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: QKLNY

Calculation Name: 1AOE-A-Xray547

Preferred Name: Dihydrofolate reductase

Target Type: SINGLE PROTEIN

Ligand Name: nadph dihydro-nicotinamide-adenine-dinucleotide phosphate | 7-(1-ethyl-propyl)-7h-pyrrolo-[3,2-f]quinazoline-1,3-diamine

Ligand 3-letter code: NDP | GW3

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1AOE

Chain ID: A

ChEMBL ID: CHEMBL2329

UniProt ID: P22906

Base Structure: X-ray

Registration Date: 2025-09-02

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 192
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2248981.440901
FMO2-HF: Nuclear repulsion 2172204.761183
FMO2-HF: Total energy -76776.679718
FMO2-MP2: Total energy -77003.784968


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-153.153-143.86829.98-17.566-21.698-0.179
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.756 / q_NPA : 0.873
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].
3A3LYS10.8340.8863.40733.42335.3180.034-0.830-1.099-0.002
4A4PRO00.0370.0352.3931.8562.0184.225-1.053-3.3340.004
5A5ASN00.0090.0004.2201.4751.6100.002-0.088-0.0500.000
100A100LEU00.0190.0093.100-3.678-2.0370.072-0.645-1.068-0.001
101A101ASN0-0.026-0.0181.786-47.490-49.00512.631-6.499-4.616-0.078
102A102LEU0-0.0050.0063.092-10.170-8.9200.218-0.557-0.911-0.008
103A103VAL0-0.032-0.0012.3743.5274.4042.664-1.067-2.474-0.004
104A104SER0-0.019-0.0231.890-40.302-38.2197.311-4.969-4.425-0.066
105A105ASP-1-0.867-0.9304.078-31.207-31.0270.000-0.029-0.1500.000
106A106VAL0-0.042-0.0232.3333.4654.1111.213-0.353-1.5060.000
107A107GLU-1-0.746-0.8462.406-29.339-27.9221.579-1.394-1.602-0.024
108A108ARG10.8670.9164.81319.34919.482-0.001-0.005-0.1270.000
109A109VAL00.0280.0124.220-1.205-0.8240.032-0.077-0.3360.000
6A6VAL0-0.033-0.0157.013-0.552-0.5520.0000.0000.0000.000
7A7ALA00.0210.0148.7581.6111.6110.0000.0000.0000.000
8A8ILE0-0.019-0.00511.833-0.572-0.5720.0000.0000.0000.000
9A9ILE0-0.0150.00314.7790.4710.4710.0000.0000.0000.000
10A10VAL0-0.0150.00216.856-0.068-0.0680.0000.0000.0000.000
11A11ALA00.0270.02920.4720.2350.2350.0000.0000.0000.000
12A12ALA00.000-0.01424.0730.0080.0080.0000.0000.0000.000
13A13LEU0-0.0270.00726.8050.1110.1110.0000.0000.0000.000
14A14LYS10.8180.92229.9719.1339.1330.0000.0000.0000.000
15A15PRO00.035-0.00332.2170.1470.1470.0000.0000.0000.000
16A16ALA00.000-0.01432.260-0.178-0.1780.0000.0000.0000.000
17A17LEU00.0410.02526.285-0.238-0.2380.0000.0000.0000.000
18A18GLY00.0350.00927.839-0.316-0.3160.0000.0000.0000.000
19A19ILE00.006-0.03323.745-0.091-0.0910.0000.0000.0000.000
20A20GLY0-0.024-0.01727.057-0.230-0.2300.0000.0000.0000.000
21A21TYR00.0560.01429.0150.2870.2870.0000.0000.0000.000
22A22LYS10.8750.93032.2868.3738.3730.0000.0000.0000.000
23A23GLY0-0.0110.00628.6740.0260.0260.0000.0000.0000.000
24A24LYS10.9100.98228.1058.7218.7210.0000.0000.0000.000
25A25MET00.0470.01724.8020.0130.0130.0000.0000.0000.000
26A26PRO0-0.049-0.02428.9640.2790.2790.0000.0000.0000.000
27A27TRP00.0350.03426.8340.4510.4510.0000.0000.0000.000
28A28ARG10.9200.94130.2518.3778.3770.0000.0000.0000.000
29A29LEU00.0100.03028.3800.2550.2550.0000.0000.0000.000
30A30ARG10.9160.94127.7638.1748.1740.0000.0000.0000.000
31A31LYS10.7960.87327.3198.8698.8690.0000.0000.0000.000
32A32GLU-1-0.806-0.87423.394-12.170-12.1700.0000.0000.0000.000
33A33ILE00.0340.01323.124-0.459-0.4590.0000.0000.0000.000
34A34ARG10.8560.93522.1059.8889.8880.0000.0000.0000.000
35A35TYR00.0900.05219.871-0.493-0.4930.0000.0000.0000.000
36A36PHE00.0300.01317.168-0.621-0.6210.0000.0000.0000.000
37A37LYS10.8490.92817.26211.77311.7730.0000.0000.0000.000
38A38ASP-1-0.823-0.89216.731-13.338-13.3380.0000.0000.0000.000
39A39VAL0-0.017-0.01114.810-0.656-0.6560.0000.0000.0000.000
40A40THR0-0.031-0.02612.749-0.957-0.9570.0000.0000.0000.000
41A41THR0-0.060-0.04211.889-1.359-1.3590.0000.0000.0000.000
42A42ARG10.8210.90512.31314.34814.3480.0000.0000.0000.000
43A43THR0-0.0370.0038.612-0.224-0.2240.0000.0000.0000.000
44A44THR0-0.131-0.09510.3571.4771.4770.0000.0000.0000.000
45A45LYS0-0.024-0.0015.399-0.195-0.1950.0000.0000.0000.000
46A46PRO00.0040.00810.324-0.432-0.4320.0000.0000.0000.000
47A47ASN0-0.030-0.02511.0971.1291.1290.0000.0000.0000.000
48A48THR0-0.0070.0116.380-1.509-1.5090.0000.0000.0000.000
49A49ARG10.8820.9427.21828.67328.6730.0000.0000.0000.000
50A50ASN00.018-0.0146.365-4.199-4.1990.0000.0000.0000.000
51A51ALA00.0150.0066.4200.1750.1750.0000.0000.0000.000
52A52VAL0-0.025-0.0158.0141.3951.3950.0000.0000.0000.000
53A53ILE00.0070.0057.741-0.151-0.1510.0000.0000.0000.000
54A54MET0-0.0070.01111.9871.8991.8990.0000.0000.0000.000
55A55GLY00.0300.01615.451-0.652-0.6520.0000.0000.0000.000
56A56ARG10.8620.90717.95613.70613.7060.0000.0000.0000.000
57A57LYS10.9330.96020.07012.91612.9160.0000.0000.0000.000
58A58THR00.0140.02219.7910.4890.4890.0000.0000.0000.000
59A59TRP00.0780.02517.5060.2860.2860.0000.0000.0000.000
60A60GLU-1-0.896-0.94420.566-12.386-12.3860.0000.0000.0000.000
61A61SER0-0.059-0.03123.7860.4670.4670.0000.0000.0000.000
62A62ILE00.0400.03220.1140.4540.4540.0000.0000.0000.000
63A63PRO0-0.001-0.00724.383-0.038-0.0380.0000.0000.0000.000
64A64GLN00.005-0.02125.089-0.082-0.0820.0000.0000.0000.000
65A65LYS10.9320.97825.49210.16810.1680.0000.0000.0000.000
66A66PHE0-0.022-0.01823.6940.1690.1690.0000.0000.0000.000
67A67ARG10.8790.97720.23412.81612.8160.0000.0000.0000.000
68A68PRO00.0240.00816.3210.4370.4370.0000.0000.0000.000
69A69LEU0-0.046-0.01916.0320.6980.6980.0000.0000.0000.000
70A70PRO00.0300.01915.640-0.980-0.9800.0000.0000.0000.000
71A71ASP-1-0.860-0.93114.402-15.709-15.7090.0000.0000.0000.000
72A72ARG10.8130.90210.84716.01816.0180.0000.0000.0000.000
73A73LEU0-0.0030.0126.8250.4540.4540.0000.0000.0000.000
74A74ASN0-0.050-0.03210.4050.8680.8680.0000.0000.0000.000
75A75ILE00.0310.0157.051-0.245-0.2450.0000.0000.0000.000
76A76ILE0-0.042-0.01211.6111.4481.4480.0000.0000.0000.000
77A77LEU00.0160.00211.219-0.488-0.4880.0000.0000.0000.000
78A78SER0-0.020-0.03215.1231.7341.7340.0000.0000.0000.000
79A79ARG10.8130.88017.31813.81813.8180.0000.0000.0000.000
80A80SER0-0.0150.00119.2120.2480.2480.0000.0000.0000.000
81A81TYR0-0.067-0.03315.7640.6290.6290.0000.0000.0000.000
82A82GLU-1-0.839-0.91515.543-18.580-18.5800.0000.0000.0000.000
83A83ASN0-0.060-0.05410.000-0.867-0.8670.0000.0000.0000.000
84A84GLU-1-0.915-0.94911.913-18.812-18.8120.0000.0000.0000.000
85A85ILE0-0.010-0.0148.503-1.250-1.2500.0000.0000.0000.000
86A86ILE0-0.025-0.00512.4841.2311.2310.0000.0000.0000.000
87A87ASP-1-0.826-0.92815.053-17.460-17.4600.0000.0000.0000.000
88A88ASP-1-0.833-0.91012.018-25.917-25.9170.0000.0000.0000.000
89A89ASN0-0.031-0.01811.865-2.176-2.1760.0000.0000.0000.000
90A90ILE0-0.025-0.00213.639-0.060-0.0600.0000.0000.0000.000
91A91ILE00.0610.0287.798-0.481-0.4810.0000.0000.0000.000
92A92HIS10.8270.91711.99920.94320.9430.0000.0000.0000.000
93A93ALA00.0920.04310.320-1.819-1.8190.0000.0000.0000.000
94A94SER00.0490.03412.4441.0301.0300.0000.0000.0000.000
95A95SER0-0.036-0.01311.5280.2000.2000.0000.0000.0000.000
96A96ILE00.0750.0408.511-1.840-1.8400.0000.0000.0000.000
97A97GLU-1-0.789-0.8666.861-37.044-37.0440.0000.0000.0000.000
98A98SER0-0.014-0.0016.087-6.094-6.0940.0000.0000.0000.000
99A99SER0-0.027-0.0406.507-3.318-3.3180.0000.0000.0000.000
110A110PHE00.0280.0146.9641.5681.5680.0000.0000.0000.000
111A111ILE0-0.030-0.01210.765-0.272-0.2720.0000.0000.0000.000
112A112ILE00.023-0.00613.0151.0711.0710.0000.0000.0000.000
113A113GLY00.0130.03516.0820.8970.8970.0000.0000.0000.000
114A114GLY00.020-0.00717.969-0.621-0.6210.0000.0000.0000.000
115A115ALA00.0600.00520.414-0.499-0.4990.0000.0000.0000.000
116A116GLU-1-0.854-0.90821.676-13.335-13.3350.0000.0000.0000.000
117A117ILE00.0170.01115.538-0.223-0.2230.0000.0000.0000.000
118A118TYR00.003-0.01817.421-0.227-0.2270.0000.0000.0000.000
119A119ASN0-0.019-0.02519.060-0.154-0.1540.0000.0000.0000.000
120A120GLU-1-0.914-0.93018.653-14.203-14.2030.0000.0000.0000.000
121A121LEU0-0.018-0.02812.791-0.447-0.4470.0000.0000.0000.000
122A122ILE00.0230.03115.362-0.685-0.6850.0000.0000.0000.000
123A123ASN0-0.006-0.00617.6450.2920.2920.0000.0000.0000.000
124A124ASN0-0.0100.00711.727-0.454-0.4540.0000.0000.0000.000
125A125SER00.0330.00613.383-0.326-0.3260.0000.0000.0000.000
126A126LEU0-0.0040.0046.708-0.223-0.2230.0000.0000.0000.000
127A127VAL0-0.049-0.0089.798-0.483-0.4830.0000.0000.0000.000
128A128SER00.0430.00411.6080.7470.7470.0000.0000.0000.000
129A129HIS00.0050.00913.2410.3900.3900.0000.0000.0000.000
130A130LEU0-0.0140.00014.703-0.590-0.5900.0000.0000.0000.000
131A131LEU0-0.020-0.00815.5060.5070.5070.0000.0000.0000.000
132A132ILE00.0240.00318.463-0.184-0.1840.0000.0000.0000.000
133A133THR0-0.031-0.02721.8950.2550.2550.0000.0000.0000.000
134A134GLU-1-0.806-0.88324.456-9.930-9.9300.0000.0000.0000.000
135A135ILE00.002-0.00827.6130.2100.2100.0000.0000.0000.000
136A136GLU-1-0.871-0.94430.259-8.662-8.6620.0000.0000.0000.000
137A137HIS00.0570.01533.954-0.040-0.0400.0000.0000.0000.000
138A138PRO0-0.015-0.00237.1620.0030.0030.0000.0000.0000.000
139A139SER0-0.035-0.02640.1530.1840.1840.0000.0000.0000.000
140A140PRO00.0260.02636.483-0.056-0.0560.0000.0000.0000.000
141A141GLU-1-0.868-0.92437.715-7.444-7.4440.0000.0000.0000.000
142A142SER0-0.050-0.02940.0930.0800.0800.0000.0000.0000.000
143A143ILE0-0.065-0.02934.631-0.064-0.0640.0000.0000.0000.000
144A144GLU-1-0.911-0.95036.774-7.745-7.7450.0000.0000.0000.000
145A145MET0-0.097-0.03931.895-0.395-0.3950.0000.0000.0000.000
146A146ASP-1-0.826-0.89931.917-9.335-9.3350.0000.0000.0000.000
147A147THR0-0.068-0.02926.850-0.260-0.2600.0000.0000.0000.000
148A148PHE00.0310.01228.300-0.045-0.0450.0000.0000.0000.000
149A149LEU0-0.0340.00122.507-0.408-0.4080.0000.0000.0000.000
150A150LYS10.9310.96524.58212.15712.1570.0000.0000.0000.000
151A151PHE00.034-0.00119.763-0.418-0.4180.0000.0000.0000.000
152A152PRO00.0400.03722.5020.3750.3750.0000.0000.0000.000
153A153LEU00.018-0.00723.028-0.262-0.2620.0000.0000.0000.000
154A154GLU-1-0.864-0.92325.591-10.395-10.3950.0000.0000.0000.000
155A155SER0-0.031-0.01623.3200.1190.1190.0000.0000.0000.000
156A156TRP0-0.046-0.02516.299-0.654-0.6540.0000.0000.0000.000
157A157THR0-0.005-0.01222.6560.6790.6790.0000.0000.0000.000
158A158LYS10.8470.92922.7489.7099.7090.0000.0000.0000.000
159A159GLN0-0.002-0.01720.8190.6360.6360.0000.0000.0000.000
160A160PRO00.0210.01223.9720.1730.1730.0000.0000.0000.000
161A161LYS10.8380.88524.2129.3799.3790.0000.0000.0000.000
162A162SER00.0210.01623.943-0.137-0.1370.0000.0000.0000.000
163A163GLU-1-0.818-0.89020.428-12.629-12.6290.0000.0000.0000.000
164A164LEU0-0.0020.00919.317-0.658-0.6580.0000.0000.0000.000
165A165GLN0-0.015-0.02619.383-0.120-0.1200.0000.0000.0000.000
166A166LYS10.8290.88618.66312.14912.1490.0000.0000.0000.000
167A167PHE0-0.0230.00812.249-0.628-0.6280.0000.0000.0000.000
168A168VAL00.002-0.00514.875-0.912-0.9120.0000.0000.0000.000
169A169GLY00.0350.04517.136-0.083-0.0830.0000.0000.0000.000
170A170ASP-1-0.833-0.90818.284-12.280-12.2800.0000.0000.0000.000
171A171THR0-0.083-0.04418.2090.3460.3460.0000.0000.0000.000
172A172VAL00.0180.00220.9350.1140.1140.0000.0000.0000.000
173A173LEU0-0.0050.01021.687-0.077-0.0770.0000.0000.0000.000
174A174GLU-1-0.846-0.89325.440-8.873-8.8730.0000.0000.0000.000
175A175ASP-1-0.826-0.90528.166-9.625-9.6250.0000.0000.0000.000
176A176ASP-1-0.880-0.92530.802-8.176-8.1760.0000.0000.0000.000
177A177ILE0-0.0010.01227.8070.2800.2800.0000.0000.0000.000
178A178LYS10.8950.93731.9497.8917.8910.0000.0000.0000.000
179A179GLU-1-0.838-0.90830.848-9.227-9.2270.0000.0000.0000.000
180A180GLY0-0.0030.00135.116-0.064-0.0640.0000.0000.0000.000
181A181ASP-1-0.893-0.94938.403-7.253-7.2530.0000.0000.0000.000
182A182PHE0-0.037-0.01633.286-0.067-0.0670.0000.0000.0000.000
183A183THR00.005-0.00933.8310.1020.1020.0000.0000.0000.000
184A184TYR0-0.035-0.04727.268-0.237-0.2370.0000.0000.0000.000
185A185ASN00.0200.00528.330-0.002-0.0020.0000.0000.0000.000
186A186TYR00.0250.00922.746-0.205-0.2050.0000.0000.0000.000
187A187THR0-0.033-0.03223.2170.2210.2210.0000.0000.0000.000
188A188LEU00.0240.01516.725-0.473-0.4730.0000.0000.0000.000
189A189TRP0-0.013-0.01219.3210.6280.6280.0000.0000.0000.000
190A190THR00.0070.00517.446-0.647-0.6470.0000.0000.0000.000
191A191ARG10.8500.92415.11016.84216.8420.0000.0000.0000.000
192A192LYS0-0.054-0.00919.721-1.668-1.6680.0000.0000.0000.000