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

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FMODB ID: JVM89

Calculation Name: 1OP0-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-acetamido-2-deoxy-beta-d-glucopyranose | alpha-l-fucopyranose

Ligand 3-letter code: NAG | FUC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1OP0

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I8X1

Base Structure: X-ray

Registration Date: 2025-10-05

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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2857852.872863
FMO2-HF: Nuclear repulsion 2766580.249059
FMO2-HF: Total energy -91272.623804
FMO2-MP2: Total energy -91530.779717


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(A:16:VAL)


Summations of interaction energy for fragment #1(A:16:VAL)
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.
-204.903-188.65731.925-20.529-27.646-0.219
Interaction energy analysis for fragmet #1(A:16:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.735 / q_NPA : 0.863
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].
3A18GLY00.0370.0093.1872.4384.4240.168-0.931-1.223-0.002
4A19GLY0-0.036-0.0313.6913.9444.2000.004-0.054-0.2060.000
5A20ASN0-0.078-0.0304.3991.7751.839-0.001-0.001-0.0610.000
7A22CYS0-0.082-0.0352.674-8.079-5.7801.297-1.327-2.269-0.016
119A138ILE00.0230.0332.4500.2261.0681.404-0.398-1.8480.001
120A139MET0-0.028-0.0382.439-3.048-1.7600.896-0.880-1.304-0.003
121A140GLY00.0370.0252.9434.7674.6780.6940.508-1.114-0.003
122A141TRP0-0.014-0.0113.446-9.008-8.6410.010-0.052-0.325-0.002
123A142GLY00.0670.0333.2679.62810.0540.019-0.150-0.295-0.001
124A143SER0-0.042-0.0322.746-17.230-15.0281.180-1.803-1.578-0.019
125A144ILE00.0260.0141.917-32.215-31.8606.301-3.715-2.942-0.048
126A145THR0-0.088-0.0454.1727.9268.042-0.001-0.024-0.0910.000
133A152PRO0-0.0050.0244.2626.2266.315-0.001-0.007-0.0810.000
137A156TYR00.0420.0022.5344.3235.5200.595-0.428-1.365-0.001
138A158ALA00.0140.0022.5780.9691.5741.553-0.499-1.660-0.002
139A159ASN0-0.0060.0083.694-0.109-0.0450.0050.080-0.1490.000
171A189ASP-1-0.771-0.8713.962-32.569-32.354-0.001-0.040-0.1740.000
172A190THR0-0.028-0.0082.481-15.960-12.4371.645-2.365-2.803-0.022
173A191CYS0-0.0440.0043.27810.89311.4710.017-0.082-0.513-0.001
174A192GLY00.0800.0304.8690.9381.026-0.001-0.005-0.0830.000
176A194ASP-1-0.804-0.8911.960-132.030-132.33316.143-8.329-7.512-0.100
177A195SER00.0030.0054.7175.8085.886-0.001-0.027-0.0500.000
6A21GLU-1-0.815-0.8925.497-30.726-30.7260.0000.0000.0000.000
8A23ASP-1-0.763-0.8928.293-17.464-17.4640.0000.0000.0000.000
9A24ILE0-0.052-0.02611.711-0.811-0.8110.0000.0000.0000.000
10A25ASN0-0.087-0.07513.9181.1871.1870.0000.0000.0000.000
11A26GLU-1-0.808-0.8799.045-26.438-26.4380.0000.0000.0000.000
12A27HIS10.8600.9329.02224.99424.9940.0000.0000.0000.000
13A28ARG10.8640.92510.98914.89814.8980.0000.0000.0000.000
14A29PHE00.0580.0429.4980.6720.6720.0000.0000.0000.000
15A30LEU0-0.045-0.0186.981-0.185-0.1850.0000.0000.0000.000
16A31VAL0-0.028-0.01311.0850.9410.9410.0000.0000.0000.000
17A32ALA00.0050.00710.676-2.120-2.1200.0000.0000.0000.000
18A33PHE00.0130.00311.5152.3932.3930.0000.0000.0000.000
19A34PHE0-0.018-0.01512.754-1.807-1.8070.0000.0000.0000.000
20A35ASN00.1310.05815.2460.7960.7960.0000.0000.0000.000
21A36THR00.010-0.00717.852-0.729-0.7290.0000.0000.0000.000
22A38THR0-0.042-0.00716.2650.4740.4740.0000.0000.0000.000
23A39GLY00.0050.00714.392-0.707-0.7070.0000.0000.0000.000
24A40PHE0-0.039-0.0419.7950.4740.4740.0000.0000.0000.000
25A41PHE0-0.013-0.00310.575-1.505-1.5050.0000.0000.0000.000
26A42CYS0-0.080-0.0259.147-2.838-2.8380.0000.0000.0000.000
27A43GLY00.0190.0227.942-0.108-0.1080.0000.0000.0000.000
28A44GLY00.0460.0208.8541.8991.8990.0000.0000.0000.000
29A45THR0-0.034-0.01411.047-1.486-1.4860.0000.0000.0000.000
30A46LEU0-0.0060.00413.0951.0911.0910.0000.0000.0000.000
31A47ILE00.0160.00616.415-0.068-0.0680.0000.0000.0000.000
32A48ASN0-0.011-0.00618.6210.3900.3900.0000.0000.0000.000
33A49PRO00.026-0.01021.370-0.403-0.4030.0000.0000.0000.000
34A50GLU-1-0.905-0.95723.771-10.757-10.7570.0000.0000.0000.000
35A51TRP00.0200.02521.613-0.132-0.1320.0000.0000.0000.000
36A52VAL00.008-0.00815.341-0.447-0.4470.0000.0000.0000.000
37A53VAL0-0.0050.00615.2630.5850.5850.0000.0000.0000.000
38A54THR00.012-0.00312.146-1.436-1.4360.0000.0000.0000.000
39A55ALA00.0370.02212.3170.8610.8610.0000.0000.0000.000
40A56ALA0-0.0010.00914.2700.3380.3380.0000.0000.0000.000
41A57HIS10.7790.85211.39123.88023.8800.0000.0000.0000.000
42A59ASP-1-0.793-0.87714.972-14.455-14.4550.0000.0000.0000.000
43A60SER0-0.010-0.00618.1980.0250.0250.0000.0000.0000.000
44A62THR0-0.019-0.03020.3890.2340.2340.0000.0000.0000.000
45A63ASP-1-0.969-0.97222.154-13.015-13.0150.0000.0000.0000.000
46A64PHE0-0.045-0.02117.842-0.820-0.8200.0000.0000.0000.000
47A65GLN0-0.046-0.02518.6480.5740.5740.0000.0000.0000.000
48A66MET0-0.0280.00016.087-1.210-1.2100.0000.0000.0000.000
49A67GLN00.0240.02114.9741.4501.4500.0000.0000.0000.000
50A68LEU0-0.006-0.01014.506-1.455-1.4550.0000.0000.0000.000
51A69GLY00.0580.02015.1780.7710.7710.0000.0000.0000.000
52A70VAL0-0.0040.02112.5340.3330.3330.0000.0000.0000.000
53A71HIS0-0.020-0.03210.361-1.045-1.0450.0000.0000.0000.000
54A72SER00.0340.00711.345-2.503-2.5030.0000.0000.0000.000
55A73LYS10.8760.9428.78033.35433.3540.0000.0000.0000.000
56A74LYS10.8150.89813.94621.79521.7950.0000.0000.0000.000
57A75VAL0-0.065-0.03216.2491.1011.1010.0000.0000.0000.000
58A76LEU00.0390.02617.153-0.692-0.6920.0000.0000.0000.000
59A77ASN0-0.058-0.04215.8500.7300.7300.0000.0000.0000.000
60A78GLU-1-0.865-0.94619.711-13.877-13.8770.0000.0000.0000.000
61A79ASP-1-0.779-0.84321.072-14.164-14.1640.0000.0000.0000.000
62A80GLU-1-0.815-0.88717.447-18.050-18.0500.0000.0000.0000.000
63A81GLN0-0.030-0.02319.2191.3301.3300.0000.0000.0000.000
64A82THR00.0190.00119.290-0.553-0.5530.0000.0000.0000.000
65A83ARG10.6820.82720.27213.65413.6540.0000.0000.0000.000
66A84ASN00.019-0.00820.821-0.855-0.8550.0000.0000.0000.000
67A85PRO00.0140.01120.9500.2050.2050.0000.0000.0000.000
68A86LYS10.9110.97222.71010.75510.7550.0000.0000.0000.000
69A87GLU-1-0.877-0.94125.140-9.974-9.9740.0000.0000.0000.000
70A88LYS10.8340.89221.62213.19513.1950.0000.0000.0000.000
71A89PHE00.0280.01522.8400.4420.4420.0000.0000.0000.000
72A90ILE00.0500.02220.922-0.759-0.7590.0000.0000.0000.000
73A91CYS0-0.037-0.01622.9330.2220.2220.0000.0000.0000.000
74A92PRO00.0340.01424.922-0.036-0.0360.0000.0000.0000.000
75A93ASN0-0.040-0.02127.9970.0550.0550.0000.0000.0000.000
76A94LYS10.8290.91720.77814.07614.0760.0000.0000.0000.000
77A95ASN0-0.017-0.01525.6180.3680.3680.0000.0000.0000.000
78A95ASN00.000-0.01624.286-0.973-0.9730.0000.0000.0000.000
79A96ASN0-0.050-0.02224.213-0.294-0.2940.0000.0000.0000.000
80A97GLU-1-0.809-0.85022.899-12.232-12.2320.0000.0000.0000.000
81A98VAL0-0.013-0.02316.611-0.096-0.0960.0000.0000.0000.000
82A99LEU00.0260.00915.421-0.715-0.7150.0000.0000.0000.000
83A100ASP-1-0.779-0.86318.435-12.546-12.5460.0000.0000.0000.000
84A101LYS10.8250.89920.47911.65611.6560.0000.0000.0000.000
85A102ASP-1-0.702-0.78814.435-20.032-20.0320.0000.0000.0000.000
86A103ILE0-0.049-0.02315.589-1.305-1.3050.0000.0000.0000.000
87A104MET0-0.047-0.00917.0441.1311.1310.0000.0000.0000.000
88A105LEU0-0.038-0.00217.699-0.780-0.7800.0000.0000.0000.000
89A106ILE00.012-0.00917.6650.4940.4940.0000.0000.0000.000
90A107LYS10.8740.95521.02910.41910.4190.0000.0000.0000.000
91A108LEU0-0.004-0.01719.708-0.118-0.1180.0000.0000.0000.000
92A109ASP-1-0.812-0.89623.613-11.864-11.8640.0000.0000.0000.000
93A110LYS10.9430.96425.59711.17611.1760.0000.0000.0000.000
94A111PRO00.0610.04024.962-0.484-0.4840.0000.0000.0000.000
95A112ILE0-0.0170.01620.5270.0750.0750.0000.0000.0000.000
96A113SER0-0.031-0.03123.8900.5870.5870.0000.0000.0000.000
97A114ASN0-0.011-0.01222.252-0.550-0.5500.0000.0000.0000.000
98A115SER0-0.008-0.03021.3380.4690.4690.0000.0000.0000.000
99A116LYS10.9340.98520.03514.33514.3350.0000.0000.0000.000
100A117HIS10.7960.86816.49715.75015.7500.0000.0000.0000.000
101A118ILE00.0290.03516.433-1.137-1.1370.0000.0000.0000.000
102A119ALA0-0.029-0.02917.3870.9810.9810.0000.0000.0000.000
103A120PRO0-0.0180.00216.852-0.845-0.8450.0000.0000.0000.000
104A121LEU0-0.024-0.00212.8470.2200.2200.0000.0000.0000.000
105A122SER0-0.016-0.00716.6830.1570.1570.0000.0000.0000.000
106A123LEU00.0220.00017.642-0.651-0.6510.0000.0000.0000.000
107A124PRO0-0.0430.00817.5320.3990.3990.0000.0000.0000.000
108A125SER00.0260.00719.3960.2730.2730.0000.0000.0000.000
109A127SER0-0.047-0.02220.9720.5010.5010.0000.0000.0000.000
110A128PRO00.0460.02620.729-0.557-0.5570.0000.0000.0000.000
111A129PRO0-0.0010.01916.940-0.070-0.0700.0000.0000.0000.000
112A131SER00.0250.01018.4080.5790.5790.0000.0000.0000.000
113A132VAL00.0320.01417.771-0.822-0.8220.0000.0000.0000.000
114A133GLY0-0.010-0.00116.9900.6260.6260.0000.0000.0000.000
115A134SER0-0.070-0.03215.843-0.277-0.2770.0000.0000.0000.000
116A135VAL00.003-0.00311.626-0.853-0.8530.0000.0000.0000.000
117A136CYS0-0.032-0.0059.7330.1240.1240.0000.0000.0000.000
118A137ARG10.8190.8775.62426.77026.7700.0000.0000.0000.000
127A146PRO00.0350.0246.331-2.462-2.4620.0000.0000.0000.000
128A147VAL00.0250.0178.1351.1911.1910.0000.0000.0000.000
129A148LYS10.9760.98210.93622.55922.5590.0000.0000.0000.000
130A149GLU-1-0.871-0.9227.732-33.512-33.5120.0000.0000.0000.000
131A150THR0-0.055-0.0516.8855.3505.3500.0000.0000.0000.000
132A151PHE00.0180.0056.151-7.231-7.2310.0000.0000.0000.000
134A153ASP-1-0.780-0.8927.389-22.858-22.8580.0000.0000.0000.000
135A154VAL0-0.0350.0028.1691.4021.4020.0000.0000.0000.000
136A155PRO0-0.0110.0085.892-5.438-5.4380.0000.0000.0000.000
140A160ILE0-0.038-0.0135.654-0.203-0.2030.0000.0000.0000.000
141A161ASN00.0180.0038.5060.9100.9100.0000.0000.0000.000
142A162LEU00.0520.01711.438-1.176-1.1760.0000.0000.0000.000
143A163LEU0-0.062-0.03612.3971.2491.2490.0000.0000.0000.000
144A164ASP-1-0.821-0.91615.358-13.153-13.1530.0000.0000.0000.000
145A165HIS10.8720.92818.01114.09214.0920.0000.0000.0000.000
146A166ALA00.0200.00319.373-0.223-0.2230.0000.0000.0000.000
147A167VAL0-0.035-0.01216.0540.0830.0830.0000.0000.0000.000
148A168CYS00.0080.01613.257-1.456-1.4560.0000.0000.0000.000
149A169GLN0-0.010-0.01017.2130.0150.0150.0000.0000.0000.000
150A170ALA0-0.022-0.00420.9030.3850.3850.0000.0000.0000.000
151A171GLY00.0220.01817.6180.1640.1640.0000.0000.0000.000
152A172TYR0-0.116-0.07512.092-0.550-0.5500.0000.0000.0000.000
153A172PRO00.0100.01019.0510.3180.3180.0000.0000.0000.000
154A173GLU-1-0.811-0.88917.952-16.118-16.1180.0000.0000.0000.000
155A174LEU0-0.060-0.02817.351-0.193-0.1930.0000.0000.0000.000
156A175LEU00.0140.01420.4440.4770.4770.0000.0000.0000.000
157A176ALA0-0.061-0.03422.276-0.471-0.4710.0000.0000.0000.000
158A177GLU-1-0.854-0.93724.064-11.453-11.4530.0000.0000.0000.000
159A178TYR0-0.056-0.05119.678-0.381-0.3810.0000.0000.0000.000
160A179ARG10.8440.91020.31611.56911.5690.0000.0000.0000.000
161A180THR0-0.007-0.00416.051-0.703-0.7030.0000.0000.0000.000
162A181LEU0-0.036-0.02013.6200.7340.7340.0000.0000.0000.000
163A183ALA0-0.008-0.0039.3260.7660.7660.0000.0000.0000.000
164A184GLY00.0600.0278.018-1.799-1.7990.0000.0000.0000.000
165A185ILE0-0.042-0.0219.0991.2791.2790.0000.0000.0000.000
166A186VAL00.0490.02511.364-0.531-0.5310.0000.0000.0000.000
167A186GLN00.0110.00312.9870.1730.1730.0000.0000.0000.000
168A186GLY00.0200.01810.6930.0880.0880.0000.0000.0000.000
169A187GLY0-0.053-0.0419.2070.5960.5960.0000.0000.0000.000
170A188LYS10.8610.9365.30324.28724.2870.0000.0000.0000.000
175A193GLY00.0320.0135.229-7.508-7.5080.0000.0000.0000.000
178A196GLY00.0470.0138.4070.2280.2280.0000.0000.0000.000
179A197GLY0-0.0020.0106.7071.8691.8690.0000.0000.0000.000
180A198PRO0-0.023-0.0106.9771.1951.1950.0000.0000.0000.000
181A199LEU0-0.025-0.0036.621-3.322-3.3220.0000.0000.0000.000
182A200ILE0-0.019-0.0138.6552.4242.4240.0000.0000.0000.000
183A202ASN00.005-0.01413.2810.8820.8820.0000.0000.0000.000
184A207GLY00.0130.01114.0690.7900.7900.0000.0000.0000.000
185A208GLN00.0040.00015.1130.3310.3310.0000.0000.0000.000
186A209PHE00.0340.00311.837-0.963-0.9630.0000.0000.0000.000
187A210GLN00.030-0.01113.1700.7530.7530.0000.0000.0000.000
188A211GLY00.0050.00711.8760.8130.8130.0000.0000.0000.000
189A212ILE00.0000.00810.509-1.041-1.0410.0000.0000.0000.000
190A213VAL0-0.064-0.0335.1810.7370.7370.0000.0000.0000.000
191A214SER0-0.044-0.0318.3470.4390.4390.0000.0000.0000.000
192A215TYR0-0.022-0.05410.955-0.331-0.3310.0000.0000.0000.000
193A216GLY00.0350.0209.491-1.578-1.5780.0000.0000.0000.000
194A217ALA0-0.0070.00910.2541.8551.8550.0000.0000.0000.000
195A218HIS00.0030.0049.608-1.504-1.5040.0000.0000.0000.000
196A219PRO0-0.009-0.02411.0611.9631.9630.0000.0000.0000.000
197A221GLY00.006-0.0058.0010.3770.3770.0000.0000.0000.000
198A221GLN0-0.015-0.0178.7193.3113.3110.0000.0000.0000.000
199A222GLY00.0350.02312.487-0.122-0.1220.0000.0000.0000.000
200A223PRO0-0.047-0.03813.9450.1830.1830.0000.0000.0000.000
201A224LYS10.8460.92813.49218.71418.7140.0000.0000.0000.000
202A225PRO00.0000.00910.684-1.707-1.7070.0000.0000.0000.000
203A226GLY00.0850.0678.4750.2360.2360.0000.0000.0000.000
204A227ILE00.017-0.0109.4562.1622.1620.0000.0000.0000.000
205A228TYR0-0.033-0.0285.828-0.779-0.7790.0000.0000.0000.000
206A229THR00.004-0.00811.6841.3051.3050.0000.0000.0000.000
207A230ASN0-0.009-0.01614.328-0.948-0.9480.0000.0000.0000.000
208A231VAL00.0110.00314.4960.7640.7640.0000.0000.0000.000
209A232PHE00.0330.01017.3330.7450.7450.0000.0000.0000.000
210A233ASP-1-0.854-0.90820.400-12.336-12.3360.0000.0000.0000.000
211A234TYR00.0250.00019.1440.4020.4020.0000.0000.0000.000
212A235THR0-0.038-0.02021.2650.3360.3360.0000.0000.0000.000
213A236ASP-1-0.776-0.87123.138-9.910-9.9100.0000.0000.0000.000
214A237TRP0-0.033-0.01021.544-0.036-0.0360.0000.0000.0000.000
215A238ILE00.0280.01019.7030.1130.1130.0000.0000.0000.000
216A239GLN0-0.032-0.02424.0050.1610.1610.0000.0000.0000.000
217A240ARG10.8310.90126.5809.9399.9390.0000.0000.0000.000
218A241ASN00.012-0.00625.9180.3040.3040.0000.0000.0000.000
219A242ILE0-0.047-0.02122.9080.1400.1400.0000.0000.0000.000
220A243ALA0-0.077-0.03627.3870.2200.2200.0000.0000.0000.000
221A244GLY00.0050.00630.3650.3460.3460.0000.0000.0000.000
222A245ASN0-0.072-0.03831.8420.1410.1410.0000.0000.0000.000
223A246THR0-0.001-0.02028.843-0.113-0.1130.0000.0000.0000.000
224A247ASP-1-0.933-0.94730.533-8.983-8.9830.0000.0000.0000.000
225A248ALA0-0.0340.00029.7990.0320.0320.0000.0000.0000.000
226A249THR0-0.004-0.00629.288-0.346-0.3460.0000.0000.0000.000
227A251PRO00.0130.01624.7760.3870.3870.0000.0000.0000.000
228A252PRO-1-0.797-0.88426.327-11.795-11.7950.0000.0000.0000.000