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: M8K2Z

Calculation Name: 1D1D-A-Other547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1D1D

Chain ID: A

ChEMBL ID:

UniProt ID: O92954

Base Structure: SolutionNMR

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 220
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2293607.448606
FMO2-HF: Nuclear repulsion 2210597.503133
FMO2-HF: Total energy -83009.945473
FMO2-MP2: Total energy -83253.365057


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:11:TRP)


Summations of interaction energy for fragment #1(A:11:TRP)
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.
-12.081-5.05210.138-6.525-10.642-0.049
Interaction energy analysis for fragmet #1(A:11:TRP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.904
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].
3A13PRO00.0070.0163.8451.9083.583-0.016-0.654-1.004-0.001
105A115GLY0-0.0050.0023.202-0.565-0.1230.014-0.160-0.297-0.001
106A116ASN0-0.048-0.0312.187-20.164-17.7624.407-2.719-4.090-0.039
107A117PRO00.0550.0302.1040.3431.7015.719-2.528-4.550-0.004
108A118GLN00.015-0.0113.2552.7873.8740.015-0.463-0.639-0.004
109A119GLY00.0430.0295.2855.1625.227-0.001-0.001-0.0620.000
4A14LEU00.0790.0455.8503.1403.1400.0000.0000.0000.000
5A15GLU-1-0.886-0.9618.973-20.100-20.1000.0000.0000.0000.000
6A16PRO00.0510.01611.4921.3121.3120.0000.0000.0000.000
7A17LYS10.9400.99214.05319.27519.2750.0000.0000.0000.000
8A18LEU0-0.003-0.00216.2931.1581.1580.0000.0000.0000.000
9A19ILE00.0700.04413.6640.8530.8530.0000.0000.0000.000
10A20THR0-0.006-0.02017.5300.9270.9270.0000.0000.0000.000
11A21ARG10.9640.98219.72313.57713.5770.0000.0000.0000.000
12A22LEU0-0.0100.01020.2020.6860.6860.0000.0000.0000.000
13A23ALA00.0350.01620.3220.4980.4980.0000.0000.0000.000
14A24ASP-1-0.888-0.92222.410-10.708-10.7080.0000.0000.0000.000
15A25THR0-0.023-0.00825.2610.6330.6330.0000.0000.0000.000
16A26VAL0-0.004-0.00524.0000.4200.4200.0000.0000.0000.000
17A27ARG10.8670.91826.34811.06911.0690.0000.0000.0000.000
18A28THR0-0.100-0.06228.0200.4490.4490.0000.0000.0000.000
19A29LYS10.8540.93230.06910.42910.4290.0000.0000.0000.000
20A30GLY00.0370.03630.9060.2740.2740.0000.0000.0000.000
21A31LEU00.0450.01425.202-0.022-0.0220.0000.0000.0000.000
22A32ARG10.8160.90328.9289.2209.2200.0000.0000.0000.000
23A33SER0-0.0210.00730.6490.2480.2480.0000.0000.0000.000
24A34PRO00.013-0.00930.819-0.265-0.2650.0000.0000.0000.000
25A35ILE00.018-0.00329.265-0.205-0.2050.0000.0000.0000.000
26A36THR0-0.020-0.00825.621-0.356-0.3560.0000.0000.0000.000
27A37MET0-0.056-0.00925.085-0.476-0.4760.0000.0000.0000.000
28A38ALA00.0600.04225.654-0.373-0.3730.0000.0000.0000.000
29A39GLU-1-0.797-0.92124.727-11.144-11.1440.0000.0000.0000.000
30A40VAL0-0.029-0.01420.409-0.669-0.6690.0000.0000.0000.000
31A41GLU-1-0.907-0.97620.987-12.364-12.3640.0000.0000.0000.000
32A42ALA0-0.037-0.01022.384-0.236-0.2360.0000.0000.0000.000
33A43LEU0-0.076-0.04217.280-0.398-0.3980.0000.0000.0000.000
34A44MET0-0.053-0.03116.806-0.712-0.7120.0000.0000.0000.000
35A45SER0-0.0170.01918.4830.0020.0020.0000.0000.0000.000
36A46SER0-0.029-0.00415.7610.2740.2740.0000.0000.0000.000
37A47PRO0-0.026-0.02514.229-0.215-0.2150.0000.0000.0000.000
38A48LEU00.0050.00411.089-1.052-1.0520.0000.0000.0000.000
39A49LEU0-0.0050.0046.4351.0151.0150.0000.0000.0000.000
40A50PRO00.0360.0239.7371.0341.0340.0000.0000.0000.000
41A51HIS00.004-0.0106.749-1.166-1.1660.0000.0000.0000.000
42A52ASP-1-0.848-0.9197.348-34.025-34.0250.0000.0000.0000.000
43A53VAL0-0.014-0.0019.8591.8591.8590.0000.0000.0000.000
44A54THR0-0.056-0.02610.8431.2091.2090.0000.0000.0000.000
45A55ASN0-0.033-0.01610.1991.8921.8920.0000.0000.0000.000
46A56LEU00.0510.00712.3321.2811.2810.0000.0000.0000.000
47A57MET00.0170.00314.8150.8700.8700.0000.0000.0000.000
48A58ARG10.9450.97615.12517.42117.4210.0000.0000.0000.000
49A59VAL0-0.085-0.03115.2760.6650.6650.0000.0000.0000.000
50A60ILE0-0.035-0.01517.9680.7900.7900.0000.0000.0000.000
51A61LEU0-0.042-0.01820.4670.8610.8610.0000.0000.0000.000
52A62GLY00.0230.01520.565-0.505-0.5050.0000.0000.0000.000
53A63PRO00.0540.00720.0780.0510.0510.0000.0000.0000.000
54A64ALA00.0220.02221.114-0.074-0.0740.0000.0000.0000.000
55A65PRO00.0040.00123.743-0.013-0.0130.0000.0000.0000.000
56A66TYR0-0.011-0.00514.402-0.348-0.3480.0000.0000.0000.000
57A67ALA00.0360.01319.902-0.426-0.4260.0000.0000.0000.000
58A68LEU00.0310.01821.326-0.022-0.0220.0000.0000.0000.000
59A69TRP0-0.070-0.03715.523-0.115-0.1150.0000.0000.0000.000
60A70MET00.016-0.00714.237-0.254-0.2540.0000.0000.0000.000
61A71ASP-1-0.944-0.94019.436-11.623-11.6230.0000.0000.0000.000
62A72ALA00.0500.01722.8360.0140.0140.0000.0000.0000.000
63A73TRP0-0.028-0.02112.986-0.194-0.1940.0000.0000.0000.000
64A74GLY00.0480.02720.205-0.264-0.2640.0000.0000.0000.000
65A75VAL0-0.0150.00721.0260.1220.1220.0000.0000.0000.000
66A76GLN0-0.010-0.00922.4430.0500.0500.0000.0000.0000.000
67A77LEU00.000-0.00416.5500.0880.0880.0000.0000.0000.000
68A78GLN0-0.035-0.04321.2110.3970.3970.0000.0000.0000.000
69A79THR0-0.016-0.00124.1060.4640.4640.0000.0000.0000.000
70A80VAL0-0.0130.00221.4070.3290.3290.0000.0000.0000.000
71A81ILE0-0.0010.00420.6050.2290.2290.0000.0000.0000.000
72A82ALA00.0260.01924.5780.3850.3850.0000.0000.0000.000
73A83ALA0-0.033-0.02127.4300.4090.4090.0000.0000.0000.000
74A84ALA0-0.012-0.01225.5140.3020.3020.0000.0000.0000.000
75A85THR0-0.076-0.05027.2160.0900.0900.0000.0000.0000.000
76A86ARG10.8870.95329.3439.5769.5760.0000.0000.0000.000
77A87ASP-1-0.839-0.91731.095-9.266-9.2660.0000.0000.0000.000
78A88PRO0-0.039-0.02030.046-0.409-0.4090.0000.0000.0000.000
79A89ARG10.8700.91529.3979.1869.1860.0000.0000.0000.000
80A90HIS00.0550.04024.614-0.501-0.5010.0000.0000.0000.000
81A91PRO00.0170.01122.185-0.188-0.1880.0000.0000.0000.000
82A92ALA00.0500.01820.338-0.671-0.6710.0000.0000.0000.000
83A93ASN0-0.0160.00020.804-0.600-0.6000.0000.0000.0000.000
84A94GLY00.0500.03420.406-0.075-0.0750.0000.0000.0000.000
85A95GLN00.030-0.00121.465-0.434-0.4340.0000.0000.0000.000
86A96GLY00.0180.00224.5450.4750.4750.0000.0000.0000.000
87A97ARG10.9580.96126.7988.9958.9950.0000.0000.0000.000
88A98GLY0-0.033-0.00128.4490.1390.1390.0000.0000.0000.000
89A99GLU-1-0.860-0.91120.745-14.795-14.7950.0000.0000.0000.000
90A100ARG10.8770.95023.97210.87910.8790.0000.0000.0000.000
91A101THR00.0470.02720.508-0.581-0.5810.0000.0000.0000.000
92A102ASN0-0.003-0.03119.1340.3300.3300.0000.0000.0000.000
93A103LEU00.0340.01618.546-0.748-0.7480.0000.0000.0000.000
94A104ASP-1-0.840-0.92415.427-17.512-17.5120.0000.0000.0000.000
95A105ARG10.7970.89414.01115.42015.4200.0000.0000.0000.000
96A106LEU00.0310.01413.843-1.231-1.2310.0000.0000.0000.000
97A107LYS10.9470.97912.78115.81415.8140.0000.0000.0000.000
98A108GLY0-0.001-0.0069.647-1.778-1.7780.0000.0000.0000.000
99A109LEU0-0.048-0.0379.247-1.990-1.9900.0000.0000.0000.000
100A110ALA00.0010.00711.5640.8630.8630.0000.0000.0000.000
101A111ASP-1-0.861-0.94211.168-20.907-20.9070.0000.0000.0000.000
102A112GLY0-0.016-0.00610.0050.6380.6380.0000.0000.0000.000
103A113MET0-0.075-0.0208.578-2.268-2.2680.0000.0000.0000.000
104A114VAL00.0520.0396.657-4.559-4.5590.0000.0000.0000.000
110A120GLN00.0220.0057.3025.1065.1060.0000.0000.0000.000
111A121ALA0-0.009-0.0098.1402.9692.9690.0000.0000.0000.000
112A122ALA0-0.0310.0009.7622.0982.0980.0000.0000.0000.000
113A123LEU0-0.043-0.01711.5522.0012.0010.0000.0000.0000.000
114A124LEU0-0.053-0.02311.7281.7781.7780.0000.0000.0000.000
115A125ARG10.8740.95514.58314.11614.1160.0000.0000.0000.000
116A126PRO00.0320.00116.680-0.186-0.1860.0000.0000.0000.000
117A127GLY00.017-0.00617.4441.1611.1610.0000.0000.0000.000
118A128GLU-1-0.850-0.93414.540-19.774-19.7740.0000.0000.0000.000
119A129LEU00.0860.04711.5300.4450.4450.0000.0000.0000.000
120A130VAL0-0.0030.01815.2460.0130.0130.0000.0000.0000.000
121A131ALA0-0.0040.00718.4180.5870.5870.0000.0000.0000.000
122A132ILE00.0080.00713.6960.5760.5760.0000.0000.0000.000
123A133THR00.015-0.00315.9970.1430.1430.0000.0000.0000.000
124A134ALA00.0310.00717.8020.5270.5270.0000.0000.0000.000
125A135SER0-0.073-0.04819.1540.4610.4610.0000.0000.0000.000
126A136ALA00.0320.00817.6770.4800.4800.0000.0000.0000.000
127A137LEU00.0840.03419.7600.4260.4260.0000.0000.0000.000
128A138GLN0-0.062-0.03622.7240.8970.8970.0000.0000.0000.000
129A139ALA00.0300.02021.5380.4320.4320.0000.0000.0000.000
130A140PHE0-0.007-0.00221.4260.3390.3390.0000.0000.0000.000
131A141ARG10.9080.94523.89410.79310.7930.0000.0000.0000.000
132A142GLU-1-0.901-0.94126.658-9.639-9.6390.0000.0000.0000.000
133A143VAL0-0.013-0.00123.7880.3500.3500.0000.0000.0000.000
134A144ALA0-0.042-0.01326.8700.2350.2350.0000.0000.0000.000
135A145ARG10.8730.94328.9029.8379.8370.0000.0000.0000.000
136A146LEU00.0600.03529.5200.3510.3510.0000.0000.0000.000
137A147ALA0-0.015-0.01930.472-0.084-0.0840.0000.0000.0000.000
138A148GLU-1-0.897-0.93829.871-9.118-9.1180.0000.0000.0000.000
139A149PRO0-0.062-0.02528.614-0.400-0.4000.0000.0000.0000.000
140A150ALA00.0480.03726.4270.1120.1120.0000.0000.0000.000
141A151GLY00.023-0.01224.362-0.264-0.2640.0000.0000.0000.000
142A152PRO0-0.017-0.00519.5890.1260.1260.0000.0000.0000.000
143A153TRP00.055-0.01119.573-0.287-0.2870.0000.0000.0000.000
144A154ALA0-0.045-0.01323.0750.3100.3100.0000.0000.0000.000
145A155ASP-1-0.847-0.92425.592-10.309-10.3090.0000.0000.0000.000
146A156ILE0-0.114-0.03921.5380.1320.1320.0000.0000.0000.000
147A157THR00.0230.00126.0030.1790.1790.0000.0000.0000.000
148A158GLN0-0.034-0.01829.203-0.218-0.2180.0000.0000.0000.000
149A159GLY00.0340.01830.2130.3270.3270.0000.0000.0000.000
150A160PRO0-0.064-0.05532.725-0.073-0.0730.0000.0000.0000.000
151A161SER00.0020.00733.6910.1740.1740.0000.0000.0000.000
152A162GLU-1-0.872-0.93028.496-9.551-9.5510.0000.0000.0000.000
153A163SER00.0310.01727.9520.2120.2120.0000.0000.0000.000
154A164PHE00.0410.01927.675-0.353-0.3530.0000.0000.0000.000
155A165VAL00.0350.00823.691-0.312-0.3120.0000.0000.0000.000
156A166ASP-1-0.936-0.95523.406-12.132-12.1320.0000.0000.0000.000
157A167PHE00.0420.01322.902-0.590-0.5900.0000.0000.0000.000
158A168ALA0-0.0020.00123.312-0.387-0.3870.0000.0000.0000.000
159A169ASN0-0.004-0.00619.294-0.797-0.7970.0000.0000.0000.000
160A170ARG10.9110.96118.47111.52511.5250.0000.0000.0000.000
161A171LEU00.0080.01319.424-0.538-0.5380.0000.0000.0000.000
162A172ILE0-0.012-0.00516.198-0.331-0.3310.0000.0000.0000.000
163A173LYS10.9500.97812.07818.53718.5370.0000.0000.0000.000
164A174ALA0-0.0010.00414.952-0.956-0.9560.0000.0000.0000.000
165A175VAL0-0.029-0.01316.577-0.338-0.3380.0000.0000.0000.000
166A176GLU-1-0.963-0.98812.127-19.420-19.4200.0000.0000.0000.000
167A177GLY0-0.041-0.00611.951-1.517-1.5170.0000.0000.0000.000
168A178SER0-0.056-0.03613.1330.8400.8400.0000.0000.0000.000
169A179ASP-1-0.894-0.95514.618-16.071-16.0710.0000.0000.0000.000
170A180LEU00.0010.00316.1320.9720.9720.0000.0000.0000.000
171A181PRO00.005-0.00216.212-0.966-0.9660.0000.0000.0000.000
172A182PRO0-0.027-0.02215.3210.0210.0210.0000.0000.0000.000
173A183SER0-0.048-0.03417.2300.4490.4490.0000.0000.0000.000
174A184ALA00.0810.03020.6810.2510.2510.0000.0000.0000.000
175A185ARG10.9640.99914.25919.02619.0260.0000.0000.0000.000
176A186ALA00.006-0.01318.617-0.427-0.4270.0000.0000.0000.000
177A187PRO00.0090.01421.4370.3460.3460.0000.0000.0000.000
178A188VAL00.0450.02222.1910.4320.4320.0000.0000.0000.000
179A189ILE00.0210.01918.9130.2630.2630.0000.0000.0000.000
180A190ILE0-0.017-0.00623.5550.4390.4390.0000.0000.0000.000
181A191ASP-1-0.925-0.96126.695-9.651-9.6510.0000.0000.0000.000
182A192CYS00.0150.00225.7320.3210.3210.0000.0000.0000.000
183A193PHE0-0.024-0.01124.1920.2800.2800.0000.0000.0000.000
184A194ARG10.9110.96929.6299.8629.8620.0000.0000.0000.000
185A195GLN0-0.057-0.00928.9240.4130.4130.0000.0000.0000.000
186A196LYS10.9310.96632.5038.9068.9060.0000.0000.0000.000
187A197SER0-0.047-0.02331.5080.0820.0820.0000.0000.0000.000
188A198GLN00.0320.00733.4170.0510.0510.0000.0000.0000.000
189A199PRO00.0220.00036.498-0.126-0.1260.0000.0000.0000.000
190A200ASP-1-0.914-0.94537.920-7.747-7.7470.0000.0000.0000.000
191A201ILE00.0750.03031.751-0.039-0.0390.0000.0000.0000.000
192A202GLN00.0450.04534.314-0.129-0.1290.0000.0000.0000.000
193A203GLN0-0.008-0.02235.456-0.123-0.1230.0000.0000.0000.000
194A204LEU0-0.0460.00034.0540.0400.0400.0000.0000.0000.000
195A205ILE00.005-0.00730.340-0.095-0.0950.0000.0000.0000.000
196A206ARG10.8360.90533.4058.0358.0350.0000.0000.0000.000
197A207ALA0-0.0170.00436.4120.1150.1150.0000.0000.0000.000
198A208ALA0-0.0140.00832.3450.0180.0180.0000.0000.0000.000
199A209PRO0-0.0070.01032.8870.0940.0940.0000.0000.0000.000
200A210SER00.014-0.01832.670-0.258-0.2580.0000.0000.0000.000
201A211THR0-0.042-0.01931.165-0.026-0.0260.0000.0000.0000.000
202A212LEU0-0.0120.00527.921-0.234-0.2340.0000.0000.0000.000
203A213THR0-0.016-0.01826.6820.1370.1370.0000.0000.0000.000
204A214THR00.033-0.01021.724-0.277-0.2770.0000.0000.0000.000
205A215PRO00.0050.00319.4180.4980.4980.0000.0000.0000.000
206A216GLY00.0320.00221.083-0.440-0.4400.0000.0000.0000.000
207A217GLU-1-0.883-0.91222.683-11.435-11.4350.0000.0000.0000.000
208A218ILE00.0020.01025.9950.4000.4000.0000.0000.0000.000
209A219ILE00.0170.00722.9050.3680.3680.0000.0000.0000.000
210A220LYS10.9830.98925.85810.81810.8180.0000.0000.0000.000
211A221TYR0-0.017-0.01927.8520.3430.3430.0000.0000.0000.000
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