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: Z9K4N

Calculation Name: 1D02-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D02

Chain ID: A

ChEMBL ID:

UniProt ID: P43642

Base Structure: X-ray

Registration Date: 2025-10-11

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 197
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2226534.957195
FMO2-HF: Nuclear repulsion 2148070.605037
FMO2-HF: Total energy -78464.352157
FMO2-MP2: Total energy -78698.877619


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:LEU)


Summations of interaction energy for fragment #1(A:6:LEU)
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.
-101.959-93.9816.446-11.416-13.008-0.13
Interaction energy analysis for fragmet #1(A:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.913
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].
3A8GLY00.1150.0533.829-1.0230.418-0.005-0.634-0.8010.001
34A39LYS10.8240.9252.42866.37567.6362.419-0.963-2.717-0.006
35A40TYR00.0100.0114.294-1.580-1.4370.000-0.020-0.1230.000
84A89THR0-0.038-0.0474.519-0.586-0.459-0.001-0.018-0.1090.000
85A90GLU-1-0.839-0.9242.123-140.656-135.81814.026-9.730-9.134-0.125
86A91THR0-0.040-0.0413.8223.6793.8480.007-0.051-0.1240.000
4A9ARG10.8940.9546.36231.46131.4610.0000.0000.0000.000
5A10LEU00.0420.0257.815-1.593-1.5930.0000.0000.0000.000
6A11ASN0-0.018-0.00410.6191.7141.7140.0000.0000.0000.000
7A12TRP00.056-0.00212.7091.4751.4750.0000.0000.0000.000
8A13GLN0-0.030-0.00815.6100.4540.4540.0000.0000.0000.000
9A14ALA00.0570.04515.6340.9580.9580.0000.0000.0000.000
10A15LEU0-0.0170.00017.0690.8630.8630.0000.0000.0000.000
11A16ALA0-0.008-0.00818.9140.8280.8280.0000.0000.0000.000
12A17GLY00.0210.01020.6060.6970.6970.0000.0000.0000.000
13A18LEU0-0.0080.00021.0830.5560.5560.0000.0000.0000.000
14A19LYS10.9200.96522.98011.79911.7990.0000.0000.0000.000
15A20ALA0-0.035-0.02224.9520.4770.4770.0000.0000.0000.000
16A21SER0-0.062-0.04225.8450.4120.4120.0000.0000.0000.000
17A22GLY0-0.017-0.00327.6740.2940.2940.0000.0000.0000.000
18A23ALA0-0.0070.01226.6080.2450.2450.0000.0000.0000.000
19A24GLU-1-0.912-0.96128.016-10.564-10.5640.0000.0000.0000.000
20A25GLN00.0020.01023.152-0.254-0.2540.0000.0000.0000.000
21A26ASN00.013-0.00724.299-0.070-0.0700.0000.0000.0000.000
22A27LEU00.0440.01520.244-0.386-0.3860.0000.0000.0000.000
23A28TYR00.006-0.02120.096-0.602-0.6020.0000.0000.0000.000
24A29ASN00.025-0.00119.361-0.915-0.9150.0000.0000.0000.000
25A30VAL0-0.0070.00619.214-0.475-0.4750.0000.0000.0000.000
26A31PHE00.027-0.00715.037-0.627-0.6270.0000.0000.0000.000
27A32ASN0-0.029-0.01614.781-1.739-1.7390.0000.0000.0000.000
28A33ALA00.0440.03914.469-0.924-0.9240.0000.0000.0000.000
29A34VAL0-0.039-0.01613.424-0.817-0.8170.0000.0000.0000.000
30A35PHE00.011-0.00810.514-1.798-1.7980.0000.0000.0000.000
31A36GLU-1-0.876-0.9259.793-19.068-19.0680.0000.0000.0000.000
32A37GLY0-0.003-0.0038.5270.0300.0300.0000.0000.0000.000
33A38THR0-0.093-0.0306.108-3.176-3.1760.0000.0000.0000.000
36A41VAL00.0300.0207.8951.0361.0360.0000.0000.0000.000
37A42LEU0-0.0140.00010.6070.2970.2970.0000.0000.0000.000
38A43TYR0-0.065-0.05712.5590.9980.9980.0000.0000.0000.000
39A44GLU-1-0.893-0.95617.082-11.908-11.9080.0000.0000.0000.000
40A45LYS10.9080.95920.75110.58710.5870.0000.0000.0000.000
41A46PRO0-0.0080.00818.5870.1160.1160.0000.0000.0000.000
42A47LYS10.9770.96620.31512.68812.6880.0000.0000.0000.000
43A48HIS00.0310.01814.9901.4341.4340.0000.0000.0000.000
44A49LEU00.0450.03220.3490.1980.1980.0000.0000.0000.000
45A50LYS10.8440.91823.59510.95010.9500.0000.0000.0000.000
46A51ASN00.0070.00725.9600.6930.6930.0000.0000.0000.000
47A52LEU0-0.044-0.01625.304-0.222-0.2220.0000.0000.0000.000
48A53TYR00.009-0.01929.1460.0850.0850.0000.0000.0000.000
49A54ALA00.0130.02732.7200.2440.2440.0000.0000.0000.000
50A55GLN00.0330.00428.9840.4010.4010.0000.0000.0000.000
51A56VAL0-0.051-0.02134.089-0.036-0.0360.0000.0000.0000.000
52A57VAL00.0190.00736.0510.1880.1880.0000.0000.0000.000
53A58LEU0-0.0100.00338.9830.0040.0040.0000.0000.0000.000
54A59PRO00.009-0.00541.8910.0700.0700.0000.0000.0000.000
55A60ASP-1-0.842-0.93245.067-6.611-6.6110.0000.0000.0000.000
56A61ASP-1-0.991-0.97047.986-5.991-5.9910.0000.0000.0000.000
57A62VAL00.0370.00444.4450.0450.0450.0000.0000.0000.000
58A63ILE0-0.021-0.00843.3910.0040.0040.0000.0000.0000.000
59A64LYS10.8650.92747.2176.1426.1420.0000.0000.0000.000
60A65GLU-1-0.912-0.94450.232-5.822-5.8220.0000.0000.0000.000
61A66ILE0-0.065-0.02144.344-0.047-0.0470.0000.0000.0000.000
62A67PHE0-0.020-0.01845.9260.0730.0730.0000.0000.0000.000
63A68ASN0-0.014-0.01145.483-0.294-0.2940.0000.0000.0000.000
64A69PRO0-0.031-0.01842.5760.1070.1070.0000.0000.0000.000
65A70LEU00.0110.00944.840-0.036-0.0360.0000.0000.0000.000
66A71ILE0-0.046-0.02738.275-0.060-0.0600.0000.0000.0000.000
67A72ASP-1-0.738-0.81537.529-8.095-8.0950.0000.0000.0000.000
68A73LEU0-0.016-0.00536.963-0.226-0.2260.0000.0000.0000.000
69A74SER0-0.082-0.05234.859-0.265-0.2650.0000.0000.0000.000
70A75THR0-0.039-0.04532.854-0.308-0.3080.0000.0000.0000.000
71A76THR0-0.057-0.03232.651-0.185-0.1850.0000.0000.0000.000
72A77GLN0-0.010-0.00326.545-0.334-0.3340.0000.0000.0000.000
73A78TRP00.0230.01030.996-0.049-0.0490.0000.0000.0000.000
74A79GLY00.0510.02228.571-0.163-0.1630.0000.0000.0000.000
75A80VAL0-0.055-0.02425.6190.3330.3330.0000.0000.0000.000
76A81SER0-0.049-0.04725.010-0.109-0.1090.0000.0000.0000.000
77A82PRO00.0120.03122.1130.3560.3560.0000.0000.0000.000
78A83ALA00.0040.01424.1270.0300.0300.0000.0000.0000.000
79A84PHE00.0120.01118.482-0.008-0.0080.0000.0000.0000.000
80A85ALA0-0.0040.00016.5290.3060.3060.0000.0000.0000.000
81A86ILE0-0.0070.01412.139-0.065-0.0650.0000.0000.0000.000
82A87GLU-1-0.794-0.8619.117-23.360-23.3600.0000.0000.0000.000
83A88ASN0-0.012-0.0185.291-4.666-4.6660.0000.0000.0000.000
87A92HIS10.8130.9037.00132.70732.7070.0000.0000.0000.000
88A93LYS10.8620.9499.54427.66227.6620.0000.0000.0000.000
89A94ILE0-0.050-0.04411.093-1.028-1.0280.0000.0000.0000.000
90A95LEU00.0240.02913.8870.9830.9830.0000.0000.0000.000
91A96PHE00.004-0.01616.4700.1530.1530.0000.0000.0000.000
92A97GLY00.0460.01719.4510.1390.1390.0000.0000.0000.000
93A98GLU-1-0.878-0.95021.566-10.944-10.9440.0000.0000.0000.000
94A99ILE00.0220.01924.061-0.106-0.1060.0000.0000.0000.000
95A100LYS10.7660.87227.26210.84810.8480.0000.0000.0000.000
96A101ARG10.9150.95627.51710.43410.4340.0000.0000.0000.000
97A102GLN0-0.021-0.02533.2000.1370.1370.0000.0000.0000.000
98A103ASP-1-0.867-0.92436.660-7.898-7.8980.0000.0000.0000.000
99A104GLY0-0.014-0.02839.425-0.100-0.1000.0000.0000.0000.000
100A105TRP0-0.081-0.04040.7490.1030.1030.0000.0000.0000.000
101A106VAL00.0050.00239.685-0.093-0.0930.0000.0000.0000.000
102A107GLU-1-0.753-0.85442.096-7.451-7.4510.0000.0000.0000.000
103A108GLY0-0.014-0.01045.378-0.041-0.0410.0000.0000.0000.000
104A109LYS10.8720.95342.8497.2737.2730.0000.0000.0000.000
105A110ASP-1-0.814-0.89847.706-6.157-6.1570.0000.0000.0000.000
106A111PRO0-0.043-0.04046.900-0.167-0.1670.0000.0000.0000.000
107A112SER0-0.017-0.00546.795-0.151-0.1510.0000.0000.0000.000
108A113ALA00.0100.00644.669-0.033-0.0330.0000.0000.0000.000
109A114GLY00.0570.03442.302-0.139-0.1390.0000.0000.0000.000
110A115ARG10.8740.92742.7986.5756.5750.0000.0000.0000.000
111A116GLY0-0.0190.00641.7800.0300.0300.0000.0000.0000.000
112A117ASN00.009-0.01939.923-0.055-0.0550.0000.0000.0000.000
113A118ALA00.0360.02837.985-0.118-0.1180.0000.0000.0000.000
114A119HIS0-0.007-0.01134.120-0.189-0.1890.0000.0000.0000.000
115A120GLU-1-0.832-0.90434.050-8.153-8.1530.0000.0000.0000.000
116A121ARG10.9000.95132.9618.8278.8270.0000.0000.0000.000
117A122SER0-0.060-0.04129.834-0.252-0.2520.0000.0000.0000.000
118A123CYS00.0270.00830.311-0.402-0.4020.0000.0000.0000.000
119A124LYS10.9650.99430.1099.9239.9230.0000.0000.0000.000
120A125LEU0-0.020-0.00125.2400.0280.0280.0000.0000.0000.000
121A126PHE00.0470.03227.942-0.352-0.3520.0000.0000.0000.000
122A127THR0-0.033-0.01730.3250.1790.1790.0000.0000.0000.000
123A128PRO00.0470.01430.051-0.350-0.3500.0000.0000.0000.000
124A129GLY0-0.019-0.00629.816-0.220-0.2200.0000.0000.0000.000
125A130LEU0-0.020-0.01627.322-0.316-0.3160.0000.0000.0000.000
126A131LEU00.0430.03625.588-0.542-0.5420.0000.0000.0000.000
127A132LYS11.0061.00624.4829.9529.9520.0000.0000.0000.000
128A133ALA0-0.0040.01024.179-0.459-0.4590.0000.0000.0000.000
129A134TYR00.032-0.00521.437-0.353-0.3530.0000.0000.0000.000
130A135ARG10.7490.86119.88513.21713.2170.0000.0000.0000.000
131A136THR0-0.057-0.03219.449-0.677-0.6770.0000.0000.0000.000
132A137ILE0-0.063-0.03918.705-0.631-0.6310.0000.0000.0000.000
133A138GLY00.0100.02015.978-0.640-0.6400.0000.0000.0000.000
134A139GLY00.0510.02614.960-1.510-1.5100.0000.0000.0000.000
135A140ILE0-0.023-0.00515.398-0.352-0.3520.0000.0000.0000.000
136A141ASN0-0.051-0.05117.4731.7831.7830.0000.0000.0000.000
137A142ASP-1-0.858-0.91117.761-15.917-15.9170.0000.0000.0000.000
138A143GLU-1-0.811-0.90819.827-12.460-12.4600.0000.0000.0000.000
139A144GLU-1-0.897-0.90119.887-14.908-14.9080.0000.0000.0000.000
140A145ILE0-0.071-0.01918.4240.3390.3390.0000.0000.0000.000
141A146LEU00.0040.00521.8480.2080.2080.0000.0000.0000.000
142A147PRO0-0.012-0.00519.792-0.580-0.5800.0000.0000.0000.000
143A148PHE0-0.019-0.02220.170-0.314-0.3140.0000.0000.0000.000
144A149TRP00.0010.00618.552-0.238-0.2380.0000.0000.0000.000
145A150VAL0-0.027-0.01322.2090.1000.1000.0000.0000.0000.000
146A151VAL00.0240.01822.8210.1140.1140.0000.0000.0000.000
147A152PHE00.003-0.01225.8380.4040.4040.0000.0000.0000.000
148A153GLU-1-0.793-0.90427.174-11.155-11.1550.0000.0000.0000.000
149A154GLY00.0600.02330.9740.2610.2610.0000.0000.0000.000
150A155ASP-1-0.821-0.91534.610-8.137-8.1370.0000.0000.0000.000
151A156ILE0-0.038-0.01433.8670.0530.0530.0000.0000.0000.000
152A157THR0-0.028-0.03531.223-0.037-0.0370.0000.0000.0000.000
153A158ARG10.7860.85033.9518.0288.0280.0000.0000.0000.000
154A159ASP-1-0.747-0.83536.934-7.555-7.5550.0000.0000.0000.000
155A160PRO00.0080.01138.687-0.194-0.1940.0000.0000.0000.000
156A161LYS10.9460.97440.7387.0297.0290.0000.0000.0000.000
157A162ARG10.8220.89937.1807.7337.7330.0000.0000.0000.000
158A163VAL00.0590.03233.944-0.227-0.2270.0000.0000.0000.000
159A164ARG10.8710.94235.1537.6527.6520.0000.0000.0000.000
160A165GLU-1-0.794-0.87537.233-8.219-8.2190.0000.0000.0000.000
161A166ILE00.0010.00431.369-0.092-0.0920.0000.0000.0000.000
162A167THR0-0.041-0.03332.584-0.276-0.2760.0000.0000.0000.000
163A168PHE0-0.020-0.00933.511-0.151-0.1510.0000.0000.0000.000
164A169TRP0-0.016-0.02233.391-0.158-0.1580.0000.0000.0000.000
165A170TYR00.0070.00326.829-0.235-0.2350.0000.0000.0000.000
166A171ASP-1-0.820-0.86930.159-9.996-9.9960.0000.0000.0000.000
167A172HIS10.8280.90027.71210.64810.6480.0000.0000.0000.000
168A173TYR00.0100.00824.960-0.098-0.0980.0000.0000.0000.000
169A174GLN0-0.031-0.04826.456-0.180-0.1800.0000.0000.0000.000
170A175ASP-1-0.784-0.87621.803-13.575-13.5750.0000.0000.0000.000
171A176ASN0-0.008-0.00521.473-0.350-0.3500.0000.0000.0000.000
172A177TYR0-0.046-0.03123.7760.1860.1860.0000.0000.0000.000
173A178PHE00.0060.00523.657-0.322-0.3220.0000.0000.0000.000
174A179MET0-0.0190.00825.7590.3660.3660.0000.0000.0000.000
175A180TRP0-0.0040.00024.969-0.072-0.0720.0000.0000.0000.000
176A181ARG10.8770.93028.10510.09010.0900.0000.0000.0000.000
177A182PRO00.019-0.00930.876-0.170-0.1700.0000.0000.0000.000
178A183ASN0-0.014-0.01232.3140.0730.0730.0000.0000.0000.000
179A184GLU-1-0.795-0.87227.853-10.752-10.7520.0000.0000.0000.000
180A185SER0-0.0190.00024.675-0.131-0.1310.0000.0000.0000.000
181A186GLY00.0640.01822.435-0.123-0.1230.0000.0000.0000.000
182A187GLU-1-0.969-0.98720.082-14.266-14.2660.0000.0000.0000.000
183A188LYS10.8670.91920.29310.48110.4810.0000.0000.0000.000
184A189LEU0-0.0190.00520.652-0.211-0.2110.0000.0000.0000.000
185A190VAL00.014-0.00115.353-0.594-0.5940.0000.0000.0000.000
186A191GLN0-0.008-0.00617.026-0.577-0.5770.0000.0000.0000.000
187A192HIS00.0350.02018.374-0.397-0.3970.0000.0000.0000.000
188A193PHE00.0520.01311.679-0.419-0.4190.0000.0000.0000.000
189A194ASN0-0.009-0.00612.943-2.774-2.7740.0000.0000.0000.000
190A195GLU-1-0.959-0.97614.207-17.083-17.0830.0000.0000.0000.000
191A196LYS10.8100.91017.02413.47513.4750.0000.0000.0000.000
192A197LEU0-0.009-0.00216.339-0.151-0.1510.0000.0000.0000.000
193A198LYS10.8270.9049.59227.87027.8700.0000.0000.0000.000
194A199LYS10.9060.95711.09516.43516.4350.0000.0000.0000.000
195A200TYR0-0.044-0.05412.049-0.628-0.6280.0000.0000.0000.000
196A201LEU0-0.032-0.02910.1080.6360.6360.0000.0000.0000.000
197A202ASP-2-1.707-1.8076.525-75.481-75.4810.0000.0000.0000.000