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: 87V5Y

Calculation Name: 5O7N-B-Xray547

Preferred Name:

Target Type:

Ligand Name: (2~{r})-1-[(2~{s})-2-(phenylmethyl)-3-sulfanyl-propanoyl]piperidine-2-carboxylic acid | 1,2-ethanediol | formic acid | zinc ion

Ligand 3-letter code: 9NK | EDO | FMT | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5O7N

Chain ID: B

ChEMBL ID:

UniProt ID: A0A173

Base Structure: X-ray

Registration Date: 2025-10-04

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 232
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2779555.134123
FMO2-HF: Nuclear repulsion 2694180.637421
FMO2-HF: Total energy -85374.496702
FMO2-MP2: Total energy -85629.75293


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:32:GLU)


Summations of interaction energy for fragment #1(A:32: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.
-13.504-10.8260.652-1.154-2.175-0.003
Interaction energy analysis for fragmet #1(A:32:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.097 / q_NPA : -0.060
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].
3A34PRO00.0060.0253.8641.1482.559-0.012-0.514-0.8850.001
7A38GLU-1-0.842-0.8845.142-6.638-6.623-0.0010.000-0.0140.000
16A47TYR00.001-0.0012.233-5.900-4.6480.665-0.640-1.276-0.004
4A35THR0-0.045-0.0585.8191.6301.6300.0000.0000.0000.000
5A36VAL00.022-0.0168.7780.4620.4620.0000.0000.0000.000
6A37SER0-0.012-0.01210.8520.2820.2820.0000.0000.0000.000
8A39ILE0-0.032-0.0069.4920.2780.2780.0000.0000.0000.000
9A40PRO00.0110.03012.1030.0180.0180.0000.0000.0000.000
10A41VAL00.0300.02015.773-0.044-0.0440.0000.0000.0000.000
11A42GLY0-0.024-0.00718.3900.1560.1560.0000.0000.0000.000
12A43GLU-1-0.904-0.93814.112-0.786-0.7860.0000.0000.0000.000
13A44VAL0-0.018-0.01613.706-0.164-0.1640.0000.0000.0000.000
14A45ARG10.7470.8598.4532.0582.0580.0000.0000.0000.000
15A46LEU00.0340.0179.775-0.124-0.1240.0000.0000.0000.000
17A48GLN0-0.049-0.0337.2570.7050.7050.0000.0000.0000.000
18A49ILE0-0.069-0.0307.099-1.005-1.0050.0000.0000.0000.000
19A50ALA00.0270.0039.3720.3030.3030.0000.0000.0000.000
20A51ASP-1-0.900-0.94012.2470.0760.0760.0000.0000.0000.000
21A52GLY0-0.026-0.00515.132-0.081-0.0810.0000.0000.0000.000
22A53VAL0-0.009-0.00313.445-0.056-0.0560.0000.0000.0000.000
23A54TRP00.0540.01910.631-0.216-0.2160.0000.0000.0000.000
24A55SER00.007-0.0039.8430.1150.1150.0000.0000.0000.000
25A56HIS0-0.070-0.02811.216-0.177-0.1770.0000.0000.0000.000
26A57ILE00.0120.0028.799-0.193-0.1930.0000.0000.0000.000
27A58ALA00.0370.02412.4360.2870.2870.0000.0000.0000.000
28A59THR0-0.022-0.03213.615-0.196-0.1960.0000.0000.0000.000
29A60GLN00.0110.00916.2720.2370.2370.0000.0000.0000.000
30A61SER0-0.031-0.01019.987-0.067-0.0670.0000.0000.0000.000
31A62PHE0-0.014-0.01822.4110.0440.0440.0000.0000.0000.000
32A63ASP-1-0.863-0.93724.744-0.842-0.8420.0000.0000.0000.000
33A64GLY0-0.058-0.02526.1140.0220.0220.0000.0000.0000.000
34A65ALA0-0.0270.00421.825-0.008-0.0080.0000.0000.0000.000
35A66VAL0-0.005-0.01717.0870.0340.0340.0000.0000.0000.000
36A67TYR0-0.020-0.00217.535-0.149-0.1490.0000.0000.0000.000
37A68PRO00.0460.02713.0410.0750.0750.0000.0000.0000.000
38A69SER0-0.035-0.02214.9420.2100.2100.0000.0000.0000.000
39A70ASN0-0.016-0.01311.982-0.638-0.6380.0000.0000.0000.000
40A71GLY00.0620.04114.7830.3650.3650.0000.0000.0000.000
41A72LEU0-0.062-0.03313.825-0.443-0.4430.0000.0000.0000.000
42A73ILE00.0090.00714.2450.2410.2410.0000.0000.0000.000
43A74VAL0-0.003-0.00515.785-0.127-0.1270.0000.0000.0000.000
44A75ARG10.8640.91318.3480.1760.1760.0000.0000.0000.000
45A76ASP-1-0.905-0.96820.266-0.457-0.4570.0000.0000.0000.000
46A77GLY0-0.0030.00923.9540.0360.0360.0000.0000.0000.000
47A78ASP-1-0.881-0.92723.827-0.016-0.0160.0000.0000.0000.000
48A79GLU-1-0.877-0.90424.822-0.312-0.3120.0000.0000.0000.000
49A80LEU0-0.027-0.01918.783-0.047-0.0470.0000.0000.0000.000
50A81LEU0-0.027-0.00921.5710.0380.0380.0000.0000.0000.000
51A82LEU0-0.001-0.00618.693-0.090-0.0900.0000.0000.0000.000
52A83ILE0-0.032-0.02119.0370.1040.1040.0000.0000.0000.000
53A84ASP-1-0.665-0.80119.156-1.610-1.6100.0000.0000.0000.000
54A85THR0-0.019-0.00420.466-0.067-0.0670.0000.0000.0000.000
55A86ALA00.0110.00518.087-0.141-0.1410.0000.0000.0000.000
56A87TRP0-0.032-0.00119.267-0.083-0.0830.0000.0000.0000.000
57A88GLY00.0760.03921.7060.0360.0360.0000.0000.0000.000
58A89ALA00.0390.01723.447-0.028-0.0280.0000.0000.0000.000
59A90LYS10.9070.94523.7310.5140.5140.0000.0000.0000.000
60A91ASN00.0710.02819.1220.1500.1500.0000.0000.0000.000
61A92THR00.0300.00019.691-0.078-0.0780.0000.0000.0000.000
62A93ALA0-0.027-0.00721.8710.0430.0430.0000.0000.0000.000
63A94ALA0-0.0050.00118.2630.0580.0580.0000.0000.0000.000
64A95LEU00.0060.00516.4220.0200.0200.0000.0000.0000.000
65A96LEU0-0.0050.00117.9840.0260.0260.0000.0000.0000.000
66A97ALA0-0.0020.00419.9030.0800.0800.0000.0000.0000.000
67A98GLU-1-0.801-0.88013.154-0.240-0.2400.0000.0000.0000.000
68A99ILE00.010-0.00515.5270.0600.0600.0000.0000.0000.000
69A100GLU-1-0.932-0.96217.2080.0130.0130.0000.0000.0000.000
70A101LYS10.7950.88113.9200.1170.1170.0000.0000.0000.000
71A102GLN0-0.104-0.07410.1310.1810.1810.0000.0000.0000.000
72A103ILE0-0.065-0.02714.5500.1000.1000.0000.0000.0000.000
73A104GLY00.0060.02917.1060.0770.0770.0000.0000.0000.000
74A105LEU0-0.046-0.02520.1360.0330.0330.0000.0000.0000.000
75A106PRO0-0.0040.01022.112-0.076-0.0760.0000.0000.0000.000
76A107VAL00.0230.00421.228-0.033-0.0330.0000.0000.0000.000
77A108THR0-0.042-0.04023.9480.0120.0120.0000.0000.0000.000
78A109ARG10.8990.94925.7600.5100.5100.0000.0000.0000.000
79A110ALA00.0370.01924.235-0.058-0.0580.0000.0000.0000.000
80A111VAL0-0.021-0.00824.0310.0750.0750.0000.0000.0000.000
81A112SER0-0.009-0.01323.780-0.078-0.0780.0000.0000.0000.000
82A113THR0-0.061-0.05922.1690.0640.0640.0000.0000.0000.000
83A114HIS0-0.013-0.02123.7910.0060.0060.0000.0000.0000.000
84A115PHE00.012-0.00627.324-0.037-0.0370.0000.0000.0000.000
85A116HIS00.0430.04226.177-0.048-0.0480.0000.0000.0000.000
86A117ASP-1-0.793-0.90626.397-0.839-0.8390.0000.0000.0000.000
87A118ASP-1-0.854-0.93721.170-1.445-1.4450.0000.0000.0000.000
88A119ARG10.7390.86218.7211.5621.5620.0000.0000.0000.000
89A120VAL00.0250.01423.8300.0260.0260.0000.0000.0000.000
90A121GLY00.0700.04625.8970.0620.0620.0000.0000.0000.000
91A122GLY0-0.067-0.04924.815-0.084-0.0840.0000.0000.0000.000
92A123VAL00.0390.02126.4600.0150.0150.0000.0000.0000.000
93A124ASP-1-0.828-0.91328.288-0.451-0.4510.0000.0000.0000.000
94A125VAL0-0.094-0.04225.4730.0450.0450.0000.0000.0000.000
95A126LEU0-0.008-0.00523.2530.0360.0360.0000.0000.0000.000
96A127ARG10.7860.87027.2500.5280.5280.0000.0000.0000.000
97A128ALA0-0.052-0.02630.6210.0410.0410.0000.0000.0000.000
98A129ALA0-0.056-0.02327.2670.0400.0400.0000.0000.0000.000
99A130GLY0-0.0100.00229.2520.0180.0180.0000.0000.0000.000
100A131VAL0-0.035-0.00225.7040.0040.0040.0000.0000.0000.000
101A132ALA0-0.019-0.01128.932-0.002-0.0020.0000.0000.0000.000
102A133THR00.0360.01827.804-0.035-0.0350.0000.0000.0000.000
103A134TYR0-0.006-0.01428.6110.0600.0600.0000.0000.0000.000
104A135ALA00.0600.02428.599-0.067-0.0670.0000.0000.0000.000
105A136SER00.0750.04030.4340.0690.0690.0000.0000.0000.000
106A137PRO00.016-0.00832.707-0.002-0.0020.0000.0000.0000.000
107A138SER0-0.062-0.02433.9760.0310.0310.0000.0000.0000.000
108A139THR00.032-0.00529.2660.0180.0180.0000.0000.0000.000
109A140ARG10.8140.90732.5290.4780.4780.0000.0000.0000.000
110A141ARG10.9821.00334.7130.4810.4810.0000.0000.0000.000
111A142LEU00.0000.00033.4700.0210.0210.0000.0000.0000.000
112A143ALA00.0100.01032.310-0.003-0.0030.0000.0000.0000.000
113A144GLU-1-0.969-0.99134.057-0.397-0.3970.0000.0000.0000.000
114A145VAL0-0.093-0.05037.7150.0210.0210.0000.0000.0000.000
115A146GLU-1-0.942-0.96133.087-0.584-0.5840.0000.0000.0000.000
116A147GLY0-0.040-0.00836.1670.0060.0060.0000.0000.0000.000
117A148ASN0-0.058-0.02730.1990.0260.0260.0000.0000.0000.000
118A149GLU-1-0.817-0.90229.457-0.648-0.6480.0000.0000.0000.000
119A150ILE00.0440.02631.599-0.040-0.0400.0000.0000.0000.000
120A151PRO0-0.003-0.00129.5200.0340.0340.0000.0000.0000.000
121A152THR00.0010.01031.9310.0240.0240.0000.0000.0000.000
122A153HIS0-0.018-0.00132.9200.0310.0310.0000.0000.0000.000
123A154SER00.010-0.00133.387-0.041-0.0410.0000.0000.0000.000
124A155LEU0-0.056-0.01728.5600.0160.0160.0000.0000.0000.000
125A156GLU-1-0.896-0.97033.172-0.429-0.4290.0000.0000.0000.000
126A157GLY0-0.030-0.01634.514-0.016-0.0160.0000.0000.0000.000
127A158LEU0-0.017-0.01029.682-0.021-0.0210.0000.0000.0000.000
128A159SER0-0.033-0.01833.487-0.023-0.0230.0000.0000.0000.000
129A160SER0-0.030-0.00736.0540.0110.0110.0000.0000.0000.000
130A161SER0-0.006-0.01533.198-0.028-0.0280.0000.0000.0000.000
131A162GLY0-0.035-0.01931.6150.0280.0280.0000.0000.0000.000
132A163ASP-1-0.843-0.89932.518-0.494-0.4940.0000.0000.0000.000
133A164ALA0-0.014-0.02129.568-0.058-0.0580.0000.0000.0000.000
134A165VAL0-0.0030.00929.7820.0540.0540.0000.0000.0000.000
135A166ARG10.8720.93727.5040.3990.3990.0000.0000.0000.000
136A167PHE0-0.024-0.01926.1650.0500.0500.0000.0000.0000.000
137A168GLY00.0450.02526.014-0.043-0.0430.0000.0000.0000.000
138A169PRO0-0.0150.01021.8550.0360.0360.0000.0000.0000.000
139A170VAL0-0.0070.00020.845-0.055-0.0550.0000.0000.0000.000
140A171GLU-1-0.881-0.91423.434-0.605-0.6050.0000.0000.0000.000
141A172LEU0-0.013-0.00824.128-0.107-0.1070.0000.0000.0000.000
142A173PHE00.0310.00425.7740.0730.0730.0000.0000.0000.000
143A174TYR00.008-0.00927.081-0.053-0.0530.0000.0000.0000.000
144A175PRO0-0.0220.00426.1880.0490.0490.0000.0000.0000.000
145A176GLY00.0970.04229.0910.0410.0410.0000.0000.0000.000
146A177ALA0-0.025-0.00430.061-0.050-0.0500.0000.0000.0000.000
147A178ALA00.012-0.01926.707-0.009-0.0090.0000.0000.0000.000
148A179HIS0-0.046-0.00725.064-0.006-0.0060.0000.0000.0000.000
149A180SER0-0.015-0.03727.1920.0090.0090.0000.0000.0000.000
150A181THR00.0480.00529.943-0.010-0.0100.0000.0000.0000.000
151A182ASP-1-0.775-0.84730.506-0.783-0.7830.0000.0000.0000.000
152A183ASN0-0.0090.00625.808-0.037-0.0370.0000.0000.0000.000
153A184LEU00.0040.00426.0130.0290.0290.0000.0000.0000.000
154A185VAL0-0.062-0.02221.954-0.099-0.0990.0000.0000.0000.000
155A186VAL0-0.003-0.01220.4660.1150.1150.0000.0000.0000.000
156A187TYR0-0.026-0.03419.142-0.195-0.1950.0000.0000.0000.000
157A188VAL00.0450.01417.3710.1310.1310.0000.0000.0000.000
158A189PRO00.012-0.00318.967-0.043-0.0430.0000.0000.0000.000
159A190SER0-0.036-0.01719.542-0.029-0.0290.0000.0000.0000.000
160A191ALA00.0260.01514.7180.0820.0820.0000.0000.0000.000
161A192SER0-0.0310.00115.563-0.141-0.1410.0000.0000.0000.000
162A193VAL00.0050.01013.220-0.182-0.1820.0000.0000.0000.000
163A194LEU0-0.011-0.00415.8120.2110.2110.0000.0000.0000.000
164A195TYR0-0.035-0.04715.406-0.334-0.3340.0000.0000.0000.000
165A196GLY00.0450.01117.4630.2330.2330.0000.0000.0000.000
166A197GLY00.0840.04218.9720.1360.1360.0000.0000.0000.000
167A198CYS0-0.070-0.03519.504-0.201-0.2010.0000.0000.0000.000
168A199ALA00.0310.03421.5720.0440.0440.0000.0000.0000.000
169A200ILE0-0.027-0.00217.3960.0630.0630.0000.0000.0000.000
170A201TYR00.014-0.00618.257-0.066-0.0660.0000.0000.0000.000
171A202GLU-1-0.815-0.88912.674-3.585-3.5850.0000.0000.0000.000
172A203LEU00.037-0.00913.4910.2920.2920.0000.0000.0000.000
173A204SER0-0.032-0.02512.8400.2970.2970.0000.0000.0000.000
174A205ARG10.8300.93815.6491.7241.7240.0000.0000.0000.000
175A206THR00.0300.00118.7970.0450.0450.0000.0000.0000.000
176A207SER00.0090.00721.7760.0870.0870.0000.0000.0000.000
177A208ALA00.0540.02423.323-0.110-0.1100.0000.0000.0000.000
178A209GLY0-0.015-0.01024.025-0.017-0.0170.0000.0000.0000.000
179A210ASN00.0130.00224.7380.1200.1200.0000.0000.0000.000
180A211VAL0-0.005-0.01927.028-0.050-0.0500.0000.0000.0000.000
181A212ALA0-0.015-0.00129.6680.0430.0430.0000.0000.0000.000
182A213ASP-1-0.823-0.90530.962-0.702-0.7020.0000.0000.0000.000
183A214ALA0-0.047-0.01329.664-0.001-0.0010.0000.0000.0000.000
184A215ASP-1-0.855-0.92331.440-0.565-0.5650.0000.0000.0000.000
185A216LEU0-0.039-0.04230.216-0.031-0.0310.0000.0000.0000.000
186A217ALA0-0.049-0.01432.447-0.006-0.0060.0000.0000.0000.000
187A218GLU-1-0.792-0.87432.864-0.601-0.6010.0000.0000.0000.000
188A219TRP0-0.0290.00124.0670.0030.0030.0000.0000.0000.000
189A220PRO0-0.056-0.04628.380-0.048-0.0480.0000.0000.0000.000
190A221THR00.0340.02429.220-0.021-0.0210.0000.0000.0000.000
191A222SER0-0.003-0.01628.7020.0190.0190.0000.0000.0000.000
192A223ILE0-0.028-0.01523.901-0.035-0.0350.0000.0000.0000.000
193A224GLU-1-0.959-0.96726.034-0.644-0.6440.0000.0000.0000.000
194A225ARG10.7840.85928.4640.6530.6530.0000.0000.0000.000
195A226ILE0-0.0040.00622.2510.0040.0040.0000.0000.0000.000
196A227GLN0-0.035-0.02223.135-0.065-0.0650.0000.0000.0000.000
197A228GLN0-0.075-0.04925.1080.0580.0580.0000.0000.0000.000
198A229HIS10.8410.94026.5560.7690.7690.0000.0000.0000.000
199A230TYR0-0.054-0.05321.937-0.004-0.0040.0000.0000.0000.000
200A231PRO0-0.011-0.00622.145-0.101-0.1010.0000.0000.0000.000
201A232GLU-1-0.830-0.90621.585-0.853-0.8530.0000.0000.0000.000
202A233ALA0-0.0180.00517.996-0.033-0.0330.0000.0000.0000.000
203A234GLN0-0.078-0.04814.633-0.034-0.0340.0000.0000.0000.000
204A235PHE0-0.022-0.0117.396-0.317-0.3170.0000.0000.0000.000
205A236VAL00.0210.01012.8820.2150.2150.0000.0000.0000.000
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