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: M357Z

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 OptHSide
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 -2709044.391943
FMO2-HF: Nuclear repulsion 2619393.90277
FMO2-HF: Total energy -89650.489172
FMO2-MP2: Total energy -89911.782955


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.
-17.129-17.16714.15-6.205-7.9070.039
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 : 0.038 / q_NPA : 0.018
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].
3A195LEU00.0010.0142.588-3.987-0.8701.655-1.807-2.9650.015
4A196GLN00.0460.0071.895-9.138-13.35712.456-3.956-4.2810.022
5A197THR0-0.0070.0033.734-2.832-1.7680.039-0.442-0.6610.002
6A198LEU0-0.025-0.0065.988-0.307-0.3070.0000.0000.0000.000
7A199LYS10.9010.9316.714-0.050-0.0500.0000.0000.0000.000
8A200ASN00.019-0.0017.496-0.194-0.1940.0000.0000.0000.000
9A201GLU-1-0.910-0.9369.3940.4820.4820.0000.0000.0000.000
10A202LEU0-0.010-0.00511.335-0.079-0.0790.0000.0000.0000.000
11A203ILE00.0580.02710.903-0.058-0.0580.0000.0000.0000.000
12A204ARG10.8470.91113.410-0.065-0.0650.0000.0000.0000.000
13A205ALA0-0.0090.00415.347-0.014-0.0140.0000.0000.0000.000
14A206ILE00.011-0.00816.742-0.011-0.0110.0000.0000.0000.000
15A207SER00.001-0.00917.299-0.027-0.0270.0000.0000.0000.000
16A208GLU-1-0.847-0.90518.1720.0180.0180.0000.0000.0000.000
17A209GLU-1-0.829-0.91121.3970.0920.0920.0000.0000.0000.000
18A210LYS10.8960.94221.600-0.020-0.0200.0000.0000.0000.000
19A211ASN00.0000.01322.234-0.010-0.0100.0000.0000.0000.000
20A212LYS10.8630.92024.651-0.077-0.0770.0000.0000.0000.000
21A213THR0-0.031-0.01027.548-0.005-0.0050.0000.0000.0000.000
22A214GLN0-0.052-0.03326.688-0.008-0.0080.0000.0000.0000.000
23A215ASN0-0.034-0.00929.193-0.009-0.0090.0000.0000.0000.000
24A216ASN0-0.0030.00931.2060.0000.0000.0000.0000.0000.000
25A217PHE0-0.042-0.03732.1580.0010.0010.0000.0000.0000.000
26A218GLY00.0080.01335.3740.0000.0000.0000.0000.0000.000
27A219PHE0-0.0070.01237.8480.0020.0020.0000.0000.0000.000
28A220ARG10.8610.90839.4590.0020.0020.0000.0000.0000.000
29A221GLU-1-0.773-0.82042.7370.0090.0090.0000.0000.0000.000
30A222THR0-0.0020.00444.311-0.003-0.0030.0000.0000.0000.000
31A223TYR0-0.032-0.04547.740-0.001-0.0010.0000.0000.0000.000
32A224ASP-1-0.802-0.88650.7890.0110.0110.0000.0000.0000.000
33A225GLN0-0.014-0.04146.8710.0040.0040.0000.0000.0000.000
34A226PHE00.029-0.00943.2950.0020.0020.0000.0000.0000.000
35A227LYS10.8670.93947.839-0.012-0.0120.0000.0000.0000.000
36A228MET0-0.0400.00044.2740.0020.0020.0000.0000.0000.000
37A229LYS10.8280.91749.434-0.008-0.0080.0000.0000.0000.000
38A230ASP-1-0.839-0.89350.9200.0090.0090.0000.0000.0000.000
39A231SER00.0730.00651.4730.0010.0010.0000.0000.0000.000
40A232ALA0-0.019-0.00947.2180.0000.0000.0000.0000.0000.000
41A233PHE0-0.022-0.02243.0780.0010.0010.0000.0000.0000.000
42A234GLU-1-0.833-0.88847.8600.0120.0120.0000.0000.0000.000
43A235LEU0-0.081-0.02649.4530.0000.0000.0000.0000.0000.000
44A236LEU0-0.036-0.02443.7080.0030.0030.0000.0000.0000.000
45A237ASP-1-0.863-0.91646.5050.0130.0130.0000.0000.0000.000
46A238VAL0-0.076-0.04440.7260.0030.0030.0000.0000.0000.000
47A239ILE00.0420.00838.2180.0010.0010.0000.0000.0000.000
48A240SER0-0.148-0.07335.8560.0000.0000.0000.0000.0000.000
49A241SER0-0.066-0.05937.763-0.004-0.0040.0000.0000.0000.000
50A242ALA00.0550.04037.8080.0020.0020.0000.0000.0000.000
51A243LYS10.9550.95932.9320.0170.0170.0000.0000.0000.000
52A244VAL0-0.042-0.02537.717-0.003-0.0030.0000.0000.0000.000
53A245TYR0-0.0070.00240.579-0.001-0.0010.0000.0000.0000.000
54A246ASP-1-0.885-0.96042.9190.0090.0090.0000.0000.0000.000
55A247ARG10.9770.98542.197-0.021-0.0210.0000.0000.0000.000
56A248SER0-0.0080.00745.7370.0010.0010.0000.0000.0000.000
57A249TYR0-0.068-0.03146.725-0.001-0.0010.0000.0000.0000.000
58A250ALA0-0.0240.00244.657-0.001-0.0010.0000.0000.0000.000
59A251PRO00.0230.01844.8800.0010.0010.0000.0000.0000.000
60A252GLN00.0590.02546.5790.0020.0020.0000.0000.0000.000
61A253LEU0-0.0150.00142.369-0.002-0.0020.0000.0000.0000.000
62A254ASN00.0320.02645.864-0.001-0.0010.0000.0000.0000.000
63A255SER0-0.025-0.00347.938-0.003-0.0030.0000.0000.0000.000
64A256ASN0-0.028-0.02647.7400.0010.0010.0000.0000.0000.000
65A257THR00.0030.00746.360-0.002-0.0020.0000.0000.0000.000
66A258PRO00.0260.00042.5810.0010.0010.0000.0000.0000.000
67A259GLU-1-0.878-0.94740.830-0.004-0.0040.0000.0000.0000.000
68A260ALA00.0060.00741.1610.0030.0030.0000.0000.0000.000
69A261GLU-1-0.850-0.90041.670-0.002-0.0020.0000.0000.0000.000
70A262ASN0-0.051-0.02435.3320.0050.0050.0000.0000.0000.000
71A263GLU-1-0.728-0.84737.6210.0260.0260.0000.0000.0000.000
72A264ARG10.8170.87438.924-0.004-0.0040.0000.0000.0000.000
73A265ASN0-0.051-0.05336.9750.0020.0020.0000.0000.0000.000
74A266LYS10.8690.94332.666-0.016-0.0160.0000.0000.0000.000
75A267PHE00.0250.01035.6730.0060.0060.0000.0000.0000.000
76A268TYR0-0.033-0.06137.7550.0040.0040.0000.0000.0000.000
77A269ALA00.0450.03432.4610.0020.0020.0000.0000.0000.000
78A270LEU0-0.083-0.01533.2980.0070.0070.0000.0000.0000.000
79A271MET0-0.062-0.01434.5970.0080.0080.0000.0000.0000.000
80A272ASP-1-0.880-0.92831.8110.0540.0540.0000.0000.0000.000
81A273PHE0-0.060-0.03732.419-0.004-0.0040.0000.0000.0000.000
82A274ASP-1-0.860-0.90636.7600.0260.0260.0000.0000.0000.000
83A275GLN00.009-0.01738.8540.0010.0010.0000.0000.0000.000
84A276TYR00.001-0.00842.260-0.001-0.0010.0000.0000.0000.000
85A277LYS10.8730.94837.002-0.053-0.0530.0000.0000.0000.000
86A278ILE0-0.031-0.01639.2190.0010.0010.0000.0000.0000.000
87A279GLU-1-0.875-0.92643.0970.0180.0180.0000.0000.0000.000
88A280GLN00.0240.01445.1150.0020.0020.0000.0000.0000.000
89A281PHE00.000-0.01843.1150.0020.0020.0000.0000.0000.000
90A282GLY00.028-0.00945.8450.0000.0000.0000.0000.0000.000
91A283SER00.0060.00347.9040.0000.0000.0000.0000.0000.000
92A284ILE0-0.020-0.00447.5210.0000.0000.0000.0000.0000.000
93A285MET0-0.071-0.03646.6680.0010.0010.0000.0000.0000.000
94A286GLU-1-0.898-0.95550.2910.0170.0170.0000.0000.0000.000
95A287ALA0-0.028-0.01153.386-0.001-0.0010.0000.0000.0000.000
96A288LEU0-0.041-0.02750.5150.0000.0000.0000.0000.0000.000
97A289TYR0-0.042-0.05053.5440.0010.0010.0000.0000.0000.000
98A290ASN0-0.065-0.01955.419-0.002-0.0020.0000.0000.0000.000
99A291GLU-1-0.871-0.91458.3150.0210.0210.0000.0000.0000.000
100A292ASN00.0470.00357.6590.0020.0020.0000.0000.0000.000
101A293GLN0-0.024-0.00357.2140.0000.0000.0000.0000.0000.000
102A294ASN0-0.066-0.04753.9420.0030.0030.0000.0000.0000.000
103A295HIS0-0.012-0.00752.6490.0020.0020.0000.0000.0000.000
104A296SER0-0.020-0.01251.0910.0010.0010.0000.0000.0000.000
105A297LEU00.0230.02148.0370.0020.0020.0000.0000.0000.000
106A298ILE00.0420.03847.7310.0020.0020.0000.0000.0000.000
107A299ARG10.9150.94646.792-0.026-0.0260.0000.0000.0000.000
108A300GLU-1-0.883-0.92343.6850.0490.0490.0000.0000.0000.000
109A301LEU0-0.025-0.02843.4040.0030.0030.0000.0000.0000.000
110A302MET00.0180.02242.1120.0030.0030.0000.0000.0000.000
111A303ILE00.0030.01340.7260.0010.0010.0000.0000.0000.000
112A304SER0-0.060-0.02438.9900.0040.0040.0000.0000.0000.000
113A305GLY00.0830.04037.2560.0050.0050.0000.0000.0000.000
114A306LEU00.0360.01336.2770.0030.0030.0000.0000.0000.000
115A307GLY00.000-0.00435.8800.0000.0000.0000.0000.0000.000
116A308THR0-0.063-0.05332.3090.0070.0070.0000.0000.0000.000
117A309GLN00.003-0.01830.1900.0130.0130.0000.0000.0000.000
118A310ILE00.0210.02031.1250.0000.0000.0000.0000.0000.000
119A311SER0-0.030-0.02130.4360.0000.0000.0000.0000.0000.000
120A312PHE0-0.005-0.00225.5060.0090.0090.0000.0000.0000.000
121A313GLU-1-0.786-0.87826.2940.0370.0370.0000.0000.0000.000
122A314LEU0-0.020-0.00726.440-0.005-0.0050.0000.0000.0000.000
123A315ALA00.0090.00624.3420.0020.0020.0000.0000.0000.000
124A316LEU0-0.012-0.00721.7650.0130.0130.0000.0000.0000.000
125A317GLU-1-0.886-0.93921.1690.0010.0010.0000.0000.0000.000
126A318GLU-1-0.835-0.92721.7890.0570.0570.0000.0000.0000.000
127A319ILE0-0.029-0.02517.1900.0120.0120.0000.0000.0000.000
128A320ASN0-0.0050.00017.1670.0300.0300.0000.0000.0000.000
129A321LYS10.9340.96317.049-0.042-0.0420.0000.0000.0000.000
130A322LYS10.7970.90717.234-0.121-0.1210.0000.0000.0000.000
131A323ILE0-0.011-0.00511.6910.0270.0270.0000.0000.0000.000
132A324GLU-1-0.960-0.96712.935-0.144-0.1440.0000.0000.0000.000
133A325ILE00.0180.00114.700-0.047-0.0470.0000.0000.0000.000
134A326PHE00.023-0.00512.584-0.016-0.0160.0000.0000.0000.000
135A327ASN00.0420.0259.105-0.062-0.0620.0000.0000.0000.000
136A328GLN00.0380.01611.113-0.130-0.1300.0000.0000.0000.000
137A329ASP-1-0.807-0.87713.909-0.063-0.0630.0000.0000.0000.000
138A330TYR0-0.066-0.0335.1260.2870.2870.0000.0000.0000.000
139A331LEU0-0.028-0.0159.452-0.118-0.1180.0000.0000.0000.000
140A332ASN0-0.132-0.07711.542-0.018-0.0180.0000.0000.0000.000
141A333ALA0-0.024-0.00912.7810.0380.0380.0000.0000.0000.000
142A334LYS10.8820.93713.7650.1140.1140.0000.0000.0000.000
143A335ILE0-0.068-0.02611.4980.0640.0640.0000.0000.0000.000
144A336ASN00.0920.05410.8080.0420.0420.0000.0000.0000.000
145A337SER00.045-0.0026.1620.0160.0160.0000.0000.0000.000
146A338PHE00.0120.0177.9320.4520.4520.0000.0000.0000.000
147A339ASP-1-0.836-0.92210.6080.3770.3770.0000.0000.0000.000
148A340PHE00.0290.0047.1980.0850.0850.0000.0000.0000.000
149A341THR0-0.035-0.0357.7320.3300.3300.0000.0000.0000.000
150A342MET00.0020.0089.562-0.019-0.0190.0000.0000.0000.000
151A343LYS10.9701.00212.891-0.335-0.3350.0000.0000.0000.000
152A344LEU00.0050.0078.325-0.031-0.0310.0000.0000.0000.000
153A345LYS10.8820.93312.221-0.996-0.9960.0000.0000.0000.000
154A346GLU-1-0.901-0.94613.6720.2440.2440.0000.0000.0000.000
155A347LEU00.008-0.00114.383-0.048-0.0480.0000.0000.0000.000
156A348LYS10.8750.93613.171-0.612-0.6120.0000.0000.0000.000
157A349SER0-0.045-0.02516.203-0.048-0.0480.0000.0000.0000.000
158A350LYS10.8960.94819.157-0.265-0.2650.0000.0000.0000.000
159A351LEU00.0340.02217.760-0.026-0.0260.0000.0000.0000.000
160A352ASN0-0.007-0.02118.578-0.035-0.0350.0000.0000.0000.000
161A353GLN0-0.0020.01721.901-0.008-0.0080.0000.0000.0000.000
162A354ILE0-0.016-0.01223.329-0.018-0.0180.0000.0000.0000.000
163A355LEU00.0260.02621.720-0.017-0.0170.0000.0000.0000.000
164A356ASP-1-0.873-0.91925.7700.1650.1650.0000.0000.0000.000
165A357LYS10.8600.93627.759-0.142-0.1420.0000.0000.0000.000
166A358ARG10.8370.89628.797-0.075-0.0750.0000.0000.0000.000
167A359LYS10.7880.87526.119-0.149-0.1490.0000.0000.0000.000
168A360GLU-1-0.870-0.92931.4790.0950.0950.0000.0000.0000.000
169A361TRP0-0.005-0.01333.726-0.005-0.0050.0000.0000.0000.000
170A362SER00.0410.00934.286-0.007-0.0070.0000.0000.0000.000
171A363ARG10.9280.97030.268-0.115-0.1150.0000.0000.0000.000
172A364GLN0-0.030-0.02037.380-0.008-0.0080.0000.0000.0000.000
173A365ALA0-0.0050.00539.319-0.004-0.0040.0000.0000.0000.000
174A366ASP-1-0.820-0.90637.9290.0540.0540.0000.0000.0000.000
175A367GLY0-0.033-0.00941.264-0.003-0.0030.0000.0000.0000.000
176A368LEU0-0.018-0.01443.369-0.003-0.0030.0000.0000.0000.000
177A369ILE00.0380.02042.520-0.003-0.0030.0000.0000.0000.000
178A370ALA0-0.0110.01044.696-0.003-0.0030.0000.0000.0000.000
179A371ASN0-0.125-0.05946.607-0.003-0.0030.0000.0000.0000.000
180A372ALA00.0480.00949.106-0.002-0.0020.0000.0000.0000.000
181A373SER0-0.043-0.02948.369-0.002-0.0020.0000.0000.0000.000
182A374SER0-0.024-0.00450.455-0.002-0.0020.0000.0000.0000.000
183A375ASN00.014-0.00553.195-0.001-0.0010.0000.0000.0000.000
184A376SER00.0810.05352.880-0.001-0.0010.0000.0000.0000.000
185A377SER00.007-0.00355.0360.0000.0000.0000.0000.0000.000
186A378LEU0-0.050-0.01957.905-0.001-0.0010.0000.0000.0000.000
187A379SER0-0.084-0.02957.3040.0010.0010.0000.0000.0000.000
188A380ASP-1-0.768-0.86759.3660.0280.0280.0000.0000.0000.000
189A381SER00.0820.03757.6520.0020.0020.0000.0000.0000.000
190A382LYS10.9390.97356.762-0.031-0.0310.0000.0000.0000.000
191A383SER0-0.067-0.09156.6480.0020.0020.0000.0000.0000.000
192A384LEU00.0280.04552.0650.0020.0020.0000.0000.0000.000
193A385ALA00.0580.02552.4310.0020.0020.0000.0000.0000.000
194A386GLU-1-0.857-0.92151.8660.0420.0420.0000.0000.0000.000
195A387TYR00.0160.00748.6770.0030.0030.0000.0000.0000.000
196A388ILE00.0520.02846.7480.0030.0030.0000.0000.0000.000
197A389LYS10.8490.90947.278-0.037-0.0370.0000.0000.0000.000
198A390LYS10.8350.92548.038-0.042-0.0420.0000.0000.0000.000
199A391ARG10.8280.90746.343-0.054-0.0540.0000.0000.0000.000
200A392TYR00.0220.01042.7300.0030.0030.0000.0000.0000.000
201A393LEU00.0220.02742.5860.0020.0020.0000.0000.0000.000
202A394ASP-1-0.837-0.91542.3160.0660.0660.0000.0000.0000.000
203A395ASN0-0.051-0.03038.9630.0070.0070.0000.0000.0000.000
204A396MET0-0.034-0.00237.7890.0040.0040.0000.0000.0000.000
205A397GLN0-0.024-0.04637.8360.0040.0040.0000.0000.0000.000
206A398ASN0-0.040-0.02836.4510.0050.0050.0000.0000.0000.000
207A399ALA0-0.027-0.00233.6640.0070.0070.0000.0000.0000.000
208A400ARG10.9840.99833.024-0.055-0.0550.0000.0000.0000.000
209A401GLN0-0.028-0.02933.726-0.004-0.0040.0000.0000.0000.000
210A402SER0-0.0060.01730.4560.0080.0080.0000.0000.0000.000
211A403VAL00.0030.00628.2740.0110.0110.0000.0000.0000.000
212A404LEU0-0.0070.00328.9020.0040.0040.0000.0000.0000.000
213A405GLU-1-0.865-0.93930.2540.1070.1070.0000.0000.0000.000
214A406ALA0-0.0140.00225.3340.0080.0080.0000.0000.0000.000
215A407TYR00.028-0.00625.4920.0080.0080.0000.0000.0000.000
216A408ILE0-0.003-0.00726.388-0.001-0.0010.0000.0000.0000.000
217A409SER0-0.093-0.04525.1050.0060.0060.0000.0000.0000.000
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