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: 1NVLZ

Calculation Name: 5GMI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GMI

Chain ID: A

ChEMBL ID:

UniProt ID: Q99JX3

Base Structure: X-ray

Registration Date: 2023-09-23

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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2464417.734308
FMO2-HF: Nuclear repulsion 2379468.980775
FMO2-HF: Total energy -84948.753533
FMO2-MP2: Total energy -85198.214578


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:-14:SER)


Summations of interaction energy for fragment #1(A:-14:SER)
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.
-10.565-5.8371.529-2.854-3.4040.024
Interaction energy analysis for fragmet #1(A:-14:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.002
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].
3A-12SER0-0.0290.0042.390-7.639-3.0761.526-2.758-3.3310.024
4A-11LEU00.0170.0104.104-3.099-2.9340.003-0.096-0.0730.000
5A-10TYR00.0060.0106.011-0.210-0.2100.0000.0000.0000.000
6A-9LYS10.9640.9695.5720.6220.6220.0000.0000.0000.000
7A-8LYS10.9630.9737.650-1.196-1.1960.0000.0000.0000.000
8A-7ALA00.0040.00310.606-0.131-0.1310.0000.0000.0000.000
9A-6GLY00.0050.01714.1990.0600.0600.0000.0000.0000.000
10A-5PHE00.010-0.00815.988-0.039-0.0390.0000.0000.0000.000
11A-4LEU0-0.0090.00020.3390.0120.0120.0000.0000.0000.000
12A-3VAL00.0260.01722.0550.0040.0040.0000.0000.0000.000
13A-2PRO00.0040.00124.914-0.009-0.0090.0000.0000.0000.000
14A-1ARG10.9530.96627.371-0.097-0.0970.0000.0000.0000.000
15A0GLY00.0470.04129.0300.0090.0090.0000.0000.0000.000
16A1SER0-0.0010.00825.1310.0100.0100.0000.0000.0000.000
17A2GLY00.1270.08224.911-0.010-0.0100.0000.0000.0000.000
18A3SER0-0.099-0.05424.7160.0240.0240.0000.0000.0000.000
19A4SER00.0040.00626.512-0.013-0.0130.0000.0000.0000.000
20A5GLN0-0.051-0.01129.1720.0010.0010.0000.0000.0000.000
21A6SER00.0780.01331.6530.0000.0000.0000.0000.0000.000
22A7VAL0-0.0180.00934.266-0.005-0.0050.0000.0000.0000.000
23A8GLU-1-0.883-0.97136.7950.1110.1110.0000.0000.0000.000
24A9ILE0-0.054-0.00439.640-0.007-0.0070.0000.0000.0000.000
25A10PRO00.0260.02242.2070.0000.0000.0000.0000.0000.000
26A11GLY00.012-0.00745.825-0.001-0.0010.0000.0000.0000.000
27A12GLY0-0.058-0.04242.8250.0000.0000.0000.0000.0000.000
28A13GLY0-0.041-0.00941.5140.0050.0050.0000.0000.0000.000
29A14THR00.0360.00637.2670.0040.0040.0000.0000.0000.000
30A15GLU-1-0.921-0.95039.2070.1220.1220.0000.0000.0000.000
31A16GLY00.0010.00741.757-0.005-0.0050.0000.0000.0000.000
32A17TYR0-0.154-0.19944.1930.0010.0010.0000.0000.0000.000
33A18HIS0-0.029-0.02739.058-0.003-0.0030.0000.0000.0000.000
34A19VAL0-0.010-0.00743.346-0.004-0.0040.0000.0000.0000.000
35A20LEU00.0470.02642.6630.0020.0020.0000.0000.0000.000
36A21ARG10.8920.92145.104-0.062-0.0620.0000.0000.0000.000
37A22VAL00.0290.02247.632-0.001-0.0010.0000.0000.0000.000
38A23GLN0-0.007-0.01449.879-0.001-0.0010.0000.0000.0000.000
39A24GLU-1-0.842-0.91251.9070.0460.0460.0000.0000.0000.000
40A25ASN0-0.073-0.04054.436-0.001-0.0010.0000.0000.0000.000
41A26SER00.001-0.00753.601-0.001-0.0010.0000.0000.0000.000
42A27PRO0-0.061-0.04255.9190.0000.0000.0000.0000.0000.000
43A28GLY00.0450.01752.3810.0000.0000.0000.0000.0000.000
44A29HIS00.0350.01551.2180.0030.0030.0000.0000.0000.000
45A30ARG10.8950.95151.959-0.042-0.0420.0000.0000.0000.000
46A31ALA0-0.044-0.00952.067-0.001-0.0010.0000.0000.0000.000
47A32GLY0-0.020-0.00749.1670.0010.0010.0000.0000.0000.000
48A33LEU0-0.075-0.03547.0570.0030.0030.0000.0000.0000.000
49A34GLU-1-0.826-0.94341.5370.0740.0740.0000.0000.0000.000
50A35PRO0-0.007-0.00543.2680.0050.0050.0000.0000.0000.000
51A36PHE00.0140.01434.6070.0010.0010.0000.0000.0000.000
52A37PHE00.0190.00134.9020.0070.0070.0000.0000.0000.000
53A38ASP-1-0.747-0.81539.3980.0830.0830.0000.0000.0000.000
54A39PHE00.0430.00638.1950.0010.0010.0000.0000.0000.000
55A40ILE0-0.0100.00043.099-0.003-0.0030.0000.0000.0000.000
56A41VAL00.0280.01543.1870.0020.0020.0000.0000.0000.000
57A42SER00.002-0.02746.220-0.001-0.0010.0000.0000.0000.000
58A43ILE00.0270.03749.715-0.001-0.0010.0000.0000.0000.000
59A44ASN0-0.020-0.03153.223-0.001-0.0010.0000.0000.0000.000
60A45GLY0-0.012-0.00152.914-0.002-0.0020.0000.0000.0000.000
61A46SER0-0.048-0.01052.7520.0030.0030.0000.0000.0000.000
62A47ARG10.8370.90943.068-0.096-0.0960.0000.0000.0000.000
63A48LEU0-0.049-0.02948.212-0.001-0.0010.0000.0000.0000.000
64A49ASN0-0.007-0.01845.2420.0060.0060.0000.0000.0000.000
65A50LYN0-0.0740.08847.329-0.001-0.0010.0000.0000.0000.000
66A51ASP-1-0.857-0.90047.5820.0870.0870.0000.0000.0000.000
67A52ASN00.1390.06249.554-0.003-0.0030.0000.0000.0000.000
68A53ASP-1-0.803-0.89053.3530.0630.0630.0000.0000.0000.000
69A54THR0-0.017-0.03154.242-0.003-0.0030.0000.0000.0000.000
70A55LEU0-0.005-0.00350.973-0.003-0.0030.0000.0000.0000.000
71A56LYS10.9870.98354.804-0.061-0.0610.0000.0000.0000.000
72A57ASP-1-0.883-0.94157.1820.0520.0520.0000.0000.0000.000
73A58LEU0-0.051-0.03156.010-0.003-0.0030.0000.0000.0000.000
74A59LEU0-0.0180.00654.909-0.002-0.0020.0000.0000.0000.000
75A60LYS10.9630.98359.157-0.047-0.0470.0000.0000.0000.000
76A61ALA0-0.034-0.01762.323-0.002-0.0020.0000.0000.0000.000
77A62ASN0-0.116-0.08361.165-0.002-0.0020.0000.0000.0000.000
78A63VAL0-0.0040.00662.7800.0000.0000.0000.0000.0000.000
79A64GLU-1-0.755-0.86663.9540.0390.0390.0000.0000.0000.000
80A65LYS10.9030.94963.306-0.043-0.0430.0000.0000.0000.000
81A66PRO00.0050.00659.7830.0010.0010.0000.0000.0000.000
82A67VAL0-0.036-0.02155.8050.0000.0000.0000.0000.0000.000
83A68LYS10.9350.97352.566-0.057-0.0570.0000.0000.0000.000
84A69MET0-0.0130.00050.0340.0010.0010.0000.0000.0000.000
85A70LEU0-0.020-0.01046.068-0.001-0.0010.0000.0000.0000.000
86A71ILE0-0.019-0.01543.9730.0020.0020.0000.0000.0000.000
87A72TYR00.0490.01735.065-0.001-0.0010.0000.0000.0000.000
88A73SER00.0510.03839.0520.0010.0010.0000.0000.0000.000
89A74SER00.039-0.01234.8710.0010.0010.0000.0000.0000.000
90A75LYS10.7970.92134.054-0.079-0.0790.0000.0000.0000.000
91A76THR0-0.020-0.02934.3200.0040.0040.0000.0000.0000.000
92A77LEU00.0030.01031.0650.0010.0010.0000.0000.0000.000
93A78GLH0-0.057-0.02735.8040.0000.0000.0000.0000.0000.000
94A79LEU00.003-0.00339.2570.0000.0000.0000.0000.0000.000
95A80ARG10.8030.87842.755-0.076-0.0760.0000.0000.0000.000
96A81GLU-1-0.907-0.96145.8140.0620.0620.0000.0000.0000.000
97A82ALA00.0080.01949.484-0.002-0.0020.0000.0000.0000.000
98A83SER0-0.048-0.02551.2840.0000.0000.0000.0000.0000.000
99A84VAL00.0550.01153.8510.0000.0000.0000.0000.0000.000
100A85THR0-0.024-0.00655.948-0.001-0.0010.0000.0000.0000.000
101A86PRO0-0.035-0.01058.2330.0000.0000.0000.0000.0000.000
102A87SER00.006-0.01059.660-0.002-0.0020.0000.0000.0000.000
103A88ASN0-0.034-0.03661.9290.0020.0020.0000.0000.0000.000
104A89LEU0-0.044-0.01864.585-0.001-0.0010.0000.0000.0000.000
105A90TRP0-0.1020.00156.732-0.001-0.0010.0000.0000.0000.000
106A91GLY00.024-0.00262.1740.0000.0000.0000.0000.0000.000
107A92GLY0-0.012-0.01159.1080.0000.0000.0000.0000.0000.000
108A93GLN0-0.0020.00056.8690.0010.0010.0000.0000.0000.000
109A94GLY00.0380.02257.4290.0020.0020.0000.0000.0000.000
110A95LEU00.0010.00458.496-0.001-0.0010.0000.0000.0000.000
111A96LEU00.0540.01653.381-0.001-0.0010.0000.0000.0000.000
112A97GLY00.0420.01754.991-0.001-0.0010.0000.0000.0000.000
113A98VAL0-0.028-0.01749.0770.0000.0000.0000.0000.0000.000
114A99SER0-0.0430.00148.9500.0010.0010.0000.0000.0000.000
115A100ILE0-0.003-0.01147.0610.0020.0020.0000.0000.0000.000
116A101ARG10.9690.97341.236-0.107-0.1070.0000.0000.0000.000
117A102PHE00.0050.02644.5640.0010.0010.0000.0000.0000.000
118A103CYS00.0130.02039.4720.0010.0010.0000.0000.0000.000
119A104SER00.0760.03836.439-0.004-0.0040.0000.0000.0000.000
120A105PHE0-0.026-0.01836.4780.0020.0020.0000.0000.0000.000
121A106ASP-1-0.983-0.99732.0430.1920.1920.0000.0000.0000.000
122A107GLY00.0550.03730.6330.0050.0050.0000.0000.0000.000
123A108ALA00.0510.02231.3020.0030.0030.0000.0000.0000.000
124A109ASN0-0.079-0.04331.219-0.010-0.0100.0000.0000.0000.000
125A110GLU-1-0.993-0.99226.1290.2570.2570.0000.0000.0000.000
126A111ASN0-0.0110.01129.4340.0070.0070.0000.0000.0000.000
127A112VAL0-0.037-0.01831.121-0.015-0.0150.0000.0000.0000.000
128A113TRP00.0110.00530.5320.0060.0060.0000.0000.0000.000
129A114HIS0-0.041-0.02631.586-0.003-0.0030.0000.0000.0000.000
130A115VAL00.0070.00533.3440.0040.0040.0000.0000.0000.000
131A116LEU0-0.043-0.00230.053-0.005-0.0050.0000.0000.0000.000
132A117GLU-1-0.833-0.92534.1740.0850.0850.0000.0000.0000.000
133A118VAL0-0.012-0.02436.8580.0050.0050.0000.0000.0000.000
134A119GLU-1-0.846-0.91639.8530.0590.0590.0000.0000.0000.000
135A120SER00.0150.01242.1670.0010.0010.0000.0000.0000.000
136A121ASN0-0.068-0.03845.9360.0000.0000.0000.0000.0000.000
137A122SER00.0290.00842.9570.0010.0010.0000.0000.0000.000
138A123PRO00.009-0.00243.547-0.002-0.0020.0000.0000.0000.000
139A124ALA00.0470.01641.342-0.001-0.0010.0000.0000.0000.000
140A125ALA0-0.0040.00843.447-0.002-0.0020.0000.0000.0000.000
141A126LEU0-0.059-0.03345.713-0.003-0.0030.0000.0000.0000.000
142A127ALA0-0.0050.01545.706-0.002-0.0020.0000.0000.0000.000
143A128GLY0-0.039-0.01647.1150.0000.0000.0000.0000.0000.000
144A129LEU0-0.032-0.00840.4540.0000.0000.0000.0000.0000.000
145A130ARG10.8200.89442.384-0.061-0.0610.0000.0000.0000.000
146A131PRO00.0350.02038.7550.0040.0040.0000.0000.0000.000
147A132HIS00.0090.01234.231-0.002-0.0020.0000.0000.0000.000
148A133SER0-0.009-0.00336.6760.0020.0020.0000.0000.0000.000
149A134ASP-1-0.740-0.83839.2020.0730.0730.0000.0000.0000.000
150A135TYR00.000-0.01332.6500.0020.0020.0000.0000.0000.000
151A136ILE0-0.015-0.00636.558-0.005-0.0050.0000.0000.0000.000
152A137ILE0-0.002-0.01336.0070.0080.0080.0000.0000.0000.000
153A138GLY00.0510.02337.6900.0040.0040.0000.0000.0000.000
154A139ALA00.0160.02739.591-0.005-0.0050.0000.0000.0000.000
155A140ASP-1-0.881-0.92242.4360.0850.0850.0000.0000.0000.000
156A141THR0-0.012-0.01140.7360.0000.0000.0000.0000.0000.000
157A142VAL00.0110.01443.958-0.001-0.0010.0000.0000.0000.000
158A143MET0-0.036-0.01344.635-0.002-0.0020.0000.0000.0000.000
159A144ASN0-0.039-0.03840.9960.0010.0010.0000.0000.0000.000
160A145GLU-1-0.895-0.96738.9500.1200.1200.0000.0000.0000.000
161A146SER0-0.017-0.00135.6860.0090.0090.0000.0000.0000.000
162A147GLU-1-0.924-0.95133.1730.1550.1550.0000.0000.0000.000
163A148ASP-1-0.945-0.96930.5810.2130.2130.0000.0000.0000.000
164A149LEU0-0.018-0.01233.222-0.008-0.0080.0000.0000.0000.000
165A150PHE00.037-0.03530.652-0.008-0.0080.0000.0000.0000.000
166A151SER0-0.051-0.00134.112-0.004-0.0040.0000.0000.0000.000
167A152LEU00.1000.06036.277-0.006-0.0060.0000.0000.0000.000
168A153ILE0-0.107-0.01536.320-0.009-0.0090.0000.0000.0000.000
169A154GLU-1-0.788-0.89038.4490.1210.1210.0000.0000.0000.000
170A155THR0-0.105-0.08240.541-0.008-0.0080.0000.0000.0000.000
171A156HIS0-0.081-0.04942.921-0.008-0.0080.0000.0000.0000.000
172A157GLU-1-0.842-0.92542.6070.0900.0900.0000.0000.0000.000
173A158ALA0-0.022-0.02645.431-0.004-0.0040.0000.0000.0000.000
174A159LYS10.7950.90948.014-0.082-0.0820.0000.0000.0000.000
175A160PRO00.0310.01747.8030.0020.0020.0000.0000.0000.000
176A161LEU00.0310.01441.6710.0010.0010.0000.0000.0000.000
177A162LYS10.9090.97646.096-0.072-0.0720.0000.0000.0000.000
178A163LEU00.0180.00740.6880.0050.0050.0000.0000.0000.000
179A164TYR0-0.046-0.04341.677-0.004-0.0040.0000.0000.0000.000
180A165VAL0-0.012-0.01240.7090.0060.0060.0000.0000.0000.000
181A166TYR00.0290.00138.915-0.004-0.0040.0000.0000.0000.000
182A167ASN0-0.011-0.01340.0370.0000.0000.0000.0000.0000.000
183A168THR0-0.033-0.04536.869-0.002-0.0020.0000.0000.0000.000
184A169ASP-1-0.950-0.94840.2940.0460.0460.0000.0000.0000.000
185A170THR0-0.060-0.03243.539-0.001-0.0010.0000.0000.0000.000
186A171ASP-1-0.911-0.94542.1400.0620.0620.0000.0000.0000.000
187A172ASN00.020-0.00243.4620.0040.0040.0000.0000.0000.000
188A173CYS0-0.0310.01143.0310.0040.0040.0000.0000.0000.000
189A174ARG10.7840.89043.824-0.074-0.0740.0000.0000.0000.000
190A175GLU-1-0.906-0.94545.5550.0740.0740.0000.0000.0000.000
191A176VAL0-0.055-0.01944.819-0.004-0.0040.0000.0000.0000.000
192A177ILE0-0.012-0.01646.4300.0030.0030.0000.0000.0000.000
193A178ILE00.0440.01042.206-0.003-0.0030.0000.0000.0000.000
194A179THR0-0.021-0.01846.3820.0010.0010.0000.0000.0000.000
195A180PRO0-0.0340.00042.387-0.003-0.0030.0000.0000.0000.000
196A181ASN00.0710.02943.804-0.001-0.0010.0000.0000.0000.000
197A182SER00.0030.00640.405-0.002-0.0020.0000.0000.0000.000
198A183ALA0-0.045-0.01642.574-0.001-0.0010.0000.0000.0000.000
199A184TRP0-0.097-0.04341.209-0.007-0.0070.0000.0000.0000.000
200A185GLY0-0.026-0.00244.844-0.003-0.0030.0000.0000.0000.000
201A186GLY00.033-0.00441.806-0.004-0.0040.0000.0000.0000.000
202A187GLH0-0.053-0.01934.8110.0030.0030.0000.0000.0000.000
203A188GLY0-0.014-0.00537.1060.0010.0010.0000.0000.0000.000
204A189SER00.0920.03337.658-0.004-0.0040.0000.0000.0000.000
205A190LEU00.013-0.00237.996-0.004-0.0040.0000.0000.0000.000
206A191GLY00.0290.02139.551-0.005-0.0050.0000.0000.0000.000
207A192CYS0-0.038-0.02536.584-0.005-0.0050.0000.0000.0000.000
208A193GLY00.0350.04333.6310.0060.0060.0000.0000.0000.000
209A194ILE0-0.036-0.03430.858-0.003-0.0030.0000.0000.0000.000
210A195GLY00.0000.00928.6220.0080.0080.0000.0000.0000.000
211A196TYR00.0350.00824.6570.0030.0030.0000.0000.0000.000
212A197GLY00.0680.03424.4920.0190.0190.0000.0000.0000.000
213A198TYR0-0.012-0.03421.171-0.032-0.0320.0000.0000.0000.000
214A199LEU0-0.063-0.02222.064-0.016-0.0160.0000.0000.0000.000
215A200HIS0-0.058-0.02125.899-0.009-0.0090.0000.0000.0000.000
216A201ARG10.8650.91927.004-0.176-0.1760.0000.0000.0000.000
217A202ILE00.0220.02330.441-0.009-0.0090.0000.0000.0000.000
218A203PRO0-0.0010.01032.9620.0050.0050.0000.0000.0000.000
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