FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 9MYM2

Calculation Name: 1GG4-A-Xray372

Preferred Name: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1GG4

Chain ID: A

ChEMBL ID: CHEMBL2540

UniProt ID: P11880

Base Structure: X-ray

Registration Date: 2023-09-26

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 439
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6887761.277812
FMO2-HF: Nuclear repulsion 6726004.246105
FMO2-HF: Total energy -161757.031707
FMO2-MP2: Total energy -162230.993522


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-8.849-0.69823.484-9.115-22.517-0.05
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / q_NPA : -0.003
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].
3A3SER00.025-0.0123.3392.2343.8892.228-1.446-2.437-0.010
4A4VAL0-0.046-0.0042.908-0.3080.1970.083-0.086-0.501-0.001
5A5THR00.0130.0025.813-0.317-0.3170.0000.0000.0000.000
6A6LEU00.015-0.0017.987-0.033-0.0330.0000.0000.0000.000
7A7SER0-0.006-0.0229.2300.0480.0480.0000.0000.0000.000
8A8GLN00.0250.0348.3260.0060.0060.0000.0000.0000.000
9A9LEU00.018-0.0124.439-0.0460.032-0.001-0.004-0.0720.000
10A10THR0-0.088-0.0348.3920.0480.0480.0000.0000.0000.000
11A11ASP-1-0.931-0.95412.0100.0920.0920.0000.0000.0000.000
12A12ILE0-0.013-0.0057.2800.0030.0030.0000.0000.0000.000
13A13LEU0-0.074-0.0406.4740.0120.0120.0000.0000.0000.000
14A14ASN0-0.062-0.02110.620-0.004-0.0040.0000.0000.0000.000
15A15GLY0-0.053-0.03413.325-0.009-0.0090.0000.0000.0000.000
16A16GLU-1-0.930-0.96314.155-0.146-0.1460.0000.0000.0000.000
17A17LEU0-0.038-0.01612.745-0.036-0.0360.0000.0000.0000.000
18A18GLN0-0.062-0.03014.9250.0280.0280.0000.0000.0000.000
19A19GLY00.022-0.00516.510-0.014-0.0140.0000.0000.0000.000
20A20ALA0-0.029-0.00416.6450.0180.0180.0000.0000.0000.000
21A21ASP-1-0.741-0.87712.058-0.307-0.3070.0000.0000.0000.000
22A22ILE0-0.047-0.0289.1030.0070.0070.0000.0000.0000.000
23A23THR0-0.0100.0078.3710.0360.0360.0000.0000.0000.000
24A24LEU0-0.049-0.0184.157-0.350-0.1420.000-0.015-0.1930.000
25A25ASP-1-0.861-0.9383.708-1.466-1.0350.006-0.083-0.3530.000
26A26ALA00.006-0.0052.448-3.468-2.0762.929-1.740-2.581-0.016
27A27VAL00.0020.0192.174-0.483-0.8654.452-0.446-3.6250.003
28A28THR0-0.021-0.0164.0710.1740.3460.001-0.006-0.1670.000
29A29THR00.0500.0417.3680.0180.0180.0000.0000.0000.000
30A30ASP-1-0.914-0.97410.693-0.240-0.2400.0000.0000.0000.000
31A31THR00.1000.04712.155-0.054-0.0540.0000.0000.0000.000
32A32ARG10.8290.91114.7020.2210.2210.0000.0000.0000.000
33A33LYS10.8620.92210.2330.4270.4270.0000.0000.0000.000
34A34LEU00.0240.0509.838-0.125-0.1250.0000.0000.0000.000
35A35THR0-0.018-0.0177.975-0.027-0.0270.0000.0000.0000.000
36A36PRO0-0.027-0.03310.134-0.033-0.0330.0000.0000.0000.000
37A37GLY00.0420.02810.645-0.032-0.0320.0000.0000.0000.000
38A38CYS0-0.0660.0116.362-0.034-0.0340.0000.0000.0000.000
39A39LEU00.0270.0114.3970.0660.202-0.001-0.008-0.1270.000
40A40PHE00.018-0.0106.539-0.090-0.0900.0000.0000.0000.000
41A41VAL0-0.015-0.0156.7910.0660.0660.0000.0000.0000.000
42A42ALA00.0330.0149.5860.0510.0510.0000.0000.0000.000
43A43LEU0-0.014-0.01411.2730.0460.0460.0000.0000.0000.000
44A44LYS10.9870.99714.3080.1400.1400.0000.0000.0000.000
45A45GLY0-0.074-0.03417.9800.0170.0170.0000.0000.0000.000
46A46GLU-1-0.921-0.96519.784-0.068-0.0680.0000.0000.0000.000
47A47ARG10.9050.94223.5440.0780.0780.0000.0000.0000.000
48A48PHE0-0.008-0.02119.922-0.002-0.0020.0000.0000.0000.000
49A49ASP-1-0.719-0.85519.038-0.184-0.1840.0000.0000.0000.000
50A50ALA00.0280.00815.198-0.003-0.0030.0000.0000.0000.000
51A51HIS0-0.097-0.07215.405-0.052-0.0520.0000.0000.0000.000
52A52ASP-1-0.898-0.94718.067-0.180-0.1800.0000.0000.0000.000
53A53PHE0-0.073-0.00617.1590.0120.0120.0000.0000.0000.000
54A54ALA00.0370.02115.951-0.035-0.0350.0000.0000.0000.000
55A55ASP-1-0.865-0.94016.736-0.256-0.2560.0000.0000.0000.000
56A56GLN0-0.025-0.01418.302-0.011-0.0110.0000.0000.0000.000
57A57ALA00.0390.01213.164-0.015-0.0150.0000.0000.0000.000
58A58LYS10.9460.98414.6010.2590.2590.0000.0000.0000.000
59A59ALA0-0.068-0.03116.336-0.009-0.0090.0000.0000.0000.000
60A60GLY0-0.033-0.01215.9380.0150.0150.0000.0000.0000.000
61A61GLY0-0.034-0.01514.687-0.021-0.0210.0000.0000.0000.000
62A62ALA0-0.049-0.02511.053-0.074-0.0740.0000.0000.0000.000
63A63GLY00.0200.00910.1100.0850.0850.0000.0000.0000.000
64A64ALA00.0090.0028.9770.0720.0720.0000.0000.0000.000
65A65LEU0-0.014-0.0069.985-0.084-0.0840.0000.0000.0000.000
66A66LEU0-0.0130.0187.2990.0330.0330.0000.0000.0000.000
67A67VAL00.004-0.00710.3900.0260.0260.0000.0000.0000.000
68A68SER0-0.005-0.00614.0110.0150.0150.0000.0000.0000.000
69A69ARG10.8280.91716.6850.2030.2030.0000.0000.0000.000
70A70PRO00.0710.03018.189-0.023-0.0230.0000.0000.0000.000
71A71LEU0-0.037-0.01316.7150.0140.0140.0000.0000.0000.000
72A72ASP-1-0.900-0.93020.294-0.169-0.1690.0000.0000.0000.000
73A73ILE0-0.022-0.01717.569-0.004-0.0040.0000.0000.0000.000
74A74ASP-1-0.962-0.97418.730-0.243-0.2430.0000.0000.0000.000
75A75LEU0-0.048-0.04113.723-0.015-0.0150.0000.0000.0000.000
76A76PRO0-0.0080.00412.6190.0230.0230.0000.0000.0000.000
77A77GLN0-0.0030.00312.845-0.053-0.0530.0000.0000.0000.000
78A78LEU00.0340.0208.5090.0190.0190.0000.0000.0000.000
79A79ILE00.0050.00312.480-0.015-0.0150.0000.0000.0000.000
80A80VAL00.0510.02711.3630.0270.0270.0000.0000.0000.000
81A81LYS10.9450.96414.7670.0450.0450.0000.0000.0000.000
82A82ASP-1-0.858-0.94915.587-0.083-0.0830.0000.0000.0000.000
83A83THR00.0540.01112.0890.0190.0190.0000.0000.0000.000
84A84ARG10.8340.94011.1870.0410.0410.0000.0000.0000.000
85A85LEU0-0.039-0.02211.8640.0210.0210.0000.0000.0000.000
86A86ALA00.0990.0639.7950.0430.0430.0000.0000.0000.000
87A87PHE0-0.0080.0035.9250.0280.0280.0000.0000.0000.000
88A88GLY00.009-0.0126.9650.1020.1020.0000.0000.0000.000
89A89GLU-1-0.882-0.9678.8040.1920.1920.0000.0000.0000.000
90A90LEU00.0020.0072.185-0.376-0.2271.751-0.261-1.6380.001
91A91ALA0-0.017-0.0195.0870.6040.704-0.001-0.002-0.0970.000
92A92ALA0-0.024-0.0046.1550.3470.3470.0000.0000.0000.000
93A93TRP00.0310.0034.418-0.0590.131-0.001-0.011-0.1790.000
94A94VAL00.026-0.0072.699-0.675-1.3133.961-0.906-2.4170.005
95A95ARG10.8540.9185.980-1.130-1.088-0.001-0.004-0.0370.000
96A96GLN0-0.085-0.0488.125-0.197-0.1970.0000.0000.0000.000
97A97GLN0-0.034-0.0037.273-0.289-0.2890.0000.0000.0000.000
98A98VAL0-0.057-0.0036.043-0.116-0.1160.0000.0000.0000.000
99A99PRO0-0.002-0.0109.127-0.099-0.0990.0000.0000.0000.000
100A100ALA0-0.0140.01610.585-0.107-0.1070.0000.0000.0000.000
101A101ARG10.8280.89612.435-0.430-0.4300.0000.0000.0000.000
102A102VAL0-0.0040.00011.6250.0050.0050.0000.0000.0000.000
103A103VAL0-0.0030.01514.488-0.073-0.0730.0000.0000.0000.000
104A104ALA00.0240.00416.0520.0300.0300.0000.0000.0000.000
105A105LEU0-0.0180.00318.088-0.034-0.0340.0000.0000.0000.000
106A106THR00.0410.01420.164-0.005-0.0050.0000.0000.0000.000
107A107GLY00.0090.00322.865-0.002-0.0020.0000.0000.0000.000
108A108SER0-0.050-0.02626.026-0.005-0.0050.0000.0000.0000.000
109A109SER0-0.049-0.03327.969-0.005-0.0050.0000.0000.0000.000
110A110GLY00.0890.03326.7020.0060.0060.0000.0000.0000.000
111A111LYS10.9050.97921.551-0.101-0.1010.0000.0000.0000.000
112A112THR00.0410.00920.3790.0110.0110.0000.0000.0000.000
113A113SER00.0710.03721.6100.0080.0080.0000.0000.0000.000
114A114VAL00.0300.01923.0040.0060.0060.0000.0000.0000.000
115A115LYS10.8830.98616.010-0.162-0.1620.0000.0000.0000.000
116A116GLU-1-0.940-0.98019.2390.1450.1450.0000.0000.0000.000
117A117MET0-0.055-0.00920.4370.0010.0010.0000.0000.0000.000
118A118THR00.006-0.02319.6910.0010.0010.0000.0000.0000.000
119A119ALA00.000-0.00716.6490.0160.0160.0000.0000.0000.000
120A120ALA0-0.0220.00318.2020.0120.0120.0000.0000.0000.000
121A121ILE0-0.013-0.00520.990-0.009-0.0090.0000.0000.0000.000
122A122LEU00.0050.00118.031-0.005-0.0050.0000.0000.0000.000
123A123SER0-0.033-0.02217.7230.0220.0220.0000.0000.0000.000
124A124GLN0-0.098-0.04218.831-0.016-0.0160.0000.0000.0000.000
125A125CYS0-0.108-0.04420.115-0.022-0.0220.0000.0000.0000.000
126A126GLY00.0400.02617.475-0.008-0.0080.0000.0000.0000.000
127A127ASN00.0000.00111.0960.0010.0010.0000.0000.0000.000
128A128THR0-0.0280.01312.9670.1020.1020.0000.0000.0000.000
129A129LEU00.0200.0366.709-0.090-0.0900.0000.0000.0000.000
130A130TYR00.016-0.00110.976-0.028-0.0280.0000.0000.0000.000
131A131THR00.0530.02011.6540.0100.0100.0000.0000.0000.000
132A132ALA00.0090.01411.884-0.030-0.0300.0000.0000.0000.000
133A133GLY00.004-0.00513.553-0.026-0.0260.0000.0000.0000.000
134A134ASN0-0.058-0.04617.0220.0150.0150.0000.0000.0000.000
135A135LEU0-0.0060.01711.958-0.019-0.0190.0000.0000.0000.000
136A136ASN0-0.055-0.04114.2110.0260.0260.0000.0000.0000.000
137A137ASN00.1000.04716.0670.0200.0200.0000.0000.0000.000
138A138ASP-1-0.822-0.93314.6840.0300.0300.0000.0000.0000.000
139A139ILE0-0.0110.01012.019-0.003-0.0030.0000.0000.0000.000
140A140GLY00.021-0.01811.271-0.022-0.0220.0000.0000.0000.000
141A141VAL00.0340.03911.3270.0320.0320.0000.0000.0000.000
142A142PRO00.0240.0288.1260.1400.1400.0000.0000.0000.000
143A143MET00.0070.0016.9660.1330.1330.0000.0000.0000.000
144A144THR0-0.101-0.0627.062-0.133-0.1330.0000.0000.0000.000
145A145LEU0-0.010-0.0186.7390.1660.1660.0000.0000.0000.000
146A146LEU00.0320.0122.535-1.1450.4960.635-0.393-1.8830.002
147A147ARG10.8200.9292.114-5.997-5.1005.789-2.822-3.863-0.033
148A148LEU0-0.040-0.0153.2470.7511.2320.104-0.043-0.5420.001
149A149THR00.0590.0323.0273.0124.0221.551-0.831-1.730-0.002
150A150PRO00.008-0.0225.252-0.505-0.421-0.001-0.008-0.0750.000
151A151GLU-1-0.916-0.9528.2140.3610.3610.0000.0000.0000.000
152A152TYR0-0.124-0.0376.136-0.222-0.2220.0000.0000.0000.000
153A153ASP-1-0.800-0.89010.2310.4830.4830.0000.0000.0000.000
154A154TYR0-0.056-0.03613.240-0.043-0.0430.0000.0000.0000.000
155A155ALA00.0330.00210.6730.0980.0980.0000.0000.0000.000
156A156VAL0-0.048-0.02412.533-0.071-0.0710.0000.0000.0000.000
157A157ILE00.022-0.00710.808-0.020-0.0200.0000.0000.0000.000
158A158GLU-1-0.858-0.93314.3170.1070.1070.0000.0000.0000.000
159A159LEU0-0.013-0.01515.813-0.004-0.0040.0000.0000.0000.000
160A160GLY0-0.041-0.03718.497-0.016-0.0160.0000.0000.0000.000
161A161ALA0-0.032-0.02620.7300.0050.0050.0000.0000.0000.000
162A162ASN0-0.109-0.02822.996-0.002-0.0020.0000.0000.0000.000
163A163HIS0-0.045-0.03724.393-0.008-0.0080.0000.0000.0000.000
164A164GLN0-0.026-0.01825.2460.0100.0100.0000.0000.0000.000
165A165GLY0-0.0130.00323.734-0.009-0.0090.0000.0000.0000.000
166A166GLU-1-0.771-0.90020.4140.0590.0590.0000.0000.0000.000
167A167ILE00.011-0.00119.2540.0130.0130.0000.0000.0000.000
168A168ALA00.0070.00619.5570.0270.0270.0000.0000.0000.000
169A169TRP00.0260.02612.5620.0330.0330.0000.0000.0000.000
170A170THR00.0860.04614.8400.0390.0390.0000.0000.0000.000
171A171VAL0-0.0010.03715.0170.0750.0750.0000.0000.0000.000
172A172SER0-0.134-0.06316.0350.0420.0420.0000.0000.0000.000
173A173LEU00.012-0.00410.9660.0360.0360.0000.0000.0000.000
174A174THR0-0.007-0.04812.2620.1190.1190.0000.0000.0000.000
175A175ARG10.8650.96813.479-0.256-0.2560.0000.0000.0000.000
176A176PRO0-0.025-0.00115.9120.0390.0390.0000.0000.0000.000
177A177GLU-1-0.763-0.88417.0880.3900.3900.0000.0000.0000.000
178A178ALA00.0340.00119.534-0.042-0.0420.0000.0000.0000.000
179A179ALA00.0090.00920.2200.0280.0280.0000.0000.0000.000
180A180LEU00.0060.01422.240-0.021-0.0210.0000.0000.0000.000
181A181VAL0-0.0080.00623.8630.0020.0020.0000.0000.0000.000
182A182ASN00.004-0.01226.045-0.001-0.0010.0000.0000.0000.000
183A183ASN0-0.033-0.03027.792-0.010-0.0100.0000.0000.0000.000
184A184LEU00.0030.01329.7630.0030.0030.0000.0000.0000.000
185A185ALA00.0340.02432.419-0.003-0.0030.0000.0000.0000.000
186A194SER00.0680.02535.936-0.002-0.0020.0000.0000.0000.000
187A195LEU00.0370.00934.8630.0030.0030.0000.0000.0000.000
188A196ALA00.0720.03434.6410.0050.0050.0000.0000.0000.000
189A197GLY0-0.0100.00233.0590.0050.0050.0000.0000.0000.000
190A198VAL00.0360.00930.3500.0040.0040.0000.0000.0000.000
191A199ALA00.0130.00229.9080.0090.0090.0000.0000.0000.000
192A200LYS10.9210.96429.834-0.062-0.0620.0000.0000.0000.000
193A201ALA00.0270.01726.3840.0070.0070.0000.0000.0000.000
194A202LYS10.8770.94225.217-0.087-0.0870.0000.0000.0000.000
195A203GLY00.0370.01726.1000.0140.0140.0000.0000.0000.000
196A204GLU-1-0.818-0.92623.8520.1130.1130.0000.0000.0000.000
197A205ILE0-0.0070.01820.9390.0160.0160.0000.0000.0000.000
198A206PHE0-0.004-0.01922.3210.0210.0210.0000.0000.0000.000
199A207SER0-0.067-0.04423.0440.0070.0070.0000.0000.0000.000
200A208GLY0-0.022-0.01219.8500.0010.0010.0000.0000.0000.000
201A209LEU0-0.056-0.00219.6270.0320.0320.0000.0000.0000.000
202A210PRO00.0310.02419.837-0.023-0.0230.0000.0000.0000.000
203A211GLU-1-0.909-0.96222.3620.1550.1550.0000.0000.0000.000
204A212ASN0-0.029-0.01222.250-0.017-0.0170.0000.0000.0000.000
205A213GLY0-0.023-0.01323.4830.0060.0060.0000.0000.0000.000
206A214ILE0-0.050-0.02223.987-0.023-0.0230.0000.0000.0000.000
207A215ALA00.0270.01524.7910.0140.0140.0000.0000.0000.000
208A216ILE00.0020.00924.705-0.013-0.0130.0000.0000.0000.000
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210A218ASN00.0610.03130.190-0.003-0.0030.0000.0000.0000.000
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