000.000
26C84ALA00.0540.04345.978-0.048-0.0480.0000.0000.0000.000
27C85ASP-1-0.907-0.96945.0326.7256.7250.0000.0000.0000.000
28C86ALA0-0.042-0.04242.5540.1580.1580.0000.0000.0000.000
29C87ALA00.0350.00442.6170.1390.1390.0000.0000.0000.000
30C88LYS10.9140.98445.167-6.648-6.6480.0000.0000.0000.000
31C89PRO0-0.037-0.00244.7480.1410.1410.0000.0000.0000.000
32C90LEU0-0.037-0.02142.014-0.114-0.1140.0000.0000.0000.000
33C91SER00.012-0.00145.860-0.219-0.2190.0000.0000.0000.000
34C92ARG10.8990.94648.550-5.762-5.7620.0000.0000.0000.000
35C93TYR0-0.027-0.03550.803-0.015-0.0150.0000.0000.0000.000
36C94VAL00.0620.02746.8830.0180.0180.0000.0000.0000.000
37C95LEU0-0.021-0.00850.2820.0120.0120.0000.0000.0000.000
38C96ASP-1-0.827-0.89751.6316.0896.0890.0000.0000.0000.000
39C97GLN00.0630.01946.6560.1550.1550.0000.0000.0000.000
40C98GLN0-0.058-0.00847.4360.1370.1370.0000.0000.0000.000
41C99ASN0-0.123-0.06449.4590.0300.0300.0000.0000.0000.000
42C100SER00.0070.00243.9560.0570.0570.0000.0000.0000.000
43C101GLN0-0.0160.01142.523-0.208-0.2080.0000.0000.0000.000
44C102LYS10.9290.96142.629-6.840-6.8400.0000.0000.0000.000
45C103TYR0-0.002-0.00136.5740.0230.0230.0000.0000.0000.000
46C104VAL00.0130.01337.125-0.054-0.0540.0000.0000.0000.000
47C105ARG10.8580.92032.883-8.996-8.9960.0000.0000.0000.000
48C106SER0-0.0070.00433.076-0.019-0.0190.0000.0000.0000.000
49C107TRP00.0200.00327.6670.0760.0760.0000.0000.0000.000
50C108THR00.0310.03627.123-0.094-0.0940.0000.0000.0000.000
51C109LEU0-0.0400.01323.6290.5490.5490.0000.0000.0000.000
52C110PRO00.0640.00620.163-0.268-0.2680.0000.0000.0000.000
53C111SER0-0.005-0.05721.0500.5050.5050.0000.0000.0000.000
54C112THR0-0.057-0.04921.8110.0830.0830.0000.0000.0000.000
55C113VAL00.0080.00418.5880.0530.0530.0000.0000.0000.000
56C114LEU0-0.058-0.02815.8460.7470.7470.0000.0000.0000.000
57C115LYS10.9790.98717.667-12.122-12.1220.0000.0000.0000.000
58C116ALA00.0280.04220.051-0.247-0.2470.0000.0000.0000.000
59C117GLY0-0.029-0.03517.6790.8030.8030.0000.0000.0000.000
60C118GLY0-0.011-0.00115.8700.7430.7430.0000.0000.0000.000
61C119LYS10.7960.89113.288-16.809-16.8090.0000.0000.0000.000
62C120ALA00.0750.04812.8891.5771.5770.0000.0000.0000.000
63C121GLN00.0230.00213.4471.0901.0900.0000.0000.0000.000
64C122LYS10.8670.9497.480-25.082-25.0820.0000.0000.0000.000
65C123LEU0-0.012-0.0058.5752.8192.8190.0000.0000.0000.000
66C124ALA00.0570.02810.464-1.030-1.0300.0000.0000.0000.000
67C125ASN0-0.028-0.0229.8050.6440.6440.0000.0000.0000.000
68C126PHE00.0220.0235.4260.9000.9000.0000.0000.0000.000
69C127LYS10.8360.92111.210-17.698-17.6980.0000.0000.0000.000
70C128TYR00.000-0.00313.757-1.363-1.3630.0000.0000.0000.000
71C129LEU00.0260.01013.4282.1372.1370.0000.0000.0000.000
72C130ARG10.9200.97914.954-17.673-17.6730.0000.0000.0000.000
73C131CYS0-0.086-0.03615.5081.1391.1390.0000.0000.0000.000
74C132ASP-1-0.739-0.86117.66714.56314.5630.0000.0000.0000.000
75C133VAL0-0.016-0.02519.3680.7470.7470.0000.0000.0000.000
76C134GLN00.0190.04419.878-1.325-1.3250.0000.0000.0000.000
77C135VAL00.021-0.00222.1160.1250.1250.0000.0000.0000.000
78C136LYS10.9550.98325.049-11.609-11.6090.0000.0000.0000.000
79C137LEU0-0.0230.00426.6980.0750.0750.0000.0000.0000.000
80C138VAL0-0.006-0.01128.158-0.103-0.1030.0000.0000.0000.000
81C139LEU0-0.0280.01330.926-0.070-0.0700.0000.0000.0000.000
82C140ASN0-0.025-0.01734.693-0.039-0.0390.0000.0000.0000.000
83C141ALA00.0320.03336.767-0.114-0.1140.0000.0000.0000.000
84C142ASN0-0.0140.01040.443-0.148-0.1480.0000.0000.0000.000
85C143PRO00.047-0.00943.753-0.021-0.0210.0000.0000.0000.000
86C144PHE0-0.048-0.01946.269-0.127-0.1270.0000.0000.0000.000
87C145VAL0-0.023-0.00544.607-0.122-0.1220.0000.0000.0000.000
88C146ALA00.0150.02245.0870.1260.1260.0000.0000.0000.000
89C147GLY0-0.003-0.02444.573-0.057-0.0570.0000.0000.0000.000
90C148ARG10.8380.91941.314-7.265-7.2650.0000.0000.0000.000
91C149MET0-0.063-0.02938.264-0.067-0.0670.0000.0000.0000.000
92C150TYR0-0.003-0.02037.8010.0340.0340.0000.0000.0000.000
93C151LEU0-0.0150.00230.029-0.001-0.0010.0000.0000.0000.000
94C152ALA00.0490.02733.7470.0820.0820.0000.0000.0000.000
95C153TYR00.014-0.00730.0850.1560.1560.0000.0000.0000.000
96C154SER0-0.039-0.04132.188-0.170-0.1700.0000.0000.0000.000
97C155PRO00.016-0.01129.9700.1080.1080.0000.0000.0000.000
98C156TYR00.0160.00227.107-0.184-0.1840.0000.0000.0000.000
99C157ASP-1-0.760-0.84832.1598.4318.4310.0000.0000.0000.000
100C158ASP-1-0.862-0.93632.5759.6799.6790.0000.0000.0000.000
101C159LYS10.8260.92229.166-10.672-10.6720.0000.0000.0000.000
102C160VAL0-0.018-0.00134.839-0.041-0.0410.0000.0000.0000.000
103C161ASP-1-0.913-0.96637.9077.2127.2120.0000.0000.0000.000
104C162THR00.0670.03141.5580.0980.0980.0000.0000.0000.000
105C163ALA0-0.005-0.00542.8420.0250.0250.0000.0000.0000.000
106C164ARG10.8560.92640.490-7.692-7.6920.0000.0000.0000.000
107C165SER00.0240.02738.6060.1340.1340.0000.0000.0000.000
108C166VAL00.004-0.01137.010-0.231-0.2310.0000.0000.0000.000
109C167LEU0-0.055-0.03838.391-0.220-0.2200.0000.0000.0000.000
110C168GLN0-0.032-0.02341.765-0.368-0.3680.0000.0000.0000.000
111C169THR00.0430.03643.023-0.214-0.2140.0000.0000.0000.000
112C170SER00.004-0.00445.7770.0160.0160.0000.0000.0000.000
113C171ARG10.9740.98745.611-6.379-6.3790.0000.0000.0000.000
114C172ALA0-0.030-0.02945.1060.1130.1130.0000.0000.0000.000
115C173GLY00.0350.02344.6090.0920.0920.0000.0000.0000.000
116C174VAL00.0190.01240.1480.1750.1750.0000.0000.0000.000
117C175THR0-0.082-0.03640.1280.1760.1760.0000.0000.0000.000
118C176GLY0-0.0180.00041.2140.0190.0190.0000.0000.0000.000
119C177TYR0-0.050-0.02036.0700.0340.0340.0000.0000.0000.000
120C178PRO0-0.016-0.00432.943-0.092-0.0920.0000.0000.0000.000
121C179GLY00.0540.00633.5040.1860.1860.0000.0000.0000.000
122C180VAL0-0.0390.00332.005-0.054-0.0540.0000.0000.0000.000
123C181GLU-1-0.908-0.96334.9887.5877.5870.0000.0000.0000.000
124C182LEU00.0030.00334.8490.2050.2050.0000.0000.0000.000
125C183ASP-1-0.822-0.90237.6987.0097.0090.0000.0000.0000.000
126C184PHE00.019-0.03638.7530.1090.1090.0000.0000.0000.000
127C185GLN0-0.002-0.00840.9440.1410.1410.0000.0000.0000.000
128C186LEU0-0.114-0.04441.040-0.098-0.0980.0000.0000.0000.000
129C187ASP-1-0.845-0.90935.6818.4208.4200.0000.0000.0000.000
130C188ASN00.0420.01134.396-0.165-0.1650.0000.0000.0000.000
131C189SER0-0.064-0.05430.1320.3150.3150.0000.0000.0000.000
132C190VAL00.0060.03031.169-0.080-0.0800.0000.0000.0000.000
133C191GLU-1-0.935-0.98224.69212.27712.2770.0000.0000.0000.000
134C192MET0-0.016-0.00326.839-0.452-0.4520.0000.0000.0000.000
135C193THR0-0.012-0.03123.1210.3160.3160.0000.0000.0000.000
136C194ILE0-0.049-0.02224.375-0.501-0.5010.0000.0000.0000.000
137C195PRO0-0.003-0.00823.5460.6380.6380.0000.0000.0000.000
138C196TYR0-0.039-0.02920.5030.0260.0260.0000.0000.0000.000
139C197ALA0-0.015-0.00222.826-0.345-0.3450.0000.0000.0000.000
140C198SER00.0070.00323.683-0.678-0.6780.0000.0000.0000.000
141C199PHE0-0.027-0.01325.6250.0730.0730.0000.0000.0000.000
142C200GLN0-0.0070.00023.7710.0110.0110.0000.0000.0000.000
143C201GLU-1-0.890-0.95520.63614.09514.0950.0000.0000.0000.000
144C202ALA0-0.109-0.07617.4990.9740.9740.0000.0000.0000.000
145C203TYR00.0350.03018.243-0.463-0.4630.0000.0000.0000.000
146C204ASP-1-0.786-0.90317.90416.77516.7750.0000.0000.0000.000
147C205LEU0-0.018-0.02313.291-0.419-0.4190.0000.0000.0000.000
148C206VAL0-0.100-0.05116.617-0.306-0.3060.0000.0000.0000.000
149C207THR0-0.038-0.03018.729-0.570-0.5700.0000.0000.0000.000
150C208GLY00.0240.02821.165-0.506-0.5060.0000.0000.0000.000
151C209THR0-0.025-0.01222.484-0.334-0.3340.0000.0000.0000.000
152C210GLU-1-0.887-0.96522.87713.35213.3520.0000.0000.0000.000
153C211ASP-1-0.776-0.83824.46912.94312.9430.0000.0000.0000.000
154C212PHE00.0140.00021.770-0.395-0.3950.0000.0000.0000.000
155C213VAL0-0.040-0.00725.912-0.345-0.3450.0000.0000.0000.000
156C214GLN0-0.0020.02328.1870.1700.1700.0000.0000.0000.000
157C215LEU0-0.024-0.00727.732-0.110-0.1100.0000.0000.0000.000
158C216TYR00.004-0.01030.914-0.118-0.1180.0000.0000.0000.000
159C217LEU00.0500.02934.1280.0740.0740.0000.0000.0000.000
160C218PHE00.010-0.01135.794-0.207-0.2070.0000.0000.0000.000
161C219PRO00.0490.03239.5100.0620.0620.0000.0000.0000.000
162C220ILE00.0180.02041.355-0.170-0.1700.0000.0000.0000.000
163C221THR0-0.019-0.01644.216-0.156-0.1560.0000.0000.0000.000
164C222PRO0-0.049-0.01345.7320.1130.1130.0000.0000.0000.000
165C223VAL00.0390.00643.947-0.007-0.0070.0000.0000.0000.000
166C224LEU0-0.028-0.00446.681-0.150-0.1500.0000.0000.0000.000
167C225GLY00.0710.03348.7410.1100.1100.0000.0000.0000.000
168C226PRO0-0.057-0.01550.249-0.122-0.1220.0000.0000.0000.000
169C227LYS10.9510.95953.421-5.310-5.3100.0000.0000.0000.000
170C228SER0-0.041-0.04954.508-0.075-0.0750.0000.0000.0000.000
171C229GLU-1-0.889-0.94755.0235.5625.5620.0000.0000.0000.000
172C230SER0-0.0300.00555.4000.0150.0150.0000.0000.0000.000
173C231GLU-1-0.985-0.98851.7465.8505.8500.0000.0000.0000.000
174C232SER00.0210.02947.7700.0040.0040.0000.0000.0000.000
175C233SER0-0.0170.00347.2130.0320.0320.0000.0000.0000.000
176C234LYS10.9170.95539.342-7.615-7.6150.0000.0000.0000.000
177C235VAL0-0.031-0.02938.817-0.064-0.0640.0000.0000.0000.000
178C236ASP-1-0.851-0.90735.5488.6628.6620.0000.0000.0000.000
179C237ILE0-0.061-0.03932.131-0.003-0.0030.0000.0000.0000.000
180C238SER0-0.0240.00128.7310.0360.0360.0000.0000.0000.000
181C239VAL00.0040.00626.8510.1010.1010.0000.0000.0000.000
182C240TYR0-0.003-0.00123.1030.2270.2270.0000.0000.0000.000
183C241MET00.0150.00422.028-0.047-0.0470.0000.0000.0000.000
184C242TRP0-0.056-0.02416.8390.2870.2870.0000.0000.0000.000
185C243LEU00.0230.01514.952-0.478-0.4780.0000.0000.0000.000
186C244SER00.0660.02415.6120.4050.4050.0000.0000.0000.000
187C245ASN0-0.019-0.01315.612-0.076-0.0760.0000.0000.0000.000
188C246ILE0-0.049-0.01011.452-0.012-0.0120.0000.0000.0000.000
189C247SER0-0.0160.00411.6392.1922.1920.0000.0000.0000.000
190C248LEU0-0.001-0.0077.879-1.793-1.7930.0000.0000.0000.000
191C249VAL0-0.086-0.0618.8853.1463.1460.0000.0000.0000.000
192C250ILE00.0710.0559.952-1.397-1.3970.0000.0000.0000.000
193C251PRO00.0230.0279.128-0.599-0.5990.0000.0000.0000.000
194C252THR00.008-0.01411.250-1.942-1.9420.0000.0000.0000.000
195C253TYR00.0210.01313.3190.5210.5210.0000.0000.0000.000
196C254ARG10.8960.95715.531-14.989-14.9890.0000.0000.0000.000
197C255MET0-0.008-0.02514.4051.1271.1270.0000.0000.0000.000
198C256ASN00.0440.02617.205-1.029-1.0290.0000.0000.0000.000
199C257PRO0-0.099-0.01719.6690.2950.2950.0000.0000.0000.000
200C258ASP-1-0.879-0.94520.66912.79212.7920.0000.0000.0000.000