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

tag_button

FMODB ID: 8N9LY

Calculation Name: 3B77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B77

Chain ID: A

ChEMBL ID:

UniProt ID: B1YJX4

Base Structure: X-ray

Registration Date: 2023-09-27

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 190
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1998627.118457
FMO2-HF: Nuclear repulsion 1921928.730958
FMO2-HF: Total energy -76698.387499
FMO2-MP2: Total energy -76924.825934


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:14:ASP)


Summations of interaction energy for fragment #1(A:14:ASP)
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.
-36.964-31.3634.732-20.853-19.4810.193
Interaction energy analysis for fragmet #1(A:14:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.771 / q_NPA : -0.870
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].
3A16GLY00.0270.0073.82110.53312.5260.008-0.908-1.0930.005
4A17GLN0-0.118-0.0795.867-2.761-2.7610.0000.0000.0000.000
5A18VAL0-0.020-0.0149.2160.0220.0220.0000.0000.0000.000
6A19ILE0-0.036-0.01410.922-0.185-0.1850.0000.0000.0000.000
7A20HIS00.0160.00114.038-0.506-0.5060.0000.0000.0000.000
8A21PRO00.040-0.00317.7640.1370.1370.0000.0000.0000.000
9A22ASP-1-0.904-0.94420.46712.92312.9230.0000.0000.0000.000
10A23ASP-1-0.913-0.95416.95016.42716.4270.0000.0000.0000.000
11A24PHE0-0.045-0.02516.9420.7750.7750.0000.0000.0000.000
12A25ASP-1-0.798-0.88418.63414.78314.7830.0000.0000.0000.000
13A26LYS10.7300.85117.681-15.237-15.2370.0000.0000.0000.000
14A27ALA0-0.058-0.01814.5391.4371.4370.0000.0000.0000.000
15A28ALA00.0230.01813.259-0.929-0.9290.0000.0000.0000.000
16A29ALA0-0.013-0.03213.329-0.651-0.6510.0000.0000.0000.000
17A30ASP-1-0.857-0.94915.24013.71213.7120.0000.0000.0000.000
18A31ASP-1-0.914-0.94918.65414.86914.8690.0000.0000.0000.000
19A32TYR0-0.084-0.04216.828-0.685-0.6850.0000.0000.0000.000
20A33VAL0-0.044-0.00819.130-0.055-0.0550.0000.0000.0000.000
21A34LEU0-0.021-0.00921.461-0.251-0.2510.0000.0000.0000.000
22A35HIS0-0.001-0.00522.462-0.862-0.8620.0000.0000.0000.000
23A36GLU-1-0.966-0.98326.81110.71410.7140.0000.0000.0000.000
24A37ASP-1-0.962-0.98028.1489.8149.8140.0000.0000.0000.000
25A38GLY0-0.047-0.02229.317-0.140-0.1400.0000.0000.0000.000
26A39GLU-1-0.786-0.82322.34513.39813.3980.0000.0000.0000.000
27A40LYS10.9350.96023.502-12.371-12.3710.0000.0000.0000.000
28A41ILE00.0140.00817.2350.0780.0780.0000.0000.0000.000
29A42TYR0-0.105-0.09719.427-0.603-0.6030.0000.0000.0000.000
30A43PHE0-0.001-0.00712.883-0.050-0.0500.0000.0000.0000.000
31A44LEU00.0050.01712.4550.0260.0260.0000.0000.0000.000
32A45ILE00.0010.0117.5380.0640.0640.0000.0000.0000.000
33A46LYS10.8420.9197.621-27.396-27.3960.0000.0000.0000.000
34A47SER00.0570.0292.253-3.721-1.1791.545-1.831-2.2560.011
35A48LYS10.7800.8781.779-173.208-177.98731.967-15.228-11.9600.195
36A49THR0-0.042-0.0432.771-11.603-8.9420.866-1.235-2.2920.001
37A50ASP-1-0.769-0.8364.16530.30730.565-0.001-0.026-0.2310.000
38A51GLU-1-0.773-0.8865.79427.53027.5300.0000.0000.0000.000
39A52TYR0-0.022-0.0294.908-2.727-2.644-0.001-0.005-0.0770.000
40A53CYS00.0040.00610.642-0.307-0.3070.0000.0000.0000.000
41A54PHE00.0370.02411.796-0.688-0.6880.0000.0000.0000.000
42A55THR00.0630.00716.612-0.272-0.2720.0000.0000.0000.000
43A56ASN00.0240.01320.3340.3760.3760.0000.0000.0000.000
44A57LEU0-0.0050.00322.832-0.418-0.4180.0000.0000.0000.000
45A58ALA0-0.011-0.01419.857-0.287-0.2870.0000.0000.0000.000
46A59LEU0-0.0220.02912.3480.2720.2720.0000.0000.0000.000
47A60VAL00.006-0.00515.412-0.483-0.4830.0000.0000.0000.000
48A61HIS0-0.021-0.0087.680-1.513-1.5130.0000.0000.0000.000
49A62LEU0-0.0050.00610.606-1.110-1.1100.0000.0000.0000.000
50A63ASP-1-0.836-0.9308.77228.35728.3570.0000.0000.0000.000
51A64GLY00.1220.0506.497-1.438-1.4380.0000.0000.0000.000
52A65GLU-1-0.894-0.9226.89624.07324.0730.0000.0000.0000.000
53A66SER0-0.109-0.0758.261-2.943-2.9430.0000.0000.0000.000
54A67ALA00.0290.0216.8212.1052.1050.0000.0000.0000.000
55A68VAL00.001-0.0097.8772.0162.0160.0000.0000.0000.000
56A69SER0-0.005-0.01210.908-3.068-3.0680.0000.0000.0000.000
57A70SER0-0.0080.00310.749-1.565-1.5650.0000.0000.0000.000
58A71LYS10.8480.92011.828-20.270-20.2700.0000.0000.0000.000
59A72ARG10.8730.9457.243-33.492-33.4920.0000.0000.0000.000
60A73VAL0-0.030-0.00112.029-1.788-1.7880.0000.0000.0000.000
61A74LEU0-0.0180.00913.1840.8310.8310.0000.0000.0000.000
62A75TYR0-0.025-0.01512.816-1.605-1.6050.0000.0000.0000.000
63A76ARG10.8000.83916.175-13.209-13.2090.0000.0000.0000.000
64A77TYR0-0.022-0.01114.216-0.306-0.3060.0000.0000.0000.000
65A78PRO00.0310.00319.2110.0430.0430.0000.0000.0000.000
66A79TYR00.0470.01118.435-0.055-0.0550.0000.0000.0000.000
67A80ALA0-0.056-0.03022.693-0.177-0.1770.0000.0000.0000.000
68A81HIS0-0.044-0.01424.536-0.347-0.3470.0000.0000.0000.000
69A82TYR0-0.048-0.02119.8450.0760.0760.0000.0000.0000.000
70A83PRO00.003-0.00420.7980.3940.3940.0000.0000.0000.000
71A84ILE00.0280.02517.6780.3430.3430.0000.0000.0000.000
72A85ARG10.8450.90418.885-12.394-12.3940.0000.0000.0000.000
73A86HIS0-0.002-0.01518.0910.5240.5240.0000.0000.0000.000
74A87VAL00.0010.01916.5300.5870.5870.0000.0000.0000.000
75A88MET0-0.046-0.02415.135-0.776-0.7760.0000.0000.0000.000
76A89PHE00.008-0.01612.7100.6350.6350.0000.0000.0000.000
77A90GLU-1-0.848-0.89812.13816.43716.4370.0000.0000.0000.000
78A91THR0-0.018-0.01112.3760.8500.8500.0000.0000.0000.000
79A92ALA00.0250.01313.024-0.104-0.1040.0000.0000.0000.000
80A93GLY00.0310.02713.981-1.261-1.2610.0000.0000.0000.000
81A94THR0-0.065-0.05416.5980.5850.5850.0000.0000.0000.000
82A95VAL0-0.038-0.02614.8640.2400.2400.0000.0000.0000.000
83A96ASP-1-0.822-0.88811.52720.30120.3010.0000.0000.0000.000
84A97LEU00.001-0.0098.946-1.290-1.2900.0000.0000.0000.000
85A98ASP-1-0.867-0.9456.90131.60331.6030.0000.0000.0000.000
86A99VAL0-0.068-0.0289.412-2.429-2.4290.0000.0000.0000.000
87A100GLU-1-0.743-0.8256.84423.57523.5750.0000.0000.0000.000
88A101ILE0-0.058-0.0278.990-2.008-2.0080.0000.0000.0000.000
89A102LYS10.8070.8749.810-17.861-17.8610.0000.0000.0000.000
90A103PHE0-0.025-0.01411.452-0.909-0.9090.0000.0000.0000.000
91A104GLU-1-0.859-0.91313.79813.96213.9620.0000.0000.0000.000
92A105ILE00.0250.00614.896-0.475-0.4750.0000.0000.0000.000
93A106GLY00.0520.01917.4200.1600.1600.0000.0000.0000.000
94A107GLY0-0.093-0.04718.651-0.692-0.6920.0000.0000.0000.000
95A108LYS10.8260.95211.294-20.329-20.3290.0000.0000.0000.000
96A109HIS0-0.018-0.02512.7330.3590.3590.0000.0000.0000.000
97A110TYR0-0.041-0.0468.9410.4170.4170.0000.0000.0000.000
98A111SER0-0.051-0.0496.883-0.674-0.6740.0000.0000.0000.000
99A112ILE00.0020.0005.1041.2841.2840.0000.0000.0000.000
100A113ASP-1-0.825-0.9012.68325.82928.7590.349-1.611-1.667-0.019
101A114VAL0-0.042-0.0305.2133.2923.208-0.001-0.0090.0950.000
102A115ASP-1-0.708-0.8288.09522.90522.9050.0000.0000.0000.000
103A116LYS10.8280.90710.188-21.748-21.7480.0000.0000.0000.000
104A117LYS10.7610.86812.976-25.189-25.1890.0000.0000.0000.000
105A118GLN0-0.0120.00012.2550.7120.7120.0000.0000.0000.000
106A119LEU00.0230.02414.627-0.250-0.2500.0000.0000.0000.000
107A120GLU-1-0.861-0.93415.49612.98312.9830.0000.0000.0000.000
108A121HIS00.0530.03315.8110.0490.0490.0000.0000.0000.000
109A122VAL00.0270.01211.801-0.440-0.4400.0000.0000.0000.000
110A123LYS10.7470.85514.903-14.109-14.1090.0000.0000.0000.000
111A124ASP-1-0.764-0.87317.94912.52512.5250.0000.0000.0000.000
112A125LEU00.0050.01412.933-0.568-0.5680.0000.0000.0000.000
113A126TYR0-0.004-0.00216.153-0.577-0.5770.0000.0000.0000.000
114A127LYS10.8230.90617.543-12.724-12.7240.0000.0000.0000.000
115A128ALA00.0010.01019.616-0.512-0.5120.0000.0000.0000.000
116A129LEU00.0220.00814.580-0.473-0.4730.0000.0000.0000.000
117A130LEU0-0.0130.00419.176-0.397-0.3970.0000.0000.0000.000
118A131ALA00.0120.00121.413-0.459-0.4590.0000.0000.0000.000
119A132ILE0-0.018-0.00420.781-0.481-0.4810.0000.0000.0000.000
120A133ALA00.0120.01021.217-0.378-0.3780.0000.0000.0000.000
121A134GLU-1-0.983-0.98223.2779.4709.4700.0000.0000.0000.000
122A135LYS10.8730.91926.583-9.208-9.2080.0000.0000.0000.000
123A136GLN00.0130.00023.505-0.042-0.0420.0000.0000.0000.000
124A137TYR0-0.011-0.00427.184-0.386-0.3860.0000.0000.0000.000
125A138GLU-1-0.878-0.92928.7058.2448.2440.0000.0000.0000.000
126A139GLY00.0230.01130.978-0.296-0.2960.0000.0000.0000.000
127A140GLN0-0.023-0.02429.426-0.309-0.3090.0000.0000.0000.000
128A141LYS10.8240.89532.391-8.578-8.5780.0000.0000.0000.000
129A142MET0-0.012-0.00135.113-0.349-0.3490.0000.0000.0000.000
130A143LEU00.0070.00933.015-0.263-0.2630.0000.0000.0000.000
131A144GLU-1-0.818-0.87234.6677.9197.9190.0000.0000.0000.000
132A145PHE00.0090.01238.432-0.226-0.2260.0000.0000.0000.000
133A146ALA00.0260.03239.956-0.218-0.2180.0000.0000.0000.000
134A147ASN00.015-0.00638.552-0.267-0.2670.0000.0000.0000.000
135A148SER0-0.040-0.02442.134-0.179-0.1790.0000.0000.0000.000
136A149SER0-0.033-0.03244.388-0.189-0.1890.0000.0000.0000.000
137A150LEU00.0050.03545.239-0.162-0.1620.0000.0000.0000.000
138A151ASN0-0.004-0.01844.894-0.212-0.2120.0000.0000.0000.000
139A152HIS00.0160.01647.265-0.200-0.2000.0000.0000.0000.000
140A153SER0-0.009-0.01749.933-0.153-0.1530.0000.0000.0000.000
141A154VAL0-0.021-0.01850.193-0.125-0.1250.0000.0000.0000.000
142A155THR0-0.067-0.04051.832-0.109-0.1090.0000.0000.0000.000
143A156ILE0-0.054-0.02953.805-0.113-0.1130.0000.0000.0000.000
144A157LEU0-0.032-0.00754.611-0.111-0.1110.0000.0000.0000.000
145A158GLY00.0190.02457.649-0.032-0.0320.0000.0000.0000.000
146A159GLY0-0.040-0.02858.897-0.060-0.0600.0000.0000.0000.000
147A160LEU0-0.0030.00960.051-0.092-0.0920.0000.0000.0000.000
148A161ARG10.9560.97963.741-4.460-4.4600.0000.0000.0000.000
149A162GLN00.004-0.00566.1950.0080.0080.0000.0000.0000.000
150A163GLY0-0.059-0.04167.7230.0220.0220.0000.0000.0000.000
151A164ASP-1-0.893-0.94568.5884.4824.4820.0000.0000.0000.000
152A165MET0-0.0030.02063.0700.0430.0430.0000.0000.0000.000
153A166ASN00.0330.00964.767-0.018-0.0180.0000.0000.0000.000
154A167VAL00.0520.02662.7980.0840.0840.0000.0000.0000.000
155A168PRO00.0060.00261.5820.0840.0840.0000.0000.0000.000
156A169GLN0-0.0170.00458.4940.0630.0630.0000.0000.0000.000
157A170THR00.023-0.00958.9590.0720.0720.0000.0000.0000.000
158A171PHE0-0.018-0.00655.6310.0820.0820.0000.0000.0000.000
159A172LYS10.8580.92755.537-5.233-5.2330.0000.0000.0000.000
160A173ASP-1-0.780-0.89154.1305.4805.4800.0000.0000.0000.000
161A174LEU00.0030.00553.3680.0970.0970.0000.0000.0000.000
162A175SER0-0.040-0.03451.4170.1190.1190.0000.0000.0000.000
163A176GLN0-0.085-0.04847.7380.0790.0790.0000.0000.0000.000
164A177GLU-1-0.906-0.95648.5796.0346.0340.0000.0000.0000.000
165A178SER0-0.056-0.02347.9820.1740.1740.0000.0000.0000.000
166A179PHE0-0.006-0.00542.7910.1820.1820.0000.0000.0000.000
167A180ASP-1-0.784-0.90143.9046.7086.7080.0000.0000.0000.000
168A181TRP0-0.041-0.01543.6340.1480.1480.0000.0000.0000.000
169A182LEU0-0.016-0.01441.4050.1790.1790.0000.0000.0000.000
170A183GLN0-0.035-0.00539.6980.3440.3440.0000.0000.0000.000
171A184GLY00.0290.01438.7500.2130.2130.0000.0000.0000.000
172A185HIS00.002-0.00638.5840.3500.3500.0000.0000.0000.000
173A186TYR0-0.0150.00431.3280.2370.2370.0000.0000.0000.000
174A187TYR0-0.011-0.02334.2170.3890.3890.0000.0000.0000.000
175A188LYS10.8670.96333.887-7.304-7.3040.0000.0000.0000.000
176A189TRP0-0.010-0.03033.4120.1520.1520.0000.0000.0000.000
177A190ASN0-0.034-0.00830.0900.3790.3790.0000.0000.0000.000
178A191GLN0-0.029-0.01128.615-0.143-0.1430.0000.0000.0000.000
179A192LYS10.9200.93827.500-9.106-9.1060.0000.0000.0000.000
180A193ASP-1-0.800-0.86526.48810.93010.9300.0000.0000.0000.000
181A194PHE00.000-0.01123.901-0.329-0.3290.0000.0000.0000.000
182A195GLY00.0740.02224.4480.3560.3560.0000.0000.0000.000
183A196SER0-0.0070.00325.3060.3060.3060.0000.0000.0000.000
184A197PHE0-0.037-0.02424.334-0.163-0.1630.0000.0000.0000.000
185A198TYR00.0420.00117.9160.3270.3270.0000.0000.0000.000
186A199GLU-1-0.882-0.91322.86310.84310.8430.0000.0000.0000.000
187A200LYS10.8840.95425.820-9.932-9.9320.0000.0000.0000.000
188A201TYR0-0.047-0.04222.842-0.516-0.5160.0000.0000.0000.000
189A202ILE0-0.0010.00619.2990.1440.1440.0000.0000.0000.000
190A203ASN0-0.072-0.01322.480-0.084-0.0840.0000.0000.0000.000