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: K3YY3

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 OptH
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 -2598983.243916
FMO2-HF: Nuclear repulsion 2508537.448605
FMO2-HF: Total energy -90445.795311
FMO2-MP2: Total energy -90708.598564


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.
-5.564-2.3130.499-1.468-2.281-0.001
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 : 0.023 / q_NPA : 0.000
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].
3G18ALA00.0200.0043.8390.4041.997-0.019-0.822-0.7520.000
4G19ALA00.0800.0466.073-0.165-0.1650.0000.0000.0000.000
5G20ARG10.9670.9659.5150.3430.3430.0000.0000.0000.000
6G21THR0-0.022-0.03211.9150.0040.0040.0000.0000.0000.000
7G22VAL0-0.0660.0187.4610.0560.0560.0000.0000.0000.000
8G23LEU00.075-0.0105.5010.1320.1320.0000.0000.0000.000
9G24GLY00.0540.00910.025-0.079-0.0790.0000.0000.0000.000
10G25GLN0-0.094-0.02410.0620.0140.0140.0000.0000.0000.000
11G26VAL00.006-0.02312.077-0.060-0.0600.0000.0000.0000.000
12G27VAL0-0.0210.0187.3160.1030.1030.0000.0000.0000.000
13G28LEU0-0.031-0.0386.8730.1080.1080.0000.0000.0000.000
14G29PRO0-0.047-0.0187.779-0.151-0.1510.0000.0000.0000.000
15G30GLY00.0100.0006.9370.1080.1080.0000.0000.0000.000
16G31GLU-1-0.890-0.9512.994-1.519-0.7140.222-0.277-0.750-0.001
17G32GLU-1-0.846-0.9192.520-3.988-3.3230.289-0.264-0.6890.000
18G33LEU0-0.134-0.1013.842-0.724-0.5360.007-0.105-0.0900.000
19G34LEU0-0.0190.0566.4990.1720.1720.0000.0000.0000.000
20G35LEU0-0.057-0.02510.1810.0760.0760.0000.0000.0000.000
21G36PRO0-0.0180.01513.367-0.020-0.0200.0000.0000.0000.000
22G37GLU-1-0.842-0.94613.998-0.546-0.5460.0000.0000.0000.000
23G38GLN0-0.032-0.02818.0160.0040.0040.0000.0000.0000.000
24G39GLU-1-0.921-0.93819.817-0.262-0.2620.0000.0000.0000.000
25G40ASP-1-0.930-0.97216.867-0.451-0.4510.0000.0000.0000.000
26G41ALA0-0.020-0.00519.6790.0060.0060.0000.0000.0000.000
27G42GLU-1-0.760-0.85914.677-0.575-0.5750.0000.0000.0000.000
28G43GLY0-0.040-0.02816.1540.0500.0500.0000.0000.0000.000
29G44PRO0-0.119-0.06516.3320.0080.0080.0000.0000.0000.000
30G45GLY0-0.032-0.03113.9990.0000.0000.0000.0000.0000.000
31G46GLY0-0.0050.00711.365-0.063-0.0630.0000.0000.0000.000
32G47ALA00.0360.00110.9080.0820.0820.0000.0000.0000.000
33G48VAL00.0160.02011.224-0.146-0.1460.0000.0000.0000.000
34G49GLU-1-0.920-0.96810.746-1.058-1.0580.0000.0000.0000.000
35G50ARG10.7460.98311.1460.5110.5110.0000.0000.0000.000
36G74GLY0-0.009-0.00716.8590.0170.0170.0000.0000.0000.000
37G75ASP-1-0.789-0.98914.348-0.575-0.5750.0000.0000.0000.000
38G76ARG10.8250.8457.1081.6071.6070.0000.0000.0000.000
39G77LEU00.0980.0288.8370.1410.1410.0000.0000.0000.000
40G78LEU00.0330.0286.433-0.409-0.4090.0000.0000.0000.000
41G79VAL0-0.0670.0126.5410.3080.3080.0000.0000.0000.000
42G80THR00.0280.0088.792-0.019-0.0190.0000.0000.0000.000
43G81LYS10.9250.94811.5320.3690.3690.0000.0000.0000.000
44G82CYS00.0130.00211.607-0.042-0.0420.0000.0000.0000.000
45G83GLY00.0370.01312.1740.0480.0480.0000.0000.0000.000
46G84ARG10.8990.96012.1520.0570.0570.0000.0000.0000.000
47G85LEU00.0390.07111.678-0.019-0.0190.0000.0000.0000.000
48G86ARG10.7740.89613.5680.2080.2080.0000.0000.0000.000
49G87HIS10.8900.93616.2540.2310.2310.0000.0000.0000.000
50G88LYS10.9671.00018.3180.1870.1870.0000.0000.0000.000
51G89GLU-1-0.910-0.97021.378-0.180-0.1800.0000.0000.0000.000
52G90PRO00.0390.04922.9100.0120.0120.0000.0000.0000.000
53G91GLY00.0100.00925.0760.0150.0150.0000.0000.0000.000
54G92SER0-0.024-0.03926.817-0.003-0.0030.0000.0000.0000.000
55G93GLY00.0300.02929.058-0.001-0.0010.0000.0000.0000.000
56G94SER00.0020.01427.9160.0010.0010.0000.0000.0000.000
57G95GLY00.0430.03428.482-0.010-0.0100.0000.0000.0000.000
58G96GLY0-0.025-0.03526.674-0.005-0.0050.0000.0000.0000.000
59G97GLY0-0.053-0.03723.3100.0100.0100.0000.0000.0000.000
60G98VAL0-0.0010.01618.340-0.010-0.0100.0000.0000.0000.000
61G99TYR00.0190.02114.5090.0410.0410.0000.0000.0000.000
62G100TRP00.007-0.03015.994-0.008-0.0080.0000.0000.0000.000
63G101VAL00.1180.04911.8950.0040.0040.0000.0000.0000.000
64G102ASP-1-0.893-0.90114.926-0.143-0.1430.0000.0000.0000.000
65G103SER00.059-0.00216.237-0.011-0.0110.0000.0000.0000.000
66G104GLN0-0.0450.00218.505-0.005-0.0050.0000.0000.0000.000
67G105GLN0-0.037-0.01619.9990.0000.0000.0000.0000.0000.000
68G106LYS10.9370.94322.4240.0620.0620.0000.0000.0000.000
69G107ARG10.9501.00121.5450.1780.1780.0000.0000.0000.000
70G108TYR00.0520.03925.172-0.006-0.0060.0000.0000.0000.000
71G109VAL0-0.057-0.03322.557-0.006-0.0060.0000.0000.0000.000
72G110PRO00.0560.01825.7340.0020.0020.0000.0000.0000.000
73G111VAL0-0.051-0.03225.099-0.019-0.0190.0000.0000.0000.000
74G112LYS10.9430.97725.0470.1990.1990.0000.0000.0000.000
75G113GLY00.0970.03529.6910.0030.0030.0000.0000.0000.000
76G114ASP-1-0.861-0.93028.708-0.133-0.1330.0000.0000.0000.000
77G115HIS00.0100.02231.5650.0020.0020.0000.0000.0000.000
78G116VAL0-0.042-0.01532.241-0.001-0.0010.0000.0000.0000.000
79G117ILE0-0.029-0.01935.0460.0030.0030.0000.0000.0000.000
80G118GLY0-0.002-0.03136.976-0.004-0.0040.0000.0000.0000.000
81G119ILE00.0250.03037.6100.0040.0040.0000.0000.0000.000
82G120VAL00.0230.01740.307-0.005-0.0050.0000.0000.0000.000
83G121THR00.0070.00539.4310.0020.0020.0000.0000.0000.000
84G122ALA00.018-0.00741.8090.0030.0030.0000.0000.0000.000
85G123LYS10.8870.95743.7320.0560.0560.0000.0000.0000.000
86G124SER0-0.074-0.02944.4450.0040.0040.0000.0000.0000.000
87G125GLY00.0460.00845.739-0.002-0.0020.0000.0000.0000.000
88G126ASP-1-0.890-0.97146.968-0.063-0.0630.0000.0000.0000.000
89G127ILE00.0280.01341.0930.0000.0000.0000.0000.0000.000
90G128PHE00.004-0.00243.0630.0030.0030.0000.0000.0000.000
91G129LYS10.9841.01737.6720.0910.0910.0000.0000.0000.000
92G130VAL00.0240.00137.8620.0060.0060.0000.0000.0000.000
93G131ASP-1-0.837-0.90434.848-0.092-0.0920.0000.0000.0000.000
94G132VAL0-0.052-0.05031.8310.0030.0030.0000.0000.0000.000
95G133GLY0-0.063-0.03331.897-0.001-0.0010.0000.0000.0000.000
96G134GLY00.0460.03128.596-0.005-0.0050.0000.0000.0000.000
97G135SER0-0.117-0.08026.2800.0000.0000.0000.0000.0000.000
98G136GLU-1-0.876-0.93428.398-0.143-0.1430.0000.0000.0000.000
99G137PRO0-0.066-0.01431.8490.0020.0020.0000.0000.0000.000
100G138ALA00.0710.02833.197-0.007-0.0070.0000.0000.0000.000
101G139SER00.021-0.02635.3400.0080.0080.0000.0000.0000.000
102G140LEU0-0.0220.02338.645-0.001-0.0010.0000.0000.0000.000
103G141SER00.0680.03841.5310.0020.0020.0000.0000.0000.000
104G142TYR0-0.083-0.02444.2510.0040.0040.0000.0000.0000.000
105G143LEU0-0.005-0.03846.6140.0030.0030.0000.0000.0000.000
106G144SER0-0.003-0.00543.928-0.004-0.0040.0000.0000.0000.000
107G145PHE00.0460.00345.396-0.001-0.0010.0000.0000.0000.000
108G146GLU-1-0.838-0.88548.694-0.049-0.0490.0000.0000.0000.000
109G147GLY00.0140.01350.8420.0030.0030.0000.0000.0000.000
110G148ALA0-0.025-0.00752.367-0.002-0.0020.0000.0000.0000.000
111G149THR00.059-0.01454.4430.0010.0010.0000.0000.0000.000
112G150LYS10.8970.96855.4960.0450.0450.0000.0000.0000.000
113G151ARG10.9400.97053.9730.0450.0450.0000.0000.0000.000
114G152ASN00.038-0.02050.636-0.002-0.0020.0000.0000.0000.000
115G153ARG10.9911.01751.4400.0480.0480.0000.0000.0000.000
116G154PRO0-0.044-0.02153.131-0.001-0.0010.0000.0000.0000.000
117G155ASN0-0.0590.01152.3090.0000.0000.0000.0000.0000.000
118G156VAL00.1160.02947.669-0.002-0.0020.0000.0000.0000.000
119G157GLN0-0.068-0.02448.4600.0000.0000.0000.0000.0000.000
120G158VAL00.0880.05946.046-0.002-0.0020.0000.0000.0000.000
121G159GLY0-0.054-0.01545.0900.0020.0020.0000.0000.0000.000
122G160ASP-1-0.896-0.95945.966-0.047-0.0470.0000.0000.0000.000
123G161LEU0-0.007-0.02143.183-0.003-0.0030.0000.0000.0000.000
124G162ILE00.000-0.01141.2860.0010.0010.0000.0000.0000.000
125G163TYR00.0430.03737.757-0.002-0.0020.0000.0000.0000.000
126G164GLY00.0550.00438.7340.0020.0020.0000.0000.0000.000
127G165GLN00.0540.01334.8000.0020.0020.0000.0000.0000.000
128G166PHE0-0.0490.01030.2300.0040.0040.0000.0000.0000.000
129G167VAL0-0.027-0.00333.512-0.004-0.0040.0000.0000.0000.000
130G168VAL0-0.061-0.01232.201-0.008-0.0080.0000.0000.0000.000
131G169ALA00.0950.06828.5820.0050.0050.0000.0000.0000.000
132G170ASN0-0.081-0.04026.2700.0010.0010.0000.0000.0000.000
133G171LYS10.9420.95719.7660.3270.3270.0000.0000.0000.000
134G172ASP-1-0.890-0.93723.959-0.261-0.2610.0000.0000.0000.000
135G173MET0-0.079-0.01226.1590.0120.0120.0000.0000.0000.000
136G174GLU-1-0.923-0.95328.701-0.124-0.1240.0000.0000.0000.000
137G175PRO0-0.007-0.03529.7920.0020.0020.0000.0000.0000.000
138G176GLU-1-0.944-0.97432.308-0.101-0.1010.0000.0000.0000.000
139G177MET0-0.054-0.04535.529-0.002-0.0020.0000.0000.0000.000
140G178VAL0-0.070-0.01737.5030.0040.0040.0000.0000.0000.000
141G179CYS0-0.015-0.03640.363-0.001-0.0010.0000.0000.0000.000
142G180ILE00.0340.02743.0310.0020.0020.0000.0000.0000.000
143G181ASP-1-0.892-0.94242.647-0.072-0.0720.0000.0000.0000.000
144G182SER0-0.075-0.03341.0770.0000.0000.0000.0000.0000.000
145G183CYS00.0000.00040.435-0.001-0.0010.0000.0000.0000.000
146G184GLY00.0330.00042.8770.0010.0010.0000.0000.0000.000
147G185ARG10.8390.90844.4820.0750.0750.0000.0000.0000.000
148G186ALA00.0400.05046.7700.0020.0020.0000.0000.0000.000
149G187ASN0-0.032-0.06646.637-0.004-0.0040.0000.0000.0000.000
150G188GLY00.0450.04043.9350.0020.0020.0000.0000.0000.000
151G189MET0-0.092-0.01839.477-0.001-0.0010.0000.0000.0000.000
152G190GLY00.0490.03443.7530.0000.0000.0000.0000.0000.000
153G191VAL0-0.052-0.03344.972-0.001-0.0010.0000.0000.0000.000
154G192ILE0-0.046-0.00841.9840.0010.0010.0000.0000.0000.000
155G193GLY0-0.007-0.01246.1210.0010.0010.0000.0000.0000.000
156G194GLN0-0.035-0.00749.1580.0000.0000.0000.0000.0000.000
157G195ASP-1-0.869-0.93651.137-0.030-0.0300.0000.0000.0000.000
158G196GLY00.024-0.02447.812-0.001-0.0010.0000.0000.0000.000
159G197LEU0-0.038-0.02043.2540.0010.0010.0000.0000.0000.000
160G198LEU00.0290.06738.639-0.002-0.0020.0000.0000.0000.000
161G199PHE0-0.0210.00038.7040.0010.0010.0000.0000.0000.000
162G200LYS10.9520.95632.6040.0480.0480.0000.0000.0000.000
163G201VAL00.0550.06632.7970.0030.0030.0000.0000.0000.000
164G202THR00.0020.02827.251-0.008-0.0080.0000.0000.0000.000
165G203LEU00.1000.04324.7230.0000.0000.0000.0000.0000.000
166G204GLY0-0.033-0.02325.7280.0000.0000.0000.0000.0000.000
167G205LEU0-0.014-0.01626.4760.0010.0010.0000.0000.0000.000
168G206ILE00.0750.05929.1970.0000.0000.0000.0000.0000.000
169G207ARG10.7970.86321.2420.1200.1200.0000.0000.0000.000
170G208LYS10.9120.95326.9920.0400.0400.0000.0000.0000.000
171G209LEU0-0.081-0.02330.0760.0050.0050.0000.0000.0000.000
172G210LEU00.008-0.00931.9080.0020.0020.0000.0000.0000.000
173G211ALA0-0.0200.01030.515-0.004-0.0040.0000.0000.0000.000
174G212PRO00.0580.02831.4630.0050.0050.0000.0000.0000.000
175G213ASP-1-0.964-0.98131.049-0.051-0.0510.0000.0000.0000.000
176G214CYS0-0.0620.00133.5270.0060.0060.0000.0000.0000.000
177G215GLU-1-0.885-0.99735.411-0.026-0.0260.0000.0000.0000.000
178G216ILE00.008-0.02535.5310.0010.0010.0000.0000.0000.000
179G217ILE00.0890.03336.3570.0010.0010.0000.0000.0000.000
180G218GLN00.0930.06938.8080.0000.0000.0000.0000.0000.000
181G219GLH0-0.147-0.03140.9760.0030.0030.0000.0000.0000.000
182G220VAL0-0.013-0.03341.5500.0030.0030.0000.0000.0000.000
183G221GLY0-0.047-0.01144.0650.0010.0010.0000.0000.0000.000
184G222LYS10.6960.85845.8710.0210.0210.0000.0000.0000.000
185G223LEU00.025-0.00147.1310.0000.0000.0000.0000.0000.000
186G224TYR0-0.0090.07450.204-0.001-0.0010.0000.0000.0000.000
187G225PRO0-0.089-0.04952.9100.0010.0010.0000.0000.0000.000
188G226LEU00.002-0.03545.9670.0000.0000.0000.0000.0000.000
189G227GLU-1-0.881-0.93547.540-0.036-0.0360.0000.0000.0000.000
190G228ILE0-0.014-0.01042.0420.0010.0010.0000.0000.0000.000
191G229VAL0-0.0070.00639.732-0.002-0.0020.0000.0000.0000.000
192G230PHE0-0.003-0.01836.2040.0010.0010.0000.0000.0000.000
193G231GLY00.0010.00235.239-0.004-0.0040.0000.0000.0000.000
194G232MET00.0750.02928.1330.0030.0030.0000.0000.0000.000
195G233ASN0-0.035-0.00630.3120.0010.0010.0000.0000.0000.000
196G234GLY0-0.047-0.09531.4120.0030.0030.0000.0000.0000.000
197G235ARG10.8150.90132.6950.0770.0770.0000.0000.0000.000
198G236ILE00.0390.01335.847-0.001-0.0010.0000.0000.0000.000
199G237TRP0-0.0290.01039.1560.0020.0020.0000.0000.0000.000
200G238VAL00.017-0.01642.5460.0000.0000.0000.0000.0000.000
201G239LYS10.9690.98745.1570.0300.0300.0000.0000.0000.000
202G240ALA00.0110.01448.9000.0000.0000.0000.0000.0000.000
203G241LYS10.9830.98851.0810.0200.0200.0000.0000.0000.000
204G242THR00.0650.00654.100-0.001-0.0010.0000.0000.0000.000
205G243ILE00.1260.07751.417-0.001-0.0010.0000.0000.0000.000
206G244GLN00.1190.02950.657-0.002-0.0020.0000.0000.0000.000
207G245GLN0-0.0560.01950.1940.0000.0000.0000.0000.0000.000
208G246THR00.006-0.03047.696-0.001-0.0010.0000.0000.0000.000
209G247LEU0-0.015-0.00446.663-0.001-0.0010.0000.0000.0000.000
210G248ILE0-0.051-0.00845.6770.0000.0000.0000.0000.0000.000
211G249LEU00.0180.01543.7990.0000.0000.0000.0000.0000.000
212G250ALA00.0600.02642.081-0.001-0.0010.0000.0000.0000.000
213G251ASN00.0660.03840.846-0.001-0.0010.0000.0000.0000.000
214G252ILE0-0.082-0.05740.7420.0010.0010.0000.0000.0000.000
215G253LEU00.000-0.10138.5780.0000.0000.0000.0000.0000.000
216G254GLU-1-0.975-1.00236.873-0.026-0.0260.0000.0000.0000.000
217G255ALA0-0.036-0.01335.9010.0010.0010.0000.0000.0000.000
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