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: 7KQVK

Calculation Name: 3TOC-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion | 1,2-ethanediol

Ligand 3-letter code: CA | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3TOC

Chain ID: A

ChEMBL ID:

UniProt ID: Q99ZV9

Base Structure: X-ray

Registration Date: 2025-10-05

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 219
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2505855.992226
FMO2-HF: Nuclear repulsion 2416365.040617
FMO2-HF: Total energy -89490.951609
FMO2-MP2: Total energy -89750.638182


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-294.431-284.54335.065-17.436-27.514-0.178
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.695 / q_NPA : 0.854
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].
3A3LEU00.0670.0463.8110.4722.469-0.019-0.962-1.015-0.003
13A13PRO0-0.054-0.0244.778-7.859-7.781-0.001-0.025-0.0520.000
14A14LEU00.0170.0052.1015.3276.3033.367-1.390-2.952-0.004
15A15ARG10.9380.9481.957-2.2560.2855.677-4.594-3.624-0.065
16A16GLY00.0230.0244.4686.7196.827-0.001-0.031-0.0750.000
46A46PHE00.0440.0223.667-3.301-2.9200.003-0.057-0.3270.000
47A47PHE0-0.044-0.0244.2293.1413.526-0.001-0.089-0.2940.000
48A48ASP-1-0.827-0.9292.407-69.595-67.0293.473-2.795-3.244-0.031
49A49HIS00.0440.0181.939-30.647-32.73312.727-4.504-6.137-0.057
50A50LYS10.8700.9393.54141.01841.0970.026-0.008-0.0970.000
54A54ILE0-0.064-0.0262.0920.9550.3263.619-0.559-2.430-0.002
162A162LYS10.7760.8802.35729.65030.0281.130-0.362-1.1460.002
163A163LEU00.0160.0132.501-7.014-4.4212.479-1.350-3.722-0.016
164A164LEU0-0.0150.0103.9372.5382.6670.011-0.017-0.1240.000
191A191THR0-0.062-0.0372.494-5.628-5.3632.576-0.679-2.162-0.002
192A192VAL0-0.014-0.0165.2701.7841.911-0.001-0.014-0.1130.000
4A4ASN00.029-0.0046.0931.0601.0600.0000.0000.0000.000
5A5PHE00.0970.0319.6490.5930.5930.0000.0000.0000.000
6A6SER0-0.033-0.02013.103-0.105-0.1050.0000.0000.0000.000
7A7LEU0-0.024-0.00516.4240.7170.7170.0000.0000.0000.000
8A8LEU0-0.0100.01911.424-0.036-0.0360.0000.0000.0000.000
9A9ASP-1-0.834-0.90015.523-16.366-16.3660.0000.0000.0000.000
10A10GLU-1-0.995-1.00112.162-24.141-24.1410.0000.0000.0000.000
11A11PRO0-0.060-0.0398.075-0.895-0.8950.0000.0000.0000.000
12A12ILE00.0650.0497.863-1.081-1.0810.0000.0000.0000.000
17A17GLY00.0400.0216.779-2.006-2.0060.0000.0000.0000.000
18A18THR0-0.017-0.0136.620-1.044-1.0440.0000.0000.0000.000
19A19ILE00.0370.0148.8150.4990.4990.0000.0000.0000.000
20A20LEU0-0.021-0.01210.089-0.953-0.9530.0000.0000.0000.000
21A21VAL00.0010.00912.6360.7610.7610.0000.0000.0000.000
22A22LEU0-0.027-0.02314.033-0.366-0.3660.0000.0000.0000.000
23A23GLU-1-0.878-0.94217.690-13.080-13.0800.0000.0000.0000.000
24A24ASP-1-0.814-0.90221.240-11.958-11.9580.0000.0000.0000.000
25A25VAL0-0.006-0.01621.287-0.481-0.4810.0000.0000.0000.000
26A26CYS0-0.028-0.01122.5440.0110.0110.0000.0000.0000.000
27A27VAL00.0220.01117.533-0.197-0.1970.0000.0000.0000.000
28A28PHE00.0130.00616.919-0.555-0.5550.0000.0000.0000.000
29A29SER0-0.036-0.03017.636-0.435-0.4350.0000.0000.0000.000
30A30LYS10.8930.95518.36513.35213.3520.0000.0000.0000.000
31A31ILE00.0480.03112.333-0.475-0.4750.0000.0000.0000.000
32A32VAL00.0060.00913.886-0.962-0.9620.0000.0000.0000.000
33A33GLN0-0.052-0.03015.384-0.058-0.0580.0000.0000.0000.000
34A34TYR0-0.082-0.08013.8740.1540.1540.0000.0000.0000.000
35A35CYS0-0.054-0.02411.076-1.589-1.5890.0000.0000.0000.000
36A36TYR0-0.046-0.02112.031-0.177-0.1770.0000.0000.0000.000
37A37GLN0-0.072-0.04614.8770.7410.7410.0000.0000.0000.000
38A38TYR-1-0.755-0.8797.603-27.890-27.8900.0000.0000.0000.000
39A39GLU0-0.056-0.02411.106-0.229-0.2290.0000.0000.0000.000
40A40GLU-1-0.949-0.96812.877-13.874-13.8740.0000.0000.0000.000
41A41ASP-1-0.844-0.90715.496-14.850-14.8500.0000.0000.0000.000
42A42SER0-0.009-0.00113.355-1.509-1.5090.0000.0000.0000.000
43A43GLU-1-0.882-0.92414.234-16.619-16.6190.0000.0000.0000.000
44A44LEU0-0.040-0.0099.656-0.777-0.7770.0000.0000.0000.000
45A45LYS10.7650.8699.28022.75022.7500.0000.0000.0000.000
51A51MET00.0130.0085.5765.1655.1650.0000.0000.0000.000
52A52LYS10.7960.9006.08033.26233.2620.0000.0000.0000.000
53A53THR00.0920.0496.067-4.385-4.3850.0000.0000.0000.000
55A55LYS10.9180.9685.42323.35723.3570.0000.0000.0000.000
56A56GLU-1-0.815-0.9077.221-19.030-19.0300.0000.0000.0000.000
57A57SER00.0350.0159.354-0.216-0.2160.0000.0000.0000.000
58A58GLU-1-0.856-0.9255.313-28.195-28.1950.0000.0000.0000.000
59A59ILE00.0610.0354.906-2.770-2.7700.0000.0000.0000.000
60A60MET0-0.0380.0056.8112.3802.3800.0000.0000.0000.000
61A61LEU00.0300.0269.349-1.352-1.3520.0000.0000.0000.000
62A62VAL0-0.018-0.00711.9561.1041.1040.0000.0000.0000.000
63A63THR00.015-0.00314.913-0.352-0.3520.0000.0000.0000.000
64A64ASP-1-0.841-0.90918.092-11.471-11.4710.0000.0000.0000.000
65A65ILE00.0240.00118.269-0.300-0.3000.0000.0000.0000.000
66A66LEU00.0190.01120.089-0.035-0.0350.0000.0000.0000.000
67A67GLY00.0210.00423.2420.2000.2000.0000.0000.0000.000
68A68PHE0-0.041-0.01514.566-0.066-0.0660.0000.0000.0000.000
69A69ASP-1-0.817-0.91119.825-11.580-11.5800.0000.0000.0000.000
70A70VAL0-0.020-0.01417.930-0.589-0.5890.0000.0000.0000.000
71A71ASN0-0.013-0.02719.816-0.066-0.0660.0000.0000.0000.000
72A72SER00.0730.05018.9360.3260.3260.0000.0000.0000.000
73A73SER00.033-0.00921.550-0.165-0.1650.0000.0000.0000.000
74A74THR0-0.052-0.02517.1660.3110.3110.0000.0000.0000.000
75A75ILE00.0280.02016.865-0.240-0.2400.0000.0000.0000.000
76A76LEU00.0070.01719.3180.0460.0460.0000.0000.0000.000
77A77LYS10.9450.97421.86911.70411.7040.0000.0000.0000.000
78A78LEU0-0.052-0.02416.3940.1360.1360.0000.0000.0000.000
79A79ILE00.0600.03220.5630.0430.0430.0000.0000.0000.000
80A80HIS0-0.040-0.03922.4360.2800.2800.0000.0000.0000.000
81A81ALA00.0330.01622.6840.2700.2700.0000.0000.0000.000
82A82ASP-1-0.845-0.89821.342-12.844-12.8440.0000.0000.0000.000
83A83LEU00.0160.01223.3520.2300.2300.0000.0000.0000.000
84A84GLU-1-0.899-0.95526.786-9.365-9.3650.0000.0000.0000.000
85A85SER0-0.094-0.06224.6150.1090.1090.0000.0000.0000.000
86A86GLN0-0.013-0.02224.1860.5180.5180.0000.0000.0000.000
87A87PHE0-0.030-0.02128.1120.3080.3080.0000.0000.0000.000
88A88ASN0-0.019-0.01028.7380.5430.5430.0000.0000.0000.000
89A89GLU-1-0.940-0.95427.753-10.558-10.5580.0000.0000.0000.000
90A90LYS10.8750.94130.9949.5239.5230.0000.0000.0000.000
91A91PRO00.0590.03234.3860.1840.1840.0000.0000.0000.000
92A92GLU-1-0.900-0.95536.953-7.440-7.4400.0000.0000.0000.000
93A93VAL0-0.039-0.02436.6380.1580.1580.0000.0000.0000.000
94A94LYS10.8580.92634.1748.4438.4430.0000.0000.0000.000
95A95SER00.0180.02037.2060.1590.1590.0000.0000.0000.000
96A96MET0-0.021-0.01540.6590.2150.2150.0000.0000.0000.000
97A97ILE00.0080.00236.2910.1330.1330.0000.0000.0000.000
98A98ASP-1-0.774-0.87938.192-7.823-7.8230.0000.0000.0000.000
99A99LYS10.9340.97540.8486.4636.4630.0000.0000.0000.000
100A100LEU0-0.045-0.01942.3190.1780.1780.0000.0000.0000.000
101A101VAL00.0370.01639.2410.1270.1270.0000.0000.0000.000
102A102ALA00.0030.02042.6960.0970.0970.0000.0000.0000.000
103A103THR0-0.022-0.02645.3700.1520.1520.0000.0000.0000.000
104A104ILE0-0.028-0.01743.1460.1090.1090.0000.0000.0000.000
105A105THR0-0.004-0.01444.2280.0450.0450.0000.0000.0000.000
106A106GLU-1-0.965-0.97846.573-5.752-5.7520.0000.0000.0000.000
107A107LEU0-0.035-0.02149.8180.1120.1120.0000.0000.0000.000
108A108ILE00.0100.00245.6390.0780.0780.0000.0000.0000.000
109A109VAL00.0260.01448.7010.0650.0650.0000.0000.0000.000
110A110PHE0-0.060-0.02051.1970.1090.1090.0000.0000.0000.000
111A111GLU-1-0.908-0.96452.246-5.390-5.3900.0000.0000.0000.000
112A112CYS0-0.116-0.06450.6340.0110.0110.0000.0000.0000.000
113A113LEU0-0.055-0.02353.3730.0610.0610.0000.0000.0000.000
114A114GLU-1-0.949-0.97456.709-4.933-4.9330.0000.0000.0000.000
115A115ASN0-0.078-0.02855.3030.0790.0790.0000.0000.0000.000
116A116GLU-1-0.967-0.98657.437-4.928-4.9280.0000.0000.0000.000
117A117LEU0-0.079-0.03754.6170.0410.0410.0000.0000.0000.000
118A118ASP-1-0.914-0.95956.028-5.215-5.2150.0000.0000.0000.000
119A119LEU0-0.072-0.02750.935-0.095-0.0950.0000.0000.0000.000
120A120GLU-1-0.978-0.98148.087-6.077-6.0770.0000.0000.0000.000
121A121TYR0-0.044-0.03745.843-0.051-0.0510.0000.0000.0000.000
122A122ASP-1-0.903-0.95141.270-7.040-7.0400.0000.0000.0000.000
123A123GLU-1-1.027-1.01238.448-7.545-7.5450.0000.0000.0000.000
124A124ILE00.0050.00738.798-0.059-0.0590.0000.0000.0000.000
125A125THR0-0.017-0.03434.252-0.156-0.1560.0000.0000.0000.000
126A126ILE00.023-0.00932.128-0.017-0.0170.0000.0000.0000.000
127A127LEU0-0.021-0.00427.113-0.103-0.1030.0000.0000.0000.000
128A128GLU-1-0.807-0.88231.120-8.190-8.1900.0000.0000.0000.000
129A129LEU00.0030.02233.7150.0590.0590.0000.0000.0000.000
130A130ILE0-0.026-0.01228.5180.0090.0090.0000.0000.0000.000
131A131LYS10.8750.94127.6809.6529.6520.0000.0000.0000.000
132A132SER0-0.028-0.02531.4870.0820.0820.0000.0000.0000.000
133A133LEU0-0.060-0.01733.4450.1540.1540.0000.0000.0000.000
134A134GLY0-0.012-0.00131.865-0.006-0.0060.0000.0000.0000.000
135A135VAL0-0.046-0.01627.413-0.163-0.1630.0000.0000.0000.000
136A136LYS10.9520.97425.8889.1199.1190.0000.0000.0000.000
137A137VAL00.0080.00921.5170.1000.1000.0000.0000.0000.000
138A138GLU-1-0.764-0.86325.003-9.460-9.4600.0000.0000.0000.000
139A139THR0-0.058-0.04723.813-0.351-0.3510.0000.0000.0000.000
140A140GLN0-0.100-0.03826.5590.1020.1020.0000.0000.0000.000
141A141SER0-0.103-0.08029.9530.2130.2130.0000.0000.0000.000
142A142ASP-1-0.793-0.85724.539-11.215-11.2150.0000.0000.0000.000
143A143THR0-0.027-0.03426.205-0.112-0.1120.0000.0000.0000.000
144A144ILE00.010-0.01421.693-0.321-0.3210.0000.0000.0000.000
145A145PHE00.0630.03520.298-0.658-0.6580.0000.0000.0000.000
146A146GLU-1-0.810-0.88320.988-11.284-11.2840.0000.0000.0000.000
147A147LYS10.8190.90820.47912.01212.0120.0000.0000.0000.000
148A148CYS0-0.049-0.02717.210-0.679-0.6790.0000.0000.0000.000
149A149LEU00.0120.00616.653-0.981-0.9810.0000.0000.0000.000
150A150GLU0-0.048-0.04917.708-0.432-0.4320.0000.0000.0000.000
151A151ILE0-0.015-0.00513.775-0.376-0.3760.0000.0000.0000.000
152A152LEU0-0.018-0.01011.840-0.949-0.9490.0000.0000.0000.000
153A153GLN0-0.024-0.01213.750-0.345-0.3450.0000.0000.0000.000
154A154ILE0-0.034-0.01714.293-0.058-0.0580.0000.0000.0000.000
155A155PHE0-0.004-0.0106.010-0.088-0.0880.0000.0000.0000.000
156A156LYS10.9500.98911.26715.71215.7120.0000.0000.0000.000
157A157TYR0-0.100-0.06012.851-0.146-0.1460.0000.0000.0000.000
158A158LEU0-0.033-0.00111.3970.4030.4030.0000.0000.0000.000
159A159THR00.010-0.00610.108-1.255-1.2550.0000.0000.0000.000
160A160LYS10.8990.9489.66715.79815.7980.0000.0000.0000.000
161A161LYS10.7940.8916.78618.92718.9270.0000.0000.0000.000
165A165ILE00.0160.0007.291-1.728-1.7280.0000.0000.0000.000
166A166PHE00.007-0.0019.8371.7901.7900.0000.0000.0000.000
167A167VAL00.001-0.00413.193-0.717-0.7170.0000.0000.0000.000
168A168ASN0-0.019-0.02115.7980.7820.7820.0000.0000.0000.000
169A169SER00.0070.00715.8710.6290.6290.0000.0000.0000.000
170A170GLY00.030-0.00518.3300.5050.5050.0000.0000.0000.000
171A171ALA0-0.028-0.01319.6470.5700.5700.0000.0000.0000.000
172A172PHE0-0.074-0.03821.2070.6730.6730.0000.0000.0000.000
173A173LEU0-0.0060.01818.8560.2390.2390.0000.0000.0000.000
174A174THR0-0.016-0.00423.117-0.038-0.0380.0000.0000.0000.000
175A175LYS10.8790.92522.70712.16912.1690.0000.0000.0000.000
176A176ASP-1-0.872-0.94522.004-12.406-12.4060.0000.0000.0000.000
177A177GLU-1-0.823-0.88321.979-12.340-12.3400.0000.0000.0000.000
178A178VAL00.0230.00417.115-0.713-0.7130.0000.0000.0000.000
179A179ALA0-0.014-0.00617.544-1.035-1.0350.0000.0000.0000.000
180A180SER00.004-0.01218.248-0.588-0.5880.0000.0000.0000.000
181A181LEU0-0.032-0.01315.419-0.513-0.5130.0000.0000.0000.000
182A182GLN0-0.015-0.01312.285-1.812-1.8120.0000.0000.0000.000
183A183GLU-1-0.956-0.96913.920-16.242-16.2420.0000.0000.0000.000
184A184TYR00.0200.00115.092-0.685-0.6850.0000.0000.0000.000
185A185ILE0-0.002-0.0039.583-0.642-0.6420.0000.0000.0000.000
186A186SER0-0.045-0.01811.427-2.110-2.1100.0000.0000.0000.000
187A187LEU0-0.021-0.00812.628-0.581-0.5810.0000.0000.0000.000
188A188THR0-0.033-0.02712.9010.8580.8580.0000.0000.0000.000
189A189ASN0-0.128-0.06110.143-1.611-1.6110.0000.0000.0000.000
190A190LEU0-0.0050.0108.077-2.417-2.4170.0000.0000.0000.000
193A193LEU0-0.0100.0096.697-2.069-2.0690.0000.0000.0000.000
194A194PHE00.0010.0018.4801.9051.9050.0000.0000.0000.000
195A195LEU00.0260.01611.037-0.395-0.3950.0000.0000.0000.000
196A196GLU-1-0.795-0.90713.667-15.095-15.0950.0000.0000.0000.000
197A197PRO00.0030.01917.161-0.187-0.1870.0000.0000.0000.000
198A198ARG10.8990.92819.99312.88412.8840.0000.0000.0000.000
199A199GLU-1-0.730-0.84119.706-14.309-14.3090.0000.0000.0000.000
200A200LEU0-0.0080.01516.5140.7100.7100.0000.0000.0000.000
201A201TYR0-0.067-0.07219.442-0.198-0.1980.0000.0000.0000.000
202A202ASP-1-0.844-0.91121.643-13.323-13.3230.0000.0000.0000.000
203A203PHE0-0.011-0.00116.443-0.155-0.1550.0000.0000.0000.000
204A204PRO00.0370.03013.9530.0970.0970.0000.0000.0000.000
205A205GLN0-0.081-0.04413.450-0.930-0.9300.0000.0000.0000.000
206A206TYR00.0340.0039.582-0.678-0.6780.0000.0000.0000.000
207A207ILE0-0.008-0.00913.9900.3430.3430.0000.0000.0000.000
208A208LEU0-0.031-0.00914.382-0.805-0.8050.0000.0000.0000.000
209A209ASP-1-0.874-0.93018.037-13.730-13.7300.0000.0000.0000.000
210A210GLU-1-0.949-0.98321.267-12.012-12.0120.0000.0000.0000.000
211A211ASP-1-0.986-0.99323.601-12.212-12.2120.0000.0000.0000.000
212A212TYR0-0.122-0.07619.5000.1260.1260.0000.0000.0000.000
213A213PHE0-0.055-0.01419.103-0.996-0.9960.0000.0000.0000.000
214A214LEU00.0130.01213.576-0.543-0.5430.0000.0000.0000.000
215A215ILE00.0060.00217.5650.2570.2570.0000.0000.0000.000
216A216THR0-0.030-0.02414.030-1.076-1.0760.0000.0000.0000.000
217A217LYS10.7870.86616.79514.82614.8260.0000.0000.0000.000
218A218ASN0-0.067-0.04517.532-0.144-0.1440.0000.0000.0000.000
219A219MET-1-0.909-0.93012.555-17.897-17.8970.0000.0000.0000.000