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: 5377Z

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2585448.454057
FMO2-HF: Nuclear repulsion 2494992.955585
FMO2-HF: Total energy -90455.498473
FMO2-MP2: Total energy -90716.495715


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.
-4.026-2.0392.984-1.918-3.052-0.003
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 : -0.002 / q_NPA : -0.008
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].
3G18ALA00.0070.0053.8880.3771.750-0.016-0.700-0.6580.001
4G19ALA00.0830.0426.715-0.166-0.1660.0000.0000.0000.000
5G20ARG10.8970.95510.0360.1640.1640.0000.0000.0000.000
6G21THR0-0.017-0.02412.8460.0030.0030.0000.0000.0000.000
7G22VAL0-0.0370.0067.9870.0380.0380.0000.0000.0000.000
8G23LEU00.0480.0165.7630.0920.0920.0000.0000.0000.000
9G24GLY00.0430.03910.221-0.070-0.0700.0000.0000.0000.000
10G25GLN0-0.080-0.05111.663-0.029-0.0290.0000.0000.0000.000
11G26VAL0-0.049-0.03812.092-0.049-0.0490.0000.0000.0000.000
12G27VAL00.0200.0307.6680.0640.0640.0000.0000.0000.000
13G28LEU00.025-0.0096.6400.0010.0010.0000.0000.0000.000
14G29PRO0-0.065-0.0227.437-0.089-0.0890.0000.0000.0000.000
15G30GLY00.0350.0076.2860.0300.0300.0000.0000.0000.000
16G31GLU-1-0.874-0.9292.490-1.050-0.2941.024-0.663-1.116-0.002
17G32GLU-1-0.848-0.9092.046-2.770-3.0271.971-0.452-1.261-0.002
18G33LEU0-0.094-0.0583.807-0.699-0.5840.005-0.103-0.0170.000
19G34LEU00.0240.0196.5230.0860.0860.0000.0000.0000.000
20G35LEU0-0.013-0.01310.2170.0980.0980.0000.0000.0000.000
21G36PRO0-0.034-0.00813.734-0.033-0.0330.0000.0000.0000.000
22G37GLU-1-0.835-0.90215.541-0.222-0.2220.0000.0000.0000.000
23G38GLN0-0.082-0.06317.915-0.009-0.0090.0000.0000.0000.000
24G39GLU-1-0.863-0.90520.137-0.156-0.1560.0000.0000.0000.000
25G40ASP-1-0.801-0.92716.321-0.265-0.2650.0000.0000.0000.000
26G41ALA0-0.050-0.02619.2510.0020.0020.0000.0000.0000.000
27G42GLU-1-0.783-0.85614.987-0.338-0.3380.0000.0000.0000.000
28G43GLY00.0300.02816.0150.0240.0240.0000.0000.0000.000
29G44PRO0-0.034-0.01716.569-0.015-0.0150.0000.0000.0000.000
30G45GLY00.004-0.01213.9600.0040.0040.0000.0000.0000.000
31G46GLY00.0130.01011.198-0.034-0.0340.0000.0000.0000.000
32G47ALA0-0.0350.00511.1120.0640.0640.0000.0000.0000.000
33G48VAL00.0430.01311.592-0.073-0.0730.0000.0000.0000.000
34G49GLU-1-0.931-0.96110.300-0.818-0.8180.0000.0000.0000.000
35G50ARG10.8330.89811.5280.3280.3280.0000.0000.0000.000
36G74GLY00.004-0.00117.0680.0150.0150.0000.0000.0000.000
37G75ASP-1-0.842-0.89714.720-0.433-0.4330.0000.0000.0000.000
38G76ARG10.7720.8546.9371.1491.1490.0000.0000.0000.000
39G77LEU00.0270.0289.0600.1040.1040.0000.0000.0000.000
40G78LEU00.0460.0356.304-0.279-0.2790.0000.0000.0000.000
41G79VAL0-0.030-0.0196.4960.2080.2080.0000.0000.0000.000
42G80THR00.004-0.0138.160-0.047-0.0470.0000.0000.0000.000
43G81LYS10.8470.90810.9740.2960.2960.0000.0000.0000.000
44G82CYS0-0.0210.00211.5640.0030.0030.0000.0000.0000.000
45G83GLY00.0420.03012.1830.0140.0140.0000.0000.0000.000
46G84ARG10.8330.92612.5230.0370.0370.0000.0000.0000.000
47G85LEU00.0700.06611.007-0.014-0.0140.0000.0000.0000.000
48G86ARG10.8340.89413.5320.0970.0970.0000.0000.0000.000
49G87HIS10.8470.89716.4500.1190.1190.0000.0000.0000.000
50G88LYS10.9640.99218.5800.1080.1080.0000.0000.0000.000
51G89GLU-1-0.778-0.88620.523-0.103-0.1030.0000.0000.0000.000
52G90PRO00.0560.03722.7330.0080.0080.0000.0000.0000.000
53G91GLY0-0.015-0.01125.3070.0080.0080.0000.0000.0000.000
54G92SER0-0.027-0.03327.086-0.001-0.0010.0000.0000.0000.000
55G93GLY00.0390.03129.190-0.002-0.0020.0000.0000.0000.000
56G94SER0-0.0430.00327.8870.0030.0030.0000.0000.0000.000
57G95GLY00.0380.01628.546-0.006-0.0060.0000.0000.0000.000
58G96GLY0-0.021-0.02726.287-0.005-0.0050.0000.0000.0000.000
59G97GLY0-0.021-0.01323.2330.0110.0110.0000.0000.0000.000
60G98VAL00.0220.01818.390-0.007-0.0070.0000.0000.0000.000
61G99TYR0-0.073-0.04314.0270.0380.0380.0000.0000.0000.000
62G100TRP00.020-0.00815.846-0.014-0.0140.0000.0000.0000.000
63G101VAL00.0230.01411.7850.0060.0060.0000.0000.0000.000
64G102ASP-1-0.850-0.88914.919-0.057-0.0570.0000.0000.0000.000
65G103SER00.064-0.00515.7030.0000.0000.0000.0000.0000.000
66G104GLN0-0.0040.00018.209-0.005-0.0050.0000.0000.0000.000
67G105GLN0-0.027-0.01319.304-0.011-0.0110.0000.0000.0000.000
68G106LYS10.9440.96222.1820.0580.0580.0000.0000.0000.000
69G107ARG10.8920.96521.4120.1370.1370.0000.0000.0000.000
70G108TYR00.0330.02524.387-0.008-0.0080.0000.0000.0000.000
71G109VAL0-0.029-0.02721.642-0.010-0.0100.0000.0000.0000.000
72G110PRO00.0530.03324.9830.0040.0040.0000.0000.0000.000
73G111VAL0-0.059-0.02223.854-0.011-0.0110.0000.0000.0000.000
74G112LYS10.9560.95925.0320.1260.1260.0000.0000.0000.000
75G113GLY00.0620.06029.1230.0020.0020.0000.0000.0000.000
76G114ASP-1-0.860-0.93828.436-0.084-0.0840.0000.0000.0000.000
77G115HIS00.0410.03131.733-0.001-0.0010.0000.0000.0000.000
78G116VAL0-0.026-0.02032.017-0.001-0.0010.0000.0000.0000.000
79G117ILE0-0.017-0.00134.9080.0020.0020.0000.0000.0000.000
80G118GLY00.0380.01536.343-0.003-0.0030.0000.0000.0000.000
81G119ILE0-0.031-0.01637.9500.0040.0040.0000.0000.0000.000
82G120VAL0-0.0260.00040.069-0.004-0.0040.0000.0000.0000.000
83G121THR00.004-0.00539.0590.0010.0010.0000.0000.0000.000
84G122ALA00.0230.00041.6520.0020.0020.0000.0000.0000.000
85G123LYS10.8390.92443.5880.0440.0440.0000.0000.0000.000
86G124SER0-0.037-0.01844.6530.0020.0020.0000.0000.0000.000
87G125GLY00.0890.05545.597-0.002-0.0020.0000.0000.0000.000
88G126ASP-1-0.921-0.96347.110-0.046-0.0460.0000.0000.0000.000
89G127ILE00.0210.01140.8130.0000.0000.0000.0000.0000.000
90G128PHE0-0.018-0.02842.8820.0020.0020.0000.0000.0000.000
91G129LYS10.8330.92336.5280.0770.0770.0000.0000.0000.000
92G130VAL00.0080.00237.6890.0040.0040.0000.0000.0000.000
93G131ASP-1-0.784-0.89734.486-0.071-0.0710.0000.0000.0000.000
94G132VAL00.0230.00831.0120.0020.0020.0000.0000.0000.000
95G133GLY0-0.047-0.02031.2980.0020.0020.0000.0000.0000.000
96G134GLY00.0030.01227.808-0.003-0.0030.0000.0000.0000.000
97G135SER0-0.078-0.05725.825-0.001-0.0010.0000.0000.0000.000
98G136GLU-1-0.881-0.93427.912-0.117-0.1170.0000.0000.0000.000
99G137PRO0-0.058-0.02231.3480.0020.0020.0000.0000.0000.000
100G138ALA00.0340.02233.676-0.005-0.0050.0000.0000.0000.000
101G139SER00.002-0.01834.8200.0060.0060.0000.0000.0000.000
102G140LEU00.0090.00737.993-0.001-0.0010.0000.0000.0000.000
103G141SER00.0540.04540.8040.0020.0020.0000.0000.0000.000
104G142TYR0-0.067-0.05043.8250.0030.0030.0000.0000.0000.000
105G143LEU00.0020.00646.6430.0020.0020.0000.0000.0000.000
106G144SER00.0380.00243.365-0.002-0.0020.0000.0000.0000.000
107G145PHE00.007-0.00844.5650.0000.0000.0000.0000.0000.000
108G146GLU-1-0.837-0.90148.270-0.031-0.0310.0000.0000.0000.000
109G147GLY0-0.055-0.01450.5290.0010.0010.0000.0000.0000.000
110G148ALA00.0200.01051.541-0.002-0.0020.0000.0000.0000.000
111G149THR00.018-0.01053.6580.0010.0010.0000.0000.0000.000
112G150LYS10.9080.95854.8560.0330.0330.0000.0000.0000.000
113G151ARG10.9590.98653.7640.0320.0320.0000.0000.0000.000
114G152ASN00.0490.00849.540-0.001-0.0010.0000.0000.0000.000
115G153ARG10.8800.94451.2760.0370.0370.0000.0000.0000.000
116G154PRO0-0.021-0.00752.887-0.001-0.0010.0000.0000.0000.000
117G155ASN0-0.035-0.02451.6900.0010.0010.0000.0000.0000.000
118G156VAL00.0790.04246.533-0.001-0.0010.0000.0000.0000.000
119G157GLN0-0.041-0.01248.398-0.001-0.0010.0000.0000.0000.000
120G158VAL0-0.002-0.00445.199-0.001-0.0010.0000.0000.0000.000
121G159GLY0-0.0080.00044.6550.0020.0020.0000.0000.0000.000
122G160ASP-1-0.831-0.90445.280-0.036-0.0360.0000.0000.0000.000
123G161LEU0-0.014-0.01042.651-0.003-0.0030.0000.0000.0000.000
124G162ILE0-0.025-0.02140.7500.0010.0010.0000.0000.0000.000
125G163TYR0-0.012-0.00237.326-0.002-0.0020.0000.0000.0000.000
126G164GLY00.0590.01138.4610.0020.0020.0000.0000.0000.000
127G165GLN00.0380.01535.1970.0010.0010.0000.0000.0000.000
128G166PHE00.007-0.00629.7500.0010.0010.0000.0000.0000.000
129G167VAL0-0.012-0.00532.812-0.003-0.0030.0000.0000.0000.000
130G168VAL0-0.0170.00331.756-0.004-0.0040.0000.0000.0000.000
131G169ALA00.0550.01027.9140.0030.0030.0000.0000.0000.000
132G170ASN0-0.095-0.05325.5470.0050.0050.0000.0000.0000.000
133G171LYS10.7870.85417.8690.2710.2710.0000.0000.0000.000
134G172ASP-1-0.853-0.90823.640-0.192-0.1920.0000.0000.0000.000
135G173MET0-0.066-0.02526.1600.0090.0090.0000.0000.0000.000
136G174GLU-1-0.781-0.85628.942-0.088-0.0880.0000.0000.0000.000
137G175PRO0-0.010-0.00229.7770.0020.0020.0000.0000.0000.000
138G176GLU-1-0.904-0.96531.939-0.072-0.0720.0000.0000.0000.000
139G177MET0-0.073-0.04635.3760.0000.0000.0000.0000.0000.000
140G178VAL0-0.034-0.01237.3130.0020.0020.0000.0000.0000.000
141G179CYS0-0.049-0.03440.0140.0000.0000.0000.0000.0000.000
142G180ILE00.0000.00742.7810.0020.0020.0000.0000.0000.000
143G181ASP-1-0.800-0.90442.139-0.048-0.0480.0000.0000.0000.000
144G182SER0-0.053-0.03340.2760.0010.0010.0000.0000.0000.000
145G183CYS0-0.085-0.04240.388-0.001-0.0010.0000.0000.0000.000
146G184GLY00.0340.01542.8620.0010.0010.0000.0000.0000.000
147G185ARG10.8210.89843.6610.0510.0510.0000.0000.0000.000
148G186ALA00.0600.05746.9470.0010.0010.0000.0000.0000.000
149G187ASN0-0.032-0.04346.424-0.003-0.0030.0000.0000.0000.000
150G188GLY00.0100.02043.5040.0020.0020.0000.0000.0000.000
151G189MET0-0.048-0.00639.5530.0000.0000.0000.0000.0000.000
152G190GLY00.0480.01743.3030.0010.0010.0000.0000.0000.000
153G191VAL0-0.030-0.01644.282-0.001-0.0010.0000.0000.0000.000
154G192ILE0-0.024-0.00441.5140.0010.0010.0000.0000.0000.000
155G193GLY00.0050.00846.0740.0010.0010.0000.0000.0000.000
156G194GLN0-0.041-0.02849.1770.0000.0000.0000.0000.0000.000
157G195ASP-1-0.847-0.92851.016-0.021-0.0210.0000.0000.0000.000
158G196GLY00.013-0.00147.7970.0000.0000.0000.0000.0000.000
159G197LEU0-0.048-0.01243.3710.0000.0000.0000.0000.0000.000
160G198LEU00.0280.01439.1220.0000.0000.0000.0000.0000.000
161G199PHE0-0.0010.00038.1010.0000.0000.0000.0000.0000.000
162G200LYS10.9520.96932.0510.0360.0360.0000.0000.0000.000
163G201VAL00.0050.01632.4870.0030.0030.0000.0000.0000.000
164G202THR00.016-0.00127.071-0.006-0.0060.0000.0000.0000.000
165G203LEU00.0720.02924.3180.0030.0030.0000.0000.0000.000
166G204GLY0-0.038-0.02625.6770.0000.0000.0000.0000.0000.000
167G205LEU0-0.012-0.00126.3220.0030.0030.0000.0000.0000.000
168G206ILE00.0150.02428.9130.0020.0020.0000.0000.0000.000
169G207ARG10.8390.89821.0860.0690.0690.0000.0000.0000.000
170G208LYS10.8510.90027.3590.0120.0120.0000.0000.0000.000
171G209LEU0-0.022-0.00330.6230.0040.0040.0000.0000.0000.000
172G210LEU00.007-0.00532.3920.0010.0010.0000.0000.0000.000
173G211ALA00.0010.01930.277-0.002-0.0020.0000.0000.0000.000
174G212PRO00.0120.01431.8910.0030.0030.0000.0000.0000.000
175G213ASP-1-0.900-0.95531.445-0.018-0.0180.0000.0000.0000.000
176G214CYS0-0.087-0.02433.4130.0040.0040.0000.0000.0000.000
177G215GLU-1-0.801-0.89835.296-0.006-0.0060.0000.0000.0000.000
178G216ILE0-0.020-0.01235.9970.0000.0000.0000.0000.0000.000
179G217ILE00.0650.03136.4070.0000.0000.0000.0000.0000.000
180G218GLN00.0610.03138.842-0.001-0.0010.0000.0000.0000.000
181G219GLH0-0.046-0.02841.4720.0020.0020.0000.0000.0000.000
182G220VAL00.019-0.00941.5880.0010.0010.0000.0000.0000.000
183G221GLY00.0130.01644.1580.0000.0000.0000.0000.0000.000
184G222LYS10.8140.92346.0640.0070.0070.0000.0000.0000.000
185G223LEU0-0.043-0.01346.6630.0010.0010.0000.0000.0000.000
186G224TYR0-0.019-0.00349.906-0.001-0.0010.0000.0000.0000.000
187G225PRO0-0.051-0.02352.9190.0010.0010.0000.0000.0000.000
188G226LEU0-0.015-0.03245.6810.0000.0000.0000.0000.0000.000
189G227GLU-1-0.857-0.92547.785-0.023-0.0230.0000.0000.0000.000
190G228ILE0-0.007-0.02041.9520.0000.0000.0000.0000.0000.000
191G229VAL00.0140.01339.748-0.001-0.0010.0000.0000.0000.000
192G230PHE00.0090.00036.1700.0010.0010.0000.0000.0000.000
193G231GLY00.0240.01834.789-0.002-0.0020.0000.0000.0000.000
194G232MET0-0.009-0.02627.8400.0030.0030.0000.0000.0000.000
195G233ASN0-0.063-0.04229.3440.0000.0000.0000.0000.0000.000
196G234GLY00.021-0.00330.8130.0010.0010.0000.0000.0000.000
197G235ARG10.7840.89931.9920.0620.0620.0000.0000.0000.000
198G236ILE00.0140.01335.3950.0000.0000.0000.0000.0000.000
199G237TRP00.0110.01138.4170.0000.0000.0000.0000.0000.000
200G238VAL0-0.012-0.01242.0160.0010.0010.0000.0000.0000.000
201G239LYS10.8370.93844.8630.0220.0220.0000.0000.0000.000
202G240ALA00.0550.02348.6660.0000.0000.0000.0000.0000.000
203G241LYS10.9480.98151.2730.0130.0130.0000.0000.0000.000
204G242THR00.0060.00554.1880.0000.0000.0000.0000.0000.000
205G243ILE00.1000.05251.0490.0000.0000.0000.0000.0000.000
206G244GLN00.0550.02550.658-0.001-0.0010.0000.0000.0000.000
207G245GLN00.0370.00850.1730.0000.0000.0000.0000.0000.000
208G246THR0-0.0150.00247.2490.0000.0000.0000.0000.0000.000
209G247LEU00.0260.00145.847-0.001-0.0010.0000.0000.0000.000
210G248ILE0-0.0170.00145.4750.0000.0000.0000.0000.0000.000
211G249LEU00.0160.00843.5790.0010.0010.0000.0000.0000.000
212G250ALA0-0.0060.00341.9660.0000.0000.0000.0000.0000.000
213G251ASN00.0240.01040.7310.0000.0000.0000.0000.0000.000
214G252ILE0-0.017-0.01740.6640.0010.0010.0000.0000.0000.000
215G253LEU00.009-0.00538.3950.0010.0010.0000.0000.0000.000
216G254GLU-1-0.966-0.98736.419-0.021-0.0210.0000.0000.0000.000
217G255ALA0-0.015-0.00135.5970.0000.0000.0000.0000.0000.000
218G256CYS0-0.082-0.04136.3250.0030.0030.0000.0000.0000.000
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