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: 4322N

Calculation Name: 2NN6-G-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NN6

Chain ID: G

ChEMBL ID:

UniProt ID: Q9Y3B2

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2594053.069839
FMO2-HF: Nuclear repulsion 2503601.888358
FMO2-HF: Total energy -90451.18148
FMO2-MP2: Total energy -90713.049914


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(G:16:ALA)


Summations of interaction energy for fragment #1(G:16:ALA)
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.
-5.414-1.960.403-1.574-2.282-0.002
Interaction energy analysis for fragmet #1(G:16:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.006
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].
3G18ALA00.0170.0063.8390.2001.764-0.019-0.793-0.7520.000
4G19ALA00.0750.0596.125-0.136-0.1360.0000.0000.0000.000
5G20ARG10.9420.9629.5590.2900.2900.0000.0000.0000.000
6G21THR0-0.027-0.04111.964-0.005-0.0050.0000.0000.0000.000
7G22VAL0-0.0450.0147.7300.0440.0440.0000.0000.0000.000
8G23LEU00.0440.0145.6870.1210.1210.0000.0000.0000.000
9G24GLY00.0350.03310.084-0.069-0.0690.0000.0000.0000.000
10G25GLN0-0.062-0.05311.1870.0040.0040.0000.0000.0000.000
11G26VAL00.031-0.00112.148-0.052-0.0520.0000.0000.0000.000
12G27VAL00.0100.0267.4530.0750.0750.0000.0000.0000.000
13G28LEU0-0.013-0.0196.8330.1150.1150.0000.0000.0000.000
14G29PRO0-0.037-0.0137.760-0.139-0.1390.0000.0000.0000.000
15G30GLY00.009-0.0016.9580.0850.0850.0000.0000.0000.000
16G31GLU-1-0.906-0.9613.138-2.236-1.1420.131-0.418-0.806-0.002
17G32GLU-1-0.815-0.8862.551-3.195-2.5730.284-0.260-0.6460.000
18G33LEU0-0.110-0.0903.844-0.690-0.5160.007-0.103-0.0780.000
19G34LEU00.0350.0516.5110.1710.1710.0000.0000.0000.000
20G35LEU0-0.021-0.00510.1970.0590.0590.0000.0000.0000.000
21G36PRO0-0.0440.00013.394-0.019-0.0190.0000.0000.0000.000
22G37GLU-1-0.833-0.93014.719-0.394-0.3940.0000.0000.0000.000
23G38GLN0-0.085-0.06718.0310.0030.0030.0000.0000.0000.000
24G39GLU-1-0.876-0.91019.817-0.222-0.2220.0000.0000.0000.000
25G40ASP-1-0.880-0.95916.914-0.409-0.4090.0000.0000.0000.000
26G41ALA0-0.043-0.00519.7040.0030.0030.0000.0000.0000.000
27G42GLU-1-0.729-0.84714.880-0.476-0.4760.0000.0000.0000.000
28G43GLY00.0080.00016.1620.0430.0430.0000.0000.0000.000
29G44PRO0-0.071-0.04016.1770.0050.0050.0000.0000.0000.000
30G45GLY0-0.022-0.01313.9870.0000.0000.0000.0000.0000.000
31G46GLY00.0230.02111.347-0.070-0.0700.0000.0000.0000.000
32G47ALA0-0.020-0.01310.9260.0850.0850.0000.0000.0000.000
33G48VAL00.0610.04311.235-0.125-0.1250.0000.0000.0000.000
34G49GLU-1-0.900-0.95410.753-0.944-0.9440.0000.0000.0000.000
35G50ARG10.7860.92811.1250.3950.3950.0000.0000.0000.000
36G74GLY00.0100.00416.8440.0170.0170.0000.0000.0000.000
37G75ASP-1-0.809-0.92314.456-0.545-0.5450.0000.0000.0000.000
38G76ARG10.7990.8466.9191.3831.3830.0000.0000.0000.000
39G77LEU00.0410.0098.8330.1240.1240.0000.0000.0000.000
40G78LEU00.0200.0116.782-0.396-0.3960.0000.0000.0000.000
41G79VAL0-0.0520.0136.9500.3040.3040.0000.0000.0000.000
42G80THR00.008-0.0038.820-0.020-0.0200.0000.0000.0000.000
43G81LYS10.8790.92411.5610.4050.4050.0000.0000.0000.000
44G82CYS0-0.017-0.01011.587-0.037-0.0370.0000.0000.0000.000
45G83GLY00.0260.00712.1790.0560.0560.0000.0000.0000.000
46G84ARG10.9030.97112.1680.0900.0900.0000.0000.0000.000
47G85LEU00.0070.02911.182-0.013-0.0130.0000.0000.0000.000
48G86ARG10.7930.87613.5970.2320.2320.0000.0000.0000.000
49G87HIS10.8470.89516.2790.2150.2150.0000.0000.0000.000
50G88LYS10.9691.00518.3470.1860.1860.0000.0000.0000.000
51G89GLU-1-0.809-0.91120.406-0.192-0.1920.0000.0000.0000.000
52G90PRO00.0700.06522.9070.0110.0110.0000.0000.0000.000
53G91GLY0-0.019-0.00925.1030.0140.0140.0000.0000.0000.000
54G92SER0-0.013-0.03526.846-0.001-0.0010.0000.0000.0000.000
55G93GLY00.0170.02629.081-0.001-0.0010.0000.0000.0000.000
56G94SER00.0050.01228.3270.0010.0010.0000.0000.0000.000
57G95GLY00.0400.03328.500-0.009-0.0090.0000.0000.0000.000
58G96GLY0-0.027-0.03826.683-0.005-0.0050.0000.0000.0000.000
59G97GLY0-0.047-0.03023.3260.0090.0090.0000.0000.0000.000
60G98VAL0-0.0020.01218.748-0.009-0.0090.0000.0000.0000.000
61G99TYR0-0.034-0.01414.4340.0430.0430.0000.0000.0000.000
62G100TRP0-0.014-0.04716.000-0.014-0.0140.0000.0000.0000.000
63G101VAL00.0910.05011.7230.0030.0030.0000.0000.0000.000
64G102ASP-1-0.886-0.91014.934-0.162-0.1620.0000.0000.0000.000
65G103SER00.0840.01016.131-0.017-0.0170.0000.0000.0000.000
66G104GLN0-0.0250.00918.5070.0010.0010.0000.0000.0000.000
67G105GLN0-0.030-0.01419.774-0.007-0.0070.0000.0000.0000.000
68G106LYS10.9390.94922.4140.0910.0910.0000.0000.0000.000
69G107ARG10.9290.98621.7700.1920.1920.0000.0000.0000.000
70G108TYR00.0290.02525.156-0.008-0.0080.0000.0000.0000.000
71G109VAL0-0.040-0.02522.419-0.006-0.0060.0000.0000.0000.000
72G110PRO00.0770.04125.7180.0020.0020.0000.0000.0000.000
73G111VAL0-0.053-0.04524.785-0.016-0.0160.0000.0000.0000.000
74G112LYS10.9640.99125.0350.1940.1940.0000.0000.0000.000
75G113GLY00.1020.04229.6850.0020.0020.0000.0000.0000.000
76G114ASP-1-0.916-0.94829.215-0.131-0.1310.0000.0000.0000.000
77G115HIS00.0660.04732.1150.0040.0040.0000.0000.0000.000
78G116VAL0-0.048-0.01532.290-0.002-0.0020.0000.0000.0000.000
79G117ILE0-0.013-0.02335.0390.0040.0040.0000.0000.0000.000
80G118GLY0-0.023-0.02736.964-0.004-0.0040.0000.0000.0000.000
81G119ILE00.0020.01237.8610.0040.0040.0000.0000.0000.000
82G120VAL00.0320.02040.284-0.005-0.0050.0000.0000.0000.000
83G121THR00.0320.01339.2450.0020.0020.0000.0000.0000.000
84G122ALA00.0200.00041.8410.0030.0030.0000.0000.0000.000
85G123LYS10.8600.91943.7600.0570.0570.0000.0000.0000.000
86G124SER0-0.049-0.01644.5560.0040.0040.0000.0000.0000.000
87G125GLY00.0610.02645.759-0.002-0.0020.0000.0000.0000.000
88G126ASP-1-0.882-0.95047.025-0.061-0.0610.0000.0000.0000.000
89G127ILE00.0160.00340.9680.0000.0000.0000.0000.0000.000
90G128PHE0-0.009-0.00343.3600.0020.0020.0000.0000.0000.000
91G129LYS10.8550.93536.4650.1000.1000.0000.0000.0000.000
92G130VAL0-0.022-0.01138.1180.0050.0050.0000.0000.0000.000
93G131ASP-1-0.829-0.92534.950-0.099-0.0990.0000.0000.0000.000
94G132VAL0-0.016-0.02231.5840.0030.0030.0000.0000.0000.000
95G133GLY0-0.061-0.03831.876-0.002-0.0020.0000.0000.0000.000
96G134GLY00.0250.02728.571-0.006-0.0060.0000.0000.0000.000
97G135SER0-0.096-0.06426.348-0.001-0.0010.0000.0000.0000.000
98G136GLU-1-0.899-0.94828.427-0.150-0.1500.0000.0000.0000.000
99G137PRO0-0.054-0.01231.8760.0010.0010.0000.0000.0000.000
100G138ALA00.0450.01433.226-0.007-0.0070.0000.0000.0000.000
101G139SER00.020-0.01635.3700.0070.0070.0000.0000.0000.000
102G140LEU00.0110.00738.673-0.002-0.0020.0000.0000.0000.000
103G141SER00.0850.05041.5610.0020.0020.0000.0000.0000.000
104G142TYR0-0.131-0.04044.2780.0030.0030.0000.0000.0000.000
105G143LEU0-0.008-0.03646.6450.0030.0030.0000.0000.0000.000
106G144SER00.0110.00943.719-0.004-0.0040.0000.0000.0000.000
107G145PHE00.025-0.00845.246-0.001-0.0010.0000.0000.0000.000
108G146GLU-1-0.879-0.91648.682-0.048-0.0480.0000.0000.0000.000
109G147GLY00.0030.01050.8320.0030.0030.0000.0000.0000.000
110G148ALA0-0.014-0.00452.372-0.002-0.0020.0000.0000.0000.000
111G149THR00.028-0.02354.5600.0010.0010.0000.0000.0000.000
112G150LYS10.9170.97755.5230.0440.0440.0000.0000.0000.000
113G151ARG10.9670.98054.0310.0440.0440.0000.0000.0000.000
114G152ASN00.024-0.00249.940-0.001-0.0010.0000.0000.0000.000
115G153ARG10.9500.98551.1750.0490.0490.0000.0000.0000.000
116G154PRO0-0.040-0.00453.123-0.001-0.0010.0000.0000.0000.000
117G155ASN0-0.037-0.01652.2760.0000.0000.0000.0000.0000.000
118G156VAL00.1170.03547.093-0.002-0.0020.0000.0000.0000.000
119G157GLN0-0.063-0.02348.5420.0000.0000.0000.0000.0000.000
120G158VAL00.0490.04145.896-0.002-0.0020.0000.0000.0000.000
121G159GLY0-0.035-0.00945.0670.0020.0020.0000.0000.0000.000
122G160ASP-1-0.871-0.92945.947-0.051-0.0510.0000.0000.0000.000
123G161LEU0-0.020-0.02943.027-0.003-0.0030.0000.0000.0000.000
124G162ILE0-0.022-0.01041.2560.0010.0010.0000.0000.0000.000
125G163TYR00.0540.04537.667-0.002-0.0020.0000.0000.0000.000
126G164GLY00.0730.01738.7250.0030.0030.0000.0000.0000.000
127G165GLN00.0690.01935.1800.0000.0000.0000.0000.0000.000
128G166PHE0-0.0250.00430.3400.0030.0030.0000.0000.0000.000
129G167VAL0-0.043-0.01833.501-0.004-0.0040.0000.0000.0000.000
130G168VAL0-0.028-0.00632.177-0.007-0.0070.0000.0000.0000.000
131G169ALA00.0750.06628.6710.0040.0040.0000.0000.0000.000
132G170ASN0-0.078-0.03426.2580.0010.0010.0000.0000.0000.000
133G171LYS10.7980.87618.3810.3600.3600.0000.0000.0000.000
134G172ASP-1-0.879-0.93223.979-0.244-0.2440.0000.0000.0000.000
135G173MET0-0.077-0.02026.1680.0120.0120.0000.0000.0000.000
136G174GLU-1-0.835-0.88928.718-0.119-0.1190.0000.0000.0000.000
137G175PRO0-0.001-0.03730.0160.0020.0020.0000.0000.0000.000
138G176GLU-1-0.935-0.97432.334-0.095-0.0950.0000.0000.0000.000
139G177MET0-0.058-0.04335.556-0.002-0.0020.0000.0000.0000.000
140G178VAL0-0.041-0.02037.4860.0040.0040.0000.0000.0000.000
141G179CYS0-0.010-0.01740.352-0.001-0.0010.0000.0000.0000.000
142G180ILE0-0.0060.02343.0220.0020.0020.0000.0000.0000.000
143G181ASP-1-0.847-0.92442.642-0.072-0.0720.0000.0000.0000.000
144G182SER0-0.033-0.01140.9220.0010.0010.0000.0000.0000.000
145G183CYS0-0.047-0.02340.616-0.001-0.0010.0000.0000.0000.000
146G184GLY00.023-0.00742.8780.0020.0020.0000.0000.0000.000
147G185ARG10.8180.90144.3170.0720.0720.0000.0000.0000.000
148G186ALA00.0480.05446.8460.0020.0020.0000.0000.0000.000
149G187ASN0-0.026-0.05246.626-0.003-0.0030.0000.0000.0000.000
150G188GLY00.0380.03443.9360.0020.0020.0000.0000.0000.000
151G189MET0-0.065-0.02439.6990.0000.0000.0000.0000.0000.000
152G190GLY00.0570.03643.7500.0000.0000.0000.0000.0000.000
153G191VAL0-0.037-0.03244.966-0.002-0.0020.0000.0000.0000.000
154G192ILE0-0.044-0.02441.5780.0010.0010.0000.0000.0000.000
155G193GLY0-0.012-0.01046.1160.0010.0010.0000.0000.0000.000
156G194GLN0-0.035-0.00849.1540.0000.0000.0000.0000.0000.000
157G195ASP-1-0.861-0.93451.110-0.035-0.0350.0000.0000.0000.000
158G196GLY00.015-0.01247.706-0.001-0.0010.0000.0000.0000.000
159G197LEU0-0.053-0.03143.4700.0010.0010.0000.0000.0000.000
160G198LEU00.0440.07439.171-0.002-0.0020.0000.0000.0000.000
161G199PHE00.0020.00538.1300.0010.0010.0000.0000.0000.000
162G200LYS10.9430.96032.2210.0650.0650.0000.0000.0000.000
163G201VAL00.0870.04332.7670.0030.0030.0000.0000.0000.000
164G202THR0-0.0200.01127.230-0.008-0.0080.0000.0000.0000.000
165G203LEU00.1140.05924.7160.0020.0020.0000.0000.0000.000
166G204GLY0-0.030-0.01025.7440.0020.0020.0000.0000.0000.000
167G205LEU0-0.023-0.02026.4910.0020.0020.0000.0000.0000.000
168G206ILE00.0600.06129.3530.0010.0010.0000.0000.0000.000
169G207ARG10.7970.87221.3080.1430.1430.0000.0000.0000.000
170G208LYS10.8530.90327.3050.0620.0620.0000.0000.0000.000
171G209LEU0-0.059-0.02030.1000.0050.0050.0000.0000.0000.000
172G210LEU0-0.014-0.02031.9700.0030.0030.0000.0000.0000.000
173G211ALA0-0.039-0.00130.238-0.002-0.0020.0000.0000.0000.000
174G212PRO00.0580.02931.5490.0050.0050.0000.0000.0000.000
175G213ASP-1-0.950-0.97331.260-0.061-0.0610.0000.0000.0000.000
176G214CYS0-0.070-0.01933.4940.0050.0050.0000.0000.0000.000
177G215GLU-1-0.814-0.91535.442-0.031-0.0310.0000.0000.0000.000
178G216ILE00.013-0.00135.9570.0010.0010.0000.0000.0000.000
179G217ILE00.0790.04136.1980.0020.0020.0000.0000.0000.000
180G218GLN00.0830.04738.8590.0010.0010.0000.0000.0000.000
181G219GLH0-0.083-0.02941.2420.0030.0030.0000.0000.0000.000
182G220VAL0-0.002-0.02141.9010.0030.0030.0000.0000.0000.000
183G221GLY0-0.047-0.01444.0880.0010.0010.0000.0000.0000.000
184G222LYS10.7110.86145.9770.0290.0290.0000.0000.0000.000
185G223LEU00.0340.00046.9260.0000.0000.0000.0000.0000.000
186G224TYR0-0.0320.04750.154-0.001-0.0010.0000.0000.0000.000
187G225PRO0-0.066-0.03952.9280.0010.0010.0000.0000.0000.000
188G226LEU0-0.013-0.04445.7390.0000.0000.0000.0000.0000.000
189G227GLU-1-0.827-0.90647.522-0.039-0.0390.0000.0000.0000.000
190G228ILE00.000-0.01741.9490.0000.0000.0000.0000.0000.000
191G229VAL0-0.004-0.00339.676-0.001-0.0010.0000.0000.0000.000
192G230PHE0-0.003-0.01336.2080.0010.0010.0000.0000.0000.000
193G231GLY00.0180.01635.239-0.003-0.0030.0000.0000.0000.000
194G232MET00.0710.02728.0310.0020.0020.0000.0000.0000.000
195G233ASN0-0.079-0.02730.3120.0010.0010.0000.0000.0000.000
196G234GLY0-0.046-0.08331.4060.0020.0020.0000.0000.0000.000
197G235ARG10.8080.90732.6940.0890.0890.0000.0000.0000.000
198G236ILE00.0370.01735.8420.0000.0000.0000.0000.0000.000
199G237TRP0-0.0050.01039.1580.0020.0020.0000.0000.0000.000
200G238VAL0-0.023-0.01142.5460.0000.0000.0000.0000.0000.000
201G239LYS10.9130.94945.1610.0370.0370.0000.0000.0000.000
202G240ALA0-0.0040.00948.9050.0000.0000.0000.0000.0000.000
203G241LYS10.9840.98851.0900.0250.0250.0000.0000.0000.000
204G242THR0-0.029-0.00954.5700.0000.0000.0000.0000.0000.000
205G243ILE00.1030.06351.243-0.001-0.0010.0000.0000.0000.000
206G244GLN00.0940.02750.663-0.002-0.0020.0000.0000.0000.000
207G245GLN00.0780.04950.2040.0000.0000.0000.0000.0000.000
208G246THR00.002-0.01347.361-0.001-0.0010.0000.0000.0000.000
209G247LEU0-0.011-0.01346.298-0.002-0.0020.0000.0000.0000.000
210G248ILE0-0.042-0.00945.687-0.001-0.0010.0000.0000.0000.000
211G249LEU00.0390.02443.850-0.001-0.0010.0000.0000.0000.000
212G250ALA00.0300.01642.097-0.002-0.0020.0000.0000.0000.000
213G251ASN00.0340.03240.8560.0000.0000.0000.0000.0000.000
214G252ILE0-0.040-0.03840.7550.0000.0000.0000.0000.0000.000
215G253LEU0-0.002-0.02738.519-0.001-0.0010.0000.0000.0000.000
216G254GLU-1-0.991-0.99836.852-0.042-0.0420.0000.0000.0000.000
217G255ALA0-0.034-0.01035.913-0.001-0.0010.0000.0000.0000.000
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