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: YV1N2

Calculation Name: 1B8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1B8P

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZF99

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 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 327
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4769753.530473
FMO2-HF: Nuclear repulsion 4645725.534702
FMO2-HF: Total energy -124027.99577
FMO2-MP2: Total energy -124386.381635


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:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-233.972-237.75739.976-16.088-20.102-0.202
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.834 / q_NPA : 0.916
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].
3A5PRO00.0030.0083.324-9.047-6.4970.030-1.373-1.2070.002
4A6MET0-0.0080.0145.2790.6920.6920.0000.0000.0000.000
5A7ARG10.8800.9317.34421.35121.3510.0000.0000.0000.000
6A8VAL0-0.007-0.01210.0530.2260.2260.0000.0000.0000.000
7A9ALA00.0320.03012.7961.0261.0260.0000.0000.0000.000
8A10VAL0-0.020-0.01616.116-0.368-0.3680.0000.0000.0000.000
9A11THR00.0020.00018.6560.5900.5900.0000.0000.0000.000
10A12GLY00.0220.00422.4860.0070.0070.0000.0000.0000.000
11A13ALA0-0.006-0.00521.638-0.053-0.0530.0000.0000.0000.000
12A14ALA00.0240.00822.924-0.243-0.2430.0000.0000.0000.000
13A15GLY0-0.0100.00225.6880.4520.4520.0000.0000.0000.000
14A16GLN0-0.007-0.02225.206-0.644-0.6440.0000.0000.0000.000
15A17ILE0-0.033-0.01421.987-0.157-0.1570.0000.0000.0000.000
16A18CYS0-0.005-0.00220.851-0.777-0.7770.0000.0000.0000.000
17A19TYR0-0.032-0.02520.703-0.812-0.8120.0000.0000.0000.000
18A20SER0-0.055-0.02822.055-0.090-0.0900.0000.0000.0000.000
19A21LEU0-0.064-0.03016.200-0.414-0.4140.0000.0000.0000.000
20A22LEU00.0100.00016.320-1.337-1.3370.0000.0000.0000.000
21A23PHE00.0650.03915.406-1.501-1.5010.0000.0000.0000.000
22A24ARG10.8230.88614.84718.15318.1530.0000.0000.0000.000
23A25ILE0-0.025-0.02110.974-1.893-1.8930.0000.0000.0000.000
24A26ALA00.0290.02610.567-2.795-2.7950.0000.0000.0000.000
25A27ASN0-0.031-0.01911.525-1.074-1.0740.0000.0000.0000.000
26A28GLY00.0770.0428.283-1.202-1.2020.0000.0000.0000.000
27A29ASP-1-0.872-0.9197.883-26.193-26.1930.0000.0000.0000.000
28A30MET0-0.055-0.0189.7650.3740.3740.0000.0000.0000.000
29A31LEU00.002-0.0085.4921.4751.4750.0000.0000.0000.000
30A32GLY00.0580.0433.497-11.340-11.1250.000-0.060-0.1550.000
31A33LYS10.7900.8694.55629.37829.458-0.0010.000-0.0780.000
32A34ASP-1-0.787-0.8811.812-136.592-141.35623.538-10.469-8.305-0.129
33A35GLN0-0.065-0.0542.090-33.070-33.89516.082-5.798-9.460-0.074
34A36PRO00.0070.0152.95111.61210.5710.3271.612-0.897-0.001
35A37VAL0-0.013-0.0015.619-2.585-2.5850.0000.0000.0000.000
36A38ILE00.0040.0038.4242.0282.0280.0000.0000.0000.000
37A39LEU00.0070.00611.4620.2520.2520.0000.0000.0000.000
38A40GLN0-0.026-0.01314.5740.1950.1950.0000.0000.0000.000
39A41LEU00.0100.00517.4000.2080.2080.0000.0000.0000.000
40A42LEU0-0.020-0.01620.2230.6270.6270.0000.0000.0000.000
41A43GLU-1-0.821-0.91823.428-11.663-11.6630.0000.0000.0000.000
42A44ILE0-0.011-0.00426.7630.1620.1620.0000.0000.0000.000
43A45PRO00.0410.01430.349-0.061-0.0610.0000.0000.0000.000
44A46ASN0-0.033-0.01332.1650.0740.0740.0000.0000.0000.000
45A47GLU-1-0.758-0.87933.225-8.833-8.8330.0000.0000.0000.000
46A48LYS10.9770.97933.4268.6648.6640.0000.0000.0000.000
47A49ALA0-0.0080.00530.168-0.107-0.1070.0000.0000.0000.000
48A50GLN00.005-0.01227.496-0.523-0.5230.0000.0000.0000.000
49A51LYS10.8290.90728.7488.4878.4870.0000.0000.0000.000
50A52ALA0-0.027-0.00829.618-0.145-0.1450.0000.0000.0000.000
51A53LEU00.0160.00522.403-0.246-0.2460.0000.0000.0000.000
52A54GLN00.0200.00524.804-0.772-0.7720.0000.0000.0000.000
53A55GLY0-0.0080.00026.035-0.170-0.1700.0000.0000.0000.000
54A56VAL00.006-0.00621.828-0.208-0.2080.0000.0000.0000.000
55A57MET0-0.022-0.02320.533-0.481-0.4810.0000.0000.0000.000
56A58MET00.0090.01121.747-0.254-0.2540.0000.0000.0000.000
57A59GLU-1-0.805-0.87623.608-12.394-12.3940.0000.0000.0000.000
58A60ILE0-0.042-0.02517.189-0.549-0.5490.0000.0000.0000.000
59A61ASP-1-0.905-0.96118.842-16.639-16.6390.0000.0000.0000.000
60A62ASP-1-0.939-0.96420.041-12.754-12.7540.0000.0000.0000.000
61A63CYS0-0.154-0.07518.8230.2340.2340.0000.0000.0000.000
62A64ALA0-0.033-0.01217.696-0.699-0.6990.0000.0000.0000.000
63A65PHE00.008-0.00113.317-0.721-0.7210.0000.0000.0000.000
64A66PRO00.0070.00210.695-0.545-0.5450.0000.0000.0000.000
65A67LEU0-0.042-0.0086.094-1.637-1.6370.0000.0000.0000.000
66A68LEU0-0.001-0.0019.009-2.171-2.1710.0000.0000.0000.000
67A69ALA0-0.0100.0018.5601.4441.4440.0000.0000.0000.000
68A70GLY0-0.005-0.00610.6841.4441.4440.0000.0000.0000.000
69A71MET0-0.0260.00613.812-1.112-1.1120.0000.0000.0000.000
70A72THR0-0.014-0.01016.6010.5820.5820.0000.0000.0000.000
71A73ALA00.0590.03019.635-0.275-0.2750.0000.0000.0000.000
72A74HIS0-0.018-0.00220.306-0.386-0.3860.0000.0000.0000.000
73A75ALA00.0320.01324.4920.1080.1080.0000.0000.0000.000
74A76ASP-1-0.771-0.88026.398-11.180-11.1800.0000.0000.0000.000
75A77PRO00.002-0.00224.439-0.497-0.4970.0000.0000.0000.000
76A78MET0-0.0130.00323.451-0.691-0.6910.0000.0000.0000.000
77A79THR0-0.038-0.04022.637-0.440-0.4400.0000.0000.0000.000
78A80ALA0-0.0270.00520.608-0.643-0.6430.0000.0000.0000.000
79A81PHE00.023-0.01118.881-0.957-0.9570.0000.0000.0000.000
80A82LYS10.8320.90718.52514.61214.6120.0000.0000.0000.000
81A83ASP-1-0.832-0.89714.793-17.087-17.0870.0000.0000.0000.000
82A84ALA0-0.015-0.00213.910-1.437-1.4370.0000.0000.0000.000
83A85ASP-1-0.766-0.89710.092-25.562-25.5620.0000.0000.0000.000
84A86VAL0-0.040-0.02110.259-0.204-0.2040.0000.0000.0000.000
85A87ALA00.0200.01413.2040.6660.6660.0000.0000.0000.000
86A88LEU0-0.015-0.00214.0210.2990.2990.0000.0000.0000.000
87A89LEU00.0220.01018.1390.4910.4910.0000.0000.0000.000
88A90VAL00.023-0.00920.7450.4450.4450.0000.0000.0000.000
89A91GLY0-0.0170.00623.4560.6030.6030.0000.0000.0000.000
90A92ALA00.0090.01426.201-0.011-0.0110.0000.0000.0000.000
91A93ARG10.8820.94429.2928.7428.7420.0000.0000.0000.000
92A94PRO00.0300.02032.2840.0730.0730.0000.0000.0000.000
93A95ARG10.8870.92734.3297.9747.9740.0000.0000.0000.000
94A96GLY00.024-0.00537.928-0.087-0.0870.0000.0000.0000.000
95A97PRO00.025-0.00840.7440.0700.0700.0000.0000.0000.000
96A98GLY00.0030.01544.582-0.029-0.0290.0000.0000.0000.000
97A99MET0-0.0390.01938.266-0.005-0.0050.0000.0000.0000.000
98A100GLU-1-0.799-0.88743.569-6.871-6.8710.0000.0000.0000.000
99A101ARG10.7770.85137.8028.1428.1420.0000.0000.0000.000
100A102LYS10.9050.95239.9726.6626.6620.0000.0000.0000.000
101A103ASP-1-0.759-0.88940.674-7.472-7.4720.0000.0000.0000.000
102A104LEU0-0.071-0.03635.272-0.142-0.1420.0000.0000.0000.000
103A105LEU00.0160.01536.120-0.296-0.2960.0000.0000.0000.000
104A106GLU-1-0.777-0.88236.222-8.156-8.1560.0000.0000.0000.000
105A107ALA0-0.040-0.01736.601-0.185-0.1850.0000.0000.0000.000
106A108ASN0-0.013-0.02131.750-0.514-0.5140.0000.0000.0000.000
107A109ALA00.0610.04132.082-0.358-0.3580.0000.0000.0000.000
108A110GLN0-0.020-0.01133.298-0.286-0.2860.0000.0000.0000.000
109A111ILE0-0.039-0.01829.123-0.213-0.2130.0000.0000.0000.000
110A112PHE00.009-0.01925.158-0.362-0.3620.0000.0000.0000.000
111A113THR0-0.0140.00728.374-0.296-0.2960.0000.0000.0000.000
112A114VAL0-0.035-0.00229.394-0.178-0.1780.0000.0000.0000.000
113A115GLN00.016-0.00524.567-0.782-0.7820.0000.0000.0000.000
114A116GLY00.0250.01824.945-0.485-0.4850.0000.0000.0000.000
115A117LYS10.9810.98525.6889.4109.4100.0000.0000.0000.000
116A118ALA0-0.025-0.00925.037-0.041-0.0410.0000.0000.0000.000
117A119ILE0-0.006-0.00920.425-0.393-0.3930.0000.0000.0000.000
118A120ASP-1-0.801-0.88222.157-12.363-12.3630.0000.0000.0000.000
119A121ALA00.0040.01424.198-0.169-0.1690.0000.0000.0000.000
120A122VAL0-0.042-0.01721.498-0.035-0.0350.0000.0000.0000.000
121A123ALA0-0.0010.02518.145-0.618-0.6180.0000.0000.0000.000
122A124SER0-0.0120.00413.0211.0351.0350.0000.0000.0000.000
123A125ARG10.8060.87616.14414.56814.5680.0000.0000.0000.000
124A126ASN0-0.020-0.01814.5761.0581.0580.0000.0000.0000.000
125A127ILE0-0.0150.01114.573-1.129-1.1290.0000.0000.0000.000
126A128LYS10.8590.94711.43324.96124.9610.0000.0000.0000.000
127A129VAL00.0230.00915.300-0.392-0.3920.0000.0000.0000.000
128A130LEU0-0.0240.00917.1850.3530.3530.0000.0000.0000.000
129A131VAL0-0.0300.00119.2150.0820.0820.0000.0000.0000.000
130A132VAL00.000-0.02620.4430.0190.0190.0000.0000.0000.000
131A133GLY00.0000.00623.4940.4650.4650.0000.0000.0000.000
132A134ASN0-0.058-0.03926.644-0.144-0.1440.0000.0000.0000.000
133A135PRO00.0390.02929.7660.0850.0850.0000.0000.0000.000
134A136ALA00.0440.00425.6330.0050.0050.0000.0000.0000.000
135A137ASN0-0.004-0.01026.983-0.452-0.4520.0000.0000.0000.000
136A138THR00.040-0.00628.492-0.168-0.1680.0000.0000.0000.000
137A139ASN0-0.020-0.01627.8800.3440.3440.0000.0000.0000.000
138A140ALA00.0250.00724.840-0.131-0.1310.0000.0000.0000.000
139A141TYR0-0.004-0.01926.283-0.122-0.1220.0000.0000.0000.000
140A142ILE0-0.006-0.00529.1580.0830.0830.0000.0000.0000.000
141A143ALA0-0.012-0.00125.0580.0900.0900.0000.0000.0000.000
142A144MET0-0.028-0.00225.407-0.090-0.0900.0000.0000.0000.000
143A145LYS10.8930.94726.6719.9879.9870.0000.0000.0000.000
144A146SER0-0.045-0.02328.7610.4590.4590.0000.0000.0000.000
145A147ALA0-0.050-0.01924.732-0.023-0.0230.0000.0000.0000.000
146A148PRO00.0080.00826.049-0.301-0.3010.0000.0000.0000.000
147A149SER0-0.080-0.06425.057-0.079-0.0790.0000.0000.0000.000
148A150LEU0-0.021-0.00419.813-0.539-0.5390.0000.0000.0000.000
149A151PRO00.005-0.00419.2080.5680.5680.0000.0000.0000.000
150A152ALA00.0610.03021.652-0.464-0.4640.0000.0000.0000.000
151A153LYS10.8330.90517.48717.11417.1140.0000.0000.0000.000
152A154ASN0-0.010-0.00816.578-0.183-0.1830.0000.0000.0000.000
153A155PHE00.0300.02019.055-0.618-0.6180.0000.0000.0000.000
154A156THR0-0.018-0.01318.8890.2620.2620.0000.0000.0000.000
155A157ALA00.0130.00021.4780.0820.0820.0000.0000.0000.000
156A158MET0-0.0180.01020.566-0.218-0.2180.0000.0000.0000.000
157A159LEU00.018-0.01022.5490.3420.3420.0000.0000.0000.000
158A160ARG10.7880.90215.95218.72118.7210.0000.0000.0000.000
159A161LEU0-0.006-0.01321.9430.0950.0950.0000.0000.0000.000
160A162ASP-1-0.813-0.89323.965-11.205-11.2050.0000.0000.0000.000
161A163HIS00.0730.07122.6220.5050.5050.0000.0000.0000.000
162A164ASN0-0.015-0.02519.5900.4180.4180.0000.0000.0000.000
163A165ARG10.8410.92124.06511.51611.5160.0000.0000.0000.000
164A166ALA00.0550.03427.6730.3620.3620.0000.0000.0000.000
165A167LEU00.0190.00322.8710.3570.3570.0000.0000.0000.000
166A168SER0-0.031-0.02827.0180.3640.3640.0000.0000.0000.000
167A169GLN0-0.026-0.02628.4910.6390.6390.0000.0000.0000.000
168A170ILE00.0390.02829.9930.3660.3660.0000.0000.0000.000
169A171ALA00.0000.02628.5080.2280.2280.0000.0000.0000.000
170A172ALA0-0.033-0.01930.6470.2350.2350.0000.0000.0000.000
171A173LYS10.8010.91133.6748.2388.2380.0000.0000.0000.000
172A174THR0-0.022-0.04032.7890.1620.1620.0000.0000.0000.000
173A175GLY00.0040.02634.6500.1220.1220.0000.0000.0000.000
174A176LYS10.8470.92330.3709.7899.7890.0000.0000.0000.000
175A177PRO00.0240.01826.221-0.124-0.1240.0000.0000.0000.000
176A178VAL00.0550.01323.513-0.151-0.1510.0000.0000.0000.000
177A179SER0-0.032-0.01721.6620.0400.0400.0000.0000.0000.000
178A180SER0-0.036-0.02422.833-0.209-0.2090.0000.0000.0000.000
179A181ILE0-0.039-0.01825.2940.3590.3590.0000.0000.0000.000
180A182GLU-1-0.810-0.89924.355-12.908-12.9080.0000.0000.0000.000
181A183LYS10.7930.87824.81112.15212.1520.0000.0000.0000.000
182A184LEU00.0020.02126.3990.3690.3690.0000.0000.0000.000
183A185PHE0-0.020-0.01825.309-0.653-0.6530.0000.0000.0000.000
184A186VAL0-0.041-0.02526.5570.4930.4930.0000.0000.0000.000
185A187TRP0-0.024-0.00927.612-0.437-0.4370.0000.0000.0000.000
186A188GLY00.018-0.00129.9830.1820.1820.0000.0000.0000.000
187A189ASN00.022-0.01829.477-0.814-0.8140.0000.0000.0000.000
188A190HIS10.8250.91327.07811.75811.7580.0000.0000.0000.000
189A191SER0-0.073-0.06729.5530.1070.1070.0000.0000.0000.000
190A192PRO00.004-0.01033.074-0.104-0.1040.0000.0000.0000.000
191A193THR0-0.032-0.01935.6550.0880.0880.0000.0000.0000.000
192A194MET0-0.0490.01831.056-0.024-0.0240.0000.0000.0000.000
193A195TYR00.030-0.02532.2210.3470.3470.0000.0000.0000.000
194A196ALA00.0420.01630.510-0.272-0.2720.0000.0000.0000.000
195A197ASP-1-0.784-0.86630.594-9.258-9.2580.0000.0000.0000.000
196A198TYR0-0.014-0.02631.124-0.193-0.1930.0000.0000.0000.000
197A199ARG10.7250.82832.9299.0279.0270.0000.0000.0000.000
198A200TYR00.0450.02730.5330.1920.1920.0000.0000.0000.000
199A201ALA0-0.0210.01229.329-0.261-0.2610.0000.0000.0000.000
200A202GLN00.001-0.01829.0450.1210.1210.0000.0000.0000.000
201A203ILE00.005-0.00728.758-0.369-0.3690.0000.0000.0000.000
202A204ASP-1-0.847-0.91628.905-10.237-10.2370.0000.0000.0000.000
203A205GLY00.0190.02230.0240.2260.2260.0000.0000.0000.000
204A206ALA0-0.0120.00431.4960.2500.2500.0000.0000.0000.000
205A207SER0-0.013-0.04233.083-0.389-0.3890.0000.0000.0000.000
206A208VAL00.0260.00131.0140.1990.1990.0000.0000.0000.000
207A209LYS10.8700.93034.3128.3698.3690.0000.0000.0000.000
208A210ASP-1-0.858-0.91037.251-8.000-8.0000.0000.0000.0000.000
209A211MET0-0.066-0.01833.9040.1310.1310.0000.0000.0000.000
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