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: 9RZJ2

Calculation Name: 3V4C-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol

Ligand 3-letter code: PE4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3V4C

Chain ID: B

ChEMBL ID:

UniProt ID: Q92WS7

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 500
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -8932071.31947
FMO2-HF: Nuclear repulsion 8747782.742997
FMO2-HF: Total energy -184288.576473
FMO2-MP2: Total energy -184829.009546


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:PHE)


Summations of interaction energy for fragment #1(A:3:PHE)
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.
-290.442-277.87527.294-15.646-24.216-0.111
Interaction energy analysis for fragmet #1(A:3:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.792 / q_NPA : 0.872
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].
3A5PRO0-0.0210.0102.451-0.2634.4852.877-2.245-5.3800.011
4A6LYS10.8640.9273.49234.96934.6610.0730.842-0.6070.001
32A34PHE0-0.001-0.0084.647-1.932-1.829-0.001-0.003-0.0990.000
79A81ALA0-0.052-0.0092.390-6.357-5.5891.138-0.579-1.3260.000
80A82ILE00.000-0.0063.838-2.257-1.7110.006-0.076-0.477-0.001
82A84GLU-1-0.841-0.8931.740-129.501-131.27318.159-9.833-6.555-0.115
83A85ILE0-0.038-0.0092.3272.4264.0960.964-0.528-2.106-0.002
84A86GLY00.0910.0424.4704.8274.926-0.001-0.028-0.0700.000
187A189GLY00.035-0.0043.497-0.755-0.5200.017-0.038-0.2140.000
188A190THR0-0.054-0.0522.848-5.486-4.0200.350-0.808-1.009-0.010
189A191GLY00.0160.0075.2111.0011.042-0.001-0.004-0.0360.000
190A192GLU-1-0.769-0.8852.596-36.315-34.8390.285-0.615-1.146-0.005
191A193ILE0-0.0080.0012.726-1.7900.5683.388-1.282-4.4630.012
192A194VAL00.0080.0014.1561.5511.7880.014-0.084-0.1670.001
194A196GLU-1-0.896-0.9423.375-36.725-35.8250.026-0.365-0.561-0.003
5A7GLY00.0360.0335.3132.4792.4790.0000.0000.0000.000
6A8LYS10.7720.8786.76521.87821.8780.0000.0000.0000.000
7A9HIS0-0.0130.0067.975-1.376-1.3760.0000.0000.0000.000
8A10LEU0-0.0120.0019.441-0.400-0.4000.0000.0000.0000.000
9A11VAL00.012-0.01711.2210.6190.6190.0000.0000.0000.000
10A12ALA00.0220.01715.0590.1640.1640.0000.0000.0000.000
11A13GLY00.0310.02413.9950.4250.4250.0000.0000.0000.000
12A14GLU-1-0.876-0.92213.823-13.791-13.7910.0000.0000.0000.000
13A15TRP00.013-0.0106.428-1.130-1.1300.0000.0000.0000.000
14A16LEU0-0.040-0.01211.3850.2970.2970.0000.0000.0000.000
15A17ASP-1-0.833-0.90512.154-18.519-18.5190.0000.0000.0000.000
16A18GLY00.040-0.00114.1640.4490.4490.0000.0000.0000.000
17A19ALA0-0.055-0.00816.4130.2480.2480.0000.0000.0000.000
18A20GLY0-0.002-0.00217.5910.2080.2080.0000.0000.0000.000
19A21THR0-0.075-0.05312.938-0.033-0.0330.0000.0000.0000.000
20A22PHE0-0.054-0.02111.1290.9690.9690.0000.0000.0000.000
21A23ALA00.0600.03311.794-1.104-1.1040.0000.0000.0000.000
22A24SER0-0.008-0.0057.8091.1831.1830.0000.0000.0000.000
23A25ALA00.021-0.00110.5410.2060.2060.0000.0000.0000.000
24A26PRO0-0.0250.0119.7690.7890.7890.0000.0000.0000.000
25A27ALA0-0.028-0.00211.8341.5481.5480.0000.0000.0000.000
26A28HIS0-0.061-0.02810.3750.5190.5190.0000.0000.0000.000
27A29GLY00.0460.0219.032-2.108-2.1080.0000.0000.0000.000
28A30PRO0-0.048-0.0217.0852.6582.6580.0000.0000.0000.000
29A31ALA00.0180.0158.580-1.745-1.7450.0000.0000.0000.000
30A32HIS00.004-0.0075.8330.6190.6190.0000.0000.0000.000
31A33ASP-1-0.857-0.9128.641-18.696-18.6960.0000.0000.0000.000
33A35ALA00.0260.0169.9441.5241.5240.0000.0000.0000.000
34A36VAL0-0.048-0.01412.448-0.091-0.0910.0000.0000.0000.000
35A37GLY00.0370.01315.5410.3040.3040.0000.0000.0000.000
36A38THR0-0.037-0.06016.5390.2550.2550.0000.0000.0000.000
37A39VAL00.0680.02820.145-0.173-0.1730.0000.0000.0000.000
38A40GLU-1-0.852-0.90922.180-10.865-10.8650.0000.0000.0000.000
39A41LEU0-0.036-0.01216.0080.0260.0260.0000.0000.0000.000
40A42VAL00.0150.01619.084-0.200-0.2000.0000.0000.0000.000
41A43ASN00.0340.00720.4130.0870.0870.0000.0000.0000.000
42A44ARG10.8300.91619.22012.87312.8730.0000.0000.0000.000
43A45ALA00.0190.00617.800-0.001-0.0010.0000.0000.0000.000
44A46CYS0-0.034-0.01819.6620.0420.0420.0000.0000.0000.000
45A47GLU-1-0.864-0.93423.007-9.272-9.2720.0000.0000.0000.000
46A48ALA0-0.023-0.01020.5630.1610.1610.0000.0000.0000.000
47A49ALA00.0290.01621.1060.0010.0010.0000.0000.0000.000
48A50GLU-1-0.851-0.93622.668-8.936-8.9360.0000.0000.0000.000
49A51GLU-1-0.967-0.98324.986-9.388-9.3880.0000.0000.0000.000
50A52ALA0-0.032-0.00722.4560.0960.0960.0000.0000.0000.000
51A53PHE0-0.0160.00424.5140.0310.0310.0000.0000.0000.000
52A54TRP0-0.042-0.03226.9310.3140.3140.0000.0000.0000.000
53A55THR0-0.039-0.01126.1940.1470.1470.0000.0000.0000.000
54A56TYR0-0.038-0.05122.7830.0040.0040.0000.0000.0000.000
55A57GLY00.0300.01526.169-0.006-0.0060.0000.0000.0000.000
56A58TYR0-0.093-0.05828.9110.4450.4450.0000.0000.0000.000
57A59SER0-0.0450.00027.3910.0180.0180.0000.0000.0000.000
58A60SER00.0530.00629.3850.0570.0570.0000.0000.0000.000
59A61ARG00.004-0.01728.959-0.481-0.4810.0000.0000.0000.000
60A62LYS10.9560.97928.2829.2519.2510.0000.0000.0000.000
61A63GLU-1-0.827-0.87825.842-10.185-10.1850.0000.0000.0000.000
62A64ARG10.8540.93324.0109.3849.3840.0000.0000.0000.000
63A65ALA00.0040.01023.376-0.532-0.5320.0000.0000.0000.000
64A66ALA0-0.032-0.02123.532-0.463-0.4630.0000.0000.0000.000
65A67PHE00.0210.00416.559-0.715-0.7150.0000.0000.0000.000
66A68LEU00.0100.00318.810-0.844-0.8440.0000.0000.0000.000
67A69ARG10.7540.82719.09810.48910.4890.0000.0000.0000.000
68A70ALA00.0110.01217.499-0.713-0.7130.0000.0000.0000.000
69A71ILE00.0240.00113.589-1.168-1.1680.0000.0000.0000.000
70A72ALA0-0.038-0.01514.327-1.232-1.2320.0000.0000.0000.000
71A73ASP-1-0.880-0.93815.348-16.106-16.1060.0000.0000.0000.000
72A74GLU-1-0.858-0.89911.290-21.641-21.6410.0000.0000.0000.000
73A75ILE00.0120.01610.103-2.320-2.3200.0000.0000.0000.000
74A76GLU-1-0.811-0.87710.341-21.472-21.4720.0000.0000.0000.000
75A77ALA0-0.064-0.02210.899-1.159-1.1590.0000.0000.0000.000
76A78ARG10.7670.8575.98026.44726.4470.0000.0000.0000.000
77A79ALA00.0130.0066.419-3.814-3.8140.0000.0000.0000.000
78A80GLU-1-0.847-0.9456.456-30.013-30.0130.0000.0000.0000.000
81A83THR0-0.006-0.0066.4151.8511.8510.0000.0000.0000.000
85A87SER0-0.036-0.0187.7133.3713.3710.0000.0000.0000.000
86A88GLN0-0.0080.0105.3791.4351.4350.0000.0000.0000.000
87A89GLU-1-0.776-0.8736.224-27.608-27.6080.0000.0000.0000.000
88A90THR00.012-0.0239.5552.7472.7470.0000.0000.0000.000
89A91GLY00.0320.00712.1351.6551.6550.0000.0000.0000.000
90A92LEU0-0.051-0.01313.5091.2321.2320.0000.0000.0000.000
91A93PRO00.025-0.00613.406-1.402-1.4020.0000.0000.0000.000
92A94GLU-1-0.838-0.92610.586-26.947-26.9470.0000.0000.0000.000
93A95ALA0-0.022-0.00713.248-0.001-0.0010.0000.0000.0000.000
94A96ARG10.8000.89715.45117.01617.0160.0000.0000.0000.000
95A97LEU00.0070.0099.6650.6920.6920.0000.0000.0000.000
96A98ASN00.0370.01512.455-0.478-0.4780.0000.0000.0000.000
97A99GLY00.0080.00914.0040.6130.6130.0000.0000.0000.000
98A100GLU-1-0.738-0.86614.483-17.081-17.0810.0000.0000.0000.000
99A101ARG10.8680.93710.82523.51023.5100.0000.0000.0000.000
100A102GLY00.0500.03314.1440.5790.5790.0000.0000.0000.000
101A103ARG10.8340.91217.51513.96013.9600.0000.0000.0000.000
102A104THR0-0.023-0.03214.0590.7460.7460.0000.0000.0000.000
103A105THR0-0.039-0.04314.9400.8870.8870.0000.0000.0000.000
104A106GLY00.0160.00817.8570.6380.6380.0000.0000.0000.000
105A107GLN0-0.052-0.02818.7111.0941.0940.0000.0000.0000.000
106A108LEU0-0.010-0.00515.8090.5360.5360.0000.0000.0000.000
107A109ARG10.8800.92817.41815.74915.7490.0000.0000.0000.000
108A110LEU00.0180.01823.1130.4790.4790.0000.0000.0000.000
109A111PHE0-0.008-0.01822.7770.5120.5120.0000.0000.0000.000
110A112ALA00.0030.01723.9330.3730.3730.0000.0000.0000.000
111A113ASP-1-0.861-0.92625.833-10.608-10.6080.0000.0000.0000.000
112A114HIS0-0.122-0.06328.4370.5150.5150.0000.0000.0000.000
113A115ILE0-0.001-0.00926.4470.3070.3070.0000.0000.0000.000
114A116GLU-1-0.806-0.88829.026-9.960-9.9600.0000.0000.0000.000
115A117LYS10.8580.94731.7809.3479.3470.0000.0000.0000.000
116A118GLY00.0140.01833.6820.2450.2450.0000.0000.0000.000
117A119ASP-1-0.914-0.96035.240-7.802-7.8020.0000.0000.0000.000
118A120TYR-1-0.884-0.96331.218-9.032-9.0320.0000.0000.0000.000
119A121LEU00.0010.02333.6370.0400.0400.0000.0000.0000.000
120A122ASP-1-0.879-0.92636.060-7.576-7.5760.0000.0000.0000.000
121A123ARG00.0260.01438.3080.2020.2020.0000.0000.0000.000
122A124ARG10.8830.94241.2156.8756.8750.0000.0000.0000.000
123A125VAL00.0080.00344.964-0.029-0.0290.0000.0000.0000.000
124A126ASP-1-0.860-0.91047.951-5.750-5.7500.0000.0000.0000.000
125A127ALA00.0210.00651.2710.0260.0260.0000.0000.0000.000
126A128ALA00.0220.00953.7530.0550.0550.0000.0000.0000.000
127A129MET0-0.036-0.01656.2070.0360.0360.0000.0000.0000.000
128A130PRO00.002-0.00259.4780.0440.0440.0000.0000.0000.000
129A131GLU-1-0.829-0.92661.856-4.859-4.8590.0000.0000.0000.000
130A132ARG10.8050.90958.8095.1115.1110.0000.0000.0000.000
131A133GLN0-0.018-0.00864.1890.0620.0620.0000.0000.0000.000
132A134PRO0-0.010-0.03065.379-0.019-0.0190.0000.0000.0000.000
133A135ALA00.0080.01262.3200.0280.0280.0000.0000.0000.000
134A136PRO00.0720.05960.603-0.033-0.0330.0000.0000.0000.000
135A137ARG10.7350.86354.2205.4925.4920.0000.0000.0000.000
136A138GLN00.0530.02753.975-0.038-0.0380.0000.0000.0000.000
137A139GLU-1-0.800-0.86949.335-6.066-6.0660.0000.0000.0000.000
138A140ILE0-0.010-0.00447.801-0.024-0.0240.0000.0000.0000.000
139A141ARG10.8800.90744.4846.3826.3820.0000.0000.0000.000
140A142LEU0-0.047-0.02140.8910.0260.0260.0000.0000.0000.000
141A143VAL00.0510.02937.0310.0090.0090.0000.0000.0000.000
142A144GLN0-0.057-0.03134.428-0.004-0.0040.0000.0000.0000.000
143A145ARG10.8630.92732.3908.2968.2960.0000.0000.0000.000
144A146PRO00.0370.02328.6090.0530.0530.0000.0000.0000.000
145A147VAL0-0.066-0.04328.3700.2200.2200.0000.0000.0000.000
146A148GLY00.0530.02628.5390.2590.2590.0000.0000.0000.000
147A149PRO0-0.0040.00323.992-0.299-0.2990.0000.0000.0000.000
148A150VAL0-0.0130.00522.3360.2920.2920.0000.0000.0000.000
149A151ALA00.0010.01520.751-0.484-0.4840.0000.0000.0000.000
150A152VAL00.020-0.00117.5830.3110.3110.0000.0000.0000.000
151A153PHE0-0.048-0.02617.737-0.603-0.6030.0000.0000.0000.000
152A154GLY00.0100.01714.9880.2660.2660.0000.0000.0000.000
153A155ALA00.0400.00916.0660.0230.0230.0000.0000.0000.000
154A156SER0-0.034-0.02415.124-0.634-0.6340.0000.0000.0000.000
155A157ASN0-0.043-0.04615.165-0.948-0.9480.0000.0000.0000.000
156A158PHE0-0.053-0.02015.7830.0090.0090.0000.0000.0000.000
157A159PRO00.0240.01810.1500.2650.2650.0000.0000.0000.000
158A160LEU0-0.028-0.0119.188-1.159-1.1590.0000.0000.0000.000
159A161ALA00.015-0.00412.6090.7820.7820.0000.0000.0000.000
160A162PHE0-0.020-0.00916.1340.8890.8890.0000.0000.0000.000
161A163SER00.0180.00012.1230.3790.3790.0000.0000.0000.000
162A164THR0-0.0020.0039.5550.6880.6880.0000.0000.0000.000
163A165ALA00.0380.01312.7040.5110.5110.0000.0000.0000.000
164A166GLY00.0100.01114.4040.2690.2690.0000.0000.0000.000
165A167GLY0-0.008-0.00816.8830.3510.3510.0000.0000.0000.000
166A168ASP-1-0.818-0.88619.912-11.492-11.4920.0000.0000.0000.000
167A169THR00.010-0.00715.6510.5790.5790.0000.0000.0000.000
168A170ALA0-0.0100.00418.7620.2740.2740.0000.0000.0000.000
169A171ALA00.0330.01820.3710.3770.3770.0000.0000.0000.000
170A172ALA00.0040.00021.5300.4240.4240.0000.0000.0000.000
171A173LEU00.0320.01217.4000.2770.2770.0000.0000.0000.000
172A174ALA0-0.0020.01522.0730.2720.2720.0000.0000.0000.000
173A175ALA00.0210.00724.9630.3440.3440.0000.0000.0000.000
174A176GLY00.0160.01325.5670.3430.3430.0000.0000.0000.000
175A177CYS0-0.063-0.01824.5510.3160.3160.0000.0000.0000.000
176A178PRO0-0.035-0.00921.286-0.450-0.4500.0000.0000.0000.000
177A179VAL0-0.018-0.00217.4610.2220.2220.0000.0000.0000.000
178A180VAL00.0090.00217.224-0.640-0.6400.0000.0000.0000.000
179A181VAL0-0.005-0.00613.2640.2910.2910.0000.0000.0000.000
180A182LYS10.7840.88314.72714.92514.9250.0000.0000.0000.000
181A183GLY00.0440.01111.937-0.095-0.0950.0000.0000.0000.000
182A184HIS00.0210.01412.3430.0900.0900.0000.0000.0000.000
183A185SER0-0.009-0.01411.387-1.115-1.1150.0000.0000.0000.000
184A186ALA0-0.002-0.01012.041-0.584-0.5840.0000.0000.0000.000
185A187HIS0-0.0230.0178.645-0.257-0.2570.0000.0000.0000.000
186A188PRO00.0480.0427.535-0.659-0.6590.0000.0000.0000.000
193A195ALA00.0140.0007.0891.7291.7290.0000.0000.0000.000
195A197ALA0-0.0030.0047.0381.1191.1190.0000.0000.0000.000
196A198VAL00.0110.0089.5851.4431.4430.0000.0000.0000.000
197A199ASP-1-0.816-0.8979.532-18.804-18.8040.0000.0000.0000.000
198A200ALA0-0.032-0.0129.9591.0121.0120.0000.0000.0000.000
199A201ALA00.0030.00311.8161.0711.0710.0000.0000.0000.000
200A202ILE0-0.0130.01314.5840.9210.9210.0000.0000.0000.000
201A203ARG10.8210.88710.18820.02720.0270.0000.0000.0000.000
202A204LYS10.7950.89815.49517.23017.2300.0000.0000.0000.000
203A205THR0-0.051-0.05517.6140.6710.6710.0000.0000.0000.000
204A206GLY0-0.0170.00519.6740.5490.5490.0000.0000.0000.000
205A207VAL0-0.0040.01019.4460.4620.4620.0000.0000.0000.000
206A208HIS00.0690.03120.509-0.774-0.7740.0000.0000.0000.000
207A209PRO00.0370.00417.701-0.236-0.2360.0000.0000.0000.000
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