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: LZ589

Calculation Name: 1JN5-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JN5

Chain ID: B

ChEMBL ID:

UniProt ID: Q9UBU9

Base Structure: X-ray

Registration Date: 2023-09-20

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945513.88198
FMO2-HF: Nuclear repulsion 1872870.875756
FMO2-HF: Total energy -72643.006224
FMO2-MP2: Total energy -72855.132625


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(B:370:ALA)


Summations of interaction energy for fragment #1(B:370:ALA)
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.
-0.9460.073-0.006-0.456-0.5570.003
Interaction energy analysis for fragmet #1(B:370:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.018
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].
3B372PRO00.0380.0203.837-1.691-0.672-0.006-0.456-0.5570.003
4B373CYS0-0.026-0.0156.3330.4730.4730.0000.0000.0000.000
5B374LYS10.9670.9937.8680.2440.2440.0000.0000.0000.000
6B375GLY00.0140.00711.3970.0040.0040.0000.0000.0000.000
7B376SER00.0320.00314.6210.0060.0060.0000.0000.0000.000
8B377TYR0-0.0220.00915.1690.0040.0040.0000.0000.0000.000
9B378PHE00.054-0.01117.2920.0060.0060.0000.0000.0000.000
10B379GLY00.0160.02819.4050.0120.0120.0000.0000.0000.000
11B380THR00.0280.00420.4330.0050.0050.0000.0000.0000.000
12B381GLU-1-0.859-0.94623.783-0.011-0.0110.0000.0000.0000.000
13B382ASN0-0.037-0.01426.117-0.004-0.0040.0000.0000.0000.000
14B383LEU00.0800.03124.279-0.004-0.0040.0000.0000.0000.000
15B384LYS10.9320.98823.1710.0580.0580.0000.0000.0000.000
16B385SER0-0.034-0.02325.596-0.005-0.0050.0000.0000.0000.000
17B386LEU00.0120.02329.058-0.003-0.0030.0000.0000.0000.000
18B387VAL00.0270.00324.844-0.003-0.0030.0000.0000.0000.000
19B388LEU0-0.036-0.02924.326-0.005-0.0050.0000.0000.0000.000
20B389HIS00.0150.01927.997-0.005-0.0050.0000.0000.0000.000
21B390PHE00.001-0.01029.528-0.001-0.0010.0000.0000.0000.000
22B391LEU0-0.012-0.00825.423-0.001-0.0010.0000.0000.0000.000
23B392GLN0-0.0080.00529.885-0.001-0.0010.0000.0000.0000.000
24B393GLN00.0030.00232.3600.0000.0000.0000.0000.0000.000
25B394TYR00.005-0.01631.458-0.001-0.0010.0000.0000.0000.000
26B395TYR0-0.012-0.03927.872-0.001-0.0010.0000.0000.0000.000
27B396ALA0-0.0050.02933.133-0.002-0.0020.0000.0000.0000.000
28B397ILE00.0100.01436.2600.0000.0000.0000.0000.0000.000
29B398TYR0-0.0300.00332.5710.0000.0000.0000.0000.0000.000
30B399ASP-1-0.754-0.86333.169-0.059-0.0590.0000.0000.0000.000
31B400SER0-0.035-0.02036.5210.0000.0000.0000.0000.0000.000
32B401GLY0-0.028-0.00940.1390.0000.0000.0000.0000.0000.000
33B402ASP-1-0.835-0.91941.869-0.021-0.0210.0000.0000.0000.000
34B403ARG10.7250.83635.4360.0410.0410.0000.0000.0000.000
35B404GLN00.001-0.00639.9190.0030.0030.0000.0000.0000.000
36B405GLY00.0060.00241.8290.0020.0020.0000.0000.0000.000
37B406LEU00.000-0.00435.3480.0010.0010.0000.0000.0000.000
38B407LEU0-0.042-0.02238.6680.0020.0020.0000.0000.0000.000
39B408ASP-1-0.899-0.93640.934-0.008-0.0080.0000.0000.0000.000
40B409ALA0-0.061-0.02335.3720.0010.0010.0000.0000.0000.000
41B410TYR0-0.076-0.04832.4250.0010.0010.0000.0000.0000.000
42B411HIS00.0980.03536.8180.0000.0000.0000.0000.0000.000
43B412ASP-1-0.795-0.89038.6610.0000.0000.0000.0000.0000.000
44B413GLY0-0.029-0.00739.919-0.001-0.0010.0000.0000.0000.000
45B414ALA0-0.021-0.00335.2500.0020.0020.0000.0000.0000.000
46B415CYS0-0.061-0.02532.9020.0000.0000.0000.0000.0000.000
47B416CYS0-0.013-0.00431.904-0.002-0.0020.0000.0000.0000.000
48B417SER0-0.018-0.00929.3690.0040.0040.0000.0000.0000.000
49B418LEU00.0440.03728.775-0.003-0.0030.0000.0000.0000.000
50B419SER0-0.041-0.02425.6560.0010.0010.0000.0000.0000.000
51B420ILE00.0150.01526.151-0.006-0.0060.0000.0000.0000.000
52B421PRO0-0.025-0.01623.1330.0050.0050.0000.0000.0000.000
53B422PHE00.0490.00724.6940.0050.0050.0000.0000.0000.000
54B423ILE0-0.0150.00422.2760.0030.0030.0000.0000.0000.000
55B424PRO0-0.0100.01126.2640.0020.0020.0000.0000.0000.000
56B425GLN00.039-0.02327.841-0.008-0.0080.0000.0000.0000.000
57B426ASN00.0370.01827.3560.0000.0000.0000.0000.0000.000
58B427PRO00.0150.00825.0130.0030.0030.0000.0000.0000.000
59B428ALA00.0150.01428.072-0.003-0.0030.0000.0000.0000.000
60B429ARG10.8830.96527.2570.0880.0880.0000.0000.0000.000
61B430SER00.0660.03630.7830.0070.0070.0000.0000.0000.000
62B431SER00.0240.00431.476-0.003-0.0030.0000.0000.0000.000
63B432LEU00.0180.02227.7010.0000.0000.0000.0000.0000.000
64B433ALA0-0.032-0.01832.3570.0030.0030.0000.0000.0000.000
65B434GLU-1-0.915-0.95935.428-0.037-0.0370.0000.0000.0000.000
66B435TYR0-0.022-0.04531.4340.0020.0020.0000.0000.0000.000
67B436PHE0-0.072-0.03732.6870.0020.0020.0000.0000.0000.000
68B437LYS10.9380.96734.1040.0290.0290.0000.0000.0000.000
69B438ASP-1-0.794-0.87935.316-0.021-0.0210.0000.0000.0000.000
70B439SER0-0.0290.00630.2360.0000.0000.0000.0000.0000.000
71B440ARG10.8800.92230.5000.0070.0070.0000.0000.0000.000
72B441ASN00.0650.02025.6670.0040.0040.0000.0000.0000.000
73B442VAL00.0450.02527.4650.0010.0010.0000.0000.0000.000
74B443LYN00.0850.07623.9770.0010.0010.0000.0000.0000.000
75B444LYS10.8130.90626.5660.0320.0320.0000.0000.0000.000
76B445LEU00.0320.03030.3360.0010.0010.0000.0000.0000.000
77B446LYS10.9060.93330.1360.0020.0020.0000.0000.0000.000
78B447ASP-1-0.728-0.87434.8650.0020.0020.0000.0000.0000.000
79B448PRO00.010-0.00237.167-0.001-0.0010.0000.0000.0000.000
80B449THR00.0270.01738.2130.0010.0010.0000.0000.0000.000
81B450LEU0-0.012-0.01537.999-0.001-0.0010.0000.0000.0000.000
82B451ARG10.8060.88631.537-0.008-0.0080.0000.0000.0000.000
83B452PHE0-0.022-0.00135.555-0.001-0.0010.0000.0000.0000.000
84B453ARG10.9890.99537.8840.0060.0060.0000.0000.0000.000
85B454LEU0-0.0200.00134.462-0.001-0.0010.0000.0000.0000.000
86B455LEU0-0.104-0.03932.632-0.002-0.0020.0000.0000.0000.000
87B456LYS10.8470.92635.3340.0200.0200.0000.0000.0000.000
88B457HIS00.002-0.01836.3180.0000.0000.0000.0000.0000.000
89B458THR00.010-0.00238.722-0.001-0.0010.0000.0000.0000.000
90B459ARG10.8560.90439.1990.0010.0010.0000.0000.0000.000
91B460LEU00.0310.03640.243-0.002-0.0020.0000.0000.0000.000
92B461ASN0-0.020-0.02540.788-0.003-0.0030.0000.0000.0000.000
93B462VAL0-0.058-0.01935.509-0.002-0.0020.0000.0000.0000.000
94B463VAL00.020-0.01437.650-0.003-0.0030.0000.0000.0000.000
95B464ALA0-0.026-0.00539.340-0.002-0.0020.0000.0000.0000.000
96B465PHE00.0290.01533.646-0.002-0.0020.0000.0000.0000.000
97B466LEU0-0.008-0.00733.331-0.003-0.0030.0000.0000.0000.000
98B467ASN0-0.015-0.01236.987-0.005-0.0050.0000.0000.0000.000
99B468GLU-1-0.955-0.97139.658-0.023-0.0230.0000.0000.0000.000
100B469LEU0-0.081-0.02233.241-0.003-0.0030.0000.0000.0000.000
101B470PRO00.0270.02135.0660.0010.0010.0000.0000.0000.000
102B471LYS10.9190.96336.0460.0370.0370.0000.0000.0000.000
103B472THR0-0.086-0.07832.321-0.003-0.0030.0000.0000.0000.000
104B473GLN00.0300.00932.1020.0030.0030.0000.0000.0000.000
105B474HIS10.8090.90727.6940.0630.0630.0000.0000.0000.000
106B475ASP-1-0.854-0.89026.570-0.108-0.1080.0000.0000.0000.000
107B476VAL00.0470.00526.298-0.009-0.0090.0000.0000.0000.000
108B477ASN0-0.012-0.00726.0420.0010.0010.0000.0000.0000.000
109B478SER0-0.042-0.03323.106-0.010-0.0100.0000.0000.0000.000
110B479PHE0-0.080-0.03521.807-0.013-0.0130.0000.0000.0000.000
111B480VAL0-0.029-0.00515.803-0.006-0.0060.0000.0000.0000.000
112B481VAL0-0.037-0.03019.2210.0090.0090.0000.0000.0000.000
113B482ASP-1-0.873-0.92215.481-0.147-0.1470.0000.0000.0000.000
114B483ILE0-0.033-0.01418.2240.0110.0110.0000.0000.0000.000
115B484SER0-0.025-0.01617.8930.0110.0110.0000.0000.0000.000
116B485ALA0-0.007-0.00418.8890.0240.0240.0000.0000.0000.000
117B486GLN0-0.014-0.02321.915-0.012-0.0120.0000.0000.0000.000
118B487THR00.0140.01224.9080.0080.0080.0000.0000.0000.000
119B488SER00.0290.01928.021-0.004-0.0040.0000.0000.0000.000
120B489THR0-0.017-0.02731.259-0.004-0.0040.0000.0000.0000.000
121B490LEU00.0140.01825.649-0.004-0.0040.0000.0000.0000.000
122B491LEU00.0320.02025.0500.0050.0050.0000.0000.0000.000
123B492CYS0-0.0080.00522.305-0.007-0.0070.0000.0000.0000.000
124B493PHE0-0.013-0.01621.5140.0030.0030.0000.0000.0000.000
125B494SER00.001-0.00118.8600.0050.0050.0000.0000.0000.000
126B495VAL0-0.025-0.01220.434-0.010-0.0100.0000.0000.0000.000
127B496ASN00.0010.00917.1910.0050.0050.0000.0000.0000.000
128B497GLY00.0360.02020.320-0.004-0.0040.0000.0000.0000.000
129B498VAL00.005-0.00522.513-0.002-0.0020.0000.0000.0000.000
130B499PHE0-0.035-0.02025.1490.0060.0060.0000.0000.0000.000
131B500LYS10.9160.97028.8640.0670.0670.0000.0000.0000.000
132B501GLU-1-0.728-0.81231.866-0.059-0.0590.0000.0000.0000.000
133B502VAL0-0.006-0.02834.571-0.001-0.0010.0000.0000.0000.000
134B503ASP-1-0.841-0.91837.743-0.040-0.0400.0000.0000.0000.000
135B504GLY00.0680.04738.844-0.002-0.0020.0000.0000.0000.000
136B505LYS10.9260.94139.9880.0370.0370.0000.0000.0000.000
137B506SER0-0.005-0.00434.8640.0000.0000.0000.0000.0000.000
138B507ARG10.9150.96435.5300.0490.0490.0000.0000.0000.000
139B508ASP-1-0.851-0.90835.247-0.065-0.0650.0000.0000.0000.000
140B509SER00.0040.01531.011-0.006-0.0060.0000.0000.0000.000
141B510LEU0-0.035-0.01826.0160.0020.0020.0000.0000.0000.000
142B511ARG10.7230.82127.0870.0680.0680.0000.0000.0000.000
143B512ALA00.025-0.00321.707-0.005-0.0050.0000.0000.0000.000
144B513PHE0-0.057-0.03022.8570.0090.0090.0000.0000.0000.000
145B514THR00.0460.01518.458-0.012-0.0120.0000.0000.0000.000
146B515ARG10.7700.85221.5970.0480.0480.0000.0000.0000.000
147B516THR00.0110.01421.973-0.004-0.0040.0000.0000.0000.000
148B517PHE00.0130.01724.0200.0020.0020.0000.0000.0000.000
149B518ILE00.021-0.00425.6130.0040.0040.0000.0000.0000.000
150B519ALA0-0.045-0.02727.755-0.003-0.0030.0000.0000.0000.000
151B520VAL00.0190.01530.3530.0060.0060.0000.0000.0000.000
152B521PRO00.003-0.00532.770-0.004-0.0040.0000.0000.0000.000
153B522ALA00.0030.02934.9070.0000.0000.0000.0000.0000.000
154B523SER0-0.013-0.02137.6950.0000.0000.0000.0000.0000.000
155B524ASN00.0290.00739.5140.0020.0020.0000.0000.0000.000
156B525SER0-0.020-0.00135.966-0.001-0.0010.0000.0000.0000.000
157B526GLY00.0090.01835.496-0.002-0.0020.0000.0000.0000.000
158B527LEU0-0.053-0.04229.9110.0030.0030.0000.0000.0000.000
159B528CYS0-0.0020.01534.105-0.002-0.0020.0000.0000.0000.000
160B529ILE00.0180.01530.9390.0040.0040.0000.0000.0000.000
161B530VAL00.021-0.00331.677-0.001-0.0010.0000.0000.0000.000
162B531ASN0-0.032-0.02529.2770.0040.0040.0000.0000.0000.000
163B532ASP-1-0.704-0.79928.619-0.030-0.0300.0000.0000.0000.000
164B533GLU-1-0.894-0.92024.941-0.034-0.0340.0000.0000.0000.000
165B534LEU00.0140.01625.532-0.007-0.0070.0000.0000.0000.000
166B535PHE00.0560.02920.591-0.001-0.0010.0000.0000.0000.000
167B536VAL00.0140.00324.376-0.010-0.0100.0000.0000.0000.000
168B537ARG10.7790.83318.6130.1690.1690.0000.0000.0000.000
169B538ASN0-0.0020.00424.9480.0030.0030.0000.0000.0000.000
170B539ALA00.0090.01622.835-0.009-0.0090.0000.0000.0000.000
171B540SER0-0.021-0.05519.5630.0080.0080.0000.0000.0000.000
172B541SER00.034-0.00122.1580.0020.0020.0000.0000.0000.000
173B542GLU-1-0.854-0.89618.158-0.215-0.2150.0000.0000.0000.000
174B543GLU-1-0.780-0.84419.095-0.196-0.1960.0000.0000.0000.000
175B544ILE0-0.019-0.00921.3520.0070.0070.0000.0000.0000.000
176B545GLN0-0.0030.00323.4460.0080.0080.0000.0000.0000.000
177B546ARG10.9310.96117.6290.2620.2620.0000.0000.0000.000
178B547ALA0-0.027-0.01423.3800.0070.0070.0000.0000.0000.000
179B548PHE0-0.014-0.02025.4540.0100.0100.0000.0000.0000.000
180B549ALA0-0.0070.02226.1420.0080.0080.0000.0000.0000.000
181B550MET0-0.021-0.01528.1540.0020.0020.0000.0000.0000.000
182B551PRO0-0.026-0.00627.9330.0070.0070.0000.0000.0000.000
183B552ALA00.0210.01331.2430.0020.0020.0000.0000.0000.000
184B553PRO00.0100.00331.117-0.007-0.0070.0000.0000.0000.000
185B554THR0-0.001-0.00229.2700.0050.0050.0000.0000.0000.000
186B555PRO0-0.015-0.00328.741-0.008-0.0080.0000.0000.0000.000