FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

tag_button

FMODB ID: 9QNJ2

Calculation Name: 1MFB-H-Xray547

Preferred Name:

Target Type:

Ligand Name: alpha-d-galactopyranose | alpha-d-mannopyranose | alpha-l-rhamnopyranose | alpha-d-abequopyranose

Ligand 3-letter code: GLA | MAN | RAM | ABE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1MFB

Chain ID: H

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 216
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2178488.692601
FMO2-HF: Nuclear repulsion 2095697.602987
FMO2-HF: Total energy -82791.089614
FMO2-MP2: Total energy -83031.052471


3D Structure Molmil
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(H:251:GLU)


Summations of interaction energy for fragment #1(H:251:GLU)
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.
-18.594-22.60317.348-7.514-5.8240.066
Interaction energy analysis for fragmet #1(H:251:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : 0.000
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].
3H253GLN0-0.026-0.0163.3454.4066.4170.033-0.830-1.214-0.001
26H276GLY00.0300.0124.339-0.606-0.598-0.001-0.0440.0370.000
27H277TYR00.0140.0035.2013.1113.217-0.001-0.008-0.0970.000
106H357TYR0-0.056-0.0571.645-27.151-33.28517.317-6.632-4.5500.067
4H254VAL00.0140.0136.0030.0650.0650.0000.0000.0000.000
5H255GLN0-0.003-0.0039.3280.1110.1110.0000.0000.0000.000
6H256GLN00.032-0.00711.7750.4980.4980.0000.0000.0000.000
7H257SER0-0.0120.01015.504-0.240-0.2400.0000.0000.0000.000
8H258GLY00.0320.00518.6960.1640.1640.0000.0000.0000.000
9H259THR0-0.033-0.02220.1550.0950.0950.0000.0000.0000.000
10H260VAL0-0.0030.00823.404-0.092-0.0920.0000.0000.0000.000
11H261LEU0-0.011-0.00326.4590.0940.0940.0000.0000.0000.000
12H262ALA0-0.003-0.00230.179-0.052-0.0520.0000.0000.0000.000
13H263ARG10.8680.91332.6740.1510.1510.0000.0000.0000.000
14H264PRO00.0430.00535.694-0.004-0.0040.0000.0000.0000.000
15H265GLY0-0.0120.00037.478-0.025-0.0250.0000.0000.0000.000
16H266ALA0-0.032-0.00334.380-0.019-0.0190.0000.0000.0000.000
17H267SER0-0.023-0.02431.8470.0620.0620.0000.0000.0000.000
18H268VAL0-0.005-0.00227.338-0.048-0.0480.0000.0000.0000.000
19H269LYS10.9120.96824.3490.7840.7840.0000.0000.0000.000
20H270MET00.0050.02621.100-0.065-0.0650.0000.0000.0000.000
21H271SER00.007-0.01718.2370.0070.0070.0000.0000.0000.000
22H272CYS0-0.075-0.02514.920-0.072-0.0720.0000.0000.0000.000
23H273LYS10.9280.99411.3635.0685.0680.0000.0000.0000.000
24H274ALA00.0260.02210.4090.1270.1270.0000.0000.0000.000
25H275SER00.000-0.0215.840-0.854-0.8540.0000.0000.0000.000
28H278THR00.0240.0128.094-0.561-0.5610.0000.0000.0000.000
29H279PHE00.0240.00411.8770.7430.7430.0000.0000.0000.000
30H280THR00.0420.01113.6480.2800.2800.0000.0000.0000.000
31H281ASN00.0040.00713.9500.0230.0230.0000.0000.0000.000
32H282TYR0-0.036-0.01110.4220.2050.2050.0000.0000.0000.000
33H283TRP00.002-0.00214.953-0.462-0.4620.0000.0000.0000.000
34H284MET0-0.0210.00013.0630.4430.4430.0000.0000.0000.000
35H285HIS00.0400.02315.970-0.270-0.2700.0000.0000.0000.000
36H286TRP00.0350.00217.106-0.006-0.0060.0000.0000.0000.000
37H287ILE0-0.008-0.00417.6120.0280.0280.0000.0000.0000.000
38H288LYS10.8640.93620.433-0.599-0.5990.0000.0000.0000.000
39H289GLN00.0610.04320.9310.1200.1200.0000.0000.0000.000
40H290ARG10.8850.93723.403-0.575-0.5750.0000.0000.0000.000
41H291PRO00.000-0.00126.8770.0840.0840.0000.0000.0000.000
42H292GLY00.0360.02627.8730.0550.0550.0000.0000.0000.000
43H293GLN0-0.038-0.03328.396-0.041-0.0410.0000.0000.0000.000
44H294GLY00.0280.03625.3130.0200.0200.0000.0000.0000.000
45H295LEU0-0.008-0.01519.457-0.052-0.0520.0000.0000.0000.000
46H296GLU-1-0.801-0.88123.4870.7000.7000.0000.0000.0000.000
47H297TRP00.003-0.00220.191-0.080-0.0800.0000.0000.0000.000
48H298ILE0-0.011-0.00222.651-0.109-0.1090.0000.0000.0000.000
49H299GLY00.0450.00122.689-0.110-0.1100.0000.0000.0000.000
50H300ALA0-0.055-0.01019.7390.1240.1240.0000.0000.0000.000
51H301ILE00.0170.00119.947-0.109-0.1090.0000.0000.0000.000
52H302TYR00.0190.02417.809-0.011-0.0110.0000.0000.0000.000
53H303PRO00.010-0.00516.938-0.107-0.1070.0000.0000.0000.000
54H304GLY00.0160.01219.551-0.173-0.1730.0000.0000.0000.000
55H305ASN0-0.031-0.01920.786-0.016-0.0160.0000.0000.0000.000
56H306SER0-0.033-0.00723.096-0.013-0.0130.0000.0000.0000.000
57H307ALA00.0280.03324.3640.0320.0320.0000.0000.0000.000
58H308THR0-0.035-0.03423.8580.0290.0290.0000.0000.0000.000
59H309PHE0-0.0160.01023.5390.0090.0090.0000.0000.0000.000
60H310TYR00.0220.00525.041-0.006-0.0060.0000.0000.0000.000
61H311ASN0-0.016-0.01126.823-0.053-0.0530.0000.0000.0000.000
62H312HIS00.0290.00128.500-0.080-0.0800.0000.0000.0000.000
63H313LYS10.8430.90630.364-0.666-0.6660.0000.0000.0000.000
64H314PHE00.007-0.00527.846-0.031-0.0310.0000.0000.0000.000
65H315ARG10.9250.98230.414-0.426-0.4260.0000.0000.0000.000
66H316ALA00.0280.01732.218-0.040-0.0400.0000.0000.0000.000
67H317LYS10.7710.90530.042-0.190-0.1900.0000.0000.0000.000
68H318THR0-0.005-0.02826.755-0.022-0.0220.0000.0000.0000.000
69H319LYS10.9570.98928.2230.1500.1500.0000.0000.0000.000
70H320LEU00.0220.01822.592-0.060-0.0600.0000.0000.0000.000
71H321THR0-0.046-0.02823.694-0.063-0.0630.0000.0000.0000.000
72H322ALA00.0170.00019.785-0.009-0.0090.0000.0000.0000.000
73H323VAL00.0160.02120.1350.0510.0510.0000.0000.0000.000
74H324THR00.025-0.00818.338-0.265-0.2650.0000.0000.0000.000
75H325SER00.0130.01317.600-0.220-0.2200.0000.0000.0000.000
76H326THR0-0.016-0.01117.038-0.237-0.2370.0000.0000.0000.000
77H327ILE0-0.0100.00510.826-0.321-0.3210.0000.0000.0000.000
78H328THR00.001-0.00314.013-0.248-0.2480.0000.0000.0000.000
79H329ALA0-0.0020.00716.6760.2230.2230.0000.0000.0000.000
80H330TYR0-0.015-0.03518.844-0.162-0.1620.0000.0000.0000.000
81H331MET0-0.0010.01921.7800.1740.1740.0000.0000.0000.000
82H332GLU-1-0.936-0.96223.770-0.360-0.3600.0000.0000.0000.000
83H333LEU0-0.015-0.00725.8800.0920.0920.0000.0000.0000.000
84H334SER00.0420.01529.181-0.047-0.0470.0000.0000.0000.000
85H335SER00.0550.01432.9700.0380.0380.0000.0000.0000.000
86H336LEU0-0.071-0.02130.1790.0500.0500.0000.0000.0000.000
87H337THR00.024-0.00134.014-0.003-0.0030.0000.0000.0000.000
88H338ASN00.0680.03133.906-0.004-0.0040.0000.0000.0000.000
89H339GLU-1-0.860-0.94233.3670.3040.3040.0000.0000.0000.000
90H340ASP-1-0.822-0.88030.1860.3100.3100.0000.0000.0000.000
91H341SER00.0010.01428.868-0.023-0.0230.0000.0000.0000.000
92H342ALA0-0.024-0.01125.6450.0730.0730.0000.0000.0000.000
93H343VAL00.0170.02820.055-0.129-0.1290.0000.0000.0000.000
94H344TYR0-0.005-0.02721.1940.1690.1690.0000.0000.0000.000
95H345TYR00.0140.01215.534-0.129-0.1290.0000.0000.0000.000
96H347THR00.002-0.02112.4410.1320.1320.0000.0000.0000.000
97H348ARG10.8180.9166.194-6.879-6.8790.0000.0000.0000.000
98H349GLY00.0140.01811.8960.8180.8180.0000.0000.0000.000
99H350GLY00.013-0.00114.254-0.355-0.3550.0000.0000.0000.000
100H351HIS0-0.003-0.00514.905-0.291-0.2910.0000.0000.0000.000
101H352GLY00.0190.00717.0920.2990.2990.0000.0000.0000.000
102H353TYR0-0.071-0.04410.455-0.265-0.2650.0000.0000.0000.000
103H354TYR00.028-0.00116.102-0.101-0.1010.0000.0000.0000.000
104H355GLY00.0540.01512.381-0.384-0.3840.0000.0000.0000.000
105H356ASP-1-0.778-0.8338.4207.7357.7350.0000.0000.0000.000
107H358TRP0-0.005-0.0257.893-2.512-2.5120.0000.0000.0000.000
108H359GLY0-0.0110.00010.031-0.077-0.0770.0000.0000.0000.000
109H360GLN0-0.004-0.02511.2020.1880.1880.0000.0000.0000.000
110H361GLY00.0240.01813.7620.0400.0400.0000.0000.0000.000
111H362ALA0-0.011-0.00317.372-0.252-0.2520.0000.0000.0000.000
112H363SER0-0.018-0.01019.9960.1430.1430.0000.0000.0000.000
113H364LEU00.0110.00723.261-0.144-0.1440.0000.0000.0000.000
114H365THR0-0.008-0.00826.5350.0950.0950.0000.0000.0000.000
115H366VAL0-0.019-0.00930.007-0.069-0.0690.0000.0000.0000.000
116H367SER00.040-0.00133.1020.0280.0280.0000.0000.0000.000
117H368SER00.0160.00336.273-0.043-0.0430.0000.0000.0000.000
118H369ALA0-0.0230.01337.929-0.019-0.0190.0000.0000.0000.000
119H370LYS10.9560.97238.4820.0600.0600.0000.0000.0000.000
120H371THR0-0.008-0.00236.8540.0260.0260.0000.0000.0000.000
121H372THR0-0.026-0.00938.685-0.002-0.0020.0000.0000.0000.000
122H373PRO00.0230.01639.1990.0040.0040.0000.0000.0000.000
123H374PRO0-0.020-0.00138.5240.0190.0190.0000.0000.0000.000
124H375SER00.0030.00240.900-0.014-0.0140.0000.0000.0000.000
125H376VAL0-0.008-0.00841.1140.0230.0230.0000.0000.0000.000
126H377TYR0-0.019-0.01843.722-0.010-0.0100.0000.0000.0000.000
127H378PRO00.0070.00744.5440.0120.0120.0000.0000.0000.000
128H379LEU0-0.064-0.03542.3640.0040.0040.0000.0000.0000.000
129H380ALA00.0540.02845.9040.0090.0090.0000.0000.0000.000
130H381PRO0-0.016-0.02247.564-0.004-0.0040.0000.0000.0000.000
131H382GLY00.0320.01150.278-0.001-0.0010.0000.0000.0000.000
132H383SER0-0.019-0.02652.490-0.003-0.0030.0000.0000.0000.000
133H384ALA00.0510.03251.7480.0110.0110.0000.0000.0000.000
134H385ALA0-0.0150.01553.0370.0110.0110.0000.0000.0000.000
135H386GLN0-0.037-0.01054.985-0.007-0.0070.0000.0000.0000.000
136H387THR0-0.036-0.02350.2020.0130.0130.0000.0000.0000.000
137H388ASP-1-0.871-0.93151.2940.2280.2280.0000.0000.0000.000
138H389SER0-0.035-0.02348.9630.0010.0010.0000.0000.0000.000
139H390MET0-0.055-0.01241.7830.0010.0010.0000.0000.0000.000
140H391VAL00.0340.02746.0710.0040.0040.0000.0000.0000.000
141H392THR0-0.019-0.01841.3790.0030.0030.0000.0000.0000.000
142H393LEU0-0.0180.00143.238-0.011-0.0110.0000.0000.0000.000
143H394GLY00.0570.00441.2230.0240.0240.0000.0000.0000.000
144H395CYS0-0.111-0.01939.733-0.031-0.0310.0000.0000.0000.000
145H396LEU00.0080.01839.9610.0200.0200.0000.0000.0000.000
146H397VAL0-0.005-0.00737.117-0.031-0.0310.0000.0000.0000.000
147H398LYS10.9930.98338.795-0.107-0.1070.0000.0000.0000.000
148H399GLY00.0240.01740.542-0.025-0.0250.0000.0000.0000.000
149H400TYR00.000-0.02732.978-0.018-0.0180.0000.0000.0000.000
150H401PHE00.0270.00934.5520.0230.0230.0000.0000.0000.000
151H402PRO0-0.0120.00031.800-0.027-0.0270.0000.0000.0000.000
152H403GLU-1-0.778-0.87029.3540.1360.1360.0000.0000.0000.000
153H404PRO0-0.042-0.01327.541-0.050-0.0500.0000.0000.0000.000
154H405VAL00.004-0.01530.306-0.052-0.0520.0000.0000.0000.000
155H406THR0-0.049-0.02229.6440.0110.0110.0000.0000.0000.000
156H407VAL0-0.001-0.01732.344-0.008-0.0080.0000.0000.0000.000
157H408THR0-0.016-0.00133.2400.0040.0040.0000.0000.0000.000
158H409TRP00.0210.00735.641-0.002-0.0020.0000.0000.0000.000
159H410ASN00.025-0.00338.359-0.005-0.0050.0000.0000.0000.000
160H411SER0-0.007-0.00938.158-0.004-0.0040.0000.0000.0000.000
161H412GLY0-0.0050.00535.025-0.033-0.0330.0000.0000.0000.000
162H413SER0-0.039-0.02035.5020.0080.0080.0000.0000.0000.000
163H414LEU0-0.042-0.01138.2020.0230.0230.0000.0000.0000.000
164H415SER00.0220.00133.0810.0110.0110.0000.0000.0000.000
165H416SER00.0230.00833.9830.0360.0360.0000.0000.0000.000
166H417GLY00.0320.00634.887-0.017-0.0170.0000.0000.0000.000
167H418VAL0-0.043-0.01333.841-0.008-0.0080.0000.0000.0000.000
168H419HIS00.0080.01332.9810.0630.0630.0000.0000.0000.000
169H420THR0-0.0020.00131.596-0.059-0.0590.0000.0000.0000.000
170H421PHE0-0.0180.00631.2010.0500.0500.0000.0000.0000.000
171H422PRO00.0160.00128.829-0.051-0.0510.0000.0000.0000.000
172H423ALA0-0.0030.00430.771-0.007-0.0070.0000.0000.0000.000
173H424VAL0-0.018-0.00632.6200.0430.0430.0000.0000.0000.000
174H425LEU0-0.028-0.00934.238-0.041-0.0410.0000.0000.0000.000
175H426GLN00.0130.00636.5560.0010.0010.0000.0000.0000.000
176H427SER00.0090.00040.406-0.031-0.0310.0000.0000.0000.000
177H428ASP-1-0.855-0.92638.2400.1290.1290.0000.0000.0000.000
178H429LEU0-0.051-0.01638.138-0.029-0.0290.0000.0000.0000.000
179H430TYR00.0160.00731.2690.0110.0110.0000.0000.0000.000
180H431THR0-0.042-0.03036.642-0.043-0.0430.0000.0000.0000.000
181H432LEU00.0260.03732.3280.0350.0350.0000.0000.0000.000
182H433SER0-0.006-0.01435.818-0.016-0.0160.0000.0000.0000.000
183H434SER00.006-0.00435.1750.0220.0220.0000.0000.0000.000
184H435SER0-0.006-0.01436.837-0.003-0.0030.0000.0000.0000.000
185H436VAL00.0340.01337.3500.0080.0080.0000.0000.0000.000
186H437THR0-0.0110.01139.471-0.001-0.0010.0000.0000.0000.000
187H438VAL00.0040.00940.942-0.001-0.0010.0000.0000.0000.000
188H439PRO00.0570.01543.7460.0110.0110.0000.0000.0000.000
189H440SER00.003-0.02446.688-0.012-0.0120.0000.0000.0000.000
190H441SER00.0120.01549.981-0.008-0.0080.0000.0000.0000.000
191H442THR0-0.041-0.01845.803-0.014-0.0140.0000.0000.0000.000
192H443TRP00.0010.01547.895-0.011-0.0110.0000.0000.0000.000
193H444PRO0-0.028-0.04049.9380.0100.0100.0000.0000.0000.000
194H445SER0-0.043-0.02251.845-0.013-0.0130.0000.0000.0000.000
195H446GLU-1-0.864-0.90546.591-0.007-0.0070.0000.0000.0000.000
196H447THR0-0.061-0.04647.1610.0110.0110.0000.0000.0000.000
197H448VAL00.0320.02843.275-0.007-0.0070.0000.0000.0000.000
198H449THR0-0.004-0.01943.117-0.002-0.0020.0000.0000.0000.000
199H451ASN00.0420.00837.932-0.003-0.0030.0000.0000.0000.000
200H452VAL0-0.008-0.00537.1920.0140.0140.0000.0000.0000.000
201H453ALA00.0150.00434.613-0.024-0.0240.0000.0000.0000.000
202H454HIS00.0300.03234.244-0.004-0.0040.0000.0000.0000.000
203H455PRO0-0.019-0.01130.510-0.018-0.0180.0000.0000.0000.000
204H456ALA00.0170.01232.812-0.023-0.0230.0000.0000.0000.000
205H457SER00.004-0.02634.303-0.011-0.0110.0000.0000.0000.000
206H458SER00.0080.00436.582-0.008-0.0080.0000.0000.0000.000
207H459THR00.0180.01537.8360.0010.0010.0000.0000.0000.000
208H460LYS10.8300.89735.7170.2560.2560.0000.0000.0000.000
209H461VAL0-0.0090.00539.9300.0000.0000.0000.0000.0000.000
210H462ASP-1-0.804-0.87841.522-0.091-0.0910.0000.0000.0000.000
211H463LYS10.8830.92243.643-0.012-0.0120.0000.0000.0000.000
212H464LYS10.9811.00445.0320.0110.0110.0000.0000.0000.000
213H465ILE0-0.028-0.02144.1280.0040.0040.0000.0000.0000.000
214H466VAL0-0.041-0.01847.973-0.006-0.0060.0000.0000.0000.000
215H467PRO0-0.014-0.00351.7830.0110.0110.0000.0000.0000.000
216H468ARG00.0720.05051.205-0.027-0.0270.0000.0000.0000.000