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: 5J62Z

Calculation Name: 3FTD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3FTD

Chain ID: A

ChEMBL ID:

UniProt ID: O67680

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptH
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 239
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3096019.659913
FMO2-HF: Nuclear repulsion 3001424.23283
FMO2-HF: Total energy -94595.427083
FMO2-MP2: Total energy -94876.045732


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:7:SER)


Summations of interaction energy for fragment #1(A:7:SER)
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.
-10.345-5.4060.636-2.734-2.842-0.001
Interaction energy analysis for fragmet #1(A:7:SER)
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 : 0.032
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].
3A9GLY0-0.032-0.0263.614-2.8930.128-0.030-1.656-1.3360.011
4A10GLN0-0.0060.0042.533-5.246-3.7190.662-0.989-1.200-0.012
5A11HIS00.0350.0266.2610.7640.7640.0000.0000.0000.000
6A12LEU0-0.059-0.0359.8700.3840.3840.0000.0000.0000.000
7A13LEU0-0.0090.0118.203-0.079-0.0790.0000.0000.0000.000
8A14VAL0-0.002-0.01411.5960.0710.0710.0000.0000.0000.000
9A15SER0-0.001-0.00213.0520.0850.0850.0000.0000.0000.000
10A16GLU-1-0.797-0.93010.7080.3180.3180.0000.0000.0000.000
11A17GLY0-0.0250.00414.5430.0230.0230.0000.0000.0000.000
12A18VAL0-0.015-0.01417.6310.0000.0000.0000.0000.0000.000
13A19LEU00.0190.00712.134-0.014-0.0140.0000.0000.0000.000
14A20LYS10.9620.97814.456-0.351-0.3510.0000.0000.0000.000
15A21LYS10.9430.99218.120-0.028-0.0280.0000.0000.0000.000
16A22ILE0-0.018-0.02518.066-0.008-0.0080.0000.0000.0000.000
17A23ALA00.0140.00217.807-0.005-0.0050.0000.0000.0000.000
18A24GLU-1-0.918-0.95219.9080.1060.1060.0000.0000.0000.000
19A25GLU-1-0.933-0.97723.0410.0070.0070.0000.0000.0000.000
20A26LEU0-0.053-0.02920.631-0.012-0.0120.0000.0000.0000.000
21A27ASN0-0.034-0.01424.5420.0070.0070.0000.0000.0000.000
22A28ILE0-0.031-0.01620.392-0.006-0.0060.0000.0000.0000.000
23A29GLU-1-0.913-0.95624.5500.1050.1050.0000.0000.0000.000
24A30GLU-1-0.887-0.95426.2660.2000.2000.0000.0000.0000.000
25A31GLY0-0.019-0.00526.679-0.017-0.0170.0000.0000.0000.000
26A32ASN0-0.0120.00624.982-0.018-0.0180.0000.0000.0000.000
27A33THR00.0180.01623.2360.0220.0220.0000.0000.0000.000
28A34VAL0-0.010-0.00319.665-0.019-0.0190.0000.0000.0000.000
29A35VAL00.0120.00320.1670.0040.0040.0000.0000.0000.000
30A36GLU-1-0.781-0.89413.555-0.156-0.1560.0000.0000.0000.000
31A37VAL0-0.030-0.02417.455-0.036-0.0360.0000.0000.0000.000
32A38GLY0-0.047-0.03317.4070.0110.0110.0000.0000.0000.000
33A39GLY00.0330.00914.172-0.061-0.0610.0000.0000.0000.000
34A40GLY0-0.039-0.03210.6200.0970.0970.0000.0000.0000.000
35A41THR00.0300.00810.8480.0430.0430.0000.0000.0000.000
36A42GLY00.0710.0416.8700.1600.1600.0000.0000.0000.000
37A43ASN0-0.034-0.0366.4820.8010.8010.0000.0000.0000.000
38A44LEU0-0.0190.0048.4920.1810.1810.0000.0000.0000.000
39A45THR00.035-0.00110.0970.0740.0740.0000.0000.0000.000
40A46LYS10.9200.9575.299-2.842-2.8420.0000.0000.0000.000
41A47VAL0-0.0030.01110.5350.0090.0090.0000.0000.0000.000
42A48LEU0-0.015-0.01813.487-0.006-0.0060.0000.0000.0000.000
43A49LEU0-0.0080.00812.110-0.019-0.0190.0000.0000.0000.000
44A50GLN0-0.073-0.02213.5390.0970.0970.0000.0000.0000.000
45A51HIS0-0.031-0.00816.758-0.055-0.0550.0000.0000.0000.000
46A52PRO00.0380.01719.9600.0220.0220.0000.0000.0000.000
47A53LEU0-0.0290.00018.004-0.029-0.0290.0000.0000.0000.000
48A54LYS10.9860.99122.069-0.078-0.0780.0000.0000.0000.000
49A55LYS10.8580.92620.287-0.089-0.0890.0000.0000.0000.000
50A56LEU00.0010.00314.858-0.017-0.0170.0000.0000.0000.000
51A57TYR00.0180.00617.3840.0140.0140.0000.0000.0000.000
52A58VAL00.0280.01512.607-0.012-0.0120.0000.0000.0000.000
53A59ILE0-0.065-0.02715.779-0.015-0.0150.0000.0000.0000.000
54A60GLU-1-0.823-0.91411.738-0.978-0.9780.0000.0000.0000.000
55A61LEU00.0000.00015.1660.0280.0280.0000.0000.0000.000
56A62ASP-1-0.867-0.92710.613-1.702-1.7020.0000.0000.0000.000
57A63ARG10.9400.93911.7780.4500.4500.0000.0000.0000.000
58A64GLU-1-0.918-0.9366.428-3.001-3.0010.0000.0000.0000.000
59A65MET0-0.044-0.0177.327-0.472-0.4720.0000.0000.0000.000
60A66VAL0-0.046-0.0338.0820.2700.2700.0000.0000.0000.000
61A67GLU-1-0.938-0.9628.031-0.113-0.1130.0000.0000.0000.000
62A68ASN00.0200.0003.7350.1290.5200.004-0.089-0.3060.000
63A69LEU0-0.043-0.0145.5121.0741.0740.0000.0000.0000.000
64A70LYS10.9150.9677.8810.4530.4530.0000.0000.0000.000
65A71SER0-0.053-0.0195.6210.5640.5640.0000.0000.0000.000
66A72ILE0-0.066-0.0417.4730.4550.4550.0000.0000.0000.000
67A73GLY00.0030.0019.443-0.238-0.2380.0000.0000.0000.000
68A74ASP-1-0.828-0.90812.7670.4150.4150.0000.0000.0000.000
69A75GLU-1-0.879-0.93415.0470.2480.2480.0000.0000.0000.000
70A76ARG10.7070.83116.924-0.478-0.4780.0000.0000.0000.000
71A77LEU0-0.041-0.00411.246-0.069-0.0690.0000.0000.0000.000
72A78GLU-1-0.882-0.94315.8190.0180.0180.0000.0000.0000.000
73A79VAL0-0.031-0.01411.849-0.031-0.0310.0000.0000.0000.000
74A80ILE0-0.008-0.00815.2270.0060.0060.0000.0000.0000.000
75A81ASN0-0.077-0.04516.010-0.024-0.0240.0000.0000.0000.000
76A82GLU-1-0.884-0.95317.510-0.246-0.2460.0000.0000.0000.000
77A83ASP-1-0.817-0.89919.359-0.367-0.3670.0000.0000.0000.000
78A84ALA00.0660.02020.3070.0410.0410.0000.0000.0000.000
79A85SER0-0.128-0.08222.1860.0370.0370.0000.0000.0000.000
80A86LYS10.8940.93324.9990.2800.2800.0000.0000.0000.000
81A87PHE00.0330.03523.6960.0150.0150.0000.0000.0000.000
82A88PRO00.0370.03125.7880.0070.0070.0000.0000.0000.000
83A89PHE00.0630.02423.0510.0120.0120.0000.0000.0000.000
84A90CYS0-0.081-0.01926.8140.0170.0170.0000.0000.0000.000
85A91SER0-0.094-0.04027.3390.0100.0100.0000.0000.0000.000
86A92LEU00.0040.00922.6040.0050.0050.0000.0000.0000.000
87A93GLY00.005-0.00626.3440.0200.0200.0000.0000.0000.000
88A94LYS10.9200.94928.813-0.004-0.0040.0000.0000.0000.000
89A95GLU-1-0.926-0.95930.0310.0250.0250.0000.0000.0000.000
90A96LEU0-0.042-0.00425.2120.0110.0110.0000.0000.0000.000
91A97LYS10.8370.91824.411-0.070-0.0700.0000.0000.0000.000
92A98VAL00.0100.01022.7610.0010.0010.0000.0000.0000.000
93A99VAL00.0290.01018.4500.0050.0050.0000.0000.0000.000
94A100GLY00.0640.03618.079-0.025-0.0250.0000.0000.0000.000
95A101ASN00.0060.00615.7310.0810.0810.0000.0000.0000.000
96A102LEU0-0.010-0.00418.060-0.070-0.0700.0000.0000.0000.000
97A103PRO00.0530.03217.8910.0130.0130.0000.0000.0000.000
98A104TYR00.0560.00320.4870.0570.0570.0000.0000.0000.000
99A105ASN0-0.061-0.02622.5990.0210.0210.0000.0000.0000.000
100A106VAL00.0580.03321.3110.0170.0170.0000.0000.0000.000
101A107ALA00.0030.01624.3830.0250.0250.0000.0000.0000.000
102A108SER0-0.007-0.02325.2130.0270.0270.0000.0000.0000.000
103A109LEU00.0030.01026.7550.0170.0170.0000.0000.0000.000
104A110ILE00.0700.03621.4590.0160.0160.0000.0000.0000.000
105A111ILE0-0.0160.00525.7590.0220.0220.0000.0000.0000.000
106A112GLU-1-0.780-0.86728.233-0.132-0.1320.0000.0000.0000.000
107A113ASN0-0.041-0.04126.0060.0270.0270.0000.0000.0000.000
108A114THR00.0200.00226.8240.0120.0120.0000.0000.0000.000
109A115VAL0-0.031-0.00428.8620.0140.0140.0000.0000.0000.000
110A116TYR0-0.104-0.07731.9200.0140.0140.0000.0000.0000.000
111A117ASN0-0.019-0.01329.5560.0140.0140.0000.0000.0000.000
112A118LYS10.9230.95731.6590.0590.0590.0000.0000.0000.000
113A119ASP-1-0.928-0.97333.467-0.032-0.0320.0000.0000.0000.000
114A121VAL00.0080.01428.0160.0020.0020.0000.0000.0000.000
115A122PRO00.0280.02729.861-0.008-0.0080.0000.0000.0000.000
116A123LEU0-0.006-0.01427.1590.0010.0010.0000.0000.0000.000
117A124ALA00.0150.01325.792-0.002-0.0020.0000.0000.0000.000
118A125VAL0-0.0140.00622.6670.0020.0020.0000.0000.0000.000
119A126PHE00.0300.01022.436-0.015-0.0150.0000.0000.0000.000
120A127MET0-0.0400.00717.9330.0290.0290.0000.0000.0000.000
121A128VAL00.0170.01221.976-0.035-0.0350.0000.0000.0000.000
122A129GLN00.034-0.00424.328-0.009-0.0090.0000.0000.0000.000
123A130LYS10.9660.97626.2710.1440.1440.0000.0000.0000.000
124A131GLU-1-0.866-0.93228.882-0.125-0.1250.0000.0000.0000.000
125A132VAL0-0.021-0.00828.4190.0090.0090.0000.0000.0000.000
126A133ALA00.0250.00828.3830.0120.0120.0000.0000.0000.000
127A134GLU-1-0.943-0.98330.339-0.096-0.0960.0000.0000.0000.000
128A135LYS10.9350.97933.7670.1480.1480.0000.0000.0000.000
129A136LEU0-0.039-0.00329.9160.0090.0090.0000.0000.0000.000
130A137GLN00.002-0.00934.0080.0160.0160.0000.0000.0000.000
131A138GLY0-0.016-0.00335.4540.0080.0080.0000.0000.0000.000
132A139LYS10.9070.96238.3340.0480.0480.0000.0000.0000.000
133A140LYS10.9310.95736.4920.0780.0780.0000.0000.0000.000
134A141ASP-1-0.767-0.87137.204-0.111-0.1110.0000.0000.0000.000
135A142THR0-0.033-0.02738.3040.0030.0030.0000.0000.0000.000
136A143GLY0-0.005-0.01037.924-0.008-0.0080.0000.0000.0000.000
137A144TRP00.0320.01134.5580.0070.0070.0000.0000.0000.000
138A145LEU00.0130.01531.0590.0060.0060.0000.0000.0000.000
139A146SER0-0.005-0.00735.6150.0070.0070.0000.0000.0000.000
140A147VAL00.0180.01736.5160.0060.0060.0000.0000.0000.000
141A148PHE0-0.022-0.00334.4830.0060.0060.0000.0000.0000.000
142A149VAL00.0300.00732.6650.0050.0050.0000.0000.0000.000
143A150ARG10.9080.94635.5120.0800.0800.0000.0000.0000.000
144A151THR0-0.042-0.00537.9340.0070.0070.0000.0000.0000.000
145A152PHE00.004-0.02136.5140.0050.0050.0000.0000.0000.000
146A153TYR00.0020.01231.8440.0000.0000.0000.0000.0000.000
147A154ASP-1-0.842-0.90535.557-0.034-0.0340.0000.0000.0000.000
148A155VAL0-0.037-0.02931.879-0.002-0.0020.0000.0000.0000.000
149A156ASN0-0.044-0.01331.3440.0060.0060.0000.0000.0000.000
150A157TYR0-0.012-0.03429.955-0.013-0.0130.0000.0000.0000.000
151A158VAL00.0030.01226.2250.0070.0070.0000.0000.0000.000
152A159MET00.0070.00023.3170.0140.0140.0000.0000.0000.000
153A160THR00.0090.01626.852-0.015-0.0150.0000.0000.0000.000
154A161VAL00.0000.00620.7530.0130.0130.0000.0000.0000.000
155A162PRO0-0.020-0.01924.071-0.026-0.0260.0000.0000.0000.000
156A163PRO00.0540.00722.472-0.002-0.0020.0000.0000.0000.000
157A164ARG10.9960.98220.7730.1020.1020.0000.0000.0000.000
158A165PHE0-0.0260.00918.8920.0040.0040.0000.0000.0000.000
159A166PHE0-0.021-0.01216.2940.0070.0070.0000.0000.0000.000
160A167VAL0-0.0160.02414.1960.0460.0460.0000.0000.0000.000
161A168PRO00.1010.02213.949-0.104-0.1040.0000.0000.0000.000
162A169PRO0-0.013-0.00617.0080.0130.0130.0000.0000.0000.000
163A170PRO0-0.0120.02020.090-0.011-0.0110.0000.0000.0000.000
164A171LYS10.9650.96222.3410.3530.3530.0000.0000.0000.000
165A172VAL00.0060.01425.6640.0270.0270.0000.0000.0000.000
166A173GLN0-0.005-0.01525.325-0.007-0.0070.0000.0000.0000.000
167A174SER00.0130.01622.875-0.016-0.0160.0000.0000.0000.000
168A175ALA0-0.017-0.01224.8630.0210.0210.0000.0000.0000.000
169A176VAL00.0420.03022.324-0.021-0.0210.0000.0000.0000.000
170A177ILE0-0.029-0.01424.9940.0140.0140.0000.0000.0000.000
171A178LYS10.9620.98526.344-0.016-0.0160.0000.0000.0000.000
172A179LEU0-0.042-0.02028.531-0.001-0.0010.0000.0000.0000.000
173A180VAL00.0350.01030.2600.0060.0060.0000.0000.0000.000
174A181LYS10.8510.94432.9170.0260.0260.0000.0000.0000.000
175A182ASN0-0.054-0.04635.0290.0070.0070.0000.0000.0000.000
176A183GLU-1-0.856-0.92638.659-0.044-0.0440.0000.0000.0000.000
177A184LYS10.8140.92639.0680.0450.0450.0000.0000.0000.000
178A185PHE00.0200.00243.5200.0010.0010.0000.0000.0000.000
179A186PRO00.0290.03243.945-0.003-0.0030.0000.0000.0000.000
180A187VAL0-0.053-0.03642.4760.0000.0000.0000.0000.0000.000
181A188LYS10.9930.99842.8520.0430.0430.0000.0000.0000.000
182A189ASP-1-0.825-0.91942.492-0.073-0.0730.0000.0000.0000.000
183A190LEU00.0450.01136.759-0.003-0.0030.0000.0000.0000.000
184A191LYS10.9490.97535.5840.1070.1070.0000.0000.0000.000
185A192ASN0-0.050-0.02540.085-0.008-0.0080.0000.0000.0000.000
186A193TYR00.001-0.01240.765-0.001-0.0010.0000.0000.0000.000
187A194LYS10.8610.91534.8330.1350.1350.0000.0000.0000.000
188A195LYS10.9270.97540.3430.0820.0820.0000.0000.0000.000
189A196PHE00.0300.02942.880-0.002-0.0020.0000.0000.0000.000
190A197LEU00.0030.00140.354-0.001-0.0010.0000.0000.0000.000
191A198THR0-0.029-0.03638.780-0.002-0.0020.0000.0000.0000.000
192A199LYS10.9760.99241.5340.0790.0790.0000.0000.0000.000
193A200ILE00.0040.01144.985-0.001-0.0010.0000.0000.0000.000
194A201PHE00.0260.00341.7920.0000.0000.0000.0000.0000.000
195A202GLN0-0.058-0.00540.900-0.006-0.0060.0000.0000.0000.000
196A203ASN0-0.016-0.02144.5000.0040.0040.0000.0000.0000.000
197A204ARG10.9730.98542.1490.1060.1060.0000.0000.0000.000
198A205ARG10.9850.99445.7500.0870.0870.0000.0000.0000.000
199A206LYS10.8870.96548.5580.0810.0810.0000.0000.0000.000
200A207VAL00.0080.01351.057-0.001-0.0010.0000.0000.0000.000
201A208LEU00.1020.03149.759-0.002-0.0020.0000.0000.0000.000
202A209ARG10.9740.99353.3570.0520.0520.0000.0000.0000.000
203A210LYS10.8360.92154.2810.0640.0640.0000.0000.0000.000
204A211LYS10.7050.84747.3160.0790.0790.0000.0000.0000.000
205A212ILE00.0040.01550.691-0.002-0.0020.0000.0000.0000.000
206A213PRO00.0590.03054.4700.0010.0010.0000.0000.0000.000
207A214GLU-1-0.851-0.96558.180-0.043-0.0430.0000.0000.0000.000
208A215GLU-1-0.932-0.95960.084-0.039-0.0390.0000.0000.0000.000
209A216LEU00.0860.03855.8840.0010.0010.0000.0000.0000.000
210A217LEU0-0.066-0.02553.9710.0000.0000.0000.0000.0000.000
211A218LYS10.8870.95157.3710.0410.0410.0000.0000.0000.000
212A219GLU-1-0.895-0.92559.356-0.035-0.0350.0000.0000.0000.000
213A220ALA0-0.035-0.01454.8230.0010.0010.0000.0000.0000.000
214A221GLY0-0.001-0.00656.1950.0000.0000.0000.0000.0000.000
215A222ILE0-0.049-0.02452.573-0.001-0.0010.0000.0000.0000.000
216A223ASN00.0290.01056.3450.0000.0000.0000.0000.0000.000
217A224PRO00.0570.02356.224-0.003-0.0030.0000.0000.0000.000
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