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: MZM1Z

Calculation Name: 6VMZ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2,6-dichloro-n-[1-(propan-2-yl)piperidin-4-yl]benzamide | 2-acetamido-2-deoxy-beta-d-glucopyranose

Ligand 3-letter code: R3P | NAG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6VMZ

Chain ID: B

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1535325.899785
FMO2-HF: Nuclear repulsion 1463674.118979
FMO2-HF: Total energy -71651.780806
FMO2-MP2: Total energy -71857.273596


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(B:1:GLY)


Summations of interaction energy for fragment #1(B:1:GLY)
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.
-263.709-258.3628.759-7.445-6.658-0.092
Interaction energy analysis for fragmet #1(B:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.809 / q_NPA : 0.897
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].
3B3PHE0-0.028-0.0123.52112.54813.859-0.005-0.584-0.722-0.002
4B4GLY0-0.0100.0022.82810.95611.4600.015-0.206-0.312-0.001
5B5ALA00.0150.0124.1269.2119.360-0.001-0.012-0.1350.000
6B6ILE0-0.020-0.0264.1035.4295.553-0.001-0.018-0.1050.000
7B7ALA0-0.044-0.0183.499-16.621-16.0300.017-0.296-0.312-0.002
109B109ASP-1-0.794-0.9072.587-75.783-73.7070.995-1.617-1.455-0.017
110B110PHE0-0.052-0.0034.5611.6431.605-0.001-0.0060.0460.000
112B112ASP-1-0.745-0.8741.923-113.825-113.1797.741-4.704-3.682-0.070
113B113SER0-0.054-0.0155.2994.5544.538-0.001-0.0020.0190.000
8B8GLY0-0.026-0.0065.347-4.529-4.5290.0000.0000.0000.000
9B9PHE0-0.072-0.0266.1234.7654.7650.0000.0000.0000.000
10B10ILE00.0110.0077.9994.0304.0300.0000.0000.0000.000
11B11GLU-1-0.907-0.9578.409-27.204-27.2040.0000.0000.0000.000
12B12GLY0-0.031-0.0249.948-0.880-0.8800.0000.0000.0000.000
13B13GLY0-0.0100.00810.8940.4690.4690.0000.0000.0000.000
14B14TRP00.000-0.01812.2731.3451.3450.0000.0000.0000.000
15B15GLN00.024-0.00316.0920.8390.8390.0000.0000.0000.000
16B16GLY0-0.0050.01018.3700.6440.6440.0000.0000.0000.000
17B17MET0-0.054-0.00315.3110.9040.9040.0000.0000.0000.000
18B18VAL00.006-0.00118.726-0.537-0.5370.0000.0000.0000.000
19B19ASP-1-0.880-0.93921.166-13.621-13.6210.0000.0000.0000.000
20B20GLY0-0.002-0.02219.1290.4300.4300.0000.0000.0000.000
21B21TRP0-0.0050.00413.669-0.528-0.5280.0000.0000.0000.000
22B22TYR00.002-0.02811.040-1.319-1.3190.0000.0000.0000.000
23B23GLY00.006-0.00214.6591.5041.5040.0000.0000.0000.000
24B24TYR0-0.016-0.02916.118-1.102-1.1020.0000.0000.0000.000
25B25HIS00.016-0.00118.7380.7810.7810.0000.0000.0000.000
26B26HIS00.0080.01820.415-0.291-0.2910.0000.0000.0000.000
27B27SER00.004-0.03123.671-0.081-0.0810.0000.0000.0000.000
28B28ASN00.0050.01726.3520.0930.0930.0000.0000.0000.000
29B29GLU-1-0.858-0.92529.707-9.184-9.1840.0000.0000.0000.000
30B30GLN0-0.039-0.01132.5540.0990.0990.0000.0000.0000.000
31B31GLY00.0000.01531.0020.1370.1370.0000.0000.0000.000
32B32SER0-0.021-0.01325.579-0.078-0.0780.0000.0000.0000.000
33B33GLY00.0020.00424.9420.4030.4030.0000.0000.0000.000
34B34TYR0-0.013-0.01218.866-0.209-0.2090.0000.0000.0000.000
35B35ALA00.0220.01121.1490.6580.6580.0000.0000.0000.000
36B36ALA00.0230.02819.317-0.757-0.7570.0000.0000.0000.000
37B37ASP-1-0.777-0.85417.610-15.647-15.6470.0000.0000.0000.000
38B38LYS10.8710.92319.07212.62012.6200.0000.0000.0000.000
39B39GLU-1-0.890-0.92920.599-14.568-14.5680.0000.0000.0000.000
40B40SER0-0.024-0.05515.446-0.521-0.5210.0000.0000.0000.000
41B41THR0-0.011-0.01016.465-1.089-1.0890.0000.0000.0000.000
42B42GLN0-0.037-0.02617.535-0.196-0.1960.0000.0000.0000.000
43B43LYS10.9740.98817.94015.03215.0320.0000.0000.0000.000
44B44ALA00.0210.01213.851-0.242-0.2420.0000.0000.0000.000
45B45ILE00.0120.00815.702-0.213-0.2130.0000.0000.0000.000
46B46ASP-1-0.865-0.91018.237-13.692-13.6920.0000.0000.0000.000
47B47GLY0-0.022-0.01316.6500.3430.3430.0000.0000.0000.000
48B48VAL0-0.013-0.01513.818-0.096-0.0960.0000.0000.0000.000
49B49THR0-0.020-0.01816.5020.4670.4670.0000.0000.0000.000
50B50ASN0-0.005-0.01120.0680.8730.8730.0000.0000.0000.000
51B51LYS10.8230.92512.08522.91522.9150.0000.0000.0000.000
52B52VAL00.0150.00317.9620.3350.3350.0000.0000.0000.000
53B53ASN00.0180.00120.0260.4030.4030.0000.0000.0000.000
54B54SER0-0.027-0.02020.7270.5680.5680.0000.0000.0000.000
55B55ILE0-0.036-0.01917.2050.2990.2990.0000.0000.0000.000
56B56ILE00.0030.00421.8600.4250.4250.0000.0000.0000.000
57B57ASP-1-0.888-0.95225.097-10.671-10.6710.0000.0000.0000.000
58B58LYS10.7990.89623.86211.94011.9400.0000.0000.0000.000
59B59MET00.0150.01823.3030.3120.3120.0000.0000.0000.000
60B60ASN0-0.032-0.00827.6370.3610.3610.0000.0000.0000.000
61B61THR0-0.060-0.03230.6220.2890.2890.0000.0000.0000.000
62B62GLN00.0150.01629.084-0.260-0.2600.0000.0000.0000.000
63B63PHE0-0.040-0.02231.8900.2850.2850.0000.0000.0000.000
64B64GLU-1-0.925-0.95734.831-8.293-8.2930.0000.0000.0000.000
65B65ALA0-0.029-0.01337.5990.1630.1630.0000.0000.0000.000
66B66VAL0-0.026-0.02739.6740.0920.0920.0000.0000.0000.000
67B67GLY0-0.018-0.00143.4530.0500.0500.0000.0000.0000.000
68B68ARG10.8070.87943.3077.2177.2170.0000.0000.0000.000
69B69GLU-1-0.945-0.96448.716-6.169-6.1690.0000.0000.0000.000
70B70PHE00.015-0.00248.1830.0530.0530.0000.0000.0000.000
71B71ASN00.0400.01653.4400.0630.0630.0000.0000.0000.000
72B72ASN00.016-0.00355.614-0.157-0.1570.0000.0000.0000.000
73B73LEU0-0.030-0.01457.286-0.004-0.0040.0000.0000.0000.000
74B74GLU-1-0.876-0.93353.999-5.702-5.7020.0000.0000.0000.000
75B75ARG10.8600.90651.8945.8485.8480.0000.0000.0000.000
76B76ARG10.9340.96650.2335.6445.6440.0000.0000.0000.000
77B77ILE00.0200.00649.098-0.131-0.1310.0000.0000.0000.000
78B78GLU-1-0.817-0.87248.229-6.398-6.3980.0000.0000.0000.000
79B79ASN0-0.024-0.02345.071-0.245-0.2450.0000.0000.0000.000
80B80LEU0-0.030-0.00544.387-0.161-0.1610.0000.0000.0000.000
81B81ASN00.0770.03843.554-0.137-0.1370.0000.0000.0000.000
82B82LYS10.8560.91140.6087.5307.5300.0000.0000.0000.000
83B83LYS10.9410.96239.3147.6667.6660.0000.0000.0000.000
84B84MET0-0.0330.00538.816-0.159-0.1590.0000.0000.0000.000
85B85GLU-1-0.804-0.89138.038-7.763-7.7630.0000.0000.0000.000
86B86ASP-1-0.827-0.89936.591-8.252-8.2520.0000.0000.0000.000
87B87GLY00.0260.01734.667-0.272-0.2720.0000.0000.0000.000
88B88PHE0-0.016-0.02333.308-0.272-0.2720.0000.0000.0000.000
89B89LEU00.0080.00532.325-0.297-0.2970.0000.0000.0000.000
90B90ASP-1-0.913-0.93430.223-10.019-10.0190.0000.0000.0000.000
91B91VAL0-0.054-0.03128.559-0.442-0.4420.0000.0000.0000.000
92B92TRP0-0.001-0.01327.641-0.500-0.5000.0000.0000.0000.000
93B93THR0-0.0060.00325.882-0.355-0.3550.0000.0000.0000.000
94B94TYR0-0.0010.00222.713-0.731-0.7310.0000.0000.0000.000
95B95ASN0-0.042-0.03022.758-0.796-0.7960.0000.0000.0000.000
96B96ALA00.0070.00622.307-0.564-0.5640.0000.0000.0000.000
97B97GLU-1-0.934-0.97220.501-13.850-13.8500.0000.0000.0000.000
98B98LEU0-0.008-0.00317.167-1.047-1.0470.0000.0000.0000.000
99B99LEU00.0080.00617.022-1.105-1.1050.0000.0000.0000.000
100B100VAL00.0090.00116.342-1.090-1.0900.0000.0000.0000.000
101B101LEU0-0.032-0.01514.184-1.409-1.4090.0000.0000.0000.000
102B102MET00.003-0.00212.433-1.482-1.4820.0000.0000.0000.000
103B103GLU-1-0.836-0.92611.639-22.593-22.5930.0000.0000.0000.000
104B104ASN0-0.0070.01811.450-0.918-0.9180.0000.0000.0000.000
105B105GLU-1-0.942-0.9596.954-32.586-32.5860.0000.0000.0000.000
106B106ARG10.9430.9596.86620.36620.3660.0000.0000.0000.000
107B107THR0-0.041-0.0348.9270.7490.7490.0000.0000.0000.000
108B108LEU0-0.031-0.0065.065-0.350-0.3500.0000.0000.0000.000
111B111HIS00.0550.0537.1831.5491.5490.0000.0000.0000.000
114B114ASN0-0.006-0.0208.0203.3683.3680.0000.0000.0000.000
115B115VAL00.0010.0067.8652.5262.5260.0000.0000.0000.000
116B116LYS10.8930.9487.65031.37031.3700.0000.0000.0000.000
117B117ASN0-0.024-0.0249.4872.3082.3080.0000.0000.0000.000
118B118LEU0-0.0270.00012.5991.8271.8270.0000.0000.0000.000
119B119TYR0-0.031-0.04211.9891.2371.2370.0000.0000.0000.000
120B120ASP-1-0.787-0.88812.920-21.728-21.7280.0000.0000.0000.000
121B121LYS10.8630.93815.34416.54316.5430.0000.0000.0000.000
122B122VAL0-0.0020.00817.3891.1081.1080.0000.0000.0000.000
123B123ARG10.8650.92815.72219.65019.6500.0000.0000.0000.000
124B124LEU0-0.071-0.04218.8440.8680.8680.0000.0000.0000.000
125B125GLN0-0.053-0.02121.2541.2691.2690.0000.0000.0000.000
126B126LEU00.0090.00621.4340.6170.6170.0000.0000.0000.000
127B127ARG10.8710.93723.16511.96611.9660.0000.0000.0000.000
128B128ASP-1-0.786-0.86624.246-11.186-11.1860.0000.0000.0000.000
129B129ASN00.008-0.00326.9030.4490.4490.0000.0000.0000.000
130B130ALA0-0.026-0.01523.5120.1900.1900.0000.0000.0000.000
131B131LYS10.8610.93523.16112.61112.6110.0000.0000.0000.000
132B132GLU-1-0.837-0.90615.972-19.155-19.1550.0000.0000.0000.000
133B133LEU0-0.037-0.02718.5260.3350.3350.0000.0000.0000.000
134B134GLY0-0.026-0.00614.9510.0260.0260.0000.0000.0000.000
135B135ASN00.0430.01813.281-1.282-1.2820.0000.0000.0000.000
136B136GLY00.0170.00413.154-0.119-0.1190.0000.0000.0000.000
137B137CYS0-0.078-0.02213.6281.0121.0120.0000.0000.0000.000
138B138PHE00.026-0.00616.691-0.027-0.0270.0000.0000.0000.000
139B139GLU-1-0.860-0.91120.559-11.884-11.8840.0000.0000.0000.000
140B140PHE00.023-0.00424.133-0.046-0.0460.0000.0000.0000.000
141B141TYR0-0.049-0.01826.8320.1290.1290.0000.0000.0000.000
142B142HIS00.0300.03129.5160.0330.0330.0000.0000.0000.000
143B143LYS10.8260.88830.8829.1609.1600.0000.0000.0000.000
144B144CYS0-0.0280.01628.464-0.337-0.3370.0000.0000.0000.000
145B145ASP-1-0.817-0.91330.144-9.758-9.7580.0000.0000.0000.000
146B146ASN00.011-0.01329.886-0.606-0.6060.0000.0000.0000.000
147B147GLU-1-0.905-0.94129.953-9.858-9.8580.0000.0000.0000.000
148B149MET0-0.018-0.00525.723-0.628-0.6280.0000.0000.0000.000
149B150GLU-1-0.832-0.90725.673-12.439-12.4390.0000.0000.0000.000
150B151SER0-0.056-0.03326.769-0.314-0.3140.0000.0000.0000.000
151B152VAL00.0040.00122.092-0.282-0.2820.0000.0000.0000.000
152B153ARG10.7950.90522.12911.91311.9130.0000.0000.0000.000
153B154ASN0-0.060-0.03622.727-0.362-0.3620.0000.0000.0000.000
154B155GLY0-0.0150.00524.2420.0920.0920.0000.0000.0000.000
155B156THR0-0.078-0.05124.9960.3510.3510.0000.0000.0000.000
156B157TYR00.010-0.00626.4340.3630.3630.0000.0000.0000.000
157B158ASP-1-0.829-0.91528.285-9.346-9.3460.0000.0000.0000.000
158B159TYR0-0.059-0.06328.1200.3450.3450.0000.0000.0000.000
159B160PRO0-0.017-0.02430.5410.1250.1250.0000.0000.0000.000
160B161GLN0-0.064-0.00934.2200.2480.2480.0000.0000.0000.000
161B162TYR00.0440.01431.2760.1040.1040.0000.0000.0000.000
162B163SER0-0.034-0.01432.5670.0350.0350.0000.0000.0000.000
163B164GLU-1-0.822-0.89433.532-8.353-8.3530.0000.0000.0000.000
164B165GLU-1-0.883-0.93734.995-9.071-9.0710.0000.0000.0000.000
165B166ALA00.005-0.00630.867-0.031-0.0310.0000.0000.0000.000
166B167ARG10.8500.89732.8208.4278.4270.0000.0000.0000.000
167B168LEU0-0.013-0.01234.6490.0670.0670.0000.0000.0000.000
168B169LYS10.8580.95132.9069.2309.2300.0000.0000.0000.000
169B170ARG10.7280.84829.28210.35010.3500.0000.0000.0000.000
170B171GLU-1-0.884-0.92432.779-9.897-9.8970.0000.0000.0000.000
171B172GLU-1-0.927-0.96035.411-7.840-7.8400.0000.0000.0000.000
172B173ILE0-0.092-0.05138.733-0.011-0.0110.0000.0000.0000.000
173B174SER-1-0.983-0.98241.327-7.307-7.3070.0000.0000.0000.000