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: ZV44N

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1599594.167666
FMO2-HF: Nuclear repulsion 1529542.498908
FMO2-HF: Total energy -70051.668759
FMO2-MP2: Total energy -70257.33388


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.
-0.0970000000000010.4963.979-1.676-2.897-0.011
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 : -0.026 / q_NPA : -0.028
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].
3A159GLN00.0230.0032.361-0.3780.0913.980-1.670-2.779-0.011
4A160THR0-0.006-0.0094.2420.5150.639-0.001-0.006-0.1180.000
5A161TYR00.0040.0016.520-0.065-0.0650.0000.0000.0000.000
6A162ARG10.9600.98210.0670.2010.2010.0000.0000.0000.000
7A163ALA00.0210.03413.419-0.021-0.0210.0000.0000.0000.000
8A164ILE0-0.045-0.04216.7950.0130.0130.0000.0000.0000.000
9A165ALA0-0.001-0.01219.6210.0080.0080.0000.0000.0000.000
10A166ASP-1-0.826-0.89621.216-0.049-0.0490.0000.0000.0000.000
11A167TYR0-0.068-0.03721.409-0.011-0.0110.0000.0000.0000.000
12A168GLU-1-0.895-0.94623.355-0.011-0.0110.0000.0000.0000.000
13A169LYS10.9260.95624.150-0.028-0.0280.0000.0000.0000.000
14A170THR0-0.051-0.00225.7320.0050.0050.0000.0000.0000.000
15A171SER00.0610.03626.6520.0090.0090.0000.0000.0000.000
16A172GLY0-0.035-0.02626.2280.0010.0010.0000.0000.0000.000
17A173SER0-0.119-0.13722.9810.0060.0060.0000.0000.0000.000
18A174GLU-1-0.755-0.82021.452-0.061-0.0610.0000.0000.0000.000
19A175MET0-0.057-0.01514.8450.0360.0360.0000.0000.0000.000
20A176ALA0-0.026-0.01820.513-0.014-0.0140.0000.0000.0000.000
21A177LEU0-0.052-0.03016.5310.0020.0020.0000.0000.0000.000
22A178SER00.0410.04019.7890.0040.0040.0000.0000.0000.000
23A179THR0-0.002-0.01019.526-0.015-0.0150.0000.0000.0000.000
24A180GLY0-0.110-0.06617.8880.0130.0130.0000.0000.0000.000
25A181ASP-1-0.825-0.90515.870-0.011-0.0110.0000.0000.0000.000
26A182VAL0-0.068-0.0459.916-0.040-0.0400.0000.0000.0000.000
27A183VAL00.008-0.00410.8630.0640.0640.0000.0000.0000.000
28A184GLU-1-0.860-0.9275.9690.5840.5840.0000.0000.0000.000
29A185VAL0-0.024-0.0297.2130.1400.1400.0000.0000.0000.000
30A186VAL0-0.045-0.0217.783-0.264-0.2640.0000.0000.0000.000
31A187GLU-1-0.944-0.97510.141-0.251-0.2510.0000.0000.0000.000
32A188LYS10.8440.9349.2910.9530.9530.0000.0000.0000.000
33A189SER00.0830.04213.5730.0230.0230.0000.0000.0000.000
34A190GLU-1-0.947-0.97517.327-0.221-0.2210.0000.0000.0000.000
35A191SER0-0.017-0.01719.9590.0200.0200.0000.0000.0000.000
36A192GLY0-0.029-0.01619.3670.0160.0160.0000.0000.0000.000
37A193TRP0-0.0210.01119.326-0.003-0.0030.0000.0000.0000.000
38A194TRP0-0.007-0.02111.680-0.077-0.0770.0000.0000.0000.000
39A195PHE00.0390.03713.8710.0370.0370.0000.0000.0000.000
40A196CYS0-0.014-0.02011.862-0.097-0.0970.0000.0000.0000.000
41A197GLN00.0130.0098.0680.0210.0210.0000.0000.0000.000
42A198MET00.0120.01211.068-0.048-0.0480.0000.0000.0000.000
43A199LYS10.8220.9145.592-0.072-0.0720.0000.0000.0000.000
44A200ALA00.0040.00110.744-0.023-0.0230.0000.0000.0000.000
45A201LYS10.9830.99412.667-0.149-0.1490.0000.0000.0000.000
46A202ARG10.9650.9729.486-0.825-0.8250.0000.0000.0000.000
47A203GLY00.0270.00316.541-0.024-0.0240.0000.0000.0000.000
48A204TRP0-0.0070.00719.389-0.002-0.0020.0000.0000.0000.000
49A205ILE00.0240.01322.456-0.016-0.0160.0000.0000.0000.000
50A206PRO00.0220.00625.3210.0060.0060.0000.0000.0000.000
51A207ALA00.0960.05228.469-0.003-0.0030.0000.0000.0000.000
52A208SER0-0.024-0.03929.314-0.003-0.0030.0000.0000.0000.000
53A209PHE0-0.048-0.03930.069-0.009-0.0090.0000.0000.0000.000
54A210LEU0-0.0200.01025.6240.0010.0010.0000.0000.0000.000
55A211GLU-1-0.802-0.89029.9120.0940.0940.0000.0000.0000.000
56A212PRO00.0720.05429.4270.0080.0080.0000.0000.0000.000
57A213LEU00.0450.00926.677-0.011-0.0110.0000.0000.0000.000
58A214ASP-1-0.866-0.92530.7450.1210.1210.0000.0000.0000.000
59A215SER0-0.065-0.04733.250-0.012-0.0120.0000.0000.0000.000
60A216PRO0-0.041-0.01634.3040.0060.0060.0000.0000.0000.000
61A217ASP-1-0.878-0.95435.8640.0930.0930.0000.0000.0000.000
62A218GLU-1-0.870-0.91730.7010.1640.1640.0000.0000.0000.000
63A219THR0-0.019-0.02130.860-0.006-0.0060.0000.0000.0000.000
64A220GLU-1-0.993-0.99827.7860.2000.2000.0000.0000.0000.000
65A221ASP-1-0.875-0.92732.1390.1280.1280.0000.0000.0000.000
66A222PRO0-0.031-0.00534.278-0.003-0.0030.0000.0000.0000.000
67A223GLU-1-0.894-0.96236.6330.0910.0910.0000.0000.0000.000
68A224PRO0-0.065-0.03840.3020.0010.0010.0000.0000.0000.000
69A225ASN00.0190.00642.788-0.005-0.0050.0000.0000.0000.000
70A226TYR0-0.004-0.01744.5850.0000.0000.0000.0000.0000.000
71A227ALA00.0650.03947.685-0.002-0.0020.0000.0000.0000.000
72A228GLY0-0.0220.00745.722-0.002-0.0020.0000.0000.0000.000
73A229GLU-1-0.880-0.92840.4240.0960.0960.0000.0000.0000.000
74A230PRO00.0260.02544.5420.0000.0000.0000.0000.0000.000
75A231TYR0-0.016-0.03737.1910.0060.0060.0000.0000.0000.000
76A232VAL00.0070.00742.367-0.004-0.0040.0000.0000.0000.000
77A233ALA00.0130.01841.7820.0050.0050.0000.0000.0000.000
78A234ILE0-0.008-0.01536.198-0.003-0.0030.0000.0000.0000.000
79A235LYS10.9260.96236.367-0.083-0.0830.0000.0000.0000.000
80A236ALA0-0.0010.01440.6270.0010.0010.0000.0000.0000.000
81A237TYR0-0.098-0.06640.7350.0040.0040.0000.0000.0000.000
82A238THR00.0100.00643.392-0.003-0.0030.0000.0000.0000.000
83A239ALA0-0.033-0.01744.8770.0020.0020.0000.0000.0000.000
84A240VAL0-0.017-0.01443.097-0.003-0.0030.0000.0000.0000.000
85A241GLU-1-0.830-0.82942.9400.0670.0670.0000.0000.0000.000
86A242GLY0-0.006-0.01346.9340.0000.0000.0000.0000.0000.000
87A243ASP-1-0.845-0.90244.9500.0680.0680.0000.0000.0000.000
88A244GLU-1-0.781-0.87842.8570.0740.0740.0000.0000.0000.000
89A245VAL00.0100.01245.373-0.003-0.0030.0000.0000.0000.000
90A246SER0-0.011-0.00745.7730.0020.0020.0000.0000.0000.000
91A247LEU0-0.029-0.01144.354-0.001-0.0010.0000.0000.0000.000
92A248LEU00.001-0.01546.1110.0010.0010.0000.0000.0000.000
93A249GLU-1-0.961-0.99042.9110.0650.0650.0000.0000.0000.000
94A250GLY0-0.014-0.00745.230-0.003-0.0030.0000.0000.0000.000
95A251GLU-1-0.879-0.92547.0960.0520.0520.0000.0000.0000.000
96A252ALA00.005-0.00246.5860.0030.0030.0000.0000.0000.000
97A253VAL0-0.015-0.00844.404-0.002-0.0020.0000.0000.0000.000
98A254GLU-1-0.801-0.87246.2530.0620.0620.0000.0000.0000.000
99A255VAL0-0.040-0.01840.0130.0000.0000.0000.0000.0000.000
100A256ILE0-0.007-0.02143.4930.0000.0000.0000.0000.0000.000
101A257HIS00.0320.02739.321-0.004-0.0040.0000.0000.0000.000
102A258LYS10.8490.91435.953-0.107-0.1070.0000.0000.0000.000
103A259LEU0-0.0130.00835.4220.0060.0060.0000.0000.0000.000
104A260LEU00.0620.02029.6970.0010.0010.0000.0000.0000.000
105A261ASP-1-0.928-0.95930.9450.1180.1180.0000.0000.0000.000
106A262GLY0-0.038-0.02633.043-0.002-0.0020.0000.0000.0000.000
107A263TRP0-0.065-0.04133.890-0.007-0.0070.0000.0000.0000.000
108A264TRP00.0360.02134.426-0.003-0.0030.0000.0000.0000.000
109A265VAL0-0.0160.00539.366-0.004-0.0040.0000.0000.0000.000
110A266ILE0-0.010-0.01242.9120.0020.0020.0000.0000.0000.000
111A267ARG10.7890.85845.200-0.062-0.0620.0000.0000.0000.000
112A268LYS10.9220.96248.926-0.051-0.0510.0000.0000.0000.000
113A269ASP-1-0.894-0.93251.0240.0470.0470.0000.0000.0000.000
114A270ASP-1-0.910-0.95854.2640.0470.0470.0000.0000.0000.000
115A271VAL0-0.088-0.05351.8800.0000.0000.0000.0000.0000.000
116A272THR0-0.017-0.02547.8140.0010.0010.0000.0000.0000.000
117A273GLY00.0120.00246.804-0.002-0.0020.0000.0000.0000.000
118A274TYR0-0.062-0.03440.8960.0040.0040.0000.0000.0000.000
119A275PHE00.0190.00740.662-0.003-0.0030.0000.0000.0000.000
120A276PRO0-0.0140.00236.5920.0050.0050.0000.0000.0000.000
121A277SER00.0180.00434.2150.0000.0000.0000.0000.0000.000
122A278MET0-0.032-0.01931.2160.0020.0020.0000.0000.0000.000
123A279TYR0-0.038-0.02334.3230.0000.0000.0000.0000.0000.000
124A280LEU00.0300.03837.258-0.006-0.0060.0000.0000.0000.000
125A281GLN0-0.011-0.01636.2220.0030.0030.0000.0000.0000.000
126A282LYS10.9340.97636.517-0.109-0.1090.0000.0000.0000.000
127A283SER00.010-0.00640.492-0.001-0.0010.0000.0000.0000.000
128A284GLY00.0140.00743.2290.0010.0010.0000.0000.0000.000
129A285GLN0-0.032-0.00438.4570.0020.0020.0000.0000.0000.000
130A286ASP-1-0.849-0.92937.3350.0760.0760.0000.0000.0000.000
131A287VAL00.1210.05237.4110.0060.0060.0000.0000.0000.000
132A288SER00.0400.03536.6610.0050.0050.0000.0000.0000.000
133A289GLN0-0.079-0.04632.1630.0110.0110.0000.0000.0000.000
134A290ALA00.0120.01332.7250.0080.0080.0000.0000.0000.000
135A291GLN00.014-0.00733.4250.0060.0060.0000.0000.0000.000
136A292ARG10.8720.94129.914-0.091-0.0910.0000.0000.0000.000
137A293GLN0-0.074-0.03228.7410.0100.0100.0000.0000.0000.000
138A294ILE0-0.0310.01128.9460.0100.0100.0000.0000.0000.000
139A295LYS10.9500.95923.569-0.168-0.1680.0000.0000.0000.000
140A296ARG10.9040.95822.952-0.190-0.1900.0000.0000.0000.000
141A297GLY00.0210.01429.460-0.002-0.0020.0000.0000.0000.000
142A298ALA00.0130.00431.6860.0080.0080.0000.0000.0000.000
143A299PRO00.0030.01131.051-0.002-0.0020.0000.0000.0000.000
144A300PRO00.0660.05131.791-0.006-0.0060.0000.0000.0000.000
145A301ARG10.8900.95234.425-0.070-0.0700.0000.0000.0000.000
146A302ARG10.9060.93933.692-0.108-0.1080.0000.0000.0000.000
147A303SER0-0.125-0.13637.311-0.001-0.0010.0000.0000.0000.000
148A304SER0-0.0120.00137.504-0.003-0.0030.0000.0000.0000.000
149A305ILE0-0.032-0.00935.121-0.002-0.0020.0000.0000.0000.000
150A306ARG10.9380.96839.071-0.051-0.0510.0000.0000.0000.000
151A307ASN0-0.014-0.02740.576-0.003-0.0030.0000.0000.0000.000
152A308ALA00.0070.02537.2600.0010.0010.0000.0000.0000.000
153A309HIS0-0.004-0.01135.847-0.004-0.0040.0000.0000.0000.000
154A310SER0-0.037-0.02235.2000.0040.0040.0000.0000.0000.000
155A311ILE0-0.009-0.00932.338-0.006-0.0060.0000.0000.0000.000
156A312HIS10.7210.85333.531-0.106-0.1060.0000.0000.0000.000
157A313GLN00.0420.01538.388-0.001-0.0010.0000.0000.0000.000
158A314ARG10.9120.96638.556-0.084-0.0840.0000.0000.0000.000
159A315SER00.0540.02040.7860.0020.0020.0000.0000.0000.000
160A316ARG10.9450.98536.034-0.099-0.0990.0000.0000.0000.000
161A317LYS10.9060.94640.119-0.083-0.0830.0000.0000.0000.000
162A318ARG10.8800.92737.416-0.091-0.0910.0000.0000.0000.000
163A319LEU00.0010.01642.869-0.004-0.0040.0000.0000.0000.000
164A320SER00.0470.02545.6700.0020.0020.0000.0000.0000.000
165A321GLN00.1260.04245.244-0.001-0.0010.0000.0000.0000.000
166A322ASP-1-0.846-0.90749.0390.0480.0480.0000.0000.0000.000
167A323ALA0-0.012-0.00749.551-0.001-0.0010.0000.0000.0000.000
168A324TYR0-0.005-0.03142.303-0.001-0.0010.0000.0000.0000.000
169A325ARG10.9350.97949.066-0.049-0.0490.0000.0000.0000.000
170A326ARG10.8600.92152.190-0.049-0.0490.0000.0000.0000.000
171A327ASN00.0200.00648.746-0.004-0.0040.0000.0000.0000.000
172A328SER00.0120.01250.0280.0000.0000.0000.0000.0000.000
173A329VAL0-0.014-0.01351.655-0.001-0.0010.0000.0000.0000.000
174A330ARG10.8560.93354.606-0.048-0.0480.0000.0000.0000.000
175A331PHE0-0.065-0.03051.550-0.001-0.0010.0000.0000.0000.000
176A332LEU00.0340.03851.3860.0030.0030.0000.0000.0000.000