FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R91K8

Calculation Name: 1DT9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DT9

Chain ID: A

ChEMBL ID:

UniProt ID: P62495

Base Structure: X-ray

Registration Date: 2023-06-21

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 398
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5947952.028069
FMO2-HF: Nuclear repulsion 5792787.334317
FMO2-HF: Total energy -155164.693752
FMO2-MP2: Total energy -155620.526351


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:5:PRO)


Summations of interaction energy for fragment #1(A:5: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.
-1.4620.82-0.018-1.318-0.945-0.002
Interaction energy analysis for fragmet #1(A:5:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / 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].
3A7ALA00.0170.0163.932-0.8811.401-0.018-1.318-0.945-0.002
4A8ALA00.0870.0636.873-0.321-0.3210.0000.0000.0000.000
5A9ASP-1-0.798-0.8696.387-0.511-0.5110.0000.0000.0000.000
6A10ARG10.8550.8995.457-0.733-0.7330.0000.0000.0000.000
7A11ASN0-0.027-0.0337.1790.0760.0760.0000.0000.0000.000
8A12VAL00.0750.06310.4510.0310.0310.0000.0000.0000.000
9A13GLU-1-0.809-0.9028.7490.5160.5160.0000.0000.0000.000
10A14ILE0-0.042-0.01710.699-0.017-0.0170.0000.0000.0000.000
11A15TRP00.0410.01513.155-0.019-0.0190.0000.0000.0000.000
12A16LYS10.8980.93812.561-0.346-0.3460.0000.0000.0000.000
13A17ILE00.0030.02113.998-0.020-0.0200.0000.0000.0000.000
14A18LYS10.9650.98916.831-0.223-0.2230.0000.0000.0000.000
15A19LYS10.8860.95819.165-0.103-0.1030.0000.0000.0000.000
16A20LEU00.0060.00219.069-0.016-0.0160.0000.0000.0000.000
17A21ILE0-0.036-0.03519.081-0.012-0.0120.0000.0000.0000.000
18A22LYS10.9360.98022.488-0.110-0.1100.0000.0000.0000.000
19A23SER00.011-0.00224.819-0.005-0.0050.0000.0000.0000.000
20A24LEU0-0.041-0.02322.827-0.008-0.0080.0000.0000.0000.000
21A25GLU-1-0.840-0.90126.3310.1530.1530.0000.0000.0000.000
22A26ALA0-0.071-0.01528.609-0.010-0.0100.0000.0000.0000.000
23A27ALA0-0.029-0.00230.541-0.009-0.0090.0000.0000.0000.000
24A28ARG10.8990.91232.306-0.087-0.0870.0000.0000.0000.000
25A29GLY00.0130.02435.159-0.006-0.0060.0000.0000.0000.000
26A30ASN0-0.023-0.01437.426-0.001-0.0010.0000.0000.0000.000
27A31GLY0-0.0070.00039.870-0.001-0.0010.0000.0000.0000.000
28A32THR0-0.016-0.02737.3000.0010.0010.0000.0000.0000.000
29A33SER00.0240.02536.2410.0000.0000.0000.0000.0000.000
30A34MET0-0.104-0.02931.4640.0010.0010.0000.0000.0000.000
31A35ILE00.0100.00128.5970.0010.0010.0000.0000.0000.000
32A36SER00.0190.00926.3040.0070.0070.0000.0000.0000.000
33A37LEU0-0.027-0.02624.474-0.006-0.0060.0000.0000.0000.000
34A38ILE0-0.003-0.00119.8950.0220.0220.0000.0000.0000.000
35A39ILE0-0.006-0.00920.829-0.027-0.0270.0000.0000.0000.000
36A40PRO0-0.0020.03018.9060.0490.0490.0000.0000.0000.000
37A41PRO00.0400.00814.927-0.020-0.0200.0000.0000.0000.000
38A42LYS10.9000.94615.610-0.422-0.4220.0000.0000.0000.000
39A43ASP-1-0.750-0.82318.8180.2180.2180.0000.0000.0000.000
40A44GLN00.005-0.00921.3870.0220.0220.0000.0000.0000.000
41A45ILE00.1020.04420.821-0.013-0.0130.0000.0000.0000.000
42A46SER0-0.020-0.00424.505-0.007-0.0070.0000.0000.0000.000
43A47ARG10.8380.89225.617-0.231-0.2310.0000.0000.0000.000
44A48VAL00.0270.00325.324-0.012-0.0120.0000.0000.0000.000
45A49ALA0-0.011-0.02328.216-0.012-0.0120.0000.0000.0000.000
46A50LYS10.8930.96029.975-0.124-0.1240.0000.0000.0000.000
47A51MET00.0450.05430.136-0.010-0.0100.0000.0000.0000.000
48A52LEU00.0040.00128.899-0.008-0.0080.0000.0000.0000.000
49A53ALA0-0.015-0.00633.208-0.009-0.0090.0000.0000.0000.000
50A54ASP-1-0.851-0.92935.8650.1030.1030.0000.0000.0000.000
51A55GLU-1-0.838-0.90034.7890.1120.1120.0000.0000.0000.000
52A56PHE0-0.033-0.02836.972-0.007-0.0070.0000.0000.0000.000
53A57GLY00.0200.01438.710-0.007-0.0070.0000.0000.0000.000
54A58THR0-0.033-0.02940.924-0.007-0.0070.0000.0000.0000.000
55A59ALA00.008-0.00440.381-0.005-0.0050.0000.0000.0000.000
56A60SER0-0.064-0.04042.419-0.005-0.0050.0000.0000.0000.000
57A61ASN0-0.066-0.04344.578-0.007-0.0070.0000.0000.0000.000
58A62ILE0-0.0010.01842.612-0.004-0.0040.0000.0000.0000.000
59A63LYS10.8530.94147.039-0.060-0.0600.0000.0000.0000.000
60A64SER00.1210.05048.265-0.002-0.0020.0000.0000.0000.000
61A65ARG10.9090.94748.022-0.048-0.0480.0000.0000.0000.000
62A66VAL00.0940.07845.3730.0020.0020.0000.0000.0000.000
63A67ASN00.0500.01443.1040.0030.0030.0000.0000.0000.000
64A68ARG10.9680.98643.018-0.057-0.0570.0000.0000.0000.000
65A69LEU0-0.032-0.03241.6980.0030.0030.0000.0000.0000.000
66A70SER0-0.0150.00839.9400.0050.0050.0000.0000.0000.000
67A71VAL00.0630.02738.0630.0050.0050.0000.0000.0000.000
68A72LEU0-0.017-0.00637.4620.0050.0050.0000.0000.0000.000
69A73GLY00.0510.03237.1520.0050.0050.0000.0000.0000.000
70A74ALA00.0310.03133.7890.0050.0050.0000.0000.0000.000
71A75ILE00.0350.01032.8080.0080.0080.0000.0000.0000.000
72A76THR0-0.059-0.04432.7980.0040.0040.0000.0000.0000.000
73A77SER00.0120.00030.2360.0030.0030.0000.0000.0000.000
74A78VAL00.0450.01827.0720.0070.0070.0000.0000.0000.000
75A79GLN0-0.020-0.01027.8870.0100.0100.0000.0000.0000.000
76A80GLN0-0.029-0.02328.8310.0060.0060.0000.0000.0000.000
77A81ARG10.8160.90223.760-0.174-0.1740.0000.0000.0000.000
78A82LEU00.007-0.00623.5410.0110.0110.0000.0000.0000.000
79A83LYS10.8430.92524.408-0.111-0.1110.0000.0000.0000.000
80A84LEU0-0.0240.00222.669-0.010-0.0100.0000.0000.0000.000
81A85TYR0-0.067-0.03917.0410.0260.0260.0000.0000.0000.000
82A86ASN00.012-0.00518.5500.0100.0100.0000.0000.0000.000
83A87LYN00.002-0.01718.795-0.016-0.0160.0000.0000.0000.000
84A88VAL0-0.053-0.00516.7990.0250.0250.0000.0000.0000.000
85A89PRO00.0280.04313.000-0.012-0.0120.0000.0000.0000.000
86A90PRO00.0240.0109.470-0.054-0.0540.0000.0000.0000.000
87A91ASN0-0.095-0.0658.5550.0310.0310.0000.0000.0000.000
88A92GLY0-0.026-0.03512.661-0.091-0.0910.0000.0000.0000.000
89A93LEU0-0.0010.00015.8680.0240.0240.0000.0000.0000.000
90A94VAL0-0.0230.02117.537-0.037-0.0370.0000.0000.0000.000
91A95VAL00.018-0.01219.821-0.006-0.0060.0000.0000.0000.000
92A96TYR0-0.027-0.01921.583-0.004-0.0040.0000.0000.0000.000
93A97CYS0-0.068-0.02225.623-0.008-0.0080.0000.0000.0000.000
94A98GLY00.0930.04228.939-0.001-0.0010.0000.0000.0000.000
95A99THR0-0.040-0.00732.295-0.002-0.0020.0000.0000.0000.000
96A100ILE0-0.013-0.01432.4340.0010.0010.0000.0000.0000.000
97A101VAL00.0150.02135.563-0.004-0.0040.0000.0000.0000.000
98A102THR0-0.019-0.02235.6150.0040.0040.0000.0000.0000.000
99A103GLU-1-0.871-0.93937.1790.0420.0420.0000.0000.0000.000
100A104GLU-1-0.831-0.92939.1800.0380.0380.0000.0000.0000.000
101A105GLY0-0.0030.01341.662-0.002-0.0020.0000.0000.0000.000
102A106LYS10.8050.91139.787-0.039-0.0390.0000.0000.0000.000
103A107GLU-1-0.875-0.93838.4360.0720.0720.0000.0000.0000.000
104A108LYS10.9140.94832.714-0.075-0.0750.0000.0000.0000.000
105A109LYS10.8620.93133.166-0.074-0.0740.0000.0000.0000.000
106A110VAL00.0160.02127.331-0.001-0.0010.0000.0000.0000.000
107A111ASN0-0.022-0.03926.8740.0040.0040.0000.0000.0000.000
108A112ILE00.0260.02221.040-0.001-0.0010.0000.0000.0000.000
109A113ASP-1-0.774-0.84420.6290.2450.2450.0000.0000.0000.000
110A114PHE00.0560.02614.995-0.015-0.0150.0000.0000.0000.000
111A115GLU-1-0.813-0.89710.4471.2221.2220.0000.0000.0000.000
112A116PRO0-0.047-0.01612.5050.0390.0390.0000.0000.0000.000
113A117PHE00.036-0.0118.1860.2120.2120.0000.0000.0000.000
114A118LYS10.9180.95210.053-1.002-1.0020.0000.0000.0000.000
115A119PRO00.0390.05712.787-0.049-0.0490.0000.0000.0000.000
116A120ILE00.040-0.01214.788-0.022-0.0220.0000.0000.0000.000
117A121ASN0-0.027-0.02917.998-0.028-0.0280.0000.0000.0000.000
118A122THR00.0090.01920.486-0.020-0.0200.0000.0000.0000.000
119A123SER0-0.031-0.04122.407-0.025-0.0250.0000.0000.0000.000
120A124LEU0-0.056-0.01224.233-0.019-0.0190.0000.0000.0000.000
121A125TYR0-0.017-0.05326.0380.0110.0110.0000.0000.0000.000
122A126LEU00.0000.01928.998-0.012-0.0120.0000.0000.0000.000
123A127CYS00.0360.02630.8870.0020.0020.0000.0000.0000.000
124A128ASP-1-0.780-0.84833.1590.1140.1140.0000.0000.0000.000
125A129ASN0-0.020-0.02935.0000.0000.0000.0000.0000.0000.000
126A130LYS10.9270.93831.858-0.125-0.1250.0000.0000.0000.000
127A131PHE00.0180.00827.0830.0040.0040.0000.0000.0000.000
128A132HIS10.7850.85627.246-0.165-0.1650.0000.0000.0000.000
129A133THR00.034-0.00923.0730.0230.0230.0000.0000.0000.000
130A134GLU-1-0.796-0.86722.4310.2110.2110.0000.0000.0000.000
131A135ALA0-0.003-0.00320.6560.0150.0150.0000.0000.0000.000
132A136LEU0-0.037-0.01917.5440.0420.0420.0000.0000.0000.000
133A137THR00.027-0.01017.9910.0340.0340.0000.0000.0000.000
134A138ALA00.0290.03619.205-0.003-0.0030.0000.0000.0000.000
135A139LEU0-0.021-0.01812.9020.0210.0210.0000.0000.0000.000
136A140LEU0-0.112-0.04614.4720.0230.0230.0000.0000.0000.000
137A141SER00.0160.00315.879-0.062-0.0620.0000.0000.0000.000
138A142ASP-1-0.891-0.92310.9540.6300.6300.0000.0000.0000.000
139A143ASP-1-0.909-0.94914.3330.1320.1320.0000.0000.0000.000
140A144SER0-0.020-0.01113.4770.0180.0180.0000.0000.0000.000
141A145LYS10.8630.94113.695-0.221-0.2210.0000.0000.0000.000
142A146PHE00.002-0.01314.575-0.019-0.0190.0000.0000.0000.000
143A147GLY00.017-0.00617.0150.0110.0110.0000.0000.0000.000
144A148PHE0-0.0090.02018.318-0.021-0.0210.0000.0000.0000.000
145A149ILE00.0170.01120.7910.0080.0080.0000.0000.0000.000
146A150VAL0-0.032-0.02524.185-0.007-0.0070.0000.0000.0000.000
147A151ILE0-0.0170.00326.6710.0030.0030.0000.0000.0000.000
148A152ASP-1-0.755-0.87930.1300.0020.0020.0000.0000.0000.000
149A153GLY0-0.024-0.00333.895-0.003-0.0030.0000.0000.0000.000
150A154SER0-0.092-0.06937.068-0.001-0.0010.0000.0000.0000.000
151A155GLY0-0.029-0.01534.4440.0030.0030.0000.0000.0000.000
152A156ALA0-0.0010.02628.922-0.001-0.0010.0000.0000.0000.000
153A157LEU0-0.025-0.01626.9140.0040.0040.0000.0000.0000.000
154A158PHE00.0060.00423.054-0.007-0.0070.0000.0000.0000.000
155A159GLY00.0560.02123.2900.0070.0070.0000.0000.0000.000
156A160THR0-0.048-0.02618.4390.0030.0030.0000.0000.0000.000
157A161LEU00.0510.04720.2950.0000.0000.0000.0000.0000.000
158A162GLN00.0670.01117.2480.0020.0020.0000.0000.0000.000
159A163GLY00.0850.07719.6260.0040.0040.0000.0000.0000.000
160A164ASN0-0.050-0.04221.532-0.021-0.0210.0000.0000.0000.000
161A165THR0-0.047-0.02822.075-0.013-0.0130.0000.0000.0000.000
162A166ARG10.9670.99422.816-0.070-0.0700.0000.0000.0000.000
163A167GLU-1-0.898-0.95321.0590.1660.1660.0000.0000.0000.000
164A168VAL0-0.0010.01424.196-0.004-0.0040.0000.0000.0000.000
165A169LEU0-0.0100.00020.5780.0030.0030.0000.0000.0000.000
166A170HIS00.0360.01925.1240.0000.0000.0000.0000.0000.000
167A171LYS10.8880.92127.207-0.046-0.0460.0000.0000.0000.000
168A172PHE0-0.0230.00128.1660.0000.0000.0000.0000.0000.000
169A173THR0-0.003-0.02732.377-0.001-0.0010.0000.0000.0000.000
170A174VAL0-0.025-0.01334.484-0.001-0.0010.0000.0000.0000.000
171A175ASP-1-0.805-0.88537.1440.0020.0020.0000.0000.0000.000
172A176LEU00.0130.01037.079-0.001-0.0010.0000.0000.0000.000
173A177PRO00.0180.00940.9160.0010.0010.0000.0000.0000.000
174A178LYS10.8240.90542.345-0.001-0.0010.0000.0000.0000.000
175A179LYS10.9430.96646.0270.0010.0010.0000.0000.0000.000
176A180HIS00.0870.05348.724-0.001-0.0010.0000.0000.0000.000
177A181GLY0-0.009-0.00352.2540.0000.0000.0000.0000.0000.000
178A182ARG10.9810.97655.6000.0030.0030.0000.0000.0000.000
179A183GLY00.0710.04458.1090.0000.0000.0000.0000.0000.000
180A184GLY0-0.0010.01758.1580.0000.0000.0000.0000.0000.000
181A185GLN0-0.012-0.01851.075-0.001-0.0010.0000.0000.0000.000
182A186SER0-0.009-0.00854.0570.0000.0000.0000.0000.0000.000
183A187ALA00.1120.05952.2730.0000.0000.0000.0000.0000.000
184A188LEU00.0760.04448.3370.0000.0000.0000.0000.0000.000
185A189ARG10.8910.93648.5830.0110.0110.0000.0000.0000.000
186A190PHE0-0.022-0.02646.9430.0000.0000.0000.0000.0000.000
187A191ALA00.0790.04045.7160.0000.0000.0000.0000.0000.000
188A192ARG10.9450.97344.1000.0210.0210.0000.0000.0000.000
189A193LEU0-0.017-0.00943.1850.0000.0000.0000.0000.0000.000
190A194ARG10.9680.97841.4030.0160.0160.0000.0000.0000.000
191A195MET0-0.0220.00538.1650.0010.0010.0000.0000.0000.000
192A196GLU-1-0.935-0.98838.894-0.024-0.0240.0000.0000.0000.000
193A197LYS10.9300.96237.6770.0120.0120.0000.0000.0000.000
194A198ARG10.8300.94434.8180.0330.0330.0000.0000.0000.000
195A199HIS00.1230.06632.6400.0020.0020.0000.0000.0000.000
196A200ASN0-0.057-0.03232.641-0.001-0.0010.0000.0000.0000.000
197A201TYR0-0.072-0.05432.4020.0050.0050.0000.0000.0000.000
198A202VAL0-0.020-0.02929.2890.0030.0030.0000.0000.0000.000
199A203ARG10.9170.94428.2210.0280.0280.0000.0000.0000.000
200A204LYS10.9630.97727.484-0.005-0.0050.0000.0000.0000.000
201A205VAL0-0.0200.00826.3370.0070.0070.0000.0000.0000.000
202A206ALA00.0060.00624.1760.0050.0050.0000.0000.0000.000
203A207GLU-1-0.887-0.93223.179-0.038-0.0380.0000.0000.0000.000
204A208THR0-0.122-0.07723.4440.0070.0070.0000.0000.0000.000
205A209ALA00.0230.00721.1930.0110.0110.0000.0000.0000.000
206A210VAL00.0470.01317.8550.0090.0090.0000.0000.0000.000
207A211GLN0-0.068-0.03418.2430.0070.0070.0000.0000.0000.000
208A212LEU0-0.029-0.01719.2940.0130.0130.0000.0000.0000.000
209A213PHE0-0.0070.01116.1190.0170.0170.0000.0000.0000.000
210A214ILE0-0.0520.00112.7350.0220.0220.0000.0000.0000.000
211A215SER00.0090.01513.882-0.013-0.0130.0000.0000.0000.000
212A216GLY0-0.019-0.01811.7030.0330.0330.0000.0000.0000.000
213A217ASP-1-0.917-0.96810.289-0.045-0.0450.0000.0000.0000.000
214A218LYN00.0060.0146.116-0.103-0.1030.0000.0000.0000.000
215A219VAL00.0610.0259.8390.0490.0490.0000.0000.0000.000
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