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: YMZL2

Calculation Name: 3OTD-A-Xray549

Preferred Name:

Target Type:

Ligand Name: iodide ion

Ligand 3-letter code: IOD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3OTD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NWX6

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 240
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3154311.05729
FMO2-HF: Nuclear repulsion 3055042.673208
FMO2-HF: Total energy -99268.384081
FMO2-MP2: Total energy -99558.064916


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:3:LYS)


Summations of interaction energy for fragment #1(A:3: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.
-54.135-51.855-0.014-1-1.266-0.005
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.845 / q_NPA : 1.894
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].
3A5LYS10.9771.0043.83865.64767.927-0.014-1.000-1.266-0.005
4A6PHE00.0430.0005.7275.7495.7490.0000.0000.0000.000
5A7GLU-1-0.910-0.9485.755-70.935-70.9350.0000.0000.0000.000
6A8TYR00.0540.0338.2303.0583.0580.0000.0000.0000.000
7A9VAL0-0.0130.00010.3493.1433.1430.0000.0000.0000.000
8A10ARG10.8840.9229.57351.74551.7450.0000.0000.0000.000
9A11ASP-1-0.914-0.94912.344-44.823-44.8230.0000.0000.0000.000
10A12PHE0-0.071-0.03414.8281.7411.7410.0000.0000.0000.000
11A13GLU-1-0.913-0.94917.137-30.302-30.3020.0000.0000.0000.000
12A14ALA0-0.0150.00019.008-0.259-0.2590.0000.0000.0000.000
13A15ASP-1-0.851-0.91322.196-23.931-23.9310.0000.0000.0000.000
14A16ASP-1-0.762-0.84824.208-23.100-23.1000.0000.0000.0000.000
15A17THR0-0.057-0.03926.4950.6210.6210.0000.0000.0000.000
16A18CYS0-0.062-0.02128.8330.7290.7290.0000.0000.0000.000
17A19LEU00.0190.01232.546-0.164-0.1640.0000.0000.0000.000
18A20ALA00.0480.02433.4800.2760.2760.0000.0000.0000.000
19A21HIS0-0.031-0.02935.1310.0780.0780.0000.0000.0000.000
20A22CYS0-0.0400.00937.8390.6140.6140.0000.0000.0000.000
21A23TRP00.0170.00038.380-0.522-0.5220.0000.0000.0000.000
22A24VAL0-0.0120.00034.493-0.059-0.0590.0000.0000.0000.000
23A25VAL0-0.002-0.00237.8400.1960.1960.0000.0000.0000.000
24A26VAL0-0.0070.00835.285-0.282-0.2820.0000.0000.0000.000
25A27ARG10.7870.85938.09714.40314.4030.0000.0000.0000.000
26A28LEU0-0.0100.00436.744-0.437-0.4370.0000.0000.0000.000
27A29ASP-1-0.769-0.85440.493-14.020-14.0200.0000.0000.0000.000
28A30GLY00.0630.02441.746-0.345-0.3450.0000.0000.0000.000
29A31ARG10.9420.97138.11316.04216.0420.0000.0000.0000.000
30A32ASN0-0.069-0.04742.4620.0910.0910.0000.0000.0000.000
31A33PHE00.0250.01743.1520.1400.1400.0000.0000.0000.000
32A34HIS00.0430.04647.3790.0310.0310.0000.0000.0000.000
33A35ARG10.9890.98346.93413.04213.0420.0000.0000.0000.000
34A36PHE00.0190.01544.8680.0780.0780.0000.0000.0000.000
35A37ALA00.0500.02348.5640.1150.1150.0000.0000.0000.000
36A38GLU-1-0.908-0.95151.930-10.983-10.9830.0000.0000.0000.000
37A39LYS10.8470.92748.24112.75012.7500.0000.0000.0000.000
38A40HIS0-0.029-0.00147.046-0.113-0.1130.0000.0000.0000.000
39A41ASN0-0.060-0.02652.2000.1700.1700.0000.0000.0000.000
40A42PHE00.007-0.00249.3530.0480.0480.0000.0000.0000.000
41A43ALA00.0040.00455.4570.1260.1260.0000.0000.0000.000
42A44LYS10.8740.94355.60110.92610.9260.0000.0000.0000.000
43A45PRO0-0.0060.00160.0320.1780.1780.0000.0000.0000.000
44A46ASN0-0.039-0.03157.188-0.368-0.3680.0000.0000.0000.000
45A47ASP-1-0.718-0.83354.689-11.130-11.1300.0000.0000.0000.000
46A48SER00.0360.01154.608-0.184-0.1840.0000.0000.0000.000
47A49ARG10.8600.93052.97911.10411.1040.0000.0000.0000.000
48A50ALA00.0320.02050.172-0.270-0.2700.0000.0000.0000.000
49A51LEU00.0080.00549.500-0.271-0.2710.0000.0000.0000.000
50A52GLN0-0.008-0.00250.156-0.083-0.0830.0000.0000.0000.000
51A53LEU00.0140.03445.112-0.208-0.2080.0000.0000.0000.000
52A54MET0-0.0180.00544.854-0.466-0.4660.0000.0000.0000.000
53A55THR00.0110.00145.185-0.298-0.2980.0000.0000.0000.000
54A56LYS10.9310.98843.42413.93613.9360.0000.0000.0000.000
55A57CYS0-0.077-0.02541.504-0.363-0.3630.0000.0000.0000.000
56A58ALA00.006-0.00541.191-0.411-0.4110.0000.0000.0000.000
57A59GLN0-0.028-0.03142.118-0.223-0.2230.0000.0000.0000.000
58A60THR00.0220.00338.516-0.132-0.1320.0000.0000.0000.000
59A61VAL0-0.041-0.01936.960-0.448-0.4480.0000.0000.0000.000
60A62MET0-0.072-0.04337.758-0.228-0.2280.0000.0000.0000.000
61A63GLU-1-0.893-0.94639.663-14.365-14.3650.0000.0000.0000.000
62A64GLU-1-0.936-0.96434.834-17.261-17.2610.0000.0000.0000.000
63A65LEU0-0.091-0.03132.342-0.836-0.8360.0000.0000.0000.000
64A66GLU-1-0.845-0.92431.985-18.866-18.8660.0000.0000.0000.000
65A67ASP-1-0.816-0.91635.130-17.777-17.7770.0000.0000.0000.000
66A68ILE0-0.049-0.00437.0390.3150.3150.0000.0000.0000.000
67A69VAL0-0.0040.00139.7170.1870.1870.0000.0000.0000.000
68A70ILE0-0.011-0.00543.3280.3680.3680.0000.0000.0000.000
69A71ALA00.0110.01043.299-0.397-0.3970.0000.0000.0000.000
70A72TYR0-0.051-0.06045.0690.3220.3220.0000.0000.0000.000
71A73GLY00.0510.03046.545-0.331-0.3310.0000.0000.0000.000
72A74GLN0-0.091-0.05848.2500.3840.3840.0000.0000.0000.000
73A75SER00.0390.02649.594-0.186-0.1860.0000.0000.0000.000
74A76ASP-1-0.871-0.94146.914-12.833-12.8330.0000.0000.0000.000
75A77GLU-1-0.831-0.88145.093-13.679-13.6790.0000.0000.0000.000
76A78TYR00.030-0.00943.1130.2090.2090.0000.0000.0000.000
77A79SER0-0.038-0.00442.392-0.446-0.4460.0000.0000.0000.000
78A80PHE00.0160.00739.3350.2720.2720.0000.0000.0000.000
79A81VAL00.0000.00240.217-0.313-0.3130.0000.0000.0000.000
80A82PHE00.0220.00934.6530.0880.0880.0000.0000.0000.000
81A83LYS10.8090.89438.26215.79315.7930.0000.0000.0000.000
82A84ARG10.9831.00037.85914.03314.0330.0000.0000.0000.000
83A85LYS10.9120.98337.14515.71015.7100.0000.0000.0000.000
84A86THR0-0.098-0.05933.789-0.788-0.7880.0000.0000.0000.000
85A87ASN0-0.004-0.03229.786-0.748-0.7480.0000.0000.0000.000
86A88TRP0-0.0260.00528.948-1.094-1.0940.0000.0000.0000.000
87A89PHE00.0450.01124.139-1.086-1.0860.0000.0000.0000.000
88A90LYS10.9060.93622.81425.77825.7780.0000.0000.0000.000
89A91ARG10.7840.86926.96418.36618.3660.0000.0000.0000.000
90A92ARG10.8220.92020.46027.65527.6550.0000.0000.0000.000
91A93ALA00.0770.02527.6060.2730.2730.0000.0000.0000.000
92A94SER0-0.030-0.04725.9670.2750.2750.0000.0000.0000.000
93A95LYS10.8990.97221.93826.21026.2100.0000.0000.0000.000
94A96PHE00.0340.02628.1140.2910.2910.0000.0000.0000.000
95A97MET00.001-0.00230.5520.5670.5670.0000.0000.0000.000
96A98THR0-0.041-0.04427.3400.2190.2190.0000.0000.0000.000
97A99HIS0-0.0100.02526.5240.4900.4900.0000.0000.0000.000
98A100VAL00.0370.02631.0750.4190.4190.0000.0000.0000.000
99A101ALA00.0120.00033.2080.4290.4290.0000.0000.0000.000
100A102SER0-0.076-0.05830.9720.3480.3480.0000.0000.0000.000
101A103GLN00.0620.03733.0350.4010.4010.0000.0000.0000.000
102A104PHE00.0280.02635.0370.5300.5300.0000.0000.0000.000
103A105ALA0-0.006-0.01035.6460.4290.4290.0000.0000.0000.000
104A106SER0-0.025-0.01434.7480.4070.4070.0000.0000.0000.000
105A107SER00.017-0.00736.8520.4260.4260.0000.0000.0000.000
106A108TYR00.030-0.00739.9850.4590.4590.0000.0000.0000.000
107A109VAL0-0.057-0.03839.1410.3560.3560.0000.0000.0000.000
108A110PHE0-0.057-0.01739.4700.2370.2370.0000.0000.0000.000
109A111TYR00.0350.00541.0040.2950.2950.0000.0000.0000.000
110A112TRP0-0.033-0.01244.6320.2590.2590.0000.0000.0000.000
111A113ARG10.8850.90546.52512.49512.4950.0000.0000.0000.000
112A114ASP-1-0.884-0.92647.396-12.760-12.7600.0000.0000.0000.000
113A115TYR0-0.037-0.02048.0710.2640.2640.0000.0000.0000.000
114A116PHE0-0.066-0.04449.5880.2950.2950.0000.0000.0000.000
115A117GLU-1-0.897-0.92951.590-11.190-11.1900.0000.0000.0000.000
116A118ASP-1-0.907-0.95053.564-10.882-10.8820.0000.0000.0000.000
117A119GLN0-0.058-0.02451.5970.1500.1500.0000.0000.0000.000
118A120PRO00.0310.01749.738-0.252-0.2520.0000.0000.0000.000
119A121LEU00.0200.02242.8480.0410.0410.0000.0000.0000.000
120A122LEU0-0.024-0.03746.425-0.124-0.1240.0000.0000.0000.000
121A123TYR0-0.052-0.03942.4160.0670.0670.0000.0000.0000.000
122A124PRO00.0370.03038.5000.1600.1600.0000.0000.0000.000
123A125PRO0-0.0060.00440.318-0.118-0.1180.0000.0000.0000.000
124A126GLY0-0.021-0.00837.939-0.403-0.4030.0000.0000.0000.000
125A127PHE00.001-0.01737.6410.4350.4350.0000.0000.0000.000
126A128ASP-1-0.927-0.95937.188-16.451-16.4510.0000.0000.0000.000
127A129GLY00.018-0.00336.4690.1730.1730.0000.0000.0000.000
128A130ARG10.8480.92436.08914.62514.6250.0000.0000.0000.000
129A131VAL00.0300.00733.2710.0800.0800.0000.0000.0000.000
130A132VAL0-0.044-0.01736.3170.0600.0600.0000.0000.0000.000
131A133VAL00.0120.00635.498-0.111-0.1110.0000.0000.0000.000
132A134TYR0-0.005-0.00438.8460.2670.2670.0000.0000.0000.000
133A135PRO00.0160.00142.086-0.105-0.1050.0000.0000.0000.000
134A136SER0-0.005-0.00743.0330.2150.2150.0000.0000.0000.000
135A137ASN00.0950.03646.266-0.295-0.2950.0000.0000.0000.000
136A138GLN0-0.033-0.01548.1470.1290.1290.0000.0000.0000.000
137A139THR00.006-0.00446.333-0.019-0.0190.0000.0000.0000.000
138A140LEU00.0070.01544.078-0.070-0.0700.0000.0000.0000.000
139A141LYS10.9310.97447.04111.82411.8240.0000.0000.0000.000
140A142ASP-1-0.833-0.89250.450-11.981-11.9810.0000.0000.0000.000
141A143TYR0-0.028-0.02844.4680.0800.0800.0000.0000.0000.000
142A144LEU00.018-0.00146.4200.0520.0520.0000.0000.0000.000
143A145SER00.012-0.01049.6540.2470.2470.0000.0000.0000.000
144A146TRP0-0.037-0.01346.8250.0690.0690.0000.0000.0000.000
145A147ARG10.7500.84147.44712.97312.9730.0000.0000.0000.000
146A148GLN00.0640.02350.9920.2480.2480.0000.0000.0000.000
147A149ALA0-0.014-0.01554.1420.2420.2420.0000.0000.0000.000
148A150ASP-1-0.853-0.90652.304-11.973-11.9730.0000.0000.0000.000
149A151CYS00.0080.02253.7370.1730.1730.0000.0000.0000.000
150A152HIS00.0070.01055.3360.1420.1420.0000.0000.0000.000
151A153ILE0-0.003-0.00857.5850.1900.1900.0000.0000.0000.000
152A154ASN0-0.016-0.01454.2420.2880.2880.0000.0000.0000.000
153A155ASN00.0480.02957.9360.0800.0800.0000.0000.0000.000
154A156LEU0-0.046-0.00259.6550.1880.1880.0000.0000.0000.000
155A157TYR0-0.015-0.01160.6500.2280.2280.0000.0000.0000.000
156A158ASN00.012-0.00856.9050.1930.1930.0000.0000.0000.000
157A159THR0-0.003-0.02261.3810.0850.0850.0000.0000.0000.000
158A160VAL00.0220.01264.1350.1290.1290.0000.0000.0000.000
159A161PHE0-0.015-0.01161.3340.1060.1060.0000.0000.0000.000
160A162TRP00.009-0.02358.8160.0610.0610.0000.0000.0000.000
161A163ALA00.0390.05164.6260.0520.0520.0000.0000.0000.000
162A164LEU00.011-0.00968.1750.1170.1170.0000.0000.0000.000
163A165ILE0-0.050-0.01663.9490.0780.0780.0000.0000.0000.000
164A166GLN0-0.100-0.06163.9150.0170.0170.0000.0000.0000.000
165A167GLN0-0.045-0.01568.275-0.033-0.0330.0000.0000.0000.000
166A168SER0-0.0050.00271.6930.1050.1050.0000.0000.0000.000
167A169GLY0-0.0140.01271.4440.0970.0970.0000.0000.0000.000
168A170LEU0-0.069-0.02670.1370.0120.0120.0000.0000.0000.000
169A171THR00.013-0.02667.727-0.184-0.1840.0000.0000.0000.000
170A172PRO00.049-0.00262.9720.0280.0280.0000.0000.0000.000
171A173VAL00.0110.01165.125-0.049-0.0490.0000.0000.0000.000
172A174GLN00.0490.04666.411-0.024-0.0240.0000.0000.0000.000
173A175ALA00.0410.02966.2790.0730.0730.0000.0000.0000.000
174A176GLN0-0.015-0.00861.7630.0500.0500.0000.0000.0000.000
175A177GLY0-0.006-0.00665.8510.0080.0080.0000.0000.0000.000
176A178ARG10.9140.95768.9698.7978.7970.0000.0000.0000.000
177A179LEU00.0360.01965.7070.0770.0770.0000.0000.0000.000
178A180GLN0-0.0100.01764.2920.0050.0050.0000.0000.0000.000
179A181GLY0-0.016-0.00766.7320.1410.1410.0000.0000.0000.000
180A182THR0-0.052-0.01868.0230.0200.0200.0000.0000.0000.000
181A183LEU00.002-0.01767.264-0.207-0.2070.0000.0000.0000.000
182A184ALA00.003-0.01165.651-0.001-0.0010.0000.0000.0000.000
183A185ALA00.0130.00567.4450.0180.0180.0000.0000.0000.000
184A186ASP-1-0.781-0.89370.894-8.860-8.8600.0000.0000.0000.000
185A187LYS10.8570.93464.1879.7719.7710.0000.0000.0000.000
186A188ASN0-0.018-0.01268.1220.0380.0380.0000.0000.0000.000
187A189GLU-1-0.863-0.91170.837-8.255-8.2550.0000.0000.0000.000
188A190ILE0-0.0040.00171.1240.0670.0670.0000.0000.0000.000
189A191LEU0-0.026-0.01067.1200.0230.0230.0000.0000.0000.000
190A192PHE0-0.034-0.00571.7260.0540.0540.0000.0000.0000.000
191A193SER0-0.025-0.04674.9440.1050.1050.0000.0000.0000.000
192A194GLU-1-0.960-0.97674.623-8.444-8.4440.0000.0000.0000.000
193A195PHE0-0.030-0.02671.499-0.005-0.0050.0000.0000.0000.000
194A196ASN0-0.064-0.01974.0650.0760.0760.0000.0000.0000.000
195A197ILE0-0.0080.00268.677-0.022-0.0220.0000.0000.0000.000
196A198ASN00.0280.01271.618-0.078-0.0780.0000.0000.0000.000
197A199TYR00.0810.03762.101-0.124-0.1240.0000.0000.0000.000
198A200ASN0-0.038-0.03166.646-0.275-0.2750.0000.0000.0000.000
199A201ASN0-0.081-0.04667.4750.0360.0360.0000.0000.0000.000
200A202GLU-1-0.852-0.91763.681-9.801-9.8010.0000.0000.0000.000
201A203LEU00.0210.02060.931-0.036-0.0360.0000.0000.0000.000
202A204PRO0-0.001-0.01260.004-0.121-0.1210.0000.0000.0000.000
203A205MET0-0.0160.00254.714-0.115-0.1150.0000.0000.0000.000
204A206TYR0-0.001-0.01456.193-0.141-0.1410.0000.0000.0000.000
205A207ARG10.8500.93458.1369.9029.9020.0000.0000.0000.000
206A208LYS10.8470.92957.20310.86210.8620.0000.0000.0000.000
207A209GLY00.0560.05553.301-0.228-0.2280.0000.0000.0000.000
208A210THR0-0.042-0.02550.6300.2800.2800.0000.0000.0000.000
209A211VAL0-0.0130.00449.919-0.269-0.2690.0000.0000.0000.000
210A212LEU0-0.034-0.00745.5650.1320.1320.0000.0000.0000.000
211A213ILE00.0330.00247.193-0.248-0.2480.0000.0000.0000.000
212A214TRP0-0.036-0.01541.0700.2420.2420.0000.0000.0000.000
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