Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: NNZJQ

Calculation Name: 3UMF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UMF

Chain ID: A

ChEMBL ID:

UniProt ID: G4V9S0

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2112388.953816
FMO2-HF: Nuclear repulsion 2034918.090602
FMO2-HF: Total energy -77470.863214
FMO2-MP2: Total energy -77694.716555


3D Structure
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.
-21.658-14.9086.49-4.737-8.5060.032
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 : 0 / q_Mulliken : 0.118 / q_NPA : 0.051
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].
3A6LEU00.008-0.0112.044-15.256-11.5935.667-3.566-5.7650.033
4A7ALA0-0.0160.0063.000-3.957-2.6180.121-0.510-0.951-0.002
5A8LYS10.8500.9254.345-2.986-2.7910.000-0.033-0.1620.000
6A9ALA0-0.017-0.0126.408-0.082-0.0820.0000.0000.0000.000
7A10LYS10.8820.9528.103-0.747-0.7470.0000.0000.0000.000
8A11VAL0-0.002-0.0049.7510.0100.0100.0000.0000.0000.000
9A12ILE00.0010.00212.360-0.122-0.1220.0000.0000.0000.000
10A13PHE00.0300.01313.3810.0240.0240.0000.0000.0000.000
11A14VAL00.0010.00717.861-0.008-0.0080.0000.0000.0000.000
12A15LEU0-0.008-0.00121.501-0.013-0.0130.0000.0000.0000.000
13A16GLY00.0720.02224.4250.0090.0090.0000.0000.0000.000
14A17GLY00.0250.02628.1820.0000.0000.0000.0000.0000.000
15A18PRO0-0.023-0.01730.8200.0090.0090.0000.0000.0000.000
16A19GLY00.0520.03033.975-0.004-0.0040.0000.0000.0000.000
17A20SER0-0.038-0.02330.5950.0070.0070.0000.0000.0000.000
18A21GLY00.0260.00832.1460.0040.0040.0000.0000.0000.000
19A22LYS10.8810.93224.580-0.105-0.1050.0000.0000.0000.000
20A23GLY00.0200.02026.6250.0140.0140.0000.0000.0000.000
21A24THR00.0730.03027.0460.0120.0120.0000.0000.0000.000
22A25GLN0-0.042-0.02427.4190.0150.0150.0000.0000.0000.000
23A26CYS0-0.048-0.02922.8960.0160.0160.0000.0000.0000.000
24A27GLU-1-0.892-0.94323.8920.1850.1850.0000.0000.0000.000
25A28LYS10.8480.92325.950-0.119-0.1190.0000.0000.0000.000
26A29LEU0-0.027-0.01522.4050.0070.0070.0000.0000.0000.000
27A30VAL0-0.019-0.00120.3760.0230.0230.0000.0000.0000.000
28A31GLN0-0.027-0.01722.6430.0110.0110.0000.0000.0000.000
29A32LYS10.8580.95225.748-0.184-0.1840.0000.0000.0000.000
30A33PHE0-0.027-0.02521.075-0.015-0.0150.0000.0000.0000.000
31A34HIS0-0.0050.00420.3030.0690.0690.0000.0000.0000.000
32A35PHE0-0.026-0.00817.2010.0640.0640.0000.0000.0000.000
33A36ASN00.0180.01812.602-0.142-0.1420.0000.0000.0000.000
34A37HIS0-0.073-0.04815.739-0.016-0.0160.0000.0000.0000.000
35A38LEU0-0.0050.00012.1720.0150.0150.0000.0000.0000.000
36A39SER00.011-0.02016.786-0.043-0.0430.0000.0000.0000.000
37A40SER00.0450.00917.7560.0150.0150.0000.0000.0000.000
38A41GLY00.0340.02118.793-0.019-0.0190.0000.0000.0000.000
39A42ASP-1-0.835-0.90019.8840.1570.1570.0000.0000.0000.000
40A43LEU0-0.020-0.00513.8670.0120.0120.0000.0000.0000.000
41A44LEU00.0100.00517.339-0.028-0.0280.0000.0000.0000.000
42A45ARG10.9330.97019.533-0.121-0.1210.0000.0000.0000.000
43A46ALA0-0.029-0.01917.750-0.005-0.0050.0000.0000.0000.000
44A47GLU-1-0.746-0.83616.342-0.097-0.0970.0000.0000.0000.000
45A48VAL0-0.009-0.00618.848-0.012-0.0120.0000.0000.0000.000
46A49GLN0-0.044-0.02222.319-0.005-0.0050.0000.0000.0000.000
47A50SER0-0.023-0.01319.1720.0080.0080.0000.0000.0000.000
48A51GLY00.0080.01321.093-0.001-0.0010.0000.0000.0000.000
49A52SER0-0.037-0.03819.043-0.023-0.0230.0000.0000.0000.000
50A53PRO00.019-0.01420.6180.0050.0050.0000.0000.0000.000
51A54LYS10.9070.96113.6850.2330.2330.0000.0000.0000.000
52A55GLY00.0550.03120.0040.0030.0030.0000.0000.0000.000
53A56LYS10.8540.92121.5610.0480.0480.0000.0000.0000.000
54A57GLU-1-0.799-0.88123.237-0.106-0.1060.0000.0000.0000.000
55A58LEU0-0.015-0.01218.6130.0040.0040.0000.0000.0000.000
56A59LYS10.8190.88623.2960.0280.0280.0000.0000.0000.000
57A60ALA00.0230.01526.3890.0050.0050.0000.0000.0000.000
58A61MET0-0.040-0.00224.122-0.006-0.0060.0000.0000.0000.000
59A62MET0-0.024-0.01822.5100.0110.0110.0000.0000.0000.000
60A63GLU-1-0.875-0.90927.918-0.018-0.0180.0000.0000.0000.000
61A64ARG10.7590.84327.9610.0970.0970.0000.0000.0000.000
62A65GLY0-0.0220.00230.9520.0000.0000.0000.0000.0000.000
63A66GLU-1-0.875-0.92927.780-0.105-0.1050.0000.0000.0000.000
64A67LEU0-0.039-0.02224.5730.0060.0060.0000.0000.0000.000
65A68VAL00.0180.00519.931-0.017-0.0170.0000.0000.0000.000
66A69PRO00.0250.01019.123-0.001-0.0010.0000.0000.0000.000
67A70LEU00.0340.02216.441-0.001-0.0010.0000.0000.0000.000
68A71GLU-1-0.801-0.90814.429-0.375-0.3750.0000.0000.0000.000
69A72VAL0-0.0010.00513.636-0.080-0.0800.0000.0000.0000.000
70A73VAL00.004-0.00114.3340.0240.0240.0000.0000.0000.000
71A74LEU0-0.015-0.00110.9010.0760.0760.0000.0000.0000.000
72A75ALA00.0020.0049.683-0.018-0.0180.0000.0000.0000.000
73A76LEU0-0.004-0.0019.5230.0290.0290.0000.0000.0000.000
74A77LEU0-0.005-0.00511.1690.1700.1700.0000.0000.0000.000
75A78LYS10.8430.9124.1493.6233.769-0.001-0.021-0.1250.000
76A79GLU-1-0.962-0.9806.1380.5660.5660.0000.0000.0000.000
77A80ALA00.003-0.0107.9550.4430.4430.0000.0000.0000.000
78A81MET0-0.011-0.0077.2170.0390.0390.0000.0000.0000.000
79A82ILE0-0.012-0.0072.434-0.8470.4020.704-0.597-1.3560.001
80A83LYS10.9070.9626.005-0.666-0.6660.0000.0000.0000.000
81A84LEU0-0.015-0.0179.150-0.311-0.3110.0000.0000.0000.000
82A85VAL0-0.016-0.0045.664-0.303-0.3030.0000.0000.0000.000
83A86ASP-1-0.840-0.9048.9122.4492.4490.0000.0000.0000.000
84A87LYS10.9330.97811.128-0.969-0.9690.0000.0000.0000.000
85A88ASN00.0460.01312.995-0.129-0.1290.0000.0000.0000.000
86A89CYS0-0.0020.01710.9170.1220.1220.0000.0000.0000.000
87A90HIS0-0.025-0.01311.2840.0110.0110.0000.0000.0000.000
88A91PHE00.0120.0019.3500.0820.0820.0000.0000.0000.000
89A92LEU00.0100.02314.018-0.075-0.0750.0000.0000.0000.000
90A93ILE0-0.016-0.02012.7520.0340.0340.0000.0000.0000.000
91A94ASP-1-0.789-0.87716.8730.1270.1270.0000.0000.0000.000
92A95GLY0-0.058-0.02520.549-0.020-0.0200.0000.0000.0000.000
93A96TYR0-0.050-0.02714.596-0.032-0.0320.0000.0000.0000.000
94A97PRO0-0.0010.00816.9730.0340.0340.0000.0000.0000.000
95A98ARG10.9280.95118.9810.0190.0190.0000.0000.0000.000
96A99GLU-1-0.797-0.92221.356-0.072-0.0720.0000.0000.0000.000
97A100LEU00.025-0.00120.259-0.005-0.0050.0000.0000.0000.000
98A101ASP-1-0.803-0.90718.463-0.238-0.2380.0000.0000.0000.000
99A102GLN00.0060.01216.556-0.022-0.0220.0000.0000.0000.000
100A103GLY00.0340.03115.2080.0040.0040.0000.0000.0000.000
101A104ILE00.0260.01313.933-0.035-0.0350.0000.0000.0000.000
102A105LYS10.8130.88813.0320.2580.2580.0000.0000.0000.000
103A106PHE00.0460.00810.088-0.171-0.1710.0000.0000.0000.000
104A107GLU-1-0.755-0.8659.145-0.219-0.2190.0000.0000.0000.000
105A108LYS10.8510.9319.0731.0141.0140.0000.0000.0000.000
106A109GLU-1-0.862-0.9147.521-2.172-2.1720.0000.0000.0000.000
107A110VAL0-0.057-0.0165.304-0.964-0.9640.0000.0000.0000.000
108A111CYS00.017-0.0054.515-0.1170.041-0.001-0.010-0.1470.000
109A112PRO00.0060.0027.0440.1100.1100.0000.0000.0000.000
110A113CYS0-0.107-0.02310.5270.1350.1350.0000.0000.0000.000
111A114LEU00.0020.00113.033-0.053-0.0530.0000.0000.0000.000
112A115CYS0-0.049-0.02814.569-0.031-0.0310.0000.0000.0000.000
113A116VAL00.0240.00417.4600.0290.0290.0000.0000.0000.000
114A117ILE00.0130.01520.180-0.015-0.0150.0000.0000.0000.000
115A118ASN0-0.038-0.02623.057-0.002-0.0020.0000.0000.0000.000
116A119PHE0-0.021-0.01625.169-0.003-0.0030.0000.0000.0000.000
117A120ASP-1-0.876-0.93929.0430.0250.0250.0000.0000.0000.000
118A121VAL0-0.023-0.02431.7610.0050.0050.0000.0000.0000.000
119A122SER00.030-0.00735.329-0.003-0.0030.0000.0000.0000.000
120A123GLU-1-0.715-0.82438.1370.0080.0080.0000.0000.0000.000
121A124GLU-1-0.796-0.88440.1520.0200.0200.0000.0000.0000.000
122A125VAL0-0.054-0.01938.1760.0030.0030.0000.0000.0000.000
123A126MET0-0.0230.00937.3760.0040.0040.0000.0000.0000.000
124A127ARG10.8640.89439.484-0.008-0.0080.0000.0000.0000.000
125A128LYS10.9380.97843.073-0.034-0.0340.0000.0000.0000.000
126A129ARG10.7620.88035.760-0.058-0.0580.0000.0000.0000.000
127A130LEU0-0.055-0.04037.1000.0030.0030.0000.0000.0000.000
128A131LEU0-0.0140.02041.6220.0000.0000.0000.0000.0000.000
129A132LYS10.9050.95444.918-0.018-0.0180.0000.0000.0000.000
130A133ARG10.8790.92145.106-0.036-0.0360.0000.0000.0000.000
131A134ALA0-0.050-0.01950.059-0.001-0.0010.0000.0000.0000.000
132A135GLU-1-0.905-0.94952.0730.0080.0080.0000.0000.0000.000
133A136THR00.0200.01949.8860.0000.0000.0000.0000.0000.000
134A137SER0-0.051-0.04951.5970.0010.0010.0000.0000.0000.000
135A138ASN00.024-0.00351.8690.0010.0010.0000.0000.0000.000
136A139ARG10.9020.96848.904-0.022-0.0220.0000.0000.0000.000
137A140VAL0-0.039-0.02847.4680.0010.0010.0000.0000.0000.000
138A141ASP-1-0.742-0.85647.4100.0080.0080.0000.0000.0000.000
139A142ASP-1-0.895-0.93046.0070.0000.0000.0000.0000.0000.000
140A143ASN00.0060.00543.457-0.002-0.0020.0000.0000.0000.000
141A144GLU-1-0.831-0.93042.4840.0220.0220.0000.0000.0000.000
142A145GLU-1-0.719-0.85542.7540.0020.0020.0000.0000.0000.000
143A146THR0-0.005-0.00739.447-0.003-0.0030.0000.0000.0000.000
144A147ILE0-0.062-0.03637.8290.0000.0000.0000.0000.0000.000
145A148VAL0-0.0060.00837.9720.0010.0010.0000.0000.0000.000
146A149LYS10.8610.91638.5630.0040.0040.0000.0000.0000.000
147A150ARG10.9510.99233.646-0.021-0.0210.0000.0000.0000.000
148A151PHE0-0.024-0.01533.863-0.001-0.0010.0000.0000.0000.000
149A152ARG10.8870.90534.1360.0000.0000.0000.0000.0000.000
150A153THR0-0.005-0.01232.120-0.005-0.0050.0000.0000.0000.000
151A154PHE0-0.020-0.00726.630-0.005-0.0050.0000.0000.0000.000
152A155ASN00.0130.01129.611-0.007-0.0070.0000.0000.0000.000
153A156GLU-1-0.818-0.90330.655-0.031-0.0310.0000.0000.0000.000
154A157LEU0-0.038-0.01026.780-0.006-0.0060.0000.0000.0000.000
155A158THR0-0.009-0.02125.254-0.006-0.0060.0000.0000.0000.000
156A159LYS10.8180.91126.1100.0200.0200.0000.0000.0000.000
157A160PRO00.0130.00925.5530.0000.0000.0000.0000.0000.000
158A161VAL0-0.020-0.00620.336-0.009-0.0090.0000.0000.0000.000
159A162ILE00.0240.00522.4260.0050.0050.0000.0000.0000.000
160A163GLU-1-0.811-0.87924.765-0.025-0.0250.0000.0000.0000.000
161A164HIS00.0050.00917.546-0.014-0.0140.0000.0000.0000.000
162A165TYR0-0.030-0.05815.6300.0050.0050.0000.0000.0000.000
163A166LYS10.8430.91021.5020.0230.0230.0000.0000.0000.000
164A167GLN0-0.040-0.03124.516-0.004-0.0040.0000.0000.0000.000
165A168GLN0-0.052-0.02316.9340.0110.0110.0000.0000.0000.000
166A169ASN0-0.055-0.02521.1070.0040.0040.0000.0000.0000.000
167A170LYS10.8600.93614.6310.0490.0490.0000.0000.0000.000
168A171VAL0-0.048-0.01820.8020.0240.0240.0000.0000.0000.000
169A172ILE0-0.0060.00321.684-0.005-0.0050.0000.0000.0000.000
170A173THR0-0.003-0.00824.8450.0030.0030.0000.0000.0000.000
171A174ILE0-0.065-0.03027.3120.0030.0030.0000.0000.0000.000
172A175ASP-1-0.809-0.86329.9660.0460.0460.0000.0000.0000.000
173A176ALA00.0260.00031.8030.0070.0070.0000.0000.0000.000
174A177SER0-0.060-0.06033.8510.0000.0000.0000.0000.0000.000
175A178GLY00.0030.00836.983-0.002-0.0020.0000.0000.0000.000
176A179THR00.033-0.00337.8510.0020.0020.0000.0000.0000.000
177A180VAL00.0660.01633.2550.0030.0030.0000.0000.0000.000
178A181ASP-1-0.825-0.89933.4590.1180.1180.0000.0000.0000.000
179A182ALA00.0220.01934.1590.0040.0040.0000.0000.0000.000
180A183ILE0-0.022-0.00130.7720.0020.0020.0000.0000.0000.000
181A184PHE00.0020.00727.0440.0040.0040.0000.0000.0000.000
182A185ASP-1-0.819-0.91129.4400.1360.1360.0000.0000.0000.000
183A186LYS10.8460.93130.500-0.076-0.0760.0000.0000.0000.000
184A187VAL00.023-0.00725.0380.0010.0010.0000.0000.0000.000
185A188ASN0-0.037-0.05026.0760.0250.0250.0000.0000.0000.000
186A189HIS0-0.084-0.03426.7800.0030.0030.0000.0000.0000.000
187A190GLU-1-0.770-0.86326.0230.0780.0780.0000.0000.0000.000
188A191LEU00.0520.02320.4980.0000.0000.0000.0000.0000.000
189A192GLN0-0.0110.00421.7330.0140.0140.0000.0000.0000.000
190A193LYS10.8280.90323.048-0.079-0.0790.0000.0000.0000.000
191A194PHE00.0280.02218.330-0.011-0.0110.0000.0000.0000.000
192A195GLY00.0230.01618.0170.0290.0290.0000.0000.0000.000
193A196VAL0-0.068-0.03217.5390.0480.0480.0000.0000.0000.000
194A197LYS10.9540.97520.134-0.165-0.1650.0000.0000.0000.000