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: M9M9Z

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 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 439
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6889471.074162
FMO2-HF: Nuclear repulsion 6727711.857458
FMO2-HF: Total energy -161759.216704
FMO2-MP2: Total energy -162233.003097


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.
-15.883-15.14136.408-12.636-24.511-0.081
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 : -0.075 / q_NPA : -0.026
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].
3A3SER00.005-0.0443.3153.2264.4742.521-1.350-2.418-0.011
4A4VAL0-0.087-0.0252.700-0.673-0.1140.241-0.124-0.676-0.001
5A5THR00.015-0.0045.725-0.195-0.1950.0000.0000.0000.000
6A6LEU00.0180.0027.658-0.047-0.0470.0000.0000.0000.000
7A7SER0-0.019-0.0549.1980.0150.0150.0000.0000.0000.000
8A8GLN00.0020.0188.2820.0220.0220.0000.0000.0000.000
9A9LEU00.021-0.0074.289-0.0830.012-0.001-0.008-0.0870.000
10A10THR0-0.092-0.0278.3280.0370.0370.0000.0000.0000.000
11A11ASP-1-0.929-0.95411.958-0.007-0.0070.0000.0000.0000.000
12A12ILE0-0.014-0.0047.0740.0050.0050.0000.0000.0000.000
13A13LEU0-0.068-0.0396.5200.0150.0150.0000.0000.0000.000
14A14ASN0-0.064-0.02710.5800.0050.0050.0000.0000.0000.000
15A15GLY0-0.043-0.03113.3160.0020.0020.0000.0000.0000.000
16A16GLU-1-0.901-0.93514.135-0.064-0.0640.0000.0000.0000.000
17A17LEU0-0.036-0.01712.580-0.015-0.0150.0000.0000.0000.000
18A18GLN0-0.077-0.05214.9130.0180.0180.0000.0000.0000.000
19A19GLY00.026-0.00316.3320.0010.0010.0000.0000.0000.000
20A20ALA0-0.036-0.00616.4360.0030.0030.0000.0000.0000.000
21A21ASP-1-0.731-0.84111.901-0.149-0.1490.0000.0000.0000.000
22A22ILE0-0.052-0.0328.7370.0180.0180.0000.0000.0000.000
23A23THR00.0050.0108.215-0.030-0.0300.0000.0000.0000.000
24A24LEU0-0.038-0.0103.835-0.311-0.0590.002-0.030-0.2240.000
25A25ASP-1-0.790-0.8813.6980.0480.4810.005-0.084-0.3540.000
26A26ALA0-0.001-0.0022.443-2.132-0.6472.915-1.753-2.646-0.015
27A27VAL0-0.0080.0082.260-1.202-1.3513.852-0.249-3.4540.002
28A28THR0-0.016-0.0134.1000.2670.4450.000-0.009-0.1690.000
29A29THR00.0580.0437.437-0.061-0.0610.0000.0000.0000.000
30A30ASP-1-0.861-0.93210.6340.1070.1070.0000.0000.0000.000
31A31THR00.1040.05112.2060.0170.0170.0000.0000.0000.000
32A32ARG10.8390.91514.743-0.075-0.0750.0000.0000.0000.000
33A33LYS10.7890.87810.281-0.160-0.1600.0000.0000.0000.000
34A34LEU00.0260.0509.8710.0460.0460.0000.0000.0000.000
35A35THR0-0.014-0.0177.7910.0510.0510.0000.0000.0000.000
36A36PRO0-0.020-0.03110.145-0.071-0.0710.0000.0000.0000.000
37A37GLY00.0370.02810.5200.0190.0190.0000.0000.0000.000
38A38CYS0-0.0730.0106.372-0.048-0.0480.0000.0000.0000.000
39A39LEU00.0280.0074.597-0.0890.039-0.001-0.006-0.1210.000
40A40PHE00.011-0.0136.5850.0420.0420.0000.0000.0000.000
41A41VAL0-0.017-0.0166.634-0.010-0.0100.0000.0000.0000.000
42A42ALA00.0290.0209.4870.0420.0420.0000.0000.0000.000
43A43LEU0-0.016-0.00911.2750.0030.0030.0000.0000.0000.000
44A44LYS10.9510.97614.3050.0370.0370.0000.0000.0000.000
45A45GLY0-0.066-0.03017.9890.0020.0020.0000.0000.0000.000
46A46GLU-1-0.927-0.96519.832-0.007-0.0070.0000.0000.0000.000
47A47ARG10.9060.93723.610-0.011-0.0110.0000.0000.0000.000
48A48PHE0-0.006-0.01719.8560.0050.0050.0000.0000.0000.000
49A49ASP-1-0.709-0.84019.060-0.030-0.0300.0000.0000.0000.000
50A50ALA0-0.046-0.03216.2420.0020.0020.0000.0000.0000.000
51A51HIS00.0230.00815.380-0.010-0.0100.0000.0000.0000.000
52A52ASP-1-0.883-0.93918.089-0.018-0.0180.0000.0000.0000.000
53A53PHE0-0.085-0.04617.5340.0080.0080.0000.0000.0000.000
54A54ALA00.0400.02116.1080.0010.0010.0000.0000.0000.000
55A55ASP-1-0.862-0.93416.846-0.022-0.0220.0000.0000.0000.000
56A56GLN0-0.034-0.02018.3070.0030.0030.0000.0000.0000.000
57A57ALA00.0390.00413.3000.0110.0110.0000.0000.0000.000
58A58LYS10.8260.90714.6800.0340.0340.0000.0000.0000.000
59A59ALA0-0.055-0.02416.3770.0070.0070.0000.0000.0000.000
60A60GLY0-0.036-0.01315.9190.0100.0100.0000.0000.0000.000
61A61GLY0-0.034-0.01514.6370.0240.0240.0000.0000.0000.000
62A62ALA0-0.047-0.02611.044-0.002-0.0020.0000.0000.0000.000
63A63GLY00.0170.01010.0670.0150.0150.0000.0000.0000.000
64A64ALA00.001-0.0038.8410.0070.0070.0000.0000.0000.000
65A65LEU0-0.012-0.0039.999-0.018-0.0180.0000.0000.0000.000
66A66LEU0-0.0150.0087.273-0.001-0.0010.0000.0000.0000.000
67A67VAL00.006-0.00810.4420.0300.0300.0000.0000.0000.000
68A68SER00.0220.00613.9120.0020.0020.0000.0000.0000.000
69A69ARG10.8010.90516.6350.0420.0420.0000.0000.0000.000
70A70PRO00.0450.01918.252-0.007-0.0070.0000.0000.0000.000
71A71LEU0-0.037-0.01417.1160.0080.0080.0000.0000.0000.000
72A72ASP-1-0.905-0.93820.301-0.034-0.0340.0000.0000.0000.000
73A73ILE0-0.018-0.01217.3600.0040.0040.0000.0000.0000.000
74A74ASP-1-0.886-0.93418.691-0.042-0.0420.0000.0000.0000.000
75A75LEU0-0.002-0.00213.5120.0060.0060.0000.0000.0000.000
76A76PRO0-0.0080.00212.5220.0030.0030.0000.0000.0000.000
77A77GLN00.0130.01912.760-0.023-0.0230.0000.0000.0000.000
78A78LEU00.0240.0168.7390.0020.0020.0000.0000.0000.000
79A79ILE00.0000.00212.502-0.002-0.0020.0000.0000.0000.000
80A80VAL00.0410.02711.4480.0060.0060.0000.0000.0000.000
81A81LYS10.9580.96814.7820.0310.0310.0000.0000.0000.000
82A82ASP-1-0.881-0.96815.636-0.021-0.0210.0000.0000.0000.000
83A83THR00.0440.01112.0980.0030.0030.0000.0000.0000.000
84A84ARG10.8120.90311.2640.0020.0020.0000.0000.0000.000
85A85LEU0-0.049-0.02312.0180.0120.0120.0000.0000.0000.000
86A86ALA00.1080.0709.9050.0220.0220.0000.0000.0000.000
87A87PHE00.0010.0025.8330.0240.0240.0000.0000.0000.000
88A88GLY00.015-0.0147.1720.0990.0990.0000.0000.0000.000
89A89GLU-1-0.874-0.9659.0650.0740.0740.0000.0000.0000.000
90A90LEU00.0100.0072.577-0.712-0.0790.783-0.179-1.2370.000
91A91ALA0-0.024-0.0125.3310.6280.6280.0000.0000.0000.000
92A92ALA0-0.020-0.0026.452-0.024-0.0240.0000.0000.0000.000
93A93TRP00.0350.0073.952-0.337-0.0780.001-0.024-0.2350.000
94A94VAL00.0370.0062.761-0.106-1.3594.479-0.825-2.4000.004
95A95ARG10.8620.9275.949-0.605-0.6050.0000.0000.0000.000
96A96GLN0-0.098-0.0548.082-0.194-0.1940.0000.0000.0000.000
97A97GLN0-0.053-0.0147.227-0.155-0.1550.0000.0000.0000.000
98A98VAL0-0.0490.0035.516-0.157-0.1570.0000.0000.0000.000
99A99PRO00.000-0.0098.8980.1060.1060.0000.0000.0000.000
100A100ALA0-0.0280.0069.5010.0620.0620.0000.0000.0000.000
101A101ARG10.8310.88111.4440.1660.1660.0000.0000.0000.000
102A102VAL0-0.0070.00411.246-0.010-0.0100.0000.0000.0000.000
103A103VAL0-0.0120.00613.9340.0370.0370.0000.0000.0000.000
104A104ALA00.0200.00315.782-0.010-0.0100.0000.0000.0000.000
105A105LEU0-0.0220.00017.8160.0080.0080.0000.0000.0000.000
106A106THR00.0320.01119.9350.0020.0020.0000.0000.0000.000
107A107GLY00.0210.00822.639-0.001-0.0010.0000.0000.0000.000
108A108SER0-0.065-0.02925.8360.0010.0010.0000.0000.0000.000
109A109SER0-0.026-0.01727.8200.0010.0010.0000.0000.0000.000
110A110GLY00.0760.03226.556-0.002-0.0020.0000.0000.0000.000
111A111LYS10.8920.97321.3840.0080.0080.0000.0000.0000.000
112A112THR00.004-0.00320.577-0.004-0.0040.0000.0000.0000.000
113A113SER00.0530.03821.505-0.001-0.0010.0000.0000.0000.000
114A114VAL00.0440.02322.660-0.002-0.0020.0000.0000.0000.000
115A115LYS10.8290.95215.8200.0110.0110.0000.0000.0000.000
116A116GLU-1-0.849-0.95218.941-0.010-0.0100.0000.0000.0000.000
117A117MET0-0.055-0.01220.3370.0000.0000.0000.0000.0000.000
118A118THR00.003-0.02118.929-0.001-0.0010.0000.0000.0000.000
119A119ALA00.001-0.00516.416-0.007-0.0070.0000.0000.0000.000
120A120ALA0-0.0170.01617.886-0.003-0.0030.0000.0000.0000.000
121A121ILE0-0.003-0.00420.6360.0030.0030.0000.0000.0000.000
122A122LEU00.006-0.00117.1090.0010.0010.0000.0000.0000.000
123A123SER0-0.041-0.02817.131-0.008-0.0080.0000.0000.0000.000
124A124GLN0-0.098-0.04218.1010.0080.0080.0000.0000.0000.000
125A125CYS0-0.112-0.04819.0780.0060.0060.0000.0000.0000.000
126A126GLY00.0290.01816.487-0.001-0.0010.0000.0000.0000.000
127A127ASN0-0.029-0.0239.7290.0550.0550.0000.0000.0000.000
128A128THR0-0.0280.00512.228-0.063-0.0630.0000.0000.0000.000
129A129LEU00.0160.0266.5080.0730.0730.0000.0000.0000.000
130A130TYR00.0130.00610.625-0.001-0.0010.0000.0000.0000.000
131A131THR00.0510.02111.5670.0020.0020.0000.0000.0000.000
132A132ALA00.0070.01411.8500.0180.0180.0000.0000.0000.000
133A133GLY00.0210.00213.5310.0030.0030.0000.0000.0000.000
134A134ASN0-0.076-0.05417.006-0.007-0.0070.0000.0000.0000.000
135A135LEU0-0.0060.01912.0410.0030.0030.0000.0000.0000.000
136A136ASN0-0.045-0.04114.079-0.009-0.0090.0000.0000.0000.000
137A137ASN00.0680.03416.2660.0000.0000.0000.0000.0000.000
138A138ASP-1-0.772-0.87914.9450.0040.0040.0000.0000.0000.000
139A139ILE0-0.0120.00612.2480.0070.0070.0000.0000.0000.000
140A140GLY00.025-0.01111.3030.0090.0090.0000.0000.0000.000
141A141VAL00.0380.03211.287-0.018-0.0180.0000.0000.0000.000
142A142PRO00.0360.0348.252-0.033-0.0330.0000.0000.0000.000
143A143MET00.004-0.0017.0350.0250.0250.0000.0000.0000.000
144A144THR0-0.094-0.0506.738-0.065-0.0650.0000.0000.0000.000
145A145LEU0-0.005-0.0146.543-0.249-0.2490.0000.0000.0000.000
146A146LEU00.0320.0072.316-1.947-0.9542.390-0.668-2.7150.000
147A147ARG10.8230.9311.890-4.923-7.89811.315-4.181-4.160-0.038
148A148LEU0-0.049-0.0143.1320.2790.8670.222-0.028-0.782-0.001
149A149THR00.024-0.0061.955-6.741-8.6337.684-3.073-2.719-0.021
150A150PRO00.008-0.0154.1950.5220.6820.000-0.045-0.1140.000
151A151GLU-1-0.851-0.9017.292-0.348-0.3480.0000.0000.0000.000
152A152TYR0-0.090-0.0185.7140.2600.2600.0000.0000.0000.000
153A153ASP-1-0.813-0.8989.204-0.195-0.1950.0000.0000.0000.000
154A154TYR0-0.044-0.02812.2410.0260.0260.0000.0000.0000.000
155A155ALA00.0270.00410.058-0.050-0.0500.0000.0000.0000.000
156A156VAL0-0.042-0.02111.9430.0430.0430.0000.0000.0000.000
157A157ILE00.014-0.00810.3490.0070.0070.0000.0000.0000.000
158A158GLU-1-0.811-0.90914.0820.0030.0030.0000.0000.0000.000
159A159LEU00.003-0.01315.3440.0030.0030.0000.0000.0000.000
160A160GLY0-0.032-0.03218.2780.0010.0010.0000.0000.0000.000
161A161ALA0-0.044-0.01920.8030.0010.0010.0000.0000.0000.000
162A162ASN0-0.126-0.04922.6470.0000.0000.0000.0000.0000.000
163A163HIS0-0.047-0.04024.4460.0000.0000.0000.0000.0000.000
164A164GLN0-0.004-0.00125.492-0.001-0.0010.0000.0000.0000.000
165A165GLY0-0.024-0.00923.9860.0010.0010.0000.0000.0000.000
166A166GLU-1-0.741-0.87720.661-0.001-0.0010.0000.0000.0000.000
167A167ILE00.0200.00819.5160.0020.0020.0000.0000.0000.000
168A168ALA0-0.010-0.00619.8430.0000.0000.0000.0000.0000.000
169A169TRP00.0180.02212.9780.0020.0020.0000.0000.0000.000
170A170THR00.0620.03815.0720.0050.0050.0000.0000.0000.000
171A171VAL0-0.0100.01415.3140.0000.0000.0000.0000.0000.000
172A172SER0-0.126-0.05916.349-0.001-0.0010.0000.0000.0000.000
173A173LEU0-0.0050.00111.0490.0020.0020.0000.0000.0000.000
174A174THR0-0.005-0.02712.3490.0130.0130.0000.0000.0000.000
175A175ARG10.8750.97013.436-0.019-0.0190.0000.0000.0000.000
176A176PRO0-0.029-0.00115.879-0.016-0.0160.0000.0000.0000.000
177A177GLU-1-0.766-0.87316.943-0.106-0.1060.0000.0000.0000.000
178A178ALA00.008-0.00719.3470.0100.0100.0000.0000.0000.000
179A179ALA00.0080.01519.944-0.006-0.0060.0000.0000.0000.000
180A180LEU00.0170.01122.0350.0040.0040.0000.0000.0000.000
181A181VAL0-0.0060.00923.6080.0010.0010.0000.0000.0000.000
182A182ASN0-0.011-0.02425.7930.0000.0000.0000.0000.0000.000
183A183ASN0-0.008-0.01127.5720.0020.0020.0000.0000.0000.000
184A184LEU00.0260.02429.5480.0000.0000.0000.0000.0000.000
185A185ALA00.0200.01532.2050.0000.0000.0000.0000.0000.000
186A194SER00.0480.00435.8350.0000.0000.0000.0000.0000.000
187A195LEU00.0410.02534.7180.0000.0000.0000.0000.0000.000
188A196ALA00.0700.03334.593-0.001-0.0010.0000.0000.0000.000
189A197GLY00.0180.01433.326-0.001-0.0010.0000.0000.0000.000
190A198VAL00.015-0.00530.4440.0000.0000.0000.0000.0000.000
191A199ALA00.0170.00929.871-0.001-0.0010.0000.0000.0000.000
192A200LYS10.9090.94829.3920.0070.0070.0000.0000.0000.000
193A201ALA00.0070.00726.677-0.001-0.0010.0000.0000.0000.000
194A202LYS10.8820.93825.6030.0080.0080.0000.0000.0000.000
195A203GLY00.0300.01825.895-0.002-0.0020.0000.0000.0000.000
196A204GLU-1-0.807-0.91524.060-0.009-0.0090.0000.0000.0000.000
197A205ILE0-0.0080.01420.4510.0000.0000.0000.0000.0000.000
198A206PHE0-0.002-0.01722.283-0.003-0.0030.0000.0000.0000.000
199A207SER0-0.058-0.03523.2180.0000.0000.0000.0000.0000.000
200A208GLY0-0.002-0.01119.8100.0030.0030.0000.0000.0000.000
201A209LEU0-0.0380.00419.584-0.004-0.0040.0000.0000.0000.000
202A210PRO00.0380.02719.9780.0060.0060.0000.0000.0000.000
203A211GLU-1-0.901-0.95622.324-0.023-0.0230.0000.0000.0000.000
204A212ASN0-0.034-0.01021.9660.0040.0040.0000.0000.0000.000
205A213GLY00.021-0.00223.361-0.004-0.0040.0000.0000.0000.000
206A214ILE0-0.051-0.02423.7730.0050.0050.0000.0000.0000.000
207A215ALA00.0320.02324.557-0.003-0.0030.0000.0000.0000.000
208A216ILE00.0030.00624.3050.0020.0020.0000.0000.0000.000
209A217MET0-0.041-0.02527.3260.0010.0010.0000.0000.0000.000
210A218ASN00.0300.01629.9000.0000.0000.0000.0000.0000.000
211A219ALA0-0.0020.00432.2160.0010.0010.0000.0000.0000.000
212A220ASP-1-0.818-0.88535.651-0.010-0.0100.0000.0000.0000.000
213A221ASN0-0.105-0.06533.8890.0010.0010.0000.0000.0000.000
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