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: 74J7K

Calculation Name: 3DD5-C-Xray547

Preferred Name:

Target Type:

Ligand Name: diethyl phosphonate

Ligand 3-letter code: DEP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DD5

Chain ID: C

ChEMBL ID:

UniProt ID: P11373

Base Structure: X-ray

Registration Date: 2025-10-06

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 191
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2023135.650268
FMO2-HF: Nuclear repulsion 1951874.433591
FMO2-HF: Total energy -71261.216678
FMO2-MP2: Total energy -71468.829287


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(C:32:SER)


Summations of interaction energy for fragment #1(C:32:SER)
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.
-31.613-25.9420.372-3.036-3.006-0.023
Interaction energy analysis for fragmet #1(C:32:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.842 / q_NPA : 0.914
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].
3C34THR0-0.023-0.0102.49213.16215.6240.201-1.178-1.485-0.002
4C35ARG10.7310.8152.73020.53223.6010.172-1.841-1.399-0.021
38C69PRO0-0.008-0.0244.574-0.145-0.005-0.001-0.017-0.1220.000
5C36ASN00.0520.0205.4025.1975.1970.0000.0000.0000.000
6C37GLU-1-0.724-0.8067.684-33.808-33.8080.0000.0000.0000.000
7C38LEU0-0.0020.02310.8301.8961.8960.0000.0000.0000.000
8C39GLU-1-0.880-0.92712.054-18.404-18.4040.0000.0000.0000.000
9C40THR0-0.068-0.06911.2391.3591.3590.0000.0000.0000.000
10C41GLY00.0340.04913.8140.8740.8740.0000.0000.0000.000
11C42SER00.008-0.00815.5091.0181.0180.0000.0000.0000.000
12C43SER00.0700.01519.268-0.276-0.2760.0000.0000.0000.000
13C44SER0-0.068-0.03522.1530.3950.3950.0000.0000.0000.000
14C45ALA0-0.040-0.02419.0120.2990.2990.0000.0000.0000.000
15C46CYS0-0.022-0.01218.728-0.828-0.8280.0000.0000.0000.000
16C47PRO0-0.0040.02816.2700.5790.5790.0000.0000.0000.000
17C48LYS10.8490.91418.98213.77113.7710.0000.0000.0000.000
18C49VAL0-0.034-0.01616.2300.4710.4710.0000.0000.0000.000
19C50ILE0-0.0010.00115.263-1.032-1.0320.0000.0000.0000.000
20C51TYR00.002-0.00510.1151.6341.6340.0000.0000.0000.000
21C52ILE0-0.014-0.00912.537-1.792-1.7920.0000.0000.0000.000
22C53PHE00.0080.01910.4351.1361.1360.0000.0000.0000.000
23C54ALA0-0.013-0.00112.541-0.863-0.8630.0000.0000.0000.000
24C55ARG10.8320.91710.72125.76025.7600.0000.0000.0000.000
25C56ALA00.0480.03213.0091.6331.6330.0000.0000.0000.000
26C57SER00.025-0.02714.857-0.692-0.6920.0000.0000.0000.000
27C58THR0-0.073-0.03715.0350.3090.3090.0000.0000.0000.000
28C59GLU-1-0.745-0.82910.387-27.584-27.5840.0000.0000.0000.000
29C60PRO00.0130.0137.0610.4830.4830.0000.0000.0000.000
30C61GLY0-0.016-0.0146.742-2.949-2.9490.0000.0000.0000.000
31C62ASN0-0.002-0.0196.978-0.943-0.9430.0000.0000.0000.000
32C63MET0-0.0030.0175.5844.0534.0530.0000.0000.0000.000
33C64GLY00.0260.0187.7323.1893.1890.0000.0000.0000.000
34C65ILE0-0.085-0.0575.334-6.982-6.9820.0000.0000.0000.000
35C66SER00.005-0.0086.9761.1871.1870.0000.0000.0000.000
36C67ALA00.0260.0059.189-1.009-1.0090.0000.0000.0000.000
37C68GLY00.0020.0049.2330.4880.4880.0000.0000.0000.000
39C70ILE00.0360.0386.6281.2901.2900.0000.0000.0000.000
40C71VAL0-0.001-0.0029.5331.4581.4580.0000.0000.0000.000
41C72ALA0-0.036-0.0097.2601.1861.1860.0000.0000.0000.000
42C73ASP-1-0.865-0.9336.671-35.149-35.1490.0000.0000.0000.000
43C74ALA0-0.083-0.0459.3692.1672.1670.0000.0000.0000.000
44C75LEU0-0.0020.00012.4621.6161.6160.0000.0000.0000.000
45C76GLU-1-0.764-0.8748.143-31.320-31.3200.0000.0000.0000.000
46C77ARG10.8960.95812.22119.38419.3840.0000.0000.0000.000
47C78ILE0-0.094-0.04014.5011.2471.2470.0000.0000.0000.000
48C79TYR00.015-0.00816.1091.3451.3450.0000.0000.0000.000
49C80GLY00.0480.04415.1630.6540.6540.0000.0000.0000.000
50C81ALA00.005-0.01710.908-0.054-0.0540.0000.0000.0000.000
51C82ASN0-0.059-0.03212.635-0.773-0.7730.0000.0000.0000.000
52C83ASP-1-0.806-0.89915.550-14.757-14.7570.0000.0000.0000.000
53C84VAL0-0.039-0.02312.2980.6530.6530.0000.0000.0000.000
54C85TRP0-0.0320.00112.165-0.927-0.9270.0000.0000.0000.000
55C86VAL00.017-0.0067.5311.0711.0710.0000.0000.0000.000
56C87GLN0-0.052-0.0329.122-1.716-1.7160.0000.0000.0000.000
57C88GLY00.0760.0368.8161.2971.2970.0000.0000.0000.000
58C89VAL0-0.041-0.0269.9471.0331.0330.0000.0000.0000.000
59C90GLY00.020-0.00611.719-0.983-0.9830.0000.0000.0000.000
60C91GLY00.0410.01912.3691.5191.5190.0000.0000.0000.000
61C92PRO0-0.002-0.01015.241-0.106-0.1060.0000.0000.0000.000
62C93TYR0-0.085-0.04314.6321.4101.4100.0000.0000.0000.000
63C94LEU00.0390.01415.157-1.592-1.5920.0000.0000.0000.000
64C95ALA0-0.0360.00315.155-0.732-0.7320.0000.0000.0000.000
65C96ASP-1-0.794-0.87517.154-14.903-14.9030.0000.0000.0000.000
66C97LEU00.0640.00119.9140.3570.3570.0000.0000.0000.000
67C98ALA00.0020.01822.0380.4830.4830.0000.0000.0000.000
68C99SER0-0.017-0.05122.5230.6060.6060.0000.0000.0000.000
69C100ASN0-0.077-0.04121.5470.0360.0360.0000.0000.0000.000
70C101PHE0-0.016-0.00925.2200.3140.3140.0000.0000.0000.000
71C102LEU0-0.0230.01026.0510.4800.4800.0000.0000.0000.000
72C103PRO00.0130.00129.198-0.155-0.1550.0000.0000.0000.000
73C104ASP-1-0.872-0.93927.259-10.886-10.8860.0000.0000.0000.000
74C105GLY0-0.051-0.02825.969-0.314-0.3140.0000.0000.0000.000
75C106THR00.014-0.00620.558-0.683-0.6830.0000.0000.0000.000
76C107SER00.0480.03221.5010.5650.5650.0000.0000.0000.000
77C108SER00.0300.00623.210-0.422-0.4220.0000.0000.0000.000
78C109ALA00.0180.00422.326-0.093-0.0930.0000.0000.0000.000
79C110ALA00.0300.02118.950-0.513-0.5130.0000.0000.0000.000
80C111ILE00.0250.01819.684-0.516-0.5160.0000.0000.0000.000
81C112ASN0-0.012-0.01922.2210.0670.0670.0000.0000.0000.000
82C113GLU-1-0.837-0.90815.840-18.345-18.3450.0000.0000.0000.000
83C114ALA00.0320.01417.765-0.517-0.5170.0000.0000.0000.000
84C115ARG10.8690.92718.75912.05112.0510.0000.0000.0000.000
85C116ARG10.7810.89015.96318.23218.2320.0000.0000.0000.000
86C117LEU00.0070.00714.0580.0950.0950.0000.0000.0000.000
87C118PHE00.031-0.00517.888-0.001-0.0010.0000.0000.0000.000
88C119THR0-0.039-0.03520.3140.6170.6170.0000.0000.0000.000
89C120LEU0-0.0090.00216.8330.4610.4610.0000.0000.0000.000
90C121ALA00.0210.01118.2930.0700.0700.0000.0000.0000.000
91C122ASN0-0.009-0.00219.8730.5180.5180.0000.0000.0000.000
92C123THR0-0.101-0.06323.1130.3510.3510.0000.0000.0000.000
93C124LYS10.7920.91516.52118.09418.0940.0000.0000.0000.000
94C126PRO00.0290.02622.462-0.208-0.2080.0000.0000.0000.000
95C127ASN0-0.036-0.02825.3150.2980.2980.0000.0000.0000.000
96C128ALA00.0210.04120.2890.1090.1090.0000.0000.0000.000
97C129ALA00.0090.00421.1910.3530.3530.0000.0000.0000.000
98C130ILE0-0.0150.00218.540-0.902-0.9020.0000.0000.0000.000
99C131VAL0-0.0070.00016.1220.7770.7770.0000.0000.0000.000
100C132SER00.006-0.01316.215-0.816-0.8160.0000.0000.0000.000
101C133GLY00.0380.01815.5270.6920.6920.0000.0000.0000.000
102C134GLY00.0040.00615.550-0.860-0.8600.0000.0000.0000.000
103C135TYR00.0150.00013.4880.6260.6260.0000.0000.0000.000
104C136SER00.0730.04216.514-0.182-0.1820.0000.0000.0000.000
105C137GLN00.0440.07018.679-0.151-0.1510.0000.0000.0000.000
106C138GLY00.0270.00716.8130.3680.3680.0000.0000.0000.000
107C139THR0-0.064-0.05717.8030.4240.4240.0000.0000.0000.000
108C140ALA00.0380.03420.7130.4870.4870.0000.0000.0000.000
109C141VAL0-0.050-0.01517.5360.4050.4050.0000.0000.0000.000
110C142MET00.0260.03816.2560.6540.6540.0000.0000.0000.000
111C143ALA0-0.0010.00521.0580.5070.5070.0000.0000.0000.000
112C144GLY00.0570.02824.3680.5570.5570.0000.0000.0000.000
113C145SER0-0.066-0.05921.3050.3450.3450.0000.0000.0000.000
114C146ILE00.0540.01821.0970.4940.4940.0000.0000.0000.000
115C147SER0-0.0130.00224.7870.4580.4580.0000.0000.0000.000
116C148GLY0-0.023-0.01927.9100.4490.4490.0000.0000.0000.000
117C149LEU0-0.0390.00223.1040.0600.0600.0000.0000.0000.000
118C150SER00.0240.00027.6500.3200.3200.0000.0000.0000.000
119C151THR00.014-0.01129.384-0.308-0.3080.0000.0000.0000.000
120C152THR0-0.0010.01229.706-0.174-0.1740.0000.0000.0000.000
121C153ILE00.0950.04424.058-0.127-0.1270.0000.0000.0000.000
122C154LYS10.8270.91925.61610.06810.0680.0000.0000.0000.000
123C155ASN0-0.033-0.01427.460-0.135-0.1350.0000.0000.0000.000
124C156GLN00.0170.00822.7680.1320.1320.0000.0000.0000.000
125C157ILE0-0.022-0.00921.631-0.359-0.3590.0000.0000.0000.000
126C158LYS10.8870.92922.75012.33512.3350.0000.0000.0000.000
127C159GLY00.007-0.00622.1020.4940.4940.0000.0000.0000.000
128C160VAL0-0.046-0.01320.224-0.717-0.7170.0000.0000.0000.000
129C161VAL00.0080.01117.1670.5250.5250.0000.0000.0000.000
130C162LEU0-0.053-0.02918.713-0.862-0.8620.0000.0000.0000.000
131C163PHE00.0420.01515.3860.4350.4350.0000.0000.0000.000
132C164GLY00.0870.03219.148-0.451-0.4510.0000.0000.0000.000
133C165TYR0-0.032-0.05621.409-0.303-0.3030.0000.0000.0000.000
134C166THR00.0480.01122.4030.6090.6090.0000.0000.0000.000
135C167LYS10.8380.93325.01011.54211.5420.0000.0000.0000.000
136C168ASN0-0.015-0.00626.9810.2400.2400.0000.0000.0000.000
137C169LEU0-0.0030.00928.6250.2920.2920.0000.0000.0000.000
138C170GLN00.0110.00329.6500.2220.2220.0000.0000.0000.000
139C171ASN0-0.022-0.01628.3630.5050.5050.0000.0000.0000.000
140C172LEU0-0.038-0.02131.962-0.019-0.0190.0000.0000.0000.000
141C173GLY00.0360.02929.7610.0870.0870.0000.0000.0000.000
142C174ARG10.8530.92628.7449.5549.5540.0000.0000.0000.000
143C175ILE00.0480.04423.533-0.090-0.0900.0000.0000.0000.000
144C176PRO00.0330.01328.0620.3010.3010.0000.0000.0000.000
145C177ASN0-0.039-0.03530.050-0.376-0.3760.0000.0000.0000.000
146C178PHE00.0500.03925.2040.0860.0860.0000.0000.0000.000
147C179GLU-1-0.836-0.89129.399-9.763-9.7630.0000.0000.0000.000
148C180THR00.0350.00428.945-0.364-0.3640.0000.0000.0000.000
149C181SER0-0.024-0.01529.219-0.327-0.3270.0000.0000.0000.000
150C182LYS10.8700.94625.98411.13811.1380.0000.0000.0000.000
151C183THR0-0.060-0.04724.742-0.660-0.6600.0000.0000.0000.000
152C184GLU-1-0.847-0.89922.973-11.798-11.7980.0000.0000.0000.000
153C185VAL0-0.040-0.02923.044-0.647-0.6470.0000.0000.0000.000
154C186TYR0-0.024-0.01719.8060.0550.0550.0000.0000.0000.000
155C187CYS0-0.059-0.01722.015-0.564-0.5640.0000.0000.0000.000
156C188ASP-1-0.810-0.90223.131-11.478-11.4780.0000.0000.0000.000
157C189ILE0-0.013-0.00124.9930.1120.1120.0000.0000.0000.000
158C190ALA00.0150.01625.5950.4030.4030.0000.0000.0000.000
159C191ASP-1-0.808-0.89121.922-13.720-13.7200.0000.0000.0000.000
160C192ALA00.0220.00225.0760.2060.2060.0000.0000.0000.000
161C193VAL0-0.038-0.01322.6820.3270.3270.0000.0000.0000.000
162C195TYR0-0.056-0.04027.2530.4980.4980.0000.0000.0000.000
163C196GLY0-0.022-0.01329.8220.3550.3550.0000.0000.0000.000
164C197THR0-0.042-0.00930.0510.1090.1090.0000.0000.0000.000
165C198LEU00.012-0.00826.064-0.398-0.3980.0000.0000.0000.000
166C199PHE0-0.021-0.00726.4230.3320.3320.0000.0000.0000.000
167C200ILE00.001-0.00523.110-0.538-0.5380.0000.0000.0000.000
168C201LEU00.0350.00623.1920.4650.4650.0000.0000.0000.000
169C202PRO0-0.043-0.01119.996-0.552-0.5520.0000.0000.0000.000
170C203ALA00.0130.00919.1190.6700.6700.0000.0000.0000.000
171C204HIS00.0100.00617.059-1.370-1.3700.0000.0000.0000.000
172C205PHE0-0.008-0.00612.9600.1780.1780.0000.0000.0000.000
173C206LEU00.0270.01115.8630.0510.0510.0000.0000.0000.000
174C207TYR0-0.045-0.04016.4690.4180.4180.0000.0000.0000.000
175C208GLN00.0320.01411.678-0.951-0.9510.0000.0000.0000.000
176C209THR00.014-0.00915.351-0.532-0.5320.0000.0000.0000.000
177C210ASP-1-0.843-0.92818.142-14.042-14.0420.0000.0000.0000.000
178C211ALA0-0.013-0.00713.082-0.038-0.0380.0000.0000.0000.000
179C212ALA00.0160.00514.110-0.562-0.5620.0000.0000.0000.000
180C213VAL0-0.060-0.03015.0960.2480.2480.0000.0000.0000.000
181C214ALA0-0.0100.01018.8150.3410.3410.0000.0000.0000.000
182C215ALA00.0740.03316.9910.3690.3690.0000.0000.0000.000
183C216PRO0-0.020-0.00915.7830.3710.3710.0000.0000.0000.000
184C217ARG10.9540.97518.38512.35412.3540.0000.0000.0000.000
185C218PHE0-0.0200.00121.7610.4970.4970.0000.0000.0000.000
186C219LEU00.0350.00616.8230.4830.4830.0000.0000.0000.000
187C220GLN0-0.003-0.00120.3810.0610.0610.0000.0000.0000.000
188C221ALA0-0.050-0.02221.6590.3820.3820.0000.0000.0000.000
189C222ARG10.8200.90723.59712.20312.2030.0000.0000.0000.000
190C223ILE0-0.060-0.01918.8510.1360.1360.0000.0000.0000.000
191C224GLY-1-0.849-0.89423.326-12.229-12.2290.0000.0000.0000.000