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

tag_button

FMODB ID: 89KVY

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2464934.030492
FMO2-HF: Nuclear repulsion 2379983.212183
FMO2-HF: Total energy -84950.818309
FMO2-MP2: Total energy -85200.137779


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.
-10.36-7.0294.084-3.314-4.1010.027
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 : 0.027 / q_NPA : 0.014
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-12SER0-0.041-0.0212.136-7.762-4.6214.071-3.294-3.9180.026
4A-11LEU00.0080.0053.806-2.920-2.7300.013-0.020-0.1830.001
5A-10TYR00.0150.0205.962-0.297-0.2970.0000.0000.0000.000
6A-9LYS10.9640.9815.4150.4750.4750.0000.0000.0000.000
7A-8LYS10.9800.9857.466-0.386-0.3860.0000.0000.0000.000
8A-7ALA0-0.007-0.00510.337-0.101-0.1010.0000.0000.0000.000
9A-6GLY00.0070.01413.8690.0460.0460.0000.0000.0000.000
10A-5PHE00.006-0.00915.618-0.024-0.0240.0000.0000.0000.000
11A-4LEU00.0040.00620.4120.0100.0100.0000.0000.0000.000
12A-3VAL00.0380.01822.1180.0030.0030.0000.0000.0000.000
13A-2PRO00.0040.01225.001-0.005-0.0050.0000.0000.0000.000
14A-1ARG10.8400.88727.713-0.049-0.0490.0000.0000.0000.000
15A0GLY00.0630.04729.1910.0060.0060.0000.0000.0000.000
16A1SER0-0.010-0.00925.2540.0010.0010.0000.0000.0000.000
17A2GLY00.0670.04424.676-0.004-0.0040.0000.0000.0000.000
18A3SER0-0.098-0.05724.6410.0130.0130.0000.0000.0000.000
19A4SER0-0.0130.01226.273-0.005-0.0050.0000.0000.0000.000
20A5GLN0-0.063-0.02528.8750.0020.0020.0000.0000.0000.000
21A6SER00.020-0.01431.493-0.002-0.0020.0000.0000.0000.000
22A7VAL0-0.030-0.00734.314-0.004-0.0040.0000.0000.0000.000
23A8GLU-1-0.898-0.97536.5610.0650.0650.0000.0000.0000.000
24A9ILE0-0.0520.00539.082-0.004-0.0040.0000.0000.0000.000
25A10PRO00.0130.00142.1020.0000.0000.0000.0000.0000.000
26A11GLY00.016-0.00845.8380.0000.0000.0000.0000.0000.000
27A12GLY0-0.0140.00242.6600.0000.0000.0000.0000.0000.000
28A13GLY0-0.0010.01241.4070.0040.0040.0000.0000.0000.000
29A14THR00.025-0.00636.266-0.003-0.0030.0000.0000.0000.000
30A15GLU-1-0.873-0.93438.9290.0730.0730.0000.0000.0000.000
31A16GLY00.0190.00341.600-0.003-0.0030.0000.0000.0000.000
32A17TYR0-0.032-0.02243.8020.0010.0010.0000.0000.0000.000
33A18HIS0-0.0040.01538.915-0.002-0.0020.0000.0000.0000.000
34A19VAL0-0.011-0.02043.211-0.003-0.0030.0000.0000.0000.000
35A20LEU00.0610.03242.4730.0010.0010.0000.0000.0000.000
36A21ARG10.8990.94644.903-0.033-0.0330.0000.0000.0000.000
37A22VAL00.0250.02147.435-0.001-0.0010.0000.0000.0000.000
38A23GLN00.0220.00849.674-0.001-0.0010.0000.0000.0000.000
39A24GLU-1-0.840-0.91552.8700.0220.0220.0000.0000.0000.000
40A25ASN0-0.058-0.03253.942-0.001-0.0010.0000.0000.0000.000
41A26SER00.0050.01453.4930.0000.0000.0000.0000.0000.000
42A27PRO0-0.067-0.03755.8300.0000.0000.0000.0000.0000.000
43A28GLY00.0480.02152.0880.0000.0000.0000.0000.0000.000
44A29HIS00.0180.01051.1860.0010.0010.0000.0000.0000.000
45A30ARG10.8520.90952.208-0.023-0.0230.0000.0000.0000.000
46A31ALA0-0.033-0.00651.983-0.001-0.0010.0000.0000.0000.000
47A32GLY0-0.0120.00749.2780.0010.0010.0000.0000.0000.000
48A33LEU0-0.039-0.02046.7070.0020.0020.0000.0000.0000.000
49A34GLU-1-0.757-0.86740.9990.0390.0390.0000.0000.0000.000
50A35PRO0-0.007-0.00642.8730.0030.0030.0000.0000.0000.000
51A36PHE00.0400.02134.4610.0000.0000.0000.0000.0000.000
52A37PHE00.0200.01034.5700.0030.0030.0000.0000.0000.000
53A38ASP-1-0.738-0.81339.0780.0460.0460.0000.0000.0000.000
54A39PHE00.0330.00838.3420.0000.0000.0000.0000.0000.000
55A40ILE0-0.025-0.01243.079-0.001-0.0010.0000.0000.0000.000
56A41VAL00.0110.01843.4250.0020.0020.0000.0000.0000.000
57A42SER00.0450.00046.1490.0010.0010.0000.0000.0000.000
58A43ILE00.0110.01649.807-0.001-0.0010.0000.0000.0000.000
59A44ASN0-0.037-0.04153.3780.0000.0000.0000.0000.0000.000
60A45GLY00.0150.01752.975-0.001-0.0010.0000.0000.0000.000
61A46SER0-0.019-0.00252.3680.0020.0020.0000.0000.0000.000
62A47ARG10.7650.87243.199-0.057-0.0570.0000.0000.0000.000
63A48LEU0-0.042-0.02647.881-0.001-0.0010.0000.0000.0000.000
64A49ASN0-0.041-0.03345.6500.0030.0030.0000.0000.0000.000
65A50LYN0-0.091-0.03347.3060.0000.0000.0000.0000.0000.000
66A51ASP-1-0.857-0.91147.3810.0520.0520.0000.0000.0000.000
67A52ASN00.0640.03649.351-0.003-0.0030.0000.0000.0000.000
68A53ASP-1-0.717-0.85353.2350.0350.0350.0000.0000.0000.000
69A54THR0-0.054-0.03354.657-0.002-0.0020.0000.0000.0000.000
70A55LEU00.0290.01651.114-0.001-0.0010.0000.0000.0000.000
71A56LYS10.8540.91454.997-0.036-0.0360.0000.0000.0000.000
72A57ASP-1-0.835-0.92057.4310.0290.0290.0000.0000.0000.000
73A58LEU0-0.007-0.00556.249-0.001-0.0010.0000.0000.0000.000
74A59LEU0-0.0030.00854.861-0.001-0.0010.0000.0000.0000.000
75A60LYS10.8750.92659.247-0.030-0.0300.0000.0000.0000.000
76A61ALA0-0.045-0.02262.424-0.001-0.0010.0000.0000.0000.000
77A62ASN0-0.087-0.06360.970-0.002-0.0020.0000.0000.0000.000
78A63VAL00.0100.01162.8670.0000.0000.0000.0000.0000.000
79A64GLU-1-0.713-0.80563.8440.0220.0220.0000.0000.0000.000
80A65LYS10.8740.93363.398-0.025-0.0250.0000.0000.0000.000
81A66PRO00.0000.00259.9850.0010.0010.0000.0000.0000.000
82A67VAL0-0.044-0.02656.0820.0000.0000.0000.0000.0000.000
83A68LYS10.8560.92352.391-0.034-0.0340.0000.0000.0000.000
84A69MET0-0.025-0.01950.5450.0010.0010.0000.0000.0000.000
85A70LEU0-0.0190.00546.033-0.001-0.0010.0000.0000.0000.000
86A71ILE00.004-0.00643.9830.0010.0010.0000.0000.0000.000
87A72TYR00.0570.03135.034-0.001-0.0010.0000.0000.0000.000
88A73SER00.016-0.00639.479-0.001-0.0010.0000.0000.0000.000
89A74SER00.0350.00434.5960.0000.0000.0000.0000.0000.000
90A75LYS10.7980.90534.096-0.042-0.0420.0000.0000.0000.000
91A76THR0-0.022-0.02334.5590.0010.0010.0000.0000.0000.000
92A77LEU00.0030.01930.7040.0010.0010.0000.0000.0000.000
93A78GLH0-0.050-0.04935.4180.0010.0010.0000.0000.0000.000
94A79LEU0-0.013-0.00738.9080.0000.0000.0000.0000.0000.000
95A80ARG10.7940.86842.479-0.042-0.0420.0000.0000.0000.000
96A81GLU-1-0.827-0.90045.4580.0360.0360.0000.0000.0000.000
97A82ALA00.0150.01149.147-0.001-0.0010.0000.0000.0000.000
98A83SER0-0.009-0.01051.1390.0000.0000.0000.0000.0000.000
99A84VAL00.0070.00654.004-0.001-0.0010.0000.0000.0000.000
100A85THR0-0.010-0.00655.9990.0000.0000.0000.0000.0000.000
101A86PRO0-0.035-0.01357.8770.0000.0000.0000.0000.0000.000
102A87SER0-0.029-0.04559.612-0.001-0.0010.0000.0000.0000.000
103A88ASN0-0.069-0.06461.6900.0010.0010.0000.0000.0000.000
104A89LEU0-0.061-0.01564.380-0.001-0.0010.0000.0000.0000.000
105A90TRP0-0.0300.00656.699-0.001-0.0010.0000.0000.0000.000
106A91GLY00.0210.01662.5470.0000.0000.0000.0000.0000.000
107A92GLY0-0.015-0.01959.0880.0000.0000.0000.0000.0000.000
108A93GLN0-0.031-0.01056.6330.0010.0010.0000.0000.0000.000
109A94GLY00.0390.01257.3720.0010.0010.0000.0000.0000.000
110A95LEU0-0.003-0.00959.1440.0000.0000.0000.0000.0000.000
111A96LEU00.0480.01253.2340.0000.0000.0000.0000.0000.000
112A97GLY00.0310.01754.8990.0000.0000.0000.0000.0000.000
113A98VAL0-0.044-0.03149.0820.0000.0000.0000.0000.0000.000
114A99SER0-0.0270.01948.9070.0010.0010.0000.0000.0000.000
115A100ILE0-0.017-0.02246.9460.0010.0010.0000.0000.0000.000
116A101ARG10.9390.96141.080-0.063-0.0630.0000.0000.0000.000
117A102PHE0-0.0010.01044.1920.0010.0010.0000.0000.0000.000
118A103CYS00.0220.00639.1760.0010.0010.0000.0000.0000.000
119A104SER00.0490.03036.515-0.002-0.0020.0000.0000.0000.000
120A105PHE00.005-0.00637.0820.0000.0000.0000.0000.0000.000
121A106ASP-1-0.892-0.93931.8090.1070.1070.0000.0000.0000.000
122A107GLY00.0340.02330.2090.0000.0000.0000.0000.0000.000
123A108ALA00.0260.00731.0670.0020.0020.0000.0000.0000.000
124A109ASN0-0.067-0.03930.844-0.006-0.0060.0000.0000.0000.000
125A110GLU-1-0.863-0.92226.0270.1370.1370.0000.0000.0000.000
126A111ASN0-0.043-0.00829.3160.0110.0110.0000.0000.0000.000
127A112VAL0-0.046-0.01930.900-0.009-0.0090.0000.0000.0000.000
128A113TRP00.0310.00730.1330.0040.0040.0000.0000.0000.000
129A114HIS0-0.028-0.00131.392-0.001-0.0010.0000.0000.0000.000
130A115VAL00.010-0.00433.2170.0030.0030.0000.0000.0000.000
131A116LEU0-0.0300.00129.897-0.003-0.0030.0000.0000.0000.000
132A117GLU-1-0.821-0.89633.6730.0440.0440.0000.0000.0000.000
133A118VAL0-0.015-0.02336.6610.0040.0040.0000.0000.0000.000
134A119GLU-1-0.841-0.91039.7050.0290.0290.0000.0000.0000.000
135A120SER00.000-0.01042.0930.0000.0000.0000.0000.0000.000
136A121ASN0-0.060-0.04245.8830.0000.0000.0000.0000.0000.000
137A122SER00.0430.04242.9540.0010.0010.0000.0000.0000.000
138A123PRO00.0090.00243.636-0.001-0.0010.0000.0000.0000.000
139A124ALA00.0510.02441.2710.0000.0000.0000.0000.0000.000
140A125ALA0-0.015-0.00643.356-0.001-0.0010.0000.0000.0000.000
141A126LEU0-0.055-0.02645.641-0.002-0.0020.0000.0000.0000.000
142A127ALA00.0030.01345.426-0.001-0.0010.0000.0000.0000.000
143A128GLY0-0.025-0.00746.7410.0000.0000.0000.0000.0000.000
144A129LEU0-0.0120.00640.1600.0000.0000.0000.0000.0000.000
145A130ARG10.7990.87642.032-0.031-0.0310.0000.0000.0000.000
146A131PRO00.0240.01838.4600.0020.0020.0000.0000.0000.000
147A132HIS00.0160.01533.131-0.001-0.0010.0000.0000.0000.000
148A133SER00.0090.01036.3180.0010.0010.0000.0000.0000.000
149A134ASP-1-0.717-0.81038.8040.0380.0380.0000.0000.0000.000
150A135TYR0-0.006-0.01332.2340.0010.0010.0000.0000.0000.000
151A136ILE0-0.019-0.00236.395-0.003-0.0030.0000.0000.0000.000
152A137ILE0-0.016-0.01935.7650.0050.0050.0000.0000.0000.000
153A138GLY00.0490.02437.5570.0020.0020.0000.0000.0000.000
154A139ALA00.0120.01339.480-0.003-0.0030.0000.0000.0000.000
155A140ASP-1-0.874-0.90542.1720.0490.0490.0000.0000.0000.000
156A141THR0-0.020-0.01140.4600.0000.0000.0000.0000.0000.000
157A142VAL00.0040.00143.8000.0000.0000.0000.0000.0000.000
158A143MET0-0.067-0.02645.414-0.001-0.0010.0000.0000.0000.000
159A144ASN0-0.011-0.02541.367-0.001-0.0010.0000.0000.0000.000
160A145GLU-1-0.834-0.89339.3570.0750.0750.0000.0000.0000.000
161A146SER0-0.051-0.04935.4140.0070.0070.0000.0000.0000.000
162A147GLU-1-0.895-0.93633.6730.0850.0850.0000.0000.0000.000
163A148ASP-1-0.965-0.98630.2650.1230.1230.0000.0000.0000.000
164A149LEU00.0010.00433.315-0.004-0.0040.0000.0000.0000.000
165A150PHE00.012-0.02630.201-0.004-0.0040.0000.0000.0000.000
166A151SER0-0.0050.01334.244-0.003-0.0030.0000.0000.0000.000
167A152LEU00.0060.01336.291-0.004-0.0040.0000.0000.0000.000
168A153ILE0-0.047-0.02236.153-0.005-0.0050.0000.0000.0000.000
169A154GLU-1-0.822-0.92137.2100.0730.0730.0000.0000.0000.000
170A155THR0-0.039-0.02140.696-0.005-0.0050.0000.0000.0000.000
171A156HIS0-0.024-0.01843.017-0.006-0.0060.0000.0000.0000.000
172A157GLU-1-0.792-0.85242.5380.0480.0480.0000.0000.0000.000
173A158ALA0-0.035-0.03145.092-0.002-0.0020.0000.0000.0000.000
174A159LYS10.8040.90947.918-0.048-0.0480.0000.0000.0000.000
175A160PRO00.0160.01247.6980.0020.0020.0000.0000.0000.000
176A161LEU00.0340.01541.6870.0000.0000.0000.0000.0000.000
177A162LYS10.9170.96545.861-0.041-0.0410.0000.0000.0000.000
178A163LEU00.0140.00940.3730.0030.0030.0000.0000.0000.000
179A164TYR0-0.021-0.03441.545-0.003-0.0030.0000.0000.0000.000
180A165VAL0-0.012-0.02040.2480.0030.0030.0000.0000.0000.000
181A166TYR0-0.019-0.04838.699-0.002-0.0020.0000.0000.0000.000
182A167ASN0-0.029-0.03340.135-0.001-0.0010.0000.0000.0000.000
183A168THR0-0.002-0.03036.961-0.002-0.0020.0000.0000.0000.000
184A169ASP-1-0.980-0.95540.4160.0200.0200.0000.0000.0000.000
185A170THR0-0.073-0.05443.589-0.001-0.0010.0000.0000.0000.000
186A171ASP-1-0.860-0.89840.7980.0360.0360.0000.0000.0000.000
187A172ASN0-0.007-0.01443.2360.0030.0030.0000.0000.0000.000
188A173CYS0-0.0340.01042.8070.0020.0020.0000.0000.0000.000
189A174ARG10.7250.83343.218-0.039-0.0390.0000.0000.0000.000
190A175GLU-1-0.885-0.93545.1490.0410.0410.0000.0000.0000.000
191A176VAL0-0.043-0.02144.428-0.002-0.0020.0000.0000.0000.000
192A177ILE0-0.024-0.01946.5050.0020.0020.0000.0000.0000.000
193A178ILE00.0290.01642.311-0.002-0.0020.0000.0000.0000.000
194A179THR0-0.013-0.01746.4780.0010.0010.0000.0000.0000.000
195A180PRO0-0.0120.00842.139-0.002-0.0020.0000.0000.0000.000
196A181ASN00.0530.01943.568-0.001-0.0010.0000.0000.0000.000
197A182SER0-0.037-0.03440.6450.0000.0000.0000.0000.0000.000
198A183ALA0-0.062-0.02442.3770.0000.0000.0000.0000.0000.000
199A184TRP0-0.083-0.02141.359-0.004-0.0040.0000.0000.0000.000
200A185GLY0-0.007-0.00644.560-0.002-0.0020.0000.0000.0000.000
201A186GLY00.0090.00541.474-0.002-0.0020.0000.0000.0000.000
202A187GLH0-0.077-0.07734.2690.0020.0020.0000.0000.0000.000
203A188GLY00.0230.01737.2700.0030.0030.0000.0000.0000.000
204A189SER0-0.010-0.03438.145-0.003-0.0030.0000.0000.0000.000
205A190LEU00.0370.01337.660-0.002-0.0020.0000.0000.0000.000
206A191GLY00.0110.00639.711-0.003-0.0030.0000.0000.0000.000
207A192CYS0-0.025-0.02837.025-0.004-0.0040.0000.0000.0000.000
208A193GLY00.0380.04933.6340.0040.0040.0000.0000.0000.000
209A194ILE0-0.048-0.03531.180-0.002-0.0020.0000.0000.0000.000
210A195GLY00.0160.01728.5570.0050.0050.0000.0000.0000.000
211A196TYR00.006-0.01125.1630.0030.0030.0000.0000.0000.000
212A197GLY00.0560.03124.4130.0080.0080.0000.0000.0000.000
213A198TYR0-0.080-0.09421.891-0.011-0.0110.0000.0000.0000.000
214A199LEU0-0.063-0.02321.987-0.010-0.0100.0000.0000.0000.000
215A200HIS0-0.063-0.02225.796-0.005-0.0050.0000.0000.0000.000
216A201ARG10.8810.94027.260-0.094-0.0940.0000.0000.0000.000
217A202ILE00.0230.02730.441-0.005-0.0050.0000.0000.0000.000
218A203PRO00.0000.00932.8930.0030.0030.0000.0000.0000.000
219A204THR0-0.022-0.03332.7090.0030.0030.0000.0000.0000.000
220A205ARG10.8220.90734.211-0.039-0.0390.0000.0000.0000.000
221A206PRO0-0.0010.00133.5120.0030.0030.0000.0000.0000.000
222A207PHE0-0.012-0.01434.3200.0000.0000.0000.0000.0000.000
223A208GLU-1-0.783-0.83237.0250.0450.0450.0000.0000.0000.000