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: G5721

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 OptHSide
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 -2465503.198799
FMO2-HF: Nuclear repulsion 2380553.043203
FMO2-HF: Total energy -84950.155596
FMO2-MP2: Total energy -85199.550266


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.
-10.561-5.9662.276-3.134-3.7370.027
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 : 0.018 / q_NPA : 0.006
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-12SER0-0.031-0.0012.282-8.224-3.7782.271-3.039-3.6780.026
4A-11LEU00.0100.0084.034-2.769-2.6200.005-0.095-0.0590.001
5A-10TYR00.0100.0116.005-0.118-0.1180.0000.0000.0000.000
6A-9LYS10.9690.9725.5920.2190.2190.0000.0000.0000.000
7A-8LYS10.9670.9777.699-0.112-0.1120.0000.0000.0000.000
8A-7ALA0-0.0010.00110.607-0.058-0.0580.0000.0000.0000.000
9A-6GLY00.0050.01714.2390.0380.0380.0000.0000.0000.000
10A-5PHE00.011-0.00715.743-0.021-0.0210.0000.0000.0000.000
11A-4LEU0-0.0050.00120.3180.0110.0110.0000.0000.0000.000
12A-3VAL00.0280.01721.9450.0010.0010.0000.0000.0000.000
13A-2PRO00.0010.00324.813-0.003-0.0030.0000.0000.0000.000
14A-1ARG10.8650.90027.229-0.028-0.0280.0000.0000.0000.000
15A0GLY00.0460.04028.8670.0050.0050.0000.0000.0000.000
16A1SER00.0020.00424.8810.0030.0030.0000.0000.0000.000
17A2GLY00.1020.06924.665-0.002-0.0020.0000.0000.0000.000
18A3SER0-0.111-0.06524.4810.0100.0100.0000.0000.0000.000
19A4SER00.0150.02926.304-0.005-0.0050.0000.0000.0000.000
20A5GLN0-0.072-0.03628.9170.0020.0020.0000.0000.0000.000
21A6SER00.0680.01431.426-0.001-0.0010.0000.0000.0000.000
22A7VAL0-0.0200.00234.211-0.001-0.0010.0000.0000.0000.000
23A8GLU-1-0.891-0.96236.5940.0500.0500.0000.0000.0000.000
24A9ILE0-0.052-0.01139.259-0.004-0.0040.0000.0000.0000.000
25A10PRO00.0360.03041.9780.0010.0010.0000.0000.0000.000
26A11GLY0-0.002-0.01645.599-0.001-0.0010.0000.0000.0000.000
27A12GLY0-0.049-0.03842.5720.0010.0010.0000.0000.0000.000
28A13GLY0-0.041-0.01241.2450.0030.0030.0000.0000.0000.000
29A14THR00.0320.00036.169-0.001-0.0010.0000.0000.0000.000
30A15GLU-1-0.897-0.93738.9290.0580.0580.0000.0000.0000.000
31A16GLY00.0130.00541.471-0.002-0.0020.0000.0000.0000.000
32A17TYR0-0.022-0.02043.9150.0010.0010.0000.0000.0000.000
33A18HIS0-0.017-0.01338.666-0.001-0.0010.0000.0000.0000.000
34A19VAL0-0.016-0.01243.091-0.002-0.0020.0000.0000.0000.000
35A20LEU00.0450.02542.0860.0000.0000.0000.0000.0000.000
36A21ARG10.9100.94644.869-0.023-0.0230.0000.0000.0000.000
37A22VAL00.0200.02047.4250.0000.0000.0000.0000.0000.000
38A23GLN00.005-0.00149.677-0.001-0.0010.0000.0000.0000.000
39A24GLU-1-0.842-0.91452.6000.0130.0130.0000.0000.0000.000
40A25ASN0-0.047-0.03054.2630.0000.0000.0000.0000.0000.000
41A26SER00.0310.01553.4080.0000.0000.0000.0000.0000.000
42A27PRO0-0.055-0.03655.7410.0000.0000.0000.0000.0000.000
43A28GLY00.0460.01252.1830.0000.0000.0000.0000.0000.000
44A29HIS00.0180.00651.0520.0010.0010.0000.0000.0000.000
45A30ARG10.8470.91951.803-0.015-0.0150.0000.0000.0000.000
46A31ALA0-0.040-0.00651.998-0.001-0.0010.0000.0000.0000.000
47A32GLY0-0.020-0.00649.0180.0010.0010.0000.0000.0000.000
48A33LEU0-0.063-0.02746.8940.0010.0010.0000.0000.0000.000
49A34GLU-1-0.765-0.88641.0070.0230.0230.0000.0000.0000.000
50A35PRO00.008-0.00343.0720.0020.0020.0000.0000.0000.000
51A36PHE00.0090.00834.344-0.001-0.0010.0000.0000.0000.000
52A37PHE00.0410.00834.8380.0030.0030.0000.0000.0000.000
53A38ASP-1-0.747-0.82139.1990.0310.0310.0000.0000.0000.000
54A39PHE00.0340.00638.1610.0010.0010.0000.0000.0000.000
55A40ILE0-0.020-0.00442.868-0.001-0.0010.0000.0000.0000.000
56A41VAL00.0070.00843.0540.0020.0020.0000.0000.0000.000
57A42SER00.043-0.01145.9790.0010.0010.0000.0000.0000.000
58A43ILE00.0210.03549.479-0.001-0.0010.0000.0000.0000.000
59A44ASN0-0.014-0.02752.9910.0000.0000.0000.0000.0000.000
60A45GLY00.0080.00952.6970.0000.0000.0000.0000.0000.000
61A46SER0-0.028-0.00452.5160.0010.0010.0000.0000.0000.000
62A47ARG10.7940.89942.876-0.045-0.0450.0000.0000.0000.000
63A48LEU0-0.057-0.03447.890-0.001-0.0010.0000.0000.0000.000
64A49ASN0-0.007-0.01245.2330.0020.0020.0000.0000.0000.000
65A50LYN0-0.130-0.05747.0370.0000.0000.0000.0000.0000.000
66A51ASP-1-0.844-0.89147.2410.0420.0420.0000.0000.0000.000
67A52ASN00.1050.04349.246-0.002-0.0020.0000.0000.0000.000
68A53ASP-1-0.730-0.84553.0450.0290.0290.0000.0000.0000.000
69A54THR0-0.032-0.03254.038-0.002-0.0020.0000.0000.0000.000
70A55LEU00.0110.00650.720-0.001-0.0010.0000.0000.0000.000
71A56LYS10.8610.91154.537-0.029-0.0290.0000.0000.0000.000
72A57ASP-1-0.812-0.90756.9100.0240.0240.0000.0000.0000.000
73A58LEU0-0.041-0.02255.858-0.001-0.0010.0000.0000.0000.000
74A59LEU0-0.011-0.00254.522-0.001-0.0010.0000.0000.0000.000
75A60LYS10.8700.93158.912-0.023-0.0230.0000.0000.0000.000
76A61ALA0-0.023-0.01162.051-0.001-0.0010.0000.0000.0000.000
77A62ASN0-0.084-0.05260.831-0.001-0.0010.0000.0000.0000.000
78A63VAL00.0100.01662.5580.0000.0000.0000.0000.0000.000
79A64GLU-1-0.708-0.81563.7330.0150.0150.0000.0000.0000.000
80A65LYS10.8500.92363.221-0.019-0.0190.0000.0000.0000.000
81A66PRO00.0100.00559.5010.0010.0010.0000.0000.0000.000
82A67VAL0-0.056-0.03555.7360.0000.0000.0000.0000.0000.000
83A68LYS10.8470.91352.207-0.025-0.0250.0000.0000.0000.000
84A69MET0-0.019-0.00950.0320.0010.0010.0000.0000.0000.000
85A70LEU0-0.027-0.01145.693-0.001-0.0010.0000.0000.0000.000
86A71ILE0-0.017-0.01543.7710.0010.0010.0000.0000.0000.000
87A72TYR00.0390.01434.879-0.001-0.0010.0000.0000.0000.000
88A73SER00.0430.02639.0070.0000.0000.0000.0000.0000.000
89A74SER00.0290.00134.6790.0000.0000.0000.0000.0000.000
90A75LYS10.7640.88733.866-0.025-0.0250.0000.0000.0000.000
91A76THR0-0.004-0.02134.1750.0000.0000.0000.0000.0000.000
92A77LEU0-0.0010.01730.8770.0000.0000.0000.0000.0000.000
93A78GLH0-0.053-0.05835.6300.0000.0000.0000.0000.0000.000
94A79LEU00.0020.00039.0940.0000.0000.0000.0000.0000.000
95A80ARG10.7960.86642.579-0.028-0.0280.0000.0000.0000.000
96A81GLU-1-0.831-0.90345.6520.0260.0260.0000.0000.0000.000
97A82ALA00.0150.01949.315-0.001-0.0010.0000.0000.0000.000
98A83SER0-0.011-0.01051.1140.0010.0010.0000.0000.0000.000
99A84VAL00.011-0.00453.684-0.001-0.0010.0000.0000.0000.000
100A85THR0-0.0090.00255.7600.0000.0000.0000.0000.0000.000
101A86PRO0-0.038-0.00857.8740.0000.0000.0000.0000.0000.000
102A87SER0-0.022-0.04559.445-0.001-0.0010.0000.0000.0000.000
103A88ASN0-0.072-0.06161.7100.0010.0010.0000.0000.0000.000
104A89LEU0-0.035-0.01164.3640.0000.0000.0000.0000.0000.000
105A90TRP0-0.0810.00956.384-0.001-0.0010.0000.0000.0000.000
106A91GLY00.0270.00261.9570.0000.0000.0000.0000.0000.000
107A92GLY0-0.019-0.01058.9030.0000.0000.0000.0000.0000.000
108A93GLN00.0000.00256.7790.0010.0010.0000.0000.0000.000
109A94GLY00.0330.01757.1960.0010.0010.0000.0000.0000.000
110A95LEU00.0040.00358.234-0.001-0.0010.0000.0000.0000.000
111A96LEU00.0490.01152.899-0.001-0.0010.0000.0000.0000.000
112A97GLY00.0370.00954.781-0.001-0.0010.0000.0000.0000.000
113A98VAL0-0.042-0.02648.9260.0000.0000.0000.0000.0000.000
114A99SER0-0.0340.00748.5990.0010.0010.0000.0000.0000.000
115A100ILE0-0.019-0.01946.7950.0000.0000.0000.0000.0000.000
116A101ARG10.9890.99540.573-0.050-0.0500.0000.0000.0000.000
117A102PHE00.0160.03244.1140.0000.0000.0000.0000.0000.000
118A103CYS00.0150.00938.9340.0010.0010.0000.0000.0000.000
119A104SER00.0660.03936.164-0.002-0.0020.0000.0000.0000.000
120A105PHE0-0.022-0.01736.4600.0000.0000.0000.0000.0000.000
121A106ASP-1-0.962-0.99131.8500.0850.0850.0000.0000.0000.000
122A107GLY00.0410.02930.3760.0030.0030.0000.0000.0000.000
123A108ALA00.0360.01731.0320.0010.0010.0000.0000.0000.000
124A109ASN0-0.066-0.03930.828-0.004-0.0040.0000.0000.0000.000
125A110GLU-1-0.970-0.99125.9160.1010.1010.0000.0000.0000.000
126A111ASN0-0.0190.01229.1830.0050.0050.0000.0000.0000.000
127A112VAL0-0.036-0.02230.862-0.007-0.0070.0000.0000.0000.000
128A113TRP00.007-0.00230.0050.0010.0010.0000.0000.0000.000
129A114HIS0-0.023-0.00331.336-0.002-0.0020.0000.0000.0000.000
130A115VAL00.0150.00533.1300.0020.0020.0000.0000.0000.000
131A116LEU0-0.0380.00129.853-0.004-0.0040.0000.0000.0000.000
132A117GLU-1-0.825-0.90233.8060.0270.0270.0000.0000.0000.000
133A118VAL0-0.013-0.02636.6890.0030.0030.0000.0000.0000.000
134A119GLU-1-0.843-0.91239.7170.0190.0190.0000.0000.0000.000
135A120SER00.014-0.00142.0550.0000.0000.0000.0000.0000.000
136A121ASN0-0.071-0.04645.8180.0010.0010.0000.0000.0000.000
137A122SER00.0400.03642.8720.0010.0010.0000.0000.0000.000
138A123PRO00.010-0.00543.471-0.001-0.0010.0000.0000.0000.000
139A124ALA00.0460.01441.1940.0000.0000.0000.0000.0000.000
140A125ALA0-0.0110.00343.287-0.001-0.0010.0000.0000.0000.000
141A126LEU0-0.048-0.02245.537-0.001-0.0010.0000.0000.0000.000
142A127ALA0-0.0030.01845.488-0.001-0.0010.0000.0000.0000.000
143A128GLY0-0.033-0.01646.8930.0000.0000.0000.0000.0000.000
144A129LEU0-0.023-0.00240.184-0.001-0.0010.0000.0000.0000.000
145A130ARG10.8110.88442.184-0.020-0.0200.0000.0000.0000.000
146A131PRO00.0270.01438.5870.0020.0020.0000.0000.0000.000
147A132HIS00.0120.02033.688-0.002-0.0020.0000.0000.0000.000
148A133SER00.000-0.00636.5260.0000.0000.0000.0000.0000.000
149A134ASP-1-0.729-0.82039.0280.0240.0240.0000.0000.0000.000
150A135TYR0-0.005-0.01332.3620.0000.0000.0000.0000.0000.000
151A136ILE0-0.022-0.00736.321-0.002-0.0020.0000.0000.0000.000
152A137ILE00.012-0.01035.7530.0040.0040.0000.0000.0000.000
153A138GLY00.0380.02037.4320.0020.0020.0000.0000.0000.000
154A139ALA00.0120.02339.308-0.003-0.0030.0000.0000.0000.000
155A140ASP-1-0.877-0.90842.1980.0390.0390.0000.0000.0000.000
156A141THR0-0.015-0.01640.4670.0000.0000.0000.0000.0000.000
157A142VAL00.0050.00443.7710.0000.0000.0000.0000.0000.000
158A143MET0-0.054-0.01145.288-0.001-0.0010.0000.0000.0000.000
159A144ASN0-0.019-0.03540.905-0.001-0.0010.0000.0000.0000.000
160A145GLU-1-0.838-0.90838.9520.0630.0630.0000.0000.0000.000
161A146SER0-0.054-0.04335.5560.0060.0060.0000.0000.0000.000
162A147GLU-1-0.898-0.94433.0760.0710.0710.0000.0000.0000.000
163A148ASP-1-0.959-0.97230.0530.1040.1040.0000.0000.0000.000
164A149LEU0-0.013-0.00833.046-0.003-0.0030.0000.0000.0000.000
165A150PHE00.037-0.02930.280-0.003-0.0030.0000.0000.0000.000
166A151SER0-0.0310.01334.099-0.002-0.0020.0000.0000.0000.000
167A152LEU00.0520.03236.219-0.003-0.0030.0000.0000.0000.000
168A153ILE0-0.108-0.05436.233-0.004-0.0040.0000.0000.0000.000
169A154GLU-1-0.802-0.90537.4020.0630.0630.0000.0000.0000.000
170A155THR0-0.033-0.00640.467-0.004-0.0040.0000.0000.0000.000
171A156HIS0-0.073-0.04942.853-0.005-0.0050.0000.0000.0000.000
172A157GLU-1-0.829-0.90742.4830.0420.0420.0000.0000.0000.000
173A158ALA0-0.012-0.01845.358-0.002-0.0020.0000.0000.0000.000
174A159LYS10.7760.89347.779-0.040-0.0400.0000.0000.0000.000
175A160PRO00.0290.01547.7270.0010.0010.0000.0000.0000.000
176A161LEU00.0360.02241.5230.0010.0010.0000.0000.0000.000
177A162LYS10.9280.98945.947-0.032-0.0320.0000.0000.0000.000
178A163LEU00.0100.00740.2990.0030.0030.0000.0000.0000.000
179A164TYR0-0.035-0.06041.369-0.003-0.0030.0000.0000.0000.000
180A165VAL0-0.023-0.01740.4870.0020.0020.0000.0000.0000.000
181A166TYR0-0.037-0.05638.770-0.001-0.0010.0000.0000.0000.000
182A167ASN0-0.013-0.02139.842-0.001-0.0010.0000.0000.0000.000
183A168THR00.000-0.02636.707-0.001-0.0010.0000.0000.0000.000
184A169ASP-1-0.965-0.94940.1470.0080.0080.0000.0000.0000.000
185A170THR0-0.061-0.04243.4100.0000.0000.0000.0000.0000.000
186A171ASP-1-0.847-0.88641.0560.0180.0180.0000.0000.0000.000
187A172ASN0-0.018-0.03043.3050.0030.0030.0000.0000.0000.000
188A173CYS0-0.0260.01842.8670.0010.0010.0000.0000.0000.000
189A174ARG10.7530.84943.511-0.026-0.0260.0000.0000.0000.000
190A175GLU-1-0.908-0.94745.3150.0310.0310.0000.0000.0000.000
191A176VAL0-0.060-0.02744.575-0.002-0.0020.0000.0000.0000.000
192A177ILE0-0.018-0.02146.2030.0020.0020.0000.0000.0000.000
193A178ILE00.0330.00942.090-0.002-0.0020.0000.0000.0000.000
194A179THR0-0.012-0.01746.2270.0010.0010.0000.0000.0000.000
195A180PRO0-0.0240.00442.261-0.002-0.0020.0000.0000.0000.000
196A181ASN00.0570.02543.7380.0000.0000.0000.0000.0000.000
197A182SER0-0.005-0.00940.8950.0000.0000.0000.0000.0000.000
198A183ALA0-0.066-0.02842.4930.0000.0000.0000.0000.0000.000
199A184TRP0-0.087-0.03841.111-0.004-0.0040.0000.0000.0000.000
200A185GLY0-0.028-0.00544.771-0.002-0.0020.0000.0000.0000.000
201A186GLY00.022-0.00341.736-0.003-0.0030.0000.0000.0000.000
202A187GLH0-0.073-0.04534.6920.0030.0030.0000.0000.0000.000
203A188GLY00.000-0.00237.0400.0000.0000.0000.0000.0000.000
204A189SER00.0930.03237.587-0.002-0.0020.0000.0000.0000.000
205A190LEU00.009-0.00237.960-0.002-0.0020.0000.0000.0000.000
206A191GLY00.0320.02039.471-0.003-0.0030.0000.0000.0000.000
207A192CYS0-0.047-0.03036.631-0.003-0.0030.0000.0000.0000.000
208A193GLY00.0430.04833.4780.0040.0040.0000.0000.0000.000
209A194ILE0-0.053-0.04330.612-0.001-0.0010.0000.0000.0000.000
210A195GLY00.0120.01428.4030.0030.0030.0000.0000.0000.000
211A196TYR00.0230.00224.6890.0020.0020.0000.0000.0000.000
212A197GLY00.0710.03224.2670.0070.0070.0000.0000.0000.000
213A198TYR0-0.007-0.03221.612-0.014-0.0140.0000.0000.0000.000
214A199LEU0-0.067-0.02121.997-0.010-0.0100.0000.0000.0000.000
215A200HIS0-0.072-0.03025.751-0.004-0.0040.0000.0000.0000.000
216A201ARG10.8820.93626.921-0.060-0.0600.0000.0000.0000.000
217A202ILE00.0220.02430.259-0.005-0.0050.0000.0000.0000.000
218A203PRO0-0.0070.00632.8190.0010.0010.0000.0000.0000.000
219A204THR0-0.034-0.02832.3220.0030.0030.0000.0000.0000.000
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