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: MR2QZ

Calculation Name: 1ISP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1ISP

Chain ID: A

ChEMBL ID:

UniProt ID: P37957

Base Structure: X-ray

Registration Date: 2025-10-03

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 179
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1856502.872921
FMO2-HF: Nuclear repulsion 1789572.203663
FMO2-HF: Total energy -66930.669257
FMO2-MP2: Total energy -67127.647335


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:2:GLU)


Summations of interaction energy for fragment #1(A:2: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.
-4.559-1.8180.025-1.452-1.313-0.001
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.032
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].
3A4ASN0-0.0020.0053.261-12.701-10.0480.026-1.449-1.230-0.001
30A31TRP0-0.042-0.0245.5493.9984.086-0.001-0.003-0.0830.000
4A5PRO0-0.0060.0026.0121.4031.4030.0000.0000.0000.000
5A6VAL0-0.0080.0047.9090.7070.7070.0000.0000.0000.000
6A7VAL00.0060.00310.6100.0670.0670.0000.0000.0000.000
7A8MET0-0.039-0.01513.1730.2490.2490.0000.0000.0000.000
8A9VAL00.0220.01316.964-0.080-0.0800.0000.0000.0000.000
9A10HIS00.0260.02020.4890.0690.0690.0000.0000.0000.000
10A11GLY00.0490.02123.853-0.034-0.0340.0000.0000.0000.000
11A12ILE00.0230.01127.305-0.030-0.0300.0000.0000.0000.000
12A13GLY0-0.036-0.01230.8040.0310.0310.0000.0000.0000.000
13A14GLY0-0.047-0.00927.6500.0140.0140.0000.0000.0000.000
14A15ALA00.015-0.00425.974-0.038-0.0380.0000.0000.0000.000
15A16SER0-0.034-0.05720.7220.0850.0850.0000.0000.0000.000
16A17PHE00.007-0.00921.1330.0620.0620.0000.0000.0000.000
17A18ASN0-0.035-0.01523.1460.0700.0700.0000.0000.0000.000
18A19PHE00.0390.00718.3060.0880.0880.0000.0000.0000.000
19A20ALA00.0070.01818.8030.1050.1050.0000.0000.0000.000
20A21GLY00.0350.01519.1900.1050.1050.0000.0000.0000.000
21A22ILE00.0290.01715.4520.1790.1790.0000.0000.0000.000
22A23LYS10.8700.91214.5000.6580.6580.0000.0000.0000.000
23A24SER0-0.051-0.01914.3890.1940.1940.0000.0000.0000.000
24A25TYR00.0340.01613.4830.3740.3740.0000.0000.0000.000
25A26LEU00.0500.02610.2870.4320.4320.0000.0000.0000.000
26A27VAL0-0.0200.0029.9770.8790.8790.0000.0000.0000.000
27A28SER0-0.064-0.03811.0770.5270.5270.0000.0000.0000.000
28A29GLN0-0.042-0.0149.7890.6530.6530.0000.0000.0000.000
29A30GLY00.0370.0267.0081.9341.9340.0000.0000.0000.000
31A32SER00.0320.0105.966-1.180-1.1800.0000.0000.0000.000
32A33ARG11.0100.9967.873-1.047-1.0470.0000.0000.0000.000
33A34ASP-1-0.851-0.9299.393-3.163-3.1630.0000.0000.0000.000
34A35LYS10.8700.9325.8873.7393.7390.0000.0000.0000.000
35A36LEU0-0.0210.0138.9090.0900.0900.0000.0000.0000.000
36A37TYR00.0750.04410.1450.1170.1170.0000.0000.0000.000
37A38ALA0-0.073-0.05014.1180.2390.2390.0000.0000.0000.000
38A39VAL0-0.0040.02517.584-0.071-0.0710.0000.0000.0000.000
39A40ASP-1-0.770-0.85920.529-0.233-0.2330.0000.0000.0000.000
40A41PHE0-0.065-0.03623.300-0.065-0.0650.0000.0000.0000.000
41A42TRP00.0400.01327.0260.0540.0540.0000.0000.0000.000
42A43ASP-1-0.738-0.81130.411-0.191-0.1910.0000.0000.0000.000
43A44LYS10.9490.96431.2670.1640.1640.0000.0000.0000.000
44A45THR0-0.028-0.04633.3360.0300.0300.0000.0000.0000.000
45A46GLY0-0.0030.00130.1540.0160.0160.0000.0000.0000.000
46A47THR0-0.018-0.01830.255-0.009-0.0090.0000.0000.0000.000
47A48ASN00.031-0.00528.913-0.037-0.0370.0000.0000.0000.000
48A49TYR00.0070.00628.993-0.050-0.0500.0000.0000.0000.000
49A50ASN0-0.016-0.00830.776-0.052-0.0520.0000.0000.0000.000
50A51ASN00.006-0.01226.200-0.060-0.0600.0000.0000.0000.000
51A52GLY00.0090.01124.953-0.058-0.0580.0000.0000.0000.000
52A53PRO00.022-0.00224.315-0.093-0.0930.0000.0000.0000.000
53A54VAL0-0.029-0.00223.728-0.075-0.0750.0000.0000.0000.000
54A55LEU0-0.008-0.00518.671-0.082-0.0820.0000.0000.0000.000
55A56SER0-0.033-0.04319.885-0.150-0.1500.0000.0000.0000.000
56A57ARG10.9720.98220.2070.7300.7300.0000.0000.0000.000
57A58PHE0-0.018-0.01016.049-0.115-0.1150.0000.0000.0000.000
58A59VAL00.011-0.00614.859-0.181-0.1810.0000.0000.0000.000
59A60GLN0-0.016-0.00815.378-0.205-0.2050.0000.0000.0000.000
60A61LYS10.8780.93216.4411.2781.2780.0000.0000.0000.000
61A62VAL00.0050.00311.529-0.194-0.1940.0000.0000.0000.000
62A63LEU0-0.0460.00211.564-0.645-0.6450.0000.0000.0000.000
63A64ASP-1-0.851-0.91912.677-2.464-2.4640.0000.0000.0000.000
64A65GLU-1-0.900-0.94013.917-1.933-1.9330.0000.0000.0000.000
65A66THR0-0.085-0.0698.245-0.570-0.5700.0000.0000.0000.000
66A67GLY00.0150.0269.119-0.985-0.9850.0000.0000.0000.000
67A68ALA0-0.060-0.0287.845-0.249-0.2490.0000.0000.0000.000
68A69LYS10.9290.9558.8965.1235.1230.0000.0000.0000.000
69A70LYS10.8280.9089.6532.5632.5630.0000.0000.0000.000
70A71VAL00.0210.0139.512-0.976-0.9760.0000.0000.0000.000
71A72ASP-1-0.768-0.8678.742-0.929-0.9290.0000.0000.0000.000
72A73ILE0-0.017-0.01711.685-0.044-0.0440.0000.0000.0000.000
73A74VAL0-0.0060.00114.0840.2740.2740.0000.0000.0000.000
74A75ALA0-0.008-0.00216.756-0.090-0.0900.0000.0000.0000.000
75A76HIS0-0.011-0.01420.4050.0500.0500.0000.0000.0000.000
76A77SER00.0100.00423.604-0.097-0.0970.0000.0000.0000.000
77A78MET00.0140.00526.585-0.001-0.0010.0000.0000.0000.000
78A79GLY00.0780.05223.933-0.046-0.0460.0000.0000.0000.000
79A80GLY00.0070.00522.836-0.070-0.0700.0000.0000.0000.000
80A81ALA00.0140.01223.905-0.051-0.0510.0000.0000.0000.000
81A82ASN00.007-0.00824.729-0.046-0.0460.0000.0000.0000.000
82A83THR0-0.012-0.01819.445-0.099-0.0990.0000.0000.0000.000
83A84LEU0-0.024-0.01022.192-0.072-0.0720.0000.0000.0000.000
84A85TYR00.0070.00123.963-0.037-0.0370.0000.0000.0000.000
85A86TYR00.0350.02617.548-0.006-0.0060.0000.0000.0000.000
86A87ILE0-0.042-0.01818.915-0.064-0.0640.0000.0000.0000.000
87A88LYS10.9050.96622.5110.2730.2730.0000.0000.0000.000
88A89ASN0-0.048-0.04026.2370.0300.0300.0000.0000.0000.000
89A90LEU0-0.0190.01124.7920.0050.0050.0000.0000.0000.000
90A91ASP-1-0.770-0.84421.551-1.106-1.1060.0000.0000.0000.000
91A92GLY00.0470.00719.378-0.130-0.1300.0000.0000.0000.000
92A93GLY0-0.0060.00318.627-0.083-0.0830.0000.0000.0000.000
93A94ASN00.0000.00317.4780.0110.0110.0000.0000.0000.000
94A95LYS10.8790.92514.9491.2501.2500.0000.0000.0000.000
95A96VAL0-0.0050.00113.689-0.263-0.2630.0000.0000.0000.000
96A97ALA0-0.0210.00410.1850.0240.0240.0000.0000.0000.000
97A98ASN0-0.020-0.0258.5910.5530.5530.0000.0000.0000.000
98A99VAL00.0140.00412.570-0.208-0.2080.0000.0000.0000.000
99A100VAL0-0.020-0.00814.1340.2030.2030.0000.0000.0000.000
100A101THR0-0.025-0.00616.963-0.102-0.1020.0000.0000.0000.000
101A102LEU0-0.012-0.01018.9500.1080.1080.0000.0000.0000.000
102A103GLY00.0720.01722.728-0.064-0.0640.0000.0000.0000.000
103A104GLY00.0160.01725.036-0.051-0.0510.0000.0000.0000.000
104A105ALA00.0230.01025.8460.0200.0200.0000.0000.0000.000
105A106ASN00.012-0.02323.713-0.078-0.0780.0000.0000.0000.000
106A107ARG10.7740.86627.372-0.146-0.1460.0000.0000.0000.000
107A108LEU0-0.029-0.00330.652-0.011-0.0110.0000.0000.0000.000
108A109THR0-0.083-0.04227.509-0.028-0.0280.0000.0000.0000.000
109A110THR0-0.048-0.03726.063-0.021-0.0210.0000.0000.0000.000
110A111GLY00.0540.03728.7050.0290.0290.0000.0000.0000.000
111A112LYS10.8200.91823.7680.0510.0510.0000.0000.0000.000
112A113ALA00.0220.01421.513-0.043-0.0430.0000.0000.0000.000
113A114LEU00.0180.01722.548-0.012-0.0120.0000.0000.0000.000
114A115PRO00.0250.00820.661-0.033-0.0330.0000.0000.0000.000
115A116GLY00.0610.03719.741-0.080-0.0800.0000.0000.0000.000
116A117THR0-0.031-0.04120.4110.0450.0450.0000.0000.0000.000
117A118ASP-1-0.799-0.88815.301-1.536-1.5360.0000.0000.0000.000
118A119PRO0-0.042-0.01818.8760.1000.1000.0000.0000.0000.000
119A120ASN0-0.031-0.01316.5290.1790.1790.0000.0000.0000.000
120A121GLN0-0.066-0.03212.7800.1320.1320.0000.0000.0000.000
121A122LYS10.8210.90716.228-0.032-0.0320.0000.0000.0000.000
122A123ILE0-0.0080.01115.4850.0440.0440.0000.0000.0000.000
123A124LEU0-0.0110.00612.1130.1540.1540.0000.0000.0000.000
124A125TYR0-0.014-0.02615.2340.0130.0130.0000.0000.0000.000
125A126THR00.006-0.00315.7540.2030.2030.0000.0000.0000.000
126A127SER0-0.082-0.04618.285-0.080-0.0800.0000.0000.0000.000
127A128ILE00.0250.02218.0290.0480.0480.0000.0000.0000.000
128A129TYR00.0400.02022.514-0.076-0.0760.0000.0000.0000.000
129A130SER0-0.003-0.02226.2470.0620.0620.0000.0000.0000.000
130A131SER00.017-0.00529.079-0.052-0.0520.0000.0000.0000.000
131A132ALA0-0.0080.00131.938-0.032-0.0320.0000.0000.0000.000
132A133ASP-1-0.819-0.90429.5880.2840.2840.0000.0000.0000.000
133A134MET0-0.027-0.01832.442-0.028-0.0280.0000.0000.0000.000
134A135ILE0-0.033-0.00932.657-0.023-0.0230.0000.0000.0000.000
135A136VAL0-0.043-0.02329.536-0.036-0.0360.0000.0000.0000.000
136A137MET00.0530.03431.6440.0390.0390.0000.0000.0000.000
137A138ASN00.032-0.00730.2400.0110.0110.0000.0000.0000.000
138A139TYR00.0090.00030.0280.0170.0170.0000.0000.0000.000
139A140LEU0-0.0010.00131.143-0.023-0.0230.0000.0000.0000.000
140A141SER00.0170.00326.184-0.015-0.0150.0000.0000.0000.000
141A142ARG10.9070.97725.878-0.347-0.3470.0000.0000.0000.000
142A143LEU00.0120.01822.812-0.049-0.0490.0000.0000.0000.000
143A144ASP-1-0.808-0.89425.3720.1570.1570.0000.0000.0000.000
144A145GLY00.0470.02124.255-0.060-0.0600.0000.0000.0000.000
145A146ALA0-0.0080.00320.8960.0140.0140.0000.0000.0000.000
146A147ARG10.8120.90016.233-1.508-1.5080.0000.0000.0000.000
147A148ASN0-0.067-0.04120.6680.0020.0020.0000.0000.0000.000
148A149VAL00.007-0.00220.7150.0170.0170.0000.0000.0000.000
149A150GLN0-0.025-0.01423.899-0.026-0.0260.0000.0000.0000.000
150A151ILE0-0.0010.00023.7120.0510.0510.0000.0000.0000.000
151A152HIS00.0670.03526.930-0.097-0.0970.0000.0000.0000.000
152A153GLY00.0300.01829.4270.0430.0430.0000.0000.0000.000
153A154VAL0-0.0250.00826.2740.0100.0100.0000.0000.0000.000
154A155GLY00.0800.05529.548-0.028-0.0280.0000.0000.0000.000
155A156HIS0-0.011-0.02628.9390.0010.0010.0000.0000.0000.000
156A157ILE00.0450.01727.5280.0130.0130.0000.0000.0000.000
157A158GLY00.0290.01826.4990.0250.0250.0000.0000.0000.000
158A159LEU0-0.028-0.01923.9080.0910.0910.0000.0000.0000.000
159A160LEU0-0.026-0.01321.6740.1010.1010.0000.0000.0000.000
160A161TYR0-0.052-0.02521.5870.0760.0760.0000.0000.0000.000
161A162SER00.0490.03622.3720.0380.0380.0000.0000.0000.000
162A163SER00.0300.00920.1840.0720.0720.0000.0000.0000.000
163A164GLN00.0310.02019.3190.2000.2000.0000.0000.0000.000
164A165VAL00.0230.01519.3670.1210.1210.0000.0000.0000.000
165A166ASN00.0330.00616.6970.0110.0110.0000.0000.0000.000
166A167SER0-0.019-0.01015.0190.3750.3750.0000.0000.0000.000
167A168LEU00.0160.00514.5930.2800.2800.0000.0000.0000.000
168A169ILE0-0.011-0.00513.153-0.031-0.0310.0000.0000.0000.000
169A170LYS10.8680.9359.211-5.590-5.5900.0000.0000.0000.000
170A171GLU-1-0.825-0.89510.1152.8902.8900.0000.0000.0000.000
171A172GLY0-0.0110.00211.3220.0880.0880.0000.0000.0000.000
172A173LEU0-0.046-0.0368.934-0.388-0.3880.0000.0000.0000.000
173A174ASN0-0.031-0.0246.2352.2582.2580.0000.0000.0000.000
174A175GLY00.0310.0297.822-0.041-0.0410.0000.0000.0000.000
175A176GLY0-0.0020.00510.077-0.235-0.2350.0000.0000.0000.000
176A177GLY0-0.021-0.01513.087-0.158-0.1580.0000.0000.0000.000
177A178GLN0-0.003-0.02115.176-0.076-0.0760.0000.0000.0000.000
178A179ASN0-0.006-0.02317.871-0.053-0.0530.0000.0000.0000.000
179A180THR-1-0.814-0.87420.0750.0160.0160.0000.0000.0000.000