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: 2NV3R

Calculation Name: 1JVA-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JVA

Chain ID: B

ChEMBL ID:

UniProt ID: P17255

Base Structure: X-ray

Registration Date: 2023-09-24

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 430
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7376927.794418
FMO2-HF: Nuclear repulsion 7208263.861982
FMO2-HF: Total energy -168663.932435
FMO2-MP2: Total energy -169158.272291


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:279:ILE)


Summations of interaction energy for fragment #1(B:279:ILE)
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.
-1.9230.43-0.002-1.151-1.20.002
Interaction energy analysis for fragmet #1(B:279:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.012
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].
3B281TYR00.0100.0073.879-2.0960.257-0.002-1.151-1.2000.002
4B282VAL00.0600.0266.2930.2810.2810.0000.0000.0000.000
5B283GLY00.0150.0429.7450.0890.0890.0000.0000.0000.000
6B284SER0-0.038-0.03312.7120.0410.0410.0000.0000.0000.000
7B285PHE00.0210.00214.4480.0140.0140.0000.0000.0000.000
8B286ALA00.0490.01816.688-0.013-0.0130.0000.0000.0000.000
9B287LYS10.9761.00318.4450.1250.1250.0000.0000.0000.000
10B288GLY00.0000.00220.5420.0110.0110.0000.0000.0000.000
11B289THR0-0.088-0.05520.9530.0120.0120.0000.0000.0000.000
12B290ASN00.0130.01123.524-0.006-0.0060.0000.0000.0000.000
13B291VAL00.000-0.00123.552-0.006-0.0060.0000.0000.0000.000
14B292LEU0-0.015-0.00126.7350.0120.0120.0000.0000.0000.000
15B293MET00.0310.02227.490-0.019-0.0190.0000.0000.0000.000
16B294ALA0-0.027-0.03530.5300.0060.0060.0000.0000.0000.000
17B295ASP-1-0.796-0.87232.221-0.105-0.1050.0000.0000.0000.000
18B296GLY0-0.023-0.00334.3200.0080.0080.0000.0000.0000.000
19B297SER0-0.055-0.03533.5510.0030.0030.0000.0000.0000.000
20B298ILE0-0.032-0.04330.240-0.008-0.0080.0000.0000.0000.000
21B299GLU-1-0.860-0.93427.290-0.133-0.1330.0000.0000.0000.000
22B300CYS0-0.052-0.02825.408-0.006-0.0060.0000.0000.0000.000
23B301ILE00.0320.00619.326-0.002-0.0020.0000.0000.0000.000
24B302GLU-1-0.901-0.96320.476-0.178-0.1780.0000.0000.0000.000
25B303ASN0-0.056-0.03221.5200.0000.0000.0000.0000.0000.000
26B304ILE00.0110.03322.7570.0010.0010.0000.0000.0000.000
27B305GLU-1-0.904-0.95822.185-0.154-0.1540.0000.0000.0000.000
28B306VAL0-0.010-0.02519.833-0.011-0.0110.0000.0000.0000.000
29B307GLY00.0090.01222.5510.0180.0180.0000.0000.0000.000
30B308ASN0-0.0100.00925.1440.0150.0150.0000.0000.0000.000
31B309LYS10.8340.89525.8570.1410.1410.0000.0000.0000.000
32B310VAL00.0190.02724.6460.0110.0110.0000.0000.0000.000
33B311MET0-0.023-0.00227.9050.0020.0020.0000.0000.0000.000
34B312GLY00.0840.03928.480-0.014-0.0140.0000.0000.0000.000
35B313LYS10.8010.86227.0650.2000.2000.0000.0000.0000.000
36B314ASP-1-0.812-0.89831.252-0.142-0.1420.0000.0000.0000.000
37B315GLY0-0.0040.00033.7950.0070.0070.0000.0000.0000.000
38B316ARG10.8970.95632.4170.1160.1160.0000.0000.0000.000
39B317PRO00.0460.01330.138-0.007-0.0070.0000.0000.0000.000
40B318ARG10.7410.85525.2570.1800.1800.0000.0000.0000.000
41B319GLU-1-0.866-0.92324.353-0.175-0.1750.0000.0000.0000.000
42B320VAL00.0020.00420.320-0.022-0.0220.0000.0000.0000.000
43B321ILE00.0390.02318.1070.0140.0140.0000.0000.0000.000
44B322LYS10.8270.90811.0040.7200.7200.0000.0000.0000.000
45B323LEU00.0270.02016.270-0.007-0.0070.0000.0000.0000.000
46B324PRO0-0.046-0.00811.915-0.004-0.0040.0000.0000.0000.000
47B325ARG10.8710.94011.7190.3990.3990.0000.0000.0000.000
48B326GLY00.0200.0149.390-0.103-0.1030.0000.0000.0000.000
49B327ARG10.8050.8928.8230.1720.1720.0000.0000.0000.000
50B328GLU-1-0.767-0.8947.347-1.248-1.2480.0000.0000.0000.000
51B329THR00.0240.0119.4080.0940.0940.0000.0000.0000.000
52B330MET0-0.0330.02112.241-0.120-0.1200.0000.0000.0000.000
53B331TYR0-0.010-0.05013.8060.0190.0190.0000.0000.0000.000
54B332SER0-0.0090.00518.033-0.015-0.0150.0000.0000.0000.000
55B333VAL0-0.034-0.00721.1110.0140.0140.0000.0000.0000.000
56B334VAL00.009-0.00923.5250.0050.0050.0000.0000.0000.000
57B335GLN00.0200.02227.333-0.003-0.0030.0000.0000.0000.000
58B336LYS10.8360.89830.3360.0770.0770.0000.0000.0000.000
59B337SER00.0150.01832.4050.0020.0020.0000.0000.0000.000
60B351PRO00.007-0.01136.4580.0000.0000.0000.0000.0000.000
61B352GLU-1-0.813-0.90635.126-0.069-0.0690.0000.0000.0000.000
62B353LEU0-0.080-0.02432.088-0.005-0.0050.0000.0000.0000.000
63B354LEU00.0290.00929.578-0.003-0.0030.0000.0000.0000.000
64B355LYS10.9090.95226.7100.0920.0920.0000.0000.0000.000
65B356PHE00.0110.01319.8290.0010.0010.0000.0000.0000.000
66B357THR00.0480.01518.5050.0110.0110.0000.0000.0000.000
67B358CYS0-0.057-0.00416.230-0.001-0.0010.0000.0000.0000.000
68B359ASN00.0810.02210.4870.0920.0920.0000.0000.0000.000
69B360ALA0-0.003-0.00310.3480.0160.0160.0000.0000.0000.000
70B361THR0-0.043-0.0338.591-0.056-0.0560.0000.0000.0000.000
71B362ASN0-0.031-0.01510.912-0.052-0.0520.0000.0000.0000.000
72B363GLU-1-0.843-0.89714.251-0.428-0.4280.0000.0000.0000.000
73B364LEU0-0.028-0.01216.6230.0340.0340.0000.0000.0000.000
74B365VAL00.0320.01719.967-0.003-0.0030.0000.0000.0000.000
75B366VAL0-0.068-0.03222.5230.0230.0230.0000.0000.0000.000
76B367ARG10.8870.93525.0940.1310.1310.0000.0000.0000.000
77B368THR00.002-0.00527.588-0.001-0.0010.0000.0000.0000.000
78B369PRO0-0.0290.00229.923-0.001-0.0010.0000.0000.0000.000
79B370ARG10.8410.92232.9900.0850.0850.0000.0000.0000.000
80B371SER0-0.033-0.01834.8770.0050.0050.0000.0000.0000.000
81B372VAL00.0390.01036.576-0.001-0.0010.0000.0000.0000.000
82B373ARG10.9300.98239.3730.0450.0450.0000.0000.0000.000
83B374ARG10.9390.97141.7420.0340.0340.0000.0000.0000.000
84B375LEU0-0.066-0.02741.8800.0000.0000.0000.0000.0000.000
85B376SER00.0510.03645.9850.0000.0000.0000.0000.0000.000
86B377ARG10.8550.91238.7010.0290.0290.0000.0000.0000.000
87B378THR00.0760.04646.4930.0000.0000.0000.0000.0000.000
88B379ILE0-0.061-0.03641.4400.0000.0000.0000.0000.0000.000
89B380LYS10.9420.96043.1560.0100.0100.0000.0000.0000.000
90B381GLY00.0340.02646.9630.0010.0010.0000.0000.0000.000
91B382VAL00.0150.01748.2790.0000.0000.0000.0000.0000.000
92B383GLU-1-0.886-0.94748.624-0.018-0.0180.0000.0000.0000.000
93B384TYR0-0.068-0.03344.6790.0000.0000.0000.0000.0000.000
94B385PHE00.0420.02146.627-0.001-0.0010.0000.0000.0000.000
95B386GLU-1-0.792-0.85939.254-0.036-0.0360.0000.0000.0000.000
96B387VAL0-0.009-0.00839.9660.0000.0000.0000.0000.0000.000
97B388ILE0-0.052-0.01936.0840.0000.0000.0000.0000.0000.000
98B389THR0-0.020-0.04734.7820.0020.0020.0000.0000.0000.000
99B390PHE0-0.034-0.00931.7110.0000.0000.0000.0000.0000.000
100B391GLU-1-0.765-0.84630.453-0.074-0.0740.0000.0000.0000.000
101B392MET00.0230.02823.3240.0020.0020.0000.0000.0000.000
102B393GLY00.0020.00525.4640.0120.0120.0000.0000.0000.000
103B394GLN00.0310.02120.601-0.016-0.0160.0000.0000.0000.000
104B395LYS10.8620.91819.6740.1180.1180.0000.0000.0000.000
105B396LYS10.8750.94615.3640.0440.0440.0000.0000.0000.000
106B397ALA00.0300.02113.3860.0190.0190.0000.0000.0000.000
107B398PRO00.005-0.01413.1430.0210.0210.0000.0000.0000.000
108B399ASP-1-0.794-0.8568.423-0.442-0.4420.0000.0000.0000.000
109B400GLY0-0.015-0.00710.029-0.023-0.0230.0000.0000.0000.000
110B401ARG10.7490.8129.6210.5520.5520.0000.0000.0000.000
111B402ILE0-0.033-0.02012.9370.0660.0660.0000.0000.0000.000
112B403VAL00.0370.02814.723-0.032-0.0320.0000.0000.0000.000
113B404GLU-1-0.912-0.96617.153-0.187-0.1870.0000.0000.0000.000
114B405LEU0-0.022-0.02419.709-0.014-0.0140.0000.0000.0000.000
115B406VAL00.0320.01922.5450.0180.0180.0000.0000.0000.000
116B407LYS10.8320.91824.5550.1000.1000.0000.0000.0000.000
117B408GLU-1-0.827-0.89227.699-0.060-0.0600.0000.0000.0000.000
118B409VAL0-0.057-0.03030.4020.0030.0030.0000.0000.0000.000
119B410SER0-0.048-0.05132.9420.0010.0010.0000.0000.0000.000
120B411LYS10.8450.90134.2080.0630.0630.0000.0000.0000.000
121B412SER00.0140.00338.7010.0010.0010.0000.0000.0000.000
122B413TYR0-0.050-0.03741.692-0.001-0.0010.0000.0000.0000.000
123B414PRO00.0310.01644.8280.0000.0000.0000.0000.0000.000
124B415ILE00.002-0.01048.438-0.001-0.0010.0000.0000.0000.000
125B416SER0-0.016-0.01851.203-0.001-0.0010.0000.0000.0000.000
126B417GLU-1-0.898-0.93547.823-0.025-0.0250.0000.0000.0000.000
127B418GLY00.0460.03552.186-0.001-0.0010.0000.0000.0000.000
128B419PRO0-0.050-0.04450.109-0.001-0.0010.0000.0000.0000.000
129B420GLU-1-0.881-0.91649.227-0.032-0.0320.0000.0000.0000.000
130B421ARG10.9860.97940.7260.0370.0370.0000.0000.0000.000
131B422ALA0-0.031-0.01944.561-0.003-0.0030.0000.0000.0000.000
132B423ASN0-0.006-0.01944.808-0.004-0.0040.0000.0000.0000.000
133B424GLU-1-0.824-0.88944.002-0.043-0.0430.0000.0000.0000.000
134B425LEU0-0.0030.00038.308-0.003-0.0030.0000.0000.0000.000
135B426VAL0-0.023-0.02140.981-0.004-0.0040.0000.0000.0000.000
136B427GLU-1-0.822-0.89242.331-0.056-0.0560.0000.0000.0000.000
137B428SER00.0470.01339.570-0.003-0.0030.0000.0000.0000.000
138B429TYR0-0.037-0.03734.266-0.004-0.0040.0000.0000.0000.000
139B430ARG10.9040.94838.6020.0490.0490.0000.0000.0000.000
140B431LYS10.8410.90040.4370.0520.0520.0000.0000.0000.000
141B432ALA0-0.0110.01235.789-0.002-0.0020.0000.0000.0000.000
142B433SER0-0.050-0.03734.915-0.009-0.0090.0000.0000.0000.000
143B434ASN00.0320.02235.8160.0020.0020.0000.0000.0000.000
144B435LYS10.8540.92631.4620.1290.1290.0000.0000.0000.000
145B436ALA00.0430.01636.2630.0000.0000.0000.0000.0000.000
146B437TYR0-0.009-0.00831.9590.0010.0010.0000.0000.0000.000
147B438PHE00.0080.00528.282-0.001-0.0010.0000.0000.0000.000
148B439GLU-1-0.799-0.89027.639-0.138-0.1380.0000.0000.0000.000
149B440TRP00.001-0.00621.199-0.002-0.0020.0000.0000.0000.000
150B441THR00.000-0.02618.7550.0170.0170.0000.0000.0000.000
151B442ILE0-0.028-0.00617.6950.0090.0090.0000.0000.0000.000
152B443GLU-1-0.706-0.79810.715-0.841-0.8410.0000.0000.0000.000
153B444ALA00.0110.00514.9300.0590.0590.0000.0000.0000.000
154B445ARG10.8460.9157.7620.9440.9440.0000.0000.0000.000
155B446ASP-1-0.758-0.85014.045-0.339-0.3390.0000.0000.0000.000
156B447LEU0-0.029-0.00916.3280.0400.0400.0000.0000.0000.000
157B448SER0-0.040-0.02617.5820.0300.0300.0000.0000.0000.000
158B449LEU0-0.027-0.00815.9600.0280.0280.0000.0000.0000.000
159B450LEU00.0200.02420.4750.0130.0130.0000.0000.0000.000
160B451GLY00.0360.02723.7120.0130.0130.0000.0000.0000.000
161B452SER00.008-0.00527.280-0.007-0.0070.0000.0000.0000.000
162B453HIS10.8560.88529.5530.0520.0520.0000.0000.0000.000
163B454VAL00.0490.03726.7790.0000.0000.0000.0000.0000.000
164B455ARG10.8820.93724.0990.1150.1150.0000.0000.0000.000
165B456LYS10.9150.95527.1780.0710.0710.0000.0000.0000.000
166B457ALA0-0.033-0.00530.4970.0020.0020.0000.0000.0000.000
167B458THR00.0290.00624.8150.0020.0020.0000.0000.0000.000
168B459TYR0-0.079-0.01928.2820.0040.0040.0000.0000.0000.000
169B460GLN00.0800.04523.262-0.020-0.0200.0000.0000.0000.000
170B461THR00.009-0.01827.0050.0150.0150.0000.0000.0000.000
171B462TYR0-0.001-0.01528.445-0.009-0.0090.0000.0000.0000.000
172B463ALA00.0230.00431.0080.0060.0060.0000.0000.0000.000
173B464PRO0-0.0120.00932.9180.0010.0010.0000.0000.0000.000
174B465ILE00.0060.00534.534-0.006-0.0060.0000.0000.0000.000
175B466LEU0-0.041-0.02936.2560.0070.0070.0000.0000.0000.000
176B467TYR0-0.012-0.01236.2430.0030.0030.0000.0000.0000.000
177B468GLU-1-0.859-0.90838.159-0.072-0.0720.0000.0000.0000.000
178B469ASN0-0.0220.00540.8320.0040.0040.0000.0000.0000.000
179B470ASP-1-0.869-0.96442.613-0.060-0.0600.0000.0000.0000.000
180B471HIS00.0320.02245.1030.0030.0030.0000.0000.0000.000
181B472PHE0-0.011-0.00846.9780.0030.0030.0000.0000.0000.000
182B473PHE00.0180.00549.6690.0040.0040.0000.0000.0000.000
183B474ASP-1-0.874-0.93547.488-0.057-0.0570.0000.0000.0000.000
184B475TYR0-0.118-0.07850.9390.0020.0020.0000.0000.0000.000
185B476MET0-0.0230.02052.6160.0020.0020.0000.0000.0000.000
186B477GLN0-0.006-0.00254.5020.0030.0030.0000.0000.0000.000
187B478LYS10.8370.92750.9050.0500.0500.0000.0000.0000.000
188B479SER0-0.019-0.02056.0490.0020.0020.0000.0000.0000.000
189B480LYS10.8800.92558.7470.0340.0340.0000.0000.0000.000
190B481PHE00.0840.02057.2600.0010.0010.0000.0000.0000.000
191B482HIS00.0280.03561.6310.0000.0000.0000.0000.0000.000
192B483LEU0-0.0170.01259.297-0.001-0.0010.0000.0000.0000.000
193B484THR00.009-0.00659.1940.0010.0010.0000.0000.0000.000
194B485ILE0-0.020-0.00355.701-0.001-0.0010.0000.0000.0000.000
195B486GLU-1-0.791-0.89556.060-0.042-0.0420.0000.0000.0000.000
196B487GLY00.0520.02656.5680.0000.0000.0000.0000.0000.000
197B488PRO00.017-0.01952.0210.0000.0000.0000.0000.0000.000
198B489LYS10.8240.91149.6080.0560.0560.0000.0000.0000.000
199B490VAL00.0120.00853.9770.0000.0000.0000.0000.0000.000
200B491LEU00.0340.01755.1470.0010.0010.0000.0000.0000.000
201B492ALA00.001-0.00351.3650.0000.0000.0000.0000.0000.000
202B493TYR0-0.045-0.05153.2240.0000.0000.0000.0000.0000.000
203B494LEU00.001-0.00155.3770.0010.0010.0000.0000.0000.000
204B495LEU0-0.003-0.00152.7950.0010.0010.0000.0000.0000.000
205B496GLY00.0040.00452.4080.0000.0000.0000.0000.0000.000
206B497LEU0-0.018-0.02153.3520.0000.0000.0000.0000.0000.000
207B498TRP0-0.037-0.01553.0130.0000.0000.0000.0000.0000.000
208B499ILE00.001-0.00449.9330.0010.0010.0000.0000.0000.000
209B500GLY0-0.0010.00253.1990.0000.0000.0000.0000.0000.000
210B501ASP-1-0.806-0.85954.669-0.032-0.0320.0000.0000.0000.000
211B502GLY00.0000.00057.7970.0010.0010.0000.0000.0000.000
212B503LEU0-0.023-0.00557.9680.0000.0000.0000.0000.0000.000
213B504SER00.004-0.02555.841-0.001-0.0010.0000.0000.0000.000
214B505ASP-1-0.816-0.86957.204-0.028-0.0280.0000.0000.0000.000
215B506ARG10.8190.86860.0040.0270.0270.0000.0000.0000.000
216B507ALA00.0100.01460.519-0.001-0.0010.0000.0000.0000.000
217B508THR0-0.067-0.04261.5240.0010.0010.0000.0000.0000.000
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