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: 8945Y

Calculation Name: 3B8M-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3B8M

Chain ID: C

ChEMBL ID:

UniProt ID: Q8XBV8

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 260
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2875889.307105
FMO2-HF: Nuclear repulsion 2773176.180827
FMO2-HF: Total energy -102713.126279
FMO2-MP2: Total energy -103018.381256


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(C:64:LYS)


Summations of interaction energy for fragment #1(C:64: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.
-86.224-78.3746.019-6.141-7.729-0.061
Interaction energy analysis for fragmet #1(C:64:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.925 / q_NPA : 0.967
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].
3C66THR00.0260.0083.861-2.213-0.398-0.015-0.930-0.8700.003
4C67SER0-0.033-0.0056.0972.0182.0180.0000.0000.0000.000
5C68ALA00.033-0.0089.5050.0920.0920.0000.0000.0000.000
6C69ALA00.0200.01812.3680.3020.3020.0000.0000.0000.000
7C70VAL00.0070.00516.089-0.055-0.0550.0000.0000.0000.000
8C71VAL0-0.0110.00719.0920.3610.3610.0000.0000.0000.000
9C72THR00.0280.00522.132-0.072-0.0720.0000.0000.0000.000
10C73PRO0-0.015-0.01125.712-0.009-0.0090.0000.0000.0000.000
11C74PRO00.0060.04228.7670.0620.0620.0000.0000.0000.000
12C75GLU-1-0.797-0.88730.233-8.828-8.8280.0000.0000.0000.000
13C76PRO0-0.021-0.03433.1530.0110.0110.0000.0000.0000.000
14C77VAL00.0380.01934.1480.0870.0870.0000.0000.0000.000
15C78GLN0-0.002-0.00328.5020.0900.0900.0000.0000.0000.000
16C79TRP00.012-0.01731.610-0.140-0.1400.0000.0000.0000.000
17C80GLN0-0.0280.00336.5390.1950.1950.0000.0000.0000.000
18C81GLU-1-0.803-0.90837.051-7.240-7.2400.0000.0000.0000.000
19C82LEU00.0360.02635.5880.1400.1400.0000.0000.0000.000
20C83GLU-1-0.760-0.86439.255-6.594-6.5940.0000.0000.0000.000
21C84LYS10.8050.90141.0617.3437.3430.0000.0000.0000.000
22C85THR0-0.041-0.01741.8800.1680.1680.0000.0000.0000.000
23C86PHE00.0290.00238.6090.0800.0800.0000.0000.0000.000
24C87THR00.0110.00044.5930.1680.1680.0000.0000.0000.000
25C88LYS10.8330.91244.3436.7446.7440.0000.0000.0000.000
26C89LEU00.0150.01144.8980.1090.1090.0000.0000.0000.000
27C90ARG10.8200.89245.1416.4496.4490.0000.0000.0000.000
28C91VAL0-0.043-0.01550.3170.1140.1140.0000.0000.0000.000
29C92LEU0-0.064-0.02850.9920.1170.1170.0000.0000.0000.000
30C93ASP-1-0.836-0.90753.631-5.430-5.4300.0000.0000.0000.000
31C94LEU0-0.019-0.00447.180-0.007-0.0070.0000.0000.0000.000
32C95ASP-1-0.856-0.92147.842-6.331-6.3310.0000.0000.0000.000
33C96ILE0-0.048-0.02442.593-0.070-0.0700.0000.0000.0000.000
34C97LYS10.8410.91838.9197.2987.2980.0000.0000.0000.000
35C98ILE00.0200.01934.749-0.032-0.0320.0000.0000.0000.000
36C99ASP-1-0.856-0.89735.362-7.772-7.7720.0000.0000.0000.000
37C100ARG10.9090.94832.8027.9127.9120.0000.0000.0000.000
38C101THR00.004-0.01831.283-0.347-0.3470.0000.0000.0000.000
39C102GLU-1-0.844-0.93430.911-7.861-7.8610.0000.0000.0000.000
40C103ALA00.0310.01030.774-0.207-0.2070.0000.0000.0000.000
41C104PHE00.0330.02223.828-0.265-0.2650.0000.0000.0000.000
42C105ASN00.007-0.00726.257-0.546-0.5460.0000.0000.0000.000
43C106LEU0-0.049-0.01526.944-0.240-0.2400.0000.0000.0000.000
44C107PHE00.0350.00620.397-0.157-0.1570.0000.0000.0000.000
45C108ILE00.0180.01321.228-0.428-0.4280.0000.0000.0000.000
46C109LYS10.9160.96822.2528.9988.9980.0000.0000.0000.000
47C110LYS10.7890.87723.7509.6639.6630.0000.0000.0000.000
48C111PHE00.0520.02715.032-0.301-0.3010.0000.0000.0000.000
49C112GLN0-0.041-0.02118.449-0.781-0.7810.0000.0000.0000.000
50C113SER0-0.0240.00019.680-0.053-0.0530.0000.0000.0000.000
51C114VAL00.0740.02317.402-0.213-0.2130.0000.0000.0000.000
52C115SER00.0250.00919.222-0.283-0.2830.0000.0000.0000.000
53C116LEU00.0010.01021.6230.0630.0630.0000.0000.0000.000
54C117LEU0-0.0040.01813.765-0.311-0.3110.0000.0000.0000.000
55C118GLU-1-0.872-0.94317.244-14.868-14.8680.0000.0000.0000.000
56C119GLU-1-0.907-0.91918.675-11.616-11.6160.0000.0000.0000.000
57C120TYR00.0280.02914.846-0.453-0.4530.0000.0000.0000.000
58C121LEU0-0.012-0.02012.753-0.385-0.3850.0000.0000.0000.000
59C122ARG10.8230.88116.41713.67813.6780.0000.0000.0000.000
60C123SER0-0.038-0.03819.3930.5860.5860.0000.0000.0000.000
61C124SER0-0.0040.00916.5930.3670.3670.0000.0000.0000.000
62C125PRO00.0450.01717.985-0.720-0.7200.0000.0000.0000.000
63C126TYR0-0.018-0.03511.672-1.189-1.1890.0000.0000.0000.000
64C127VAL0-0.023-0.00812.883-1.609-1.6090.0000.0000.0000.000
65C128MET0-0.042-0.01014.703-0.511-0.5110.0000.0000.0000.000
66C129ASP-1-0.864-0.92617.039-16.107-16.1070.0000.0000.0000.000
67C130GLN0-0.098-0.04110.618-3.449-3.4490.0000.0000.0000.000
68C131LEU00.0310.02412.453-1.641-1.6410.0000.0000.0000.000
69C132LYS10.7740.8507.58334.66734.6670.0000.0000.0000.000
70C133GLU-1-0.808-0.8647.827-39.016-39.0160.0000.0000.0000.000
71C134ALA0-0.0010.0008.182-2.048-2.0480.0000.0000.0000.000
72C135LYS10.8200.89610.78220.94320.9430.0000.0000.0000.000
73C136ILE0-0.043-0.01712.8630.9080.9080.0000.0000.0000.000
74C137ASP-1-0.824-0.90816.356-17.508-17.5080.0000.0000.0000.000
75C138GLU-1-0.816-0.90018.514-13.800-13.8000.0000.0000.0000.000
76C139LEU0-0.079-0.04221.8420.3640.3640.0000.0000.0000.000
77C140ASP-1-0.847-0.91216.641-17.492-17.4920.0000.0000.0000.000
78C141LEU00.0500.03517.153-0.944-0.9440.0000.0000.0000.000
79C142HIS00.0380.02917.602-0.262-0.2620.0000.0000.0000.000
80C143ARG10.8390.90116.42016.94616.9460.0000.0000.0000.000
81C144ALA00.0170.01413.372-0.812-0.8120.0000.0000.0000.000
82C145ILE00.0100.00412.984-1.000-1.0000.0000.0000.0000.000
83C146VAL00.0210.01514.359-0.216-0.2160.0000.0000.0000.000
84C147ALA00.0470.03711.149-0.235-0.2350.0000.0000.0000.000
85C148LEU00.0020.0038.532-1.833-1.8330.0000.0000.0000.000
86C149SER0-0.022-0.03210.5440.1090.1090.0000.0000.0000.000
87C150GLU-1-0.876-0.93110.595-21.076-21.0760.0000.0000.0000.000
88C151LYS10.7050.8345.99325.46825.4680.0000.0000.0000.000
89C152MET00.0010.0378.610-0.638-0.6380.0000.0000.0000.000
90C153LYS10.8370.9169.11120.15920.1590.0000.0000.0000.000
91C154ALA00.0350.01112.898-0.030-0.0300.0000.0000.0000.000
92C155VAL0-0.014-0.00615.4130.1570.1570.0000.0000.0000.000
93C156ASP-1-0.783-0.88818.154-10.544-10.5440.0000.0000.0000.000
94C157ASP-1-0.770-0.83819.328-12.716-12.7160.0000.0000.0000.000
95C158ASN0-0.057-0.04921.4170.3270.3270.0000.0000.0000.000
96C159ALA0-0.0100.01922.7750.4630.4630.0000.0000.0000.000
97C160SER0-0.0100.00520.2730.0880.0880.0000.0000.0000.000
98C161LYS10.8840.93522.26810.55610.5560.0000.0000.0000.000
99C162LYS10.8060.88625.3668.3978.3970.0000.0000.0000.000
100C163LYS10.8680.91027.3959.7479.7470.0000.0000.0000.000
101C164ASP-1-0.860-0.90830.469-7.692-7.6920.0000.0000.0000.000
102C165GLU-1-0.828-0.89731.621-8.128-8.1280.0000.0000.0000.000
103C166PRO0-0.066-0.03330.868-0.313-0.3130.0000.0000.0000.000
104C167SER0-0.025-0.01127.7460.0590.0590.0000.0000.0000.000
105C168LEU0-0.007-0.00330.0650.1480.1480.0000.0000.0000.000
106C169TYR0-0.0010.00225.3580.2360.2360.0000.0000.0000.000
107C170THR00.0020.00626.321-0.152-0.1520.0000.0000.0000.000
108C171SER0-0.061-0.07722.6340.1850.1850.0000.0000.0000.000
109C172TRP00.0320.01119.4180.0640.0640.0000.0000.0000.000
110C173THR00.0250.00414.323-0.239-0.2390.0000.0000.0000.000
111C174LEU0-0.060-0.02615.0800.1750.1750.0000.0000.0000.000
112C175SER00.000-0.0119.726-0.162-0.1620.0000.0000.0000.000
113C176PHE00.0220.0038.0780.3910.3910.0000.0000.0000.000
114C177THR0-0.029-0.0242.549-0.830-0.4190.746-0.363-0.7940.000
115C178ALA00.0360.0253.5891.2551.7430.004-0.166-0.3260.000
116C179PRO0-0.009-0.0152.147-16.716-14.0414.860-3.573-3.962-0.046
117C180THR00.006-0.0072.934-10.429-8.0170.425-1.106-1.731-0.018
118C181SER00.0370.0145.0391.7761.825-0.001-0.003-0.0460.000
119C182GLU-1-0.761-0.8607.023-22.076-22.0760.0000.0000.0000.000
120C183GLH0-0.010-0.0217.386-0.894-0.8940.0000.0000.0000.000
121C184ALA0-0.033-0.0195.8541.4911.4910.0000.0000.0000.000
122C185GLN0-0.034-0.0367.7901.2811.2810.0000.0000.0000.000
123C186THR0-0.044-0.04511.4121.7801.7800.0000.0000.0000.000
124C187VAL00.0080.00610.2991.2881.2880.0000.0000.0000.000
125C188LEU0-0.057-0.01111.2861.1501.1500.0000.0000.0000.000
126C189SER0-0.038-0.03312.9371.0771.0770.0000.0000.0000.000
127C190GLY00.0310.02315.8650.7580.7580.0000.0000.0000.000
128C191TYR0-0.003-0.01615.3720.8240.8240.0000.0000.0000.000
129C192ILE00.0160.00216.2490.8320.8320.0000.0000.0000.000
130C193ASP-1-0.865-0.92018.904-12.577-12.5770.0000.0000.0000.000
131C194TYR0-0.061-0.06420.1370.5030.5030.0000.0000.0000.000
132C195ILE0-0.006-0.00820.0410.6470.6470.0000.0000.0000.000
133C196SER0-0.060-0.05422.6690.6230.6230.0000.0000.0000.000
134C197ALA00.0070.00924.9130.4820.4820.0000.0000.0000.000
135C198LEU00.0130.01524.2980.4860.4860.0000.0000.0000.000
136C199VAL0-0.028-0.01426.3760.3930.3930.0000.0000.0000.000
137C200VAL0-0.0150.01628.9080.3810.3810.0000.0000.0000.000
138C201LYS10.8560.91030.6958.8528.8520.0000.0000.0000.000
139C202GLU-1-0.766-0.87331.024-8.942-8.9420.0000.0000.0000.000
140C203SER0-0.041-0.03132.3490.3000.3000.0000.0000.0000.000
141C204ILE00.003-0.01134.8480.2750.2750.0000.0000.0000.000
142C205GLU-1-0.816-0.88335.732-7.928-7.9280.0000.0000.0000.000
143C206ASN0-0.025-0.02236.1760.3840.3840.0000.0000.0000.000
144C207VAL0-0.027-0.01138.9850.1860.1860.0000.0000.0000.000
145C208ARG10.7970.86238.3177.6647.6640.0000.0000.0000.000
146C209ASN00.0760.03340.3530.1740.1740.0000.0000.0000.000
147C210LYS10.8890.95239.7857.3367.3360.0000.0000.0000.000
148C211LEU00.0130.00845.3540.1340.1340.0000.0000.0000.000
149C212GLU-1-0.948-0.95145.863-6.335-6.3350.0000.0000.0000.000
150C213ILE00.0320.01447.0830.1510.1510.0000.0000.0000.000
151C214LYS10.7710.86949.5205.6855.6850.0000.0000.0000.000
152C215THR0-0.005-0.02650.8480.1590.1590.0000.0000.0000.000
153C216GLN0-0.086-0.05151.9820.0190.0190.0000.0000.0000.000
154C217PHE0-0.011-0.00353.6310.1410.1410.0000.0000.0000.000
155C218GLU-1-0.776-0.88455.489-5.127-5.1270.0000.0000.0000.000
156C219LYS10.9740.99556.9845.4485.4480.0000.0000.0000.000
157C220GLU-1-0.872-0.93056.507-5.296-5.2960.0000.0000.0000.000
158C221LYS10.7910.89259.4264.9804.9800.0000.0000.0000.000
159C222LEU00.0040.00961.2140.1040.1040.0000.0000.0000.000
160C223ALA00.0000.00163.0280.0970.0970.0000.0000.0000.000
161C224GLN00.0520.02762.5000.1130.1130.0000.0000.0000.000
162C225ASP-1-0.774-0.87764.425-4.664-4.6640.0000.0000.0000.000
163C226ARG10.8580.90566.7094.5444.5440.0000.0000.0000.000
164C227ILE00.0200.01667.6940.0770.0770.0000.0000.0000.000
165C228LYS10.8160.89965.6704.6774.6770.0000.0000.0000.000
166C229MET00.0100.00471.1980.0440.0440.0000.0000.0000.000
167C230LYS10.8810.93573.4464.0304.0300.0000.0000.0000.000
168C231ASN00.017-0.00273.6400.0720.0720.0000.0000.0000.000
169C232GLN00.000-0.00575.6590.0750.0750.0000.0000.0000.000
170C233LEU00.0160.03177.5730.0490.0490.0000.0000.0000.000
171C234ASP-1-0.806-0.88479.504-3.850-3.8500.0000.0000.0000.000
172C235ALA0-0.023-0.01880.3730.0570.0570.0000.0000.0000.000
173C236ASN0-0.042-0.03680.2140.0810.0810.0000.0000.0000.000
174C237ILE00.0090.01482.8400.0560.0560.0000.0000.0000.000
175C238GLN0-0.047-0.03085.1600.0800.0800.0000.0000.0000.000
176C239ARG10.7860.87484.2023.6723.6720.0000.0000.0000.000
177C240LEU00.0220.00787.4670.0410.0410.0000.0000.0000.000
178C241ASN00.0020.00189.2940.0180.0180.0000.0000.0000.000
179C242TYR00.0280.01689.2680.0480.0480.0000.0000.0000.000
180C243SER00.0030.00291.4120.0260.0260.0000.0000.0000.000
181C244LEU0-0.031-0.00493.3560.0340.0340.0000.0000.0000.000
182C245ASP-1-0.889-0.94295.467-3.236-3.2360.0000.0000.0000.000
183C246ILE0-0.003-0.01194.6220.0470.0470.0000.0000.0000.000
184C247ALA0-0.0010.00396.8110.0350.0350.0000.0000.0000.000
185C248ASN0-0.067-0.04698.7220.0660.0660.0000.0000.0000.000
186C249ALA0-0.028-0.005101.1490.0360.0360.0000.0000.0000.000
187C250ALA0-0.020-0.005100.9880.0310.0310.0000.0000.0000.000
188C251GLY0-0.013-0.003102.9570.0180.0180.0000.0000.0000.000
189C252ILE0-0.0110.00599.2000.0160.0160.0000.0000.0000.000
190C253LYS10.9340.962100.1983.0343.0340.0000.0000.0000.000
191C254LYS10.9140.97399.7933.0173.0170.0000.0000.0000.000
192C255PRO00.0180.00996.3580.0060.0060.0000.0000.0000.000
193C256VAL0-0.0280.00897.2130.0370.0370.0000.0000.0000.000
194C257TYR0-0.026-0.01598.263-0.019-0.0190.0000.0000.0000.000
195C265ASP-1-0.729-0.80692.234-3.348-3.3480.0000.0000.0000.000
196C266ASP-1-0.883-0.94592.409-3.372-3.3720.0000.0000.0000.000
197C267PRO0-0.040-0.02288.534-0.030-0.0300.0000.0000.0000.000
198C268ASP-1-0.856-0.90587.417-3.614-3.6140.0000.0000.0000.000
199C269PHE0-0.057-0.04288.648-0.038-0.0380.0000.0000.0000.000
200C270SER0-0.074-0.03889.7880.0330.0330.0000.0000.0000.000
201C271ILE00.047-0.00491.778-0.001-0.0010.0000.0000.0000.000
202C272SER0-0.047-0.04892.8000.0220.0220.0000.0000.0000.000
203C273LEU0-0.030-0.01590.8700.0200.0200.0000.0000.0000.000
204C274GLY00.0370.02294.4590.0180.0180.0000.0000.0000.000
205C275ALA00.004-0.01696.298-0.032-0.0320.0000.0000.0000.000
206C276ASP-1-0.887-0.96396.820-3.134-3.1340.0000.0000.0000.000
207C277GLY0-0.036-0.01294.786-0.018-0.0180.0000.0000.0000.000
208C278ILE0-0.025-0.01792.030-0.047-0.0470.0000.0000.0000.000
209C279GLU-1-0.904-0.95192.069-3.258-3.2580.0000.0000.0000.000
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211C281LYS10.7980.88184.9523.6023.6020.0000.0000.0000.000
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