FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: 97VL2

Calculation Name: 5T50-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion | 1,2-ethanediol

Ligand 3-letter code: CA | EDO

Ligand of Interest (LOI):

PDB ID: 5T50

Chain ID: A

ChEMBL ID:

UniProt ID: P86993

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 229
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2902939.707127
FMO2-HF: Nuclear repulsion 2815273.730844
FMO2-HF: Total energy -87665.976282
FMO2-MP2: Total energy -87929.355287


3D Structure
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:SER)


Summations of interaction energy for fragment #1(A:1:SER)
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.
-164.987-170.94139.309-17.869-15.483-0.115
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.786 / q_NPA : 0.873
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].
3A3LEU00.0050.0113.8263.1544.608-0.010-0.597-0.847-0.001
54A54PHE00.0090.0102.821-2.426-0.6020.511-0.847-1.4870.007
55A55GLN00.001-0.0111.665-24.444-32.27821.731-8.012-5.886-0.032
56A56LEU00.020-0.0032.010-30.362-30.9376.709-3.322-2.812-0.039
57A57ARG10.9360.9754.58843.03943.148-0.001-0.013-0.0940.000
58A58ASP-1-0.875-0.9213.495-55.333-54.7830.007-0.252-0.305-0.002
59A59THR0-0.021-0.0121.879-30.649-32.97010.365-4.398-3.645-0.047
60A60SER00.0250.0264.0469.0639.296-0.001-0.131-0.101-0.001
225A225SER0-0.013-0.0303.9505.5376.034-0.001-0.281-0.2140.000
227A227SER0-0.017-0.0354.574-8.066-7.957-0.001-0.016-0.0920.000
4A4SER0-0.041-0.0226.2011.6501.6500.0000.0000.0000.000
5A5PHE00.0240.0189.7970.8910.8910.0000.0000.0000.000
6A6ASN0-0.008-0.03013.1900.1640.1640.0000.0000.0000.000
7A7TYR00.0120.00515.3000.0780.0780.0000.0000.0000.000
8A8PRO0-0.004-0.01519.7580.2450.2450.0000.0000.0000.000
9A9ASN0-0.008-0.00122.9040.1460.1460.0000.0000.0000.000
10A10PHE0-0.012-0.01819.120-0.584-0.5840.0000.0000.0000.000
11A11GLN0-0.083-0.04923.9500.1970.1970.0000.0000.0000.000
12A12SER0-0.038-0.02321.9610.2470.2470.0000.0000.0000.000
13A13VAL0-0.018-0.03220.860-0.247-0.2470.0000.0000.0000.000
14A14GLU-1-0.842-0.89218.905-14.033-14.0330.0000.0000.0000.000
15A15ASP-1-0.849-0.91213.868-19.643-19.6430.0000.0000.0000.000
16A16ILE0-0.0600.00314.969-1.106-1.1060.0000.0000.0000.000
17A17THR0-0.033-0.01916.0430.9260.9260.0000.0000.0000.000
18A18PHE00.028-0.00117.970-0.180-0.1800.0000.0000.0000.000
19A19GLN00.0260.01219.216-0.148-0.1480.0000.0000.0000.000
20A20GLY00.0050.01322.808-0.096-0.0960.0000.0000.0000.000
21A21GLY0-0.028-0.03726.0710.1660.1660.0000.0000.0000.000
22A22ALA0-0.0120.01823.7430.2040.2040.0000.0000.0000.000
23A23SER0-0.064-0.04025.6280.1530.1530.0000.0000.0000.000
24A24PRO00.0730.04124.548-0.024-0.0240.0000.0000.0000.000
25A25ARG10.8700.93226.51910.69210.6920.0000.0000.0000.000
26A26ASN0-0.0080.00529.261-0.162-0.1620.0000.0000.0000.000
27A27GLU-1-0.813-0.88627.404-10.515-10.5150.0000.0000.0000.000
28A28THR0-0.040-0.01425.663-0.366-0.3660.0000.0000.0000.000
29A29LEU0-0.0050.00219.7390.1380.1380.0000.0000.0000.000
30A30GLN0-0.025-0.01624.3730.1310.1310.0000.0000.0000.000
31A31LEU00.016-0.00722.407-0.150-0.1500.0000.0000.0000.000
32A32THR0-0.015-0.01525.7850.0730.0730.0000.0000.0000.000
33A33PRO00.0140.01929.1350.1320.1320.0000.0000.0000.000
34A34THR00.0280.01332.0170.0790.0790.0000.0000.0000.000
35A35ASP-1-0.825-0.92435.412-7.816-7.8160.0000.0000.0000.000
36A36SER0-0.004-0.01138.556-0.073-0.0730.0000.0000.0000.000
37A37ASN0-0.082-0.03140.8870.2230.2230.0000.0000.0000.000
38A38GLY0-0.0060.00938.4280.0530.0530.0000.0000.0000.000
39A39ILE0-0.054-0.03238.679-0.114-0.1140.0000.0000.0000.000
40A40PRO0-0.036-0.01135.292-0.067-0.0670.0000.0000.0000.000
41A41ILE0-0.029-0.00334.9950.2410.2410.0000.0000.0000.000
42A42ARG10.9580.98634.9797.5097.5090.0000.0000.0000.000
43A43GLN0-0.0200.00534.2230.0110.0110.0000.0000.0000.000
44A44ARG10.8760.94531.0599.0549.0540.0000.0000.0000.000
45A45ALA00.0920.03926.230-0.024-0.0240.0000.0000.0000.000
46A46GLY00.0060.00924.7550.2600.2600.0000.0000.0000.000
47A47HIS10.7840.88719.13514.73814.7380.0000.0000.0000.000
48A48ALA00.0310.02119.6790.4610.4610.0000.0000.0000.000
49A49VAL0-0.026-0.01314.292-0.290-0.2900.0000.0000.0000.000
50A50TYR00.0160.0219.646-0.086-0.0860.0000.0000.0000.000
51A51SER0-0.035-0.04512.062-0.347-0.3470.0000.0000.0000.000
52A52GLN0-0.0070.0097.4212.0292.0290.0000.0000.0000.000
53A53PRO0-0.038-0.0236.350-1.115-1.1150.0000.0000.0000.000
61A61PHE0-0.037-0.0316.061-4.508-4.5080.0000.0000.0000.000
62A62TYR0-0.018-0.0238.2253.1843.1840.0000.0000.0000.000
63A63THR0-0.046-0.03511.763-0.759-0.7590.0000.0000.0000.000
64A64THR0-0.015-0.00513.9031.2021.2020.0000.0000.0000.000
65A65PHE00.0340.00717.678-0.281-0.2810.0000.0000.0000.000
66A66THR00.0170.03520.1220.3510.3510.0000.0000.0000.000
67A67PHE00.006-0.00623.824-0.138-0.1380.0000.0000.0000.000
68A68VAL00.0080.01525.8190.3850.3850.0000.0000.0000.000
69A69ILE00.0130.00928.150-0.163-0.1630.0000.0000.0000.000
70A70ARG10.9450.97430.9828.8088.8080.0000.0000.0000.000
71A71THR00.0130.00934.2490.0400.0400.0000.0000.0000.000
72A72THR0-0.034-0.03436.4510.1250.1250.0000.0000.0000.000
73A73SER0-0.008-0.00539.6550.2270.2270.0000.0000.0000.000
74A74ASN00.0560.01639.847-0.262-0.2620.0000.0000.0000.000
75A75SER0-0.041-0.01239.560-0.051-0.0510.0000.0000.0000.000
76A76PRO0-0.046-0.01035.0180.0920.0920.0000.0000.0000.000
77A77ALA00.0300.02833.6440.0220.0220.0000.0000.0000.000
78A78ASP-1-0.828-0.95530.023-9.630-9.6300.0000.0000.0000.000
79A79GLY00.0680.04728.434-0.130-0.1300.0000.0000.0000.000
80A80PHE0-0.083-0.05821.8520.0240.0240.0000.0000.0000.000
81A81ALA00.0230.01520.2270.0820.0820.0000.0000.0000.000
82A82ILE0-0.0060.01414.8720.0290.0290.0000.0000.0000.000
83A83PHE0-0.050-0.04515.7130.1140.1140.0000.0000.0000.000
84A84ILE00.0500.0279.341-0.820-0.8200.0000.0000.0000.000
85A85ALA00.0220.00312.2101.3551.3550.0000.0000.0000.000
86A86PRO00.0300.02311.331-1.652-1.6520.0000.0000.0000.000
87A87PRO0-0.003-0.0159.4221.3231.3230.0000.0000.0000.000
88A88ASP-1-0.907-0.94812.209-17.508-17.5080.0000.0000.0000.000
89A89PHE0-0.046-0.01115.2701.2641.2640.0000.0000.0000.000
90A90PRO00.0060.00217.186-0.075-0.0750.0000.0000.0000.000
91A91VAL0-0.051-0.03520.525-0.247-0.2470.0000.0000.0000.000
92A92LYS10.9040.97521.09714.58814.5880.0000.0000.0000.000
93A93ARG10.8170.89925.04910.24110.2410.0000.0000.0000.000
94A94TYR0-0.021-0.01427.672-0.335-0.3350.0000.0000.0000.000
95A95GLY00.0340.00729.9950.0890.0890.0000.0000.0000.000
96A96GLY00.0920.04129.449-0.377-0.3770.0000.0000.0000.000
97A97TYR0-0.026-0.00927.470-0.205-0.2050.0000.0000.0000.000
98A98LEU00.0130.00124.586-0.604-0.6040.0000.0000.0000.000
99A99GLY00.0380.04423.985-0.525-0.5250.0000.0000.0000.000
100A100LEU0-0.053-0.01619.170-0.630-0.6300.0000.0000.0000.000
101A101PHE00.0080.00721.648-0.296-0.2960.0000.0000.0000.000
102A102GLU-1-0.723-0.87424.910-10.733-10.7330.0000.0000.0000.000
103A103PRO00.025-0.00128.101-0.071-0.0710.0000.0000.0000.000
104A104ASN0-0.042-0.02131.3410.0790.0790.0000.0000.0000.000
105A105THR0-0.040-0.02026.467-0.106-0.1060.0000.0000.0000.000
106A106ALA00.0220.02026.324-0.393-0.3930.0000.0000.0000.000
107A107THR00.0250.02426.242-0.366-0.3660.0000.0000.0000.000
108A108ASN0-0.0080.00026.638-0.290-0.2900.0000.0000.0000.000
109A109THR00.0420.01022.441-0.175-0.1750.0000.0000.0000.000
110A110SER0-0.009-0.00521.738-0.674-0.6740.0000.0000.0000.000
111A111ALA0-0.060-0.02123.548-0.003-0.0030.0000.0000.0000.000
112A112ASN0-0.093-0.04720.674-0.025-0.0250.0000.0000.0000.000
113A113LYS10.9360.97813.09522.25222.2520.0000.0000.0000.000
114A114VAL00.002-0.00315.374-0.702-0.7020.0000.0000.0000.000
115A115VAL00.0070.01413.6450.8260.8260.0000.0000.0000.000
116A116ALA0-0.019-0.01015.147-0.752-0.7520.0000.0000.0000.000
117A117VAL00.0090.00916.8910.3680.3680.0000.0000.0000.000
118A118GLU-1-0.847-0.89219.367-12.509-12.5090.0000.0000.0000.000
119A119PHE0-0.015-0.02020.8910.1850.1850.0000.0000.0000.000
120A120ASP-1-0.794-0.88825.787-10.481-10.4810.0000.0000.0000.000
121A121THR0-0.059-0.09128.7110.2670.2670.0000.0000.0000.000
122A122TRP0-0.032-0.02332.1260.5900.5900.0000.0000.0000.000
123A123VAL0-0.0330.00433.061-0.134-0.1340.0000.0000.0000.000
124A124ASN0-0.015-0.02832.6030.0600.0600.0000.0000.0000.000
125A125THR0-0.065-0.04934.9870.0550.0550.0000.0000.0000.000
126A126GLU-1-0.874-0.91134.437-8.820-8.8200.0000.0000.0000.000
127A127TRP0-0.029-0.02630.214-0.051-0.0510.0000.0000.0000.000
128A128LYS10.8880.94432.3368.8258.8250.0000.0000.0000.000
129A129GLU-1-0.717-0.84930.652-10.534-10.5340.0000.0000.0000.000
130A130PRO0-0.019-0.01231.0790.3750.3750.0000.0000.0000.000
131A131ARG10.9630.98234.1977.7107.7100.0000.0000.0000.000
132A132TYR0-0.042-0.03132.5510.2080.2080.0000.0000.0000.000
133A133ARG10.8790.95732.7748.4938.4930.0000.0000.0000.000
134A134HIS10.8330.90728.02210.66610.6660.0000.0000.0000.000
135A135ILE00.0370.03524.085-0.114-0.1140.0000.0000.0000.000
136A136GLY00.014-0.00624.2210.3610.3610.0000.0000.0000.000
137A137ILE0-0.0180.00718.407-0.523-0.5230.0000.0000.0000.000
138A138ASP0-0.021-0.05519.8910.7050.7050.0000.0000.0000.000
139A139VAL00.0390.00517.264-1.037-1.0370.0000.0000.0000.000
140A140ASN0-0.0080.00317.4960.1860.1860.0000.0000.0000.000
141A141SER00.016-0.00220.2650.6910.6910.0000.0000.0000.000
142A142ILE00.0090.01023.192-0.469-0.4690.0000.0000.0000.000
143A143VAL0-0.043-0.01625.5340.3280.3280.0000.0000.0000.000
144A144SER0-0.026-0.01424.010-0.224-0.2240.0000.0000.0000.000
145A145VAL0-0.049-0.01520.7460.4390.4390.0000.0000.0000.000
146A146ARG10.9180.97022.81712.43212.4320.0000.0000.0000.000
147A147VAL00.0240.01124.320-0.287-0.2870.0000.0000.0000.000
148A148THR0-0.019-0.01326.9930.3330.3330.0000.0000.0000.000
149A149ARG10.9030.95529.2318.5508.5500.0000.0000.0000.000
150A150TRP00.001-0.00228.892-0.223-0.2230.0000.0000.0000.000
151A151GLN00.0460.00931.6530.4110.4110.0000.0000.0000.000
152A152ASP-1-0.805-0.89834.679-8.634-8.6340.0000.0000.0000.000
153A153LYS10.8770.93736.9808.4368.4360.0000.0000.0000.000
154A154ASP-1-0.744-0.84332.071-9.533-9.5330.0000.0000.0000.000
155A155VAL0-0.0190.01832.147-0.105-0.1050.0000.0000.0000.000
156A156PHE0-0.051-0.03833.673-0.030-0.0300.0000.0000.0000.000
157A157SER0-0.042-0.02933.6110.1740.1740.0000.0000.0000.000
158A158ARG10.8790.93834.5058.3308.3300.0000.0000.0000.000
159A159SER00.0090.00832.6890.0290.0290.0000.0000.0000.000
160A160ILE0-0.005-0.00228.029-0.174-0.1740.0000.0000.0000.000
161A161ALA00.0070.02227.4410.0800.0800.0000.0000.0000.000
162A162THR0-0.004-0.01122.860-0.319-0.3190.0000.0000.0000.000
163A163ALA0-0.0050.00020.6400.3130.3130.0000.0000.0000.000
164A164HIS00.0410.04518.183-1.084-1.0840.0000.0000.0000.000
165A165VAL0-0.006-0.01614.1050.6640.6640.0000.0000.0000.000
166A166GLY00.0280.01412.338-1.054-1.0540.0000.0000.0000.000
167A167TYR0-0.058-0.0438.1031.3091.3090.0000.0000.0000.000
168A168ASP-1-0.753-0.8449.779-25.235-25.2350.0000.0000.0000.000
169A169GLY00.0670.0198.0440.8360.8360.0000.0000.0000.000
170A170ILE0-0.030-0.0029.0380.6970.6970.0000.0000.0000.000
171A171SER0-0.081-0.08212.0990.9640.9640.0000.0000.0000.000
172A172LYS10.8530.93311.09626.72326.7230.0000.0000.0000.000
173A173ILE0-0.0120.00713.4871.2411.2410.0000.0000.0000.000
174A174LEU00.0100.01813.092-1.385-1.3850.0000.0000.0000.000
175A175THR0-0.017-0.01914.9231.9411.9410.0000.0000.0000.000
176A176ALA00.0130.01316.552-0.943-0.9430.0000.0000.0000.000
177A177PHE0-0.018-0.00919.2400.7810.7810.0000.0000.0000.000
178A178VAL0-0.005-0.00121.804-0.366-0.3660.0000.0000.0000.000
179A179THR00.0130.00124.5130.3130.3130.0000.0000.0000.000
180A180TYR00.0520.03027.361-0.251-0.2510.0000.0000.0000.000
181A181PRO0-0.0130.00230.5040.1150.1150.0000.0000.0000.000
182A182ASP-1-0.917-0.95932.980-8.134-8.1340.0000.0000.0000.000
183A183GLY0-0.014-0.01133.9010.2900.2900.0000.0000.0000.000
184A184GLY0-0.038-0.01732.415-0.038-0.0380.0000.0000.0000.000
185A185ASN0-0.019-0.02528.443-0.484-0.4840.0000.0000.0000.000
186A186TYR0-0.086-0.06126.4880.3580.3580.0000.0000.0000.000
187A187VAL00.0350.01023.020-0.472-0.4720.0000.0000.0000.000
188A188LEU0-0.083-0.02321.9240.5000.5000.0000.0000.0000.000
189A189SER00.031-0.00619.625-0.429-0.4290.0000.0000.0000.000
190A190HIS0-0.017-0.02118.3321.2561.2560.0000.0000.0000.000
191A191VAL00.0310.02717.369-0.928-0.9280.0000.0000.0000.000
192A192VAL0-0.027-0.02414.2670.8820.8820.0000.0000.0000.000
193A193ASP-1-0.784-0.88011.845-26.946-26.9460.0000.0000.0000.000
194A194LEU0-0.012-0.0179.5370.7980.7980.0000.0000.0000.000
195A195ALA0-0.0070.0047.999-1.830-1.8300.0000.0000.0000.000
196A196GLU-1-0.939-0.9659.176-20.267-20.2670.0000.0000.0000.000
197A197ILE0-0.051-0.02412.7801.1021.1020.0000.0000.0000.000
198A198PHE0-0.082-0.0608.9091.9231.9230.0000.0000.0000.000
199A199PRO00.0200.0278.424-3.958-3.9580.0000.0000.0000.000
200A200GLY0-0.035-0.0327.7170.2070.2070.0000.0000.0000.000
201A201ASP-1-0.881-0.9225.927-41.114-41.1140.0000.0000.0000.000
202A202VAL0-0.052-0.0276.4784.4334.4330.0000.0000.0000.000
203A203ARG10.9180.9847.40218.33718.3370.0000.0000.0000.000
204A204ILE00.0390.0139.9990.2700.2700.0000.0000.0000.000
205A205GLY00.0300.00511.7430.5710.5710.0000.0000.0000.000
206A206PHE00.0040.01115.4320.1200.1200.0000.0000.0000.000
207A207SER0-0.041-0.05119.0270.1160.1160.0000.0000.0000.000
208A208GLY00.0430.02821.6180.0920.0920.0000.0000.0000.000
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