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: 7G9RK

Calculation Name: 2YN7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YN7

Chain ID: A

ChEMBL ID:

UniProt ID: O50955

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2717294.22142
FMO2-HF: Nuclear repulsion 2627642.971579
FMO2-HF: Total energy -89651.249841
FMO2-MP2: Total energy -89912.763314


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(A:193:SER)


Summations of interaction energy for fragment #1(A:193:SER)
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.
-14.802-8.253.963-4.565-5.9490.029
Interaction energy analysis for fragmet #1(A:193:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.108 / q_NPA : 0.061
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].
3A195LEU00.0080.0322.854-4.579-0.9330.600-1.953-2.2920.013
4A196GLN00.0360.0032.130-8.367-6.4423.358-2.184-3.1000.015
5A197THR0-0.030-0.0193.566-1.993-1.0120.005-0.428-0.5570.001
6A198LEU0-0.020-0.0105.8620.0570.0570.0000.0000.0000.000
7A199LYS10.8960.9437.0550.0790.0790.0000.0000.0000.000
8A200ASN00.0480.0137.9830.0100.0100.0000.0000.0000.000
9A201GLU-1-0.869-0.8989.714-0.099-0.0990.0000.0000.0000.000
10A202LEU00.0380.01811.6740.0130.0130.0000.0000.0000.000
11A203ILE00.0310.01111.193-0.007-0.0070.0000.0000.0000.000
12A204ARG10.8450.92213.1910.3010.3010.0000.0000.0000.000
13A205ALA00.0180.01815.7180.0170.0170.0000.0000.0000.000
14A206ILE00.010-0.00717.4130.0110.0110.0000.0000.0000.000
15A207SER0-0.008-0.01417.5490.0050.0050.0000.0000.0000.000
16A208GLU-1-0.854-0.92017.885-0.201-0.2010.0000.0000.0000.000
17A209GLU-1-0.827-0.90121.643-0.059-0.0590.0000.0000.0000.000
18A210LYS10.8820.93621.8870.0570.0570.0000.0000.0000.000
19A211ASN0-0.0030.01522.3630.0080.0080.0000.0000.0000.000
20A212LYS10.8400.89824.4550.0810.0810.0000.0000.0000.000
21A213THR0-0.030-0.01627.6480.0020.0020.0000.0000.0000.000
22A214GLN0-0.010-0.01027.1860.0060.0060.0000.0000.0000.000
23A215ASN0-0.063-0.01129.241-0.002-0.0020.0000.0000.0000.000
24A216ASN00.025-0.00131.3300.0000.0000.0000.0000.0000.000
25A217PHE0-0.046-0.02531.6460.0000.0000.0000.0000.0000.000
26A218GLY00.0190.01835.1270.0000.0000.0000.0000.0000.000
27A219PHE0-0.054-0.01938.0120.0030.0030.0000.0000.0000.000
28A220ARG10.8360.89539.7690.0300.0300.0000.0000.0000.000
29A221GLU-1-0.759-0.81942.772-0.024-0.0240.0000.0000.0000.000
30A222THR0-0.0140.00144.7210.0000.0000.0000.0000.0000.000
31A223TYR0-0.033-0.04748.1530.0010.0010.0000.0000.0000.000
32A224ASP-1-0.759-0.85150.931-0.020-0.0200.0000.0000.0000.000
33A225GLN0-0.028-0.04246.9870.0020.0020.0000.0000.0000.000
34A226PHE00.035-0.00543.7220.0000.0000.0000.0000.0000.000
35A227LYS10.8460.90648.1430.0200.0200.0000.0000.0000.000
36A228MET0-0.0420.01744.2410.0020.0020.0000.0000.0000.000
37A229LYS10.8300.91649.4150.0170.0170.0000.0000.0000.000
38A230ASP-1-0.826-0.89451.002-0.015-0.0150.0000.0000.0000.000
39A231SER00.0760.00651.7550.0010.0010.0000.0000.0000.000
40A232ALA0-0.028-0.02047.4060.0010.0010.0000.0000.0000.000
41A233PHE0-0.038-0.03243.1540.0010.0010.0000.0000.0000.000
42A234GLU-1-0.853-0.89647.939-0.012-0.0120.0000.0000.0000.000
43A235LEU0-0.053-0.01050.0200.0010.0010.0000.0000.0000.000
44A236LEU0-0.030-0.02144.1980.0010.0010.0000.0000.0000.000
45A237ASP-1-0.853-0.90446.808-0.010-0.0100.0000.0000.0000.000
46A238VAL0-0.058-0.03041.0750.0000.0000.0000.0000.0000.000
47A239ILE00.0420.02039.0420.0010.0010.0000.0000.0000.000
48A240SER0-0.148-0.10336.4790.0010.0010.0000.0000.0000.000
49A241SER0-0.035-0.03738.3450.0000.0000.0000.0000.0000.000
50A242ALA00.0490.04437.9960.0010.0010.0000.0000.0000.000
51A243LYS10.9430.95633.5770.0210.0210.0000.0000.0000.000
52A244VAL0-0.041-0.02338.244-0.002-0.0020.0000.0000.0000.000
53A245TYR00.0010.00741.2340.0000.0000.0000.0000.0000.000
54A246ASP-1-0.839-0.93143.318-0.006-0.0060.0000.0000.0000.000
55A247ARG10.9130.94842.3110.0040.0040.0000.0000.0000.000
56A248SER0-0.036-0.00646.2080.0000.0000.0000.0000.0000.000
57A249TYR0-0.064-0.03547.4150.0000.0000.0000.0000.0000.000
58A250ALA0-0.028-0.00544.905-0.001-0.0010.0000.0000.0000.000
59A251PRO00.0120.01145.2820.0010.0010.0000.0000.0000.000
60A252GLN00.0630.02746.9230.0000.0000.0000.0000.0000.000
61A253LEU0-0.038-0.01242.789-0.001-0.0010.0000.0000.0000.000
62A254ASN00.0410.03546.328-0.002-0.0020.0000.0000.0000.000
63A255SER0-0.0170.00648.514-0.001-0.0010.0000.0000.0000.000
64A256ASN0-0.018-0.01848.0110.0000.0000.0000.0000.0000.000
65A257THR00.0020.00046.7240.0000.0000.0000.0000.0000.000
66A258PRO00.0190.00342.523-0.001-0.0010.0000.0000.0000.000
67A259GLU-1-0.868-0.93940.952-0.022-0.0220.0000.0000.0000.000
68A260ALA00.0100.01241.3900.0000.0000.0000.0000.0000.000
69A261GLU-1-0.816-0.88641.873-0.030-0.0300.0000.0000.0000.000
70A262ASN0-0.050-0.02535.5730.0000.0000.0000.0000.0000.000
71A263GLU-1-0.708-0.83938.142-0.017-0.0170.0000.0000.0000.000
72A264ARG10.7860.85939.5810.0220.0220.0000.0000.0000.000
73A265ASN0-0.023-0.03937.368-0.003-0.0030.0000.0000.0000.000
74A266LYS10.8500.94033.3070.0260.0260.0000.0000.0000.000
75A267PHE00.014-0.00136.1820.0000.0000.0000.0000.0000.000
76A268TYR0-0.034-0.06338.4440.0000.0000.0000.0000.0000.000
77A269ALA00.0300.02132.817-0.002-0.0020.0000.0000.0000.000
78A270LEU0-0.088-0.02433.449-0.002-0.0020.0000.0000.0000.000
79A271MET0-0.056-0.00734.7990.0000.0000.0000.0000.0000.000
80A272ASP-1-0.839-0.90831.777-0.043-0.0430.0000.0000.0000.000
81A273PHE0-0.029-0.01332.581-0.003-0.0030.0000.0000.0000.000
82A274ASP-1-0.835-0.90436.690-0.036-0.0360.0000.0000.0000.000
83A275GLN00.007-0.01338.8320.0040.0040.0000.0000.0000.000
84A276TYR0-0.028-0.01142.2650.0020.0020.0000.0000.0000.000
85A277LYS10.8410.91936.8160.0300.0300.0000.0000.0000.000
86A278ILE0-0.037-0.01539.4540.0020.0020.0000.0000.0000.000
87A279GLU-1-0.865-0.92643.167-0.019-0.0190.0000.0000.0000.000
88A280GLN0-0.0050.00745.3010.0020.0020.0000.0000.0000.000
89A281PHE00.0240.00243.3530.0020.0020.0000.0000.0000.000
90A282GLY00.028-0.00346.1790.0020.0020.0000.0000.0000.000
91A283SER00.0270.00048.2110.0010.0010.0000.0000.0000.000
92A284ILE0-0.020-0.00247.7900.0010.0010.0000.0000.0000.000
93A285MET0-0.066-0.03647.0270.0020.0020.0000.0000.0000.000
94A286GLU-1-0.889-0.95150.690-0.014-0.0140.0000.0000.0000.000
95A287ALA0-0.006-0.00453.8570.0010.0010.0000.0000.0000.000
96A288LEU0-0.062-0.03250.6790.0010.0010.0000.0000.0000.000
97A289TYR0-0.043-0.05654.1230.0010.0010.0000.0000.0000.000
98A290ASN0-0.052-0.01555.7510.0000.0000.0000.0000.0000.000
99A291GLU-1-0.877-0.91958.323-0.006-0.0060.0000.0000.0000.000
100A292ASN00.0560.00857.7200.0000.0000.0000.0000.0000.000
101A293GLN0-0.039-0.01757.3370.0000.0000.0000.0000.0000.000
102A294ASN0-0.044-0.02654.3350.0010.0010.0000.0000.0000.000
103A295HIS0-0.010-0.01552.9810.0000.0000.0000.0000.0000.000
104A296SER0-0.039-0.01551.6250.0000.0000.0000.0000.0000.000
105A297LEU00.0010.01048.2820.0000.0000.0000.0000.0000.000
106A298ILE00.0410.02648.0960.0000.0000.0000.0000.0000.000
107A299ARG10.9060.95547.2060.0050.0050.0000.0000.0000.000
108A300GLU-1-0.832-0.90843.105-0.001-0.0010.0000.0000.0000.000
109A301LEU0-0.008-0.00443.4800.0000.0000.0000.0000.0000.000
110A302MET00.0260.03242.358-0.001-0.0010.0000.0000.0000.000
111A303ILE0-0.022-0.00741.134-0.001-0.0010.0000.0000.0000.000
112A304SER0-0.060-0.03239.3050.0000.0000.0000.0000.0000.000
113A305GLY00.0800.03837.6460.0000.0000.0000.0000.0000.000
114A306LEU00.0220.00136.631-0.001-0.0010.0000.0000.0000.000
115A307GLY00.0290.01536.145-0.001-0.0010.0000.0000.0000.000
116A308THR0-0.050-0.03232.6570.0030.0030.0000.0000.0000.000
117A309GLN0-0.003-0.00930.4900.0020.0020.0000.0000.0000.000
118A310ILE00.0140.01131.381-0.002-0.0020.0000.0000.0000.000
119A311SER0-0.032-0.02930.8150.0010.0010.0000.0000.0000.000
120A312PHE0-0.007-0.00925.9320.0040.0040.0000.0000.0000.000
121A313GLU-1-0.795-0.88526.578-0.033-0.0330.0000.0000.0000.000
122A314LEU0-0.017-0.00326.712-0.002-0.0020.0000.0000.0000.000
123A315ALA00.001-0.00224.6090.0030.0030.0000.0000.0000.000
124A316LEU0-0.003-0.00521.8990.0050.0050.0000.0000.0000.000
125A317GLU-1-0.885-0.93221.769-0.047-0.0470.0000.0000.0000.000
126A318GLU-1-0.840-0.91522.0780.0080.0080.0000.0000.0000.000
127A319ILE00.014-0.00817.4660.0120.0120.0000.0000.0000.000
128A320ASN0-0.0010.00917.7440.0030.0030.0000.0000.0000.000
129A321LYS10.9030.95317.6510.0110.0110.0000.0000.0000.000
130A322LYS10.8080.89317.604-0.038-0.0380.0000.0000.0000.000
131A323ILE0-0.013-0.01112.2390.0280.0280.0000.0000.0000.000
132A324GLU-1-0.950-0.97013.284-0.086-0.0860.0000.0000.0000.000
133A325ILE00.0110.00015.073-0.014-0.0140.0000.0000.0000.000
134A326PHE00.023-0.00413.0290.0030.0030.0000.0000.0000.000
135A327ASN00.0220.0199.996-0.035-0.0350.0000.0000.0000.000
136A328GLN00.0210.00711.586-0.056-0.0560.0000.0000.0000.000
137A329ASP-1-0.825-0.90114.3650.0180.0180.0000.0000.0000.000
138A330TYR0-0.062-0.0345.0980.2360.2360.0000.0000.0000.000
139A331LEU0-0.023-0.0139.474-0.051-0.0510.0000.0000.0000.000
140A332ASN0-0.098-0.05311.7520.0100.0100.0000.0000.0000.000
141A333ALA0-0.021-0.00712.9110.0230.0230.0000.0000.0000.000
142A334LYS10.8730.93213.9240.0240.0240.0000.0000.0000.000
143A335ILE0-0.046-0.01011.8790.0290.0290.0000.0000.0000.000
144A336ASN00.0330.01410.8040.0520.0520.0000.0000.0000.000
145A337SER00.0450.0076.073-0.019-0.0190.0000.0000.0000.000
146A338PHE00.0200.0217.7800.3240.3240.0000.0000.0000.000
147A339ASP-1-0.781-0.89310.3670.2680.2680.0000.0000.0000.000
148A340PHE00.0290.0077.6380.0160.0160.0000.0000.0000.000
149A341THR0-0.026-0.0377.5090.2160.2160.0000.0000.0000.000
150A342MET00.0140.0229.380-0.100-0.1000.0000.0000.0000.000
151A343LYS10.9610.99913.072-0.263-0.2630.0000.0000.0000.000
152A344LEU00.0080.0098.556-0.041-0.0410.0000.0000.0000.000
153A345LYS10.8710.92012.421-0.509-0.5090.0000.0000.0000.000
154A346GLU-1-0.898-0.93913.7970.0960.0960.0000.0000.0000.000
155A347LEU00.003-0.00114.857-0.034-0.0340.0000.0000.0000.000
156A348LYS10.8360.89613.388-0.032-0.0320.0000.0000.0000.000
157A349SER0-0.015-0.01016.469-0.029-0.0290.0000.0000.0000.000
158A350LYS10.8270.90119.367-0.112-0.1120.0000.0000.0000.000
159A351LEU00.0320.01918.081-0.013-0.0130.0000.0000.0000.000
160A352ASN0-0.003-0.01318.953-0.025-0.0250.0000.0000.0000.000
161A353GLN0-0.049-0.01422.217-0.002-0.0020.0000.0000.0000.000
162A354ILE00.004-0.00323.314-0.006-0.0060.0000.0000.0000.000
163A355LEU00.0270.02021.604-0.006-0.0060.0000.0000.0000.000
164A356ASP-1-0.837-0.90425.732-0.023-0.0230.0000.0000.0000.000
165A357LYS10.8690.95828.080-0.015-0.0150.0000.0000.0000.000
166A358ARG10.7970.86929.0250.0350.0350.0000.0000.0000.000
167A359LYS10.7760.86526.2760.0260.0260.0000.0000.0000.000
168A360GLU-1-0.846-0.89631.557-0.008-0.0080.0000.0000.0000.000
169A361TRP00.006-0.00534.030-0.001-0.0010.0000.0000.0000.000
170A362SER00.0340.02034.3660.0000.0000.0000.0000.0000.000
171A363ARG10.8690.92230.2220.0140.0140.0000.0000.0000.000
172A364GLN0-0.011-0.02137.3170.0010.0010.0000.0000.0000.000
173A365ALA0-0.0080.00339.4740.0000.0000.0000.0000.0000.000
174A366ASP-1-0.815-0.90837.890-0.027-0.0270.0000.0000.0000.000
175A367GLY0-0.008-0.00341.2590.0000.0000.0000.0000.0000.000
176A368LEU0-0.0360.00343.3470.0010.0010.0000.0000.0000.000
177A369ILE00.0380.01842.4370.0000.0000.0000.0000.0000.000
178A370ALA0-0.0130.00144.6090.0000.0000.0000.0000.0000.000
179A371ASN0-0.085-0.02746.5530.0010.0010.0000.0000.0000.000
180A372ALA00.0730.02749.3220.0000.0000.0000.0000.0000.000
181A373SER0-0.025-0.02448.1750.0000.0000.0000.0000.0000.000
182A374SER0-0.023-0.00550.3120.0000.0000.0000.0000.0000.000
183A375ASN0-0.022-0.02253.2050.0010.0010.0000.0000.0000.000
184A376SER00.0570.04652.9350.0010.0010.0000.0000.0000.000
185A377SER00.003-0.00855.3130.0010.0010.0000.0000.0000.000
186A378LEU0-0.054-0.01757.9900.0000.0000.0000.0000.0000.000
187A379SER0-0.028-0.01957.6470.0010.0010.0000.0000.0000.000
188A380ASP-1-0.797-0.88059.790-0.005-0.0050.0000.0000.0000.000
189A381SER00.0990.04057.5080.0000.0000.0000.0000.0000.000
190A382LYS10.9070.96356.7880.0040.0040.0000.0000.0000.000
191A383SER0-0.073-0.08356.8580.0010.0010.0000.0000.0000.000
192A384LEU0-0.0040.02052.3470.0000.0000.0000.0000.0000.000
193A385ALA00.0490.01952.5190.0000.0000.0000.0000.0000.000
194A386GLU-1-0.864-0.92452.042-0.001-0.0010.0000.0000.0000.000
195A387TYR0-0.020-0.02048.3220.0010.0010.0000.0000.0000.000
196A388ILE00.0740.03346.8150.0010.0010.0000.0000.0000.000
197A389LYS10.8520.90847.4550.0020.0020.0000.0000.0000.000
198A390LYS10.8550.92848.8430.0020.0020.0000.0000.0000.000
199A391ARG10.7990.90446.4670.0030.0030.0000.0000.0000.000
200A392TYR00.0080.00443.1200.0000.0000.0000.0000.0000.000
201A393LEU00.0300.02842.4040.0000.0000.0000.0000.0000.000
202A394ASP-1-0.839-0.91442.4440.0040.0040.0000.0000.0000.000
203A395ASN0-0.054-0.02339.0140.0030.0030.0000.0000.0000.000
204A396MET0-0.013-0.00137.8970.0010.0010.0000.0000.0000.000
205A397GLN0-0.034-0.03838.0910.0010.0010.0000.0000.0000.000
206A398ASN0-0.037-0.04136.5990.0040.0040.0000.0000.0000.000
207A399ALA0-0.052-0.01533.8540.0030.0030.0000.0000.0000.000
208A400ARG10.9790.99533.2290.0000.0000.0000.0000.0000.000
209A401GLN0-0.074-0.04233.896-0.001-0.0010.0000.0000.0000.000
210A402SER00.0230.01730.4960.0020.0020.0000.0000.0000.000
211A403VAL0-0.0080.00828.4830.0050.0050.0000.0000.0000.000
212A404LEU00.0170.01729.1350.0020.0020.0000.0000.0000.000
213A405GLU-1-0.846-0.93330.4260.0250.0250.0000.0000.0000.000
214A406ALA0-0.0160.00325.4450.0060.0060.0000.0000.0000.000
215A407TYR00.036-0.01125.7740.0050.0050.0000.0000.0000.000
216A408ILE0-0.004-0.00926.6360.0030.0030.0000.0000.0000.000
217A409SER0-0.081-0.04325.1060.0070.0070.0000.0000.0000.000
218A410ILE0-0.0120.00320.9230.0140.0140.0000.0000.0000.000
219A411MET0-0.0150.04522.8210.0010.0010.0000.0000.0000.000