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: GRQQ1

Calculation Name: 2PX4-A-Xray547

Preferred Name:

Target Type:

Ligand Name: s-adenosyl-l-homocysteine | unknown atom or ion

Ligand 3-letter code: SAH | UNX

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PX4

Chain ID: A

ChEMBL ID:

UniProt ID: P05769

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 263
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -3642520.817497
FMO2-HF: Nuclear repulsion 3536814.541542
FMO2-HF: Total energy -105706.275955
FMO2-MP2: Total energy -106009.672839


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:6:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
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.
-56.137-51.13639.945-22.318-22.629-0.239
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.636 / q_NPA : 1.793
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].
3A8LEU00.0440.0073.469-7.824-6.0420.024-0.851-0.955-0.002
5A10GLU-1-0.744-0.8712.193-127.705-122.6726.182-4.855-6.360-0.050
6A11GLN0-0.016-0.0072.182-15.133-11.6623.755-2.432-4.795-0.017
7A12TRP0-0.037-0.0113.5886.2066.3900.0200.010-0.2140.000
9A14GLU-1-0.797-0.8741.745-184.182-189.65129.964-14.190-10.305-0.170
4A9GLY00.0190.0075.9784.1674.1670.0000.0000.0000.000
8A13LYS10.8060.9076.08852.10852.1080.0000.0000.0000.000
10A15LYS10.9710.9865.88768.93468.9340.0000.0000.0000.000
11A16LEU0-0.047-0.0158.0795.5365.5360.0000.0000.0000.000
12A17ASN0-0.061-0.0618.3837.0707.0700.0000.0000.0000.000
13A18ALA0-0.0080.0098.8952.0042.0040.0000.0000.0000.000
14A19MET0-0.067-0.00110.9042.9152.9150.0000.0000.0000.000
15A20GLY00.0710.04113.8781.3331.3330.0000.0000.0000.000
16A21LYS10.9300.95417.33923.85023.8500.0000.0000.0000.000
17A22GLU-1-0.862-0.93620.312-24.140-24.1400.0000.0000.0000.000
18A23GLU-1-0.801-0.89414.686-35.875-35.8750.0000.0000.0000.000
19A24PHE00.0720.02715.8900.1630.1630.0000.0000.0000.000
20A25PHE0-0.070-0.06518.1810.3940.3940.0000.0000.0000.000
21A26SER0-0.023-0.01221.6091.1421.1420.0000.0000.0000.000
22A27TYR00.005-0.01413.4390.1640.1640.0000.0000.0000.000
23A28ARG10.8570.94818.31326.57626.5760.0000.0000.0000.000
24A29LYS10.9630.96819.27623.00423.0040.0000.0000.0000.000
25A30GLU-1-0.755-0.86919.703-24.888-24.8880.0000.0000.0000.000
26A31ALA0-0.015-0.01620.698-1.121-1.1210.0000.0000.0000.000
27A32ILE0-0.096-0.01720.629-0.377-0.3770.0000.0000.0000.000
28A33LEU00.0140.01823.1620.7090.7090.0000.0000.0000.000
29A34GLU-1-0.895-0.96925.611-23.235-23.2350.0000.0000.0000.000
30A35VAL00.0230.03227.9510.4750.4750.0000.0000.0000.000
31A36ASP-1-0.808-0.89031.177-17.465-17.4650.0000.0000.0000.000
32A37ARG10.7200.82231.12818.19818.1980.0000.0000.0000.000
33A38THR0-0.039-0.02534.1320.0840.0840.0000.0000.0000.000
34A39GLU-1-0.792-0.90636.750-14.604-14.6040.0000.0000.0000.000
35A40ALA0-0.0020.00936.3970.2910.2910.0000.0000.0000.000
36A41ARG10.8810.93430.01119.00719.0070.0000.0000.0000.000
37A42ARG10.8870.94236.99014.44814.4480.0000.0000.0000.000
38A43ALA00.0430.02740.1610.3560.3560.0000.0000.0000.000
39A44ARG10.9020.94537.82715.89415.8940.0000.0000.0000.000
40A45ARG10.8080.88140.07514.07614.0760.0000.0000.0000.000
41A46GLU-1-0.832-0.88143.422-13.221-13.2210.0000.0000.0000.000
42A47GLY00.0760.04445.449-0.076-0.0760.0000.0000.0000.000
43A48ASN0-0.016-0.02942.9350.2700.2700.0000.0000.0000.000
44A49LYS10.9480.96843.00814.04114.0410.0000.0000.0000.000
45A50VAL00.0160.01444.918-0.068-0.0680.0000.0000.0000.000
46A51GLY00.0400.03646.1530.1370.1370.0000.0000.0000.000
47A52GLY00.0480.03743.023-0.279-0.2790.0000.0000.0000.000
48A53HIS0-0.057-0.03539.484-0.296-0.2960.0000.0000.0000.000
49A54PRO00.0040.01334.943-0.003-0.0030.0000.0000.0000.000
50A55VAL00.0610.04434.313-0.216-0.2160.0000.0000.0000.000
51A56SER0-0.041-0.03230.336-0.659-0.6590.0000.0000.0000.000
52A57ARG11.0030.99223.93323.52023.5200.0000.0000.0000.000
53A58GLY00.0470.03027.728-0.526-0.5260.0000.0000.0000.000
54A59THR00.006-0.01828.724-0.233-0.2330.0000.0000.0000.000
55A60ALA00.0520.02929.8230.1410.1410.0000.0000.0000.000
56A61LYS10.8530.94222.95324.62724.6270.0000.0000.0000.000
57A62LEU00.0350.02927.877-0.175-0.1750.0000.0000.0000.000
58A63ARG10.8310.88930.28018.16118.1610.0000.0000.0000.000
59A64TRP00.0210.00025.525-0.232-0.2320.0000.0000.0000.000
60A65LEU00.014-0.00525.079-0.101-0.1010.0000.0000.0000.000
61A66VAL0-0.0010.00629.2240.1550.1550.0000.0000.0000.000
62A67GLU-1-0.893-0.93632.856-17.920-17.9200.0000.0000.0000.000
63A68ARG10.7670.87228.87120.15520.1550.0000.0000.0000.000
64A69ARG10.8710.93531.36317.01817.0180.0000.0000.0000.000
65A70PHE00.0280.00426.593-0.192-0.1920.0000.0000.0000.000
66A71VAL00.0010.01629.019-0.411-0.4110.0000.0000.0000.000
67A72GLN0-0.020-0.01831.3500.1650.1650.0000.0000.0000.000
68A73PRO0-0.027-0.01233.8780.3240.3240.0000.0000.0000.000
69A74ILE0-0.011-0.01136.2520.4450.4450.0000.0000.0000.000
70A75GLY00.0780.05338.710-0.312-0.3120.0000.0000.0000.000
71A76LYS10.8640.94038.88815.53815.5380.0000.0000.0000.000
72A77VAL00.001-0.01434.726-0.464-0.4640.0000.0000.0000.000
73A78VAL0-0.003-0.00332.8290.2980.2980.0000.0000.0000.000
74A79ASP-1-0.802-0.89731.249-19.593-19.5930.0000.0000.0000.000
75A80LEU00.0320.00228.4020.2810.2810.0000.0000.0000.000
76A81GLY00.036-0.00527.829-0.827-0.8270.0000.0000.0000.000
77A82CYS0-0.0220.01628.909-0.178-0.1780.0000.0000.0000.000
78A83GLY00.0130.01031.0740.1360.1360.0000.0000.0000.000
79A84ARG10.8250.89530.74219.43419.4340.0000.0000.0000.000
80A85GLY00.0900.02833.8430.5890.5890.0000.0000.0000.000
81A86GLY0-0.100-0.03732.5040.2810.2810.0000.0000.0000.000
82A87TRP00.0050.01225.7670.1530.1530.0000.0000.0000.000
83A88SER00.022-0.02532.8610.4680.4680.0000.0000.0000.000
84A89TYR00.0340.00036.0090.3020.3020.0000.0000.0000.000
85A90TYR00.0370.02034.5540.3390.3390.0000.0000.0000.000
86A91ALA00.0270.01035.5070.3040.3040.0000.0000.0000.000
87A92ALA00.0320.02037.2960.2830.2830.0000.0000.0000.000
88A93THR0-0.057-0.03139.3470.3740.3740.0000.0000.0000.000
89A94MET0-0.0240.01037.0240.0690.0690.0000.0000.0000.000
90A95LYS10.9971.00240.44513.85213.8520.0000.0000.0000.000
91A96ASN00.003-0.00341.4950.5600.5600.0000.0000.0000.000
92A97VAL0-0.0280.00738.817-0.073-0.0730.0000.0000.0000.000
93A98GLN0-0.054-0.04441.924-0.001-0.0010.0000.0000.0000.000
94A99GLU-1-0.829-0.92341.808-14.329-14.3290.0000.0000.0000.000
95A100VAL0-0.0230.00237.231-0.446-0.4460.0000.0000.0000.000
96A101ARG10.8550.93437.54715.21815.2180.0000.0000.0000.000
97A102GLY00.0240.01434.821-0.525-0.5250.0000.0000.0000.000
98A103TYR0-0.047-0.05433.0750.6160.6160.0000.0000.0000.000
99A104THR0-0.001-0.01431.395-1.010-1.0100.0000.0000.0000.000
100A105LYS10.9120.96226.19522.75922.7590.0000.0000.0000.000
101A106GLY00.0080.01932.0290.4760.4760.0000.0000.0000.000
102A107GLY00.0360.01132.491-0.469-0.4690.0000.0000.0000.000
103A108PRO0-0.012-0.03033.282-0.264-0.2640.0000.0000.0000.000
104A109GLY0-0.008-0.00230.058-0.483-0.4830.0000.0000.0000.000
105A110HIS0-0.0200.01025.675-0.838-0.8380.0000.0000.0000.000
106A111GLU-1-0.927-0.97129.203-20.238-20.2380.0000.0000.0000.000
107A112GLU-1-0.750-0.84132.379-16.883-16.8830.0000.0000.0000.000
108A113PRO0-0.025-0.02035.911-0.130-0.1300.0000.0000.0000.000
109A114MET0-0.071-0.03337.3800.1640.1640.0000.0000.0000.000
110A115LEU00.0290.01839.462-0.043-0.0430.0000.0000.0000.000
111A116MET0-0.085-0.03240.1440.0980.0980.0000.0000.0000.000
112A117GLN00.0070.00043.4070.1150.1150.0000.0000.0000.000
113A118SER00.0180.00541.1900.3110.3110.0000.0000.0000.000
114A119TYR0-0.027-0.01244.2190.1660.1660.0000.0000.0000.000
115A120GLY00.0330.01043.778-0.312-0.3120.0000.0000.0000.000
116A121TRP0-0.020-0.01543.870-0.142-0.1420.0000.0000.0000.000
117A122ASN0-0.0030.00244.945-0.235-0.2350.0000.0000.0000.000
118A123ILE00.0120.02243.1450.1390.1390.0000.0000.0000.000
119A124VAL0-0.029-0.00639.628-0.371-0.3710.0000.0000.0000.000
120A125THR0-0.062-0.01941.0710.2520.2520.0000.0000.0000.000
121A126MET0-0.021-0.00137.392-0.615-0.6150.0000.0000.0000.000
122A127LYS10.9130.96037.64015.01315.0130.0000.0000.0000.000
123A128SER00.020-0.03035.893-0.653-0.6530.0000.0000.0000.000
124A129GLY00.0230.01735.7500.3920.3920.0000.0000.0000.000
125A130VAL0-0.080-0.03833.4740.1120.1120.0000.0000.0000.000
126A131ASP-1-0.847-0.93028.657-21.798-21.7980.0000.0000.0000.000
127A132VAL00.012-0.02327.3080.3710.3710.0000.0000.0000.000
128A133PHE0-0.082-0.04322.906-0.331-0.3310.0000.0000.0000.000
129A134TYR0-0.0010.00428.306-0.232-0.2320.0000.0000.0000.000
130A135LYS10.8280.93531.97417.01917.0190.0000.0000.0000.000
131A136PRO00.0230.01932.788-0.401-0.4010.0000.0000.0000.000
132A137SER00.015-0.00831.5900.2420.2420.0000.0000.0000.000
133A138GLU-1-0.832-0.89834.260-15.442-15.4420.0000.0000.0000.000
134A139ILE00.0420.01335.922-0.394-0.3940.0000.0000.0000.000
135A140SER0-0.032-0.02334.7980.0310.0310.0000.0000.0000.000
136A141ASP-1-0.809-0.88536.383-15.519-15.5190.0000.0000.0000.000
137A142THR0-0.039-0.02933.110-0.393-0.3930.0000.0000.0000.000
138A143LEU0-0.013-0.00528.4270.2070.2070.0000.0000.0000.000
139A144LEU0-0.022-0.01128.991-0.611-0.6110.0000.0000.0000.000
140A145CYS0-0.0050.00325.0190.1230.1230.0000.0000.0000.000
141A146ASP-1-0.792-0.87724.322-25.228-25.2280.0000.0000.0000.000
142A147ILE0-0.002-0.00222.496-0.526-0.5260.0000.0000.0000.000
143A148GLY00.009-0.01819.656-1.058-1.0580.0000.0000.0000.000
144A149GLU-1-0.916-0.93820.206-25.651-25.6510.0000.0000.0000.000
145A150SER00.0020.00316.040-0.826-0.8260.0000.0000.0000.000
146A151SER0-0.025-0.01713.9401.6851.6850.0000.0000.0000.000
147A152PRO00.0560.03111.812-1.802-1.8020.0000.0000.0000.000
148A153SER00.003-0.0119.475-3.409-3.4090.0000.0000.0000.000
149A154ALA00.0570.0096.8623.2103.2100.0000.0000.0000.000
150A155GLU-1-0.786-0.8786.921-62.140-62.1400.0000.0000.0000.000
151A156ILE00.001-0.00110.3593.5523.5520.0000.0000.0000.000
152A157GLU-1-0.771-0.88211.661-40.292-40.2920.0000.0000.0000.000
153A158GLU-1-0.806-0.8869.525-47.769-47.7690.0000.0000.0000.000
154A159GLN0-0.004-0.00212.2854.3504.3500.0000.0000.0000.000
155A160ARG10.8670.92215.53233.60133.6010.0000.0000.0000.000
156A161THR0-0.021-0.03214.5551.8441.8440.0000.0000.0000.000
157A162LEU0-0.022-0.00813.7371.4221.4220.0000.0000.0000.000
158A163ARG11.0051.01517.28025.54725.5470.0000.0000.0000.000
159A164ILE0-0.025-0.00819.1451.3831.3830.0000.0000.0000.000
160A165LEU00.014-0.00416.9011.0921.0920.0000.0000.0000.000
161A166GLU-1-0.996-0.98120.870-24.472-24.4720.0000.0000.0000.000
162A167MET00.0180.02322.8191.1071.1070.0000.0000.0000.000
163A168VAL0-0.004-0.02223.4730.9150.9150.0000.0000.0000.000
164A169SER0-0.053-0.03823.7260.3900.3900.0000.0000.0000.000
165A170ASP-1-0.880-0.92426.232-19.784-19.7840.0000.0000.0000.000
166A171TRP0-0.014-0.00628.9851.1241.1240.0000.0000.0000.000
167A172LEU00.0420.01326.0120.5510.5510.0000.0000.0000.000
168A173SER0-0.105-0.06129.8940.5820.5820.0000.0000.0000.000
169A174ARG10.8800.93731.72317.57017.5700.0000.0000.0000.000
170A175GLY00.0090.01833.4750.4900.4900.0000.0000.0000.000
171A176PRO0-0.061-0.00631.4940.2940.2940.0000.0000.0000.000
172A177LYS10.9580.96932.13515.47715.4770.0000.0000.0000.000
173A178GLU-1-0.811-0.87332.140-18.890-18.8900.0000.0000.0000.000
174A179PHE00.015-0.01325.0380.1000.1000.0000.0000.0000.000
175A180CYS0-0.058-0.01826.281-0.697-0.6970.0000.0000.0000.000
176A181ILE00.0470.02122.0000.3730.3730.0000.0000.0000.000
177A182LYS10.8420.93519.57626.62326.6230.0000.0000.0000.000
178A183ILE0-0.0070.00915.207-0.351-0.3510.0000.0000.0000.000
179A184LEU0-0.022-0.01614.723-0.630-0.6300.0000.0000.0000.000
180A185CYS0-0.029-0.00910.219-2.910-2.9100.0000.0000.0000.000
181A186PRO0-0.005-0.01411.557-1.794-1.7940.0000.0000.0000.000
182A187TYR00.005-0.0116.2212.7702.7700.0000.0000.0000.000
183A188MET00.0120.0216.307-8.865-8.8650.0000.0000.0000.000
184A189PRO00.0410.0105.5494.9744.9740.0000.0000.0000.000
185A190LYS10.9690.9828.21549.44949.4490.0000.0000.0000.000
186A191VAL0-0.036-0.01311.0233.6623.6620.0000.0000.0000.000
187A192ILE0-0.0120.0038.8882.5602.5600.0000.0000.0000.000
188A193GLU-1-0.868-0.93112.035-37.878-37.8780.0000.0000.0000.000
189A194LYS10.9170.97414.36629.93029.9300.0000.0000.0000.000
190A195LEU00.024-0.00814.7001.9211.9210.0000.0000.0000.000
191A196GLU-1-0.874-0.94714.827-33.412-33.4120.0000.0000.0000.000
192A197SER0-0.064-0.04218.2151.9011.9010.0000.0000.0000.000
193A198LEU0-0.037-0.01420.1891.4441.4440.0000.0000.0000.000
194A199GLN0-0.102-0.05220.5090.3130.3130.0000.0000.0000.000
195A200ARG10.8880.93118.32529.39129.3910.0000.0000.0000.000
196A201ARG10.9150.98724.27021.95521.9550.0000.0000.0000.000
197A202PHE0-0.016-0.02425.3220.7570.7570.0000.0000.0000.000
198A203GLY00.0390.04025.9670.5130.5130.0000.0000.0000.000
199A204GLY00.0700.03124.673-0.800-0.8000.0000.0000.0000.000
200A205GLY0-0.001-0.00521.746-0.501-0.5010.0000.0000.0000.000
201A206LEU0-0.017-0.01116.0260.1820.1820.0000.0000.0000.000
202A207VAL00.0060.01420.043-0.243-0.2430.0000.0000.0000.000
203A208ARG10.7930.90016.65532.51132.5110.0000.0000.0000.000
204A209VAL00.0410.02719.8970.8870.8870.0000.0000.0000.000
205A210PRO00.0080.00621.543-1.003-1.0030.0000.0000.0000.000
206A211LEU00.0410.02622.962-0.197-0.1970.0000.0000.0000.000
207A212SER0-0.140-0.09219.3190.7050.7050.0000.0000.0000.000
208A213ARG10.8550.92519.73924.21124.2110.0000.0000.0000.000
209A214ASN00.0220.00215.757-1.346-1.3460.0000.0000.0000.000
210A215SER00.0010.00014.449-1.525-1.5250.0000.0000.0000.000
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