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: Y1JG2

Calculation Name: 5DOC-B-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol | zinc ion

Ligand 3-letter code: GOL | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5DOC

Chain ID: B

ChEMBL ID:

UniProt ID: P16794

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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2420436.157329
FMO2-HF: Nuclear repulsion 2336826.891526
FMO2-HF: Total energy -83609.265803
FMO2-MP2: Total energy -83844.479914


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:17:LYS)


Summations of interaction energy for fragment #1(A:17:LYS)
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.
-323.829-315.13120.879-15.381-14.194-0.181
Interaction energy analysis for fragmet #1(A:17:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.582 / q_NPA : 1.784
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].
3A19SER00.0760.0423.8432.4854.354-0.017-0.870-0.983-0.001
14A30ARG10.9380.9962.98998.10199.3340.409-0.476-1.166-0.005
17A33THR0-0.044-0.0204.039-5.094-4.9220.000-0.022-0.1500.000
27A43GLU-1-0.856-0.9311.777-169.844-169.75914.425-8.851-5.659-0.109
28A44GLN00.0180.0213.3125.6696.4240.013-0.185-0.582-0.001
29A45VAL00.017-0.0182.144-51.022-46.8185.981-5.430-4.755-0.062
30A46SER00.0030.0033.14315.60015.8750.0680.479-0.821-0.003
31A47ARG10.9220.9244.36345.41745.5220.000-0.026-0.0780.000
4A20ILE0-0.052-0.0236.2422.3272.3270.0000.0000.0000.000
5A21CYS0-0.015-0.0068.8333.7373.7370.0000.0000.0000.000
6A22LEU0-0.0280.00011.920-0.739-0.7390.0000.0000.0000.000
7A23PRO00.0060.00014.6741.1701.1700.0000.0000.0000.000
8A24PHE00.0220.0049.930-0.989-0.9890.0000.0000.0000.000
9A25ASN00.0220.01214.6810.6480.6480.0000.0000.0000.000
10A26PHE00.0560.00613.050-2.243-2.2430.0000.0000.0000.000
11A27HIS00.0060.00414.903-2.088-2.0880.0000.0000.0000.000
12A28SER0-0.060-0.02712.2750.4830.4830.0000.0000.0000.000
13A29HIS0-0.079-0.0489.712-2.307-2.3070.0000.0000.0000.000
15A31GLN00.0620.0248.311-4.465-4.4650.0000.0000.0000.000
16A32HIS0-0.001-0.0187.326-4.310-4.3100.0000.0000.0000.000
18A34CYS0-0.0160.0376.5648.3808.3800.0000.0000.0000.000
19A35LEU00.0050.0026.491-10.084-10.0840.0000.0000.0000.000
20A36ASP-1-0.892-0.9245.523-58.622-58.6220.0000.0000.0000.000
21A37ILE00.0050.0087.311-3.830-3.8300.0000.0000.0000.000
22A38SER00.0910.0538.8883.1483.1480.0000.0000.0000.000
23A39PRO0-0.002-0.00711.462-0.609-0.6090.0000.0000.0000.000
24A40TYR0-0.035-0.0119.5361.8651.8650.0000.0000.0000.000
25A41GLY0-0.018-0.0018.572-1.743-1.7430.0000.0000.0000.000
26A42ASN00.0340.0228.4201.7491.7490.0000.0000.0000.000
32A48ILE0-0.065-0.0337.5033.4313.4310.0000.0000.0000.000
33A49ALA0-0.020-0.0064.8432.4402.4400.0000.0000.0000.000
34A50CYS0-0.056-0.0086.298-4.834-4.8340.0000.0000.0000.000
35A51THR00.1140.0577.8442.6682.6680.0000.0000.0000.000
36A52SER00.0360.0149.9243.5353.5350.0000.0000.0000.000
37A53CYS0-0.106-0.06611.1702.3262.3260.0000.0000.0000.000
38A54GLU-1-0.942-0.95311.387-42.292-42.2920.0000.0000.0000.000
39A55ASP-1-0.915-0.94814.418-32.258-32.2580.0000.0000.0000.000
40A56ASN0-0.098-0.03514.9452.8722.8720.0000.0000.0000.000
41A57ARG10.9540.96417.93125.18225.1820.0000.0000.0000.000
42A58ILE00.006-0.00419.171-0.644-0.6440.0000.0000.0000.000
43A59LEU00.0270.02116.7621.2001.2000.0000.0000.0000.000
44A60PRO0-0.055-0.01720.6360.4390.4390.0000.0000.0000.000
45A61THR00.028-0.02621.916-0.819-0.8190.0000.0000.0000.000
46A62ALA00.0490.00323.0850.6680.6680.0000.0000.0000.000
47A63SER0-0.018-0.00824.6410.7810.7810.0000.0000.0000.000
48A64ASP-1-0.805-0.87225.926-22.019-22.0190.0000.0000.0000.000
49A65ALA0-0.002-0.00125.5960.6480.6480.0000.0000.0000.000
50A66MET0-0.0110.01127.7160.6830.6830.0000.0000.0000.000
51A67VAL0-0.003-0.00530.5620.7630.7630.0000.0000.0000.000
52A68ALA0-0.020-0.00429.9260.6490.6490.0000.0000.0000.000
53A69PHE00.0180.00631.5220.4070.4070.0000.0000.0000.000
54A70ILE0-0.002-0.00933.0810.5760.5760.0000.0000.0000.000
55A71ASN0-0.064-0.03735.4020.9310.9310.0000.0000.0000.000
56A72GLN00.0630.05733.8850.0290.0290.0000.0000.0000.000
57A73THR00.0000.00436.057-0.027-0.0270.0000.0000.0000.000
58A74SER0-0.022-0.00938.5290.5370.5370.0000.0000.0000.000
59A75ASN0-0.072-0.04633.680-0.266-0.2660.0000.0000.0000.000
60A76ILE00.0250.02134.326-0.498-0.4980.0000.0000.0000.000
61A77MET00.0510.02134.991-0.346-0.3460.0000.0000.0000.000
62A78LYS10.9090.97528.55920.67920.6790.0000.0000.0000.000
63A79ASN00.0410.00630.086-0.992-0.9920.0000.0000.0000.000
64A80ARG10.9150.95931.17018.54218.5420.0000.0000.0000.000
65A81ASN00.0810.02727.5580.9620.9620.0000.0000.0000.000
66A82PHE00.0190.01128.5750.0140.0140.0000.0000.0000.000
67A83TYR0-0.026-0.04730.5250.2020.2020.0000.0000.0000.000
68A84TYR0-0.006-0.01532.4350.2480.2480.0000.0000.0000.000
69A85GLY00.0690.04730.9000.2450.2450.0000.0000.0000.000
70A86PHE0-0.002-0.00931.767-0.045-0.0450.0000.0000.0000.000
71A87CYS0-0.018-0.00633.9620.4330.4330.0000.0000.0000.000
72A88LYS10.9540.97136.55115.30115.3010.0000.0000.0000.000
73A89SER00.0140.01738.3010.5320.5320.0000.0000.0000.000
74A90SER00.0540.01839.164-0.391-0.3910.0000.0000.0000.000
75A91GLU-1-0.969-0.97640.749-14.883-14.8830.0000.0000.0000.000
76A92LEU00.0100.00334.996-0.214-0.2140.0000.0000.0000.000
77A93LEU00.0240.03136.369-0.403-0.4030.0000.0000.0000.000
78A94LYS10.9640.98737.72014.05214.0520.0000.0000.0000.000
79A95LEU00.0200.03336.747-0.016-0.0160.0000.0000.0000.000
80A96SER0-0.012-0.01833.486-0.430-0.4300.0000.0000.0000.000
81A97THR0-0.135-0.08834.917-0.105-0.1050.0000.0000.0000.000
82A98ASN0-0.054-0.03537.4230.3030.3030.0000.0000.0000.000
83A99GLN00.0390.02631.6390.3790.3790.0000.0000.0000.000
84A100PRO00.0320.01731.263-0.479-0.4790.0000.0000.0000.000
85A101PRO00.0310.01026.885-0.386-0.3860.0000.0000.0000.000
86A102ILE00.0250.02126.904-0.904-0.9040.0000.0000.0000.000
87A103PHE00.0100.00127.527-0.484-0.4840.0000.0000.0000.000
88A104GLN0-0.043-0.04125.951-0.382-0.3820.0000.0000.0000.000
89A105ILE00.0150.00221.566-0.920-0.9200.0000.0000.0000.000
90A106TYR00.0220.01122.501-0.633-0.6330.0000.0000.0000.000
91A107TYR0-0.018-0.01423.774-0.337-0.3370.0000.0000.0000.000
92A108LEU0-0.054-0.03220.688-0.270-0.2700.0000.0000.0000.000
93A109LEU00.0460.00717.553-1.174-1.1740.0000.0000.0000.000
94A110HIS00.0420.03319.950-0.806-0.8060.0000.0000.0000.000
95A111ALA0-0.086-0.04221.7390.2050.2050.0000.0000.0000.000
96A112ALA0-0.047-0.01716.368-0.422-0.4220.0000.0000.0000.000
97A113ASN0-0.031-0.02815.208-1.140-1.1400.0000.0000.0000.000
98A114HIS0-0.027-0.03019.3091.7341.7340.0000.0000.0000.000
99A115ASP-1-0.843-0.88620.745-25.340-25.3400.0000.0000.0000.000
100A116ILE0-0.061-0.03620.519-0.909-0.9090.0000.0000.0000.000
101A117VAL00.0070.00623.1701.0641.0640.0000.0000.0000.000
102A118PRO0-0.058-0.02025.493-0.533-0.5330.0000.0000.0000.000
103A119PHE00.0450.00926.6770.8250.8250.0000.0000.0000.000
104A120MET0-0.046-0.00928.555-0.761-0.7610.0000.0000.0000.000
105A121HIS10.8310.90729.51120.75320.7530.0000.0000.0000.000
106A122ALA00.006-0.00633.002-0.409-0.4090.0000.0000.0000.000
107A123GLU-1-0.874-0.92434.752-18.003-18.0030.0000.0000.0000.000
108A124ASP-1-0.850-0.92036.911-16.470-16.4700.0000.0000.0000.000
109A125GLY0-0.038-0.01739.1090.1600.1600.0000.0000.0000.000
110A126ARG10.7960.89733.60417.87017.8700.0000.0000.0000.000
111A127LEU0-0.068-0.03731.9900.0210.0210.0000.0000.0000.000
112A128HIS00.0890.04829.037-1.104-1.1040.0000.0000.0000.000
113A129MET0-0.052-0.03224.7250.6880.6880.0000.0000.0000.000
114A130HIS0-0.004-0.01224.088-0.159-0.1590.0000.0000.0000.000
115A131VAL0-0.007-0.00921.1940.9710.9710.0000.0000.0000.000
116A132ILE00.0140.01620.981-1.532-1.5320.0000.0000.0000.000
117A133PHE0-0.001-0.01217.2440.2200.2200.0000.0000.0000.000
118A134GLU-1-0.871-0.94520.211-22.822-22.8220.0000.0000.0000.000
119A135ASN0-0.068-0.04018.1231.3171.3170.0000.0000.0000.000
120A136PRO0-0.018-0.01116.603-0.615-0.6150.0000.0000.0000.000
121A137ASP-1-0.885-0.95513.326-40.609-40.6090.0000.0000.0000.000
122A138VAL0-0.042-0.02212.4792.0092.0090.0000.0000.0000.000
123A139HIS00.012-0.0257.739-1.842-1.8420.0000.0000.0000.000
124A140ILE0-0.004-0.00110.5584.1104.1100.0000.0000.0000.000
125A141PRO00.0630.00710.951-3.922-3.9220.0000.0000.0000.000
126A142CYS0-0.001-0.0229.6601.5121.5120.0000.0000.0000.000
127A143ASP-1-0.883-0.91911.527-37.168-37.1680.0000.0000.0000.000
128A144CYS00.0280.02815.0292.3652.3650.0000.0000.0000.000
129A145ILE00.0290.02711.4091.8421.8420.0000.0000.0000.000
130A146THR0-0.036-0.02114.0572.2802.2800.0000.0000.0000.000
131A147GLN0-0.0010.01716.5053.3503.3500.0000.0000.0000.000
132A148MET00.0400.01517.8041.1941.1940.0000.0000.0000.000
133A149LEU00.0090.00815.5861.3771.3770.0000.0000.0000.000
134A150THR0-0.083-0.05019.8311.5021.5020.0000.0000.0000.000
135A151ALA0-0.042-0.02322.2531.2811.2810.0000.0000.0000.000
136A152ALA00.0020.00422.1750.8990.8990.0000.0000.0000.000
137A153ARG10.8890.94022.94224.40424.4040.0000.0000.0000.000
138A154GLU-1-0.945-0.96624.333-20.730-20.7300.0000.0000.0000.000
139A155ASP-1-0.794-0.87826.810-20.045-20.0450.0000.0000.0000.000
140A156TYR0-0.004-0.00625.1590.6290.6290.0000.0000.0000.000
141A157SER0-0.035-0.00122.674-1.006-1.0060.0000.0000.0000.000
142A158VAL00.0350.02119.0010.4520.4520.0000.0000.0000.000
143A159THR0-0.066-0.05217.844-1.270-1.2700.0000.0000.0000.000
144A160LEU00.0230.03612.6051.4271.4270.0000.0000.0000.000
145A161ASN00.030-0.00515.980-2.388-2.3880.0000.0000.0000.000
146A162ILE00.0230.02313.7020.0810.0810.0000.0000.0000.000
147A163VAL0-0.013-0.00817.5630.6180.6180.0000.0000.0000.000
148A164ARG10.8540.91421.40521.29721.2970.0000.0000.0000.000
149A165ASP-1-0.912-0.93919.823-26.676-26.6760.0000.0000.0000.000
150A166HIS10.8430.92519.49126.03226.0320.0000.0000.0000.000
151A167VAL00.0550.03514.395-0.254-0.2540.0000.0000.0000.000
152A168VAL00.002-0.00117.2801.5751.5750.0000.0000.0000.000
153A169ILE0-0.015-0.00515.671-1.603-1.6030.0000.0000.0000.000
154A170SER00.0040.01519.2891.9031.9030.0000.0000.0000.000
155A171VAL0-0.027-0.02421.773-1.292-1.2920.0000.0000.0000.000
156A172LEU00.0300.02524.3980.8870.8870.0000.0000.0000.000
157A173CYS0-0.042-0.01826.974-0.317-0.3170.0000.0000.0000.000
158A174HIS0-0.011-0.01525.3841.1391.1390.0000.0000.0000.000
159A175ALA0-0.025-0.01830.7920.7910.7910.0000.0000.0000.000
160A176VAL00.004-0.00632.156-0.511-0.5110.0000.0000.0000.000
161A177SER0-0.035-0.01932.2650.7050.7050.0000.0000.0000.000
162A178ALA0-0.037-0.02535.0440.1420.1420.0000.0000.0000.000
163A179SER00.0190.00335.939-0.452-0.4520.0000.0000.0000.000
164A180SER0-0.031-0.01936.4770.3790.3790.0000.0000.0000.000
165A181VAL0-0.026-0.00735.9570.3700.3700.0000.0000.0000.000
166A182LYS10.9740.98738.93313.72913.7290.0000.0000.0000.000
167A183ILE00.0300.03136.9810.1420.1420.0000.0000.0000.000
168A184ASP-1-0.870-0.93640.881-13.432-13.4320.0000.0000.0000.000
169A185VAL00.0430.00242.079-0.118-0.1180.0000.0000.0000.000
170A186THR0-0.0060.01143.443-0.085-0.0850.0000.0000.0000.000
171A187ILE0-0.038-0.02943.8580.0380.0380.0000.0000.0000.000
172A188LEU0-0.014-0.01037.606-0.070-0.0700.0000.0000.0000.000
173A189GLN0-0.009-0.02241.689-0.371-0.3710.0000.0000.0000.000
174A190ARG10.8630.91743.20113.21813.2180.0000.0000.0000.000
175A191LYS10.8740.92841.21514.70514.7050.0000.0000.0000.000
176A192ILE0-0.014-0.00837.769-0.233-0.2330.0000.0000.0000.000
177A193ASP-1-0.878-0.93040.949-14.041-14.0410.0000.0000.0000.000
178A194GLU-1-0.912-0.93944.202-13.121-13.1210.0000.0000.0000.000
179A195MET0-0.114-0.03935.791-0.187-0.1870.0000.0000.0000.000
180A196ASP-1-0.875-0.91941.245-14.149-14.1490.0000.0000.0000.000
181A197ILE0-0.053-0.04136.276-0.460-0.4600.0000.0000.0000.000
182A198PRO0-0.0130.00235.6900.3060.3060.0000.0000.0000.000
183A199ASN00.0160.01137.250-0.058-0.0580.0000.0000.0000.000
184A200ASP-1-0.789-0.89932.728-18.147-18.1470.0000.0000.0000.000
185A201VAL00.0040.00732.225-0.510-0.5100.0000.0000.0000.000
186A202SER0-0.029-0.01433.259-0.249-0.2490.0000.0000.0000.000
187A203GLU-1-0.933-0.97834.319-16.857-16.8570.0000.0000.0000.000
188A204SER0-0.139-0.06529.240-0.590-0.5900.0000.0000.0000.000
189A205PHE00.0260.00630.439-0.462-0.4620.0000.0000.0000.000
190A206GLU-1-0.859-0.91832.429-16.700-16.7000.0000.0000.0000.000
191A207ARG10.8770.92527.15620.85020.8500.0000.0000.0000.000
192A208TYR0-0.044-0.02725.353-0.665-0.6650.0000.0000.0000.000
193A209LYS10.9110.96529.19916.35016.3500.0000.0000.0000.000
194A210GLU-1-0.886-0.95530.143-18.655-18.6550.0000.0000.0000.000
195A211LEU0-0.003-0.00123.731-0.143-0.1430.0000.0000.0000.000
196A212ILE00.0160.00927.712-0.360-0.3600.0000.0000.0000.000
197A213GLN0-0.0010.00329.6450.3750.3750.0000.0000.0000.000
198A214GLU-1-0.892-0.93425.900-22.740-22.7400.0000.0000.0000.000
199A215LEU0-0.030-0.02523.544-0.368-0.3680.0000.0000.0000.000
200A216CYS0-0.089-0.05227.6150.1270.1270.0000.0000.0000.000
201A217GLN0-0.091-0.04130.3440.8890.8890.0000.0000.0000.000
202A218SER-1-0.846-0.89527.637-21.053-21.0530.0000.0000.0000.000