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: 4J16N

Calculation Name: 1B77-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B77

Chain ID: A

ChEMBL ID:

UniProt ID: O80164

Base Structure: X-ray

Registration Date: 2023-09-24

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 228
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2604987.346188
FMO2-HF: Nuclear repulsion 2516836.736304
FMO2-HF: Total energy -88150.609884
FMO2-MP2: Total energy -88407.699518


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-36.041-33.05739.279-14.268-27.997-0.12
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : 0.004
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].
3A3LEU0-0.017-0.0192.309-3.454-0.4902.299-1.894-3.3690.000
4A4SER00.016-0.0174.7800.4700.558-0.001-0.011-0.0760.000
5A5LYS10.8760.9058.5200.5130.5130.0000.0000.0000.000
6A6ASP-1-0.897-0.94211.283-0.269-0.2690.0000.0000.0000.000
7A7THR0-0.013-0.0255.3450.2150.2150.0000.0000.0000.000
8A8ILE00.0050.0027.5210.1680.1680.0000.0000.0000.000
9A9ALA0-0.019-0.0109.4020.1110.1110.0000.0000.0000.000
10A10ILE00.0130.01010.7880.0580.0580.0000.0000.0000.000
11A11LEU00.0130.0075.5650.0860.0860.0000.0000.0000.000
12A12LYS10.8960.94010.2750.1280.1280.0000.0000.0000.000
13A13ASN0-0.0030.01613.3410.0330.0330.0000.0000.0000.000
14A14PHE00.0280.01010.9130.0140.0140.0000.0000.0000.000
15A15ALA00.0190.01713.3820.0210.0210.0000.0000.0000.000
16A16SER0-0.082-0.04314.905-0.005-0.0050.0000.0000.0000.000
17A17ILE0-0.056-0.02916.484-0.008-0.0080.0000.0000.0000.000
18A18ASN0-0.055-0.04416.109-0.009-0.0090.0000.0000.0000.000
19A19SER00.0220.02715.8050.0020.0020.0000.0000.0000.000
20A20GLY00.0250.01513.436-0.002-0.0020.0000.0000.0000.000
21A21ILE0-0.053-0.0268.802-0.049-0.0490.0000.0000.0000.000
22A22LEU0-0.025-0.01610.2630.0160.0160.0000.0000.0000.000
23A23LEU0-0.0110.0043.802-0.381-0.1590.001-0.030-0.1930.000
24A24SER0-0.004-0.0466.9960.0150.0150.0000.0000.0000.000
25A25GLN0-0.068-0.0376.457-0.111-0.1110.0000.0000.0000.000
26A26GLY00.0090.0236.742-0.439-0.4390.0000.0000.0000.000
27A27LYS10.8240.9116.2490.5960.5960.0000.0000.0000.000
28A28PHE0-0.026-0.0288.109-0.142-0.1420.0000.0000.0000.000
29A29ILE00.0270.0306.2810.2220.2220.0000.0000.0000.000
30A30MET0-0.0120.0069.179-0.140-0.1400.0000.0000.0000.000
31A31THR00.0030.00011.9630.0760.0760.0000.0000.0000.000
32A32ARG10.8800.91714.399-0.181-0.1810.0000.0000.0000.000
33A33ALA00.0380.04418.1310.0160.0160.0000.0000.0000.000
34A34VAL00.0370.00920.5010.0040.0040.0000.0000.0000.000
35A35ASN00.0310.04222.1190.0050.0050.0000.0000.0000.000
36A36GLY00.0140.00623.001-0.008-0.0080.0000.0000.0000.000
37A37THR0-0.031-0.02623.991-0.001-0.0010.0000.0000.0000.000
38A38THR00.0450.03420.334-0.009-0.0090.0000.0000.0000.000
39A39TYR0-0.052-0.05816.7510.0280.0280.0000.0000.0000.000
40A40ALA00.0080.00715.822-0.027-0.0270.0000.0000.0000.000
41A41GLU-1-0.830-0.89113.7950.1720.1720.0000.0000.0000.000
42A42ALA00.0350.01011.619-0.042-0.0420.0000.0000.0000.000
43A43ASN0-0.0040.00511.1440.0880.0880.0000.0000.0000.000
44A44ILE0-0.017-0.0055.383-0.037-0.0370.0000.0000.0000.000
45A45SER00.0350.0139.1880.0210.0210.0000.0000.0000.000
46A46ASP-1-0.774-0.8333.827-1.450-1.3250.000-0.020-0.1050.000
47A47GLU-1-0.888-0.9593.7920.1020.5170.001-0.104-0.3110.000
48A48ILE0-0.019-0.0012.382-3.828-4.34911.449-4.788-6.140-0.011
49A49ASP-1-0.809-0.9251.926-20.279-22.98412.708-1.679-8.324-0.073
50A50PHE0-0.014-0.0142.565-2.430-0.8681.931-0.749-2.7440.000
51A51ASP-1-0.779-0.8745.1092.5872.7960.000-0.024-0.1850.000
52A52VAL0-0.022-0.0055.929-0.428-0.4280.0000.0000.0000.000
53A53ALA00.0080.0118.5810.1350.1350.0000.0000.0000.000
54A54LEU00.0030.0057.397-0.086-0.0860.0000.0000.0000.000
55A55TYR00.0320.01211.584-0.045-0.0450.0000.0000.0000.000
56A56ASP-1-0.812-0.87814.2980.0610.0610.0000.0000.0000.000
57A57LEU00.0200.0048.6810.0040.0040.0000.0000.0000.000
58A58ASN00.0550.03111.739-0.081-0.0810.0000.0000.0000.000
59A59SER0-0.051-0.05414.316-0.058-0.0580.0000.0000.0000.000
60A60PHE00.0260.0205.497-0.048-0.0480.0000.0000.0000.000
61A61LEU0-0.004-0.0098.135-0.097-0.0970.0000.0000.0000.000
62A62SER0-0.075-0.04810.708-0.069-0.0690.0000.0000.0000.000
63A63ILE00.0020.01611.646-0.022-0.0220.0000.0000.0000.000
64A64LEU00.0090.0046.403-0.032-0.0320.0000.0000.0000.000
65A65SER0-0.123-0.06310.457-0.044-0.0440.0000.0000.0000.000
66A66LEU0-0.058-0.02913.7160.0310.0310.0000.0000.0000.000
67A67VAL0-0.038-0.00710.5050.0260.0260.0000.0000.0000.000
68A68SER0-0.010-0.03212.2750.0240.0240.0000.0000.0000.000
69A69ASP-1-0.838-0.91411.322-0.518-0.5180.0000.0000.0000.000
70A70ASP-1-0.963-0.9778.696-0.503-0.5030.0000.0000.0000.000
71A71ALA0-0.013-0.0117.7150.0740.0740.0000.0000.0000.000
72A72GLU-1-0.821-0.8733.5821.6522.5780.087-0.499-0.5140.001
73A73ILE0-0.026-0.0242.109-1.0680.8221.408-1.007-2.2920.000
74A74SER00.0030.0081.952-7.900-10.2289.396-3.417-3.652-0.037
75A75MET0-0.0160.0064.1831.0961.2330.000-0.046-0.0920.000
76A76HIS0-0.0060.0037.401-0.172-0.1720.0000.0000.0000.000
77A77THR0-0.030-0.04010.5400.0560.0560.0000.0000.0000.000
78A78ASP-1-0.849-0.91313.7620.0080.0080.0000.0000.0000.000
79A79GLY00.0070.00912.2320.0310.0310.0000.0000.0000.000
80A80ASN0-0.059-0.04411.7130.1510.1510.0000.0000.0000.000
81A81ILE00.0160.0146.481-0.051-0.0510.0000.0000.0000.000
82A82LYS10.8750.9377.7680.3110.3110.0000.0000.0000.000
83A83ILE00.0330.0236.607-0.363-0.3630.0000.0000.0000.000
84A84ALA0-0.030-0.0257.4550.1940.1940.0000.0000.0000.000
85A85ASP-1-0.714-0.8219.235-0.333-0.3330.0000.0000.0000.000
86A86THR0-0.012-0.01512.0510.0630.0630.0000.0000.0000.000
87A87ARG10.8680.93614.9800.1480.1480.0000.0000.0000.000
88A88SER0-0.013-0.03414.9150.0230.0230.0000.0000.0000.000
89A89THR0-0.067-0.03711.466-0.013-0.0130.0000.0000.0000.000
90A90VAL0-0.0090.01611.8070.0450.0450.0000.0000.0000.000
91A91TYR00.015-0.00111.086-0.068-0.0680.0000.0000.0000.000
92A92TRP00.010-0.00310.569-0.042-0.0420.0000.0000.0000.000
93A93PRO0-0.0050.00511.9970.0310.0310.0000.0000.0000.000
94A94ALA00.0170.01411.3140.0740.0740.0000.0000.0000.000
95A95ALA0-0.050-0.02212.511-0.084-0.0840.0000.0000.0000.000
96A96ASP-1-0.781-0.87313.9700.3230.3230.0000.0000.0000.000
97A97LYS10.8650.93811.885-0.714-0.7140.0000.0000.0000.000
98A98SER0-0.080-0.05216.296-0.017-0.0170.0000.0000.0000.000
99A99THR0-0.065-0.04817.653-0.023-0.0230.0000.0000.0000.000
100A100ILE0-0.019-0.00513.617-0.015-0.0150.0000.0000.0000.000
101A101VAL00.0050.01217.9460.0000.0000.0000.0000.0000.000
102A102PHE00.000-0.00714.3370.0300.0300.0000.0000.0000.000
103A103PRO0-0.027-0.00214.591-0.035-0.0350.0000.0000.0000.000
104A104ASN00.007-0.01315.5030.0370.0370.0000.0000.0000.000
105A105LYS10.9350.96917.051-0.174-0.1740.0000.0000.0000.000
106A106PRO00.0760.03316.067-0.006-0.0060.0000.0000.0000.000
107A107ILE0-0.051-0.02217.688-0.016-0.0160.0000.0000.0000.000
108A108GLN0-0.007-0.00919.752-0.005-0.0050.0000.0000.0000.000
109A109PHE0-0.021-0.00923.352-0.004-0.0040.0000.0000.0000.000
110A110PRO0-0.0100.01125.439-0.002-0.0020.0000.0000.0000.000
111A111VAL0-0.012-0.01329.161-0.003-0.0030.0000.0000.0000.000
112A112ALA0-0.031-0.01630.5040.0000.0000.0000.0000.0000.000
113A113SER00.0250.01532.236-0.001-0.0010.0000.0000.0000.000
114A114VAL0-0.0120.00234.353-0.003-0.0030.0000.0000.0000.000
115A115ILE0-0.038-0.02330.8540.0030.0030.0000.0000.0000.000
116A116THR00.0310.01531.953-0.003-0.0030.0000.0000.0000.000
117A117GLU-1-0.848-0.90130.169-0.008-0.0080.0000.0000.0000.000
118A118ILE00.0160.01228.1560.0010.0010.0000.0000.0000.000
119A119LYS10.8550.91528.6000.0100.0100.0000.0000.0000.000
120A120ALA00.0130.00026.7620.0020.0020.0000.0000.0000.000
121A121GLU-1-0.907-0.96528.079-0.027-0.0270.0000.0000.0000.000
122A122ASP-1-0.829-0.91831.463-0.009-0.0090.0000.0000.0000.000
123A123LEU0-0.008-0.00124.7870.0020.0020.0000.0000.0000.000
124A124GLN00.0090.01128.536-0.001-0.0010.0000.0000.0000.000
125A125GLN0-0.0100.00429.5230.0030.0030.0000.0000.0000.000
126A126LEU00.0550.03330.6380.0010.0010.0000.0000.0000.000
127A127LEU00.0280.01925.8140.0020.0020.0000.0000.0000.000
128A128ARG10.8330.91928.5440.0280.0280.0000.0000.0000.000
129A129VAL0-0.003-0.00332.0060.0010.0010.0000.0000.0000.000
130A130SER00.034-0.00332.7480.0020.0020.0000.0000.0000.000
131A131ARG10.8950.94627.5960.0020.0020.0000.0000.0000.000
132A132GLY0-0.016-0.00134.3410.0010.0010.0000.0000.0000.000
133A133LEU0-0.022-0.00337.4830.0000.0000.0000.0000.0000.000
134A134GLN0-0.046-0.02737.1680.0020.0020.0000.0000.0000.000
135A135ILE0-0.0450.00034.8080.0020.0020.0000.0000.0000.000
136A136ASP-1-0.782-0.86833.9550.0240.0240.0000.0000.0000.000
137A137THR0-0.021-0.02433.6000.0040.0040.0000.0000.0000.000
138A138ILE0-0.005-0.00931.079-0.004-0.0040.0000.0000.0000.000
139A139ALA00.0080.00235.3340.0030.0030.0000.0000.0000.000
140A140ILE0-0.026-0.00431.776-0.003-0.0030.0000.0000.0000.000
141A141THR0-0.028-0.03136.4490.0020.0020.0000.0000.0000.000
142A142ASN00.0120.01639.8250.0000.0000.0000.0000.0000.000
143A143LYS10.8740.90242.239-0.007-0.0070.0000.0000.0000.000
144A144ASP-1-0.871-0.92044.8110.0060.0060.0000.0000.0000.000
145A145GLY00.0360.03346.123-0.001-0.0010.0000.0000.0000.000
146A146LYS10.8120.89141.581-0.002-0.0020.0000.0000.0000.000
147A147ILE00.0010.01235.9750.0020.0020.0000.0000.0000.000
148A148VAL0-0.017-0.01638.612-0.002-0.0020.0000.0000.0000.000
149A149ILE0-0.010-0.00232.7340.0030.0030.0000.0000.0000.000
150A150ASN00.0150.02737.024-0.004-0.0040.0000.0000.0000.000
151A151GLY00.0480.01037.3760.0020.0020.0000.0000.0000.000
152A152TYR0-0.008-0.01437.837-0.002-0.0020.0000.0000.0000.000
153A153ASN00.026-0.00738.0310.0020.0020.0000.0000.0000.000
154A154LYS10.8470.91838.542-0.029-0.0290.0000.0000.0000.000
155A155VAL0-0.025-0.01439.2760.0000.0000.0000.0000.0000.000
156A156GLU-1-0.837-0.89441.9440.0110.0110.0000.0000.0000.000
157A157ASP-1-0.797-0.88843.4670.0140.0140.0000.0000.0000.000
158A158SER00.0270.02142.8660.0010.0010.0000.0000.0000.000
159A159GLY00.000-0.00143.5170.0020.0020.0000.0000.0000.000
160A160LEU0-0.033-0.00738.7900.0000.0000.0000.0000.0000.000
161A161THR0-0.041-0.03843.388-0.001-0.0010.0000.0000.0000.000
162A162ARG10.7930.87445.557-0.014-0.0140.0000.0000.0000.000
163A163PRO0-0.0160.01142.3860.0000.0000.0000.0000.0000.000
164A164LYS10.8170.89640.992-0.011-0.0110.0000.0000.0000.000
165A165TYR0-0.025-0.03635.908-0.001-0.0010.0000.0000.0000.000
166A166SER0-0.034-0.03139.6610.0020.0020.0000.0000.0000.000
167A167LEU00.0050.01633.843-0.002-0.0020.0000.0000.0000.000
168A168THR00.0030.00038.0170.0020.0020.0000.0000.0000.000
169A169LEU0-0.049-0.01533.313-0.001-0.0010.0000.0000.0000.000
170A170THR0-0.006-0.00735.487-0.001-0.0010.0000.0000.0000.000
171A171ASP-1-0.814-0.89538.2840.0020.0020.0000.0000.0000.000
172A172TYR0-0.054-0.05739.9220.0010.0010.0000.0000.0000.000
173A173ASP-1-0.902-0.94142.1090.0060.0060.0000.0000.0000.000
174A174GLY0-0.043-0.01542.9910.0000.0000.0000.0000.0000.000
175A175SER0-0.039-0.03644.0140.0000.0000.0000.0000.0000.000
176A176ASN0-0.0460.00342.1960.0010.0010.0000.0000.0000.000
177A177ASN0-0.003-0.00243.529-0.002-0.0020.0000.0000.0000.000
178A178PHE00.012-0.01138.1890.0020.0020.0000.0000.0000.000
179A179ASN0-0.0090.01339.809-0.004-0.0040.0000.0000.0000.000
180A180PHE00.0460.00234.4380.0020.0020.0000.0000.0000.000
181A181VAL00.0120.01235.390-0.002-0.0020.0000.0000.0000.000
182A182ILE0-0.003-0.01129.2140.0040.0040.0000.0000.0000.000
183A183ASN00.0440.02229.422-0.009-0.0090.0000.0000.0000.000
184A184MET0-0.025-0.01129.5270.0010.0010.0000.0000.0000.000
185A185ALA0-0.020-0.01427.962-0.001-0.0010.0000.0000.0000.000
186A186ASN0-0.035-0.04924.7900.0010.0010.0000.0000.0000.000
187A187MET00.0010.01524.2660.0070.0070.0000.0000.0000.000
188A188LYS10.8220.90220.367-0.070-0.0700.0000.0000.0000.000
189A189ILE0-0.0160.01520.2360.0010.0010.0000.0000.0000.000
190A190GLN00.0210.01415.7810.0010.0010.0000.0000.0000.000
191A191PRO0-0.010-0.00420.4050.0020.0020.0000.0000.0000.000
192A192GLY00.0500.01222.017-0.011-0.0110.0000.0000.0000.000
193A193ASN0-0.016-0.00523.8470.0080.0080.0000.0000.0000.000
194A194TYR0-0.051-0.03920.6260.0000.0000.0000.0000.0000.000
195A195LYS10.9140.95425.487-0.019-0.0190.0000.0000.0000.000
196A196VAL0-0.028-0.02126.2950.0040.0040.0000.0000.0000.000
197A197MET0-0.052-0.01725.099-0.003-0.0030.0000.0000.0000.000
198A198LEU00.0270.01329.1160.0050.0050.0000.0000.0000.000
199A199TRP00.019-0.00731.0870.0010.0010.0000.0000.0000.000
200A200GLY00.0680.02632.9750.0020.0020.0000.0000.0000.000
201A201ALA0-0.030-0.01035.696-0.002-0.0020.0000.0000.0000.000
202A202GLY00.0220.01237.4350.0020.0020.0000.0000.0000.000
203A203ASP-1-0.789-0.88437.5340.0490.0490.0000.0000.0000.000
204A204LYS10.7640.88433.304-0.051-0.0510.0000.0000.0000.000
205A205VAL00.0330.01533.350-0.003-0.0030.0000.0000.0000.000
206A206ALA0-0.005-0.00928.0350.0050.0050.0000.0000.0000.000
207A207ALA00.0220.01528.045-0.005-0.0050.0000.0000.0000.000
208A208LYS10.8370.91220.354-0.061-0.0610.0000.0000.0000.000
209A209PHE00.0140.00723.518-0.008-0.0080.0000.0000.0000.000
210A210GLU-1-0.800-0.89821.4150.0420.0420.0000.0000.0000.000
211A211SER00.013-0.00119.817-0.012-0.0120.0000.0000.0000.000
212A212SER0-0.039-0.02920.0520.0070.0070.0000.0000.0000.000
213A213GLN0-0.0180.00615.8660.0010.0010.0000.0000.0000.000
214A214VAL00.0220.01214.5730.0060.0060.0000.0000.0000.000
215A215SER00.0150.01316.756-0.007-0.0070.0000.0000.0000.000
216A216TYR00.000-0.02017.4500.0140.0140.0000.0000.0000.000
217A217VAL0-0.032-0.01820.434-0.007-0.0070.0000.0000.0000.000
218A218ILE0-0.029-0.01322.7440.0100.0100.0000.0000.0000.000
219A219ALA0-0.0050.00625.500-0.004-0.0040.0000.0000.0000.000
220A220MET0-0.050-0.00728.447-0.003-0.0030.0000.0000.0000.000
221A221GLU-1-0.840-0.91531.8770.0510.0510.0000.0000.0000.000
222A222ALA0-0.008-0.00934.521-0.002-0.0020.0000.0000.0000.000
223A223ASP-1-0.861-0.92937.3480.0300.0300.0000.0000.0000.000
224A224SER0-0.038-0.02436.012-0.003-0.0030.0000.0000.0000.000
225A225THR0-0.045-0.01638.5620.0000.0000.0000.0000.0000.000
226A226HIS0-0.056-0.04338.660-0.002-0.0020.0000.0000.0000.000
227A227ASP-1-0.769-0.86141.5140.0210.0210.0000.0000.0000.000
228A228PHE0-0.055-0.02138.8840.0010.0010.0000.0000.0000.000