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: 24Y7R

Calculation Name: 1Y1X-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | calcium ion

Ligand 3-letter code: SO4 | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Y1X

Chain ID: A

ChEMBL ID:

UniProt ID: Q4QG08

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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1888666.737039
FMO2-HF: Nuclear repulsion 1816354.403232
FMO2-HF: Total energy -72312.333807
FMO2-MP2: Total energy -72522.702342


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:10:PRO)


Summations of interaction energy for fragment #1(A:10:PRO)
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.
-83.112-69.77.247-7.723-12.932-0.07
Interaction energy analysis for fragmet #1(A:10:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.926
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].
3A12SER00.002-0.0012.68710.02112.9100.074-1.425-1.538-0.003
4A13THR0-0.0050.0022.785-14.063-12.3260.318-0.884-1.171-0.011
5A14GLY00.0700.0565.3323.8063.841-0.001-0.001-0.0310.000
45A54SER0-0.053-0.0162.074-1.855-1.9811.882-0.708-1.049-0.001
46A55SER00.014-0.0113.3105.9726.5640.020-0.191-0.421-0.002
47A56ALA0-0.017-0.0112.485-24.144-20.7691.838-2.273-2.939-0.030
48A57GLY0-0.010-0.0083.0196.4087.8230.087-0.599-0.903-0.004
49A58VAL0-0.018-0.0112.8290.6592.0070.401-0.530-1.218-0.006
50A59PRO0-0.020-0.0192.128-10.516-8.3052.541-1.326-3.425-0.012
51A60PHE00.0420.0383.2317.8187.7540.0870.214-0.237-0.001
6A15VAL00.006-0.0177.1891.0351.0350.0000.0000.0000.000
7A16TYR00.0150.0079.8442.2802.2800.0000.0000.0000.000
8A17ALA00.0610.0437.4430.5350.5350.0000.0000.0000.000
9A18PRO0-0.016-0.0059.4461.8291.8290.0000.0000.0000.000
10A19SER00.0280.01112.3641.0061.0060.0000.0000.0000.000
11A20ALA0-0.044-0.00410.4130.5430.5430.0000.0000.0000.000
12A21ARG10.9550.96012.37216.97416.9740.0000.0000.0000.000
13A22HIS0-0.049-0.0198.4722.6782.6780.0000.0000.0000.000
14A23MET0-0.0020.01814.0450.3080.3080.0000.0000.0000.000
15A24ASN0-0.016-0.01316.645-0.340-0.3400.0000.0000.0000.000
16A25ASP-1-0.762-0.88117.900-16.185-16.1850.0000.0000.0000.000
17A26ASN0-0.076-0.04620.093-0.055-0.0550.0000.0000.0000.000
18A27GLN0-0.010-0.00119.681-0.028-0.0280.0000.0000.0000.000
19A28GLU-1-0.844-0.92222.656-11.185-11.1850.0000.0000.0000.000
20A29LEU0-0.029-0.00821.482-0.620-0.6200.0000.0000.0000.000
21A30MET00.0230.00221.337-0.724-0.7240.0000.0000.0000.000
22A31GLU-1-0.881-0.92920.341-13.413-13.4130.0000.0000.0000.000
23A32TRP0-0.013-0.03413.960-1.229-1.2290.0000.0000.0000.000
24A33PHE0-0.029-0.00216.518-0.971-0.9710.0000.0000.0000.000
25A34ARG10.9960.98016.85212.97912.9790.0000.0000.0000.000
26A35ALA0-0.039-0.00113.960-0.427-0.4270.0000.0000.0000.000
27A36VAL0-0.077-0.04211.867-1.846-1.8460.0000.0000.0000.000
28A37ASP-1-0.785-0.89513.065-16.394-16.3940.0000.0000.0000.000
29A38THR0-0.068-0.04210.9260.7910.7910.0000.0000.0000.000
30A39ASP-1-0.888-0.92914.055-16.920-16.9200.0000.0000.0000.000
31A40GLY0-0.062-0.01616.3770.8650.8650.0000.0000.0000.000
32A41SER0-0.016-0.00218.4261.0271.0270.0000.0000.0000.000
33A42GLY0-0.040-0.02620.5470.7260.7260.0000.0000.0000.000
34A43ALA0-0.055-0.03720.1640.4920.4920.0000.0000.0000.000
35A44ILE0-0.063-0.01614.364-0.831-0.8310.0000.0000.0000.000
36A45SER00.1010.03613.856-0.371-0.3710.0000.0000.0000.000
37A46VAL00.026-0.00111.709-1.255-1.2550.0000.0000.0000.000
38A47PRO0-0.002-0.0229.370-1.926-1.9260.0000.0000.0000.000
39A48GLU00.0110.0238.610-2.955-2.9550.0000.0000.0000.000
40A49LEU00.0470.0239.685-1.640-1.6400.0000.0000.0000.000
41A50ASN0-0.088-0.0555.666-4.826-4.8260.0000.0000.0000.000
42A51ALA0-0.0020.0064.931-5.061-5.0610.0000.0000.0000.000
43A52ALA00.0070.0045.774-2.759-2.7590.0000.0000.0000.000
44A53LEU0-0.017-0.0077.7140.7990.7990.0000.0000.0000.000
52A61SER0-0.005-0.0046.478-0.569-0.5690.0000.0000.0000.000
53A62LEU00.0380.0228.7280.7000.7000.0000.0000.0000.000
54A63ALA00.0760.04410.2191.2431.2430.0000.0000.0000.000
55A64THR0-0.050-0.05012.0090.7050.7050.0000.0000.0000.000
56A65THR0-0.027-0.01910.007-0.042-0.0420.0000.0000.0000.000
57A66GLU-1-0.891-0.94712.448-18.480-18.4800.0000.0000.0000.000
58A67LYS10.8550.94015.36015.45615.4560.0000.0000.0000.000
59A68LEU0-0.022-0.02413.3180.8580.8580.0000.0000.0000.000
60A69LEU00.0090.01315.5810.5420.5420.0000.0000.0000.000
61A70HIS00.0140.01117.4220.6260.6260.0000.0000.0000.000
62A71MET0-0.048-0.01620.2560.5340.5340.0000.0000.0000.000
63A72TYR0-0.034-0.02219.8040.8080.8080.0000.0000.0000.000
64A73ASP-1-0.746-0.85921.076-12.437-12.4370.0000.0000.0000.000
65A74LYS10.7260.84322.88112.32012.3200.0000.0000.0000.000
66A75ASN0-0.033-0.02026.0500.2150.2150.0000.0000.0000.000
67A76HIS0-0.056-0.01924.8190.1070.1070.0000.0000.0000.000
68A77SER00.0010.00323.440-0.035-0.0350.0000.0000.0000.000
69A78GLY0-0.034-0.01720.527-0.151-0.1510.0000.0000.0000.000
70A79GLU-1-0.975-1.00317.971-16.912-16.9120.0000.0000.0000.000
71A80ILE0-0.045-0.01118.1610.4560.4560.0000.0000.0000.000
72A81THR00.0450.00420.309-0.328-0.3280.0000.0000.0000.000
73A82PHE0-0.028-0.03522.458-0.106-0.1060.0000.0000.0000.000
74A83ASP-1-0.873-0.91923.622-11.352-11.3520.0000.0000.0000.000
75A84GLU-1-0.766-0.88023.059-12.403-12.4030.0000.0000.0000.000
76A85PHE0-0.011-0.01316.341-0.417-0.4170.0000.0000.0000.000
77A86LYS10.9650.99420.85310.20010.2000.0000.0000.0000.000
78A87ASP-1-0.881-0.94422.776-11.639-11.6390.0000.0000.0000.000
79A88LEU00.0210.02516.511-0.317-0.3170.0000.0000.0000.000
80A89HIS10.8720.93717.59214.55714.5570.0000.0000.0000.000
81A90HIS0-0.025-0.02918.674-0.322-0.3220.0000.0000.0000.000
82A91PHE00.0260.01918.939-0.076-0.0760.0000.0000.0000.000
83A92ILE00.0420.02813.687-0.322-0.3220.0000.0000.0000.000
84A93LEU0-0.024-0.00916.238-0.618-0.6180.0000.0000.0000.000
85A94SER0-0.064-0.03918.1070.1100.1100.0000.0000.0000.000
86A95MET00.0010.01415.8460.0970.0970.0000.0000.0000.000
87A96ARG10.7750.89612.74719.46719.4670.0000.0000.0000.000
88A97GLU-1-0.891-0.93815.537-13.505-13.5050.0000.0000.0000.000
89A98GLY0-0.023-0.02219.0110.2960.2960.0000.0000.0000.000
90A99PHE0-0.012-0.00913.8170.1690.1690.0000.0000.0000.000
91A100ARG10.8040.88516.12716.27416.2740.0000.0000.0000.000
92A101LYS10.9100.96917.46312.37112.3710.0000.0000.0000.000
93A102ARG10.8010.89319.60113.22213.2220.0000.0000.0000.000
94A103ASP-1-0.705-0.84915.061-18.855-18.8550.0000.0000.0000.000
95A104SER0-0.070-0.05818.4240.2070.2070.0000.0000.0000.000
96A105SER0-0.071-0.02817.5430.6970.6970.0000.0000.0000.000
97A106GLY0-0.058-0.02015.663-0.004-0.0040.0000.0000.0000.000
98A107ASP-1-0.925-0.96813.490-20.655-20.6550.0000.0000.0000.000
99A108GLY0-0.048-0.01910.907-2.087-2.0870.0000.0000.0000.000
100A109ARG10.7220.83411.21021.02221.0220.0000.0000.0000.000
101A110LEU00.0170.03414.6390.7860.7860.0000.0000.0000.000
102A111ASP-1-0.781-0.89718.156-13.294-13.2940.0000.0000.0000.000
103A112SER0-0.005-0.01820.8710.4760.4760.0000.0000.0000.000
104A113ASN00.007-0.01023.6050.5270.5270.0000.0000.0000.000
105A114GLU-1-0.739-0.83320.363-14.485-14.4850.0000.0000.0000.000
106A115VAL0-0.008-0.01120.2150.1140.1140.0000.0000.0000.000
107A116ARG10.7920.85422.92811.42611.4260.0000.0000.0000.000
108A117ALA00.0140.00625.8030.3480.3480.0000.0000.0000.000
109A118ALA0-0.046-0.01422.5840.3000.3000.0000.0000.0000.000
110A119LEU0-0.0110.00324.5590.1880.1880.0000.0000.0000.000
111A120LEU00.0310.01526.5590.3210.3210.0000.0000.0000.000
112A121SER0-0.040-0.02527.5670.3460.3460.0000.0000.0000.000
113A122SER0-0.081-0.03728.6210.2090.2090.0000.0000.0000.000
114A123GLY00.0040.00730.2830.2150.2150.0000.0000.0000.000
115A124TYR0-0.021-0.00831.8220.2200.2200.0000.0000.0000.000
116A125GLN00.0120.00932.607-0.174-0.1740.0000.0000.0000.000
117A126VAL00.0130.00029.965-0.008-0.0080.0000.0000.0000.000
118A127SER00.0200.01933.077-0.035-0.0350.0000.0000.0000.000
119A128GLU-1-0.702-0.82630.002-10.753-10.7530.0000.0000.0000.000
120A129GLN0-0.001-0.00530.744-0.509-0.5090.0000.0000.0000.000
121A130THR00.0230.00330.243-0.200-0.2000.0000.0000.0000.000
122A131PHE00.0070.00524.383-0.348-0.3480.0000.0000.0000.000
123A132GLN0-0.024-0.02126.252-0.729-0.7290.0000.0000.0000.000
124A133ALA0-0.041-0.01626.123-0.426-0.4260.0000.0000.0000.000
125A134LEU0-0.011-0.00324.566-0.345-0.3450.0000.0000.0000.000
126A135MET00.0290.02120.176-0.659-0.6590.0000.0000.0000.000
127A136ARG10.9230.96121.22510.92810.9280.0000.0000.0000.000
128A137LYS10.8840.94922.18412.19412.1940.0000.0000.0000.000
129A138PHE00.0410.01218.745-0.263-0.2630.0000.0000.0000.000
130A139ASP-1-0.759-0.87616.802-18.230-18.2300.0000.0000.0000.000
131A140ARG10.7400.85111.94421.81921.8190.0000.0000.0000.000
132A141GLN00.0100.0119.417-0.090-0.0900.0000.0000.0000.000
133A142ARG10.8810.94714.54614.52214.5220.0000.0000.0000.000
134A143ARG10.9160.94810.47823.97223.9720.0000.0000.0000.000
135A144GLY0-0.0010.01117.4680.2200.2200.0000.0000.0000.000
136A145SER0-0.026-0.01416.7240.0650.0650.0000.0000.0000.000
137A146LEU0-0.047-0.00115.848-0.601-0.6010.0000.0000.0000.000
138A147GLY00.0390.01311.726-0.264-0.2640.0000.0000.0000.000
139A148PHE00.0340.0009.0781.4301.4300.0000.0000.0000.000
140A149ASP-1-0.787-0.9029.680-26.125-26.1250.0000.0000.0000.000
141A150ASP-1-0.802-0.89011.672-20.238-20.2380.0000.0000.0000.000
142A151TYR0-0.005-0.00214.5731.4391.4390.0000.0000.0000.000
143A152VAL00.0340.02413.2101.1771.1770.0000.0000.0000.000
144A153GLU-1-0.818-0.88915.259-16.936-16.9360.0000.0000.0000.000
145A154LEU0-0.030-0.00617.5911.0411.0410.0000.0000.0000.000
146A155SER0-0.028-0.02818.7091.0421.0420.0000.0000.0000.000
147A156ILE0-0.007-0.00817.4090.7690.7690.0000.0000.0000.000
148A157PHE00.0000.00321.2540.7400.7400.0000.0000.0000.000
149A158VAL00.0370.00123.5500.6370.6370.0000.0000.0000.000
150A159CYS0-0.070-0.01524.1070.6900.6900.0000.0000.0000.000
151A160ARG10.8970.94423.61512.82912.8290.0000.0000.0000.000
152A161VAL00.0090.00527.6050.4590.4590.0000.0000.0000.000
153A162ARG10.8840.93525.78311.48011.4800.0000.0000.0000.000
154A163ASN0-0.0030.00228.2800.4340.4340.0000.0000.0000.000
155A164VAL00.0120.01431.6870.3390.3390.0000.0000.0000.000
156A165PHE0-0.027-0.01833.5210.2880.2880.0000.0000.0000.000
157A166ALA0-0.010-0.01434.7230.2820.2820.0000.0000.0000.000
158A167PHE0-0.0260.01036.2300.2300.2300.0000.0000.0000.000
159A168TYR00.026-0.00237.6860.3330.3330.0000.0000.0000.000
160A169ASP-1-0.781-0.85339.387-7.346-7.3460.0000.0000.0000.000
161A170ARG10.8540.91141.1037.2657.2650.0000.0000.0000.000
162A171GLU-1-0.932-0.96343.648-6.433-6.4330.0000.0000.0000.000
163A172ARG10.8420.92737.5497.9457.9450.0000.0000.0000.000
164A173THR00.000-0.01942.1340.0140.0140.0000.0000.0000.000
165A174GLY0-0.010-0.00639.8410.0380.0380.0000.0000.0000.000
166A175GLN0-0.091-0.04840.359-0.040-0.0400.0000.0000.0000.000
167A176VAL00.0170.01438.2790.0050.0050.0000.0000.0000.000
168A177THR0-0.027-0.02341.5320.1220.1220.0000.0000.0000.000
169A178PHE0-0.0010.00237.481-0.053-0.0530.0000.0000.0000.000
170A179THR00.0400.03943.0750.0700.0700.0000.0000.0000.000
171A180PHE00.027-0.00539.539-0.159-0.1590.0000.0000.0000.000
172A181ASP-1-0.897-0.94840.631-7.546-7.5460.0000.0000.0000.000
173A182THR00.0570.01640.056-0.205-0.2050.0000.0000.0000.000
174A183PHE0-0.0140.00935.813-0.223-0.2230.0000.0000.0000.000
175A184ILE0-0.0070.00535.766-0.318-0.3180.0000.0000.0000.000
176A185GLY00.0280.01635.207-0.265-0.2650.0000.0000.0000.000
177A186GLY00.0160.00234.717-0.218-0.2180.0000.0000.0000.000
178A187SER0-0.036-0.04332.193-0.350-0.3500.0000.0000.0000.000
179A188VAL0-0.029-0.02030.637-0.401-0.4010.0000.0000.0000.000
180A189SER0-0.035-0.01029.971-0.235-0.2350.0000.0000.0000.000
181A190ILE0-0.063-0.04227.037-0.299-0.2990.0000.0000.0000.000
182A191LEU-1-0.856-0.88923.924-13.242-13.2420.0000.0000.0000.000