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: 52G7Z

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 OptAll
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 -2678820.377187
FMO2-HF: Nuclear repulsion 2592816.684176
FMO2-HF: Total energy -86003.693011
FMO2-MP2: Total energy -86254.155419


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.
-0.2342.6080.053-1.232-1.661-0.003
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 : -0.009 / 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].
3A50VAL0-0.022-0.0073.8551.2112.383-0.009-0.550-0.6120.002
4A51PHE00.0430.0146.569-0.132-0.1320.0000.0000.0000.000
5A52ARG10.9490.98010.1830.3780.3780.0000.0000.0000.000
6A53GLN0-0.020-0.01313.539-0.006-0.0060.0000.0000.0000.000
7A54LEU0-0.071-0.04316.906-0.003-0.0030.0000.0000.0000.000
8A55ALA00.0450.02419.8030.0160.0160.0000.0000.0000.000
9A56PRO00.0280.01221.438-0.002-0.0020.0000.0000.0000.000
10A57ASN0-0.043-0.01821.9260.0150.0150.0000.0000.0000.000
11A58VAL00.0450.04219.378-0.012-0.0120.0000.0000.0000.000
12A59TRP00.0350.00314.6150.0200.0200.0000.0000.0000.000
13A60GLN0-0.022-0.00911.7470.1050.1050.0000.0000.0000.000
14A61HIS0-0.062-0.0209.904-0.110-0.1100.0000.0000.0000.000
15A62THR00.014-0.0156.9750.2620.2620.0000.0000.0000.000
16A63SER00.0070.0175.256-0.683-0.6830.0000.0000.0000.000
17A64TYR0-0.008-0.0203.5610.7391.0990.002-0.057-0.3040.000
18A65LEU00.0480.0325.6010.0610.0610.0000.0000.0000.000
19A66ASP-1-0.921-0.9558.0480.3600.3600.0000.0000.0000.000
20A67MET0-0.0070.0059.885-0.086-0.0860.0000.0000.0000.000
21A68PRO00.0340.01013.4620.0340.0340.0000.0000.0000.000
22A69GLY00.000-0.00616.515-0.025-0.0250.0000.0000.0000.000
23A70PHE0-0.087-0.04714.618-0.009-0.0090.0000.0000.0000.000
24A71GLY00.0490.04412.185-0.003-0.0030.0000.0000.0000.000
25A72ALA00.003-0.0126.651-0.082-0.0820.0000.0000.0000.000
26A73VAL00.0050.0188.664-0.154-0.1540.0000.0000.0000.000
27A74ALA00.0330.0108.156-0.218-0.2180.0000.0000.0000.000
28A75SER0-0.058-0.0428.8100.3380.3380.0000.0000.0000.000
29A76ASN0-0.023-0.0049.762-0.457-0.4570.0000.0000.0000.000
30A77GLY00.0660.02912.1810.0910.0910.0000.0000.0000.000
31A78LEU0-0.062-0.02814.4030.0040.0040.0000.0000.0000.000
32A79ILE00.0240.02512.016-0.003-0.0030.0000.0000.0000.000
33A80VAL00.012-0.00216.6700.0220.0220.0000.0000.0000.000
34A81ARG10.9100.96620.2120.0620.0620.0000.0000.0000.000
35A82ASP-1-0.825-0.91821.885-0.097-0.0970.0000.0000.0000.000
36A83GLY00.0210.01025.4330.0030.0030.0000.0000.0000.000
37A84GLY0-0.0030.00025.8880.0040.0040.0000.0000.0000.000
38A85ARG10.7730.87023.6700.1070.1070.0000.0000.0000.000
39A86VAL00.0080.00217.2440.0040.0040.0000.0000.0000.000
40A87LEU0-0.0070.00520.316-0.001-0.0010.0000.0000.0000.000
41A88VAL00.000-0.00914.783-0.005-0.0050.0000.0000.0000.000
42A89VAL0-0.033-0.01217.1840.0300.0300.0000.0000.0000.000
43A90ASP-1-0.718-0.87715.677-0.479-0.4790.0000.0000.0000.000
44A91THR0-0.032-0.01513.0880.0090.0090.0000.0000.0000.000
45A92ALA0-0.026-0.0067.973-0.082-0.0820.0000.0000.0000.000
46A93TRP0-0.009-0.0107.7500.4000.4000.0000.0000.0000.000
47A94THR00.0490.0237.4510.1220.1220.0000.0000.0000.000
48A95ASP-1-0.738-0.8669.928-0.616-0.6160.0000.0000.0000.000
49A96ASP-1-0.904-0.9417.684-0.724-0.7240.0000.0000.0000.000
50A97GLN0-0.015-0.0193.6250.1090.3160.001-0.036-0.1720.000
51A98THR00.0420.0036.3150.1870.1870.0000.0000.0000.000
52A99ALA00.0260.0129.5120.1630.1630.0000.0000.0000.000
53A100GLN0-0.031-0.0243.139-2.329-1.2260.059-0.589-0.573-0.005
54A101ILE0-0.0040.0006.9380.3580.3580.0000.0000.0000.000
55A102LEU0-0.009-0.0038.9260.1520.1520.0000.0000.0000.000
56A103ASN00.009-0.0039.1410.0150.0150.0000.0000.0000.000
57A104TRP00.0230.0118.492-0.009-0.0090.0000.0000.0000.000
58A105ILE00.0070.00510.4490.0000.0000.0000.0000.0000.000
59A106LYS10.8660.93113.7100.0010.0010.0000.0000.0000.000
60A107GLN0-0.054-0.03112.460-0.033-0.0330.0000.0000.0000.000
61A108GLU-1-0.918-0.95912.4640.2740.2740.0000.0000.0000.000
62A109ILE0-0.073-0.03915.414-0.035-0.0350.0000.0000.0000.000
63A110ASN0-0.048-0.00717.293-0.009-0.0090.0000.0000.0000.000
64A111LEU0-0.025-0.00119.084-0.004-0.0040.0000.0000.0000.000
65A112PRO0-0.0060.00319.274-0.011-0.0110.0000.0000.0000.000
66A113VAL00.025-0.00416.143-0.001-0.0010.0000.0000.0000.000
67A114ALA0-0.022-0.00419.611-0.004-0.0040.0000.0000.0000.000
68A115LEU0-0.042-0.01821.8100.0050.0050.0000.0000.0000.000
69A116ALA00.0000.00118.282-0.012-0.0120.0000.0000.0000.000
70A117VAL0-0.017-0.00620.0840.0210.0210.0000.0000.0000.000
71A118VAL00.0240.01218.180-0.040-0.0400.0000.0000.0000.000
72A119THR0-0.046-0.06019.3690.0320.0320.0000.0000.0000.000
73A120HIS0-0.049-0.04318.1070.0530.0530.0000.0000.0000.000
74A121ALA00.0380.01420.544-0.033-0.0330.0000.0000.0000.000
75A122HIS10.7740.86818.7770.2540.2540.0000.0000.0000.000
76A123GLN00.0970.02712.8090.0170.0170.0000.0000.0000.000
77A124ASP-1-0.811-0.90413.044-0.544-0.5440.0000.0000.0000.000
78A125LYS10.7420.88213.5210.5190.5190.0000.0000.0000.000
79A126MET00.0330.02515.8670.0250.0250.0000.0000.0000.000
80A127GLY00.0400.02813.7440.0430.0430.0000.0000.0000.000
81A128GLY0-0.041-0.01512.668-0.050-0.0500.0000.0000.0000.000
82A129MET0-0.0010.00313.5250.0090.0090.0000.0000.0000.000
83A130ASP-1-0.780-0.88716.637-0.220-0.2200.0000.0000.0000.000
84A131ALA0-0.045-0.02212.7230.0340.0340.0000.0000.0000.000
85A132LEU0-0.047-0.02914.6910.0390.0390.0000.0000.0000.000
86A133HIS0-0.002-0.00316.8560.0400.0400.0000.0000.0000.000
87A134ALA0-0.0120.00117.0190.0280.0280.0000.0000.0000.000
88A135ALA0-0.053-0.01816.2620.0250.0250.0000.0000.0000.000
89A136GLY0-0.008-0.00318.3850.0180.0180.0000.0000.0000.000
90A137ILE0-0.057-0.01316.8570.0090.0090.0000.0000.0000.000
91A138ALA0-0.011-0.00421.015-0.005-0.0050.0000.0000.0000.000
92A139THR00.016-0.00319.9090.0010.0010.0000.0000.0000.000
93A140TYR0-0.032-0.03222.5740.0260.0260.0000.0000.0000.000
94A141ALA00.0900.04323.230-0.025-0.0250.0000.0000.0000.000
95A142ASN0-0.012-0.00625.1400.0280.0280.0000.0000.0000.000
96A143ALA00.0350.02027.883-0.005-0.0050.0000.0000.0000.000
97A144LEU00.001-0.00129.718-0.001-0.0010.0000.0000.0000.000
98A145SER00.002-0.04124.3320.0000.0000.0000.0000.0000.000
99A146ASN0-0.001-0.01625.802-0.021-0.0210.0000.0000.0000.000
100A147GLN0-0.064-0.03027.2810.0040.0040.0000.0000.0000.000
101A148LEU0-0.0030.00026.4550.0060.0060.0000.0000.0000.000
102A149ALA00.001-0.00323.3770.0010.0010.0000.0000.0000.000
103A150PRO00.0220.00524.283-0.003-0.0030.0000.0000.0000.000
104A151GLN0-0.055-0.01626.4750.0120.0120.0000.0000.0000.000
105A152GLU-1-0.878-0.91921.290-0.223-0.2230.0000.0000.0000.000
106A153GLY0-0.022-0.00621.931-0.015-0.0150.0000.0000.0000.000
107A154MET0-0.0590.00117.588-0.038-0.0380.0000.0000.0000.000
108A155VAL00.0050.00519.7300.0250.0250.0000.0000.0000.000
109A156ALA00.007-0.00621.453-0.018-0.0180.0000.0000.0000.000
110A157ALA0-0.009-0.01723.221-0.007-0.0070.0000.0000.0000.000
111A158GLN0-0.006-0.00623.3230.0270.0270.0000.0000.0000.000
112A159HIS10.8240.92326.2300.1610.1610.0000.0000.0000.000
113A160SER00.0410.01727.364-0.017-0.0170.0000.0000.0000.000
114A161LEU0-0.021-0.00326.5720.0090.0090.0000.0000.0000.000
115A162THR0-0.024-0.03830.460-0.003-0.0030.0000.0000.0000.000
116A163PHE00.014-0.00528.950-0.004-0.0040.0000.0000.0000.000
117A164ALA00.0520.04135.0390.0050.0050.0000.0000.0000.000
118A165ALA00.004-0.01037.509-0.003-0.0030.0000.0000.0000.000
119A166ASN0-0.027-0.01538.008-0.003-0.0030.0000.0000.0000.000
120A167GLY00.0770.04634.448-0.001-0.0010.0000.0000.0000.000
121A168TRP0-0.060-0.02531.151-0.012-0.0120.0000.0000.0000.000
122A169VAL0-0.0080.00030.2410.0030.0030.0000.0000.0000.000
123A170GLU-1-0.846-0.90033.007-0.085-0.0850.0000.0000.0000.000
124A171PRO00.002-0.01534.261-0.004-0.0040.0000.0000.0000.000
125A172ALA0-0.029-0.00834.417-0.002-0.0020.0000.0000.0000.000
126A173THR0-0.031-0.00931.947-0.003-0.0030.0000.0000.0000.000
127A174ALA00.0030.00229.798-0.009-0.0090.0000.0000.0000.000
128A175PRO0-0.0020.00530.1140.0050.0050.0000.0000.0000.000
129A176ASN0-0.001-0.02029.761-0.007-0.0070.0000.0000.0000.000
130A177PHE00.0910.04526.507-0.005-0.0050.0000.0000.0000.000
131A178GLY00.0390.03427.157-0.007-0.0070.0000.0000.0000.000
132A179PRO0-0.0110.00325.3650.0030.0030.0000.0000.0000.000
133A180LEU00.0180.00922.187-0.004-0.0040.0000.0000.0000.000
134A181LYS10.8180.90826.4670.1120.1120.0000.0000.0000.000
135A182VAL00.0240.00125.994-0.008-0.0080.0000.0000.0000.000
136A183PHE00.0080.00528.1220.0130.0130.0000.0000.0000.000
137A184TYR00.011-0.01228.499-0.012-0.0120.0000.0000.0000.000
138A185PRO0-0.073-0.03428.3400.0100.0100.0000.0000.0000.000
139A186GLY00.0590.03831.2400.0100.0100.0000.0000.0000.000
140A187PRO00.001-0.00230.454-0.011-0.0110.0000.0000.0000.000
141A188GLY0-0.005-0.00928.8860.0070.0070.0000.0000.0000.000
142A189HIS0-0.073-0.03020.925-0.008-0.0080.0000.0000.0000.000
143A190THR00.0520.00023.6160.0010.0010.0000.0000.0000.000
144A191SER00.0740.02626.6890.0060.0060.0000.0000.0000.000
145A192ASP-1-0.765-0.82325.192-0.201-0.2010.0000.0000.0000.000
146A193ASN0-0.0020.01024.619-0.006-0.0060.0000.0000.0000.000
147A194ILE0-0.0250.00324.5510.0190.0190.0000.0000.0000.000
148A195THR0-0.081-0.04024.055-0.016-0.0160.0000.0000.0000.000
149A196VAL00.012-0.00723.1920.0120.0120.0000.0000.0000.000
150A197GLY00.0350.02724.679-0.008-0.0080.0000.0000.0000.000
151A198ILE0-0.037-0.01521.5190.0000.0000.0000.0000.0000.000
152A199ASP-1-0.820-0.90826.198-0.085-0.0850.0000.0000.0000.000
153A200GLY0-0.0010.00328.410-0.002-0.0020.0000.0000.0000.000
154A201THR0-0.098-0.06225.003-0.001-0.0010.0000.0000.0000.000
155A202ASP-1-0.797-0.87627.242-0.099-0.0990.0000.0000.0000.000
156A203ILE0-0.040-0.01721.574-0.006-0.0060.0000.0000.0000.000
157A204ALA0-0.0040.00024.3830.0060.0060.0000.0000.0000.000
158A205PHE0-0.0160.00016.6460.0000.0000.0000.0000.0000.000
159A206GLY00.0530.01321.7570.0130.0130.0000.0000.0000.000
160A207GLY00.0540.02419.4540.0120.0120.0000.0000.0000.000
161A208CYS0-0.062-0.01518.430-0.034-0.0340.0000.0000.0000.000
162A209LEU00.0120.04320.4940.0190.0190.0000.0000.0000.000
163A210ILE0-0.050-0.00723.0940.0180.0180.0000.0000.0000.000
164A211LYS10.8690.93721.0140.1890.1890.0000.0000.0000.000
165A212ASP-1-0.751-0.87020.159-0.184-0.1840.0000.0000.0000.000
166A213SER0-0.079-0.08422.4610.0170.0170.0000.0000.0000.000
167A214LYS10.8220.91222.3990.1460.1460.0000.0000.0000.000
168A215ALA00.0090.02522.2110.0120.0120.0000.0000.0000.000
169A216LYS10.9210.94823.5780.0920.0920.0000.0000.0000.000
170A217SER00.0200.01024.9670.0050.0050.0000.0000.0000.000
171A218LEU00.0190.01324.524-0.011-0.0110.0000.0000.0000.000
172A219GLY00.0020.00522.199-0.017-0.0170.0000.0000.0000.000
173A220ASN00.003-0.01120.9000.0230.0230.0000.0000.0000.000
174A221LEU00.0200.00123.820-0.012-0.0120.0000.0000.0000.000
175A222GLY0-0.0100.00825.8090.0070.0070.0000.0000.0000.000
176A223ASP-1-0.805-0.88824.265-0.177-0.1770.0000.0000.0000.000
177A224ALA0-0.045-0.01227.326-0.001-0.0010.0000.0000.0000.000
178A225ASP-1-0.762-0.85728.932-0.088-0.0880.0000.0000.0000.000
179A226THR0-0.028-0.04330.9640.0000.0000.0000.0000.0000.000
180A227GLU-1-0.822-0.87833.132-0.065-0.0650.0000.0000.0000.000
181A228HIS0-0.051-0.05334.4370.0060.0060.0000.0000.0000.000
182A229TYR0-0.007-0.01825.230-0.003-0.0030.0000.0000.0000.000
183A230ALA00.012-0.00131.625-0.005-0.0050.0000.0000.0000.000
184A231ALA0-0.0240.00233.8800.0020.0020.0000.0000.0000.000
185A232SER00.035-0.00730.6480.0020.0020.0000.0000.0000.000
186A233ALA0-0.004-0.01129.408-0.007-0.0070.0000.0000.0000.000
187A234ARG10.7440.81830.4010.0820.0820.0000.0000.0000.000
188A235ALA00.0120.02232.8820.0020.0020.0000.0000.0000.000
189A236PHE00.0500.01625.0140.0000.0000.0000.0000.0000.000
190A237GLY0-0.024-0.01530.2220.0000.0000.0000.0000.0000.000
191A238ALA0-0.033-0.02331.5890.0040.0040.0000.0000.0000.000
192A239ALA00.0110.02231.4750.0050.0050.0000.0000.0000.000
193A240PHE00.0160.00828.2250.0020.0020.0000.0000.0000.000
194A241PRO0-0.025-0.00131.083-0.002-0.0020.0000.0000.0000.000
195A242LYS10.9130.93332.9450.0770.0770.0000.0000.0000.000
196A243ALA00.0170.04127.2590.0030.0030.0000.0000.0000.000
197A244SER0-0.036-0.05028.132-0.005-0.0050.0000.0000.0000.000
198A245MET0-0.029-0.00521.484-0.012-0.0120.0000.0000.0000.000
199A246ILE0-0.005-0.00422.839-0.004-0.0040.0000.0000.0000.000
200A247VAL00.0320.00816.974-0.013-0.0130.0000.0000.0000.000
201A248MET0-0.024-0.00317.6900.0330.0330.0000.0000.0000.000
202A249SER00.0560.01715.360-0.065-0.0650.0000.0000.0000.000
203A250HIS10.7530.85913.0030.4620.4620.0000.0000.0000.000
204A251SER00.014-0.00114.9030.0200.0200.0000.0000.0000.000
205A252ALA0-0.005-0.00415.260-0.042-0.0420.0000.0000.0000.000
206A253PRO0-0.026-0.02115.7370.0380.0380.0000.0000.0000.000
207A254ASP-1-0.745-0.83518.897-0.126-0.1260.0000.0000.0000.000
208A255SER00.0150.00822.2360.0050.0050.0000.0000.0000.000
209A256ARG10.8830.91725.9010.1030.1030.0000.0000.0000.000
210A257ALA0-0.0100.00527.7120.0030.0030.0000.0000.0000.000
211A258ALA00.0290.01923.9350.0050.0050.0000.0000.0000.000
212A259ILE00.0230.02025.8440.0010.0010.0000.0000.0000.000
213A260THR0-0.036-0.01828.1890.0080.0080.0000.0000.0000.000
214A261HIS0-0.048-0.03326.2340.0120.0120.0000.0000.0000.000
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