FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2026-04-18

All entries: 88827

Number of unique PDB entries: 32070

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FMODB ID: 3Z2LL

Calculation Name: 1DOA-B-Xray547

Preferred Name: Cell division control protein 42 homolog

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-diphosphate | geran-8-yl geran | o-methylcysteine | magnesium ion

Ligand 3-letter code: GDP | GER | CMT | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1DOA

Chain ID: B

ChEMBL ID: CHEMBL6088

UniProt ID: P60953

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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2155016.944643
FMO2-HF: Nuclear repulsion 2074674.304567
FMO2-HF: Total energy -80342.640076
FMO2-MP2: Total energy -80577.77844


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:5:GLU)


Summations of interaction energy for fragment #1(A:5:GLU)
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.
-16.839-10.2411.986-3.528-5.0560.02
Interaction energy analysis for fragmet #1(A:5:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.094 / q_NPA : -0.063
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].
3A7THR00.0230.0082.244-2.0630.8650.727-1.573-2.082-0.005
4A8ALA00.0780.0652.580-2.8090.5201.174-1.767-2.7360.021
5A9GLU-1-0.875-0.9513.5940.3550.6960.085-0.188-0.2380.004
6A10GLN0-0.044-0.0246.3680.2920.2920.0000.0000.0000.000
7A11LEU0-0.014-0.0078.026-1.461-1.4610.0000.0000.0000.000
8A12ALA00.0800.03510.520-0.895-0.8950.0000.0000.0000.000
9A13GLN0-0.047-0.01611.4650.1580.1580.0000.0000.0000.000
10A14ILE0-0.045-0.0299.799-0.422-0.4220.0000.0000.0000.000
11A15ALA00.0390.05213.660-0.397-0.3970.0000.0000.0000.000
12A16ALA0-0.094-0.05416.963-0.050-0.0500.0000.0000.0000.000
13A17GLU-1-0.896-0.95018.5160.8480.8480.0000.0000.0000.000
14A18ASN0-0.052-0.03920.283-0.046-0.0460.0000.0000.0000.000
15A19GLU-1-0.921-0.96822.1780.8740.8740.0000.0000.0000.000
16A20GLU-1-0.867-0.93125.6390.9200.9200.0000.0000.0000.000
17A21ASP-1-0.960-0.98026.4120.5450.5450.0000.0000.0000.000
18A22GLU-1-0.946-0.95729.4220.5550.5550.0000.0000.0000.000
19A23HIS0-0.097-0.05130.923-0.105-0.1050.0000.0000.0000.000
20A24SER0-0.052-0.02334.589-0.057-0.0570.0000.0000.0000.000
21A25VAL0-0.044-0.02837.7350.0180.0180.0000.0000.0000.000
22A26ASN00.0040.00137.095-0.027-0.0270.0000.0000.0000.000
23A27TYR0-0.034-0.02040.478-0.014-0.0140.0000.0000.0000.000
24A28LYS10.9170.95842.285-0.286-0.2860.0000.0000.0000.000
25A29PRO00.0430.02842.033-0.016-0.0160.0000.0000.0000.000
26A30PRO0-0.0190.01044.532-0.003-0.0030.0000.0000.0000.000
27A31ALA0-0.028-0.02547.8820.0110.0110.0000.0000.0000.000
28A32GLN0-0.058-0.03946.714-0.021-0.0210.0000.0000.0000.000
29A33LYS10.8860.96950.254-0.147-0.1470.0000.0000.0000.000
30A34SER0-0.001-0.02652.170-0.005-0.0050.0000.0000.0000.000
31A35ILE0-0.007-0.03051.861-0.007-0.0070.0000.0000.0000.000
32A36GLN0-0.047-0.01955.485-0.010-0.0100.0000.0000.0000.000
33A37GLU-1-0.778-0.87056.4880.1440.1440.0000.0000.0000.000
34A38ILE0-0.026-0.01454.562-0.004-0.0040.0000.0000.0000.000
35A39GLN0-0.046-0.02658.064-0.010-0.0100.0000.0000.0000.000
36A40GLU-1-1.013-1.00860.8780.0930.0930.0000.0000.0000.000
37A41LEU0-0.080-0.03058.2250.0010.0010.0000.0000.0000.000
38A42ASP-1-0.862-0.92562.3260.0870.0870.0000.0000.0000.000
39A43LYS10.9160.96564.876-0.057-0.0570.0000.0000.0000.000
40A44ASP-1-0.902-0.95966.9080.0560.0560.0000.0000.0000.000
41A45ASP-1-0.779-0.89165.3920.0370.0370.0000.0000.0000.000
42A46GLU-1-0.885-0.95365.7670.0090.0090.0000.0000.0000.000
43A47SER0-0.035-0.00863.755-0.007-0.0070.0000.0000.0000.000
44A48LEU00.0430.00759.596-0.004-0.0040.0000.0000.0000.000
45A49ARG10.8470.92661.000-0.031-0.0310.0000.0000.0000.000
46A50LYS10.8500.92061.527-0.004-0.0040.0000.0000.0000.000
47A51TYR0-0.0030.00154.040-0.007-0.0070.0000.0000.0000.000
48A52LYS10.9160.96156.997-0.072-0.0720.0000.0000.0000.000
49A53GLU-1-0.883-0.92457.076-0.002-0.0020.0000.0000.0000.000
50A54ALA0-0.050-0.03056.380-0.005-0.0050.0000.0000.0000.000
51A55LEU0-0.038-0.01051.428-0.006-0.0060.0000.0000.0000.000
52A56LEU0-0.023-0.01052.2960.0040.0040.0000.0000.0000.000
53A57GLY00.0080.03154.387-0.002-0.0020.0000.0000.0000.000
54A58ARG10.8390.87856.1940.0090.0090.0000.0000.0000.000
55A59VAL0-0.047-0.02758.530-0.007-0.0070.0000.0000.0000.000
56A60ALA0-0.014-0.00155.2600.0010.0010.0000.0000.0000.000
57A61VAL00.0630.04553.8700.0010.0010.0000.0000.0000.000
58A62SER0-0.014-0.01551.8710.0020.0020.0000.0000.0000.000
59A63ALA0-0.029-0.01651.4690.0060.0060.0000.0000.0000.000
60A64ASP-1-0.847-0.92351.5880.1180.1180.0000.0000.0000.000
61A65PRO0-0.035-0.02351.5890.0080.0080.0000.0000.0000.000
62A66ASN0-0.012-0.01848.3950.0210.0210.0000.0000.0000.000
63A67VAL00.0060.02446.3160.0040.0040.0000.0000.0000.000
64A68PRO00.0580.03743.1290.0020.0020.0000.0000.0000.000
65A69ASN00.0340.01845.689-0.029-0.0290.0000.0000.0000.000
66A70VAL00.0340.02240.187-0.019-0.0190.0000.0000.0000.000
67A71VAL0-0.009-0.00840.9440.0140.0140.0000.0000.0000.000
68A72VAL00.0220.00334.984-0.024-0.0240.0000.0000.0000.000
69A73THR0-0.044-0.01137.9010.0040.0040.0000.0000.0000.000
70A74ARG10.7990.87034.3530.1860.1860.0000.0000.0000.000
71A75LEU00.0070.02228.0240.0110.0110.0000.0000.0000.000
72A76THR0-0.021-0.03531.156-0.014-0.0140.0000.0000.0000.000
73A77LEU0-0.024-0.00425.0430.0110.0110.0000.0000.0000.000
74A78VAL0-0.032-0.01529.168-0.040-0.0400.0000.0000.0000.000
75A79CYS00.004-0.00926.512-0.052-0.0520.0000.0000.0000.000
76A80SER0-0.0040.00129.005-0.024-0.0240.0000.0000.0000.000
77A81THR0-0.024-0.02624.826-0.048-0.0480.0000.0000.0000.000
78A82ALA00.0210.01525.946-0.110-0.1100.0000.0000.0000.000
79A83PRO0-0.038-0.02125.6790.0720.0720.0000.0000.0000.000
80A84GLY0-0.024-0.00327.8240.0560.0560.0000.0000.0000.000
81A85PRO00.005-0.00628.693-0.021-0.0210.0000.0000.0000.000
82A86LEU0-0.021-0.00124.075-0.018-0.0180.0000.0000.0000.000
83A87GLU-1-0.826-0.90028.628-0.244-0.2440.0000.0000.0000.000
84A88LEU0-0.018-0.00226.555-0.005-0.0050.0000.0000.0000.000
85A89ASP-1-0.795-0.88730.727-0.126-0.1260.0000.0000.0000.000
86A90LEU0-0.054-0.02830.8640.0270.0270.0000.0000.0000.000
87A91THR0-0.025-0.01834.5790.0230.0230.0000.0000.0000.000
88A92GLY0-0.0090.00137.370-0.024-0.0240.0000.0000.0000.000
89A93ASP-1-0.929-0.97333.9400.0770.0770.0000.0000.0000.000
90A94LEU00.0660.03031.139-0.023-0.0230.0000.0000.0000.000
91A95GLU-1-0.856-0.92729.3950.4240.4240.0000.0000.0000.000
92A96SER0-0.035-0.00428.2530.0080.0080.0000.0000.0000.000
93A97PHE00.0340.01126.370-0.043-0.0430.0000.0000.0000.000
94A98LYS10.8230.90923.980-0.499-0.4990.0000.0000.0000.000
95A99LYS10.8740.93323.0650.0100.0100.0000.0000.0000.000
96A100GLN00.0170.01723.714-0.124-0.1240.0000.0000.0000.000
97A101SER0-0.026-0.02119.9790.0680.0680.0000.0000.0000.000
98A102PHE00.0170.02021.072-0.174-0.1740.0000.0000.0000.000
99A103VAL0-0.028-0.01518.233-0.041-0.0410.0000.0000.0000.000
100A104LEU00.0480.02118.8600.0930.0930.0000.0000.0000.000
101A105LYS10.8680.95718.0751.9211.9210.0000.0000.0000.000
102A106GLU-1-0.750-0.87213.106-4.453-4.4530.0000.0000.0000.000
103A107GLY0-0.058-0.03617.026-0.057-0.0570.0000.0000.0000.000
104A108VAL0-0.053-0.01119.2080.0940.0940.0000.0000.0000.000
105A109GLU-1-0.861-0.92822.540-0.720-0.7200.0000.0000.0000.000
106A110TYR0-0.092-0.04922.494-0.073-0.0730.0000.0000.0000.000
107A111ARG10.9160.94327.1560.3380.3380.0000.0000.0000.000
108A112ILE00.0430.01726.336-0.043-0.0430.0000.0000.0000.000
109A113LYS10.8260.90230.1500.2700.2700.0000.0000.0000.000
110A114ILE00.0060.01132.1330.0080.0080.0000.0000.0000.000
111A115SER00.0340.01834.701-0.018-0.0180.0000.0000.0000.000
112A116PHE0-0.018-0.00337.7240.0240.0240.0000.0000.0000.000
113A117ARG10.9170.95940.0680.0060.0060.0000.0000.0000.000
114A118VAL00.0280.02543.5560.0190.0190.0000.0000.0000.000
115A119ASN0-0.073-0.04545.645-0.029-0.0290.0000.0000.0000.000
116A120ARG10.8280.89848.906-0.126-0.1260.0000.0000.0000.000
117A121GLU-1-0.774-0.90149.6050.1140.1140.0000.0000.0000.000
118A122ILE0-0.0070.00047.574-0.008-0.0080.0000.0000.0000.000
119A123VAL0-0.0100.00741.7970.0160.0160.0000.0000.0000.000
120A124SER0-0.027-0.04744.009-0.024-0.0240.0000.0000.0000.000
121A125GLY00.0400.01140.7410.0200.0200.0000.0000.0000.000
122A126MET0-0.041-0.01537.6000.0290.0290.0000.0000.0000.000
123A127LYS10.9720.97233.752-0.364-0.3640.0000.0000.0000.000
124A128TYR0-0.039-0.01626.1690.0270.0270.0000.0000.0000.000
125A129ILE0-0.011-0.00227.602-0.018-0.0180.0000.0000.0000.000
126A130GLN00.0220.01523.315-0.081-0.0810.0000.0000.0000.000
127A131HIS-1-0.857-0.91022.5210.9360.9360.0000.0000.0000.000
128A132THR0-0.038-0.03216.830-0.072-0.0720.0000.0000.0000.000
129A133TYR-1-0.853-0.93616.5221.7491.7490.0000.0000.0000.000
130A134ARG10.8150.8937.319-1.884-1.8840.0000.0000.0000.000
131A135LYS10.7790.8645.381-13.397-13.3970.0000.0000.0000.000
132A136GLY00.0210.01612.4030.2360.2360.0000.0000.0000.000
133A137VAL0-0.0170.00012.352-0.131-0.1310.0000.0000.0000.000
134A138LYS00.0030.00514.962-0.013-0.0130.0000.0000.0000.000
135A139ILE0-0.095-0.07112.7130.2940.2940.0000.0000.0000.000
136A140ASP-1-0.797-0.89016.1270.5620.5620.0000.0000.0000.000
137A141LYS10.9270.98519.469-1.006-1.0060.0000.0000.0000.000
138A142THR0-0.009-0.00123.287-0.083-0.0830.0000.0000.0000.000
139A143ASP-1-0.885-0.93925.7660.4810.4810.0000.0000.0000.000
140A144TYR0-0.064-0.06625.710-0.034-0.0340.0000.0000.0000.000
141A145MET0-0.055-0.01831.4810.0030.0030.0000.0000.0000.000
142A146VAL0-0.015-0.00635.197-0.036-0.0360.0000.0000.0000.000
143A147GLY00.0100.01237.313-0.029-0.0290.0000.0000.0000.000
144A148SER0-0.015-0.01340.6670.0190.0190.0000.0000.0000.000
145A149TYR0-0.051-0.02440.460-0.029-0.0290.0000.0000.0000.000
146A150GLY00.0630.03345.7510.0170.0170.0000.0000.0000.000
147A151PRO0-0.0130.00048.020-0.011-0.0110.0000.0000.0000.000
148A152ARG10.8320.92046.2170.0390.0390.0000.0000.0000.000
149A153ALA00.0170.01149.0840.0020.0020.0000.0000.0000.000
150A154GLU-1-0.928-0.96447.112-0.093-0.0930.0000.0000.0000.000
151A155GLU-1-0.928-0.96042.125-0.082-0.0820.0000.0000.0000.000
152A156TYR0-0.032-0.03042.042-0.016-0.0160.0000.0000.0000.000
153A157GLU-1-0.822-0.89738.871-0.201-0.2010.0000.0000.0000.000
154A158PHE00.0070.00234.238-0.008-0.0080.0000.0000.0000.000
155A159LEU0-0.039-0.02334.432-0.017-0.0170.0000.0000.0000.000
156A160THR00.0660.04730.0780.0060.0060.0000.0000.0000.000
157A161PRO00.006-0.00330.553-0.053-0.0530.0000.0000.0000.000
158A162MET0-0.057-0.01028.3000.0030.0030.0000.0000.0000.000
159A163GLU-1-0.801-0.86724.459-0.065-0.0650.0000.0000.0000.000
160A164GLU-1-0.929-0.96721.648-0.995-0.9950.0000.0000.0000.000
161A165ALA0-0.010-0.00119.3530.0800.0800.0000.0000.0000.000
162A166PRO00.0420.01615.141-0.250-0.2500.0000.0000.0000.000
163A167LYS10.9770.97513.7151.7651.7650.0000.0000.0000.000
164A168GLY00.0040.00011.3400.1020.1020.0000.0000.0000.000
165A169MET0-0.083-0.0678.750-1.436-1.4360.0000.0000.0000.000
166A170LEU00.0160.0165.427-3.336-3.3360.0000.0000.0000.000
167A171ALA00.0400.0297.444-0.451-0.4510.0000.0000.0000.000
168A172ARG10.7990.8938.7767.4977.4970.0000.0000.0000.000
169A173GLY0-0.034-0.0129.920-0.261-0.2610.0000.0000.0000.000
170A174SER0-0.011-0.02310.590-0.185-0.1850.0000.0000.0000.000
171A175TYR0-0.044-0.03912.2360.7710.7710.0000.0000.0000.000
172A176ASN0-0.059-0.02815.221-0.126-0.1260.0000.0000.0000.000
173A177ILE00.0360.01618.3100.1190.1190.0000.0000.0000.000
174A178LYS10.8610.94021.165-1.034-1.0340.0000.0000.0000.000
175A179SER00.0530.03124.319-0.001-0.0010.0000.0000.0000.000
176A180ARG10.8780.92927.359-0.529-0.5290.0000.0000.0000.000
177A181PHE00.0090.01230.995-0.022-0.0220.0000.0000.0000.000
178A182THR0-0.035-0.03934.0910.0240.0240.0000.0000.0000.000
179A183ASP-1-0.743-0.87136.4150.2390.2390.0000.0000.0000.000
180A184ASP-1-0.833-0.91038.8610.2750.2750.0000.0000.0000.000
181A185ASP-1-0.894-0.92841.0290.2640.2640.0000.0000.0000.000
182A186ARG10.8510.92237.369-0.450-0.4500.0000.0000.0000.000
183A187THR0-0.0130.00038.7430.0260.0260.0000.0000.0000.000
184A188ASP-1-0.861-0.91334.1360.4350.4350.0000.0000.0000.000
185A189HIS0-0.081-0.05937.266-0.021-0.0210.0000.0000.0000.000
186A190LEU0-0.028-0.01433.400-0.024-0.0240.0000.0000.0000.000
187A191SER00.0200.02030.5620.0150.0150.0000.0000.0000.000
188A192TRP00.000-0.00827.436-0.010-0.0100.0000.0000.0000.000
189A193GLU-1-0.856-0.92323.6120.7090.7090.0000.0000.0000.000
190A194TRP0-0.037-0.02723.184-0.136-0.1360.0000.0000.0000.000
191A195ASN0-0.0030.01318.7950.2550.2550.0000.0000.0000.000
192A196LEU00.0400.03618.349-0.170-0.1700.0000.0000.0000.000
193A197THR0-0.052-0.03013.9630.1290.1290.0000.0000.0000.000
194A198ILE00.0300.03713.607-0.132-0.1320.0000.0000.0000.000
195A199LYS10.8570.90313.7981.9841.9840.0000.0000.0000.000
196A200LYS10.9720.97812.4914.8034.8030.0000.0000.0000.000
197A201GLU-1-0.919-0.96014.615-2.139-2.1390.0000.0000.0000.000
198A202TRP00.023-0.00318.1020.0260.0260.0000.0000.0000.000
199A203LYS10.8850.94220.8721.1601.1600.0000.0000.0000.000
200A204ASP-2-1.774-1.85515.634-5.270-5.2700.0000.0000.0000.000