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: MNQ1Z

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 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 430
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -7376351.817502
FMO2-HF: Nuclear repulsion 7207692.151451
FMO2-HF: Total energy -168659.66605
FMO2-MP2: Total energy -169154.385297


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.
-4.566-2.1030.089-0.984-1.5680.002
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 : -0.002 / q_NPA : -0.022
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].
3B281TYR0-0.0130.0073.483-2.966-0.5030.089-0.984-1.5680.002
4B282VAL00.0610.0296.0180.1040.1040.0000.0000.0000.000
5B283GLY00.0240.0269.3710.0000.0000.0000.0000.0000.000
6B284SER0-0.051-0.06012.259-0.062-0.0620.0000.0000.0000.000
7B285PHE0-0.008-0.01814.2730.0370.0370.0000.0000.0000.000
8B286ALA00.0770.03516.785-0.030-0.0300.0000.0000.0000.000
9B287LYS11.0031.00418.3820.1600.1600.0000.0000.0000.000
10B288GLY0-0.0050.01020.5770.0130.0130.0000.0000.0000.000
11B289THR0-0.055-0.03120.9720.0170.0170.0000.0000.0000.000
12B290ASN0-0.0170.00023.601-0.010-0.0100.0000.0000.0000.000
13B291VAL0-0.003-0.01023.3590.0050.0050.0000.0000.0000.000
14B292LEU0-0.0070.00426.6060.0030.0030.0000.0000.0000.000
15B293MET00.0390.01726.322-0.005-0.0050.0000.0000.0000.000
16B294ALA0-0.039-0.03829.8940.0070.0070.0000.0000.0000.000
17B295ASP-1-0.807-0.83831.540-0.060-0.0600.0000.0000.0000.000
18B296GLY0-0.037-0.02333.6530.0040.0040.0000.0000.0000.000
19B297SER0-0.097-0.09033.0360.0010.0010.0000.0000.0000.000
20B298ILE0-0.035-0.03030.017-0.002-0.0020.0000.0000.0000.000
21B299GLU-1-0.865-0.94727.070-0.106-0.1060.0000.0000.0000.000
22B300CYS0-0.068-0.01725.1230.0010.0010.0000.0000.0000.000
23B301ILE00.0320.00318.803-0.005-0.0050.0000.0000.0000.000
24B302GLU-1-0.926-0.98020.423-0.152-0.1520.0000.0000.0000.000
25B303ASN0-0.048-0.03221.454-0.018-0.0180.0000.0000.0000.000
26B304ILE00.0230.04622.3120.0040.0040.0000.0000.0000.000
27B305GLU-1-0.963-0.98221.906-0.150-0.1500.0000.0000.0000.000
28B306VAL0-0.013-0.02319.3290.0060.0060.0000.0000.0000.000
29B307GLY0-0.0110.01022.1470.0090.0090.0000.0000.0000.000
30B308ASN0-0.030-0.00624.8340.0120.0120.0000.0000.0000.000
31B309LYS10.9770.97625.4320.0780.0780.0000.0000.0000.000
32B310VAL00.0240.02924.3420.0050.0050.0000.0000.0000.000
33B311MET0-0.0020.00127.2600.0060.0060.0000.0000.0000.000
34B312GLY00.0710.03228.155-0.002-0.0020.0000.0000.0000.000
35B313LYS10.8810.93927.5910.0220.0220.0000.0000.0000.000
36B314ASP-1-0.820-0.92130.720-0.036-0.0360.0000.0000.0000.000
37B315GLY0-0.040-0.01932.8470.0020.0020.0000.0000.0000.000
38B316ARG10.9090.96231.9010.0340.0340.0000.0000.0000.000
39B317PRO00.013-0.01029.899-0.002-0.0020.0000.0000.0000.000
40B318ARG10.7500.88324.8440.0560.0560.0000.0000.0000.000
41B319GLU-1-0.941-0.96623.636-0.111-0.1110.0000.0000.0000.000
42B320VAL00.0010.00419.743-0.004-0.0040.0000.0000.0000.000
43B321ILE00.0230.00417.165-0.005-0.0050.0000.0000.0000.000
44B322LYS10.9470.97410.5820.4330.4330.0000.0000.0000.000
45B323LEU00.0300.00015.2770.0180.0180.0000.0000.0000.000
46B324PRO0-0.066-0.01511.271-0.036-0.0360.0000.0000.0000.000
47B325ARG10.9630.97410.9290.3770.3770.0000.0000.0000.000
48B326GLY00.0230.0118.741-0.138-0.1380.0000.0000.0000.000
49B327ARG10.8800.9608.5040.4540.4540.0000.0000.0000.000
50B328GLU-1-0.801-0.9207.223-0.334-0.3340.0000.0000.0000.000
51B329THR00.0100.0119.6230.0300.0300.0000.0000.0000.000
52B330MET0-0.0200.01812.342-0.020-0.0200.0000.0000.0000.000
53B331TYR00.0500.00714.0830.0410.0410.0000.0000.0000.000
54B332SER0-0.0170.00117.902-0.015-0.0150.0000.0000.0000.000
55B333VAL0-0.050-0.02420.8900.0170.0170.0000.0000.0000.000
56B334VAL00.0230.00123.394-0.009-0.0090.0000.0000.0000.000
57B335GLN00.0560.03227.1270.0050.0050.0000.0000.0000.000
58B336LYS10.8830.96029.914-0.030-0.0300.0000.0000.0000.000
59B337SER00.0140.02231.930-0.001-0.0010.0000.0000.0000.000
60B351PRO0-0.027-0.03136.1650.0000.0000.0000.0000.0000.000
61B352GLU-1-0.809-0.90236.090-0.013-0.0130.0000.0000.0000.000
62B353LEU0-0.077-0.03931.8160.0000.0000.0000.0000.0000.000
63B354LEU00.0140.01929.641-0.005-0.0050.0000.0000.0000.000
64B355LYS10.9120.94026.5210.0310.0310.0000.0000.0000.000
65B356PHE00.0260.01119.875-0.004-0.0040.0000.0000.0000.000
66B357THR00.0510.02918.4520.0170.0170.0000.0000.0000.000
67B358CYS0-0.0670.00016.351-0.008-0.0080.0000.0000.0000.000
68B359ASN00.1440.06110.6370.0970.0970.0000.0000.0000.000
69B360ALA0-0.017-0.02210.4340.0350.0350.0000.0000.0000.000
70B361THR0-0.011-0.0078.7730.0790.0790.0000.0000.0000.000
71B362ASN0-0.0220.01110.949-0.018-0.0180.0000.0000.0000.000
72B363GLU-1-0.948-0.96414.2250.0710.0710.0000.0000.0000.000
73B364LEU0-0.059-0.04216.603-0.021-0.0210.0000.0000.0000.000
74B365VAL00.0490.03119.9760.0140.0140.0000.0000.0000.000
75B366VAL0-0.063-0.03422.766-0.003-0.0030.0000.0000.0000.000
76B367ARG10.9620.98525.155-0.008-0.0080.0000.0000.0000.000
77B368THR0-0.015-0.00627.8850.0020.0020.0000.0000.0000.000
78B369PRO0-0.0190.00330.038-0.001-0.0010.0000.0000.0000.000
79B370ARG10.8820.96533.266-0.036-0.0360.0000.0000.0000.000
80B371SER0-0.040-0.03135.037-0.004-0.0040.0000.0000.0000.000
81B372VAL00.0610.02837.1870.0030.0030.0000.0000.0000.000
82B373ARG10.9250.97339.875-0.046-0.0460.0000.0000.0000.000
83B374ARG10.9710.99642.484-0.032-0.0320.0000.0000.0000.000
84B375LEU0-0.052-0.02142.637-0.002-0.0020.0000.0000.0000.000
85B376SER00.0230.02446.4390.0010.0010.0000.0000.0000.000
86B377ARG10.9160.95539.804-0.059-0.0590.0000.0000.0000.000
87B378THR00.0650.04247.1340.0000.0000.0000.0000.0000.000
88B379ILE0-0.068-0.02942.5040.0020.0020.0000.0000.0000.000
89B380LYS10.9310.94644.501-0.055-0.0550.0000.0000.0000.000
90B381GLY00.0380.01647.9200.0000.0000.0000.0000.0000.000
91B382VAL00.0090.03248.979-0.002-0.0020.0000.0000.0000.000
92B383GLU-1-0.881-0.94149.2240.0360.0360.0000.0000.0000.000
93B384TYR0-0.049-0.03246.0990.0010.0010.0000.0000.0000.000
94B385PHE00.0230.01447.258-0.002-0.0020.0000.0000.0000.000
95B386GLU-1-0.838-0.90040.0440.0600.0600.0000.0000.0000.000
96B387VAL0-0.030-0.02440.253-0.003-0.0030.0000.0000.0000.000
97B388ILE0-0.015-0.00436.7770.0040.0040.0000.0000.0000.000
98B389THR00.003-0.02335.499-0.004-0.0040.0000.0000.0000.000
99B390PHE0-0.0550.00832.0180.0060.0060.0000.0000.0000.000
100B391GLU-1-0.875-0.94430.9300.0680.0680.0000.0000.0000.000
101B392MET00.0120.02123.5850.0050.0050.0000.0000.0000.000
102B393GLY00.0080.00826.074-0.003-0.0030.0000.0000.0000.000
103B394GLN00.015-0.00321.8360.0100.0100.0000.0000.0000.000
104B395LYS10.9250.96720.975-0.202-0.2020.0000.0000.0000.000
105B396LYS10.9190.98116.781-0.391-0.3910.0000.0000.0000.000
106B397ALA00.0410.02214.445-0.034-0.0340.0000.0000.0000.000
107B398PRO0-0.003-0.01214.2500.0440.0440.0000.0000.0000.000
108B399ASP-1-0.753-0.8449.8270.9280.9280.0000.0000.0000.000
109B400GLY0-0.058-0.03511.4330.1200.1200.0000.0000.0000.000
110B401ARG10.8120.86110.451-0.662-0.6620.0000.0000.0000.000
111B402ILE0-0.055-0.02414.063-0.055-0.0550.0000.0000.0000.000
112B403VAL00.0550.03215.515-0.017-0.0170.0000.0000.0000.000
113B404GLU-1-0.902-0.95018.0050.0990.0990.0000.0000.0000.000
114B405LEU0-0.005-0.00820.302-0.010-0.0100.0000.0000.0000.000
115B406VAL00.0300.01423.111-0.002-0.0020.0000.0000.0000.000
116B407LYS10.8100.90125.296-0.137-0.1370.0000.0000.0000.000
117B408GLU-1-0.828-0.88828.3920.0590.0590.0000.0000.0000.000
118B409VAL0-0.044-0.01731.6330.0060.0060.0000.0000.0000.000
119B410SER0-0.061-0.06933.712-0.006-0.0060.0000.0000.0000.000
120B411LYS10.9280.96835.765-0.070-0.0700.0000.0000.0000.000
121B412SER00.014-0.00339.596-0.002-0.0020.0000.0000.0000.000
122B413TYR0-0.040-0.01142.8110.0020.0020.0000.0000.0000.000
123B414PRO00.0230.02046.045-0.001-0.0010.0000.0000.0000.000
124B415ILE00.015-0.00149.554-0.001-0.0010.0000.0000.0000.000
125B416SER0-0.017-0.01652.101-0.001-0.0010.0000.0000.0000.000
126B417GLU-1-0.901-0.94748.6270.0420.0420.0000.0000.0000.000
127B418GLY00.0480.03453.092-0.001-0.0010.0000.0000.0000.000
128B419PRO0-0.090-0.07050.6250.0020.0020.0000.0000.0000.000
129B420GLU-1-0.847-0.91349.8220.0320.0320.0000.0000.0000.000
130B421ARG11.0501.03641.173-0.051-0.0510.0000.0000.0000.000
131B422ALA0-0.063-0.02845.4190.0020.0020.0000.0000.0000.000
132B423ASN00.002-0.04745.4480.0020.0020.0000.0000.0000.000
133B424GLU-1-0.844-0.90145.1720.0390.0390.0000.0000.0000.000
134B425LEU0-0.008-0.00538.9770.0010.0010.0000.0000.0000.000
135B426VAL0-0.040-0.03641.8580.0000.0000.0000.0000.0000.000
136B427GLU-1-0.899-0.95542.8860.0310.0310.0000.0000.0000.000
137B428SER00.0780.02740.2430.0000.0000.0000.0000.0000.000
138B429TYR0-0.069-0.06134.679-0.001-0.0010.0000.0000.0000.000
139B430ARG10.8620.92739.248-0.032-0.0320.0000.0000.0000.000
140B431LYS10.9450.99641.496-0.031-0.0310.0000.0000.0000.000
141B432ALA0-0.0190.00136.3990.0000.0000.0000.0000.0000.000
142B433SER0-0.057-0.03535.1020.0010.0010.0000.0000.0000.000
143B434ASN00.0580.03936.3680.0010.0010.0000.0000.0000.000
144B435LYS10.8700.95931.818-0.029-0.0290.0000.0000.0000.000
145B436ALA00.0410.00936.8160.0030.0030.0000.0000.0000.000
146B437TYR0-0.005-0.03131.4810.0010.0010.0000.0000.0000.000
147B438PHE0-0.010-0.00528.4740.0000.0000.0000.0000.0000.000
148B439GLU-1-0.909-0.97327.8480.0100.0100.0000.0000.0000.000
149B440TRP00.015-0.00521.7340.0060.0060.0000.0000.0000.000
150B441THR00.0220.00418.617-0.008-0.0080.0000.0000.0000.000
151B442ILE0-0.020-0.00118.1470.0180.0180.0000.0000.0000.000
152B443GLU-1-0.721-0.83411.3410.3120.3120.0000.0000.0000.000
153B444ALA00.0030.00214.9090.0150.0150.0000.0000.0000.000
154B445ARG10.8250.9118.135-0.290-0.2900.0000.0000.0000.000
155B446ASP-1-0.811-0.89914.6240.3590.3590.0000.0000.0000.000
156B447LEU0-0.011-0.00816.673-0.011-0.0110.0000.0000.0000.000
157B448SER0-0.045-0.02318.538-0.003-0.0030.0000.0000.0000.000
158B449LEU0-0.007-0.00216.858-0.002-0.0020.0000.0000.0000.000
159B450LEU0-0.052-0.01120.990-0.007-0.0070.0000.0000.0000.000
160B451GLY00.0290.02424.165-0.002-0.0020.0000.0000.0000.000
161B452SER00.015-0.00527.660-0.008-0.0080.0000.0000.0000.000
162B453HIS10.8260.86529.920-0.065-0.0650.0000.0000.0000.000
163B454VAL00.0740.04426.920-0.006-0.0060.0000.0000.0000.000
164B455ARG10.9050.97624.163-0.065-0.0650.0000.0000.0000.000
165B456LYS10.9320.95027.360-0.045-0.0450.0000.0000.0000.000
166B457ALA0-0.034-0.00230.581-0.006-0.0060.0000.0000.0000.000
167B458THR00.0260.01025.228-0.002-0.0020.0000.0000.0000.000
168B459TYR0-0.097-0.03428.375-0.003-0.0030.0000.0000.0000.000
169B460GLN00.0730.03922.929-0.005-0.0050.0000.0000.0000.000
170B461THR0-0.001-0.01727.0810.0010.0010.0000.0000.0000.000
171B462TYR0-0.009-0.01628.318-0.003-0.0030.0000.0000.0000.000
172B463ALA00.0270.00230.7740.0050.0050.0000.0000.0000.000
173B464PRO0-0.029-0.00832.638-0.003-0.0030.0000.0000.0000.000
174B465ILE00.0100.00034.378-0.002-0.0020.0000.0000.0000.000
175B466LEU0-0.028-0.02135.7780.0020.0020.0000.0000.0000.000
176B467TYR00.0110.01035.7490.0010.0010.0000.0000.0000.000
177B468GLU-1-0.904-0.93137.770-0.023-0.0230.0000.0000.0000.000
178B469ASN0-0.0350.01740.5520.0010.0010.0000.0000.0000.000
179B470ASP-1-0.803-0.94142.013-0.026-0.0260.0000.0000.0000.000
180B471HIS0-0.0100.01244.5780.0010.0010.0000.0000.0000.000
181B472PHE0-0.021-0.01346.4750.0010.0010.0000.0000.0000.000
182B473PHE0-0.013-0.00949.1990.0010.0010.0000.0000.0000.000
183B474ASP-1-0.887-0.95146.758-0.032-0.0320.0000.0000.0000.000
184B475TYR0-0.112-0.05650.2120.0010.0010.0000.0000.0000.000
185B476MET00.0180.00951.9300.0010.0010.0000.0000.0000.000
186B477GLN0-0.0040.03953.8040.0010.0010.0000.0000.0000.000
187B478LYS10.8950.96850.8210.0300.0300.0000.0000.0000.000
188B479SER0-0.056-0.04655.5790.0000.0000.0000.0000.0000.000
189B480LYS10.9160.94658.1490.0190.0190.0000.0000.0000.000
190B481PHE00.0580.00157.1320.0000.0000.0000.0000.0000.000
191B482HIS0-0.0220.00861.3470.0000.0000.0000.0000.0000.000
192B483LEU00.0300.03058.6840.0000.0000.0000.0000.0000.000
193B484THR0-0.003-0.01758.4290.0010.0010.0000.0000.0000.000
194B485ILE0-0.0140.00955.251-0.001-0.0010.0000.0000.0000.000
195B486GLU-1-0.862-0.95355.810-0.014-0.0140.0000.0000.0000.000
196B487GLY00.0130.01056.7370.0000.0000.0000.0000.0000.000
197B488PRO00.051-0.00751.7790.0000.0000.0000.0000.0000.000
198B489LYS10.9050.95949.9910.0190.0190.0000.0000.0000.000
199B490VAL00.0430.03253.9560.0000.0000.0000.0000.0000.000
200B491LEU00.0370.02754.2380.0000.0000.0000.0000.0000.000
201B492ALA00.008-0.00651.1370.0000.0000.0000.0000.0000.000
202B493TYR0-0.068-0.04852.9490.0000.0000.0000.0000.0000.000
203B494LEU00.001-0.01155.0950.0000.0000.0000.0000.0000.000
204B495LEU00.0010.00752.2190.0000.0000.0000.0000.0000.000
205B496GLY00.0150.00352.3310.0000.0000.0000.0000.0000.000
206B497LEU0-0.021-0.02253.2940.0000.0000.0000.0000.0000.000
207B498TRP0-0.0050.00752.8750.0000.0000.0000.0000.0000.000
208B499ILE0-0.030-0.03550.0180.0000.0000.0000.0000.0000.000
209B500GLY0-0.041-0.03553.3560.0000.0000.0000.0000.0000.000
210B501ASP-1-0.793-0.86254.730-0.011-0.0110.0000.0000.0000.000
211B502GLY00.0130.01057.9140.0000.0000.0000.0000.0000.000
212B503LEU0-0.052-0.01058.0720.0000.0000.0000.0000.0000.000
213B504SER00.005-0.03055.3100.0000.0000.0000.0000.0000.000
214B505ASP-1-0.826-0.86557.204-0.016-0.0160.0000.0000.0000.000
215B506ARG10.8520.88159.9120.0140.0140.0000.0000.0000.000
216B507ALA0-0.0080.03160.3080.0000.0000.0000.0000.0000.000
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