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: 9RZ32

Calculation Name: 3UMF-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3UMF

Chain ID: A

ChEMBL ID:

UniProt ID: G4V9S0

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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2110277.757902
FMO2-HF: Nuclear repulsion 2032807.397731
FMO2-HF: Total energy -77470.360171
FMO2-MP2: Total energy -77694.187724


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:4:GLN)


Summations of interaction energy for fragment #1(A:4:GLN)
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.
-27.774-25.17718.838-8.39-13.048-0.044
Interaction energy analysis for fragmet #1(A:4:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.833 / q_NPA : 0.900
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].
3A6LEU00.0060.0011.7302.2913.6907.853-3.316-5.936-0.008
4A7ALA0-0.0090.0013.280-0.580-0.285-0.0070.322-0.611-0.001
5A8LYS00.0180.0155.0945.7285.893-0.001-0.010-0.1530.000
75A78LYS10.8860.9412.21921.10321.0083.548-1.255-2.1990.019
79A82ILE0-0.014-0.0113.754-2.382-1.9020.007-0.145-0.3420.001
107A110VAL0-0.045-0.0163.255-0.7810.1790.013-0.391-0.583-0.002
108A111CYS00.001-0.0081.871-25.533-26.2057.426-3.572-3.183-0.053
109A112PRO00.0150.0074.5074.2784.343-0.001-0.023-0.0410.000
6A9ALA0-0.037-0.0105.9804.0234.0230.0000.0000.0000.000
7A10LYS10.9190.9707.83419.70019.7000.0000.0000.0000.000
8A11VAL00.0060.0017.9471.5661.5660.0000.0000.0000.000
9A12ILE00.0060.00510.8900.3900.3900.0000.0000.0000.000
10A13PHE00.0260.01210.7640.1930.1930.0000.0000.0000.000
11A14VAL00.0060.00915.5000.6000.6000.0000.0000.0000.000
12A15LEU0-0.009-0.00419.1290.2590.2590.0000.0000.0000.000
13A16GLY00.0620.01821.9420.1520.1520.0000.0000.0000.000
14A17GLY00.0200.02625.686-0.061-0.0610.0000.0000.0000.000
15A18PRO0-0.027-0.01828.380-0.014-0.0140.0000.0000.0000.000
16A19GLY00.0560.03031.6360.1100.1100.0000.0000.0000.000
17A20SER0-0.041-0.02028.1600.0110.0110.0000.0000.0000.000
18A21GLY00.0350.01229.750-0.053-0.0530.0000.0000.0000.000
19A22LYS10.8930.93222.74111.49211.4920.0000.0000.0000.000
20A23GLY00.0240.02525.089-0.334-0.3340.0000.0000.0000.000
21A24THR00.0720.03025.945-0.190-0.1900.0000.0000.0000.000
22A25GLN0-0.034-0.02025.898-0.230-0.2300.0000.0000.0000.000
23A26CYS0-0.024-0.00621.729-0.425-0.4250.0000.0000.0000.000
24A27GLU-1-0.900-0.94923.245-10.473-10.4730.0000.0000.0000.000
25A28LYS10.8770.94825.6569.4139.4130.0000.0000.0000.000
26A29LEU0-0.019-0.00621.328-0.112-0.1120.0000.0000.0000.000
27A30VAL0-0.016-0.00420.256-0.358-0.3580.0000.0000.0000.000
28A31GLN0-0.040-0.02422.475-0.028-0.0280.0000.0000.0000.000
29A32LYS10.8720.95725.31411.30911.3090.0000.0000.0000.000
30A33PHE00.005-0.00320.7030.1280.1280.0000.0000.0000.000
31A34HIS0-0.0060.00720.027-1.174-1.1740.0000.0000.0000.000
32A35PHE00.003-0.00116.951-0.733-0.7330.0000.0000.0000.000
33A36ASN0-0.0060.01212.4631.9231.9230.0000.0000.0000.000
34A37HIS0-0.056-0.04015.861-0.187-0.1870.0000.0000.0000.000
35A38LEU0-0.0020.00211.8420.0680.0680.0000.0000.0000.000
36A39SER00.019-0.00815.9840.0920.0920.0000.0000.0000.000
37A40SER00.0370.00316.945-0.191-0.1910.0000.0000.0000.000
38A41GLY00.0300.01717.8670.1000.1000.0000.0000.0000.000
39A42ASP-1-0.833-0.90419.583-11.983-11.9830.0000.0000.0000.000
40A43LEU0-0.026-0.00713.412-0.023-0.0230.0000.0000.0000.000
41A44LEU00.0180.01117.2720.0300.0300.0000.0000.0000.000
42A45ARG10.9270.96519.34510.73010.7300.0000.0000.0000.000
43A46ALA0-0.031-0.01818.1880.3480.3480.0000.0000.0000.000
44A47GLU-1-0.751-0.85916.774-13.744-13.7440.0000.0000.0000.000
45A48VAL0-0.0170.00419.3200.3310.3310.0000.0000.0000.000
46A49GLN0-0.046-0.02622.9080.6780.6780.0000.0000.0000.000
47A50SER0-0.0060.00020.2740.2110.2110.0000.0000.0000.000
48A51GLY0-0.0080.00322.3660.1140.1140.0000.0000.0000.000
49A52SER0-0.036-0.03419.9880.3890.3890.0000.0000.0000.000
50A53PRO00.008-0.02222.0150.2350.2350.0000.0000.0000.000
51A54LYS10.9040.95814.76015.14015.1400.0000.0000.0000.000
52A55GLY00.0520.03321.0390.0810.0810.0000.0000.0000.000
53A56LYS10.9030.94822.28710.14610.1460.0000.0000.0000.000
54A57GLU-1-0.799-0.87623.643-9.571-9.5710.0000.0000.0000.000
55A58LEU00.000-0.01218.7350.0950.0950.0000.0000.0000.000
56A59LYS10.8910.94123.4119.1009.1000.0000.0000.0000.000
57A60ALA00.0030.00226.5420.2590.2590.0000.0000.0000.000
58A61MET0-0.0130.00122.5780.0210.0210.0000.0000.0000.000
59A62MET0-0.043-0.02522.4330.1840.1840.0000.0000.0000.000
60A63GLU-1-0.950-0.96027.597-8.267-8.2670.0000.0000.0000.000
61A64ARG10.7670.84928.1229.5199.5190.0000.0000.0000.000
62A65GLY0-0.0220.00430.3420.1530.1530.0000.0000.0000.000
63A66GLU-1-0.880-0.93226.868-9.541-9.5410.0000.0000.0000.000
64A67LEU0-0.026-0.01923.697-0.192-0.1920.0000.0000.0000.000
65A68VAL00.0020.00119.022-0.134-0.1340.0000.0000.0000.000
66A69PRO00.0170.00818.123-0.275-0.2750.0000.0000.0000.000
67A70LEU00.0320.02214.140-0.346-0.3460.0000.0000.0000.000
68A71GLU-1-0.823-0.92913.019-15.614-15.6140.0000.0000.0000.000
69A72VAL0-0.014-0.00112.553-0.754-0.7540.0000.0000.0000.000
70A73VAL00.010-0.00213.587-0.423-0.4230.0000.0000.0000.000
71A74LEU0-0.019-0.0098.927-0.681-0.6810.0000.0000.0000.000
72A75ALA0-0.0040.0038.813-1.408-1.4080.0000.0000.0000.000
73A76LEU00.0080.0079.214-0.830-0.8300.0000.0000.0000.000
74A77LEU0-0.008-0.0049.831-0.423-0.4230.0000.0000.0000.000
76A79GLU-1-0.968-0.9796.522-19.736-19.7360.0000.0000.0000.000
77A80ALA00.010-0.0068.734-0.709-0.7090.0000.0000.0000.000
78A81MET0-0.015-0.0106.1970.0720.0720.0000.0000.0000.000
80A83LYS10.9330.9716.96316.82116.8210.0000.0000.0000.000
81A84LEU00.0080.00210.0911.4491.4490.0000.0000.0000.000
82A85VAL0-0.026-0.0096.3730.7490.7490.0000.0000.0000.000
83A86ASP-1-0.830-0.9109.573-28.508-28.5080.0000.0000.0000.000
84A87LYS10.8170.92011.85317.79317.7930.0000.0000.0000.000
85A88ASN00.0390.00113.3050.4970.4970.0000.0000.0000.000
86A89CYS00.0230.02710.885-0.432-0.4320.0000.0000.0000.000
87A90HIS0-0.023-0.01111.089-1.605-1.6050.0000.0000.0000.000
88A91PHE0-0.012-0.0079.4720.5300.5300.0000.0000.0000.000
89A92LEU00.0150.02613.278-0.145-0.1450.0000.0000.0000.000
90A93ILE0-0.007-0.01311.1400.0310.0310.0000.0000.0000.000
91A94ASP-1-0.812-0.89215.044-11.977-11.9770.0000.0000.0000.000
92A95GLY0-0.061-0.02618.7190.2540.2540.0000.0000.0000.000
93A96TYR0-0.047-0.02412.2590.4780.4780.0000.0000.0000.000
94A97PRO0-0.0010.01114.502-0.271-0.2710.0000.0000.0000.000
95A98ARG10.9770.96016.49611.80711.8070.0000.0000.0000.000
96A99GLU-1-0.863-0.93418.786-11.257-11.2570.0000.0000.0000.000
97A100LEU00.034-0.00417.650-0.640-0.6400.0000.0000.0000.000
98A101ASP-1-0.827-0.92016.202-14.739-14.7390.0000.0000.0000.000
99A102GLN00.0140.00614.263-1.235-1.2350.0000.0000.0000.000
100A103GLY00.0320.02212.733-1.042-1.0420.0000.0000.0000.000
101A104ILE00.0260.01411.500-1.507-1.5070.0000.0000.0000.000
102A105LYS10.8490.92210.86113.67813.6780.0000.0000.0000.000
103A106PHE00.0360.0127.459-1.413-1.4130.0000.0000.0000.000
104A107GLU-1-0.773-0.8706.667-23.858-23.8580.0000.0000.0000.000
105A108LYS10.8040.9216.92519.23919.2390.0000.0000.0000.000
106A109GLU-1-0.841-0.9155.859-25.857-25.8570.0000.0000.0000.000
110A113CYS0-0.093-0.0228.266-0.530-0.5300.0000.0000.0000.000
111A114LEU0-0.008-0.00110.8830.0550.0550.0000.0000.0000.000
112A115CYS0-0.036-0.01813.3180.8630.8630.0000.0000.0000.000
113A116VAL00.0130.00115.537-0.572-0.5720.0000.0000.0000.000
114A117ILE00.0220.01717.9980.5970.5970.0000.0000.0000.000
115A118ASN00.004-0.00521.062-0.097-0.0970.0000.0000.0000.000
116A119PHE0-0.026-0.02323.2220.3280.3280.0000.0000.0000.000
117A120ASP-1-0.905-0.95526.718-9.378-9.3780.0000.0000.0000.000
118A121VAL0-0.034-0.02729.2890.2050.2050.0000.0000.0000.000
119A122SER00.0400.00932.866-0.085-0.0850.0000.0000.0000.000
120A123GLU-1-0.730-0.82235.685-7.389-7.3890.0000.0000.0000.000
121A124GLU-1-0.816-0.90837.510-7.413-7.4130.0000.0000.0000.000
122A125VAL0-0.038-0.01035.7930.1160.1160.0000.0000.0000.000
123A126MET0-0.0070.01234.8130.0600.0600.0000.0000.0000.000
124A127ARG10.8480.89036.8467.0637.0630.0000.0000.0000.000
125A128LYS10.9230.96740.1627.3907.3900.0000.0000.0000.000
126A129ARG10.7830.88933.6018.4428.4420.0000.0000.0000.000
127A130LEU0-0.041-0.02634.488-0.072-0.0720.0000.0000.0000.000
128A131LEU0-0.0230.01639.0000.0590.0590.0000.0000.0000.000
129A132LYS10.8670.93342.3176.3836.3830.0000.0000.0000.000
130A133ARG10.7980.87146.0546.0146.0140.0000.0000.0000.000
131A134ALA00.0200.02844.5770.0800.0800.0000.0000.0000.000
132A135GLU-1-0.839-0.88846.698-5.653-5.6530.0000.0000.0000.000
133A136THR00.006-0.02450.3500.0210.0210.0000.0000.0000.000
134A137SER0-0.017-0.00752.8270.0870.0870.0000.0000.0000.000
135A138ASN0-0.055-0.01847.1100.1010.1010.0000.0000.0000.000
136A139ARG10.9530.97048.9795.8815.8810.0000.0000.0000.000
137A140VAL0-0.045-0.02445.359-0.021-0.0210.0000.0000.0000.000
138A141ASP-1-0.800-0.89645.291-6.363-6.3630.0000.0000.0000.000
139A142ASP-1-0.819-0.89644.870-6.517-6.5170.0000.0000.0000.000
140A143ASN0-0.008-0.01641.647-0.259-0.2590.0000.0000.0000.000
141A144GLU-1-0.782-0.91140.415-6.746-6.7460.0000.0000.0000.000
142A145GLU-1-0.773-0.88640.369-7.099-7.0990.0000.0000.0000.000
143A146THR0-0.050-0.03137.265-0.193-0.1930.0000.0000.0000.000
144A147ILE0-0.047-0.02735.490-0.297-0.2970.0000.0000.0000.000
145A148VAL00.0000.00635.638-0.250-0.2500.0000.0000.0000.000
146A149LYS10.8440.91336.2336.8996.8990.0000.0000.0000.000
147A150ARG10.9661.00031.2688.1788.1780.0000.0000.0000.000
148A151PHE0-0.015-0.01531.432-0.304-0.3040.0000.0000.0000.000
149A152ARG10.8770.89831.6597.1627.1620.0000.0000.0000.000
150A153THR0-0.005-0.01029.604-0.134-0.1340.0000.0000.0000.000
151A154PHE0-0.020-0.00424.158-0.262-0.2620.0000.0000.0000.000
152A155ASN00.0030.00727.083-0.255-0.2550.0000.0000.0000.000
153A156GLU-1-0.832-0.90228.179-9.114-9.1140.0000.0000.0000.000
154A157LEU0-0.025-0.00623.987-0.165-0.1650.0000.0000.0000.000
155A158THR00.000-0.01822.697-0.350-0.3500.0000.0000.0000.000
156A159LYS10.8260.91223.5318.5588.5580.0000.0000.0000.000
157A160PRO00.0230.01123.049-0.226-0.2260.0000.0000.0000.000
158A161VAL0-0.018-0.00617.755-0.397-0.3970.0000.0000.0000.000
159A162ILE00.005-0.00419.838-0.503-0.5030.0000.0000.0000.000
160A163GLU-1-0.870-0.93322.151-11.065-11.0650.0000.0000.0000.000
161A164HIS0-0.0060.00315.314-0.227-0.2270.0000.0000.0000.000
162A165TYR0-0.040-0.06413.096-0.061-0.0610.0000.0000.0000.000
163A166LYS10.9250.96919.02610.54110.5410.0000.0000.0000.000
164A167GLN0-0.037-0.02322.049-0.201-0.2010.0000.0000.0000.000
165A168GLN0-0.056-0.02515.111-0.758-0.7580.0000.0000.0000.000
166A169ASN0-0.036-0.01319.465-0.065-0.0650.0000.0000.0000.000
167A170LYS10.8880.94412.72120.13120.1310.0000.0000.0000.000
168A171VAL0-0.062-0.02118.954-0.235-0.2350.0000.0000.0000.000
169A172ILE00.0050.01120.7780.5360.5360.0000.0000.0000.000
170A173THR0-0.017-0.01623.1300.0400.0400.0000.0000.0000.000
171A174ILE0-0.060-0.02825.5820.1900.1900.0000.0000.0000.000
172A175ASP-1-0.784-0.85728.136-8.481-8.4810.0000.0000.0000.000
173A176ALA00.018-0.00129.7530.0110.0110.0000.0000.0000.000
174A177SER0-0.059-0.05531.8170.2440.2440.0000.0000.0000.000
175A178GLY0-0.0030.00535.1490.2450.2450.0000.0000.0000.000
176A179THR00.022-0.00736.187-0.080-0.0800.0000.0000.0000.000
177A180VAL00.0490.01031.866-0.194-0.1940.0000.0000.0000.000
178A181ASP-1-0.863-0.92732.160-8.947-8.9470.0000.0000.0000.000
179A182ALA00.0480.02632.965-0.222-0.2220.0000.0000.0000.000
180A183ILE0-0.034-0.01029.160-0.228-0.2280.0000.0000.0000.000
181A184PHE00.0120.00726.209-0.309-0.3090.0000.0000.0000.000
182A185ASP-1-0.891-0.94828.441-9.738-9.7380.0000.0000.0000.000
183A186LYS10.8400.91529.2399.7309.7300.0000.0000.0000.000
184A187VAL00.024-0.00623.720-0.310-0.3100.0000.0000.0000.000
185A188ASN00.009-0.00624.865-0.854-0.8540.0000.0000.0000.000
186A189HIS0-0.069-0.03725.574-0.170-0.1700.0000.0000.0000.000
187A190GLU-1-0.790-0.86224.785-10.939-10.9390.0000.0000.0000.000
188A191LEU00.0410.00819.343-0.481-0.4810.0000.0000.0000.000
189A192GLN00.0130.01621.145-0.466-0.4660.0000.0000.0000.000
190A193LYS10.7980.88223.13010.95210.9520.0000.0000.0000.000
191A194PHE00.0010.00617.235-0.266-0.2660.0000.0000.0000.000
192A195GLY00.0060.01017.647-1.032-1.0320.0000.0000.0000.000
193A196VAL0-0.087-0.05617.270-0.975-0.9750.0000.0000.0000.000
194A197LYS00.0590.03619.999-1.100-1.1000.0000.0000.0000.000