FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 82RJY

Calculation Name: 2NRA-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NRA

Chain ID: C

ChEMBL ID:

UniProt ID: P03067

Base Structure: X-ray

Registration Date: 2023-06-19

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 252
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3427756.798632
FMO2-HF: Nuclear repulsion 3328214.977764
FMO2-HF: Total energy -99541.820869
FMO2-MP2: Total energy -99840.329103


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:9:VAL)


Summations of interaction energy for fragment #1(C:9:VAL)
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.
-6.871-1.7580.578-2.573-3.1170.008
Interaction energy analysis for fragmet #1(C:9:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.035
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].
3C11LYS10.9910.9793.860-0.3681.310-0.005-0.983-0.6890.006
4C12LYS10.9730.9976.798-0.179-0.1790.0000.0000.0000.000
5C13THR0-0.019-0.0352.342-1.1550.9280.554-1.215-1.4210.002
6C14LYS10.9200.9615.2940.3920.476-0.001-0.004-0.0790.000
7C15ILE00.0320.0366.734-0.294-0.2940.0000.0000.0000.000
8C16ARG10.9010.9428.8230.4230.4230.0000.0000.0000.000
9C17HIS10.8960.97012.282-0.074-0.0740.0000.0000.0000.000
10C18ARG10.9811.00115.2960.1660.1660.0000.0000.0000.000
11C19ASN00.0310.03319.0900.0290.0290.0000.0000.0000.000
12C20GLU-1-0.848-0.91721.088-0.051-0.0510.0000.0000.0000.000
13C21LEU00.0030.01016.6470.0080.0080.0000.0000.0000.000
14C22ASN0-0.051-0.04619.2640.0140.0140.0000.0000.0000.000
15C23HIS00.1170.07820.3960.0210.0210.0000.0000.0000.000
16C24THR00.0780.05020.3830.0080.0080.0000.0000.0000.000
17C25LEU0-0.037-0.02215.2330.0210.0210.0000.0000.0000.000
18C26ALA0-0.033-0.01818.8430.0330.0330.0000.0000.0000.000
19C27GLN00.016-0.01821.2390.0060.0060.0000.0000.0000.000
20C28LEU0-0.0570.01316.9690.0050.0050.0000.0000.0000.000
21C29PRO00.1030.04220.3270.0330.0330.0000.0000.0000.000
22C30LEU0-0.0150.01117.4020.0180.0180.0000.0000.0000.000
23C31PRO0-0.0180.00016.5700.0560.0560.0000.0000.0000.000
24C32ALA00.1080.05115.4930.0410.0410.0000.0000.0000.000
25C33LYS10.7950.92214.892-0.238-0.2380.0000.0000.0000.000
26C34ARG10.8630.92312.256-0.616-0.6160.0000.0000.0000.000
27C35VAL0-0.0130.01010.8570.1040.1040.0000.0000.0000.000
28C36MET00.0660.02710.698-0.045-0.0450.0000.0000.0000.000
29C37TYR0-0.005-0.0149.319-0.069-0.0690.0000.0000.0000.000
30C38MET0-0.028-0.0084.9930.0230.0230.0000.0000.0000.000
31C39ALA00.0530.0246.179-0.430-0.4300.0000.0000.0000.000
32C40LEU00.000-0.0098.177-0.273-0.2730.0000.0000.0000.000
33C41ALA0-0.067-0.0313.377-0.330-0.0650.018-0.067-0.2160.000
34C42LEU0-0.071-0.0283.928-2.063-1.5990.002-0.122-0.344-0.001
35C43ILE0-0.018-0.0035.5190.1090.1090.0000.0000.0000.000
36C44ASP-1-0.812-0.8977.588-0.975-0.9750.0000.0000.0000.000
37C45SER0-0.051-0.0428.9130.2260.2260.0000.0000.0000.000
38C46LYS10.7400.86311.2960.8450.8450.0000.0000.0000.000
39C47GLU-1-0.809-0.87812.394-0.538-0.5380.0000.0000.0000.000
40C48PRO00.006-0.00214.4830.0010.0010.0000.0000.0000.000
41C49LEU00.0490.03412.565-0.090-0.0900.0000.0000.0000.000
42C50GLU-1-0.910-0.96814.064-0.566-0.5660.0000.0000.0000.000
43C51ARG10.9260.97316.8990.3050.3050.0000.0000.0000.000
44C52GLY0-0.037-0.02219.2590.0250.0250.0000.0000.0000.000
45C53ARG10.9030.9708.9100.9940.9940.0000.0000.0000.000
46C54VAL00.0340.01014.2270.0260.0260.0000.0000.0000.000
47C55PHE0-0.052-0.0259.128-0.114-0.1140.0000.0000.0000.000
48C56LYS10.9300.97010.6750.2900.2900.0000.0000.0000.000
49C57ILE0-0.010-0.0088.317-0.076-0.0760.0000.0000.0000.000
50C58ARG11.0301.0098.558-0.077-0.0770.0000.0000.0000.000
51C59ALA0-0.0010.0049.6190.2310.2310.0000.0000.0000.000
52C60GLU-1-0.910-0.96110.2290.6520.6520.0000.0000.0000.000
53C61ASP-1-0.840-0.9235.6451.1461.1460.0000.0000.0000.000
54C62LEU0-0.001-0.0097.6280.4950.4950.0000.0000.0000.000
55C63ALA0-0.0230.0019.3090.1010.1010.0000.0000.0000.000
56C64ALA00.0260.0157.955-0.026-0.0260.0000.0000.0000.000
57C65LEU0-0.048-0.0293.864-0.617-0.2330.010-0.157-0.2380.001
58C66ALA0-0.057-0.0418.345-0.194-0.1940.0000.0000.0000.000
59C67LYS10.8680.94811.640-1.036-1.0360.0000.0000.0000.000
60C68ILE0-0.0200.00213.724-0.151-0.1510.0000.0000.0000.000
61C69THR00.0420.00815.0580.0390.0390.0000.0000.0000.000
62C70PRO00.1190.03514.9180.0000.0000.0000.0000.0000.000
63C71SER00.0110.01616.324-0.015-0.0150.0000.0000.0000.000
64C72LEU0-0.004-0.00417.886-0.026-0.0260.0000.0000.0000.000
65C73ALA00.0290.02513.480-0.020-0.0200.0000.0000.0000.000
66C74TYR00.0410.02315.457-0.010-0.0100.0000.0000.0000.000
67C75ARG10.9670.99117.244-0.292-0.2920.0000.0000.0000.000
68C76GLN0-0.011-0.01916.1010.0310.0310.0000.0000.0000.000
69C77LEU00.0310.02412.210-0.022-0.0220.0000.0000.0000.000
70C78LYS10.9290.98215.468-0.167-0.1670.0000.0000.0000.000
71C79GLU-1-0.938-0.99318.7810.1270.1270.0000.0000.0000.000
72C80GLY00.0020.00116.905-0.018-0.0180.0000.0000.0000.000
73C81GLY00.015-0.00717.321-0.027-0.0270.0000.0000.0000.000
74C82LYS10.9780.98618.027-0.129-0.1290.0000.0000.0000.000
75C83LEU00.000-0.00420.428-0.015-0.0150.0000.0000.0000.000
76C84LEU0-0.026-0.01814.968-0.012-0.0120.0000.0000.0000.000
77C85GLY0-0.0070.01519.372-0.021-0.0210.0000.0000.0000.000
78C86ALA0-0.0100.00021.626-0.013-0.0130.0000.0000.0000.000
79C87SER0-0.075-0.04120.8850.0010.0010.0000.0000.0000.000
80C88LYS10.9470.96722.913-0.021-0.0210.0000.0000.0000.000
81C89ILE0-0.066-0.04221.8370.0130.0130.0000.0000.0000.000
82C90SER0-0.052-0.03423.901-0.004-0.0040.0000.0000.0000.000
83C91LEU00.007-0.00925.6360.0000.0000.0000.0000.0000.000
84C92ARG10.9600.98527.844-0.028-0.0280.0000.0000.0000.000
85C93GLY00.0840.00930.6930.0020.0020.0000.0000.0000.000
86C94ASP-1-0.894-0.94332.706-0.022-0.0220.0000.0000.0000.000
87C95ASP-1-0.919-0.96727.832-0.029-0.0290.0000.0000.0000.000
88C96ILE0-0.065-0.02928.829-0.008-0.0080.0000.0000.0000.000
89C97ILE0-0.023-0.00330.840-0.006-0.0060.0000.0000.0000.000
90C98ALA0-0.057-0.02328.180-0.006-0.0060.0000.0000.0000.000
91C99LEU00.0420.02924.659-0.005-0.0050.0000.0000.0000.000
92C100ALA00.0080.00327.923-0.009-0.0090.0000.0000.0000.000
93C101LYS10.9150.97130.8620.0550.0550.0000.0000.0000.000
94C102GLU-1-0.980-0.99924.761-0.120-0.1200.0000.0000.0000.000
95C103LEU0-0.051-0.03124.232-0.012-0.0120.0000.0000.0000.000
96C104ASN0-0.0400.01027.512-0.009-0.0090.0000.0000.0000.000
97C113SER0-0.085-0.05936.5820.0010.0010.0000.0000.0000.000
98C114GLU-1-0.929-0.97233.144-0.076-0.0760.0000.0000.0000.000
99C115GLU-1-0.921-0.94133.472-0.060-0.0600.0000.0000.0000.000
100C116LEU0-0.023-0.01228.530-0.006-0.0060.0000.0000.0000.000
101C117ASP-1-0.840-0.89826.351-0.058-0.0580.0000.0000.0000.000
102C118LEU00.0100.00625.978-0.009-0.0090.0000.0000.0000.000
103C119ASN00.0420.02223.4160.0260.0260.0000.0000.0000.000
104C120ILE0-0.026-0.01117.461-0.015-0.0150.0000.0000.0000.000
105C121ILE0-0.066-0.05216.692-0.027-0.0270.0000.0000.0000.000
106C122GLU-1-0.897-0.94320.017-0.108-0.1080.0000.0000.0000.000
107C123TRP00.0180.00518.1530.0030.0030.0000.0000.0000.000
108C124ILE0-0.027-0.01716.872-0.011-0.0110.0000.0000.0000.000
109C125ALA00.0220.02818.1420.0120.0120.0000.0000.0000.000
110C126TYR0-0.021-0.01316.2300.0080.0080.0000.0000.0000.000
111C127SER00.0390.02017.694-0.032-0.0320.0000.0000.0000.000
112C128PRO0-0.110-0.09119.6520.0230.0230.0000.0000.0000.000
113C129ASP-1-0.835-0.93621.8310.1110.1110.0000.0000.0000.000
114C130GLU-1-0.856-0.89217.9600.0500.0500.0000.0000.0000.000
115C131GLY0-0.082-0.02316.0130.0070.0070.0000.0000.0000.000
116C132TYR0-0.075-0.06612.6760.0580.0580.0000.0000.0000.000
117C133LEU0-0.029-0.00413.170-0.009-0.0090.0000.0000.0000.000
118C134SER0-0.005-0.01313.215-0.057-0.0570.0000.0000.0000.000
119C135LEU00.0090.00812.4570.0450.0450.0000.0000.0000.000
120C136LYS10.9900.99515.0950.1190.1190.0000.0000.0000.000
121C137PHE00.0110.00412.3650.0380.0380.0000.0000.0000.000
122C138THR00.0510.02717.822-0.019-0.0190.0000.0000.0000.000
123C139ARG11.0210.97820.4370.1730.1730.0000.0000.0000.000
124C140THR00.0340.01021.984-0.013-0.0130.0000.0000.0000.000
125C141ILE0-0.008-0.00517.3000.0020.0020.0000.0000.0000.000
126C142GLU-1-0.850-0.92217.662-0.284-0.2840.0000.0000.0000.000
127C143PRO00.0390.03817.731-0.032-0.0320.0000.0000.0000.000
128C144TYR0-0.066-0.05918.3790.0100.0100.0000.0000.0000.000
129C145ILE0-0.126-0.08511.7890.0100.0100.0000.0000.0000.000
130C146SER00.0210.01014.288-0.050-0.0500.0000.0000.0000.000
131C147SER0-0.0420.00415.4760.0360.0360.0000.0000.0000.000
132C148LEU00.0570.03017.3350.0000.0000.0000.0000.0000.000
133C149ILE00.036-0.00814.5260.0260.0260.0000.0000.0000.000
134C150GLY0-0.063-0.00318.6320.0200.0200.0000.0000.0000.000
135C151LYS11.0170.99322.0320.0790.0790.0000.0000.0000.000
136C152LYS10.9540.93920.0130.0570.0570.0000.0000.0000.000
137C153ASN0-0.027-0.01520.748-0.006-0.0060.0000.0000.0000.000
138C154LYS11.0061.01121.9730.0970.0970.0000.0000.0000.000
139C155PHE0-0.042-0.00217.179-0.002-0.0020.0000.0000.0000.000
140C156THR00.0350.00315.9780.0290.0290.0000.0000.0000.000
141C157THR0-0.021-0.01711.703-0.050-0.0500.0000.0000.0000.000
142C158GLN0-0.005-0.01711.725-0.033-0.0330.0000.0000.0000.000
143C159LEU00.0480.0349.228-0.043-0.0430.0000.0000.0000.000
144C160LEU00.0220.0264.434-0.220-0.0650.000-0.025-0.1300.000
145C161THR00.011-0.0067.609-0.116-0.1160.0000.0000.0000.000
146C162ALA00.0540.0248.905-0.162-0.1620.0000.0000.0000.000
147C163SER0-0.016-0.01510.390-0.149-0.1490.0000.0000.0000.000
148C164LEU00.0070.0117.433-0.127-0.1270.0000.0000.0000.000
149C165ARG10.9250.96710.908-1.317-1.3170.0000.0000.0000.000
150C166LEU0-0.0130.00914.288-0.102-0.1020.0000.0000.0000.000
151C167SER0-0.079-0.06917.090-0.048-0.0480.0000.0000.0000.000
152C168SER00.0700.03419.203-0.039-0.0390.0000.0000.0000.000
153C169GLN00.0630.03121.2410.0220.0220.0000.0000.0000.000
154C170TYR00.0390.02122.357-0.002-0.0020.0000.0000.0000.000
155C171SER00.006-0.02520.306-0.014-0.0140.0000.0000.0000.000
156C172SER0-0.032-0.01017.9220.0260.0260.0000.0000.0000.000
157C173SER00.0420.02818.9860.0010.0010.0000.0000.0000.000
158C174LEU00.0070.00921.305-0.018-0.0180.0000.0000.0000.000
159C175TYR0-0.068-0.08613.5680.0020.0020.0000.0000.0000.000
160C176GLN00.0100.00316.993-0.008-0.0080.0000.0000.0000.000
161C177LEU00.0030.01718.388-0.030-0.0300.0000.0000.0000.000
162C178ILE0-0.004-0.01920.452-0.023-0.0230.0000.0000.0000.000
163C179ARG10.8390.90414.266-0.208-0.2080.0000.0000.0000.000
164C180LYS10.9410.97418.584-0.055-0.0550.0000.0000.0000.000
165C181HIS10.8050.91620.350-0.077-0.0770.0000.0000.0000.000
166C182TYR00.0030.01117.164-0.005-0.0050.0000.0000.0000.000
167C183SER0-0.030-0.01020.378-0.016-0.0160.0000.0000.0000.000
168C184ASN00.030-0.00622.874-0.027-0.0270.0000.0000.0000.000
169C185PHE0-0.0110.00517.097-0.015-0.0150.0000.0000.0000.000
170C186LYS10.9520.99721.6950.0110.0110.0000.0000.0000.000
171C187LYS10.9810.96024.460-0.063-0.0630.0000.0000.0000.000
172C188LYS10.9040.95825.146-0.062-0.0620.0000.0000.0000.000
173C189ASN0-0.0040.01624.034-0.021-0.0210.0000.0000.0000.000
174C190TYR00.023-0.00126.4540.0090.0090.0000.0000.0000.000
175C191PHE0-0.032-0.01325.632-0.009-0.0090.0000.0000.0000.000
176C192ILE00.0150.00729.5680.0070.0070.0000.0000.0000.000
177C193ILE0-0.0010.00228.920-0.003-0.0030.0000.0000.0000.000
178C194SER0-0.0240.00132.4360.0010.0010.0000.0000.0000.000
179C195VAL00.0340.00733.4800.0040.0040.0000.0000.0000.000
180C196ASP-1-0.852-0.93933.4900.0610.0610.0000.0000.0000.000
181C197GLU-1-0.825-0.90229.9500.0460.0460.0000.0000.0000.000
182C198LEU0-0.070-0.03627.8880.0070.0070.0000.0000.0000.000
183C199LYS10.8740.92628.952-0.066-0.0660.0000.0000.0000.000
184C200GLU-1-0.849-0.92229.9790.0530.0530.0000.0000.0000.000
185C201GLU-1-0.982-1.00324.9920.0740.0740.0000.0000.0000.000
186C202LEU0-0.157-0.09024.9060.0160.0160.0000.0000.0000.000
187C203ILE0-0.022-0.00625.1580.0140.0140.0000.0000.0000.000
188C204ALA0-0.078-0.03127.9420.0060.0060.0000.0000.0000.000
189C205TYR0-0.016-0.02829.349-0.005-0.0050.0000.0000.0000.000
190C206THR0-0.078-0.03031.9950.0090.0090.0000.0000.0000.000
191C207PHE00.0320.01931.800-0.002-0.0020.0000.0000.0000.000
192C208ASP-1-0.861-0.95336.9450.0520.0520.0000.0000.0000.000
193C209LYS10.9210.97739.149-0.035-0.0350.0000.0000.0000.000
194C210ASP-1-0.913-0.95441.6890.0340.0340.0000.0000.0000.000
195C211GLY0-0.024-0.00540.449-0.003-0.0030.0000.0000.0000.000
196C212ASN0-0.040-0.03038.9910.0040.0040.0000.0000.0000.000
197C213ILE0-0.023-0.00135.4160.0030.0030.0000.0000.0000.000
198C214GLU-1-0.853-0.91236.8200.0530.0530.0000.0000.0000.000
199C215TYR0-0.037-0.03233.9430.0080.0080.0000.0000.0000.000
200C216LYS10.9750.97730.583-0.109-0.1090.0000.0000.0000.000
201C217TYR0-0.056-0.02132.1210.0050.0050.0000.0000.0000.000
202C218PRO00.0280.02036.7740.0000.0000.0000.0000.0000.000
203C219ASP-1-0.840-0.91039.8830.0680.0680.0000.0000.0000.000
204C220PHE00.0570.00835.6060.0060.0060.0000.0000.0000.000
205C221PRO0-0.009-0.01037.5720.0060.0060.0000.0000.0000.000
206C222ILE00.0500.03037.7740.0070.0070.0000.0000.0000.000
207C223PHE00.0400.01930.9590.0080.0080.0000.0000.0000.000
208C224LYS10.8890.94533.329-0.082-0.0820.0000.0000.0000.000
209C225ARG10.8680.90233.003-0.095-0.0950.0000.0000.0000.000
210C226ASP-1-0.845-0.89332.9470.1280.1280.0000.0000.0000.000
211C227VAL0-0.023-0.01028.3440.0120.0120.0000.0000.0000.000
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