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: 2MN3R

Calculation Name: 1YA9-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YA9

Chain ID: A

ChEMBL ID:

UniProt ID: P08226

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1747717.000442
FMO2-HF: Nuclear repulsion 1676321.795658
FMO2-HF: Total energy -71395.204784
FMO2-MP2: Total energy -71602.498556


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:4:PRO)


Summations of interaction energy for fragment #1(A:4: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.
-55.315-51.453-0.023-1.741-2.098-0.009
Interaction energy analysis for fragmet #1(A:4:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.829 / q_NPA : 0.888
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].
3A6VAL00.0140.0243.5477.92211.572-0.022-1.702-1.926-0.009
4A7THR00.0020.0044.398-6.772-6.560-0.001-0.039-0.1720.000
5A8ASP-1-0.885-0.9416.366-32.821-32.8210.0000.0000.0000.000
6A9GLN0-0.052-0.0348.3832.5882.5880.0000.0000.0000.000
7A10LEU00.0140.02111.9051.9861.9860.0000.0000.0000.000
8A11GLU-1-0.853-0.92014.658-15.603-15.6030.0000.0000.0000.000
9A12TRP0-0.030-0.03015.5610.5200.5200.0000.0000.0000.000
10A13GLN0-0.017-0.02210.0980.2470.2470.0000.0000.0000.000
11A14SER00.0600.03312.041-1.069-1.0690.0000.0000.0000.000
12A15ASN0-0.072-0.04813.110-0.715-0.7150.0000.0000.0000.000
13A16GLN0-0.017-0.0119.5800.9430.9430.0000.0000.0000.000
14A17PRO00.0340.0287.771-0.675-0.6750.0000.0000.0000.000
15A18TRP00.0540.0118.857-0.122-0.1220.0000.0000.0000.000
16A19GLU-1-0.807-0.88011.939-16.895-16.8950.0000.0000.0000.000
17A20GLN0-0.015-0.0166.925-2.265-2.2650.0000.0000.0000.000
18A21ALA0-0.0200.0089.482-0.415-0.4150.0000.0000.0000.000
19A22LEU00.0220.00910.4541.1951.1950.0000.0000.0000.000
20A23ASN0-0.014-0.01512.2491.9571.9570.0000.0000.0000.000
21A24ARG10.9230.9696.37934.81034.8100.0000.0000.0000.000
22A25PHE00.0280.01111.6001.3161.3160.0000.0000.0000.000
23A26TRP00.000-0.02714.6061.3271.3270.0000.0000.0000.000
24A27ASP-1-0.831-0.91414.221-17.342-17.3420.0000.0000.0000.000
25A28TYR0-0.008-0.02514.4721.2301.2300.0000.0000.0000.000
26A29LEU00.003-0.00216.3931.1461.1460.0000.0000.0000.000
27A30ARG10.7610.86517.55716.50716.5070.0000.0000.0000.000
28A31TRP00.0060.02719.0790.5030.5030.0000.0000.0000.000
29A32VAL00.0590.03320.1250.7550.7550.0000.0000.0000.000
30A33GLN0-0.081-0.04922.6340.5830.5830.0000.0000.0000.000
31A34THR0-0.047-0.04124.3470.6220.6220.0000.0000.0000.000
32A35LEU0-0.066-0.02726.3960.4550.4550.0000.0000.0000.000
33A36SER00.0620.03725.6770.3180.3180.0000.0000.0000.000
34A37ASP-1-0.878-0.95228.091-9.753-9.7530.0000.0000.0000.000
35A38GLN0-0.049-0.03021.4850.2590.2590.0000.0000.0000.000
36A39VAL0-0.034-0.00523.016-0.216-0.2160.0000.0000.0000.000
37A40GLN0-0.045-0.02725.1590.2350.2350.0000.0000.0000.000
38A41GLU-1-0.817-0.89127.423-9.890-9.8900.0000.0000.0000.000
39A42GLU-1-0.843-0.92420.913-13.983-13.9830.0000.0000.0000.000
40A43LEU0-0.065-0.02623.687-0.344-0.3440.0000.0000.0000.000
41A44GLN0-0.087-0.05325.697-0.077-0.0770.0000.0000.0000.000
42A45SER00.0610.03223.914-0.011-0.0110.0000.0000.0000.000
43A46SER0-0.085-0.05824.367-0.294-0.2940.0000.0000.0000.000
44A47GLN00.0370.02317.6800.3570.3570.0000.0000.0000.000
45A48VAL00.0440.02619.254-0.663-0.6630.0000.0000.0000.000
46A49THR0-0.061-0.03219.614-0.106-0.1060.0000.0000.0000.000
47A50GLN0-0.0300.01118.330-0.628-0.6280.0000.0000.0000.000
48A51GLU-1-0.778-0.86814.938-18.367-18.3670.0000.0000.0000.000
49A52LEU0-0.011-0.00414.741-0.894-0.8940.0000.0000.0000.000
50A53THR00.027-0.02116.4580.0400.0400.0000.0000.0000.000
51A54ALA00.0320.02412.230-0.220-0.2200.0000.0000.0000.000
52A55LEU0-0.0040.00010.507-1.202-1.2020.0000.0000.0000.000
53A56MET0-0.061-0.01412.927-0.038-0.0380.0000.0000.0000.000
54A57GLU-1-0.918-0.96114.258-16.856-16.8560.0000.0000.0000.000
55A58ASP-1-0.851-0.9047.945-31.537-31.5370.0000.0000.0000.000
56A59THR0-0.019-0.02611.043-0.296-0.2960.0000.0000.0000.000
57A60MET0-0.058-0.04213.0850.8730.8730.0000.0000.0000.000
58A61THR0-0.049-0.02411.6891.3521.3520.0000.0000.0000.000
59A62GLU-1-0.850-0.9357.702-29.079-29.0790.0000.0000.0000.000
60A63VAL0-0.066-0.02811.9620.9410.9410.0000.0000.0000.000
61A64LYS10.8370.91715.53516.68116.6810.0000.0000.0000.000
62A65ALA00.0250.02812.4090.8360.8360.0000.0000.0000.000
63A66TYR00.0810.04213.7881.0401.0400.0000.0000.0000.000
64A67LYS10.8110.88815.28713.90113.9010.0000.0000.0000.000
65A68LYS10.8760.94117.62015.31615.3160.0000.0000.0000.000
66A69GLU-1-0.775-0.88014.098-18.476-18.4760.0000.0000.0000.000
67A70LEU0-0.013-0.01817.7010.7580.7580.0000.0000.0000.000
68A71GLU-1-0.950-0.96620.275-11.535-11.5350.0000.0000.0000.000
69A72GLU-1-0.966-0.98818.821-14.793-14.7930.0000.0000.0000.000
70A73GLN0-0.054-0.02617.2330.6740.6740.0000.0000.0000.000
71A74LEU0-0.075-0.01922.6150.4690.4690.0000.0000.0000.000
72A75GLY0-0.043-0.03725.7700.2270.2270.0000.0000.0000.000
73A76PRO00.0290.01329.066-0.225-0.2250.0000.0000.0000.000
74A77VAL00.0000.03129.8440.2120.2120.0000.0000.0000.000
75A78ALA00.0160.01632.4390.1040.1040.0000.0000.0000.000
76A79GLU-1-0.899-0.95433.290-8.941-8.9410.0000.0000.0000.000
77A80GLU-1-0.851-0.93133.216-8.340-8.3400.0000.0000.0000.000
78A81THR0-0.039-0.02531.791-0.061-0.0610.0000.0000.0000.000
79A82ARG10.9991.01727.7239.9749.9740.0000.0000.0000.000
80A83ALA0-0.0040.00129.140-0.299-0.2990.0000.0000.0000.000
81A84ARG10.8460.91031.0649.0789.0780.0000.0000.0000.000
82A85LEU00.0420.01727.400-0.097-0.0970.0000.0000.0000.000
83A86GLY00.0350.02326.079-0.400-0.4000.0000.0000.0000.000
84A87LYS10.9040.94526.7039.1609.1600.0000.0000.0000.000
85A88GLU-1-0.858-0.91628.420-9.887-9.8870.0000.0000.0000.000
86A89VAL00.0400.01921.696-0.122-0.1220.0000.0000.0000.000
87A90GLN0-0.036-0.00523.724-0.427-0.4270.0000.0000.0000.000
88A91ALA00.0310.00325.330-0.128-0.1280.0000.0000.0000.000
89A92ALA0-0.039-0.01624.1970.1190.1190.0000.0000.0000.000
90A93GLN00.0500.02519.644-0.550-0.5500.0000.0000.0000.000
91A94ALA00.0160.01222.410-0.229-0.2290.0000.0000.0000.000
92A95ARG10.8250.91325.20910.92710.9270.0000.0000.0000.000
93A96LEU00.0130.01318.3840.0650.0650.0000.0000.0000.000
94A97GLY00.0560.01721.155-0.271-0.2710.0000.0000.0000.000
95A98ALA00.0450.02522.1300.0240.0240.0000.0000.0000.000
96A99ASP0-0.100-0.09923.7900.3750.3750.0000.0000.0000.000
97A100MET0-0.048-0.01116.1430.0550.0550.0000.0000.0000.000
98A101GLU-1-0.928-0.95821.776-11.847-11.8470.0000.0000.0000.000
99A102ASP-1-0.941-0.97624.115-10.029-10.0290.0000.0000.0000.000
100A103LEU0-0.038-0.03121.8200.2890.2890.0000.0000.0000.000
101A104ARG10.9410.96520.96913.42513.4250.0000.0000.0000.000
102A105ASN00.0190.00623.625-0.072-0.0720.0000.0000.0000.000
103A106ARG10.8380.93027.1219.8229.8220.0000.0000.0000.000
104A107LEU00.0090.00323.0260.3460.3460.0000.0000.0000.000
105A108GLY00.0250.01426.8540.1410.1410.0000.0000.0000.000
106A109GLN0-0.035-0.02628.1380.3770.3770.0000.0000.0000.000
107A110TYR00.0170.00929.4120.3350.3350.0000.0000.0000.000
108A111ARG10.9170.96724.96811.57811.5780.0000.0000.0000.000
109A112ASN0-0.010-0.00930.6190.0960.0960.0000.0000.0000.000
110A113GLU-1-0.798-0.89133.625-8.491-8.4910.0000.0000.0000.000
111A114VAL00.0430.02532.5870.2400.2400.0000.0000.0000.000
112A115HIS00.0110.00530.9650.3230.3230.0000.0000.0000.000
113A116THR0-0.100-0.06035.7080.2610.2610.0000.0000.0000.000
114A117MET0-0.040-0.01038.0770.2080.2080.0000.0000.0000.000
115A118LEU0-0.022-0.01238.3360.0700.0700.0000.0000.0000.000
116A119GLY00.0330.02034.9170.0160.0160.0000.0000.0000.000
117A120GLN0-0.043-0.01135.412-0.170-0.1700.0000.0000.0000.000
118A121SER00.0420.01233.811-0.183-0.1830.0000.0000.0000.000
119A122THR00.0230.00136.1440.0200.0200.0000.0000.0000.000
120A123GLU-1-0.890-0.95936.858-7.939-7.9390.0000.0000.0000.000
121A124GLU-1-0.942-0.96137.372-7.681-7.6810.0000.0000.0000.000
122A125ILE00.0170.00434.947-0.141-0.1410.0000.0000.0000.000
123A126ARG10.9320.97532.4778.5288.5280.0000.0000.0000.000
124A127ALA00.0200.01833.003-0.272-0.2720.0000.0000.0000.000
125A128ARG10.8210.89734.6988.1468.1460.0000.0000.0000.000
126A129LEU00.0220.02128.054-0.132-0.1320.0000.0000.0000.000
127A130SER00.0420.01629.613-0.306-0.3060.0000.0000.0000.000
128A131THR0-0.042-0.03530.198-0.224-0.2240.0000.0000.0000.000
129A132HIS0-0.029-0.02030.7320.0530.0530.0000.0000.0000.000
130A133LEU00.0660.02224.985-0.170-0.1700.0000.0000.0000.000
131A134ARG10.9310.98126.8639.5119.5110.0000.0000.0000.000
132A135LYS10.8980.95128.4758.8438.8430.0000.0000.0000.000
133A136MET0-0.0250.00326.355-0.022-0.0220.0000.0000.0000.000
134A137ARG10.9240.96522.40612.06112.0610.0000.0000.0000.000
135A138LYS10.9710.97624.4059.8379.8370.0000.0000.0000.000
136A139ARG10.8450.94327.09710.18310.1830.0000.0000.0000.000
137A140LEU00.0580.02819.4150.0400.0400.0000.0000.0000.000
138A141MET0-0.0310.00022.221-0.199-0.1990.0000.0000.0000.000
139A142ARG11.0341.02723.43110.09410.0940.0000.0000.0000.000
140A143ASP-1-0.788-0.87324.917-10.999-10.9990.0000.0000.0000.000
141A144ALA00.0120.01219.668-0.210-0.2100.0000.0000.0000.000
142A145GLU-1-0.907-0.95221.359-12.260-12.2600.0000.0000.0000.000
143A146ASP-1-0.907-0.96223.299-10.596-10.5960.0000.0000.0000.000
144A147LEU0-0.055-0.02918.8970.2380.2380.0000.0000.0000.000
145A148GLN0-0.014-0.01718.0650.6610.6610.0000.0000.0000.000
146A149LYS10.9390.98120.97310.56110.5610.0000.0000.0000.000
147A150ARG10.8200.89224.32710.60910.6090.0000.0000.0000.000
148A151LEU00.0320.01517.8730.2660.2660.0000.0000.0000.000
149A152ALA00.0050.01521.791-0.024-0.0240.0000.0000.0000.000
150A153VAL0-0.056-0.03423.2480.3170.3170.0000.0000.0000.000
151A154TYR00.013-0.00422.8660.3560.3560.0000.0000.0000.000
152A155LYS10.8830.95917.86815.80515.8050.0000.0000.0000.000
153A156ALA0-0.012-0.01123.3210.2150.2150.0000.0000.0000.000
154A157GLY00.0600.04126.813-0.141-0.1410.0000.0000.0000.000
155A158ALA0-0.0010.00227.9630.4020.4020.0000.0000.0000.000
156A159ARG10.7660.88226.20211.35711.3570.0000.0000.0000.000
157A160GLU-1-0.853-0.94830.415-10.043-10.0430.0000.0000.0000.000
158A161GLY00.003-0.03431.7930.1780.1780.0000.0000.0000.000
159A162ALA0-0.052-0.00632.7940.0800.0800.0000.0000.0000.000
160A163GLU-1-0.771-0.87928.458-9.795-9.7950.0000.0000.0000.000
161A164ARG10.8040.88931.5169.1539.1530.0000.0000.0000.000
162A165GLY00.0800.03628.7820.1170.1170.0000.0000.0000.000
163A166VAL0-0.033-0.01929.255-0.205-0.2050.0000.0000.0000.000
164A167SER0-0.078-0.06330.8320.1420.1420.0000.0000.0000.000
165A168ALA00.0690.03628.8640.0160.0160.0000.0000.0000.000
166A169ILE0-0.016-0.00526.387-0.150-0.1500.0000.0000.0000.000
167A170ARG10.9430.96129.1698.9148.9140.0000.0000.0000.000
168A171GLU-1-0.866-0.90932.535-9.024-9.0240.0000.0000.0000.000
169A172ARG10.9080.96423.88212.25612.2560.0000.0000.0000.000
170A173LEU0-0.056-0.02628.133-0.125-0.1250.0000.0000.0000.000
171A174GLY00.0070.03131.5240.1330.1330.0000.0000.0000.000
172A175PRO0-0.059-0.06735.270-0.061-0.0610.0000.0000.0000.000
173A176LEU0-0.024-0.00435.4670.0080.0080.0000.0000.0000.000
174A177VAL-1-0.946-0.95438.472-7.484-7.4840.0000.0000.0000.000