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: 1NYQZ

Calculation Name: 2F2F-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2F2F

Chain ID: B

ChEMBL ID:

UniProt ID: O87120

Base Structure: X-ray

Registration Date: 2023-09-23

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 261
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3572374.759055
FMO2-HF: Nuclear repulsion 3471964.388406
FMO2-HF: Total energy -100410.37065
FMO2-MP2: Total energy -100707.778461


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:23:ASN)


Summations of interaction energy for fragment #1(B:23:ASN)
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.
-47.479-38.43625.458-15.78-18.717-0.123
Interaction energy analysis for fragmet #1(B:23:ASN)
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 : -0.007
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].
3B25SER0-0.040-0.0382.583-2.1081.5240.567-1.872-2.3270.002
4B26ASP-1-0.893-0.9211.939-13.537-12.3717.668-4.569-4.264-0.049
5B27PHE0-0.070-0.0363.0172.2082.8090.019-0.185-0.4350.001
6B28LYS10.8310.8977.5241.3331.3330.0000.0000.0000.000
7B29VAL00.0270.0178.9330.3310.3310.0000.0000.0000.000
8B30ALA00.001-0.01111.7230.1060.1060.0000.0000.0000.000
9B31THR00.0130.00415.4470.0350.0350.0000.0000.0000.000
10B32TRP0-0.055-0.03718.3180.0200.0200.0000.0000.0000.000
11B33ASN00.004-0.00122.1200.0420.0420.0000.0000.0000.000
12B34LEU00.0170.03225.0280.0140.0140.0000.0000.0000.000
13B35GLN0-0.013-0.02427.1150.0070.0070.0000.0000.0000.000
14B36GLY00.0240.01729.7180.0160.0160.0000.0000.0000.000
15B37SER0-0.043-0.03031.2720.0130.0130.0000.0000.0000.000
16B38SER00.0300.00734.883-0.004-0.0040.0000.0000.0000.000
17B39ALA00.0130.02237.4310.0060.0060.0000.0000.0000.000
18B40VAL0-0.023-0.01333.9950.0000.0000.0000.0000.0000.000
19B41ASN00.034-0.00129.316-0.013-0.0130.0000.0000.0000.000
20B42GLU-1-0.727-0.83330.653-0.209-0.2090.0000.0000.0000.000
21B43SER00.0110.00730.965-0.013-0.0130.0000.0000.0000.000
22B44LYS10.8480.92829.0980.2740.2740.0000.0000.0000.000
23B45TRP00.0420.00622.493-0.041-0.0410.0000.0000.0000.000
24B46ASN0-0.057-0.05726.595-0.021-0.0210.0000.0000.0000.000
25B47ILE0-0.0020.01428.871-0.001-0.0010.0000.0000.0000.000
26B48ASN00.0170.01226.1620.0000.0000.0000.0000.0000.000
27B49VAL00.0190.01821.633-0.038-0.0380.0000.0000.0000.000
28B50ARG10.8450.92422.2710.2120.2120.0000.0000.0000.000
29B51GLN00.0150.01323.134-0.036-0.0360.0000.0000.0000.000
30B52LEU00.0480.03020.034-0.029-0.0290.0000.0000.0000.000
31B53LEU0-0.0070.01917.281-0.080-0.0800.0000.0000.0000.000
32B54SER0-0.081-0.04019.1340.0260.0260.0000.0000.0000.000
33B55GLY00.0300.00520.115-0.038-0.0380.0000.0000.0000.000
34B56GLU-1-0.927-0.97417.375-0.548-0.5480.0000.0000.0000.000
35B57GLN0-0.013-0.00915.641-0.117-0.1170.0000.0000.0000.000
36B58GLY00.0150.03716.612-0.064-0.0640.0000.0000.0000.000
37B59ALA0-0.035-0.02314.356-0.109-0.1090.0000.0000.0000.000
38B60ASP-1-0.826-0.89710.211-1.398-1.3980.0000.0000.0000.000
39B61ILE0-0.024-0.0148.6210.2000.2000.0000.0000.0000.000
40B62LEU0-0.021-0.00612.591-0.105-0.1050.0000.0000.0000.000
41B63MET0-0.0150.01612.8870.1680.1680.0000.0000.0000.000
42B64VAL0-0.011-0.01317.5310.0080.0080.0000.0000.0000.000
43B65GLN0-0.020-0.01719.4080.0430.0430.0000.0000.0000.000
44B66GLU-1-0.735-0.84523.743-0.292-0.2920.0000.0000.0000.000
45B67ALA00.0390.02324.1850.0100.0100.0000.0000.0000.000
46B68GLY00.0280.03326.2630.0140.0140.0000.0000.0000.000
47B69SER0-0.0380.00628.8100.0130.0130.0000.0000.0000.000
48B70LEU00.0290.01024.098-0.021-0.0210.0000.0000.0000.000
49B71PRO00.0060.00825.8740.0160.0160.0000.0000.0000.000
50B72SER0-0.027-0.04028.8660.0140.0140.0000.0000.0000.000
51B73SER0-0.031-0.01129.7020.0080.0080.0000.0000.0000.000
52B74ALA0-0.047-0.02425.6140.0020.0020.0000.0000.0000.000
53B75VAL0-0.023-0.01626.1130.0140.0140.0000.0000.0000.000
54B76ARG10.7920.87824.9750.0140.0140.0000.0000.0000.000
55B77THR0-0.025-0.04521.9300.0130.0130.0000.0000.0000.000
56B78SER00.014-0.00725.217-0.003-0.0030.0000.0000.0000.000
57B79ARG10.7770.89716.034-0.172-0.1720.0000.0000.0000.000
58B80VAL00.0220.01623.927-0.032-0.0320.0000.0000.0000.000
59B81ILE0-0.013-0.02019.2790.0300.0300.0000.0000.0000.000
60B82GLN0-0.0140.00221.879-0.010-0.0100.0000.0000.0000.000
61B83HIS00.0140.00622.0020.0070.0070.0000.0000.0000.000
62B84GLY00.0270.01025.6010.0090.0090.0000.0000.0000.000
63B85GLY00.0030.00327.358-0.006-0.0060.0000.0000.0000.000
64B86THR0-0.0030.00024.930-0.006-0.0060.0000.0000.0000.000
65B87PRO00.0060.02226.1730.0130.0130.0000.0000.0000.000
66B88ILE0-0.0100.00019.670-0.030-0.0300.0000.0000.0000.000
67B89GLU-1-0.782-0.85223.145-0.031-0.0310.0000.0000.0000.000
68B90GLU-1-0.720-0.80218.6150.0020.0020.0000.0000.0000.000
69B91TYR0-0.037-0.03421.5770.0240.0240.0000.0000.0000.000
70B92THR0-0.0120.00020.718-0.015-0.0150.0000.0000.0000.000
71B93TRP0-0.007-0.01322.151-0.005-0.0050.0000.0000.0000.000
72B94ASN00.0400.00222.689-0.028-0.0280.0000.0000.0000.000
73B95LEU00.0240.01820.4750.0040.0040.0000.0000.0000.000
74B96GLY00.0050.01924.690-0.004-0.0040.0000.0000.0000.000
75B97THR00.006-0.00326.9510.0110.0110.0000.0000.0000.000
76B98ARG10.9980.98228.8720.0530.0530.0000.0000.0000.000
77B99SER00.0190.01630.5130.0060.0060.0000.0000.0000.000
78B100ARG10.9340.96425.8890.1110.1110.0000.0000.0000.000
79B101PRO00.0300.03124.666-0.023-0.0230.0000.0000.0000.000
80B102ASN00.006-0.00421.102-0.036-0.0360.0000.0000.0000.000
81B103MET00.0080.01220.319-0.027-0.0270.0000.0000.0000.000
82B104VAL00.0000.02317.682-0.046-0.0460.0000.0000.0000.000
83B105TYR00.019-0.00816.4090.0590.0590.0000.0000.0000.000
84B106ILE0-0.036-0.02917.979-0.076-0.0760.0000.0000.0000.000
85B107TYR00.003-0.01015.3470.0590.0590.0000.0000.0000.000
86B108TYR0-0.034-0.04019.350-0.044-0.0440.0000.0000.0000.000
87B109SER00.034-0.00422.5650.0330.0330.0000.0000.0000.000
88B110ARG10.8500.92624.4270.1010.1010.0000.0000.0000.000
89B111LEU00.0320.00124.8990.0190.0190.0000.0000.0000.000
90B112ASP-1-0.753-0.84328.890-0.161-0.1610.0000.0000.0000.000
91B113VAL00.024-0.02631.9120.0060.0060.0000.0000.0000.000
92B114GLY0-0.0120.00934.4490.0090.0090.0000.0000.0000.000
93B115ALA0-0.019-0.01635.7920.0050.0050.0000.0000.0000.000
94B116ASN0-0.0550.00232.186-0.006-0.0060.0000.0000.0000.000
95B117ARG10.8480.88431.6340.2270.2270.0000.0000.0000.000
96B118VAL0-0.048-0.03628.780-0.024-0.0240.0000.0000.0000.000
97B119ASN0-0.036-0.02726.9130.0080.0080.0000.0000.0000.000
98B120LEU0-0.0050.00021.844-0.028-0.0280.0000.0000.0000.000
99B121ALA0-0.006-0.01220.9550.0450.0450.0000.0000.0000.000
100B122ILE00.0000.00914.139-0.058-0.0580.0000.0000.0000.000
101B123VAL0-0.0230.00117.3810.0800.0800.0000.0000.0000.000
102B124SER00.032-0.00412.442-0.197-0.1970.0000.0000.0000.000
103B125ARG10.8270.89713.1750.6290.6290.0000.0000.0000.000
104B126ARG10.9250.9805.6050.5850.5850.0000.0000.0000.000
105B127GLN0-0.0040.00912.577-0.041-0.0410.0000.0000.0000.000
106B128ALA00.0330.01912.0950.0320.0320.0000.0000.0000.000
107B129ASP-1-0.786-0.86910.2081.0541.0540.0000.0000.0000.000
108B130GLU-1-0.854-0.91213.0080.6650.6650.0000.0000.0000.000
109B131ALA00.000-0.01014.168-0.107-0.1070.0000.0000.0000.000
110B132PHE0-0.024-0.00912.1660.0480.0480.0000.0000.0000.000
111B133ILE0-0.008-0.00817.640-0.065-0.0650.0000.0000.0000.000
112B134VAL0-0.0140.00117.2970.0440.0440.0000.0000.0000.000
113B135HIS00.0250.00420.398-0.057-0.0570.0000.0000.0000.000
114B136SER00.0110.02323.5380.0140.0140.0000.0000.0000.000
115B137ASP-1-0.810-0.90524.983-0.172-0.1720.0000.0000.0000.000
116B138SER0-0.021-0.01928.2130.0110.0110.0000.0000.0000.000
117B139SER0-0.017-0.00825.592-0.005-0.0050.0000.0000.0000.000
118B140VAL0-0.005-0.00127.8990.0060.0060.0000.0000.0000.000
119B141LEU0-0.065-0.02030.6840.0120.0120.0000.0000.0000.000
120B142GLN00.024-0.00132.1200.0090.0090.0000.0000.0000.000
121B143SER0-0.074-0.03727.227-0.003-0.0030.0000.0000.0000.000
122B144ARG10.8510.90825.3350.3080.3080.0000.0000.0000.000
123B145PRO00.0110.01822.639-0.024-0.0240.0000.0000.0000.000
124B146ALA00.0020.01217.666-0.029-0.0290.0000.0000.0000.000
125B147VAL00.006-0.00118.8640.0610.0610.0000.0000.0000.000
126B148GLY00.0390.00215.014-0.106-0.1060.0000.0000.0000.000
127B149ILE0-0.062-0.01811.5420.1130.1130.0000.0000.0000.000
128B150ARG10.7900.8718.928-1.346-1.3460.0000.0000.0000.000
129B151ILE0-0.025-0.0116.365-0.043-0.0430.0000.0000.0000.000
130B152GLY00.0200.0105.7520.0150.0150.0000.0000.0000.000
131B153THR00.0070.0053.922-1.228-1.016-0.001-0.034-0.1770.000
132B154ASP-1-0.804-0.8932.106-7.159-7.4447.946-3.563-4.098-0.055
133B155VAL0-0.029-0.0245.192-0.070-0.016-0.001-0.002-0.0510.000
134B156PHE00.0140.0005.457-0.181-0.1810.0000.0000.0000.000
135B157PHE00.033-0.00310.6530.2400.2400.0000.0000.0000.000
136B158THR0-0.0030.00414.311-0.124-0.1240.0000.0000.0000.000
137B159VAL00.007-0.00517.4320.0830.0830.0000.0000.0000.000
138B160HIS0-0.031-0.04820.156-0.037-0.0370.0000.0000.0000.000
139B161ALA00.0270.05423.7510.0430.0430.0000.0000.0000.000
140B162LEU0-0.021-0.01525.2990.0110.0110.0000.0000.0000.000
141B163ALA00.0290.00529.140-0.014-0.0140.0000.0000.0000.000
142B164THR0-0.034-0.00730.870-0.001-0.0010.0000.0000.0000.000
143B165GLY00.0330.01230.1480.0080.0080.0000.0000.0000.000
144B166GLY00.0350.01826.494-0.015-0.0150.0000.0000.0000.000
145B167SER0-0.027-0.01326.214-0.023-0.0230.0000.0000.0000.000
146B168ASP-1-0.725-0.84526.272-0.300-0.3000.0000.0000.0000.000
147B169ALA00.0110.00422.140-0.001-0.0010.0000.0000.0000.000
148B170VAL00.0060.00321.607-0.032-0.0320.0000.0000.0000.000
149B171SER0-0.025-0.03621.835-0.008-0.0080.0000.0000.0000.000
150B172LEU0-0.016-0.01420.2360.0080.0080.0000.0000.0000.000
151B173ILE0-0.0010.00516.124-0.013-0.0130.0000.0000.0000.000
152B174ARG10.7880.88017.6910.2270.2270.0000.0000.0000.000
153B175ASN00.037-0.00619.4020.0310.0310.0000.0000.0000.000
154B176ILE0-0.0030.02113.9750.0710.0710.0000.0000.0000.000
155B177PHE00.0480.00714.4010.0850.0850.0000.0000.0000.000
156B178THR0-0.006-0.01116.0690.0600.0600.0000.0000.0000.000
157B179THR0-0.069-0.04416.4180.0790.0790.0000.0000.0000.000
158B180PHE0-0.030-0.01412.1120.0960.0960.0000.0000.0000.000
159B181THR00.0550.04611.3490.1110.1110.0000.0000.0000.000
160B182SER0-0.028-0.03213.6320.0580.0580.0000.0000.0000.000
161B183SER0-0.055-0.01817.1940.0370.0370.0000.0000.0000.000
162B184PRO00.0070.03314.939-0.021-0.0210.0000.0000.0000.000
163B185SER00.001-0.01417.5060.0040.0040.0000.0000.0000.000
164B186SER0-0.082-0.06716.427-0.052-0.0520.0000.0000.0000.000
165B187PRO00.0180.00015.9880.0120.0120.0000.0000.0000.000
166B188GLU-1-0.788-0.87612.4741.1061.1060.0000.0000.0000.000
167B189ARG10.8500.92211.342-0.251-0.2510.0000.0000.0000.000
168B190ARG10.8320.91811.772-0.530-0.5300.0000.0000.0000.000
169B191GLY0-0.008-0.0028.182-0.262-0.2620.0000.0000.0000.000
170B192TYR0-0.043-0.0216.8291.1721.1720.0000.0000.0000.000
171B193SER00.0540.0453.180-2.724-1.6690.062-0.535-0.5820.006
172B194TRP0-0.037-0.0215.962-0.122-0.1220.0000.0000.0000.000
173B195MET0-0.0030.0038.336-0.512-0.5120.0000.0000.0000.000
174B196VAL0-0.021-0.01110.0790.2340.2340.0000.0000.0000.000
175B197VAL00.008-0.00512.897-0.072-0.0720.0000.0000.0000.000
176B198GLY00.0150.00215.6660.0930.0930.0000.0000.0000.000
177B199ASP-1-0.777-0.88919.380-0.461-0.4610.0000.0000.0000.000
178B200PHE00.0270.00017.4150.0660.0660.0000.0000.0000.000
179B201ASN0-0.069-0.03623.1580.0510.0510.0000.0000.0000.000
180B202ARG10.8600.93024.2690.4300.4300.0000.0000.0000.000
181B203ALA00.0610.04424.691-0.041-0.0410.0000.0000.0000.000
182B204PRO00.0570.02720.2300.0180.0180.0000.0000.0000.000
183B205VAL00.0480.02421.893-0.001-0.0010.0000.0000.0000.000
184B206ASN0-0.0100.00323.7350.0240.0240.0000.0000.0000.000
185B207LEU00.0320.02119.7500.0370.0370.0000.0000.0000.000
186B208GLU-1-0.804-0.89019.038-0.622-0.6220.0000.0000.0000.000
187B209ALA0-0.030-0.01921.3820.0240.0240.0000.0000.0000.000
188B210ALA0-0.014-0.00824.6320.0320.0320.0000.0000.0000.000
189B211LEU00.0280.00718.1340.0290.0290.0000.0000.0000.000
190B212ARG10.8010.87821.4770.5390.5390.0000.0000.0000.000
191B213GLN0-0.0230.00122.7900.0220.0220.0000.0000.0000.000
192B214GLU-1-0.823-0.88122.251-0.217-0.2170.0000.0000.0000.000
193B215PRO00.0260.00320.845-0.036-0.0360.0000.0000.0000.000
194B216ALA0-0.036-0.01019.091-0.039-0.0390.0000.0000.0000.000
195B217VAL00.0810.04916.911-0.022-0.0220.0000.0000.0000.000
196B218SER0-0.0190.00415.876-0.092-0.0920.0000.0000.0000.000
197B219GLU-1-0.846-0.90116.291-0.427-0.4270.0000.0000.0000.000
198B220ASN0-0.074-0.04712.616-0.078-0.0780.0000.0000.0000.000
199B221THR0-0.029-0.01811.639-0.071-0.0710.0000.0000.0000.000
200B222ILE00.0210.0169.9760.0860.0860.0000.0000.0000.000
201B223ILE0-0.018-0.00812.576-0.105-0.1050.0000.0000.0000.000
202B224ILE0-0.0050.00110.1620.0030.0030.0000.0000.0000.000
203B225ALA00.022-0.01314.7820.0160.0160.0000.0000.0000.000
204B226PRO0-0.024-0.00417.969-0.007-0.0070.0000.0000.0000.000
205B227THR0-0.006-0.02220.3390.0080.0080.0000.0000.0000.000
206B228GLU-1-0.898-0.92723.475-0.476-0.4760.0000.0000.0000.000
207B229PRO0-0.006-0.00524.669-0.029-0.0290.0000.0000.0000.000
208B230THR00.008-0.02822.277-0.008-0.0080.0000.0000.0000.000
209B231HIS00.0520.05425.3710.0090.0090.0000.0000.0000.000
210B232ARG10.8290.90128.8150.3230.3230.0000.0000.0000.000
211B233SER0-0.062-0.03831.8300.0110.0110.0000.0000.0000.000
212B234GLY00.0150.00931.4770.0130.0130.0000.0000.0000.000
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214B236ILE00.0070.00922.973-0.011-0.0110.0000.0000.0000.000
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