Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 1NNYZ

Calculation Name: 4R3O-N-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R3O

Chain ID: N

ChEMBL ID:

UniProt ID: P25786

Base Structure: X-ray

Registration Date: 2023-09-21

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2543828.82125
FMO2-HF: Nuclear repulsion 2457710.132738
FMO2-HF: Total energy -86118.688512
FMO2-MP2: Total energy -86364.623011


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(N:1:THR)


Summations of interaction energy for fragment #1(N:1:THR)
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.
-33.636-33.55234.14-15.939-18.286-0.1
Interaction energy analysis for fragmet #1(N:1:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.059
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].
3N3ASN0-0.023-0.0122.474-2.959-0.1401.057-1.616-2.2610.002
4N4PRO0-0.0120.0152.533-0.8300.6281.912-1.029-2.341-0.009
5N5MET0-0.020-0.0153.2880.4590.0230.0570.565-0.1860.000
6N6VAL0-0.039-0.0216.412-0.142-0.1420.0000.0000.0000.000
7N7THR0-0.039-0.0156.282-0.221-0.2210.0000.0000.0000.000
8N8GLY00.0440.0288.7450.1780.1780.0000.0000.0000.000
9N9THR0-0.038-0.03011.032-0.186-0.1860.0000.0000.0000.000
10N10SER0-0.011-0.00513.696-0.104-0.1040.0000.0000.0000.000
11N11VAL0-0.0470.00414.9900.0290.0290.0000.0000.0000.000
12N12LEU0-0.005-0.01117.681-0.004-0.0040.0000.0000.0000.000
13N13GLY00.0420.01021.223-0.012-0.0120.0000.0000.0000.000
14N14VAL0-0.004-0.01123.684-0.003-0.0030.0000.0000.0000.000
15N15LYS10.8140.90827.0730.3070.3070.0000.0000.0000.000
16N16PHE0-0.048-0.02529.3490.0050.0050.0000.0000.0000.000
17N17GLU-1-0.880-0.95232.658-0.164-0.1640.0000.0000.0000.000
18N18GLY00.0090.01534.9980.0040.0040.0000.0000.0000.000
19N19GLY00.010-0.01930.9100.0020.0020.0000.0000.0000.000
20N20VAL0-0.065-0.01625.227-0.010-0.0100.0000.0000.0000.000
21N21VAL0-0.0060.00526.3150.0030.0030.0000.0000.0000.000
22N22ILE0-0.002-0.01219.776-0.024-0.0240.0000.0000.0000.000
23N23ALA00.0070.00821.7490.0330.0330.0000.0000.0000.000
24N24ALA00.0260.00717.130-0.057-0.0570.0000.0000.0000.000
25N25ASP-1-0.788-0.88717.210-0.401-0.4010.0000.0000.0000.000
26N26MET0-0.053-0.01817.547-0.032-0.0320.0000.0000.0000.000
27N27LEU0-0.071-0.02115.3760.0550.0550.0000.0000.0000.000
28N28GLY00.0320.01012.264-0.091-0.0910.0000.0000.0000.000
29N29SER0-0.024-0.01612.5540.1290.1290.0000.0000.0000.000
30N30TYR00.000-0.0089.759-0.087-0.0870.0000.0000.0000.000
31N31GLY00.0680.03210.6360.0440.0440.0000.0000.0000.000
32N32SER00.0190.00812.299-0.072-0.0720.0000.0000.0000.000
33N33LEU00.0150.02315.298-0.001-0.0010.0000.0000.0000.000
34N34ALA00.0760.03415.316-0.020-0.0200.0000.0000.0000.000
35N35ARG10.8790.94313.180-0.200-0.2000.0000.0000.0000.000
36N36PHE00.012-0.00112.7300.0370.0370.0000.0000.0000.000
37N37ARG10.9620.98616.3710.0480.0480.0000.0000.0000.000
38N38ASN00.0190.01418.3060.0100.0100.0000.0000.0000.000
39N39ILE0-0.0170.01112.8630.0320.0320.0000.0000.0000.000
40N40SER00.0320.01217.054-0.049-0.0490.0000.0000.0000.000
41N41ARG10.7800.89813.1440.5980.5980.0000.0000.0000.000
42N42ILE00.0260.00815.241-0.092-0.0920.0000.0000.0000.000
43N43MET0-0.043-0.00214.4420.0460.0460.0000.0000.0000.000
44N44ARG10.9560.98118.1280.1890.1890.0000.0000.0000.000
45N45VAL0-0.045-0.02717.553-0.005-0.0050.0000.0000.0000.000
46N46ASN00.1420.07720.7980.0000.0000.0000.0000.0000.000
47N47ASN00.0070.00624.283-0.010-0.0100.0000.0000.0000.000
48N48SER00.0110.01026.1310.0040.0040.0000.0000.0000.000
49N49THR0-0.037-0.03221.652-0.032-0.0320.0000.0000.0000.000
50N50MET0-0.0040.01320.4870.0130.0130.0000.0000.0000.000
51N51LEU00.000-0.00513.005-0.039-0.0390.0000.0000.0000.000
52N52GLY00.0380.02115.9270.0430.0430.0000.0000.0000.000
53N53ALA0-0.019-0.01610.785-0.092-0.0920.0000.0000.0000.000
54N54SER0-0.005-0.00811.4500.1720.1720.0000.0000.0000.000
55N55GLY00.0050.0007.432-0.330-0.3300.0000.0000.0000.000
56N56ASP-1-0.786-0.9113.5570.0560.4070.010-0.059-0.3030.000
57N57TYR00.006-0.0265.507-0.458-0.4580.0000.0000.0000.000
58N58ALA0-0.0280.0004.8220.1010.1010.0000.0000.0000.000
59N59ASP-1-0.717-0.8361.640-27.956-35.41519.652-7.486-4.707-0.060
60N60PHE00.0100.0124.5810.7920.835-0.001-0.013-0.0280.000
61N61GLN0-0.033-0.0338.1340.3670.3670.0000.0000.0000.000
62N62TYR0-0.0060.0046.7400.1920.1920.0000.0000.0000.000
63N63LEU00.028-0.0028.2470.1950.1950.0000.0000.0000.000
64N64LYS10.9510.97710.2790.5990.5990.0000.0000.0000.000
65N65GLN0-0.041-0.01012.1110.1310.1310.0000.0000.0000.000
66N66VAL0-0.021-0.00811.5650.0680.0680.0000.0000.0000.000
67N67LEU00.007-0.01013.8510.0430.0430.0000.0000.0000.000
68N68GLY00.0130.01416.0150.0440.0440.0000.0000.0000.000
69N69GLN0-0.078-0.04717.3520.0450.0450.0000.0000.0000.000
70N70MET0-0.022-0.00517.381-0.010-0.0100.0000.0000.0000.000
71N71VAL0-0.011-0.00220.0040.0100.0100.0000.0000.0000.000
72N72ILE0-0.0010.00621.2620.0190.0190.0000.0000.0000.000
73N73ASP-1-0.872-0.95021.472-0.063-0.0630.0000.0000.0000.000
74N74GLU-1-0.867-0.91824.244-0.199-0.1990.0000.0000.0000.000
75N75GLU-1-0.936-0.99126.005-0.158-0.1580.0000.0000.0000.000
76N76LEU0-0.066-0.03226.5020.0130.0130.0000.0000.0000.000
77N77LEU0-0.059-0.02028.2650.0130.0130.0000.0000.0000.000
78N78GLY0-0.031-0.01331.3400.0070.0070.0000.0000.0000.000
79N79ASP-1-0.890-0.94732.066-0.103-0.1030.0000.0000.0000.000
80N80GLY0-0.0100.00833.7340.0030.0030.0000.0000.0000.000
81N81HIS0-0.143-0.07330.585-0.003-0.0030.0000.0000.0000.000
82N82SER00.0590.02127.5360.0050.0050.0000.0000.0000.000
83N83TYR0-0.084-0.04522.301-0.019-0.0190.0000.0000.0000.000
84N84SER00.0730.04725.091-0.019-0.0190.0000.0000.0000.000
85N85PRO00.0440.00923.137-0.029-0.0290.0000.0000.0000.000
86N86ARG10.8930.94322.1290.2460.2460.0000.0000.0000.000
87N87ALA00.0030.01722.429-0.026-0.0260.0000.0000.0000.000
88N88ILE00.0470.02617.972-0.034-0.0340.0000.0000.0000.000
89N89HIS0-0.005-0.01317.867-0.041-0.0410.0000.0000.0000.000
90N90SER0-0.0050.01117.616-0.080-0.0800.0000.0000.0000.000
91N91TRP00.0400.01212.845-0.082-0.0820.0000.0000.0000.000
92N92LEU00.0520.01911.388-0.050-0.0500.0000.0000.0000.000
93N93THR0-0.011-0.02712.811-0.170-0.1700.0000.0000.0000.000
94N94ARG10.8790.94813.5410.4480.4480.0000.0000.0000.000
95N95ALA00.0130.01711.0210.0370.0370.0000.0000.0000.000
96N96MET0-0.0200.0077.686-0.074-0.0740.0000.0000.0000.000
97N97TYR00.0520.0208.774-0.055-0.0550.0000.0000.0000.000
98N98SER0-0.0220.00710.7180.1860.1860.0000.0000.0000.000
99N99ARG10.8220.9012.5133.7134.5850.459-0.454-0.8760.003
100N100ARG10.9350.9696.5340.9000.9000.0000.0000.0000.000
101N101SER0-0.073-0.0478.0700.2420.2420.0000.0000.0000.000
102N102LYS10.8720.9438.168-0.036-0.0360.0000.0000.0000.000
103N103MET0-0.0030.0097.8630.3690.3690.0000.0000.0000.000
104N104ASN00.0100.0193.2691.3032.4360.481-0.619-0.9950.003
105N105PRO00.0510.0293.414-1.1560.1950.087-0.516-0.921-0.001
106N106LEU00.0020.0101.893-8.795-11.3018.744-3.420-2.819-0.035
107N107TRP00.009-0.0022.2870.7813.0591.679-1.264-2.694-0.003
108N108ASN0-0.075-0.0743.9570.5520.7320.003-0.028-0.1550.000
109N109THR0-0.0100.0007.5990.0790.0790.0000.0000.0000.000
110N110MET0-0.057-0.0239.6910.1080.1080.0000.0000.0000.000
111N111VAL00.0300.02113.6820.0660.0660.0000.0000.0000.000
112N112ILE00.0020.01216.3510.0000.0000.0000.0000.0000.000
113N113GLY00.0320.00819.1050.0230.0230.0000.0000.0000.000
114N114GLY0-0.013-0.03422.733-0.008-0.0080.0000.0000.0000.000
115N115TYR0-0.042-0.01625.4820.0060.0060.0000.0000.0000.000
116N116ALA00.018-0.00329.1340.0040.0040.0000.0000.0000.000
117N117ASP-1-0.928-0.95530.990-0.178-0.1780.0000.0000.0000.000
118N118GLY00.0060.01634.4060.0070.0070.0000.0000.0000.000
119N119GLU-1-0.900-0.94232.130-0.202-0.2020.0000.0000.0000.000
120N120SER0-0.0020.00629.737-0.009-0.0090.0000.0000.0000.000
121N121PHE0-0.042-0.02821.485-0.003-0.0030.0000.0000.0000.000
122N122LEU0-0.010-0.01422.225-0.011-0.0110.0000.0000.0000.000
123N123GLY00.0090.00821.0340.0220.0220.0000.0000.0000.000
124N124TYR0-0.038-0.03014.301-0.027-0.0270.0000.0000.0000.000
125N125VAL0-0.005-0.00612.8460.0470.0470.0000.0000.0000.000
126N126ASP-1-0.813-0.88411.537-1.522-1.5220.0000.0000.0000.000
127N127MET00.0260.0126.563-0.257-0.2570.0000.0000.0000.000
128N128LEU0-0.054-0.0408.343-0.033-0.0330.0000.0000.0000.000
129N129GLY0-0.013-0.01710.8110.2300.2300.0000.0000.0000.000
130N130VAL0-0.041-0.01012.7770.1560.1560.0000.0000.0000.000
131N131ALA00.019-0.00215.359-0.098-0.0980.0000.0000.0000.000
132N132TYR0-0.051-0.01417.9620.0770.0770.0000.0000.0000.000
133N133GLU-1-0.761-0.88021.153-0.360-0.3600.0000.0000.0000.000
134N134ALA0-0.029-0.01723.9490.0110.0110.0000.0000.0000.000
135N135PRO00.0600.03625.755-0.005-0.0050.0000.0000.0000.000
136N136SER00.0530.01225.9630.0120.0120.0000.0000.0000.000
137N137LEU0-0.064-0.01419.909-0.024-0.0240.0000.0000.0000.000
138N138ALA00.0090.00920.0630.0220.0220.0000.0000.0000.000
139N139THR00.007-0.00214.6650.0140.0140.0000.0000.0000.000
140N140GLY00.0150.00315.0070.0490.0490.0000.0000.0000.000
141N141TYR00.0350.00715.6650.0330.0330.0000.0000.0000.000
142N142GLY00.0680.03518.6530.0470.0470.0000.0000.0000.000
143N143ALA0-0.031-0.01618.8280.0410.0410.0000.0000.0000.000
144N144TYR0-0.021-0.02118.0250.0130.0130.0000.0000.0000.000
145N145LEU0-0.051-0.01622.5100.0350.0350.0000.0000.0000.000
146N146ALA00.0160.01123.1400.0210.0210.0000.0000.0000.000
147N147GLN00.023-0.00222.9750.0400.0400.0000.0000.0000.000
148N148PRO0-0.013-0.00825.2400.0170.0170.0000.0000.0000.000
149N149LEU00.0310.01928.2560.0160.0160.0000.0000.0000.000
150N150LEU00.000-0.00825.0560.0110.0110.0000.0000.0000.000
151N151ARG10.9400.97724.7630.3480.3480.0000.0000.0000.000
152N152GLU-1-0.896-0.91930.809-0.168-0.1680.0000.0000.0000.000
153N153VAL00.0200.01133.0810.0140.0140.0000.0000.0000.000
154N154LEU00.0260.00529.9560.0070.0070.0000.0000.0000.000
155N155GLU-1-0.974-1.00131.874-0.229-0.2290.0000.0000.0000.000
156N156LYS10.7630.87135.5780.1790.1790.0000.0000.0000.000
157N157GLN0-0.084-0.05137.2760.0130.0130.0000.0000.0000.000
158N158PRO0-0.020-0.00835.189-0.007-0.0070.0000.0000.0000.000
159N159VAL0-0.0080.01634.870-0.010-0.0100.0000.0000.0000.000
160N160LEU00.0220.01432.4210.0060.0060.0000.0000.0000.000
161N161SER00.044-0.02035.736-0.004-0.0040.0000.0000.0000.000
162N162GLN00.0450.01432.294-0.003-0.0030.0000.0000.0000.000
163N163THR0-0.015-0.01933.380-0.007-0.0070.0000.0000.0000.000
164N164GLU-1-0.776-0.83234.887-0.162-0.1620.0000.0000.0000.000
165N165ALA00.0110.01430.638-0.009-0.0090.0000.0000.0000.000
166N166ARG10.7570.82930.1270.1780.1780.0000.0000.0000.000
167N167ASP-1-0.824-0.90330.667-0.183-0.1830.0000.0000.0000.000
168N168LEU00.0220.01029.309-0.006-0.0060.0000.0000.0000.000
169N169VAL00.0080.00625.458-0.015-0.0150.0000.0000.0000.000
170N170GLU-1-0.799-0.89226.919-0.208-0.2080.0000.0000.0000.000
171N171ARG10.8100.89328.6770.1870.1870.0000.0000.0000.000
172N172CYS0-0.043-0.01225.221-0.004-0.0040.0000.0000.0000.000
173N173MET0-0.016-0.01020.876-0.028-0.0280.0000.0000.0000.000
174N174ARG10.8090.90424.9420.1810.1810.0000.0000.0000.000
175N175VAL0-0.019-0.01326.2210.0070.0070.0000.0000.0000.000
176N176LEU0-0.026-0.01820.228-0.006-0.0060.0000.0000.0000.000
177N177TYR00.0080.01823.2210.0070.0070.0000.0000.0000.000
178N178TYR00.0120.01924.3920.0160.0160.0000.0000.0000.000
179N179ARG10.8600.91224.3770.2080.2080.0000.0000.0000.000
180N180ASP-1-0.741-0.84917.824-0.468-0.4680.0000.0000.0000.000
181N181ALA00.0130.00719.6980.0070.0070.0000.0000.0000.000
182N182ARG10.7950.89210.6770.5160.5160.0000.0000.0000.000
183N183SER00.001-0.00316.069-0.028-0.0280.0000.0000.0000.000
184N184TYR00.024-0.01318.6280.0510.0510.0000.0000.0000.000
185N185ASN00.0290.04021.032-0.029-0.0290.0000.0000.0000.000
186N186ARG10.8470.91122.7280.1720.1720.0000.0000.0000.000
187N187PHE0-0.013-0.01121.701-0.030-0.0300.0000.0000.0000.000
188N188GLN00.0070.02021.0110.0010.0010.0000.0000.0000.000
189N189ILE00.0420.02022.963-0.032-0.0320.0000.0000.0000.000
190N190ALA0-0.015-0.00322.5420.0150.0150.0000.0000.0000.000
191N191THR00.0330.00624.515-0.019-0.0190.0000.0000.0000.000
192N192VAL0-0.0290.00125.1340.0030.0030.0000.0000.0000.000
193N193THR00.0580.03028.0130.0060.0060.0000.0000.0000.000
194N194GLU-1-0.832-0.90631.332-0.138-0.1380.0000.0000.0000.000
195N195LYS10.8100.89633.7550.1350.1350.0000.0000.0000.000
196N196GLY00.0010.01330.0430.0090.0090.0000.0000.0000.000
197N197VAL0-0.050-0.02823.689-0.012-0.0120.0000.0000.0000.000
198N198GLU-1-0.943-0.96127.165-0.163-0.1630.0000.0000.0000.000
199N199ILE0-0.050-0.04621.445-0.028-0.0280.0000.0000.0000.000
200N200GLU-1-0.754-0.83025.584-0.177-0.1770.0000.0000.0000.000
201N201GLY00.0160.00125.629-0.014-0.0140.0000.0000.0000.000
202N202PRO0-0.049-0.04425.008-0.013-0.0130.0000.0000.0000.000
203N203LEU00.0130.03426.1340.0200.0200.0000.0000.0000.000
204N204SER0-0.030-0.04526.277-0.007-0.0070.0000.0000.0000.000
205N205THR0-0.038-0.01927.0040.0040.0040.0000.0000.0000.000
206N206GLU-1-0.782-0.87829.585-0.145-0.1450.0000.0000.0000.000
207N207THR0-0.050-0.02929.491-0.007-0.0070.0000.0000.0000.000
208N208ASN0-0.031-0.03532.7750.0120.0120.0000.0000.0000.000
209N209TRP00.018-0.01028.946-0.008-0.0080.0000.0000.0000.000
210N210ASP-1-0.828-0.89136.049-0.091-0.0910.0000.0000.0000.000
211N211ILE0-0.007-0.02733.9520.0040.0040.0000.0000.0000.000
212N212ALA0-0.034-0.01136.7750.0020.0020.0000.0000.0000.000
213N213HIS0-0.025-0.01338.3830.0070.0070.0000.0000.0000.000
214N214MET0-0.031-0.00940.9140.0010.0010.0000.0000.0000.000
215N215ILE0-0.0240.00139.3340.0000.0000.0000.0000.0000.000
216N216SER0-0.024-0.01341.755-0.001-0.0010.0000.0000.0000.000
217N217GLY0-0.0210.00444.5700.0020.0020.0000.0000.0000.000