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: YR3V2

Calculation Name: 5A9D-A-Xray547

Preferred Name: Solute carrier family 15 member 1

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5A9D

Chain ID: A

ChEMBL ID: CHEMBL2073714

UniProt ID: Q9JIP7

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 188
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1887961.336144
FMO2-HF: Nuclear repulsion 1814099.144959
FMO2-HF: Total energy -73862.191186
FMO2-MP2: Total energy -74075.675338


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:391:GLY)


Summations of interaction energy for fragment #1(A:391:GLY)
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.
-35.328-35.8162.0541.722-3.288-0.031
Interaction energy analysis for fragmet #1(A:391:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.846 / q_NPA : 0.925
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].
3A393ASN00.0710.0132.70310.8817.7520.5313.501-0.903-0.013
4A394GLN0-0.038-0.0112.444-5.135-2.9991.528-1.607-2.057-0.018
5A395VAL00.0420.0274.266-3.750-3.821-0.001-0.0140.0860.000
68A458GLY0-0.022-0.0104.6711.4251.476-0.001-0.032-0.0180.000
69A459HIS10.8300.9125.67331.70931.724-0.001-0.006-0.0080.000
89A479ASN0-0.057-0.0333.5499.2379.611-0.001-0.111-0.2620.000
90A480GLN0-0.020-0.0104.4791.5301.666-0.001-0.009-0.1260.000
6A396GLN00.0090.0145.0614.3824.3820.0000.0000.0000.000
7A397ILE00.016-0.0058.5651.8771.8770.0000.0000.0000.000
8A398LYS10.8800.97512.39218.06918.0690.0000.0000.0000.000
9A399VAL00.0030.00415.1680.3210.3210.0000.0000.0000.000
10A400LEU00.007-0.00918.7080.1510.1510.0000.0000.0000.000
11A401ASN0-0.037-0.01621.9190.2690.2690.0000.0000.0000.000
12A402ILE00.000-0.01825.3730.2000.2000.0000.0000.0000.000
13A403GLY00.0430.01128.0320.3830.3830.0000.0000.0000.000
14A404ASN0-0.066-0.03830.579-0.144-0.1440.0000.0000.0000.000
15A405ASN00.0080.00032.142-0.003-0.0030.0000.0000.0000.000
16A406ASN00.0540.03329.817-0.380-0.3800.0000.0000.0000.000
17A407MET0-0.0490.01426.6850.3210.3210.0000.0000.0000.000
18A408THR0-0.0010.01224.465-0.233-0.2330.0000.0000.0000.000
19A409VAL00.0050.01419.4340.2590.2590.0000.0000.0000.000
20A410HIS00.0050.00121.319-0.440-0.4400.0000.0000.0000.000
21A411PHE00.0410.00915.453-0.100-0.1000.0000.0000.0000.000
22A412PRO0-0.019-0.01415.4390.7910.7910.0000.0000.0000.000
23A413GLY00.0100.01716.306-1.013-1.0130.0000.0000.0000.000
24A414ASN0-0.042-0.02516.470-0.358-0.3580.0000.0000.0000.000
25A415SER00.016-0.00119.263-0.434-0.4340.0000.0000.0000.000
26A416VAL0-0.012-0.00618.473-0.016-0.0160.0000.0000.0000.000
27A417THR0-0.040-0.02821.6280.1490.1490.0000.0000.0000.000
28A418LEU0-0.0120.00221.199-0.120-0.1200.0000.0000.0000.000
29A419ALA00.0470.02325.4730.3650.3650.0000.0000.0000.000
30A420GLN00.0230.02327.772-0.568-0.5680.0000.0000.0000.000
31A421MET0-0.043-0.01328.2270.0010.0010.0000.0000.0000.000
32A422SER0-0.026-0.01325.673-0.115-0.1150.0000.0000.0000.000
33A423GLN00.042-0.00120.313-0.424-0.4240.0000.0000.0000.000
34A424THR0-0.003-0.01016.3240.5160.5160.0000.0000.0000.000
35A425ASP-1-0.895-0.94818.040-16.973-16.9730.0000.0000.0000.000
36A426THR0-0.036-0.01313.418-0.912-0.9120.0000.0000.0000.000
37A427PHE0-0.036-0.02210.5000.7420.7420.0000.0000.0000.000
38A428MET00.0040.02010.843-1.183-1.1830.0000.0000.0000.000
39A429THR0-0.017-0.0165.418-3.223-3.2230.0000.0000.0000.000
40A430PHE00.0360.0188.1171.1841.1840.0000.0000.0000.000
41A431ASP-1-0.837-0.9056.236-43.895-43.8950.0000.0000.0000.000
42A432ILE00.017-0.0057.3292.9802.9800.0000.0000.0000.000
43A433ASP-1-0.886-0.9449.296-24.211-24.2110.0000.0000.0000.000
44A434LYS10.8650.9179.95729.02229.0220.0000.0000.0000.000
45A435LEU0-0.0220.00811.3591.3081.3080.0000.0000.0000.000
46A436THR00.009-0.00313.4020.8670.8670.0000.0000.0000.000
47A437SER0-0.045-0.01616.7010.9830.9830.0000.0000.0000.000
48A438ILE00.0500.02515.297-0.585-0.5850.0000.0000.0000.000
49A439ASN0-0.0050.01519.4620.7960.7960.0000.0000.0000.000
50A440ILE00.0270.01421.987-0.336-0.3360.0000.0000.0000.000
51A441SER00.0350.02325.0150.3870.3870.0000.0000.0000.000
52A442SER00.0080.00528.264-0.230-0.2300.0000.0000.0000.000
53A443SER0-0.020-0.02230.7580.2840.2840.0000.0000.0000.000
54A444GLY0-0.008-0.00733.0350.1270.1270.0000.0000.0000.000
55A445SER0-0.024-0.01533.6900.3090.3090.0000.0000.0000.000
56A446PRO00.0280.00433.909-0.246-0.2460.0000.0000.0000.000
57A447GLY0-0.0090.01633.406-0.100-0.1000.0000.0000.0000.000
58A448VAL0-0.0200.00027.482-0.255-0.2550.0000.0000.0000.000
59A449THR0-0.029-0.02425.9770.3140.3140.0000.0000.0000.000
60A450THR0-0.014-0.01422.681-0.214-0.2140.0000.0000.0000.000
61A451VAL0-0.050-0.03019.0420.3420.3420.0000.0000.0000.000
62A452ALA00.0030.00420.789-0.135-0.1350.0000.0000.0000.000
63A453HIS0-0.016-0.02015.973-0.769-0.7690.0000.0000.0000.000
64A454ASP-1-0.935-0.97016.690-17.174-17.1740.0000.0000.0000.000
65A455PHE00.004-0.00411.920-0.516-0.5160.0000.0000.0000.000
66A456GLU-1-0.871-0.92410.950-23.114-23.1140.0000.0000.0000.000
67A457GLN00.0210.0036.074-5.121-5.1210.0000.0000.0000.000
70A460ARG10.9160.9738.68529.82629.8260.0000.0000.0000.000
71A461HIS00.0240.01010.4272.7502.7500.0000.0000.0000.000
72A462THR0-0.037-0.03313.738-0.178-0.1780.0000.0000.0000.000
73A463LEU0-0.002-0.00216.8630.6760.6760.0000.0000.0000.000
74A464LEU00.0010.00018.7050.4570.4570.0000.0000.0000.000
75A465VAL00.009-0.00522.2560.0650.0650.0000.0000.0000.000
76A466TRP00.0390.00624.8380.1070.1070.0000.0000.0000.000
77A467ASN00.0190.03628.672-0.194-0.1940.0000.0000.0000.000
78A468PRO0-0.036-0.01731.8150.1080.1080.0000.0000.0000.000
79A469SER00.013-0.03528.574-0.012-0.0120.0000.0000.0000.000
80A470GLN0-0.0200.00528.287-0.183-0.1830.0000.0000.0000.000
81A471TYR00.0400.00822.029-0.430-0.4300.0000.0000.0000.000
82A472ARG10.9370.96522.47912.84512.8450.0000.0000.0000.000
83A473VAL00.0280.03816.589-0.218-0.2180.0000.0000.0000.000
84A474VAL0-0.034-0.00918.3870.7740.7740.0000.0000.0000.000
85A475LYS10.8930.93115.15218.33018.3300.0000.0000.0000.000
86A476ASP-1-0.806-0.89013.602-18.626-18.6260.0000.0000.0000.000
87A477GLY00.0200.01313.117-0.533-0.5330.0000.0000.0000.000
88A478LEU0-0.001-0.0108.498-1.549-1.5490.0000.0000.0000.000
91A481LYS10.9550.9767.21621.82421.8240.0000.0000.0000.000
92A482PRO00.0200.02210.078-1.424-1.4240.0000.0000.0000.000
93A483GLU-1-0.938-0.96910.195-25.538-25.5380.0000.0000.0000.000
94A484LYS10.8950.92513.01916.45316.4530.0000.0000.0000.000
95A485GLY00.0690.02216.8530.3340.3340.0000.0000.0000.000
96A486GLU-1-0.919-0.95410.687-28.995-28.9950.0000.0000.0000.000
97A487ASN0-0.006-0.01515.0281.4191.4190.0000.0000.0000.000
98A488GLY0-0.0080.00314.686-1.594-1.5940.0000.0000.0000.000
99A489ILE00.0430.01214.4661.2661.2660.0000.0000.0000.000
100A490ARG10.8210.91514.67713.16213.1620.0000.0000.0000.000
101A491PHE00.0470.02114.8280.8790.8790.0000.0000.0000.000
102A492VAL00.007-0.00118.631-0.117-0.1170.0000.0000.0000.000
103A493ASN0-0.025-0.00721.8380.5450.5450.0000.0000.0000.000
104A494THR0-0.037-0.04223.5740.4430.4430.0000.0000.0000.000
105A495LEU0-0.0090.00224.8860.6000.6000.0000.0000.0000.000
106A496ASN0-0.036-0.02927.122-0.324-0.3240.0000.0000.0000.000
107A497GLU-1-0.849-0.90225.517-11.021-11.0210.0000.0000.0000.000
108A498MET0-0.0040.00120.700-0.321-0.3210.0000.0000.0000.000
109A499VAL0-0.0290.00619.3260.2990.2990.0000.0000.0000.000
110A500THR00.0250.01714.310-0.790-0.7900.0000.0000.0000.000
111A501ILE0-0.0120.00714.7100.6530.6530.0000.0000.0000.000
112A502LYS10.9410.97511.46321.00521.0050.0000.0000.0000.000
113A503MET00.0670.04210.9141.4831.4830.0000.0000.0000.000
114A504SER0-0.0060.0049.731-2.051-2.0510.0000.0000.0000.000
115A505GLY0-0.023-0.0086.614-2.174-2.1740.0000.0000.0000.000
116A506LYS10.8130.9085.29330.57630.5760.0000.0000.0000.000
117A507VAL00.0050.0017.0523.7123.7120.0000.0000.0000.000
118A508TYR0-0.033-0.0249.653-2.179-2.1790.0000.0000.0000.000
119A509GLU-1-0.897-0.96912.150-22.011-22.0110.0000.0000.0000.000
120A510ASN00.000-0.01114.0280.5840.5840.0000.0000.0000.000
121A511VAL00.0230.01916.6650.4660.4660.0000.0000.0000.000
122A512THR00.0390.01118.8940.5370.5370.0000.0000.0000.000
123A513SER0-0.003-0.01622.446-0.142-0.1420.0000.0000.0000.000
124A514HIS0-0.049-0.02225.7740.0480.0480.0000.0000.0000.000
125A515ASN00.0010.01721.6410.3260.3260.0000.0000.0000.000
126A516ALA0-0.004-0.00920.828-0.070-0.0700.0000.0000.0000.000
127A517SER0-0.017-0.00915.408-0.085-0.0850.0000.0000.0000.000
128A518GLY00.0140.00615.0150.6640.6640.0000.0000.0000.000
129A519TYR0-0.043-0.04514.697-0.540-0.5400.0000.0000.0000.000
130A520GLN0-0.091-0.0557.912-6.278-6.2780.0000.0000.0000.000
131A521PHE00.0410.03310.1981.7831.7830.0000.0000.0000.000
132A522PHE00.0230.0099.128-4.155-4.1550.0000.0000.0000.000
133A523PRO00.0460.02311.0901.8001.8000.0000.0000.0000.000
134A524SER00.009-0.00114.356-0.122-0.1220.0000.0000.0000.000
135A525GLY0-0.0140.01617.370-0.624-0.6240.0000.0000.0000.000
136A526GLU-1-0.842-0.90618.632-13.805-13.8050.0000.0000.0000.000
137A527LYS10.8110.90613.75318.60118.6010.0000.0000.0000.000
138A528GLN00.0250.00816.3241.2141.2140.0000.0000.0000.000
139A529TYR0-0.023-0.04014.875-1.577-1.5770.0000.0000.0000.000
140A530THR00.0040.02415.4390.5420.5420.0000.0000.0000.000
141A531ILE0-0.010-0.00916.551-0.915-0.9150.0000.0000.0000.000
142A532ASN0-0.027-0.01918.112-0.019-0.0190.0000.0000.0000.000
143A533THR00.005-0.02720.091-0.250-0.2500.0000.0000.0000.000
144A534THR00.0120.00322.7880.0390.0390.0000.0000.0000.000
145A535ALA0-0.0200.00526.0490.4630.4630.0000.0000.0000.000
146A536VAL0-0.041-0.02626.3650.3980.3980.0000.0000.0000.000
147A537ALA00.0500.02828.768-0.088-0.0880.0000.0000.0000.000
148A538PRO00.000-0.01327.318-0.201-0.2010.0000.0000.0000.000
149A539THR0-0.011-0.00827.791-0.213-0.2130.0000.0000.0000.000
150A540CYS0-0.065-0.01827.9340.0160.0160.0000.0000.0000.000
151A541LEU00.0030.01624.315-0.260-0.2600.0000.0000.0000.000
152A542THR00.0250.00921.0130.0490.0490.0000.0000.0000.000
153A543ASP-1-0.934-0.96720.216-15.149-15.1490.0000.0000.0000.000
154A544PHE0-0.005-0.01519.9140.7820.7820.0000.0000.0000.000
155A545LYS10.8140.88119.53512.19812.1980.0000.0000.0000.000
156A546SER0-0.015-0.00718.4310.1160.1160.0000.0000.0000.000
157A547SER0-0.021-0.04020.4820.2690.2690.0000.0000.0000.000
158A548ASN0-0.038-0.03021.062-1.204-1.2040.0000.0000.0000.000
159A549LEU0-0.0220.00716.0790.1680.1680.0000.0000.0000.000
160A550ASP-1-0.781-0.88720.361-12.872-12.8720.0000.0000.0000.000
161A551PHE0-0.0150.00920.073-0.975-0.9750.0000.0000.0000.000
162A552GLY0-0.047-0.02318.6800.6190.6190.0000.0000.0000.000
163A553SER00.0120.01919.6950.5430.5430.0000.0000.0000.000
164A554ALA0-0.027-0.02519.079-1.182-1.1820.0000.0000.0000.000
165A555TYR00.0300.02419.0110.4700.4700.0000.0000.0000.000
166A556THR0-0.013-0.02519.377-1.013-1.0130.0000.0000.0000.000
167A557TYR0-0.033-0.03418.8320.3790.3790.0000.0000.0000.000
168A558VAL00.003-0.00521.443-0.357-0.3570.0000.0000.0000.000
169A559ILE00.0140.01419.5980.3490.3490.0000.0000.0000.000
170A560ARG10.8480.92324.19310.30210.3020.0000.0000.0000.000
171A561ARG10.8570.92227.5789.8749.8740.0000.0000.0000.000
172A562ALA00.0220.02830.2240.1260.1260.0000.0000.0000.000
173A563SER0-0.018-0.02631.7150.2160.2160.0000.0000.0000.000
174A564ASP-1-0.842-0.91632.728-9.411-9.4110.0000.0000.0000.000
175A565GLY00.0040.01333.8470.1020.1020.0000.0000.0000.000
176A567LEU00.004-0.00423.4060.0190.0190.0000.0000.0000.000
177A568GLU-1-0.832-0.91227.148-9.922-9.9220.0000.0000.0000.000
178A569VAL0-0.026-0.01521.693-0.375-0.3750.0000.0000.0000.000
179A570LYS10.9180.98025.01610.49410.4940.0000.0000.0000.000
180A571GLU-1-0.767-0.84322.889-14.057-14.0570.0000.0000.0000.000
181A572PHE0-0.047-0.03624.2010.8550.8550.0000.0000.0000.000
182A573GLU-1-0.895-0.94223.791-12.855-12.8550.0000.0000.0000.000
183A574ASP-1-0.820-0.86221.921-13.806-13.8060.0000.0000.0000.000
184A575ILE00.017-0.00524.174-0.070-0.0700.0000.0000.0000.000
185A576PRO0-0.001-0.00420.927-0.316-0.3160.0000.0000.0000.000
186A577PRO0-0.032-0.00118.0930.4080.4080.0000.0000.0000.000
187A578ASN0-0.021-0.01919.292-0.664-0.6640.0000.0000.0000.000
188A579THR-1-0.978-0.98016.453-17.760-17.7600.0000.0000.0000.000