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: 1N87Z

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 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 260
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2868627.058205
FMO2-HF: Nuclear repulsion 2765916.970082
FMO2-HF: Total energy -102710.088123
FMO2-MP2: Total energy -103015.297006


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.
-62.253-55.3231.521-3.859-4.591-0.023
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 : 0.891 / q_NPA : 0.937
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].
3C66THR0-0.010-0.0523.8360.1682.093-0.024-0.977-0.9240.000
4C67SER0-0.039-0.0106.3871.3151.3150.0000.0000.0000.000
5C68ALA00.0330.0029.6300.3160.3160.0000.0000.0000.000
6C69ALA00.0150.00012.6640.2880.2880.0000.0000.0000.000
7C70VAL00.0070.02416.2970.0080.0080.0000.0000.0000.000
8C71VAL0-0.0140.00819.4150.3750.3750.0000.0000.0000.000
9C72THR00.0270.00722.185-0.053-0.0530.0000.0000.0000.000
10C73PRO0-0.005-0.00725.787-0.022-0.0220.0000.0000.0000.000
11C74PRO0-0.0070.01728.7480.0290.0290.0000.0000.0000.000
12C75GLU-1-0.882-0.95030.435-8.510-8.5100.0000.0000.0000.000
13C76PRO0-0.022-0.02433.4040.0110.0110.0000.0000.0000.000
14C77VAL00.0390.02134.2900.0660.0660.0000.0000.0000.000
15C78GLN0-0.006-0.01628.9520.1050.1050.0000.0000.0000.000
16C79TRP00.012-0.00731.777-0.154-0.1540.0000.0000.0000.000
17C80GLN00.0180.03036.6660.1070.1070.0000.0000.0000.000
18C81GLU-1-0.913-0.97537.116-7.610-7.6100.0000.0000.0000.000
19C82LEU00.0400.01235.4270.1640.1640.0000.0000.0000.000
20C83GLU-1-0.885-0.94439.377-6.760-6.7600.0000.0000.0000.000
21C84LYS10.9070.94242.1236.9066.9060.0000.0000.0000.000
22C85THR0-0.069-0.02641.6580.2110.2110.0000.0000.0000.000
23C86PHE00.0530.01438.9950.1190.1190.0000.0000.0000.000
24C87THR0-0.0170.00444.9170.1600.1600.0000.0000.0000.000
25C88LYS10.9270.95845.2556.5166.5160.0000.0000.0000.000
26C89LEU00.0140.00745.1470.1010.1010.0000.0000.0000.000
27C90ARG10.9871.00946.0506.2016.2010.0000.0000.0000.000
28C91VAL0-0.031-0.00750.5450.1050.1050.0000.0000.0000.000
29C92LEU0-0.095-0.03651.8230.1090.1090.0000.0000.0000.000
30C93ASP-1-0.861-0.94453.854-5.343-5.3430.0000.0000.0000.000
31C94LEU0-0.014-0.01147.478-0.014-0.0140.0000.0000.0000.000
32C95ASP-1-0.973-0.97947.639-6.130-6.1300.0000.0000.0000.000
33C96ILE0-0.025-0.01942.658-0.085-0.0850.0000.0000.0000.000
34C97LYS10.9560.98039.9506.9976.9970.0000.0000.0000.000
35C98ILE00.0190.00734.933-0.042-0.0420.0000.0000.0000.000
36C99ASP-1-0.840-0.92635.656-7.683-7.6830.0000.0000.0000.000
37C100ARG10.9380.96833.3117.6517.6510.0000.0000.0000.000
38C101THR00.0060.00631.226-0.347-0.3470.0000.0000.0000.000
39C102GLU-1-0.956-0.97830.993-7.859-7.8590.0000.0000.0000.000
40C103ALA00.0100.00231.009-0.188-0.1880.0000.0000.0000.000
41C104PHE00.0090.01023.970-0.273-0.2730.0000.0000.0000.000
42C105ASN00.0270.00126.498-0.574-0.5740.0000.0000.0000.000
43C106LEU0-0.040-0.00427.143-0.218-0.2180.0000.0000.0000.000
44C107PHE00.0460.01020.584-0.221-0.2210.0000.0000.0000.000
45C108ILE0-0.0030.00621.506-0.401-0.4010.0000.0000.0000.000
46C109LYS10.9280.96122.3408.9058.9050.0000.0000.0000.000
47C110LYS10.8490.92023.6359.4869.4860.0000.0000.0000.000
48C111PHE00.0820.03515.003-0.320-0.3200.0000.0000.0000.000
49C112GLN0-0.021-0.00718.814-0.863-0.8630.0000.0000.0000.000
50C113SER0-0.053-0.00820.087-0.081-0.0810.0000.0000.0000.000
51C114VAL00.0960.03017.675-0.239-0.2390.0000.0000.0000.000
52C115SER00.012-0.00219.621-0.225-0.2250.0000.0000.0000.000
53C116LEU0-0.020-0.00421.9440.0390.0390.0000.0000.0000.000
54C117LEU00.0020.02113.967-0.236-0.2360.0000.0000.0000.000
55C118GLU-1-0.933-0.97617.957-14.314-14.3140.0000.0000.0000.000
56C119GLU-1-0.964-0.96918.968-11.106-11.1060.0000.0000.0000.000
57C120TYR0-0.0020.01315.5340.0670.0670.0000.0000.0000.000
58C121LEU0-0.002-0.01513.551-0.366-0.3660.0000.0000.0000.000
59C122ARG10.9020.94317.10013.42613.4260.0000.0000.0000.000
60C123SER0-0.048-0.03619.9800.3820.3820.0000.0000.0000.000
61C124SER00.0060.02316.9540.3500.3500.0000.0000.0000.000
62C125PRO00.0640.01119.014-0.546-0.5460.0000.0000.0000.000
63C126TYR00.0250.01112.133-1.251-1.2510.0000.0000.0000.000
64C127VAL0-0.046-0.03613.381-1.222-1.2220.0000.0000.0000.000
65C128MET0-0.050-0.01715.354-0.552-0.5520.0000.0000.0000.000
66C129ASP-1-0.878-0.93417.717-15.512-15.5120.0000.0000.0000.000
67C130GLN0-0.059-0.02510.988-2.189-2.1890.0000.0000.0000.000
68C131LEU00.0080.00913.772-1.067-1.0670.0000.0000.0000.000
69C132LYS10.8380.9008.25731.87531.8750.0000.0000.0000.000
70C133GLU-1-0.839-0.8828.643-35.915-35.9150.0000.0000.0000.000
71C134ALA0-0.011-0.0089.305-2.336-2.3360.0000.0000.0000.000
72C135LYS10.8090.89311.45019.73619.7360.0000.0000.0000.000
73C136ILE0-0.0150.00313.3270.6030.6030.0000.0000.0000.000
74C137ASP-1-0.810-0.90216.707-17.145-17.1450.0000.0000.0000.000
75C138GLU-1-0.848-0.91919.159-13.690-13.6900.0000.0000.0000.000
76C139LEU0-0.099-0.06222.5410.2250.2250.0000.0000.0000.000
77C140ASP-1-0.893-0.94917.721-16.299-16.2990.0000.0000.0000.000
78C141LEU00.0190.01117.640-0.996-0.9960.0000.0000.0000.000
79C142HIS00.007-0.00317.780-0.544-0.5440.0000.0000.0000.000
80C143ARG10.9560.97716.22016.81216.8120.0000.0000.0000.000
81C144ALA00.0150.01713.941-0.910-0.9100.0000.0000.0000.000
82C145ILE00.0050.00113.212-0.988-0.9880.0000.0000.0000.000
83C146VAL00.0550.03214.466-0.279-0.2790.0000.0000.0000.000
84C147ALA00.0180.02711.020-0.141-0.1410.0000.0000.0000.000
85C148LEU0-0.057-0.0289.081-1.372-1.3720.0000.0000.0000.000
86C149SER0-0.041-0.04810.6260.1200.1200.0000.0000.0000.000
87C150GLU-1-0.930-0.96111.133-19.086-19.0860.0000.0000.0000.000
88C151LYS10.8460.9224.33334.66434.754-0.001-0.004-0.0840.000
89C152MET0-0.0280.0228.814-0.418-0.4180.0000.0000.0000.000
90C153LYS10.9080.95210.24118.68818.6880.0000.0000.0000.000
91C154ALA00.0210.00513.432-0.022-0.0220.0000.0000.0000.000
92C155VAL0-0.019-0.01016.1830.1250.1250.0000.0000.0000.000
93C156ASP-1-0.837-0.91518.397-10.344-10.3440.0000.0000.0000.000
94C157ASP-1-0.766-0.88519.776-12.553-12.5530.0000.0000.0000.000
95C158ASN0-0.074-0.05722.0270.1550.1550.0000.0000.0000.000
96C159ALA0-0.048-0.01523.8080.4600.4600.0000.0000.0000.000
97C160SER0-0.023-0.00221.0900.0210.0210.0000.0000.0000.000
98C161LYS10.9600.98123.13610.08410.0840.0000.0000.0000.000
99C162LYS10.9130.96525.9658.3598.3590.0000.0000.0000.000
100C163LYS10.8590.93028.4619.4769.4760.0000.0000.0000.000
101C164ASP-1-0.914-0.96531.050-7.639-7.6390.0000.0000.0000.000
102C165GLU-1-0.861-0.93832.612-7.765-7.7650.0000.0000.0000.000
103C166PRO0-0.088-0.03431.459-0.325-0.3250.0000.0000.0000.000
104C167SER0-0.030-0.01728.2460.1240.1240.0000.0000.0000.000
105C168LEU00.0180.01130.6220.1220.1220.0000.0000.0000.000
106C169TYR0-0.024-0.00325.8320.1040.1040.0000.0000.0000.000
107C170THR00.0120.00226.225-0.142-0.1420.0000.0000.0000.000
108C171SER0-0.044-0.03822.6590.1650.1650.0000.0000.0000.000
109C172TRP00.0300.02319.759-0.031-0.0310.0000.0000.0000.000
110C173THR00.0210.01414.811-0.229-0.2290.0000.0000.0000.000
111C174LEU0-0.062-0.02815.297-0.057-0.0570.0000.0000.0000.000
112C175SER0-0.027-0.01710.199-0.580-0.5800.0000.0000.0000.000
113C176PHE00.0550.0128.5790.1460.1460.0000.0000.0000.000
114C177THR00.0260.0562.664-1.957-1.3460.317-0.319-0.6090.001
115C178ALA0-0.0090.0043.8700.0170.3700.001-0.102-0.2520.000
116C179PRO0-0.013-0.0202.409-11.803-8.4461.199-2.460-2.096-0.022
117C180THR0-0.0040.0223.330-4.669-4.0750.0290.003-0.626-0.002
118C181SER00.015-0.0135.6711.1451.1450.0000.0000.0000.000
119C182GLU-1-0.862-0.9417.338-19.258-19.2580.0000.0000.0000.000
120C183GLH0-0.009-0.0327.721-0.438-0.4380.0000.0000.0000.000
121C184ALA0-0.042-0.0226.2351.5771.5770.0000.0000.0000.000
122C185GLN0-0.024-0.0348.2871.2601.2600.0000.0000.0000.000
123C186THR00.0250.00711.6481.6231.6230.0000.0000.0000.000
124C187VAL0-0.0060.00710.8731.1801.1800.0000.0000.0000.000
125C188LEU0-0.035-0.02111.5651.1021.1020.0000.0000.0000.000
126C189SER0-0.006-0.01513.2911.0441.0440.0000.0000.0000.000
127C190GLY00.0280.03315.9890.7540.7540.0000.0000.0000.000
128C191TYR00.004-0.01815.7160.7730.7730.0000.0000.0000.000
129C192ILE0-0.0080.00116.6610.7710.7710.0000.0000.0000.000
130C193ASP-1-0.912-0.94319.303-11.912-11.9120.0000.0000.0000.000
131C194TYR0-0.017-0.01420.5850.4930.4930.0000.0000.0000.000
132C195ILE00.000-0.00220.3710.6150.6150.0000.0000.0000.000
133C196SER0-0.029-0.03522.9480.5890.5890.0000.0000.0000.000
134C197ALA00.0120.01925.3070.4350.4350.0000.0000.0000.000
135C198LEU0-0.0040.00524.5450.4470.4470.0000.0000.0000.000
136C199VAL0-0.046-0.02326.4160.3570.3570.0000.0000.0000.000
137C200VAL0-0.008-0.00129.0370.3440.3440.0000.0000.0000.000
138C201LYS10.9790.99130.7868.9718.9710.0000.0000.0000.000
139C202GLU-1-0.831-0.92631.393-8.609-8.6090.0000.0000.0000.000
140C203SER0-0.049-0.01932.5420.3030.3030.0000.0000.0000.000
141C204ILE0-0.027-0.02234.8760.2770.2770.0000.0000.0000.000
142C205GLU-1-0.941-0.97236.485-7.595-7.5950.0000.0000.0000.000
143C206ASN00.0210.01336.2080.2820.2820.0000.0000.0000.000
144C207VAL0-0.072-0.03539.3080.2120.2120.0000.0000.0000.000
145C208ARG10.8900.93238.6487.4557.4550.0000.0000.0000.000
146C209ASN00.0700.04440.2170.2370.2370.0000.0000.0000.000
147C210LYS10.9230.96340.8897.0427.0420.0000.0000.0000.000
148C211LEU0-0.0150.00045.4810.1360.1360.0000.0000.0000.000
149C212GLU-1-0.932-0.95946.204-6.180-6.1800.0000.0000.0000.000
150C213ILE00.0210.00747.0870.1490.1490.0000.0000.0000.000
151C214LYS10.8130.91849.5445.6095.6090.0000.0000.0000.000
152C215THR00.001-0.00551.2870.1660.1660.0000.0000.0000.000
153C216GLN0-0.055-0.02152.0060.0180.0180.0000.0000.0000.000
154C217PHE00.0000.00153.6550.1420.1420.0000.0000.0000.000
155C218GLU-1-0.826-0.91755.545-5.083-5.0830.0000.0000.0000.000
156C219LYS10.9780.99257.1385.3115.3110.0000.0000.0000.000
157C220GLU-1-0.906-0.96757.047-5.190-5.1900.0000.0000.0000.000
158C221LYS10.8400.94159.6524.9574.9570.0000.0000.0000.000
159C222LEU00.0090.01761.4250.1050.1050.0000.0000.0000.000
160C223ALA0-0.003-0.00763.0270.0930.0930.0000.0000.0000.000
161C224GLN00.0380.01763.4720.0810.0810.0000.0000.0000.000
162C225ASP-1-0.863-0.95265.203-4.559-4.5590.0000.0000.0000.000
163C226ARG10.8490.90067.3244.4774.4770.0000.0000.0000.000
164C227ILE00.0160.01768.3310.0740.0740.0000.0000.0000.000
165C228LYS10.9070.95267.3384.5494.5490.0000.0000.0000.000
166C229MET00.016-0.00671.1680.0480.0480.0000.0000.0000.000
167C230LYS10.9591.00273.4834.0164.0160.0000.0000.0000.000
168C231ASN00.0140.00273.7050.0760.0760.0000.0000.0000.000
169C232GLN0-0.012-0.01275.7020.0860.0860.0000.0000.0000.000
170C233LEU00.0000.02477.5750.0440.0440.0000.0000.0000.000
171C234ASP-1-0.877-0.94479.403-3.814-3.8140.0000.0000.0000.000
172C235ALA0-0.046-0.03080.5010.0560.0560.0000.0000.0000.000
173C236ASN0-0.004-0.01979.9640.0640.0640.0000.0000.0000.000
174C237ILE00.0330.02483.1980.0570.0570.0000.0000.0000.000
175C238GLN0-0.028-0.01085.3890.0840.0840.0000.0000.0000.000
176C239ARG10.8900.94584.0803.6473.6470.0000.0000.0000.000
177C240LEU0-0.0020.00687.0530.0480.0480.0000.0000.0000.000
178C241ASN0-0.022-0.03589.3130.0040.0040.0000.0000.0000.000
179C242TYR00.0140.01189.8360.0430.0430.0000.0000.0000.000
180C243SER00.0070.00191.4770.0280.0280.0000.0000.0000.000
181C244LEU0-0.014-0.00393.4080.0360.0360.0000.0000.0000.000
182C245ASP-1-0.912-0.94995.619-3.194-3.1940.0000.0000.0000.000
183C246ILE0-0.008-0.00694.7710.0460.0460.0000.0000.0000.000
184C247ALA00.0040.00797.0400.0340.0340.0000.0000.0000.000
185C248ASN0-0.016-0.01798.9220.0530.0530.0000.0000.0000.000
186C249ALA0-0.053-0.010101.3060.0370.0370.0000.0000.0000.000
187C250ALA0-0.047-0.022101.2770.0320.0320.0000.0000.0000.000
188C251GLY0-0.035-0.012103.1760.0230.0230.0000.0000.0000.000
189C252ILE0-0.037-0.01199.1290.0170.0170.0000.0000.0000.000
190C253LYS10.9940.991100.3672.9262.9260.0000.0000.0000.000
191C254LYS10.9540.979100.0352.9652.9650.0000.0000.0000.000
192C255PRO00.0320.02296.5280.0020.0020.0000.0000.0000.000
193C256VAL0-0.0070.01197.6580.0380.0380.0000.0000.0000.000
194C257TYR0-0.025-0.01597.893-0.041-0.0410.0000.0000.0000.000
195C265ASP-1-0.763-0.84692.062-3.329-3.3290.0000.0000.0000.000
196C266ASP-1-0.889-0.93492.625-3.343-3.3430.0000.0000.0000.000
197C267PRO0-0.048-0.01488.780-0.031-0.0310.0000.0000.0000.000
198C268ASP-1-0.947-0.96287.903-3.509-3.5090.0000.0000.0000.000
199C269PHE0-0.049-0.03788.746-0.044-0.0440.0000.0000.0000.000
200C270SER0-0.094-0.09189.8940.0400.0400.0000.0000.0000.000
201C271ILE00.037-0.00891.6900.0030.0030.0000.0000.0000.000
202C272SER00.0050.00193.5450.0200.0200.0000.0000.0000.000
203C273LEU0-0.073-0.02590.9070.0180.0180.0000.0000.0000.000
204C274GLY00.0290.01494.4780.0200.0200.0000.0000.0000.000
205C275ALA00.009-0.01896.283-0.031-0.0310.0000.0000.0000.000
206C276ASP-1-0.895-0.94297.105-3.115-3.1150.0000.0000.0000.000
207C277GLY0-0.055-0.02794.731-0.027-0.0270.0000.0000.0000.000
208C278ILE0-0.028-0.02991.947-0.045-0.0450.0000.0000.0000.000
209C279GLU-1-0.902-0.94292.217-3.224-3.2240.0000.0000.0000.000
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