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: K9QY3

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2677152.847697
FMO2-HF: Nuclear repulsion 2591150.276461
FMO2-HF: Total energy -86002.571236
FMO2-MP2: Total energy -86253.131109


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.
1.8244.1090.072-0.832-1.5250
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 : -0.013 / q_NPA : -0.017
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].
3A50VAL0-0.0080.0043.8081.5042.709-0.015-0.517-0.6730.002
4A51PHE00.0480.0216.385-0.097-0.0970.0000.0000.0000.000
5A52ARG10.9490.9779.9720.3810.3810.0000.0000.0000.000
6A53GLN0-0.0060.00613.115-0.007-0.0070.0000.0000.0000.000
7A54LEU0-0.078-0.04816.4520.0000.0000.0000.0000.0000.000
8A55ALA00.0440.02019.2980.0150.0150.0000.0000.0000.000
9A56PRO00.0120.00420.918-0.001-0.0010.0000.0000.0000.000
10A57ASN0-0.048-0.02521.6070.0100.0100.0000.0000.0000.000
11A58VAL00.0460.03218.890-0.009-0.0090.0000.0000.0000.000
12A59TRP00.0420.01814.1660.0100.0100.0000.0000.0000.000
13A60GLN00.002-0.00612.2560.0650.0650.0000.0000.0000.000
14A61HIS0-0.076-0.0109.772-0.131-0.1310.0000.0000.0000.000
15A62THR00.022-0.0266.8560.1910.1910.0000.0000.0000.000
16A63SER0-0.0100.0075.013-0.817-0.8170.0000.0000.0000.000
17A64TYR0-0.001-0.0243.3990.6871.0410.003-0.053-0.3040.000
18A65LEU00.0350.0195.6130.2540.2540.0000.0000.0000.000
19A66ASP-1-0.922-0.9558.2050.5130.5130.0000.0000.0000.000
20A67MET0-0.018-0.00410.008-0.069-0.0690.0000.0000.0000.000
21A68PRO00.0560.02513.5410.0250.0250.0000.0000.0000.000
22A69GLY0-0.011-0.01016.446-0.027-0.0270.0000.0000.0000.000
23A70PHE0-0.072-0.04114.863-0.010-0.0100.0000.0000.0000.000
24A71GLY00.0240.03312.350-0.001-0.0010.0000.0000.0000.000
25A72ALA00.002-0.0077.002-0.057-0.0570.0000.0000.0000.000
26A73VAL00.0110.0138.935-0.133-0.1330.0000.0000.0000.000
27A74ALA00.0090.0038.171-0.180-0.1800.0000.0000.0000.000
28A75SER0-0.013-0.0078.8910.3150.3150.0000.0000.0000.000
29A76ASN0-0.0330.0009.837-0.400-0.4000.0000.0000.0000.000
30A77GLY00.0980.03712.3130.0950.0950.0000.0000.0000.000
31A78LEU0-0.051-0.02914.355-0.005-0.0050.0000.0000.0000.000
32A79ILE00.0130.02112.007-0.001-0.0010.0000.0000.0000.000
33A80VAL00.0180.00116.5700.0190.0190.0000.0000.0000.000
34A81ARG10.9460.99420.1470.0460.0460.0000.0000.0000.000
35A82ASP-1-0.846-0.92921.816-0.075-0.0750.0000.0000.0000.000
36A83GLY00.0170.00825.3370.0030.0030.0000.0000.0000.000
37A84GLY0-0.001-0.00525.5970.0040.0040.0000.0000.0000.000
38A85ARG10.8160.88623.5640.0830.0830.0000.0000.0000.000
39A86VAL00.0130.01717.2410.0000.0000.0000.0000.0000.000
40A87LEU0-0.029-0.01520.537-0.003-0.0030.0000.0000.0000.000
41A88VAL00.0100.00215.118-0.006-0.0060.0000.0000.0000.000
42A89VAL0-0.0350.00417.3210.0220.0220.0000.0000.0000.000
43A90ASP-1-0.715-0.88215.654-0.386-0.3860.0000.0000.0000.000
44A91THR0-0.0180.00013.2740.0080.0080.0000.0000.0000.000
45A92ALA0-0.052-0.0178.075-0.069-0.0690.0000.0000.0000.000
46A93TRP00.001-0.0177.6340.3320.3320.0000.0000.0000.000
47A94THR00.0500.0247.6730.1460.1460.0000.0000.0000.000
48A95ASP-1-0.735-0.87310.059-0.458-0.4580.0000.0000.0000.000
49A96ASP-1-0.896-0.9388.003-0.475-0.4750.0000.0000.0000.000
50A97GLN0-0.024-0.0253.854-0.0120.120-0.001-0.017-0.1150.000
51A98THR00.0330.0046.8410.1340.1340.0000.0000.0000.000
52A99ALA00.0310.0199.7990.1250.1250.0000.0000.0000.000
53A100GLN0-0.039-0.0282.714-0.749-0.1550.085-0.245-0.433-0.002
54A101ILE0-0.020-0.0057.2580.3050.3050.0000.0000.0000.000
55A102LEU00.0050.0029.0680.1250.1250.0000.0000.0000.000
56A103ASN00.0000.0038.951-0.014-0.0140.0000.0000.0000.000
57A104TRP00.0180.0078.446-0.030-0.0300.0000.0000.0000.000
58A105ILE00.0180.01510.394-0.016-0.0160.0000.0000.0000.000
59A106LYS10.8190.91613.777-0.017-0.0170.0000.0000.0000.000
60A107GLN0-0.019-0.03012.244-0.041-0.0410.0000.0000.0000.000
61A108GLU-1-0.941-0.96612.4880.2620.2620.0000.0000.0000.000
62A109ILE0-0.086-0.04115.278-0.034-0.0340.0000.0000.0000.000
63A110ASN0-0.0100.01117.290-0.017-0.0170.0000.0000.0000.000
64A111LEU0-0.035-0.01319.029-0.006-0.0060.0000.0000.0000.000
65A112PRO0-0.0150.00419.431-0.006-0.0060.0000.0000.0000.000
66A113VAL00.0450.01016.545-0.001-0.0010.0000.0000.0000.000
67A114ALA0-0.037-0.01519.986-0.001-0.0010.0000.0000.0000.000
68A115LEU0-0.032-0.01721.8170.0030.0030.0000.0000.0000.000
69A116ALA00.0190.01318.573-0.010-0.0100.0000.0000.0000.000
70A117VAL0-0.020-0.00820.4050.0180.0180.0000.0000.0000.000
71A118VAL00.0290.01018.535-0.030-0.0300.0000.0000.0000.000
72A119THR0-0.088-0.10319.5810.0290.0290.0000.0000.0000.000
73A120HIS0-0.019-0.01618.0260.0380.0380.0000.0000.0000.000
74A121ALA00.0770.01220.828-0.023-0.0230.0000.0000.0000.000
75A122HIS10.8660.94718.4520.2080.2080.0000.0000.0000.000
76A123GLN00.1160.05113.702-0.036-0.0360.0000.0000.0000.000
77A124ASP-1-0.904-0.97813.043-0.420-0.4200.0000.0000.0000.000
78A125LYS10.7240.86313.5430.4730.4730.0000.0000.0000.000
79A126MET00.0000.04116.0880.0170.0170.0000.0000.0000.000
80A127GLY00.0760.05113.7660.0370.0370.0000.0000.0000.000
81A128GLY0-0.056-0.03213.271-0.008-0.0080.0000.0000.0000.000
82A129MET0-0.033-0.00713.9820.0160.0160.0000.0000.0000.000
83A130ASP-1-0.846-0.91917.107-0.165-0.1650.0000.0000.0000.000
84A131ALA0-0.041-0.02113.3400.0240.0240.0000.0000.0000.000
85A132LEU0-0.038-0.02415.2050.0300.0300.0000.0000.0000.000
86A133HIS00.0420.03817.1600.0290.0290.0000.0000.0000.000
87A134ALA0-0.0110.01517.3320.0220.0220.0000.0000.0000.000
88A135ALA0-0.060-0.02116.7110.0190.0190.0000.0000.0000.000
89A136GLY0-0.024-0.01318.8340.0140.0140.0000.0000.0000.000
90A137ILE0-0.067-0.01917.1550.0070.0070.0000.0000.0000.000
91A138ALA0-0.0140.00121.302-0.007-0.0070.0000.0000.0000.000
92A139THR00.026-0.01620.307-0.002-0.0020.0000.0000.0000.000
93A140TYR0-0.035-0.03323.1470.0200.0200.0000.0000.0000.000
94A141ALA00.0770.04123.734-0.020-0.0200.0000.0000.0000.000
95A142ASN00.0360.02625.4370.0230.0230.0000.0000.0000.000
96A143ALA00.0390.01028.101-0.004-0.0040.0000.0000.0000.000
97A144LEU0-0.015-0.00929.7000.0010.0010.0000.0000.0000.000
98A145SER0-0.004-0.06824.6570.0000.0000.0000.0000.0000.000
99A146ASN00.006-0.00626.036-0.016-0.0160.0000.0000.0000.000
100A147GLN0-0.073-0.03927.4830.0020.0020.0000.0000.0000.000
101A148LEU00.0030.00926.7510.0050.0050.0000.0000.0000.000
102A149ALA00.016-0.00323.552-0.001-0.0010.0000.0000.0000.000
103A150PRO00.0140.01824.551-0.001-0.0010.0000.0000.0000.000
104A151GLN0-0.022-0.00826.3900.0040.0040.0000.0000.0000.000
105A152GLU-1-0.944-0.96422.561-0.150-0.1500.0000.0000.0000.000
106A153GLY0-0.030-0.01522.452-0.012-0.0120.0000.0000.0000.000
107A154MET0-0.082-0.01117.492-0.027-0.0270.0000.0000.0000.000
108A155VAL00.0150.01120.2990.0190.0190.0000.0000.0000.000
109A156ALA0-0.008-0.01121.806-0.014-0.0140.0000.0000.0000.000
110A157ALA0-0.003-0.02223.404-0.005-0.0050.0000.0000.0000.000
111A158GLN0-0.001-0.01024.2610.0150.0150.0000.0000.0000.000
112A159HIS10.8440.92926.7280.1160.1160.0000.0000.0000.000
113A160SER00.0460.01627.784-0.013-0.0130.0000.0000.0000.000
114A161LEU0-0.048-0.00726.9130.0060.0060.0000.0000.0000.000
115A162THR0-0.004-0.03530.851-0.003-0.0030.0000.0000.0000.000
116A163PHE0-0.019-0.02429.128-0.002-0.0020.0000.0000.0000.000
117A164ALA00.0530.04135.2280.0040.0040.0000.0000.0000.000
118A165ALA00.0210.00137.537-0.003-0.0030.0000.0000.0000.000
119A166ASN0-0.047-0.02938.284-0.003-0.0030.0000.0000.0000.000
120A167GLY00.0860.04834.566-0.002-0.0020.0000.0000.0000.000
121A168TRP0-0.037-0.00531.240-0.009-0.0090.0000.0000.0000.000
122A169VAL00.0010.00130.9900.0030.0030.0000.0000.0000.000
123A170GLU-1-0.861-0.89233.491-0.065-0.0650.0000.0000.0000.000
124A171PRO00.019-0.00334.872-0.003-0.0030.0000.0000.0000.000
125A172ALA0-0.023-0.00534.857-0.001-0.0010.0000.0000.0000.000
126A173THR0-0.038-0.02132.697-0.002-0.0020.0000.0000.0000.000
127A174ALA0-0.009-0.00130.152-0.007-0.0070.0000.0000.0000.000
128A175PRO0-0.0180.00230.6560.0030.0030.0000.0000.0000.000
129A176ASN0-0.008-0.02530.027-0.006-0.0060.0000.0000.0000.000
130A177PHE00.0920.03627.230-0.004-0.0040.0000.0000.0000.000
131A178GLY00.0280.02827.274-0.006-0.0060.0000.0000.0000.000
132A179PRO0-0.037-0.01625.6880.0020.0020.0000.0000.0000.000
133A180LEU0-0.0050.00722.795-0.005-0.0050.0000.0000.0000.000
134A181LYS10.8900.95926.8290.0930.0930.0000.0000.0000.000
135A182VAL00.0250.00526.714-0.008-0.0080.0000.0000.0000.000
136A183PHE0-0.0020.00128.2270.0100.0100.0000.0000.0000.000
137A184TYR0-0.010-0.02328.694-0.009-0.0090.0000.0000.0000.000
138A185PRO0-0.078-0.03528.2500.0080.0080.0000.0000.0000.000
139A186GLY00.0660.04331.3020.0070.0070.0000.0000.0000.000
140A187PRO00.005-0.00630.559-0.009-0.0090.0000.0000.0000.000
141A188GLY00.0430.02928.6090.0060.0060.0000.0000.0000.000
142A189HIS0-0.053-0.01121.159-0.004-0.0040.0000.0000.0000.000
143A190THR00.0500.01823.6970.0010.0010.0000.0000.0000.000
144A191SER00.0510.00826.6700.0000.0000.0000.0000.0000.000
145A192ASP-1-0.717-0.79325.515-0.156-0.1560.0000.0000.0000.000
146A193ASN0-0.038-0.01324.671-0.007-0.0070.0000.0000.0000.000
147A194ILE0-0.0080.01524.4990.0160.0160.0000.0000.0000.000
148A195THR0-0.079-0.04124.085-0.014-0.0140.0000.0000.0000.000
149A196VAL00.017-0.00323.0490.0120.0120.0000.0000.0000.000
150A197GLY00.0300.02724.327-0.011-0.0110.0000.0000.0000.000
151A198ILE0-0.032-0.01121.5290.0020.0020.0000.0000.0000.000
152A199ASP-1-0.870-0.94326.145-0.073-0.0730.0000.0000.0000.000
153A200GLY0-0.0020.00128.473-0.001-0.0010.0000.0000.0000.000
154A201THR0-0.083-0.05024.833-0.002-0.0020.0000.0000.0000.000
155A202ASP-1-0.877-0.93226.791-0.083-0.0830.0000.0000.0000.000
156A203ILE0-0.028-0.03220.962-0.008-0.0080.0000.0000.0000.000
157A204ALA0-0.0050.00123.8180.0090.0090.0000.0000.0000.000
158A205PHE0-0.031-0.01716.754-0.002-0.0020.0000.0000.0000.000
159A206GLY00.0510.00721.5340.0160.0160.0000.0000.0000.000
160A207GLY00.0660.04019.3490.0130.0130.0000.0000.0000.000
161A208CYS0-0.060-0.03218.870-0.026-0.0260.0000.0000.0000.000
162A209LEU00.0120.03220.6320.0150.0150.0000.0000.0000.000
163A210ILE0-0.0450.00023.1070.0170.0170.0000.0000.0000.000
164A211LYS10.8780.94320.9550.1660.1660.0000.0000.0000.000
165A212ASP-1-0.760-0.90120.019-0.169-0.1690.0000.0000.0000.000
166A213SER0-0.083-0.07822.0840.0190.0190.0000.0000.0000.000
167A214LYS10.8690.94122.2580.1210.1210.0000.0000.0000.000
168A215ALA00.0110.03422.3360.0090.0090.0000.0000.0000.000
169A216LYS10.9500.96523.6100.0770.0770.0000.0000.0000.000
170A217SER00.008-0.00125.0240.0050.0050.0000.0000.0000.000
171A218LEU00.0450.01624.661-0.010-0.0100.0000.0000.0000.000
172A219GLY0-0.0090.00722.553-0.014-0.0140.0000.0000.0000.000
173A220ASN0-0.012-0.01821.0050.0220.0220.0000.0000.0000.000
174A221LEU00.009-0.01924.263-0.008-0.0080.0000.0000.0000.000
175A222GLY0-0.0280.00126.3770.0050.0050.0000.0000.0000.000
176A223ASP-1-0.841-0.91725.249-0.121-0.1210.0000.0000.0000.000
177A224ALA0-0.058-0.02327.378-0.002-0.0020.0000.0000.0000.000
178A225ASP-1-0.803-0.87528.844-0.071-0.0710.0000.0000.0000.000
179A226THR00.014-0.02331.7140.0000.0000.0000.0000.0000.000
180A227GLU-1-0.883-0.91233.455-0.056-0.0560.0000.0000.0000.000
181A228HIS0-0.044-0.04534.6260.0050.0050.0000.0000.0000.000
182A229TYR0-0.016-0.02125.396-0.004-0.0040.0000.0000.0000.000
183A230ALA00.014-0.00631.582-0.005-0.0050.0000.0000.0000.000
184A231ALA0-0.016-0.01233.478-0.002-0.0020.0000.0000.0000.000
185A232SER00.0410.00030.5380.0010.0010.0000.0000.0000.000
186A233ALA0-0.007-0.00829.312-0.006-0.0060.0000.0000.0000.000
187A234ARG10.7670.84230.2610.0690.0690.0000.0000.0000.000
188A235ALA00.0170.02932.8250.0020.0020.0000.0000.0000.000
189A236PHE00.0450.01725.0270.0000.0000.0000.0000.0000.000
190A237GLY0-0.023-0.01930.2760.0000.0000.0000.0000.0000.000
191A238ALA0-0.027-0.01931.4470.0030.0030.0000.0000.0000.000
192A239ALA00.0060.02931.4470.0050.0050.0000.0000.0000.000
193A240PHE00.0050.01028.3760.0020.0020.0000.0000.0000.000
194A241PRO0-0.020-0.00730.945-0.003-0.0030.0000.0000.0000.000
195A242LYS10.9200.94032.7730.0630.0630.0000.0000.0000.000
196A243ALA00.0260.05227.0680.0010.0010.0000.0000.0000.000
197A244SER00.005-0.01427.824-0.001-0.0010.0000.0000.0000.000
198A245MET0-0.0190.00220.950-0.008-0.0080.0000.0000.0000.000
199A246ILE0-0.005-0.01022.671-0.004-0.0040.0000.0000.0000.000
200A247VAL00.0190.01316.845-0.013-0.0130.0000.0000.0000.000
201A248MET0-0.033-0.00417.6950.0270.0270.0000.0000.0000.000
202A249SER00.0460.00415.469-0.058-0.0580.0000.0000.0000.000
203A250HIS10.8050.90213.0390.3630.3630.0000.0000.0000.000
204A251SER00.0270.03414.6610.0060.0060.0000.0000.0000.000
205A252ALA0-0.015-0.00714.692-0.034-0.0340.0000.0000.0000.000
206A253PRO0-0.021-0.02215.3340.0370.0370.0000.0000.0000.000
207A254ASP-1-0.729-0.83018.537-0.132-0.1320.0000.0000.0000.000
208A255SER00.0190.00821.9450.0080.0080.0000.0000.0000.000
209A256ARG10.8640.90425.6690.0890.0890.0000.0000.0000.000
210A257ALA0-0.034-0.01527.4030.0030.0030.0000.0000.0000.000
211A258ALA00.0410.02223.9520.0060.0060.0000.0000.0000.000
212A259ILE00.0140.02125.9030.0010.0010.0000.0000.0000.000
213A260THR0-0.032-0.01928.2130.0070.0070.0000.0000.0000.000
214A261HIS0-0.058-0.03726.0100.0110.0110.0000.0000.0000.000
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