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: 66V8Z

Calculation Name: 4N77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4N77

Chain ID: A

ChEMBL ID:

UniProt ID: Q53WH0

Base Structure: X-ray

Registration Date: 2023-06-19

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 OptHSide
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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2237493.350116
FMO2-HF: Nuclear repulsion 2162808.680518
FMO2-HF: Total energy -74684.669598
FMO2-MP2: Total energy -74909.188685


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
-6.195-2.15221.233-8.139-17.135-0.068
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.075 / q_NPA : -0.015
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].
3A4LEU0-0.066-0.0173.805-0.6891.818-0.036-1.302-1.1690.005
4A5LEU0-0.0080.0036.324-0.613-0.6130.0000.0000.0000.000
5A6ILE0-0.038-0.0279.676-0.012-0.0120.0000.0000.0000.000
6A7ARG10.9390.97812.955-0.357-0.3570.0000.0000.0000.000
7A8LEU0-0.036-0.03016.574-0.023-0.0230.0000.0000.0000.000
8A9GLN00.0600.02419.390-0.002-0.0020.0000.0000.0000.000
9A10GLY00.0660.02922.5290.0060.0060.0000.0000.0000.000
10A11PRO00.0000.01625.943-0.005-0.0050.0000.0000.0000.000
11A12LEU00.0100.00328.749-0.007-0.0070.0000.0000.0000.000
12A13GLN00.0030.00122.8460.0100.0100.0000.0000.0000.000
13A14SER0-0.060-0.02326.379-0.010-0.0100.0000.0000.0000.000
14A15TRP00.0440.02720.6870.0040.0040.0000.0000.0000.000
15A16GLY00.0370.02625.165-0.007-0.0070.0000.0000.0000.000
16A17THR00.0160.03724.3390.0020.0020.0000.0000.0000.000
17A18ARG10.8110.89025.518-0.031-0.0310.0000.0000.0000.000
18A19SER00.0750.05727.799-0.005-0.0050.0000.0000.0000.000
19A20ARG10.7780.86329.063-0.005-0.0050.0000.0000.0000.000
20A21PHE00.0620.06429.479-0.001-0.0010.0000.0000.0000.000
21A22ASP-1-0.706-0.81931.5040.0270.0270.0000.0000.0000.000
22A23HIS0-0.007-0.00531.8950.0050.0050.0000.0000.0000.000
23A24ARG10.7950.86232.796-0.020-0.0200.0000.0000.0000.000
24A25ASP-1-0.836-0.90932.3710.0290.0290.0000.0000.0000.000
25A26THR0-0.048-0.04827.7650.0070.0070.0000.0000.0000.000
26A27TRP0-0.020-0.00323.365-0.006-0.0060.0000.0000.0000.000
27A28PRO00.0290.00325.4280.0070.0070.0000.0000.0000.000
28A29TYR0-0.045-0.04620.4990.0090.0090.0000.0000.0000.000
29A30PRO0-0.019-0.00918.428-0.011-0.0110.0000.0000.0000.000
30A31THR00.000-0.01919.648-0.005-0.0050.0000.0000.0000.000
31A32LYS10.8560.89713.4230.0910.0910.0000.0000.0000.000
32A33SER0-0.016-0.01217.9770.0080.0080.0000.0000.0000.000
33A34GLY0-0.065-0.02520.5420.0050.0050.0000.0000.0000.000
34A35VAL00.0480.01914.4120.0120.0120.0000.0000.0000.000
35A36VAL00.0230.01115.0000.0200.0200.0000.0000.0000.000
36A37GLY0-0.009-0.00616.8850.0040.0040.0000.0000.0000.000
37A38LEU0-0.040-0.01316.3910.0010.0010.0000.0000.0000.000
38A39LEU00.0470.01411.8690.0110.0110.0000.0000.0000.000
39A40ALA00.0190.01115.6190.0030.0030.0000.0000.0000.000
40A41ALA0-0.027-0.01418.185-0.004-0.0040.0000.0000.0000.000
41A42ALA00.0100.00015.925-0.003-0.0030.0000.0000.0000.000
42A43LEU00.0220.01013.5400.0030.0030.0000.0000.0000.000
43A44GLY0-0.057-0.01917.406-0.012-0.0120.0000.0000.0000.000
44A45ARG10.7700.85515.342-0.045-0.0450.0000.0000.0000.000
45A46ASP-1-0.817-0.90421.5190.0380.0380.0000.0000.0000.000
46A47ARG10.9300.94123.977-0.055-0.0550.0000.0000.0000.000
47A48ARG10.8430.90225.574-0.032-0.0320.0000.0000.0000.000
48A49GLU-1-0.854-0.91121.5100.0380.0380.0000.0000.0000.000
49A50ASP-1-0.827-0.88819.830-0.031-0.0310.0000.0000.0000.000
50A51VAL0-0.030-0.02618.1530.0110.0110.0000.0000.0000.000
51A52SER0-0.029-0.03617.082-0.007-0.0070.0000.0000.0000.000
52A53ASP-1-0.739-0.83513.424-0.022-0.0220.0000.0000.0000.000
53A54LEU0-0.009-0.01412.395-0.017-0.0170.0000.0000.0000.000
54A55ALA0-0.054-0.03013.093-0.005-0.0050.0000.0000.0000.000
55A56ALA0-0.0070.00812.409-0.007-0.0070.0000.0000.0000.000
56A57LEU0-0.0320.0097.681-0.053-0.0530.0000.0000.0000.000
57A58ARG10.8860.9418.8460.3810.3810.0000.0000.0000.000
58A59MET0-0.033-0.0029.6170.0210.0210.0000.0000.0000.000
59A60GLY00.0090.00011.888-0.046-0.0460.0000.0000.0000.000
60A61VAL0-0.044-0.02613.2440.0600.0600.0000.0000.0000.000
61A62ARG10.8090.87114.114-0.264-0.2640.0000.0000.0000.000
62A63VAL0-0.052-0.03716.6030.0200.0200.0000.0000.0000.000
63A64ASP-1-0.744-0.82517.8620.1950.1950.0000.0000.0000.000
64A65ARG10.9410.95220.779-0.121-0.1210.0000.0000.0000.000
65A66LYS10.9810.98024.288-0.053-0.0530.0000.0000.0000.000
66A67GLY00.0190.02526.0100.0010.0010.0000.0000.0000.000
67A68VAL0-0.046-0.02128.577-0.006-0.0060.0000.0000.0000.000
68A69LEU00.0190.01831.5840.0030.0030.0000.0000.0000.000
69A70LYS10.9260.97033.141-0.058-0.0580.0000.0000.0000.000
70A71VAL00.0100.00035.1300.0000.0000.0000.0000.0000.000
71A72ASP-1-0.873-0.90435.2060.0550.0550.0000.0000.0000.000
72A73TYR00.005-0.01937.455-0.003-0.0030.0000.0000.0000.000
73A117LYS10.9650.99139.775-0.036-0.0360.0000.0000.0000.000
74A118ARG10.8710.92334.940-0.046-0.0460.0000.0000.0000.000
75A119TYR00.0580.04333.5870.0030.0030.0000.0000.0000.000
76A120PHE0-0.044-0.02330.7490.0020.0020.0000.0000.0000.000
77A121LEU00.0140.01625.646-0.004-0.0040.0000.0000.0000.000
78A122SER0-0.027-0.05829.1400.0050.0050.0000.0000.0000.000
79A123ASP-1-0.879-0.91928.6110.0820.0820.0000.0000.0000.000
80A124ALA00.0180.02524.9440.0000.0000.0000.0000.0000.000
81A125ALA0-0.025-0.03421.7690.0090.0090.0000.0000.0000.000
82A126PHE0-0.009-0.01218.712-0.012-0.0120.0000.0000.0000.000
83A127LEU00.0580.04712.1680.0230.0230.0000.0000.0000.000
84A128VAL0-0.035-0.02612.724-0.051-0.0510.0000.0000.0000.000
85A129GLY00.0590.0349.5170.1300.1300.0000.0000.0000.000
86A130LEU0-0.044-0.0348.005-0.177-0.1770.0000.0000.0000.000
87A131GLU-1-0.773-0.8834.598-0.774-0.608-0.001-0.051-0.1130.000
88A132GLY00.0340.0034.0710.1630.337-0.001-0.034-0.1390.000
89A133GLU-1-0.859-0.9184.041-0.782-0.6160.000-0.035-0.1310.000
90A134ARG10.8920.8972.491-0.4250.1302.888-0.919-2.5250.001
91A135ALA00.0020.0034.8180.2930.325-0.001-0.001-0.0290.000
92A136LEU00.0020.0038.1440.1280.1280.0000.0000.0000.000
93A137LEU00.0030.0022.964-0.2720.2410.056-0.132-0.438-0.001
94A138GLU-1-0.807-0.8895.6080.7280.7280.0000.0000.0000.000
95A139ALA0-0.044-0.0187.4020.0040.0040.0000.0000.0000.000
96A140LEU0-0.014-0.0159.007-0.005-0.0050.0000.0000.0000.000
97A141HIS0-0.0010.0037.845-0.032-0.0320.0000.0000.0000.000
98A142ARG10.8070.8739.403-0.511-0.5110.0000.0000.0000.000
99A143ALA0-0.011-0.00612.921-0.041-0.0410.0000.0000.0000.000
100A144LEU0-0.007-0.01511.312-0.041-0.0410.0000.0000.0000.000
101A145LYS10.8610.95414.675-0.301-0.3010.0000.0000.0000.000
102A146ASN0-0.078-0.04016.392-0.037-0.0370.0000.0000.0000.000
103A147PRO00.0060.02218.565-0.010-0.0100.0000.0000.0000.000
104A148ARG10.9200.95019.440-0.131-0.1310.0000.0000.0000.000
105A149PHE0-0.059-0.00921.547-0.016-0.0160.0000.0000.0000.000
106A150PRO0-0.007-0.01322.1580.0140.0140.0000.0000.0000.000
107A151LEU00.0120.02118.004-0.005-0.0050.0000.0000.0000.000
108A152TYR00.007-0.01722.132-0.007-0.0070.0000.0000.0000.000
109A153LEU0-0.0040.01521.0280.0050.0050.0000.0000.0000.000
110A154GLY00.0740.03523.920-0.009-0.0090.0000.0000.0000.000
111A155ARG10.7200.85825.817-0.062-0.0620.0000.0000.0000.000
112A156LYS10.9640.96927.438-0.065-0.0650.0000.0000.0000.000
113A157SER0-0.050-0.02629.221-0.006-0.0060.0000.0000.0000.000
114A158TYR0-0.036-0.02127.671-0.001-0.0010.0000.0000.0000.000
115A159VAL0-0.001-0.00826.4390.0070.0070.0000.0000.0000.000
116A160PRO0-0.0030.00121.805-0.003-0.0030.0000.0000.0000.000
117A161SER0-0.056-0.01523.952-0.001-0.0010.0000.0000.0000.000
118A162PRO00.0510.01021.077-0.009-0.0090.0000.0000.0000.000
119A163PRO00.014-0.00219.461-0.001-0.0010.0000.0000.0000.000
120A164PRO00.0470.01816.5220.0150.0150.0000.0000.0000.000
121A165TYR0-0.0380.00112.1390.0060.0060.0000.0000.0000.000
122A166LEU00.0140.01912.309-0.077-0.0770.0000.0000.0000.000
123A167PRO00.012-0.00611.9310.1430.1430.0000.0000.0000.000
124A168ASP-1-0.844-0.89110.6110.6650.6650.0000.0000.0000.000
125A169GLY00.0180.0019.5170.0600.0600.0000.0000.0000.000
126A170LEU0-0.038-0.0122.940-0.800-0.0970.113-0.252-0.5630.001
127A171VAL00.0290.0104.898-0.631-0.272-0.001-0.060-0.2980.000
128A172GLU-1-0.757-0.8612.096-3.348-1.82813.331-6.576-8.275-0.051
129A173ALA00.0120.0081.8982.324-1.3444.2591.875-2.465-0.014
130A174PRO00.0390.0332.839-0.967-0.0040.627-0.647-0.943-0.009
131A175LEU0-0.027-0.0174.6550.3290.382-0.001-0.005-0.0470.000
132A176ALA0-0.025-0.0187.2720.1650.1650.0000.0000.0000.000
133A177GLU-1-0.862-0.9357.378-0.180-0.1800.0000.0000.0000.000
134A178ALA0-0.015-0.0075.1530.1180.1180.0000.0000.0000.000
135A179LEU0-0.034-0.0277.2290.0670.0670.0000.0000.0000.000
136A180GLU-1-0.881-0.93410.599-0.005-0.0050.0000.0000.0000.000
137A181GLY0-0.019-0.01410.891-0.014-0.0140.0000.0000.0000.000
138A182TYR0-0.053-0.05010.660-0.011-0.0110.0000.0000.0000.000
139A183PRO00.0470.03212.441-0.057-0.0570.0000.0000.0000.000
140A184TYR00.0070.00516.1010.0200.0200.0000.0000.0000.000
141A185LEU0-0.002-0.02116.4760.0090.0090.0000.0000.0000.000
142A186LEU0-0.127-0.04919.526-0.006-0.0060.0000.0000.0000.000
143A187GLY00.017-0.00122.4170.0070.0070.0000.0000.0000.000
144A188GLY00.0460.02924.325-0.008-0.0080.0000.0000.0000.000
145A189LYS10.8520.91620.438-0.075-0.0750.0000.0000.0000.000
146A190PRO00.0210.01420.608-0.003-0.0030.0000.0000.0000.000
147A191PRO0-0.0030.01223.602-0.008-0.0080.0000.0000.0000.000
148A192GLU-1-0.957-0.99725.7950.0520.0520.0000.0000.0000.000
149A193ASP-1-0.850-0.91823.0760.0420.0420.0000.0000.0000.000
150A194LEU0-0.057-0.02018.7750.0050.0050.0000.0000.0000.000
151A195LEU0-0.056-0.02320.895-0.009-0.0090.0000.0000.0000.000
152A196LEU00.0290.01113.7250.0240.0240.0000.0000.0000.000
153A197ALA0-0.011-0.00317.300-0.020-0.0200.0000.0000.0000.000
154A198LEU00.0110.00512.5730.0150.0150.0000.0000.0000.000
155A199GLU-1-0.788-0.86313.568-0.094-0.0940.0000.0000.0000.000
156A200ALA0-0.046-0.03014.370-0.032-0.0320.0000.0000.0000.000
157A201GLU-1-0.896-0.95515.906-0.190-0.1900.0000.0000.0000.000
158A202GLU-1-0.932-0.94918.747-0.077-0.0770.0000.0000.0000.000
159A203GLY0-0.007-0.01620.8440.0010.0010.0000.0000.0000.000
160A204ARG10.9160.96023.2980.0270.0270.0000.0000.0000.000
161A205LEU00.0130.01523.368-0.001-0.0010.0000.0000.0000.000
162A206VAL00.0110.01021.6640.0090.0090.0000.0000.0000.000
163A207TYR00.0220.00823.357-0.007-0.0070.0000.0000.0000.000
164A208ASP-1-0.759-0.86620.7020.0140.0140.0000.0000.0000.000
165A209GLN00.0950.05716.1010.0200.0200.0000.0000.0000.000
166A210PRO0-0.028-0.02618.227-0.001-0.0010.0000.0000.0000.000
167A211ALA00.013-0.00319.909-0.010-0.0100.0000.0000.0000.000
168A212GLY00.0150.00522.402-0.006-0.0060.0000.0000.0000.000
169A213PRO00.0470.04923.2590.0050.0050.0000.0000.0000.000
170A214PHE00.0340.01119.825-0.002-0.0020.0000.0000.0000.000
171A215SER0-0.053-0.03325.1130.0010.0010.0000.0000.0000.000
172A216GLU-1-0.921-0.96327.765-0.010-0.0100.0000.0000.0000.000
173A217ARG10.8440.92127.178-0.019-0.0190.0000.0000.0000.000
174A218ARG11.0281.04025.7880.0270.0270.0000.0000.0000.000
175A219PHE0-0.021-0.01922.5730.0030.0030.0000.0000.0000.000
176A220ALA00.0390.02622.593-0.001-0.0010.0000.0000.0000.000
177A221ALA0-0.019-0.02123.2680.0060.0060.0000.0000.0000.000
178A222ARG10.8080.87216.0700.0080.0080.0000.0000.0000.000
179A223PHE00.014-0.00120.0190.0150.0150.0000.0000.0000.000
180A224VAL0-0.020-0.00518.319-0.009-0.0090.0000.0000.0000.000
181A225ARG10.8340.88515.8230.1070.1070.0000.0000.0000.000
182A226GLU-1-0.869-0.92018.8290.0190.0190.0000.0000.0000.000
183A227GLU-1-0.824-0.89017.151-0.077-0.0770.0000.0000.0000.000
184A228VAL00.000-0.01220.5680.0140.0140.0000.0000.0000.000
185A229LEU0-0.0030.00315.753-0.008-0.0080.0000.0000.0000.000
186A230PRO00.0330.00919.2630.0100.0100.0000.0000.0000.000
187A231LYS10.9270.96420.027-0.035-0.0350.0000.0000.0000.000
188A232GLU-1-0.934-0.98521.1580.0510.0510.0000.0000.0000.000
189A233ARG10.8140.92011.508-0.039-0.0390.0000.0000.0000.000
190A234VAL00.0170.01216.4370.0130.0130.0000.0000.0000.000
191A235PRO0-0.0210.00714.871-0.020-0.0200.0000.0000.0000.000
192A236GLU-1-0.930-0.97218.0020.1190.1190.0000.0000.0000.000
193A237GLY00.0080.03819.6430.0230.0230.0000.0000.0000.000
194A238PRO0-0.078-0.04620.625-0.023-0.0230.0000.0000.0000.000
195A239PRO0-0.026-0.01016.188-0.030-0.0300.0000.0000.0000.000