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: R5VL8

Calculation Name: 1M4U-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose

ligand 3-letter code: NAG

PDB ID: 1M4U

Chain ID: A

ChEMBL ID:

UniProt ID: P18075

Base Structure: X-ray

Registration Date: 2023-06-19

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1972370.138682
FMO2-HF: Nuclear repulsion 1890707.055975
FMO2-HF: Total energy -81663.082707
FMO2-MP2: Total energy -81894.097159


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:27:MET)


Summations of interaction energy for fragment #1(A:27: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.
-7.062-3.4792.979-2.995-3.568-0.016
Interaction energy analysis for fragmet #1(A:27:MET)
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 : -0.012
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].
3A29HIS00.0190.0153.046-2.0510.0030.000-0.980-1.0750.001
4A30TYR00.0290.0203.483-2.173-1.5770.011-0.306-0.300-0.002
5A31LEU00.0220.0065.9550.0630.0630.0000.0000.0000.000
6A32HIS0-0.0110.0032.394-3.290-2.3572.968-1.709-2.193-0.015
7A33ILE0-0.021-0.0206.6080.2350.2350.0000.0000.0000.000
8A34ARG10.9310.9578.9960.1190.1190.0000.0000.0000.000
9A35PRO00.0150.0238.540-0.015-0.0150.0000.0000.0000.000
10A36ALA00.0150.0066.378-0.027-0.0270.0000.0000.0000.000
11A37PRO00.0000.0018.516-0.119-0.1190.0000.0000.0000.000
12A38SER0-0.007-0.01910.1040.2540.2540.0000.0000.0000.000
13A39ASP-1-0.909-0.94412.3810.8650.8650.0000.0000.0000.000
14A40ASN0-0.073-0.03713.524-0.124-0.1240.0000.0000.0000.000
15A41LEU00.0180.02516.480-0.063-0.0630.0000.0000.0000.000
16A42PRO0-0.021-0.03020.2940.0100.0100.0000.0000.0000.000
17A43LEU0-0.0030.00118.2080.0280.0280.0000.0000.0000.000
18A44VAL0-0.020-0.00522.093-0.028-0.0280.0000.0000.0000.000
19A45ASP-1-0.778-0.85423.2730.2400.2400.0000.0000.0000.000
20A46LEU0-0.013-0.01722.4260.0010.0010.0000.0000.0000.000
21A47ILE00.0160.01324.888-0.014-0.0140.0000.0000.0000.000
22A48GLU-1-0.800-0.85926.9740.1170.1170.0000.0000.0000.000
23A49HIS00.0290.01529.111-0.005-0.0050.0000.0000.0000.000
24A50PRO00.0350.00930.837-0.003-0.0030.0000.0000.0000.000
25A51ASP-1-0.856-0.93034.0970.0470.0470.0000.0000.0000.000
26A52PRO00.0670.02435.4730.0020.0020.0000.0000.0000.000
27A53ILE0-0.060-0.00434.756-0.002-0.0020.0000.0000.0000.000
28A54PHE0-0.045-0.03831.159-0.003-0.0030.0000.0000.0000.000
29A55ASP-1-0.780-0.82833.6580.0870.0870.0000.0000.0000.000
30A56PRO00.0140.03435.009-0.007-0.0070.0000.0000.0000.000
31A57LYS10.7940.85737.600-0.055-0.0550.0000.0000.0000.000
32A58GLU-1-0.892-0.95241.4390.0450.0450.0000.0000.0000.000
33A59LYS10.9480.97441.829-0.033-0.0330.0000.0000.0000.000
34A60ASP-1-0.913-0.96638.6820.0500.0500.0000.0000.0000.000
35A61LEU00.0200.02338.9210.0050.0050.0000.0000.0000.000
36A62ASN0-0.0040.00041.1630.0020.0020.0000.0000.0000.000
37A63GLU-1-0.744-0.86241.6400.0760.0760.0000.0000.0000.000
38A64THR00.0110.00841.8040.0030.0030.0000.0000.0000.000
39A65LEU00.0250.02441.272-0.001-0.0010.0000.0000.0000.000
40A66LEU00.0100.02736.9930.0010.0010.0000.0000.0000.000
41A67ARG10.8830.92037.452-0.072-0.0720.0000.0000.0000.000
42A68SER0-0.082-0.04538.8190.0010.0010.0000.0000.0000.000
43A69LEU0-0.035-0.01434.2390.0000.0000.0000.0000.0000.000
44A70LEU0-0.029-0.01031.3880.0020.0020.0000.0000.0000.000
45A71GLY00.0490.02234.1040.0050.0050.0000.0000.0000.000
46A72GLY0-0.037-0.03535.5880.0040.0040.0000.0000.0000.000
47A73HIS00.0080.01928.5270.0140.0140.0000.0000.0000.000
48A74TYR0-0.037-0.02432.7760.0100.0100.0000.0000.0000.000
49A75ASP-1-0.775-0.90233.1170.1340.1340.0000.0000.0000.000
50A76PRO0-0.009-0.01935.2420.0040.0040.0000.0000.0000.000
51A77GLY0-0.0050.01536.942-0.002-0.0020.0000.0000.0000.000
52A78PHE0-0.052-0.05231.0720.0080.0080.0000.0000.0000.000
53A79MET0-0.0290.02730.9860.0050.0050.0000.0000.0000.000
54A80ALA00.0130.01135.331-0.007-0.0070.0000.0000.0000.000
55A81THR0-0.036-0.04537.7170.0050.0050.0000.0000.0000.000
56A82SER0-0.011-0.01040.243-0.003-0.0030.0000.0000.0000.000
57A83PRO0-0.0100.00538.737-0.001-0.0010.0000.0000.0000.000
58A84PRO0-0.0060.00540.297-0.005-0.0050.0000.0000.0000.000
59A85GLU-1-0.877-0.94038.2990.1360.1360.0000.0000.0000.000
60A86ASP-1-0.797-0.87742.1970.0880.0880.0000.0000.0000.000
61A87ARG10.8060.89645.233-0.083-0.0830.0000.0000.0000.000
62A88PRO00.004-0.00148.9400.0010.0010.0000.0000.0000.000
63A96GLY00.0180.00245.4140.0010.0010.0000.0000.0000.000
64A97GLY00.0540.02542.9220.0020.0020.0000.0000.0000.000
65A98ALA0-0.039-0.02839.8410.0070.0070.0000.0000.0000.000
66A99GLU-1-0.912-0.95740.4260.1110.1110.0000.0000.0000.000
67A100ASP-1-0.840-0.91742.9980.1080.1080.0000.0000.0000.000
68A101LEU0-0.040-0.02836.5980.0050.0050.0000.0000.0000.000
69A102ALA0-0.015-0.00638.7200.0070.0070.0000.0000.0000.000
70A103GLU-1-0.922-0.96139.9890.1050.1050.0000.0000.0000.000
71A104LEU00.0150.01138.4720.0010.0010.0000.0000.0000.000
72A105ASP-1-0.776-0.89835.3050.1790.1790.0000.0000.0000.000
73A106GLN00.0240.01537.7680.0080.0080.0000.0000.0000.000
74A107LEU0-0.009-0.00340.486-0.001-0.0010.0000.0000.0000.000
75A108LEU0-0.0040.00036.379-0.001-0.0010.0000.0000.0000.000
76A109ARG10.7560.87034.734-0.159-0.1590.0000.0000.0000.000
77A110GLN0-0.069-0.02238.000-0.005-0.0050.0000.0000.0000.000
78A111ARG10.8010.88939.927-0.115-0.1150.0000.0000.0000.000
79A112PRO00.0250.04235.3090.0020.0020.0000.0000.0000.000
80A113SER00.0230.00833.125-0.004-0.0040.0000.0000.0000.000
81A114GLY00.0140.00732.4300.0100.0100.0000.0000.0000.000
82A115ALA0-0.015-0.02132.557-0.014-0.0140.0000.0000.0000.000
83A116MET0-0.046-0.01032.6580.0070.0070.0000.0000.0000.000
84A117PRO00.0480.03429.162-0.004-0.0040.0000.0000.0000.000
85A118SER00.0390.02127.942-0.018-0.0180.0000.0000.0000.000
86A119GLU-1-0.876-0.95026.3100.2150.2150.0000.0000.0000.000
87A120ILE0-0.001-0.00330.154-0.008-0.0080.0000.0000.0000.000
88A121LYS10.9360.95933.376-0.136-0.1360.0000.0000.0000.000
89A122GLY00.0280.00733.460-0.011-0.0110.0000.0000.0000.000
90A123LEU0-0.0140.01133.634-0.005-0.0050.0000.0000.0000.000
91A124GLU-1-0.787-0.86236.6020.0880.0880.0000.0000.0000.000
92A125PHE0-0.0030.00638.369-0.002-0.0020.0000.0000.0000.000
93A126SER0-0.078-0.04940.396-0.006-0.0060.0000.0000.0000.000
94A127GLU-1-0.813-0.90039.1220.0940.0940.0000.0000.0000.000
95A128GLY00.0730.01642.5120.0030.0030.0000.0000.0000.000
96A129LEU0-0.139-0.06043.9120.0000.0000.0000.0000.0000.000
97A130ALA00.0330.00444.244-0.002-0.0020.0000.0000.0000.000
98A131GLN00.0200.00638.951-0.005-0.0050.0000.0000.0000.000
99A132GLY00.0590.03342.1520.0000.0000.0000.0000.0000.000
100A133LYS10.9110.94444.692-0.063-0.0630.0000.0000.0000.000
101A134LYS11.0231.01846.647-0.053-0.0530.0000.0000.0000.000
102A135GLN00.027-0.01646.3870.0020.0020.0000.0000.0000.000
103A136ARG10.8710.98344.476-0.086-0.0860.0000.0000.0000.000
104A137LEU00.0300.01743.718-0.001-0.0010.0000.0000.0000.000
105A138SER0-0.008-0.00546.817-0.005-0.0050.0000.0000.0000.000
106A139LYS11.0351.02445.732-0.076-0.0760.0000.0000.0000.000
107A140LYS10.9040.93546.420-0.066-0.0660.0000.0000.0000.000
108A141LEU0-0.0010.00245.7890.0020.0020.0000.0000.0000.000
109A142ARG10.7620.86137.951-0.102-0.1020.0000.0000.0000.000
110A143ARG10.9960.97841.777-0.098-0.0980.0000.0000.0000.000
111A144LYS10.9510.96742.376-0.078-0.0780.0000.0000.0000.000
112A145LEU00.0360.02639.8960.0030.0030.0000.0000.0000.000
113A146GLN00.0280.00937.223-0.001-0.0010.0000.0000.0000.000
114A147MET0-0.0060.02038.1110.0060.0060.0000.0000.0000.000
115A148TRP00.0250.02439.1820.0070.0070.0000.0000.0000.000
116A149LEU00.0570.01735.6170.0050.0050.0000.0000.0000.000
117A150TRP00.0020.00733.4020.0040.0040.0000.0000.0000.000
118A151SER00.006-0.01835.2580.0080.0080.0000.0000.0000.000
119A152GLN0-0.0420.00935.231-0.005-0.0050.0000.0000.0000.000
120A153THR0-0.020-0.03431.2300.0090.0090.0000.0000.0000.000
121A154PHE0-0.019-0.01330.8420.0190.0190.0000.0000.0000.000
122A155CYS0-0.029-0.02426.5660.0170.0170.0000.0000.0000.000
123A156PRO00.0060.02030.3100.0090.0090.0000.0000.0000.000
124A157VAL0-0.033-0.01128.2970.0090.0090.0000.0000.0000.000
125A158LEU0-0.0050.00630.920-0.015-0.0150.0000.0000.0000.000
126A159TYR0-0.014-0.03030.1780.0170.0170.0000.0000.0000.000
127A160ALA00.0280.03533.386-0.009-0.0090.0000.0000.0000.000
128A161TRP0-0.049-0.03533.7420.0110.0110.0000.0000.0000.000
129A162ASN0-0.021-0.01029.406-0.014-0.0140.0000.0000.0000.000
130A163ASP-1-0.804-0.90133.4700.1080.1080.0000.0000.0000.000
131A164LEU0-0.0110.00128.9460.0050.0050.0000.0000.0000.000
132A165GLY00.0250.01431.434-0.001-0.0010.0000.0000.0000.000
133A166SER0-0.067-0.07734.0870.0020.0020.0000.0000.0000.000
134A167ARG10.7220.82331.316-0.096-0.0960.0000.0000.0000.000
135A168PHE00.0270.00726.1560.0040.0040.0000.0000.0000.000
136A169TRP00.0260.01632.059-0.005-0.0050.0000.0000.0000.000
137A170PRO00.027-0.00533.2210.0020.0020.0000.0000.0000.000
138A171ARG10.8080.90933.985-0.099-0.0990.0000.0000.0000.000
139A172TYR00.0160.01534.6740.0030.0030.0000.0000.0000.000
140A173VAL00.0170.00529.809-0.004-0.0040.0000.0000.0000.000
141A174LYS10.8260.94132.961-0.151-0.1510.0000.0000.0000.000
142A175VAL00.009-0.00327.5700.0130.0130.0000.0000.0000.000
143A176GLY00.0300.01028.571-0.012-0.0120.0000.0000.0000.000
144A177SER00.001-0.02327.8670.0260.0260.0000.0000.0000.000
145A178CYS0-0.0060.01724.7270.0240.0240.0000.0000.0000.000
146A179PHE00.0920.04529.096-0.001-0.0010.0000.0000.0000.000
147A180SER0-0.036-0.01628.491-0.008-0.0080.0000.0000.0000.000
148A181LYS10.8660.92130.485-0.217-0.2170.0000.0000.0000.000
149A182ARG10.8970.95733.269-0.189-0.1890.0000.0000.0000.000
150A183SER00.0150.00931.6590.0140.0140.0000.0000.0000.000
151A184CYS0-0.0210.00025.6040.0080.0080.0000.0000.0000.000
152A185SER0-0.010-0.02430.3000.0040.0040.0000.0000.0000.000
153A186VAL0-0.021-0.00132.348-0.012-0.0120.0000.0000.0000.000
154A187PRO00.0160.00133.1800.0010.0010.0000.0000.0000.000
155A188GLU-1-0.906-0.94633.3360.1830.1830.0000.0000.0000.000
156A189GLY00.0230.00830.613-0.002-0.0020.0000.0000.0000.000
157A190MET0-0.092-0.02425.3950.0140.0140.0000.0000.0000.000
158A191VAL00.0590.01826.369-0.022-0.0220.0000.0000.0000.000
159A193LYS10.8960.94621.770-0.432-0.4320.0000.0000.0000.000
160A194PRO00.0810.01621.152-0.018-0.0180.0000.0000.0000.000
161A195SER0-0.069-0.03620.7820.0290.0290.0000.0000.0000.000
162A196LYS10.7780.87620.543-0.302-0.3020.0000.0000.0000.000
163A197SER00.0420.03019.052-0.019-0.0190.0000.0000.0000.000
164A198VAL0-0.010-0.00222.018-0.006-0.0060.0000.0000.0000.000
165A199HIS00.0250.01118.795-0.023-0.0230.0000.0000.0000.000
166A200LEU00.0260.03024.044-0.020-0.0200.0000.0000.0000.000
167A201THR0-0.024-0.02626.8700.0140.0140.0000.0000.0000.000
168A202VAL00.0120.00727.953-0.011-0.0110.0000.0000.0000.000
169A203LEU0-0.0080.00528.7620.0010.0010.0000.0000.0000.000
170A204ARG10.7710.85126.654-0.123-0.1230.0000.0000.0000.000
171A205TRP00.0120.01429.587-0.011-0.0110.0000.0000.0000.000
172A206ARG10.9160.94825.147-0.054-0.0540.0000.0000.0000.000
173A207CYS0-0.0230.02329.653-0.008-0.0080.0000.0000.0000.000
174A208GLN00.0420.02128.0280.0030.0030.0000.0000.0000.000
175A209ARG10.8100.90528.374-0.010-0.0100.0000.0000.0000.000
176A210ARG11.0541.01130.9570.0050.0050.0000.0000.0000.000
177A211GLY00.0590.02231.778-0.003-0.0030.0000.0000.0000.000
178A212GLY00.0750.05233.2030.0010.0010.0000.0000.0000.000
179A213GLN0-0.034-0.03334.065-0.004-0.0040.0000.0000.0000.000
180A214ARG10.9210.94233.5500.0000.0000.0000.0000.0000.000
181A216GLY00.0520.03032.786-0.006-0.0060.0000.0000.0000.000
182A217TRP0-0.0090.00332.0590.0090.0090.0000.0000.0000.000
183A218ILE0-0.031-0.01525.954-0.009-0.0090.0000.0000.0000.000
184A219PRO00.0400.01627.4440.0090.0090.0000.0000.0000.000
185A220ILE0-0.069-0.01923.9880.0010.0010.0000.0000.0000.000
186A221GLN0-0.013-0.01920.535-0.028-0.0280.0000.0000.0000.000
187A222TYR0-0.026-0.03922.8050.0230.0230.0000.0000.0000.000
188A223PRO0-0.0160.00220.305-0.009-0.0090.0000.0000.0000.000
189A224ILE00.0220.00822.872-0.008-0.0080.0000.0000.0000.000
190A225ILE0-0.023-0.02123.4620.0240.0240.0000.0000.0000.000
191A226SER0-0.009-0.00624.488-0.017-0.0170.0000.0000.0000.000
192A227GLU-1-0.814-0.89224.5450.2830.2830.0000.0000.0000.000
193A229LYS10.9470.97923.305-0.366-0.3660.0000.0000.0000.000
194A231SER00.003-0.01222.0170.0280.0280.0000.0000.0000.000
195A232CYS00.0540.04622.3910.0090.0090.0000.0000.0000.000