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: N88YQ

Calculation Name: 4DA0-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 2'-deoxy-guanosine

Ligand 3-letter code: GNG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4DA0

Chain ID: A

ChEMBL ID:

UniProt ID: O34925

Base Structure: X-ray

Registration Date: 2025-10-04

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 230
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2769865.450753
FMO2-HF: Nuclear repulsion 2681341.392071
FMO2-HF: Total energy -88524.058683
FMO2-MP2: Total energy -88779.94257


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:2:SER)


Summations of interaction energy for fragment #1(A:2: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.
-229.42-230.74839.383-20.288-17.767-0.117
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.781 / q_NPA : 0.862
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].
3A4HIS0-0.020-0.0373.03813.45015.4950.004-1.019-1.030-0.002
4A5ILE0-0.0090.0032.3088.14110.4161.719-1.597-2.3970.008
5A6GLY0-0.011-0.0091.942-33.757-32.7675.239-3.479-2.750-0.050
6A7ALA00.0210.0253.3769.0529.3320.000-0.061-0.2190.000
7A8GLU-1-0.897-0.9544.360-45.116-45.003-0.001-0.017-0.0950.000
74A75GLU-1-0.784-0.8561.578-96.740-106.05524.047-9.683-5.048-0.070
75A76LEU00.0100.0014.354-1.954-1.703-0.001-0.017-0.2330.000
78A79SER0-0.103-0.0512.497-7.658-6.5911.631-1.054-1.645-0.006
79A80TYR0-0.076-0.0452.054-15.466-14.5006.745-3.361-4.3500.003
8A9LYS10.9190.9516.82127.13227.1320.0000.0000.0000.000
9A10GLY00.0180.0027.5123.3623.3620.0000.0000.0000.000
10A11GLN0-0.0010.0128.750-0.552-0.5520.0000.0000.0000.000
11A12ILE0-0.042-0.0045.9871.1011.1010.0000.0000.0000.000
12A13ALA00.0140.00410.3310.3970.3970.0000.0000.0000.000
13A14ASP-1-0.876-0.94012.441-19.852-19.8520.0000.0000.0000.000
14A15THR0-0.025-0.01014.4260.6880.6880.0000.0000.0000.000
15A16VAL0-0.002-0.00110.504-0.201-0.2010.0000.0000.0000.000
16A17LEU00.0080.00813.8470.7560.7560.0000.0000.0000.000
17A18LEU0-0.005-0.01911.034-1.192-1.1920.0000.0000.0000.000
18A19PRO00.0190.02614.6250.9750.9750.0000.0000.0000.000
19A20GLY00.0380.01114.941-0.975-0.9750.0000.0000.0000.000
20A21ASP-1-0.850-0.93015.456-16.049-16.0490.0000.0000.0000.000
21A22PRO00.0390.01213.5030.0210.0210.0000.0000.0000.000
22A23LEU0-0.011-0.00915.419-0.036-0.0360.0000.0000.0000.000
23A24ARG10.9260.96418.98912.97812.9780.0000.0000.0000.000
24A25ALA00.0170.00814.5080.2910.2910.0000.0000.0000.000
25A26LYS10.8720.92116.60614.98614.9860.0000.0000.0000.000
26A27PHE0-0.018-0.00118.3410.3770.3770.0000.0000.0000.000
27A28ILE00.006-0.00318.5420.4920.4920.0000.0000.0000.000
28A29ALA00.0090.00517.3170.3080.3080.0000.0000.0000.000
29A30GLU-1-0.848-0.92919.439-13.857-13.8570.0000.0000.0000.000
30A31THR0-0.078-0.03422.5330.6830.6830.0000.0000.0000.000
31A32TYR0-0.042-0.03922.7210.4250.4250.0000.0000.0000.000
32A33LEU0-0.078-0.02418.056-0.009-0.0090.0000.0000.0000.000
33A34GLU-1-0.887-0.93422.158-11.655-11.6550.0000.0000.0000.000
34A35ASN0-0.108-0.07321.226-0.503-0.5030.0000.0000.0000.000
35A36VAL00.0320.02617.805-0.775-0.7750.0000.0000.0000.000
36A37GLU-1-0.861-0.91214.169-19.715-19.7150.0000.0000.0000.000
37A38CYS0-0.032-0.02513.309-0.547-0.5470.0000.0000.0000.000
38A39TYR0-0.043-0.0197.365-0.134-0.1340.0000.0000.0000.000
39A40ASN00.0030.0006.852-7.413-7.4130.0000.0000.0000.000
40A41GLU-1-0.856-0.9428.773-18.507-18.5070.0000.0000.0000.000
41A42VAL0-0.0190.0026.4462.5972.5970.0000.0000.0000.000
42A43ARG10.8600.9268.85628.98028.9800.0000.0000.0000.000
43A44GLY00.0410.03411.9731.4991.4990.0000.0000.0000.000
44A45MET0-0.059-0.0119.3312.1362.1360.0000.0000.0000.000
45A46TYR0-0.014-0.0129.805-2.158-2.1580.0000.0000.0000.000
46A47GLY00.0130.0159.7300.3180.3180.0000.0000.0000.000
47A48PHE00.006-0.00410.786-0.142-0.1420.0000.0000.0000.000
48A49THR0-0.002-0.02312.208-0.657-0.6570.0000.0000.0000.000
49A50GLY00.0860.06614.6920.5470.5470.0000.0000.0000.000
50A51THR0-0.068-0.03618.434-0.118-0.1180.0000.0000.0000.000
51A52TYR00.0710.02021.2720.4280.4280.0000.0000.0000.000
52A53LYS10.8950.94023.71610.47410.4740.0000.0000.0000.000
53A54GLY00.0200.02125.2600.2370.2370.0000.0000.0000.000
54A55LYS10.8470.92521.47812.64312.6430.0000.0000.0000.000
55A56LYS10.8630.91315.64718.55818.5580.0000.0000.0000.000
56A57ILE0-0.0080.00316.959-0.013-0.0130.0000.0000.0000.000
57A58SER00.0350.00311.953-0.356-0.3560.0000.0000.0000.000
58A59VAL0-0.0250.00013.4030.8610.8610.0000.0000.0000.000
59A60GLN0-0.052-0.0348.088-3.047-3.0470.0000.0000.0000.000
60A61GLY00.0370.02811.3331.1771.1770.0000.0000.0000.000
61A62THR00.005-0.01010.492-2.065-2.0650.0000.0000.0000.000
62A63GLY00.0200.02411.881-0.708-0.7080.0000.0000.0000.000
63A64MET0-0.023-0.01814.1870.6260.6260.0000.0000.0000.000
64A65GLY00.0410.02316.557-0.308-0.3080.0000.0000.0000.000
65A66VAL00.0500.01715.632-1.266-1.2660.0000.0000.0000.000
66A67PRO0-0.006-0.00414.320-1.209-1.2090.0000.0000.0000.000
67A68SER0-0.014-0.01011.911-1.833-1.8330.0000.0000.0000.000
68A69ILE00.0140.00510.478-2.230-2.2300.0000.0000.0000.000
69A70SER0-0.013-0.03110.506-1.181-1.1810.0000.0000.0000.000
70A71ILE0-0.0390.0066.121-1.404-1.4040.0000.0000.0000.000
71A72TYR00.0250.0075.748-4.450-4.4500.0000.0000.0000.000
72A73VAL00.0350.0216.668-1.511-1.5110.0000.0000.0000.000
73A74ASN0-0.021-0.0247.6010.8230.8230.0000.0000.0000.000
76A77ILE0-0.0010.0056.4880.6580.6580.0000.0000.0000.000
77A78GLN0-0.021-0.0236.2752.8652.8650.0000.0000.0000.000
80A81ASP-1-0.836-0.8846.866-19.620-19.6200.0000.0000.0000.000
81A82VAL0-0.0180.0019.0752.1062.1060.0000.0000.0000.000
82A83GLN00.0290.02011.2970.5090.5090.0000.0000.0000.000
83A84ASN0-0.033-0.03014.9631.1241.1240.0000.0000.0000.000
84A85LEU0-0.024-0.01511.108-0.957-0.9570.0000.0000.0000.000
85A86ILE00.0360.01715.1340.7680.7680.0000.0000.0000.000
86A87ARG10.8270.91716.88114.38214.3820.0000.0000.0000.000
87A88VAL00.0200.00317.8770.7830.7830.0000.0000.0000.000
88A89GLY00.009-0.00419.954-0.399-0.3990.0000.0000.0000.000
89A90SER0-0.038-0.01821.3270.3900.3900.0000.0000.0000.000
90A91CYS0-0.030-0.00323.932-0.254-0.2540.0000.0000.0000.000
91A92GLY00.0620.05426.6210.2680.2680.0000.0000.0000.000
92A93ALA00.0140.00529.799-0.041-0.0410.0000.0000.0000.000
93A94ILE0-0.016-0.01931.9020.1690.1690.0000.0000.0000.000
94A95ARG10.8090.88934.6148.1168.1160.0000.0000.0000.000
95A96LYS10.9380.96437.0937.0117.0110.0000.0000.0000.000
96A97ASP-1-0.877-0.91838.598-7.721-7.7210.0000.0000.0000.000
97A98VAL00.0430.03633.0900.0220.0220.0000.0000.0000.000
98A99LYS10.8560.91536.3907.6747.6740.0000.0000.0000.000
99A100VAL00.0650.02834.576-0.261-0.2610.0000.0000.0000.000
100A101ARG10.9080.94933.7668.3288.3280.0000.0000.0000.000
101A102ASP-1-0.878-0.92533.305-8.594-8.5940.0000.0000.0000.000
102A103VAL0-0.0010.00027.745-0.273-0.2730.0000.0000.0000.000
103A104ILE0-0.019-0.01627.7950.2830.2830.0000.0000.0000.000
104A105LEU00.0100.00726.137-0.467-0.4670.0000.0000.0000.000
105A106ALA00.0160.00924.1540.3660.3660.0000.0000.0000.000
106A107MET00.0200.02025.198-0.316-0.3160.0000.0000.0000.000
107A108THR0-0.036-0.03525.394-0.193-0.1930.0000.0000.0000.000
108A109SER00.000-0.02223.1420.0250.0250.0000.0000.0000.000
109A110SER0-0.0230.00425.6410.0750.0750.0000.0000.0000.000
110A111THR0-0.047-0.05223.164-0.395-0.3950.0000.0000.0000.000
111A112ASP-1-0.821-0.90225.787-10.927-10.9270.0000.0000.0000.000
112A113SER0-0.0260.00220.825-0.149-0.1490.0000.0000.0000.000
113A114GLN0-0.030-0.02323.2010.4000.4000.0000.0000.0000.000
114A115MET0-0.003-0.00116.765-0.041-0.0410.0000.0000.0000.000
115A116ASN00.0440.01320.349-0.574-0.5740.0000.0000.0000.000
116A117ARG10.9160.95322.46310.60410.6040.0000.0000.0000.000
117A118VAL0-0.036-0.01220.3970.2980.2980.0000.0000.0000.000
118A119ALA0-0.037-0.00919.9000.0370.0370.0000.0000.0000.000
119A120PHE0-0.006-0.00821.8540.1380.1380.0000.0000.0000.000
120A121GLY00.0080.01125.3470.4670.4670.0000.0000.0000.000
121A122SER0-0.090-0.04627.8400.2520.2520.0000.0000.0000.000
122A123VAL0-0.011-0.01228.0100.3090.3090.0000.0000.0000.000
123A124ASP-1-0.848-0.91127.871-10.133-10.1330.0000.0000.0000.000
124A125PHE0-0.040-0.02622.0500.1180.1180.0000.0000.0000.000
125A126ALA00.0220.01325.472-0.289-0.2890.0000.0000.0000.000
126A127PRO0-0.024-0.00221.511-0.105-0.1050.0000.0000.0000.000
127A128CYS0-0.048-0.03022.9300.6630.6630.0000.0000.0000.000
128A129ALA00.0210.02722.220-0.576-0.5760.0000.0000.0000.000
129A130ASP-1-0.758-0.89021.659-12.459-12.4590.0000.0000.0000.000
130A131PHE0-0.015-0.01223.4230.2130.2130.0000.0000.0000.000
131A132GLU-1-0.889-0.93125.208-11.766-11.7660.0000.0000.0000.000
132A133LEU00.0130.01319.6060.1520.1520.0000.0000.0000.000
133A134LEU0-0.013-0.00524.2490.2470.2470.0000.0000.0000.000
134A135LYS10.9120.96226.4669.6179.6170.0000.0000.0000.000
135A136ASN0-0.016-0.00325.8180.6220.6220.0000.0000.0000.000
136A137ALA00.0360.02025.4740.1880.1880.0000.0000.0000.000
137A138TYR0-0.018-0.01827.5570.3350.3350.0000.0000.0000.000
138A139ASP-1-0.877-0.95830.989-8.960-8.9600.0000.0000.0000.000
139A140ALA00.0010.00429.1800.2430.2430.0000.0000.0000.000
140A141ALA0-0.030-0.01030.6670.1040.1040.0000.0000.0000.000
141A142LYS10.8260.91732.2418.7008.7000.0000.0000.0000.000
142A143ASP-1-0.903-0.94234.761-8.321-8.3210.0000.0000.0000.000
143A144LYS10.7990.89931.6529.7749.7740.0000.0000.0000.000
144A145GLY0-0.018-0.00835.8470.1090.1090.0000.0000.0000.000
145A146VAL0-0.030-0.00931.8450.1370.1370.0000.0000.0000.000
146A147PRO0-0.034-0.01034.7410.1040.1040.0000.0000.0000.000
147A148VAL00.0270.00530.697-0.252-0.2520.0000.0000.0000.000
148A149THR0-0.026-0.00432.3060.2160.2160.0000.0000.0000.000
149A150VAL00.0360.00830.089-0.321-0.3210.0000.0000.0000.000
150A151GLY00.0170.00130.2070.3590.3590.0000.0000.0000.000
151A152SER0-0.0150.00728.662-0.328-0.3280.0000.0000.0000.000
152A153VAL00.0270.01024.5660.2020.2020.0000.0000.0000.000
153A154PHE00.005-0.00927.179-0.038-0.0380.0000.0000.0000.000
154A155THR0-0.015-0.01320.487-0.160-0.1600.0000.0000.0000.000
155A156ALA00.0140.02423.7300.1100.1100.0000.0000.0000.000
156A157ASP-1-0.806-0.91821.251-14.211-14.2110.0000.0000.0000.000
157A158GLN0-0.122-0.06323.1700.1330.1330.0000.0000.0000.000
158A159PHE00.0120.00324.6840.2310.2310.0000.0000.0000.000
159A160TYR0-0.019-0.00726.5150.2380.2380.0000.0000.0000.000
160A161ASN0-0.020-0.02528.959-0.010-0.0100.0000.0000.0000.000
161A162ASP-1-0.851-0.92431.337-8.066-8.0660.0000.0000.0000.000
162A163ASP-1-0.911-0.93332.880-8.495-8.4950.0000.0000.0000.000
163A164SER00.017-0.00733.868-0.084-0.0840.0000.0000.0000.000
164A165GLN0-0.095-0.05729.6180.0650.0650.0000.0000.0000.000
165A166ILE00.008-0.01031.0540.0400.0400.0000.0000.0000.000
166A167GLU-1-0.865-0.92633.883-7.701-7.7010.0000.0000.0000.000
167A168LYS10.9020.95436.8628.0388.0380.0000.0000.0000.000
168A169LEU00.007-0.00730.9340.1310.1310.0000.0000.0000.000
169A170ALA00.0610.04335.0650.0190.0190.0000.0000.0000.000
170A171LYS10.8720.92836.6647.3197.3190.0000.0000.0000.000
171A172TYR0-0.065-0.03735.9470.2080.2080.0000.0000.0000.000
172A173GLY0-0.016-0.00336.218-0.109-0.1090.0000.0000.0000.000
173A174VAL0-0.051-0.00230.449-0.130-0.1300.0000.0000.0000.000
174A175LEU00.0240.01030.7910.1800.1800.0000.0000.0000.000
175A176GLY00.0630.01029.8060.1990.1990.0000.0000.0000.000
176A177VAL0-0.0290.00226.895-0.183-0.1830.0000.0000.0000.000
177A178GLU-1-0.721-0.82721.213-13.817-13.8170.0000.0000.0000.000
178A179MET0-0.0040.01220.5230.2200.2200.0000.0000.0000.000
179A180GLU-1-0.796-0.90316.395-15.766-15.7660.0000.0000.0000.000
180A181THR0-0.011-0.03417.453-0.649-0.6490.0000.0000.0000.000
181A182THR00.0500.01819.160-0.099-0.0990.0000.0000.0000.000
182A183ALA00.0080.01314.8380.0040.0040.0000.0000.0000.000
183A184LEU0-0.0190.00013.979-0.590-0.5900.0000.0000.0000.000
184A185TYR00.013-0.02315.651-0.467-0.4670.0000.0000.0000.000
185A186THR0-0.020-0.01417.9510.3550.3550.0000.0000.0000.000
186A187LEU0-0.081-0.03611.831-0.065-0.0650.0000.0000.0000.000
187A188ALA00.0300.01914.679-0.533-0.5330.0000.0000.0000.000
188A189ALA00.0270.02315.7350.1530.1530.0000.0000.0000.000
189A190LYS10.8850.95014.18818.74918.7490.0000.0000.0000.000
190A191HIS0-0.044-0.02711.0040.8420.8420.0000.0000.0000.000
191A192GLY0-0.0080.00715.114-0.389-0.3890.0000.0000.0000.000
192A193ARG10.7320.85411.94721.22921.2290.0000.0000.0000.000
193A194LYS10.8160.91316.64213.76313.7630.0000.0000.0000.000
194A195ALA00.0340.00116.864-0.836-0.8360.0000.0000.0000.000
195A196LEU00.0080.00418.5350.8600.8600.0000.0000.0000.000
196A197SER0-0.029-0.03019.358-0.836-0.8360.0000.0000.0000.000
197A198ILE00.0090.01121.2930.6800.6800.0000.0000.0000.000
198A199LEU0-0.034-0.01521.946-0.464-0.4640.0000.0000.0000.000
199A200THR00.0460.01525.0120.2690.2690.0000.0000.0000.000
200A201VAL00.0240.01627.628-0.198-0.1980.0000.0000.0000.000
201A202SER0-0.110-0.07727.217-0.055-0.0550.0000.0000.0000.000
202A203ASP-1-0.730-0.86429.279-8.632-8.6320.0000.0000.0000.000
203A204HIS0-0.069-0.02332.352-0.223-0.2230.0000.0000.0000.000
204A205VAL00.0140.01231.3030.1150.1150.0000.0000.0000.000
205A206LEU0-0.0140.00034.4730.1860.1860.0000.0000.0000.000
206A207THR0-0.008-0.00937.8090.1280.1280.0000.0000.0000.000
207A208GLY0-0.036-0.01138.8780.2200.2200.0000.0000.0000.000
208A209GLU-1-0.995-1.00339.454-7.072-7.0720.0000.0000.0000.000
209A210GLU-1-0.932-0.96036.973-8.168-8.1680.0000.0000.0000.000
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220A221HIS0-0.0210.00626.301-0.406-0.4060.0000.0000.0000.000
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226A227ALA0-0.006-0.00521.390-0.114-0.1140.0000.0000.0000.000
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229A230SER0-0.0070.00223.3570.3370.3370.0000.0000.0000.000
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