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: 49G2N

Calculation Name: 3PG4-A-Xray372

Preferred Name: Beta-lactamase NDM-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3PG4

Chain ID: A

ChEMBL ID: CHEMBL1667695

UniProt ID: C7C422

Base Structure: X-ray

Registration Date: 2023-06-26

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2676988.635793
FMO2-HF: Nuclear repulsion 2590985.270256
FMO2-HF: Total energy -86003.365537
FMO2-MP2: Total energy -86253.879753


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:48:SER)


Summations of interaction energy for fragment #1(A:48: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.
1.5173.673-0.002-0.798-1.3590.001
Interaction energy analysis for fragmet #1(A:48:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.016
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].
3A50VAL0-0.018-0.0073.8081.6732.857-0.014-0.508-0.6620.002
4A51PHE00.0480.0236.308-0.143-0.1430.0000.0000.0000.000
5A52ARG10.9650.9859.9720.3900.3900.0000.0000.0000.000
6A53GLN0-0.0130.00013.097-0.008-0.0080.0000.0000.0000.000
7A54LEU0-0.076-0.04216.5670.0050.0050.0000.0000.0000.000
8A55ALA00.0410.01619.2820.0170.0170.0000.0000.0000.000
9A56PRO00.0250.00820.918-0.002-0.0020.0000.0000.0000.000
10A57ASN0-0.056-0.03421.5770.0100.0100.0000.0000.0000.000
11A58VAL00.0490.03718.922-0.011-0.0110.0000.0000.0000.000
12A59TRP00.0380.01614.2140.0130.0130.0000.0000.0000.000
13A60GLN0-0.023-0.01811.7100.0950.0950.0000.0000.0000.000
14A61HIS0-0.070-0.0249.745-0.149-0.1490.0000.0000.0000.000
15A62THR00.021-0.0157.0470.1990.1990.0000.0000.0000.000
16A63SER00.0070.0165.103-0.832-0.8320.0000.0000.0000.000
17A64TYR0-0.002-0.0223.6040.7971.1210.001-0.044-0.2820.000
18A65LEU00.0320.0185.6470.2020.2020.0000.0000.0000.000
19A66ASP-1-0.924-0.9558.2190.4050.4050.0000.0000.0000.000
20A67MET0-0.012-0.00210.020-0.071-0.0710.0000.0000.0000.000
21A68PRO00.0700.02713.5280.0280.0280.0000.0000.0000.000
22A69GLY0-0.025-0.01216.457-0.027-0.0270.0000.0000.0000.000
23A70PHE0-0.073-0.04314.837-0.007-0.0070.0000.0000.0000.000
24A71GLY00.0260.03412.3060.0020.0020.0000.0000.0000.000
25A72ALA00.004-0.0056.940-0.074-0.0740.0000.0000.0000.000
26A73VAL00.0050.0088.904-0.126-0.1260.0000.0000.0000.000
27A74ALA00.0190.0108.192-0.202-0.2020.0000.0000.0000.000
28A75SER0-0.0080.0048.9540.3270.3270.0000.0000.0000.000
29A76ASN0-0.023-0.0159.913-0.412-0.4120.0000.0000.0000.000
30A77GLY00.0850.05412.3900.1000.1000.0000.0000.0000.000
31A78LEU0-0.063-0.03414.445-0.004-0.0040.0000.0000.0000.000
32A79ILE00.0120.01811.849-0.003-0.0030.0000.0000.0000.000
33A80VAL00.0180.00116.4950.0230.0230.0000.0000.0000.000
34A81ARG10.9290.98720.0700.0570.0570.0000.0000.0000.000
35A82ASP-1-0.843-0.93421.739-0.087-0.0870.0000.0000.0000.000
36A83GLY00.0260.01325.2610.0030.0030.0000.0000.0000.000
37A84GLY0-0.001-0.00625.5230.0040.0040.0000.0000.0000.000
38A85ARG10.7870.87823.5160.0980.0980.0000.0000.0000.000
39A86VAL00.0080.01217.1850.0010.0010.0000.0000.0000.000
40A87LEU0-0.018-0.01120.469-0.003-0.0030.0000.0000.0000.000
41A88VAL00.002-0.00415.009-0.008-0.0080.0000.0000.0000.000
42A89VAL0-0.0290.00417.2610.0260.0260.0000.0000.0000.000
43A90ASP-1-0.732-0.88615.942-0.425-0.4250.0000.0000.0000.000
44A91THR0-0.0080.00713.3550.0060.0060.0000.0000.0000.000
45A92ALA0-0.037-0.0108.151-0.072-0.0720.0000.0000.0000.000
46A93TRP00.017-0.0157.8280.3590.3590.0000.0000.0000.000
47A94THR00.0570.0197.8010.1540.1540.0000.0000.0000.000
48A95ASP-1-0.733-0.86410.128-0.530-0.5300.0000.0000.0000.000
49A96ASP-1-0.905-0.9428.185-0.573-0.5730.0000.0000.0000.000
50A97GLN0-0.009-0.0063.9180.0430.178-0.001-0.018-0.1170.000
51A98THR00.031-0.0066.8140.1150.1150.0000.0000.0000.000
52A99ALA00.0240.0189.8440.1320.1320.0000.0000.0000.000
53A100GLN0-0.030-0.0263.281-1.192-0.6790.012-0.228-0.298-0.001
54A101ILE0-0.018-0.0037.2120.3220.3220.0000.0000.0000.000
55A102LEU00.0030.0029.0020.1460.1460.0000.0000.0000.000
56A103ASN00.0010.0019.1650.0140.0140.0000.0000.0000.000
57A104TRP00.0300.0098.332-0.026-0.0260.0000.0000.0000.000
58A105ILE00.0230.01810.3280.0020.0020.0000.0000.0000.000
59A106LYS10.8470.93313.7070.0090.0090.0000.0000.0000.000
60A107GLN0-0.047-0.04212.260-0.030-0.0300.0000.0000.0000.000
61A108GLU-1-0.927-0.95712.3460.2760.2760.0000.0000.0000.000
62A109ILE0-0.085-0.04715.278-0.029-0.0290.0000.0000.0000.000
63A110ASN0-0.040-0.00517.225-0.012-0.0120.0000.0000.0000.000
64A111LEU0-0.030-0.00918.964-0.003-0.0030.0000.0000.0000.000
65A112PRO0-0.0050.00719.365-0.010-0.0100.0000.0000.0000.000
66A113VAL00.0320.00416.442-0.001-0.0010.0000.0000.0000.000
67A114ALA0-0.038-0.01419.920-0.001-0.0010.0000.0000.0000.000
68A115LEU0-0.029-0.01521.7570.0040.0040.0000.0000.0000.000
69A116ALA00.0210.01218.484-0.012-0.0120.0000.0000.0000.000
70A117VAL0-0.028-0.01320.3440.0210.0210.0000.0000.0000.000
71A118VAL00.0230.01518.449-0.033-0.0330.0000.0000.0000.000
72A119THR0-0.061-0.08019.6790.0300.0300.0000.0000.0000.000
73A120HIS0-0.002-0.01218.2060.0420.0420.0000.0000.0000.000
74A121ALA00.0400.00920.884-0.026-0.0260.0000.0000.0000.000
75A122HIS10.8050.88618.8140.2240.2240.0000.0000.0000.000
76A123GLN00.0890.03913.0950.0130.0130.0000.0000.0000.000
77A124ASP-1-0.881-0.95213.075-0.466-0.4660.0000.0000.0000.000
78A125LYS10.7430.85713.7230.4960.4960.0000.0000.0000.000
79A126MET0-0.0190.00116.1450.0180.0180.0000.0000.0000.000
80A127GLY00.0540.04213.8160.0410.0410.0000.0000.0000.000
81A128GLY0-0.049-0.02613.318-0.011-0.0110.0000.0000.0000.000
82A129MET0-0.025-0.00514.0530.0160.0160.0000.0000.0000.000
83A130ASP-1-0.827-0.91617.317-0.191-0.1910.0000.0000.0000.000
84A131ALA0-0.036-0.02113.2760.0270.0270.0000.0000.0000.000
85A132LEU0-0.040-0.02415.2820.0310.0310.0000.0000.0000.000
86A133HIS00.0470.03217.1160.0330.0330.0000.0000.0000.000
87A134ALA0-0.0110.01517.3140.0250.0250.0000.0000.0000.000
88A135ALA0-0.058-0.02216.6530.0210.0210.0000.0000.0000.000
89A136GLY0-0.021-0.01018.7940.0170.0170.0000.0000.0000.000
90A137ILE0-0.070-0.02117.1150.0080.0080.0000.0000.0000.000
91A138ALA0-0.020-0.00221.250-0.007-0.0070.0000.0000.0000.000
92A139THR00.021-0.01020.359-0.002-0.0020.0000.0000.0000.000
93A140TYR0-0.028-0.03023.0960.0220.0220.0000.0000.0000.000
94A141ALA00.0800.04423.772-0.022-0.0220.0000.0000.0000.000
95A142ASN00.0190.00925.5080.0250.0250.0000.0000.0000.000
96A143ALA00.0380.01028.165-0.004-0.0040.0000.0000.0000.000
97A144LEU0-0.017-0.01029.8840.0010.0010.0000.0000.0000.000
98A145SER00.018-0.03624.6840.0010.0010.0000.0000.0000.000
99A146ASN0-0.014-0.01426.122-0.016-0.0160.0000.0000.0000.000
100A147GLN0-0.061-0.03127.5450.0030.0030.0000.0000.0000.000
101A148LEU00.0070.00626.8620.0060.0060.0000.0000.0000.000
102A149ALA0-0.003-0.00823.519-0.001-0.0010.0000.0000.0000.000
103A150PRO00.0250.02324.597-0.002-0.0020.0000.0000.0000.000
104A151GLN0-0.024-0.00426.4310.0060.0060.0000.0000.0000.000
105A152GLU-1-0.899-0.92522.080-0.183-0.1830.0000.0000.0000.000
106A153GLY0-0.012-0.00622.487-0.014-0.0140.0000.0000.0000.000
107A154MET0-0.078-0.01417.697-0.032-0.0320.0000.0000.0000.000
108A155VAL00.0070.00820.4500.0210.0210.0000.0000.0000.000
109A156ALA0-0.011-0.01221.869-0.015-0.0150.0000.0000.0000.000
110A157ALA00.006-0.01723.465-0.006-0.0060.0000.0000.0000.000
111A158GLN0-0.001-0.00624.2190.0200.0200.0000.0000.0000.000
112A159HIS10.8270.91926.6720.1380.1380.0000.0000.0000.000
113A160SER00.0480.01927.812-0.014-0.0140.0000.0000.0000.000
114A161LEU0-0.041-0.00327.0300.0060.0060.0000.0000.0000.000
115A162THR0-0.017-0.03530.924-0.003-0.0030.0000.0000.0000.000
116A163PHE0-0.005-0.01829.161-0.003-0.0030.0000.0000.0000.000
117A164ALA00.0500.03935.2950.0050.0050.0000.0000.0000.000
118A165ALA00.0270.00337.622-0.003-0.0030.0000.0000.0000.000
119A166ASN0-0.048-0.02938.253-0.004-0.0040.0000.0000.0000.000
120A167GLY00.0850.05134.649-0.002-0.0020.0000.0000.0000.000
121A168TRP0-0.041-0.00731.366-0.010-0.0100.0000.0000.0000.000
122A169VAL0-0.0030.00030.7880.0030.0030.0000.0000.0000.000
123A170GLU-1-0.852-0.89933.544-0.075-0.0750.0000.0000.0000.000
124A171PRO00.017-0.00834.792-0.003-0.0030.0000.0000.0000.000
125A172ALA0-0.030-0.00834.793-0.002-0.0020.0000.0000.0000.000
126A173THR0-0.033-0.01532.615-0.003-0.0030.0000.0000.0000.000
127A174ALA0-0.011-0.00330.062-0.008-0.0080.0000.0000.0000.000
128A175PRO0-0.0070.00630.6890.0040.0040.0000.0000.0000.000
129A176ASN0-0.002-0.02129.961-0.008-0.0080.0000.0000.0000.000
130A177PHE00.1020.04926.762-0.005-0.0050.0000.0000.0000.000
131A178GLY00.0440.03727.202-0.007-0.0070.0000.0000.0000.000
132A179PRO0-0.025-0.01225.5460.0030.0030.0000.0000.0000.000
133A180LEU0-0.0020.00822.574-0.005-0.0050.0000.0000.0000.000
134A181LYS10.8350.93226.7570.1050.1050.0000.0000.0000.000
135A182VAL00.0210.00526.474-0.008-0.0080.0000.0000.0000.000
136A183PHE00.0080.00428.3120.0110.0110.0000.0000.0000.000
137A184TYR00.005-0.01628.777-0.010-0.0100.0000.0000.0000.000
138A185PRO0-0.076-0.03428.2690.0080.0080.0000.0000.0000.000
139A186GLY00.0620.04431.3820.0080.0080.0000.0000.0000.000
140A187PRO0-0.008-0.01530.628-0.010-0.0100.0000.0000.0000.000
141A188GLY00.0280.01128.6770.0060.0060.0000.0000.0000.000
142A189HIS0-0.065-0.02221.241-0.006-0.0060.0000.0000.0000.000
143A190THR00.0580.01423.6780.0020.0020.0000.0000.0000.000
144A191SER00.0640.01826.7300.0040.0040.0000.0000.0000.000
145A192ASP-1-0.768-0.83225.460-0.175-0.1750.0000.0000.0000.000
146A193ASN0-0.0010.01624.744-0.008-0.0080.0000.0000.0000.000
147A194ILE0-0.0280.00424.6990.0180.0180.0000.0000.0000.000
148A195THR0-0.074-0.03724.166-0.015-0.0150.0000.0000.0000.000
149A196VAL00.012-0.00723.1890.0120.0120.0000.0000.0000.000
150A197GLY00.0340.03524.411-0.010-0.0100.0000.0000.0000.000
151A198ILE0-0.029-0.01321.4950.0010.0010.0000.0000.0000.000
152A199ASP-1-0.855-0.94226.160-0.080-0.0800.0000.0000.0000.000
153A200GLY00.0030.00728.409-0.001-0.0010.0000.0000.0000.000
154A201THR0-0.078-0.04924.740-0.002-0.0020.0000.0000.0000.000
155A202ASP-1-0.819-0.88026.820-0.089-0.0890.0000.0000.0000.000
156A203ILE0-0.038-0.02721.127-0.007-0.0070.0000.0000.0000.000
157A204ALA0-0.0020.00123.8850.0090.0090.0000.0000.0000.000
158A205PHE0-0.031-0.00816.6760.0010.0010.0000.0000.0000.000
159A206GLY00.0560.00921.6090.0170.0170.0000.0000.0000.000
160A207GLY00.0610.03219.4140.0130.0130.0000.0000.0000.000
161A208CYS0-0.047-0.01218.811-0.027-0.0270.0000.0000.0000.000
162A209LEU00.0000.03220.6930.0170.0170.0000.0000.0000.000
163A210ILE0-0.048-0.00923.2180.0180.0180.0000.0000.0000.000
164A211LYS10.8660.93521.2880.1660.1660.0000.0000.0000.000
165A212ASP-1-0.757-0.87719.850-0.183-0.1830.0000.0000.0000.000
166A213SER0-0.070-0.08622.1160.0190.0190.0000.0000.0000.000
167A214LYS10.8470.92322.2860.1290.1290.0000.0000.0000.000
168A215ALA00.0160.03222.3460.0100.0100.0000.0000.0000.000
169A216LYS10.9430.96123.6240.0820.0820.0000.0000.0000.000
170A217SER00.0110.00125.0300.0050.0050.0000.0000.0000.000
171A218LEU00.0330.01324.682-0.011-0.0110.0000.0000.0000.000
172A219GLY0-0.0060.00922.578-0.015-0.0150.0000.0000.0000.000
173A220ASN0-0.005-0.01221.2580.0210.0210.0000.0000.0000.000
174A221LEU00.012-0.01824.288-0.009-0.0090.0000.0000.0000.000
175A222GLY0-0.0250.00226.4030.0060.0060.0000.0000.0000.000
176A223ASP-1-0.808-0.90324.696-0.147-0.1470.0000.0000.0000.000
177A224ALA0-0.056-0.01527.372-0.002-0.0020.0000.0000.0000.000
178A225ASP-1-0.796-0.86928.891-0.078-0.0780.0000.0000.0000.000
179A226THR0-0.015-0.04331.5080.0000.0000.0000.0000.0000.000
180A227GLU-1-0.829-0.89633.497-0.060-0.0600.0000.0000.0000.000
181A228HIS0-0.060-0.05734.6470.0060.0060.0000.0000.0000.000
182A229TYR0-0.001-0.00325.402-0.005-0.0050.0000.0000.0000.000
183A230ALA00.019-0.00731.636-0.005-0.0050.0000.0000.0000.000
184A231ALA0-0.024-0.01433.533-0.002-0.0020.0000.0000.0000.000
185A232SER00.0540.01730.7150.0020.0020.0000.0000.0000.000
186A233ALA0-0.014-0.01229.379-0.006-0.0060.0000.0000.0000.000
187A234ARG10.7630.82230.3200.0740.0740.0000.0000.0000.000
188A235ALA00.0140.02732.9700.0020.0020.0000.0000.0000.000
189A236PHE00.0490.01825.0960.0000.0000.0000.0000.0000.000
190A237GLY0-0.024-0.01830.3470.0000.0000.0000.0000.0000.000
191A238ALA0-0.036-0.02431.5120.0040.0040.0000.0000.0000.000
192A239ALA00.0060.03131.5130.0050.0050.0000.0000.0000.000
193A240PHE00.0100.00528.2270.0030.0030.0000.0000.0000.000
194A241PRO0-0.0120.00131.015-0.003-0.0030.0000.0000.0000.000
195A242LYS10.9140.93932.8410.0690.0690.0000.0000.0000.000
196A243ALA00.0170.04427.1550.0020.0020.0000.0000.0000.000
197A244SER0-0.040-0.05527.885-0.001-0.0010.0000.0000.0000.000
198A245MET0-0.020-0.00121.112-0.010-0.0100.0000.0000.0000.000
199A246ILE0-0.007-0.01022.649-0.005-0.0050.0000.0000.0000.000
200A247VAL00.0190.00716.889-0.013-0.0130.0000.0000.0000.000
201A248MET0-0.029-0.00117.7570.0280.0280.0000.0000.0000.000
202A249SER00.0450.00615.542-0.065-0.0650.0000.0000.0000.000
203A250HIS10.7720.86812.9490.4060.4060.0000.0000.0000.000
204A251SER00.0090.00514.6930.0060.0060.0000.0000.0000.000
205A252ALA0-0.024-0.01014.675-0.035-0.0350.0000.0000.0000.000
206A253PRO0-0.010-0.01515.4370.0390.0390.0000.0000.0000.000
207A254ASP-1-0.741-0.81918.585-0.129-0.1290.0000.0000.0000.000
208A255SER00.0170.00921.9860.0070.0070.0000.0000.0000.000
209A256ARG10.8640.89925.7130.0950.0950.0000.0000.0000.000
210A257ALA0-0.032-0.01427.4670.0030.0030.0000.0000.0000.000
211A258ALA00.0390.02224.0050.0060.0060.0000.0000.0000.000
212A259ILE00.0150.01925.9430.0000.0000.0000.0000.0000.000
213A260THR0-0.031-0.02028.2630.0070.0070.0000.0000.0000.000
214A261HIS0-0.047-0.03026.1710.0110.0110.0000.0000.0000.000
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216A263ALA00.014-0.00528.2930.0040.0040.0000.0000.0000.000
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