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: JRQ99

Calculation Name: 4EMT-B-Xray549

Preferred Name:

Target Type:

Ligand Name: 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2h,7h-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6h-purin-6-one) | calcium ion

Ligand 3-letter code: C2E | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4EMT

Chain ID: B

ChEMBL ID:

UniProt ID: Q86WV6

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2007973.543267
FMO2-HF: Nuclear repulsion 1934054.277841
FMO2-HF: Total energy -73919.265425
FMO2-MP2: Total energy -74134.652806


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(B:154:SER)


Summations of interaction energy for fragment #1(B:154: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.
-109.73-102.8797.698-5.865-8.683-0.059
Interaction energy analysis for fragmet #1(B:154:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.840 / q_NPA : 0.912
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].
3B156ALA00.0370.0252.7787.1158.9170.162-0.757-1.207-0.002
4B157HIS00.0350.0072.596-6.991-4.9722.392-1.666-2.746-0.022
5B158GLY00.0360.0245.1006.7786.830-0.001-0.004-0.0460.000
134B287GLN0-0.028-0.0342.415-22.287-19.5712.855-2.571-3.000-0.029
137B290LEU0-0.024-0.0072.193-3.263-3.0012.290-0.867-1.684-0.006
6B159LEU0-0.0090.0126.8575.0735.0730.0000.0000.0000.000
7B160ALA00.0430.0258.0033.4463.4460.0000.0000.0000.000
8B161TRP00.0400.0138.3723.7533.7530.0000.0000.0000.000
9B162SER0-0.065-0.04811.0942.9252.9250.0000.0000.0000.000
10B163TYR00.0490.01812.6371.9161.9160.0000.0000.0000.000
11B164TYR00.0720.03113.7531.4611.4610.0000.0000.0000.000
12B165ILE0-0.030-0.02514.9321.5101.5100.0000.0000.0000.000
13B166GLY00.0050.00016.6421.1911.1910.0000.0000.0000.000
14B167TYR0-0.090-0.06218.2390.9910.9910.0000.0000.0000.000
15B168LEU00.0480.02616.5590.8090.8090.0000.0000.0000.000
16B169ARG10.8710.93218.90416.10016.1000.0000.0000.0000.000
17B170LEU0-0.071-0.02621.0110.6010.6010.0000.0000.0000.000
18B171ILE00.004-0.00122.4180.6160.6160.0000.0000.0000.000
19B172LEU0-0.029-0.01220.6580.5620.5620.0000.0000.0000.000
20B173PRO0-0.023-0.01324.2650.4660.4660.0000.0000.0000.000
21B174GLU-1-0.824-0.90427.450-9.988-9.9880.0000.0000.0000.000
22B175LEU0-0.0050.00726.2090.4560.4560.0000.0000.0000.000
23B176GLN00.0200.01929.3010.7150.7150.0000.0000.0000.000
24B177ALA00.0180.00431.6460.3640.3640.0000.0000.0000.000
25B178ARG10.8280.92328.08610.91310.9130.0000.0000.0000.000
26B179ILE00.0240.01029.5880.2930.2930.0000.0000.0000.000
27B180ARG10.8840.94533.9879.0019.0010.0000.0000.0000.000
28B181THR0-0.004-0.01437.0200.3180.3180.0000.0000.0000.000
29B182TYR0-0.054-0.06936.1540.2230.2230.0000.0000.0000.000
30B183ASN0-0.011-0.01936.2360.2690.2690.0000.0000.0000.000
31B184GLN0-0.063-0.02039.6870.0560.0560.0000.0000.0000.000
32B185HIS00.0100.01541.7770.2480.2480.0000.0000.0000.000
33B186TYR00.0110.01840.0250.0830.0830.0000.0000.0000.000
34B187ASN0-0.015-0.00742.261-0.160-0.1600.0000.0000.0000.000
35B188ASN00.0190.00242.5870.1410.1410.0000.0000.0000.000
36B189LEU0-0.0090.00244.985-0.079-0.0790.0000.0000.0000.000
37B190LEU00.0350.01945.7940.0420.0420.0000.0000.0000.000
38B191ARG10.8200.90838.6697.8397.8390.0000.0000.0000.000
39B192GLY00.0390.02639.2470.0670.0670.0000.0000.0000.000
40B193ALA00.0000.00138.667-0.083-0.0830.0000.0000.0000.000
41B194VAL0-0.025-0.01332.610-0.126-0.1260.0000.0000.0000.000
42B195SER00.0300.00131.4810.1010.1010.0000.0000.0000.000
43B196GLN0-0.040-0.03831.001-0.462-0.4620.0000.0000.0000.000
44B197ARG10.8050.91025.75610.87510.8750.0000.0000.0000.000
45B198LEU0-0.037-0.00822.0260.2840.2840.0000.0000.0000.000
46B199TYR00.0070.00123.163-0.530-0.5300.0000.0000.0000.000
47B200ILE0-0.012-0.01217.2560.0440.0440.0000.0000.0000.000
48B201LEU00.0280.01018.958-0.425-0.4250.0000.0000.0000.000
49B202LEU0-0.023-0.03613.143-0.887-0.8870.0000.0000.0000.000
50B203PRO00.0460.04415.908-0.270-0.2700.0000.0000.0000.000
51B204LEU00.015-0.01311.787-1.365-1.3650.0000.0000.0000.000
52B205ASP-1-0.837-0.90912.929-17.754-17.7540.0000.0000.0000.000
53B206CYS0-0.118-0.06012.029-1.212-1.2120.0000.0000.0000.000
54B207GLY00.0520.02814.7690.1900.1900.0000.0000.0000.000
55B208VAL0-0.055-0.02816.8840.4310.4310.0000.0000.0000.000
56B209PRO0-0.027-0.00219.6330.1040.1040.0000.0000.0000.000
57B210ASP-1-0.908-0.95723.413-12.492-12.4920.0000.0000.0000.000
58B211ASN0-0.034-0.00625.4640.1900.1900.0000.0000.0000.000
59B212LEU00.0390.01724.5510.0410.0410.0000.0000.0000.000
60B213SER0-0.034-0.03126.8980.1420.1420.0000.0000.0000.000
61B214MET0-0.057-0.03829.1110.3800.3800.0000.0000.0000.000
62B215ALA00.0010.01325.592-0.033-0.0330.0000.0000.0000.000
63B216ASP-1-0.687-0.82527.539-9.827-9.8270.0000.0000.0000.000
64B217PRO00.0110.02330.1890.0240.0240.0000.0000.0000.000
65B218ASN0-0.083-0.04632.8050.5080.5080.0000.0000.0000.000
66B219ILE0-0.0070.00227.2990.0650.0650.0000.0000.0000.000
67B220ARG10.8970.95031.4808.0728.0720.0000.0000.0000.000
68B221PHE0-0.012-0.01431.513-0.052-0.0520.0000.0000.0000.000
69B222LEU0-0.061-0.02133.7050.2890.2890.0000.0000.0000.000
70B223ASP-1-0.773-0.85734.390-8.149-8.1490.0000.0000.0000.000
71B224LYS10.8260.90129.10310.13710.1370.0000.0000.0000.000
72B225LEU0-0.0060.00629.6310.2600.2600.0000.0000.0000.000
73B226PRO0-0.0040.00432.643-0.163-0.1630.0000.0000.0000.000
74B227GLN0-0.0040.01033.787-0.045-0.0450.0000.0000.0000.000
75B228GLN0-0.073-0.03131.938-0.306-0.3060.0000.0000.0000.000
76B229THR0-0.045-0.03226.798-0.119-0.1190.0000.0000.0000.000
77B230GLY00.0060.01229.274-0.119-0.1190.0000.0000.0000.000
78B231ASP-1-0.845-0.89225.647-12.871-12.8710.0000.0000.0000.000
79B232HIS00.0060.00428.1870.1860.1860.0000.0000.0000.000
80B233ALA0-0.015-0.02830.4500.3140.3140.0000.0000.0000.000
81B234GLY00.0440.03533.809-0.126-0.1260.0000.0000.0000.000
82B235ILE0-0.047-0.03535.1260.2340.2340.0000.0000.0000.000
83B236LYS10.8630.91630.2569.8559.8550.0000.0000.0000.000
84B237ASP-1-0.801-0.88130.588-9.685-9.6850.0000.0000.0000.000
85B238ARG10.8360.90523.09512.93012.9300.0000.0000.0000.000
86B239VAL00.0290.00729.9420.1000.1000.0000.0000.0000.000
87B240TYR00.0480.02124.103-0.587-0.5870.0000.0000.0000.000
88B241SER00.0000.00226.9620.4840.4840.0000.0000.0000.000
89B242ASN00.026-0.00224.8730.0290.0290.0000.0000.0000.000
90B243SER0-0.011-0.01127.6170.5010.5010.0000.0000.0000.000
91B244ILE00.0130.01928.943-0.287-0.2870.0000.0000.0000.000
92B245TYR00.0280.00428.0020.0420.0420.0000.0000.0000.000
93B246GLU-1-0.858-0.92132.288-7.922-7.9220.0000.0000.0000.000
94B247LEU00.0070.00429.702-0.181-0.1810.0000.0000.0000.000
95B248LEU0-0.061-0.03433.6420.2760.2760.0000.0000.0000.000
96B249GLU-1-0.732-0.82834.800-8.884-8.8840.0000.0000.0000.000
97B250ASN0-0.051-0.03337.0280.2320.2320.0000.0000.0000.000
98B251GLY00.0360.03039.3050.2100.2100.0000.0000.0000.000
99B252GLN00.0040.00940.5790.1510.1510.0000.0000.0000.000
100B253ARG10.7980.86537.7357.4957.4950.0000.0000.0000.000
101B254ALA00.0000.00835.6790.1370.1370.0000.0000.0000.000
102B255GLY00.0870.04933.927-0.102-0.1020.0000.0000.0000.000
103B256THR0-0.057-0.04033.7950.2040.2040.0000.0000.0000.000
104B257CYS0-0.0200.02928.2820.0280.0280.0000.0000.0000.000
105B258VAL00.0390.01927.1270.1270.1270.0000.0000.0000.000
106B259LEU00.0020.00324.252-0.277-0.2770.0000.0000.0000.000
107B260GLU-1-0.775-0.86121.418-13.175-13.1750.0000.0000.0000.000
108B261TYR00.0790.03518.696-0.258-0.2580.0000.0000.0000.000
109B262ALA00.0070.00814.302-0.104-0.1040.0000.0000.0000.000
110B263THR00.0440.01415.154-1.156-1.1560.0000.0000.0000.000
111B264PRO0-0.021-0.00811.136-0.403-0.4030.0000.0000.0000.000
112B265LEU00.0390.01910.862-1.881-1.8810.0000.0000.0000.000
113B266GLN00.0580.02312.775-0.361-0.3610.0000.0000.0000.000
114B267THR0-0.037-0.00610.8220.3870.3870.0000.0000.0000.000
115B268LEU00.009-0.0026.762-1.012-1.0120.0000.0000.0000.000
116B269PHE00.0110.00310.5990.0610.0610.0000.0000.0000.000
117B270ALA00.0290.02514.0470.4460.4460.0000.0000.0000.000
118B271MET0-0.025-0.0236.482-0.220-0.2200.0000.0000.0000.000
119B272SER0-0.050-0.00511.9430.6730.6730.0000.0000.0000.000
120B273GLN0-0.058-0.03013.1932.0242.0240.0000.0000.0000.000
121B274TYR0-0.031-0.01213.9920.8540.8540.0000.0000.0000.000
122B275SER00.0320.00514.607-1.230-1.2300.0000.0000.0000.000
123B276GLN0-0.009-0.00515.443-0.746-0.7460.0000.0000.0000.000
124B277ALA0-0.0170.00110.580-0.634-0.6340.0000.0000.0000.000
125B278GLY0-0.042-0.01310.377-2.167-2.1670.0000.0000.0000.000
126B279PHE0-0.047-0.0145.526-1.658-1.6580.0000.0000.0000.000
127B280SER00.004-0.03010.3222.2582.2580.0000.0000.0000.000
128B281ARG10.9510.95611.23215.07315.0730.0000.0000.0000.000
129B282GLU-1-0.855-0.93012.345-19.486-19.4860.0000.0000.0000.000
130B283ASP-1-0.813-0.8787.114-30.754-30.7540.0000.0000.0000.000
131B284ARG10.8080.8827.51916.61516.6150.0000.0000.0000.000
132B285LEU00.0250.0269.090-1.013-1.0130.0000.0000.0000.000
133B286GLU-1-0.861-0.9256.654-28.418-28.4180.0000.0000.0000.000
135B288ALA00.0640.0355.459-0.717-0.7170.0000.0000.0000.000
136B289LYS10.9160.9558.58123.93423.9340.0000.0000.0000.000
138B291PHE0-0.035-0.0036.144-0.788-0.7880.0000.0000.0000.000
139B292CYS0-0.0180.0007.3982.0722.0720.0000.0000.0000.000
140B293ARG10.8810.9198.74125.18425.1840.0000.0000.0000.000
141B294THR0-0.050-0.0436.378-1.349-1.3490.0000.0000.0000.000
142B295LEU0-0.010-0.0108.8381.4581.4580.0000.0000.0000.000
143B296GLU-1-0.938-0.96711.895-17.796-17.7960.0000.0000.0000.000
144B297ASP-1-0.827-0.89011.293-22.898-22.8980.0000.0000.0000.000
145B298ILE0-0.059-0.03310.2270.9140.9140.0000.0000.0000.000
146B299LEU0-0.026-0.02413.9881.3631.3630.0000.0000.0000.000
147B300ALA0-0.0250.00116.6121.0811.0810.0000.0000.0000.000
148B301ASP-1-0.929-0.95816.779-16.480-16.4800.0000.0000.0000.000
149B302ALA0-0.075-0.02018.9820.5770.5770.0000.0000.0000.000
150B303PRO00.0430.01720.4740.1770.1770.0000.0000.0000.000
151B304GLU-1-0.841-0.92122.836-13.186-13.1860.0000.0000.0000.000
152B305SER0-0.013-0.02720.5520.1650.1650.0000.0000.0000.000
153B306GLN00.0300.01920.375-0.236-0.2360.0000.0000.0000.000
154B307ASN0-0.013-0.00321.7950.1850.1850.0000.0000.0000.000
155B308ASN0-0.020-0.01924.6390.8790.8790.0000.0000.0000.000
156B309CYS0-0.058-0.02720.583-0.134-0.1340.0000.0000.0000.000
157B310ARG10.8240.88621.74612.36812.3680.0000.0000.0000.000
158B311LEU00.0050.01114.984-0.054-0.0540.0000.0000.0000.000
159B312ILE00.0230.02018.8510.3800.3800.0000.0000.0000.000
160B313ALA00.0060.00115.161-0.339-0.3390.0000.0000.0000.000
161B314TYR00.0130.00917.0650.4920.4920.0000.0000.0000.000
162B315GLN0-0.034-0.02716.714-1.610-1.6100.0000.0000.0000.000
163B316GLU-1-0.876-0.94018.413-13.191-13.1910.0000.0000.0000.000
164B317PRO0-0.034-0.00721.648-0.274-0.2740.0000.0000.0000.000
165B318ALA0-0.020-0.02624.5230.0520.0520.0000.0000.0000.000
166B319ASP-1-0.852-0.88925.966-9.364-9.3640.0000.0000.0000.000
167B320ASP-1-0.886-0.93027.327-10.308-10.3080.0000.0000.0000.000
168B321SER0-0.070-0.06128.4440.1580.1580.0000.0000.0000.000
169B322SER0-0.097-0.05728.9630.1050.1050.0000.0000.0000.000
170B323PHE0-0.017-0.01923.087-0.191-0.1910.0000.0000.0000.000
171B324SER0-0.007-0.01427.8390.3210.3210.0000.0000.0000.000
172B325LEU00.0390.02622.793-0.127-0.1270.0000.0000.0000.000
173B326SER0-0.065-0.06526.501-0.095-0.0950.0000.0000.0000.000
174B327GLN0-0.012-0.02129.3630.0490.0490.0000.0000.0000.000
175B328GLU-1-0.775-0.86622.869-12.582-12.5820.0000.0000.0000.000
176B329VAL0-0.038-0.02625.104-0.286-0.2860.0000.0000.0000.000
177B330LEU0-0.025-0.01926.5980.0500.0500.0000.0000.0000.000
178B331ARG10.8190.91022.60712.45312.4530.0000.0000.0000.000
179B332HIS0-0.046-0.03822.127-0.318-0.3180.0000.0000.0000.000
180B333LEU0-0.065-0.03026.2860.0030.0030.0000.0000.0000.000
181B334ARG10.8730.89129.2369.0119.0110.0000.0000.0000.000
182B335GLN0-0.050-0.01924.8780.1020.1020.0000.0000.0000.000
183B336GLU-1-0.880-0.91127.438-11.135-11.1350.0000.0000.0000.000
184B337GLU-2-1.912-1.93831.169-17.424-17.4240.0000.0000.0000.000