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: QV22Y

Calculation Name: 1NG2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NG2

Chain ID: A

ChEMBL ID:

UniProt ID: P14598

Base Structure: X-ray

Registration Date: 2023-09-24

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1601503.989037
FMO2-HF: Nuclear repulsion 1531451.099029
FMO2-HF: Total energy -70052.890008
FMO2-MP2: Total energy -70258.463679


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:157:ILE)


Summations of interaction energy for fragment #1(A:157:ILE)
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.
-1.8361.0770.541-1.521-1.934-0.003
Interaction energy analysis for fragmet #1(A:157:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.009
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].
3A159GLN00.0500.0192.791-1.4251.3480.542-1.514-1.802-0.003
4A160THR00.0060.0114.4930.5120.652-0.001-0.007-0.1320.000
5A161TYR00.0220.0186.2920.0150.0150.0000.0000.0000.000
6A162ARG10.9200.9679.9870.2240.2240.0000.0000.0000.000
7A163ALA00.0200.03613.440-0.015-0.0150.0000.0000.0000.000
8A164ILE0-0.040-0.04716.8990.0250.0250.0000.0000.0000.000
9A165ALA0-0.009-0.00219.5940.0200.0200.0000.0000.0000.000
10A166ASP-1-0.815-0.88221.329-0.137-0.1370.0000.0000.0000.000
11A167TYR0-0.091-0.06821.469-0.007-0.0070.0000.0000.0000.000
12A168GLU-1-0.905-0.95323.315-0.125-0.1250.0000.0000.0000.000
13A169LYS10.9000.96423.8910.1310.1310.0000.0000.0000.000
14A170THR0-0.045-0.05325.4370.0170.0170.0000.0000.0000.000
15A171SER00.0210.02326.4590.0130.0130.0000.0000.0000.000
16A172GLY0-0.030-0.02826.255-0.004-0.0040.0000.0000.0000.000
17A173SER0-0.066-0.03823.861-0.005-0.0050.0000.0000.0000.000
18A174GLU-1-0.731-0.81821.559-0.225-0.2250.0000.0000.0000.000
19A175MET0-0.061-0.02914.8440.0250.0250.0000.0000.0000.000
20A176ALA00.0060.00920.341-0.012-0.0120.0000.0000.0000.000
21A177LEU0-0.060-0.03516.451-0.018-0.0180.0000.0000.0000.000
22A178SER00.0400.00820.1780.0170.0170.0000.0000.0000.000
23A179THR0-0.041-0.06119.815-0.023-0.0230.0000.0000.0000.000
24A180GLY0-0.052-0.02917.9050.0200.0200.0000.0000.0000.000
25A181ASP-1-0.811-0.88616.452-0.139-0.1390.0000.0000.0000.000
26A182VAL0-0.074-0.03610.249-0.037-0.0370.0000.0000.0000.000
27A183VAL00.0280.00410.9620.0420.0420.0000.0000.0000.000
28A184GLU-1-0.855-0.9126.272-0.362-0.3620.0000.0000.0000.000
29A185VAL0-0.001-0.0167.4940.1400.1400.0000.0000.0000.000
30A186VAL0-0.063-0.0327.735-0.500-0.5000.0000.0000.0000.000
31A187GLU-1-0.891-0.9429.794-0.628-0.6280.0000.0000.0000.000
32A188LYS10.7960.9009.4911.1571.1570.0000.0000.0000.000
33A189SER00.0510.01413.3580.0330.0330.0000.0000.0000.000
34A190GLU-1-0.955-0.98417.160-0.325-0.3250.0000.0000.0000.000
35A191SER0-0.009-0.00419.9650.0320.0320.0000.0000.0000.000
36A192GLY0-0.014-0.00219.5300.0310.0310.0000.0000.0000.000
37A193TRP0-0.031-0.01319.002-0.016-0.0160.0000.0000.0000.000
38A194TRP00.008-0.00112.178-0.090-0.0900.0000.0000.0000.000
39A195PHE00.0730.06113.3160.0350.0350.0000.0000.0000.000
40A196CYS0-0.044-0.03511.719-0.196-0.1960.0000.0000.0000.000
41A197GLN0-0.0110.0018.2760.1110.1110.0000.0000.0000.000
42A198MET00.0130.00311.582-0.062-0.0620.0000.0000.0000.000
43A199LYS10.7810.8705.7100.2420.2420.0000.0000.0000.000
44A200ALA00.0070.00410.8230.0450.0450.0000.0000.0000.000
45A201LYS10.9730.98312.5560.1100.1100.0000.0000.0000.000
46A202ARG10.9520.9759.617-0.337-0.3370.0000.0000.0000.000
47A203GLY00.0220.00716.688-0.001-0.0010.0000.0000.0000.000
48A204TRP0-0.0050.00219.565-0.007-0.0070.0000.0000.0000.000
49A205ILE00.0270.01322.534-0.011-0.0110.0000.0000.0000.000
50A206PRO00.007-0.00325.5190.0080.0080.0000.0000.0000.000
51A207ALA00.0820.04428.180-0.007-0.0070.0000.0000.0000.000
52A208SER00.002-0.01729.157-0.006-0.0060.0000.0000.0000.000
53A209PHE0-0.053-0.04230.326-0.007-0.0070.0000.0000.0000.000
54A210LEU0-0.0160.00825.777-0.005-0.0050.0000.0000.0000.000
55A211GLU-1-0.781-0.85729.8790.0270.0270.0000.0000.0000.000
56A212PRO00.0450.04529.331-0.002-0.0020.0000.0000.0000.000
57A213LEU00.0080.00226.423-0.006-0.0060.0000.0000.0000.000
58A214ASP-1-0.855-0.92430.7520.0210.0210.0000.0000.0000.000
59A215SER00.015-0.00533.377-0.004-0.0040.0000.0000.0000.000
60A216PRO0-0.031-0.01334.0500.0020.0020.0000.0000.0000.000
61A217ASP-1-0.866-0.92935.7300.0350.0350.0000.0000.0000.000
62A218GLU-1-0.841-0.91231.0510.0750.0750.0000.0000.0000.000
63A219THR0-0.038-0.02830.645-0.005-0.0050.0000.0000.0000.000
64A220GLU-1-0.958-0.98227.5890.1100.1100.0000.0000.0000.000
65A221ASP-1-0.795-0.89932.0440.0770.0770.0000.0000.0000.000
66A222PRO0-0.049-0.00133.950-0.003-0.0030.0000.0000.0000.000
67A223GLU-1-0.877-0.96336.4380.0500.0500.0000.0000.0000.000
68A224PRO0-0.095-0.03740.2150.0030.0030.0000.0000.0000.000
69A225ASN0-0.007-0.00142.796-0.004-0.0040.0000.0000.0000.000
70A226TYR00.030-0.00944.4590.0000.0000.0000.0000.0000.000
71A227ALA00.0570.05747.787-0.001-0.0010.0000.0000.0000.000
72A228GLY00.0290.03245.250-0.001-0.0010.0000.0000.0000.000
73A229GLU-1-0.818-0.90439.9580.0890.0890.0000.0000.0000.000
74A230PRO00.0150.02244.0530.0000.0000.0000.0000.0000.000
75A231TYR0-0.021-0.04036.7790.0060.0060.0000.0000.0000.000
76A232VAL00.0060.00541.786-0.004-0.0040.0000.0000.0000.000
77A233ALA00.0370.02541.3500.0050.0050.0000.0000.0000.000
78A234ILE0-0.043-0.01235.783-0.002-0.0020.0000.0000.0000.000
79A235LYS10.9280.96436.256-0.082-0.0820.0000.0000.0000.000
80A236ALA0-0.0050.01540.517-0.002-0.0020.0000.0000.0000.000
81A237TYR0-0.114-0.08241.0870.0040.0040.0000.0000.0000.000
82A238THR0-0.009-0.01243.339-0.002-0.0020.0000.0000.0000.000
83A239ALA0-0.006-0.00444.7470.0010.0010.0000.0000.0000.000
84A240VAL0-0.021-0.01742.571-0.002-0.0020.0000.0000.0000.000
85A241GLU-1-0.842-0.88142.7550.0400.0400.0000.0000.0000.000
86A242GLY0-0.013-0.01646.8650.0010.0010.0000.0000.0000.000
87A243ASP-1-0.834-0.89245.0780.0430.0430.0000.0000.0000.000
88A244GLU-1-0.750-0.84742.9210.0550.0550.0000.0000.0000.000
89A245VAL0-0.0130.00545.098-0.002-0.0020.0000.0000.0000.000
90A246SER0-0.006-0.00445.3370.0020.0020.0000.0000.0000.000
91A247LEU0-0.028-0.00544.021-0.001-0.0010.0000.0000.0000.000
92A248LEU00.016-0.00145.8070.0020.0020.0000.0000.0000.000
93A249GLU-1-0.910-0.97742.0630.0800.0800.0000.0000.0000.000
94A250GLY0-0.015-0.00644.689-0.002-0.0020.0000.0000.0000.000
95A251GLU-1-0.875-0.93046.4340.0510.0510.0000.0000.0000.000
96A252ALA0-0.011-0.00946.0440.0040.0040.0000.0000.0000.000
97A253VAL0-0.015-0.00744.126-0.003-0.0030.0000.0000.0000.000
98A254GLU-1-0.801-0.87145.7400.0550.0550.0000.0000.0000.000
99A255VAL0-0.049-0.01939.435-0.001-0.0010.0000.0000.0000.000
100A256ILE00.001-0.00542.8860.0000.0000.0000.0000.0000.000
101A257HIS00.0350.03339.466-0.004-0.0040.0000.0000.0000.000
102A258LYS10.8300.90735.820-0.092-0.0920.0000.0000.0000.000
103A259LEU0-0.037-0.00935.2190.0050.0050.0000.0000.0000.000
104A260LEU00.0810.02829.5210.0060.0060.0000.0000.0000.000
105A261ASP-1-0.858-0.90431.2010.0700.0700.0000.0000.0000.000
106A262GLY0-0.014-0.01532.952-0.002-0.0020.0000.0000.0000.000
107A263TRP0-0.079-0.04433.4740.0000.0000.0000.0000.0000.000
108A264TRP00.0250.01533.750-0.002-0.0020.0000.0000.0000.000
109A265VAL0-0.0140.00338.865-0.003-0.0030.0000.0000.0000.000
110A266ILE0-0.012-0.01342.3210.0030.0030.0000.0000.0000.000
111A267ARG10.7610.82744.717-0.053-0.0530.0000.0000.0000.000
112A268LYS10.8580.91648.047-0.044-0.0440.0000.0000.0000.000
113A269ASP-1-0.809-0.88750.4210.0420.0420.0000.0000.0000.000
114A270ASP-1-0.919-0.95053.4590.0380.0380.0000.0000.0000.000
115A271VAL0-0.075-0.04951.960-0.002-0.0020.0000.0000.0000.000
116A272THR0-0.013-0.03347.7040.0010.0010.0000.0000.0000.000
117A273GLY00.0080.00446.626-0.003-0.0030.0000.0000.0000.000
118A274TYR0-0.037-0.02040.4450.0030.0030.0000.0000.0000.000
119A275PHE00.014-0.00640.171-0.002-0.0020.0000.0000.0000.000
120A276PRO0-0.0080.00536.1170.0030.0030.0000.0000.0000.000
121A277SER00.0370.01933.0970.0010.0010.0000.0000.0000.000
122A278MET0-0.022-0.01730.2140.0020.0020.0000.0000.0000.000
123A279TYR0-0.024-0.01133.8590.0040.0040.0000.0000.0000.000
124A280LEU00.0160.01436.845-0.005-0.0050.0000.0000.0000.000
125A281GLN0-0.012-0.01636.1690.0040.0040.0000.0000.0000.000
126A282LYS10.8820.94437.691-0.099-0.0990.0000.0000.0000.000
127A283SER00.0100.00040.3270.0020.0020.0000.0000.0000.000
128A284GLY00.0210.01743.1420.0010.0010.0000.0000.0000.000
129A285GLN0-0.063-0.03238.0690.0090.0090.0000.0000.0000.000
130A286ASP-1-0.803-0.89337.2810.1060.1060.0000.0000.0000.000
131A287VAL00.1030.05237.2730.0070.0070.0000.0000.0000.000
132A288SER00.0460.04236.5450.0060.0060.0000.0000.0000.000
133A289GLN0-0.063-0.05132.6110.0160.0160.0000.0000.0000.000
134A290ALA00.0060.02332.2080.0100.0100.0000.0000.0000.000
135A291GLN00.030-0.00132.8550.0080.0080.0000.0000.0000.000
136A292ARG10.8360.92030.219-0.132-0.1320.0000.0000.0000.000
137A293GLN0-0.073-0.05828.3280.0180.0180.0000.0000.0000.000
138A294ILE0-0.0210.01428.6580.0060.0060.0000.0000.0000.000
139A295LYS10.8830.93924.369-0.214-0.2140.0000.0000.0000.000
140A296ARG10.9160.96123.115-0.167-0.1670.0000.0000.0000.000
141A297GLY00.0250.01629.308-0.003-0.0030.0000.0000.0000.000
142A298ALA00.0240.01031.1830.0060.0060.0000.0000.0000.000
143A299PRO00.0050.01130.637-0.002-0.0020.0000.0000.0000.000
144A300PRO00.0320.02831.894-0.003-0.0030.0000.0000.0000.000
145A301ARG10.8770.92634.602-0.048-0.0480.0000.0000.0000.000
146A302ARG10.8170.89033.461-0.044-0.0440.0000.0000.0000.000
147A303SER0-0.056-0.05937.243-0.002-0.0020.0000.0000.0000.000
148A304SER0-0.047-0.02937.700-0.002-0.0020.0000.0000.0000.000
149A305ILE0-0.032-0.01134.895-0.002-0.0020.0000.0000.0000.000
150A306ARG10.9370.96038.887-0.023-0.0230.0000.0000.0000.000
151A307ASN0-0.009-0.01140.632-0.002-0.0020.0000.0000.0000.000
152A308ALA00.0140.01937.513-0.001-0.0010.0000.0000.0000.000
153A309HIS0-0.009-0.00536.096-0.004-0.0040.0000.0000.0000.000
154A310SER0-0.033-0.04735.3990.0020.0020.0000.0000.0000.000
155A311ILE00.0160.01731.886-0.003-0.0030.0000.0000.0000.000
156A312HIS10.7690.88033.452-0.018-0.0180.0000.0000.0000.000
157A313GLN00.0500.02638.4670.0010.0010.0000.0000.0000.000
158A314ARG10.8500.93237.618-0.015-0.0150.0000.0000.0000.000
159A315SER00.0600.02040.3880.0000.0000.0000.0000.0000.000
160A316ARG10.8580.94036.229-0.051-0.0510.0000.0000.0000.000
161A317LYS10.8370.89739.683-0.031-0.0310.0000.0000.0000.000
162A318ARG10.8060.88436.608-0.056-0.0560.0000.0000.0000.000
163A319LEU0-0.0020.01842.471-0.003-0.0030.0000.0000.0000.000
164A320SER00.0550.02145.3540.0020.0020.0000.0000.0000.000
165A321GLN00.0920.03144.7230.0000.0000.0000.0000.0000.000
166A322ASP-1-0.756-0.83348.8230.0310.0310.0000.0000.0000.000
167A323ALA0-0.028-0.01249.490-0.001-0.0010.0000.0000.0000.000
168A324TYR0-0.012-0.03742.132-0.001-0.0010.0000.0000.0000.000
169A325ARG10.8970.94248.902-0.032-0.0320.0000.0000.0000.000
170A326ARG10.8200.88752.135-0.028-0.0280.0000.0000.0000.000
171A327ASN00.0430.02548.939-0.003-0.0030.0000.0000.0000.000
172A328SER00.0270.01849.9380.0010.0010.0000.0000.0000.000
173A329VAL0-0.020-0.00751.4640.0000.0000.0000.0000.0000.000
174A330ARG10.8280.90854.300-0.032-0.0320.0000.0000.0000.000
175A331PHE0-0.054-0.02151.296-0.001-0.0010.0000.0000.0000.000
176A332LEU00.0300.03451.2630.0030.0030.0000.0000.0000.000