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: 977G2

Calculation Name: 3WP9-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3WP9

Chain ID: A

ChEMBL ID:

UniProt ID: A5XB26

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
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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2501307.993475
FMO2-HF: Nuclear repulsion 2419374.432966
FMO2-HF: Total energy -81933.560508
FMO2-MP2: Total energy -82172.51334


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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-294.918-296.24719.533-10.001-8.203-0.102
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.791 / q_NPA : 0.875
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].
3A3PRO0-0.058-0.0163.443-3.874-2.5530.044-0.610-0.755-0.001
4A4TYR00.0410.0154.947-6.695-6.769-0.001-0.0080.0830.000
110A111PRO00.0000.0142.6111.9632.6920.414-0.305-0.838-0.002
111A112GLY00.000-0.0094.702-0.659-0.512-0.001-0.012-0.1340.000
130A131THR0-0.036-0.0424.1835.5775.667-0.001-0.005-0.0830.000
132A133ASP-1-0.918-0.9504.479-39.977-39.879-0.001-0.010-0.0870.000
133A134ASP-1-0.875-0.8941.681-136.492-140.62219.065-8.946-5.989-0.097
134A135VAL00.0050.0083.25915.96016.4500.014-0.105-0.400-0.002
5A5ALA00.0590.0316.7912.0512.0510.0000.0000.0000.000
6A6VAL0-0.0310.0078.7231.5441.5440.0000.0000.0000.000
7A7GLU-1-0.916-0.95112.433-22.363-22.3630.0000.0000.0000.000
8A8LEU0-0.016-0.02314.8601.0921.0920.0000.0000.0000.000
9A9GLY0-0.0020.01017.7610.9090.9090.0000.0000.0000.000
10A10GLU-1-0.867-0.95220.388-12.902-12.9020.0000.0000.0000.000
11A11ALA0-0.036-0.01221.1670.3320.3320.0000.0000.0000.000
12A12GLY0-0.0080.00019.270-0.139-0.1390.0000.0000.0000.000
13A13THR0-0.062-0.03319.9070.0210.0210.0000.0000.0000.000
14A14PHE0-0.052-0.01923.0440.6700.6700.0000.0000.0000.000
15A15THR0-0.023-0.00922.393-0.853-0.8530.0000.0000.0000.000
16A16ILE0-0.018-0.01223.932-0.264-0.2640.0000.0000.0000.000
17A17LEU00.0050.00825.0050.4200.4200.0000.0000.0000.000
18A18SER0-0.028-0.02426.797-0.179-0.1790.0000.0000.0000.000
19A19LYS10.9480.97428.79910.74210.7420.0000.0000.0000.000
20A20SER0-0.063-0.04931.7750.2540.2540.0000.0000.0000.000
21A21GLY00.0550.02934.1020.2050.2050.0000.0000.0000.000
22A22ILE0-0.042-0.00130.660-0.350-0.3500.0000.0000.0000.000
23A23THR0-0.018-0.01033.8710.2360.2360.0000.0000.0000.000
24A24ASP-1-0.702-0.80634.300-9.507-9.5070.0000.0000.0000.000
25A25VAL0-0.066-0.01336.1140.3410.3410.0000.0000.0000.000
26A26TYR0-0.028-0.00737.091-0.151-0.1510.0000.0000.0000.000
27A27PRO0-0.078-0.03937.3350.1830.1830.0000.0000.0000.000
28A28SER00.023-0.04032.174-0.175-0.1750.0000.0000.0000.000
29A29THR0-0.075-0.04130.3890.2910.2910.0000.0000.0000.000
30A30VAL0-0.0100.00027.414-0.369-0.3690.0000.0000.0000.000
31A31THR00.0230.01725.7330.5100.5100.0000.0000.0000.000
32A32GLY00.0320.02625.486-0.670-0.6700.0000.0000.0000.000
33A33ASN0-0.006-0.00626.0780.7970.7970.0000.0000.0000.000
34A34VAL00.0280.01127.182-0.382-0.3820.0000.0000.0000.000
35A35GLY00.0460.01129.5920.3260.3260.0000.0000.0000.000
36A36THR0-0.047-0.02430.424-0.153-0.1530.0000.0000.0000.000
37A37SER00.0360.02531.9250.3600.3600.0000.0000.0000.000
38A38PRO0-0.008-0.00832.201-0.304-0.3040.0000.0000.0000.000
39A39ILE0-0.050-0.02135.4420.3180.3180.0000.0000.0000.000
40A40THR0-0.020-0.03837.403-0.057-0.0570.0000.0000.0000.000
41A41GLY00.064-0.00538.191-0.156-0.1560.0000.0000.0000.000
42A42ALA0-0.0060.00539.274-0.081-0.0810.0000.0000.0000.000
43A43ALA0-0.049-0.01937.8950.0630.0630.0000.0000.0000.000
44A44LEU0-0.011-0.00433.655-0.250-0.2500.0000.0000.0000.000
45A45LEU0-0.052-0.03536.8340.1570.1570.0000.0000.0000.000
46A46LEU00.0120.02132.1350.0320.0320.0000.0000.0000.000
47A47ASN00.011-0.01336.7790.1340.1340.0000.0000.0000.000
48A48CYS00.001-0.02537.146-0.230-0.2300.0000.0000.0000.000
49A49ASP-1-0.836-0.90337.426-8.231-8.2310.0000.0000.0000.000
50A50GLU0-0.046-0.04734.615-0.052-0.0520.0000.0000.0000.000
51A51VAL0-0.026-0.01130.989-0.363-0.3630.0000.0000.0000.000
52A52THR00.0090.00429.4150.1350.1350.0000.0000.0000.000
53A53GLY0-0.0080.01429.5610.0100.0100.0000.0000.0000.000
54A54ALA0-0.019-0.01030.4260.3760.3760.0000.0000.0000.000
55A55MET00.0020.01131.181-0.214-0.2140.0000.0000.0000.000
56A56TYR00.000-0.00829.7510.2340.2340.0000.0000.0000.000
57A57THR00.009-0.00833.819-0.132-0.1320.0000.0000.0000.000
58A58VAL0-0.016-0.00835.5410.0130.0130.0000.0000.0000.000
59A59ASP-1-0.741-0.84237.590-7.715-7.7150.0000.0000.0000.000
60A60SER0-0.020-0.01640.394-0.137-0.1370.0000.0000.0000.000
61A61ALA0-0.053-0.02442.3490.1820.1820.0000.0000.0000.000
62A62GLY00.0300.02039.827-0.014-0.0140.0000.0000.0000.000
63A63PRO00.0120.01538.2840.2280.2280.0000.0000.0000.000
64A64LEU0-0.0210.02440.864-0.069-0.0690.0000.0000.0000.000
65A65PRO0-0.032-0.04042.5750.0160.0160.0000.0000.0000.000
66A67SER0-0.008-0.00437.330-0.175-0.1750.0000.0000.0000.000
67A68ILE0-0.038-0.01234.7850.2220.2220.0000.0000.0000.000
68A69ASN0-0.021-0.01636.619-0.319-0.3190.0000.0000.0000.000
69A70SER00.0120.00133.5080.1040.1040.0000.0000.0000.000
70A71PRO00.0280.01234.112-0.318-0.3180.0000.0000.0000.000
71A72TYR00.0000.00132.375-0.277-0.2770.0000.0000.0000.000
72A73LEU00.0270.02528.119-0.190-0.1900.0000.0000.0000.000
73A74LEU00.0120.00229.138-0.431-0.4310.0000.0000.0000.000
74A75GLU-1-0.956-0.97129.696-9.643-9.6430.0000.0000.0000.000
75A76LEU00.0110.02227.138-0.264-0.2640.0000.0000.0000.000
76A77ALA00.0450.02925.097-0.428-0.4280.0000.0000.0000.000
77A78VAL0-0.014-0.02924.986-0.488-0.4880.0000.0000.0000.000
78A79SER0-0.066-0.03826.396-0.091-0.0910.0000.0000.0000.000
79A80ASP-1-0.828-0.91321.538-14.017-14.0170.0000.0000.0000.000
80A81MET0-0.0220.01221.218-0.808-0.8080.0000.0000.0000.000
81A82GLY0-0.047-0.02622.111-0.336-0.3360.0000.0000.0000.000
82A83ILE0-0.035-0.02219.447-0.253-0.2530.0000.0000.0000.000
83A84ALA00.0680.03217.606-0.559-0.5590.0000.0000.0000.000
84A85TYR0-0.003-0.00617.518-0.761-0.7610.0000.0000.0000.000
85A86ASN0-0.016-0.02019.298-0.251-0.2510.0000.0000.0000.000
86A87ASP-1-0.818-0.87914.496-22.032-22.0320.0000.0000.0000.000
87A88ALA00.0200.00914.383-1.078-1.0780.0000.0000.0000.000
88A89ALA0-0.014-0.00615.387-0.740-0.7400.0000.0000.0000.000
89A90GLY0-0.044-0.02117.6660.1560.1560.0000.0000.0000.000
90A91ARG10.6750.8039.81626.19926.1990.0000.0000.0000.000
91A92VAL00.0100.01513.2780.8160.8160.0000.0000.0000.000
92A93PRO0-0.002-0.01210.686-0.378-0.3780.0000.0000.0000.000
93A94ALA00.017-0.00211.629-1.337-1.3370.0000.0000.0000.000
94A95ASP-1-0.870-0.9167.920-33.218-33.2180.0000.0000.0000.000
95A96HIS10.8280.9148.66228.32128.3210.0000.0000.0000.000
96A97THR00.0250.01013.347-0.228-0.2280.0000.0000.0000.000
97A98GLU-1-0.810-0.87916.994-13.862-13.8620.0000.0000.0000.000
98A99LEU00.0010.01514.1640.6630.6630.0000.0000.0000.000
99A100GLY00.0660.03418.1940.1420.1420.0000.0000.0000.000
100A101THR0-0.110-0.05620.8610.8390.8390.0000.0000.0000.000
101A102GLY00.0760.04221.3790.5280.5280.0000.0000.0000.000
102A103GLU-1-0.817-0.86221.706-13.279-13.2790.0000.0000.0000.000
103A104ILE00.019-0.01216.431-0.555-0.5550.0000.0000.0000.000
104A105GLY0-0.0030.00518.313-0.675-0.6750.0000.0000.0000.000
105A106GLY0-0.073-0.04320.4010.3540.3540.0000.0000.0000.000
106A107LEU0-0.050-0.00915.440-0.170-0.1700.0000.0000.0000.000
107A108THR0-0.024-0.02211.455-0.025-0.0250.0000.0000.0000.000
108A109LEU0-0.041-0.01510.6840.1630.1630.0000.0000.0000.000
109A110GLU-1-0.837-0.9136.133-31.634-31.6340.0000.0000.0000.000
112A113VAL0-0.036-0.0096.8781.8511.8510.0000.0000.0000.000
113A114TYR0-0.084-0.0738.6432.6052.6050.0000.0000.0000.000
114A115LYS10.9210.96813.18518.35918.3590.0000.0000.0000.000
115A116TRP0-0.027-0.02715.051-0.137-0.1370.0000.0000.0000.000
116A117SER0-0.047-0.05820.2290.3210.3210.0000.0000.0000.000
117A118SER0-0.051-0.03723.4910.4730.4730.0000.0000.0000.000
118A119ASP-1-0.831-0.90723.938-11.837-11.8370.0000.0000.0000.000
119A120VAL00.0060.01319.048-0.253-0.2530.0000.0000.0000.000
120A121ASN0-0.050-0.01822.3640.4160.4160.0000.0000.0000.000
121A122ILE00.0320.02219.494-0.498-0.4980.0000.0000.0000.000
122A123SER0-0.014-0.05822.5640.6110.6110.0000.0000.0000.000
123A124THR0-0.104-0.07023.5760.4060.4060.0000.0000.0000.000
124A125ASP-1-0.779-0.89320.782-13.712-13.7120.0000.0000.0000.000
125A126VAL0-0.0110.00915.351-0.019-0.0190.0000.0000.0000.000
126A127THR0-0.020-0.00813.2180.1580.1580.0000.0000.0000.000
127A128PHE00.0170.00610.431-0.156-0.1560.0000.0000.0000.000
128A129ASN00.0100.0238.3772.2332.2330.0000.0000.0000.000
129A130GLY0-0.011-0.0245.892-3.212-3.2120.0000.0000.0000.000
131A132MET00.0380.0116.395-0.649-0.6490.0000.0000.0000.000
135A136TRP0-0.035-0.0285.796-4.271-4.2710.0000.0000.0000.000
136A137ILE0-0.043-0.0088.8502.4762.4760.0000.0000.0000.000
137A138MET0-0.0120.01011.553-0.458-0.4580.0000.0000.0000.000
138A139GLN0-0.031-0.03314.6461.5961.5960.0000.0000.0000.000
139A140ILE00.0150.00617.1680.3480.3480.0000.0000.0000.000
140A141SER0-0.006-0.01220.6770.2090.2090.0000.0000.0000.000
141A142GLY00.0110.02323.9880.6280.6280.0000.0000.0000.000
142A143ASN0-0.069-0.06025.222-0.179-0.1790.0000.0000.0000.000
143A144LEU00.0010.01620.161-0.318-0.3180.0000.0000.0000.000
144A145ASN0-0.004-0.01423.8100.6090.6090.0000.0000.0000.000
145A146GLN00.0190.00422.082-0.263-0.2630.0000.0000.0000.000
146A147ALA00.0040.00425.0970.5210.5210.0000.0000.0000.000
147A148ASN00.009-0.01127.359-0.397-0.3970.0000.0000.0000.000
148A149ALA0-0.061-0.02828.8550.0110.0110.0000.0000.0000.000
149A150LYS10.8320.95224.07811.30111.3010.0000.0000.0000.000
150A151ARG10.9520.96121.45412.72912.7290.0000.0000.0000.000
151A152VAL0-0.0190.01416.034-0.161-0.1610.0000.0000.0000.000
152A153THR0-0.021-0.00716.4260.7400.7400.0000.0000.0000.000
153A154LEU00.0280.02212.319-1.336-1.3360.0000.0000.0000.000
154A155THR0-0.020-0.04412.0071.5141.5140.0000.0000.0000.000
155A156GLY0-0.007-0.01410.206-2.281-2.2810.0000.0000.0000.000
156A157GLY0-0.002-0.00110.303-0.793-0.7930.0000.0000.0000.000
157A158ALA0-0.0390.0008.444-0.674-0.6740.0000.0000.0000.000
158A159LEU00.0480.0219.3332.8002.8000.0000.0000.0000.000
159A160ALA00.0500.02410.904-1.685-1.6850.0000.0000.0000.000
160A161LYS10.7860.88310.78225.53525.5350.0000.0000.0000.000
161A162ASN0-0.040-0.0236.7273.5443.5440.0000.0000.0000.000
162A163ILE0-0.0130.0049.152-3.099-3.0990.0000.0000.0000.000
163A164PHE00.0380.0139.3002.5142.5140.0000.0000.0000.000
164A165TRP0-0.010-0.01913.607-0.269-0.2690.0000.0000.0000.000
165A166GLN0-0.010-0.00316.7900.4020.4020.0000.0000.0000.000
166A167VAL00.0020.00018.6430.0300.0300.0000.0000.0000.000
167A168ALA0-0.022-0.01822.1860.4270.4270.0000.0000.0000.000
168A169GLY00.0360.03025.0950.5840.5840.0000.0000.0000.000
169A170TYR0-0.0350.00127.338-0.067-0.0670.0000.0000.0000.000
170A171THR00.0440.00922.940-0.618-0.6180.0000.0000.0000.000
171A172ALA0-0.043-0.02325.8750.4420.4420.0000.0000.0000.000
172A173LEU00.0070.01523.250-0.262-0.2620.0000.0000.0000.000
173A174GLY00.0500.02427.1880.4780.4780.0000.0000.0000.000
174A175THR0-0.048-0.01929.730-0.137-0.1370.0000.0000.0000.000
175A176TYR0-0.036-0.03130.367-0.051-0.0510.0000.0000.0000.000
176A177ALA00.0120.02025.570-0.064-0.0640.0000.0000.0000.000
177A178SER00.0110.00021.5450.3730.3730.0000.0000.0000.000
178A179PHE0-0.002-0.00618.718-0.336-0.3360.0000.0000.0000.000
179A180GLU-1-0.762-0.87615.572-17.481-17.4810.0000.0000.0000.000
180A181GLY00.0130.01014.909-0.879-0.8790.0000.0000.0000.000
181A182ILE0-0.046-0.01114.4701.6161.6160.0000.0000.0000.000
182A183VAL0-0.023-0.01216.870-0.537-0.5370.0000.0000.0000.000
183A184LEU00.0060.00416.6590.8030.8030.0000.0000.0000.000
184A185SER0-0.017-0.02520.476-0.065-0.0650.0000.0000.0000.000
185A186LYS10.8380.92923.84612.80312.8030.0000.0000.0000.000
186A187THR0-0.063-0.05126.1200.6220.6220.0000.0000.0000.000
187A188LEU00.0030.01028.307-0.121-0.1210.0000.0000.0000.000
188A189ILE00.0100.01323.811-0.408-0.4080.0000.0000.0000.000
189A190SER0-0.062-0.02927.5920.4040.4040.0000.0000.0000.000
190A191VAL00.0240.00826.708-0.429-0.4290.0000.0000.0000.000
191A192ASN00.0130.01629.2760.5680.5680.0000.0000.0000.000
192A193THR00.001-0.03631.320-0.116-0.1160.0000.0000.0000.000
193A194GLY0-0.0060.00532.367-0.046-0.0460.0000.0000.0000.000
194A195THR0-0.068-0.03126.239-0.132-0.1320.0000.0000.0000.000
195A196THR0-0.009-0.00123.7540.3480.3480.0000.0000.0000.000
196A197VAL0-0.042-0.03121.336-0.298-0.2980.0000.0000.0000.000
197A198ASN00.0470.04218.7941.1861.1860.0000.0000.0000.000
198A199GLY00.044-0.00718.211-1.205-1.2050.0000.0000.0000.000
199A200ARG10.9000.95617.69917.14917.1490.0000.0000.0000.000
200A201LEU0-0.025-0.00920.411-0.402-0.4020.0000.0000.0000.000
201A202LEU00.0180.00019.5360.6240.6240.0000.0000.0000.000
202A203ALA00.0210.00723.402-0.265-0.2650.0000.0000.0000.000
203A204GLN00.0190.00423.7280.7960.7960.0000.0000.0000.000
204A205THR00.000-0.00228.0200.3310.3310.0000.0000.0000.000
205A206ALA00.0220.02331.2280.0440.0440.0000.0000.0000.000
206A207VAL00.0450.01427.716-0.335-0.3350.0000.0000.0000.000
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208A209LEU00.0300.02728.778-0.298-0.2980.0000.0000.0000.000
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