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: ZY51N

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2239666.508658
FMO2-HF: Nuclear repulsion 2164981.449875
FMO2-HF: Total energy -74685.058783
FMO2-MP2: Total energy -74909.574493


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.
-11.279-1.02110.266-7.075-13.448-0.054
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 : -0.043 / q_NPA : -0.014
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].
3A4LEU0-0.058-0.0033.860-0.0551.809-0.019-0.932-0.9120.003
4A5LEU0-0.0070.0026.463-0.585-0.5850.0000.0000.0000.000
5A6ILE0-0.044-0.0309.9190.0260.0260.0000.0000.0000.000
6A7ARG10.9070.96213.397-0.303-0.3030.0000.0000.0000.000
7A8LEU0-0.022-0.02417.017-0.010-0.0100.0000.0000.0000.000
8A9GLN00.0590.02019.729-0.004-0.0040.0000.0000.0000.000
9A10GLY00.0600.02922.8530.0080.0080.0000.0000.0000.000
10A11PRO00.0130.01526.429-0.005-0.0050.0000.0000.0000.000
11A12LEU00.0080.00129.137-0.007-0.0070.0000.0000.0000.000
12A13GLN0-0.011-0.00122.9900.0090.0090.0000.0000.0000.000
13A14SER0-0.067-0.02826.449-0.009-0.0090.0000.0000.0000.000
14A15TRP00.0480.03120.8170.0060.0060.0000.0000.0000.000
15A16GLY00.0570.02924.824-0.006-0.0060.0000.0000.0000.000
16A17THR0-0.0100.02424.2410.0020.0020.0000.0000.0000.000
17A18ARG10.8030.89324.928-0.019-0.0190.0000.0000.0000.000
18A19SER00.0610.04427.411-0.004-0.0040.0000.0000.0000.000
19A20ARG10.7830.86928.8750.0000.0000.0000.0000.0000.000
20A21PHE00.0670.06029.3110.0010.0010.0000.0000.0000.000
21A22ASP-1-0.742-0.84631.3160.0200.0200.0000.0000.0000.000
22A23HIS0-0.028-0.01931.5420.0040.0040.0000.0000.0000.000
23A24ARG10.8370.90132.631-0.012-0.0120.0000.0000.0000.000
24A25ASP-1-0.845-0.92032.3300.0170.0170.0000.0000.0000.000
25A26THR0-0.034-0.05027.5960.0070.0070.0000.0000.0000.000
26A27TRP0-0.0120.00523.354-0.004-0.0040.0000.0000.0000.000
27A28PRO00.0220.00425.4040.0070.0070.0000.0000.0000.000
28A29TYR0-0.030-0.03920.5380.0070.0070.0000.0000.0000.000
29A30PRO0-0.016-0.01218.269-0.008-0.0080.0000.0000.0000.000
30A31THR0-0.001-0.00819.400-0.007-0.0070.0000.0000.0000.000
31A32LYS10.8470.90213.2410.1130.1130.0000.0000.0000.000
32A33SER0-0.014-0.01018.0220.0090.0090.0000.0000.0000.000
33A34GLY0-0.064-0.02320.7540.0060.0060.0000.0000.0000.000
34A35VAL00.0330.01214.2800.0140.0140.0000.0000.0000.000
35A36VAL00.0510.01814.9310.0240.0240.0000.0000.0000.000
36A37GLY0-0.0030.00016.8700.0060.0060.0000.0000.0000.000
37A38LEU0-0.044-0.01616.4870.0040.0040.0000.0000.0000.000
38A39LEU00.0440.01512.1030.0170.0170.0000.0000.0000.000
39A40ALA00.0150.00615.5610.0080.0080.0000.0000.0000.000
40A41ALA0-0.036-0.01418.238-0.001-0.0010.0000.0000.0000.000
41A42ALA00.0070.00215.892-0.002-0.0020.0000.0000.0000.000
42A43LEU00.0270.00313.4780.0010.0010.0000.0000.0000.000
43A44GLY0-0.054-0.02217.418-0.012-0.0120.0000.0000.0000.000
44A45ARG10.7750.85914.996-0.075-0.0750.0000.0000.0000.000
45A46ASP-1-0.802-0.90021.6210.0410.0410.0000.0000.0000.000
46A47ARG10.9010.93124.025-0.051-0.0510.0000.0000.0000.000
47A48ARG10.8640.91725.694-0.037-0.0370.0000.0000.0000.000
48A49GLU-1-0.840-0.90521.2700.0570.0570.0000.0000.0000.000
49A50ASP-1-0.806-0.88719.490-0.016-0.0160.0000.0000.0000.000
50A51VAL0-0.054-0.03217.7960.0140.0140.0000.0000.0000.000
51A52SER0-0.018-0.03016.754-0.008-0.0080.0000.0000.0000.000
52A53ASP-1-0.723-0.83113.1560.0140.0140.0000.0000.0000.000
53A54LEU0-0.018-0.01812.070-0.017-0.0170.0000.0000.0000.000
54A55ALA0-0.042-0.02513.014-0.006-0.0060.0000.0000.0000.000
55A56ALA0-0.0160.00011.957-0.015-0.0150.0000.0000.0000.000
56A57LEU0-0.0330.0077.474-0.064-0.0640.0000.0000.0000.000
57A58ARG10.8620.9188.6610.4780.4780.0000.0000.0000.000
58A59MET0-0.040-0.0109.493-0.013-0.0130.0000.0000.0000.000
59A60GLY00.014-0.00311.970-0.043-0.0430.0000.0000.0000.000
60A61VAL0-0.038-0.01713.2650.0550.0550.0000.0000.0000.000
61A62ARG10.7740.83814.430-0.159-0.1590.0000.0000.0000.000
62A63VAL0-0.038-0.02216.7990.0220.0220.0000.0000.0000.000
63A64ASP-1-0.748-0.83718.0060.1210.1210.0000.0000.0000.000
64A65ARG10.9180.94720.969-0.083-0.0830.0000.0000.0000.000
65A66LYS10.8950.93524.266-0.024-0.0240.0000.0000.0000.000
66A67GLY00.0290.03126.1400.0000.0000.0000.0000.0000.000
67A68VAL0-0.056-0.02928.491-0.006-0.0060.0000.0000.0000.000
68A69LEU00.0050.00931.7590.0030.0030.0000.0000.0000.000
69A70LYS10.9200.97033.261-0.040-0.0400.0000.0000.0000.000
70A71VAL00.002-0.00435.251-0.001-0.0010.0000.0000.0000.000
71A72ASP-1-0.842-0.90035.4160.0420.0420.0000.0000.0000.000
72A73TYR00.0350.01337.533-0.003-0.0030.0000.0000.0000.000
73A117LYS10.9260.96739.905-0.029-0.0290.0000.0000.0000.000
74A118ARG10.8520.89834.875-0.037-0.0370.0000.0000.0000.000
75A119TYR00.0560.05433.6440.0030.0030.0000.0000.0000.000
76A120PHE0-0.033-0.01530.9130.0020.0020.0000.0000.0000.000
77A121LEU00.0130.01225.585-0.003-0.0030.0000.0000.0000.000
78A122SER0-0.018-0.04728.9520.0060.0060.0000.0000.0000.000
79A123ASP-1-0.900-0.93129.2450.0560.0560.0000.0000.0000.000
80A124ALA00.0240.02325.2010.0020.0020.0000.0000.0000.000
81A125ALA0-0.021-0.02721.9950.0100.0100.0000.0000.0000.000
82A126PHE00.0020.00318.719-0.015-0.0150.0000.0000.0000.000
83A127LEU00.0510.04812.1410.0240.0240.0000.0000.0000.000
84A128VAL0-0.028-0.02712.895-0.052-0.0520.0000.0000.0000.000
85A129GLY00.0400.0189.7610.1150.1150.0000.0000.0000.000
86A130LEU0-0.040-0.0338.069-0.122-0.1220.0000.0000.0000.000
87A131GLU-1-0.750-0.8554.468-0.852-0.640-0.001-0.067-0.1440.000
88A132GLY00.014-0.0093.6710.2310.5790.001-0.129-0.2200.000
89A133GLU-1-0.834-0.8973.257-1.183-0.5360.061-0.265-0.443-0.002
90A134ARG10.8570.8852.745-1.302-0.2812.032-0.746-2.3070.000
91A135ALA00.0090.0054.3330.3450.387-0.001-0.006-0.0350.000
92A136LEU00.001-0.0087.8780.1130.1130.0000.0000.0000.000
93A137LEU00.0090.0063.136-0.2350.1900.031-0.105-0.3510.000
94A138GLU-1-0.800-0.8895.5250.9160.9160.0000.0000.0000.000
95A139ALA0-0.057-0.0207.445-0.060-0.0600.0000.0000.0000.000
96A140LEU0-0.001-0.0069.119-0.033-0.0330.0000.0000.0000.000
97A141HIS00.0040.0048.254-0.058-0.0580.0000.0000.0000.000
98A142ARG10.8060.8679.210-0.658-0.6580.0000.0000.0000.000
99A143ALA0-0.017-0.00613.149-0.054-0.0540.0000.0000.0000.000
100A144LEU0-0.012-0.02011.423-0.048-0.0480.0000.0000.0000.000
101A145LYS10.8550.94514.781-0.287-0.2870.0000.0000.0000.000
102A146ASN0-0.074-0.03216.597-0.045-0.0450.0000.0000.0000.000
103A147PRO00.0070.02218.713-0.008-0.0080.0000.0000.0000.000
104A148ARG10.9110.95019.606-0.147-0.1470.0000.0000.0000.000
105A149PHE0-0.043-0.00521.810-0.015-0.0150.0000.0000.0000.000
106A150PRO0-0.017-0.01922.5320.0120.0120.0000.0000.0000.000
107A151LEU00.0170.02418.384-0.007-0.0070.0000.0000.0000.000
108A152TYR00.002-0.02222.545-0.006-0.0060.0000.0000.0000.000
109A153LEU0-0.0040.02021.4220.0030.0030.0000.0000.0000.000
110A154GLY00.0590.03324.112-0.010-0.0100.0000.0000.0000.000
111A155ARG10.7240.84725.851-0.045-0.0450.0000.0000.0000.000
112A156LYS10.9270.96027.400-0.062-0.0620.0000.0000.0000.000
113A157SER00.0030.00329.488-0.006-0.0060.0000.0000.0000.000
114A158TYR0-0.026-0.01227.8800.0000.0000.0000.0000.0000.000
115A159VAL00.004-0.00626.4710.0070.0070.0000.0000.0000.000
116A160PRO0-0.017-0.00621.919-0.004-0.0040.0000.0000.0000.000
117A161SER0-0.062-0.01424.0490.0030.0030.0000.0000.0000.000
118A162PRO00.0630.01021.631-0.009-0.0090.0000.0000.0000.000
119A163PRO00.0250.00520.2740.0010.0010.0000.0000.0000.000
120A164PRO00.0330.01316.9180.0110.0110.0000.0000.0000.000
121A165TYR0-0.0280.00512.511-0.009-0.0090.0000.0000.0000.000
122A166LEU00.0310.02612.502-0.067-0.0670.0000.0000.0000.000
123A167PRO0-0.011-0.00112.3170.1340.1340.0000.0000.0000.000
124A168ASP-1-0.786-0.85211.3350.5210.5210.0000.0000.0000.000
125A169GLY00.0210.00510.1160.0120.0120.0000.0000.0000.000
126A170LEU0-0.038-0.0183.749-0.2410.0080.004-0.056-0.1960.000
127A171VAL00.0160.0005.077-0.561-0.298-0.001-0.035-0.2270.000
128A172GLU-1-0.766-0.8472.148-5.131-0.9696.635-4.734-6.064-0.040
129A173ALA00.0070.0042.358-0.607-0.6521.0320.686-1.673-0.007
130A174PRO00.0350.0312.838-1.302-0.2920.493-0.682-0.821-0.008
131A175LEU0-0.031-0.0244.8920.2490.309-0.001-0.004-0.0550.000
132A176ALA0-0.029-0.0137.4100.1580.1580.0000.0000.0000.000
133A177GLU-1-0.849-0.9287.552-0.274-0.2740.0000.0000.0000.000
134A178ALA0-0.012-0.0055.5620.1160.1160.0000.0000.0000.000
135A179LEU0-0.025-0.0207.6620.1010.1010.0000.0000.0000.000
136A180GLU-1-0.855-0.91511.088-0.089-0.0890.0000.0000.0000.000
137A181GLY0-0.008-0.00911.0930.0070.0070.0000.0000.0000.000
138A182TYR0-0.039-0.05010.7170.0140.0140.0000.0000.0000.000
139A183PRO00.0380.02012.375-0.045-0.0450.0000.0000.0000.000
140A184TYR00.0340.03116.1790.0150.0150.0000.0000.0000.000
141A185LEU0-0.009-0.02716.4910.0150.0150.0000.0000.0000.000
142A186LEU0-0.146-0.05719.606-0.001-0.0010.0000.0000.0000.000
143A187GLY0-0.005-0.00822.6320.0050.0050.0000.0000.0000.000
144A188GLY00.0280.02024.505-0.008-0.0080.0000.0000.0000.000
145A189LYS10.8530.91420.731-0.031-0.0310.0000.0000.0000.000
146A190PRO00.0070.01320.9920.0000.0000.0000.0000.0000.000
147A191PRO00.0010.01623.987-0.007-0.0070.0000.0000.0000.000
148A192GLU-1-0.900-0.96626.6950.0260.0260.0000.0000.0000.000
149A193ASP-1-0.844-0.91223.4120.0080.0080.0000.0000.0000.000
150A194LEU0-0.037-0.01719.0110.0040.0040.0000.0000.0000.000
151A195LEU0-0.024-0.00820.677-0.008-0.0080.0000.0000.0000.000
152A196LEU00.0150.00213.8660.0170.0170.0000.0000.0000.000
153A197ALA00.0080.00417.166-0.013-0.0130.0000.0000.0000.000
154A198LEU00.002-0.00512.5380.0070.0070.0000.0000.0000.000
155A199GLU-1-0.771-0.86113.443-0.118-0.1180.0000.0000.0000.000
156A200ALA0-0.027-0.01413.980-0.043-0.0430.0000.0000.0000.000
157A201GLU-1-0.900-0.95415.684-0.198-0.1980.0000.0000.0000.000
158A202GLU-1-0.928-0.95418.617-0.086-0.0860.0000.0000.0000.000
159A203GLY00.002-0.01620.370-0.004-0.0040.0000.0000.0000.000
160A204ARG10.8650.93422.6660.0530.0530.0000.0000.0000.000
161A205LEU00.0050.02123.101-0.003-0.0030.0000.0000.0000.000
162A206VAL0-0.0010.00221.2550.0090.0090.0000.0000.0000.000
163A207TYR00.0350.01522.780-0.006-0.0060.0000.0000.0000.000
164A208ASP-1-0.750-0.86920.670-0.009-0.0090.0000.0000.0000.000
165A209GLN00.1040.07015.4750.0200.0200.0000.0000.0000.000
166A210PRO0-0.026-0.02917.8230.0020.0020.0000.0000.0000.000
167A211ALA00.001-0.00419.674-0.011-0.0110.0000.0000.0000.000
168A212GLY00.0310.01622.241-0.004-0.0040.0000.0000.0000.000
169A213PRO00.0430.04022.8840.0040.0040.0000.0000.0000.000
170A214PHE00.0210.01419.827-0.004-0.0040.0000.0000.0000.000
171A215SER0-0.046-0.03125.0060.0000.0000.0000.0000.0000.000
172A216GLU-1-0.909-0.95927.470-0.006-0.0060.0000.0000.0000.000
173A217ARG10.8680.92927.197-0.016-0.0160.0000.0000.0000.000
174A218ARG10.9711.00525.4610.0220.0220.0000.0000.0000.000
175A219PHE0-0.012-0.01422.0850.0040.0040.0000.0000.0000.000
176A220ALA00.0290.01622.4670.0000.0000.0000.0000.0000.000
177A221ALA0-0.025-0.01722.9300.0030.0030.0000.0000.0000.000
178A222ARG10.8140.87216.0770.0430.0430.0000.0000.0000.000
179A223PHE00.0240.00619.8320.0160.0160.0000.0000.0000.000
180A224VAL0-0.017-0.00517.931-0.013-0.0130.0000.0000.0000.000
181A225ARG10.8390.89116.0670.1450.1450.0000.0000.0000.000
182A226GLU-1-0.864-0.91318.757-0.018-0.0180.0000.0000.0000.000
183A227GLU-1-0.820-0.88217.318-0.122-0.1220.0000.0000.0000.000
184A228VAL00.001-0.01020.6540.0120.0120.0000.0000.0000.000
185A229LEU00.0050.01315.466-0.009-0.0090.0000.0000.0000.000
186A230PRO00.007-0.00419.3180.0120.0120.0000.0000.0000.000
187A231LYS10.9070.96020.214-0.011-0.0110.0000.0000.0000.000
188A232GLU-1-0.903-0.97521.3770.0130.0130.0000.0000.0000.000
189A233ARG10.7840.88811.8160.0750.0750.0000.0000.0000.000
190A234VAL00.0250.02516.4020.0040.0040.0000.0000.0000.000
191A235PRO0-0.037-0.00515.038-0.008-0.0080.0000.0000.0000.000
192A236GLU-1-0.891-0.95818.1330.0730.0730.0000.0000.0000.000
193A237GLY00.0090.03619.9260.0160.0160.0000.0000.0000.000
194A238PRO0-0.074-0.04020.883-0.019-0.0190.0000.0000.0000.000
195A239PRO0-0.060-0.03915.969-0.029-0.0290.0000.0000.0000.000