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: QKL1Y

Calculation Name: 1A3C-A-Xray547

Preferred Name:

Target Type:

Ligand Name: sulfate ion | samarium (iii) ion

Ligand 3-letter code: SO4 | SM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1A3C

Chain ID: A

ChEMBL ID:

UniProt ID: P39765

Base Structure: X-ray

Registration Date: 2025-09-02

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 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1880682.903376
FMO2-HF: Nuclear repulsion 1811043.652878
FMO2-HF: Total energy -69639.250499
FMO2-MP2: Total energy -69842.831325


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:GLN)


Summations of interaction energy for fragment #1(A:3:GLN)
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.
-97.911-94.981-0.011-1.045-1.875-0.003
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.865 / q_NPA : 0.922
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].
3A5ALA00.0340.0323.514-1.0131.002-0.016-0.901-1.098-0.003
176A178TYR0-0.023-0.0324.483-7.858-7.718-0.001-0.031-0.1080.000
177A179GLU-1-0.863-0.9453.599-27.565-26.8570.007-0.111-0.6050.000
178A180ASN-1-0.980-0.9715.375-37.450-37.383-0.001-0.002-0.0640.000
4A6VAL00.0000.0005.7181.1011.1010.0000.0000.0000.000
5A7ILE0-0.043-0.0219.4290.7230.7230.0000.0000.0000.000
6A8LEU0-0.048-0.03011.9601.8581.8580.0000.0000.0000.000
7A9ASP-1-0.795-0.89914.439-18.267-18.2670.0000.0000.0000.000
8A10GLU-1-0.816-0.91016.334-14.132-14.1320.0000.0000.0000.000
9A11GLN00.0210.02919.7340.6750.6750.0000.0000.0000.000
10A12ALA0-0.069-0.04417.9190.7910.7910.0000.0000.0000.000
11A13ILE00.0360.02317.2070.5890.5890.0000.0000.0000.000
12A14ARG10.9871.00320.81512.29912.2990.0000.0000.0000.000
13A15ARG10.8660.92120.22214.66514.6650.0000.0000.0000.000
14A16ALA0-0.044-0.01521.5980.4390.4390.0000.0000.0000.000
15A17LEU00.0350.01123.6520.3920.3920.0000.0000.0000.000
16A18THR0-0.001-0.01526.0650.5230.5230.0000.0000.0000.000
17A19ARG10.8460.93722.48112.96912.9690.0000.0000.0000.000
18A20ILE00.0280.00824.5430.2910.2910.0000.0000.0000.000
19A21ALA00.0320.02028.8410.3120.3120.0000.0000.0000.000
20A22HIS00.0380.01631.7520.4030.4030.0000.0000.0000.000
21A23GLU-1-0.935-0.97228.919-10.627-10.6270.0000.0000.0000.000
22A24MET0-0.052-0.03030.2410.2130.2130.0000.0000.0000.000
23A25ILE00.0340.03534.4170.2340.2340.0000.0000.0000.000
24A26GLU-1-0.935-0.97036.484-7.919-7.9190.0000.0000.0000.000
25A27ARG10.7630.88632.6779.4629.4620.0000.0000.0000.000
26A28ASN0-0.115-0.09035.8900.1810.1810.0000.0000.0000.000
27A29LYS10.8940.94939.3817.6717.6710.0000.0000.0000.000
28A30GLY00.0760.03939.628-0.215-0.2150.0000.0000.0000.000
29A31MET0-0.027-0.01240.5620.1600.1600.0000.0000.0000.000
30A32ASN00.1160.03841.992-0.239-0.2390.0000.0000.0000.000
31A33ASN0-0.119-0.03542.7690.0090.0090.0000.0000.0000.000
32A34CYS0-0.014-0.02437.4650.0170.0170.0000.0000.0000.000
33A35ILE00.0120.03437.418-0.048-0.0480.0000.0000.0000.000
34A36LEU00.0160.01432.659-0.184-0.1840.0000.0000.0000.000
35A37VAL00.0220.00532.5350.0400.0400.0000.0000.0000.000
36A38GLY00.0020.00928.938-0.256-0.2560.0000.0000.0000.000
37A39ILE0-0.018-0.01825.8840.2630.2630.0000.0000.0000.000
38A40LYS10.8530.90220.34514.60414.6040.0000.0000.0000.000
39A41THR00.0250.00821.7720.0160.0160.0000.0000.0000.000
40A42ARG10.8200.87816.47118.56018.5600.0000.0000.0000.000
41A43GLY00.0470.02522.2310.1760.1760.0000.0000.0000.000
42A44ILE0-0.0140.00824.7630.4350.4350.0000.0000.0000.000
43A45TYR00.0130.00523.7980.3620.3620.0000.0000.0000.000
44A46LEU0-0.029-0.01821.8970.1640.1640.0000.0000.0000.000
45A47ALA00.0090.00426.0520.3080.3080.0000.0000.0000.000
46A48LYS10.9070.96129.13610.90210.9020.0000.0000.0000.000
47A49ARG10.7070.78422.41814.00714.0070.0000.0000.0000.000
48A50LEU0-0.029-0.01927.2950.1280.1280.0000.0000.0000.000
49A51ALA00.0480.03130.4860.2330.2330.0000.0000.0000.000
50A52GLU-1-0.797-0.87432.121-9.867-9.8670.0000.0000.0000.000
51A53ARG10.7700.86127.21811.19911.1990.0000.0000.0000.000
52A54ILE00.0150.00232.8230.1730.1730.0000.0000.0000.000
53A55GLU-1-0.860-0.91335.661-8.402-8.4020.0000.0000.0000.000
54A56GLN0-0.060-0.03135.5320.3940.3940.0000.0000.0000.000
55A57ILE0-0.109-0.04133.6530.0330.0330.0000.0000.0000.000
56A58GLU-1-0.875-0.95038.112-7.609-7.6090.0000.0000.0000.000
57A59GLY0-0.046-0.00340.8170.2270.2270.0000.0000.0000.000
58A60ASN0-0.078-0.04342.4120.2370.2370.0000.0000.0000.000
59A61PRO0-0.029-0.01540.775-0.183-0.1830.0000.0000.0000.000
60A62VAL0-0.019-0.02136.3230.1080.1080.0000.0000.0000.000
61A63THR0-0.034-0.02337.797-0.127-0.1270.0000.0000.0000.000
62A64VAL0-0.009-0.01132.514-0.163-0.1630.0000.0000.0000.000
63A65GLY00.0150.00834.5850.2420.2420.0000.0000.0000.000
64A66GLU-1-0.941-0.98330.673-10.868-10.8680.0000.0000.0000.000
65A67ILE00.0230.00630.6790.3240.3240.0000.0000.0000.000
66A68ASP-1-0.821-0.88028.632-11.497-11.4970.0000.0000.0000.000
67A69ILE0-0.020-0.02026.9750.2460.2460.0000.0000.0000.000
68A70THR0-0.0160.00125.010-0.730-0.7300.0000.0000.0000.000
69A71LEU0-0.033-0.02920.1220.2540.2540.0000.0000.0000.000
70A72TYR00.007-0.00623.558-0.059-0.0590.0000.0000.0000.000
71A73ARG10.8090.87922.19811.90411.9040.0000.0000.0000.000
72A74ASP-1-0.820-0.88322.254-12.773-12.7730.0000.0000.0000.000
73A75ASP-1-0.956-0.97016.194-18.419-18.4190.0000.0000.0000.000
74A76LEU0-0.007-0.01117.345-0.844-0.8440.0000.0000.0000.000
75A77SER00.0020.00417.0610.3310.3310.0000.0000.0000.000
76A78LYS10.8790.94018.84512.75412.7540.0000.0000.0000.000
77A79LYS10.8050.88121.67113.92313.9230.0000.0000.0000.000
78A80THR00.0030.00624.8110.3300.3300.0000.0000.0000.000
79A81SER0-0.025-0.03123.4750.0710.0710.0000.0000.0000.000
80A82ASN0-0.050-0.03425.6620.2940.2940.0000.0000.0000.000
81A83ASP-1-0.807-0.89622.174-13.774-13.7740.0000.0000.0000.000
82A84GLU-1-0.768-0.86725.152-10.697-10.6970.0000.0000.0000.000
83A85PRO0-0.096-0.04325.286-0.312-0.3120.0000.0000.0000.000
84A86LEU00.0000.00627.3750.4200.4200.0000.0000.0000.000
85A87VAL00.0120.00129.547-0.350-0.3500.0000.0000.0000.000
86A88LYS10.8040.88128.27511.18011.1800.0000.0000.0000.000
87A89GLY00.0220.00832.7560.3090.3090.0000.0000.0000.000
88A90ALA0-0.031-0.02233.394-0.349-0.3490.0000.0000.0000.000
89A91ASP-1-0.927-0.94035.104-8.332-8.3320.0000.0000.0000.000
90A92ILE00.031-0.00336.015-0.287-0.2870.0000.0000.0000.000
91A93PRO0-0.0100.01438.3010.2160.2160.0000.0000.0000.000
92A94VAL0-0.032-0.02141.3140.2130.2130.0000.0000.0000.000
93A95ASP-1-0.807-0.88642.682-7.152-7.1520.0000.0000.0000.000
94A96ILE00.003-0.00239.571-0.024-0.0240.0000.0000.0000.000
95A97THR0-0.062-0.05542.939-0.050-0.0500.0000.0000.0000.000
96A98ASP-1-0.961-0.98246.009-6.596-6.5960.0000.0000.0000.000
97A99GLN00.0140.02942.828-0.051-0.0510.0000.0000.0000.000
98A100LYS10.8530.95137.9277.9677.9670.0000.0000.0000.000
99A101VAL00.0450.02335.273-0.029-0.0290.0000.0000.0000.000
100A102ILE0-0.036-0.01631.321-0.057-0.0570.0000.0000.0000.000
101A103LEU00.0250.01629.984-0.120-0.1200.0000.0000.0000.000
102A104VAL0-0.002-0.00226.405-0.183-0.1830.0000.0000.0000.000
103A105ASP-1-0.790-0.88523.130-14.115-14.1150.0000.0000.0000.000
104A106ASP-1-0.820-0.92619.281-16.604-16.6040.0000.0000.0000.000
105A107VAL0-0.055-0.04715.983-0.489-0.4890.0000.0000.0000.000
106A108LEU0-0.0060.00619.0380.2980.2980.0000.0000.0000.000
107A109TYR00.0640.01016.834-0.539-0.5390.0000.0000.0000.000
108A110THR00.0660.03320.1030.7140.7140.0000.0000.0000.000
109A111GLY00.0170.00222.7150.6070.6070.0000.0000.0000.000
110A112ARG10.7920.88224.16112.45012.4500.0000.0000.0000.000
111A113THR00.0310.00823.9150.1930.1930.0000.0000.0000.000
112A114VAL00.0310.02226.1550.2800.2800.0000.0000.0000.000
113A115ARG10.8170.89028.50510.11710.1170.0000.0000.0000.000
114A116ALA00.0070.01429.3560.3180.3180.0000.0000.0000.000
115A117GLY00.0460.01930.3890.2380.2380.0000.0000.0000.000
116A118MET0-0.052-0.03831.8370.2940.2940.0000.0000.0000.000
117A119ASP-1-0.805-0.87734.544-8.906-8.9060.0000.0000.0000.000
118A120ALA00.0280.01534.4930.2380.2380.0000.0000.0000.000
119A121LEU0-0.014-0.01734.7820.1880.1880.0000.0000.0000.000
120A122VAL0-0.058-0.02537.8740.2160.2160.0000.0000.0000.000
121A123ASP-1-0.933-0.95939.565-7.735-7.7350.0000.0000.0000.000
122A124VAL0-0.073-0.03539.1370.1710.1710.0000.0000.0000.000
123A125GLY00.0020.00241.9080.1300.1300.0000.0000.0000.000
124A126ARG10.9340.96643.3066.6316.6310.0000.0000.0000.000
125A127PRO00.0420.04139.9450.1360.1360.0000.0000.0000.000
126A128SER0-0.036-0.03542.825-0.031-0.0310.0000.0000.0000.000
127A129SER0-0.071-0.04539.287-0.028-0.0280.0000.0000.0000.000
128A130ILE00.0240.02134.315-0.052-0.0520.0000.0000.0000.000
129A131GLN0-0.0010.02833.310-0.124-0.1240.0000.0000.0000.000
130A132LEU0-0.012-0.00526.363-0.128-0.1280.0000.0000.0000.000
131A133ALA00.0190.02027.775-0.029-0.0290.0000.0000.0000.000
132A134VAL0-0.012-0.01122.322-0.185-0.1850.0000.0000.0000.000
133A135LEU00.0310.02919.0390.0800.0800.0000.0000.0000.000
134A136VAL0-0.026-0.02615.865-0.356-0.3560.0000.0000.0000.000
135A137ASP-1-0.736-0.82619.025-13.790-13.7900.0000.0000.0000.000
136A138ARG10.8550.93313.00820.93220.9320.0000.0000.0000.000
137A139GLY00.0070.00817.211-0.307-0.3070.0000.0000.0000.000
138A140HIS0-0.045-0.03216.5970.0780.0780.0000.0000.0000.000
139A141ARG10.7640.85620.71813.23713.2370.0000.0000.0000.000
140A142GLU-1-0.818-0.89522.819-13.360-13.3600.0000.0000.0000.000
141A143LEU00.0250.02326.2890.4330.4330.0000.0000.0000.000
142A144PRO0-0.0050.00228.728-0.318-0.3180.0000.0000.0000.000
143A145ILE00.0160.00927.7200.2230.2230.0000.0000.0000.000
144A146ARG10.9330.96727.3579.0929.0920.0000.0000.0000.000
145A147ALA00.0330.02125.4730.1330.1330.0000.0000.0000.000
146A148ASP-1-0.897-0.93727.483-9.511-9.5110.0000.0000.0000.000
147A149TYR00.034-0.00428.2350.2510.2510.0000.0000.0000.000
148A150ILE0-0.009-0.00722.057-0.353-0.3530.0000.0000.0000.000
149A151GLY00.0060.02221.8320.1360.1360.0000.0000.0000.000
150A152LYS10.9040.93317.71715.03515.0350.0000.0000.0000.000
151A153ASN00.0430.02819.065-0.248-0.2480.0000.0000.0000.000
152A154ILE0-0.006-0.00711.254-0.317-0.3170.0000.0000.0000.000
153A155PRO0-0.0170.00114.9170.1950.1950.0000.0000.0000.000
154A156THR00.0070.00712.150-0.905-0.9050.0000.0000.0000.000
155A157SER0-0.016-0.02210.1252.2172.2170.0000.0000.0000.000
156A158LYS10.8630.89313.05617.43917.4390.0000.0000.0000.000
157A159SER00.0280.0319.5631.2261.2260.0000.0000.0000.000
158A160GLU-1-0.795-0.8827.967-28.451-28.4510.0000.0000.0000.000
159A161LYS10.9550.9758.87328.33928.3390.0000.0000.0000.000
160A162VAL00.007-0.0049.639-2.918-2.9180.0000.0000.0000.000
161A163MET0-0.0290.00011.048-0.079-0.0790.0000.0000.0000.000
162A164VAL00.0090.00212.859-0.678-0.6780.0000.0000.0000.000
163A165GLN0-0.073-0.04010.880-0.247-0.2470.0000.0000.0000.000
164A166LEU00.0360.00315.7820.3990.3990.0000.0000.0000.000
165A167ASP-1-0.841-0.90919.362-15.203-15.2030.0000.0000.0000.000
166A168GLU-1-0.837-0.90921.079-13.353-13.3530.0000.0000.0000.000
167A169VAL0-0.073-0.03518.7270.3860.3860.0000.0000.0000.000
168A170ASP-1-0.775-0.86415.295-19.372-19.3720.0000.0000.0000.000
169A171GLN0-0.093-0.03216.534-1.219-1.2190.0000.0000.0000.000
170A172ASN00.0340.01014.5320.4980.4980.0000.0000.0000.000
171A173ASP-1-0.738-0.81016.909-15.757-15.7570.0000.0000.0000.000
172A174LEU0-0.096-0.05510.784-1.160-1.1600.0000.0000.0000.000
173A175VAL00.0030.00013.2570.3660.3660.0000.0000.0000.000
174A176ALA0-0.009-0.0098.354-0.857-0.8570.0000.0000.0000.000
175A177ILE0-0.0120.0046.6432.0522.0520.0000.0000.0000.000