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: 98GY2

Calculation Name: 5CDD-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CDD

Chain ID: C

ChEMBL ID:

UniProt ID: D1FK67

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2177025.70611
FMO2-HF: Nuclear repulsion 2099040.937105
FMO2-HF: Total energy -77984.769005
FMO2-MP2: Total energy -78213.934568


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:59:ASP)


Summations of interaction energy for fragment #1(C:59:ASP)
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.
-77.303-70.6034.912-4.832-6.7810.056
Interaction energy analysis for fragmet #1(C:59:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.764 / q_NPA : -0.870
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].
3C61HIS0-0.0080.0122.036-28.801-24.9544.572-3.536-4.8840.053
4C62SER0-0.054-0.0422.481-16.204-13.6760.340-1.220-1.6480.003
5C63ILE0-0.015-0.0044.148-6.724-6.3990.000-0.076-0.2490.000
6C64ILE00.0550.0216.397-5.142-5.1420.0000.0000.0000.000
7C65GLN00.0440.0187.433-4.758-4.7580.0000.0000.0000.000
8C66PHE0-0.064-0.0318.211-2.671-2.6710.0000.0000.0000.000
9C67LEU00.0160.00410.009-2.564-2.5640.0000.0000.0000.000
10C68GLN0-0.011-0.00711.796-2.956-2.9560.0000.0000.0000.000
11C69ARG10.9060.97210.808-22.323-22.3230.0000.0000.0000.000
12C70PRO00.0430.02814.940-0.057-0.0570.0000.0000.0000.000
13C71VAL0-0.047-0.01817.2690.1680.1680.0000.0000.0000.000
14C72LEU0-0.0050.00220.062-0.149-0.1490.0000.0000.0000.000
15C73ILE0-0.066-0.03921.6200.2750.2750.0000.0000.0000.000
16C74ASP-1-0.774-0.89225.0589.7159.7150.0000.0000.0000.000
17C75ASN00.0010.00128.7920.4470.4470.0000.0000.0000.000
18C76ILE0-0.050-0.00731.573-0.197-0.1970.0000.0000.0000.000
19C77GLU-1-0.854-0.94334.8197.6077.6070.0000.0000.0000.000
20C78ILE0-0.036-0.01537.956-0.072-0.0720.0000.0000.0000.000
21C79ILE00.0350.00440.753-0.044-0.0440.0000.0000.0000.000
22C80ALA00.003-0.01044.358-0.021-0.0210.0000.0000.0000.000
23C81GLY00.0340.03447.409-0.139-0.1390.0000.0000.0000.000
24C82THR0-0.038-0.01148.0910.0900.0900.0000.0000.0000.000
25C83THR0-0.034-0.02849.274-0.054-0.0540.0000.0000.0000.000
26C84ALA00.0080.00146.299-0.051-0.0510.0000.0000.0000.000
27C85ASP-1-0.845-0.95344.3426.9916.9910.0000.0000.0000.000
28C86ALA0-0.026-0.00641.8310.1330.1330.0000.0000.0000.000
29C87ALA00.0100.00742.1120.1330.1330.0000.0000.0000.000
30C88LYS10.8780.95044.731-6.859-6.8590.0000.0000.0000.000
31C89PRO0-0.0310.00344.7740.1380.1380.0000.0000.0000.000
32C90LEU00.0100.00041.861-0.135-0.1350.0000.0000.0000.000
33C91SER00.006-0.01145.851-0.229-0.2290.0000.0000.0000.000
34C92ARG10.9260.95448.408-5.816-5.8160.0000.0000.0000.000
35C93TYR0-0.008-0.01650.415-0.026-0.0260.0000.0000.0000.000
36C94VAL00.0570.03046.385-0.002-0.0020.0000.0000.0000.000
37C95LEU0-0.017-0.00849.744-0.003-0.0030.0000.0000.0000.000
38C96ASP-1-0.795-0.88250.9596.2456.2450.0000.0000.0000.000
39C97GLN00.0560.03146.2880.1060.1060.0000.0000.0000.000
40C98GLN0-0.052-0.00947.1850.1130.1130.0000.0000.0000.000
41C99ASN0-0.125-0.06948.8550.0670.0670.0000.0000.0000.000
42C100SER00.011-0.00544.0090.0790.0790.0000.0000.0000.000
43C101GLN0-0.0200.01242.704-0.172-0.1720.0000.0000.0000.000
44C102LYS10.8890.95842.582-6.971-6.9710.0000.0000.0000.000
45C103TYR00.005-0.00936.871-0.009-0.0090.0000.0000.0000.000
46C104VAL00.0090.01636.885-0.052-0.0520.0000.0000.0000.000
47C105ARG10.8100.88732.459-9.190-9.1900.0000.0000.0000.000
48C106SER00.0050.00532.859-0.080-0.0800.0000.0000.0000.000
49C107TRP0-0.006-0.01227.6590.0550.0550.0000.0000.0000.000
50C108THR00.0120.01027.082-0.119-0.1190.0000.0000.0000.000
51C109LEU0-0.0230.01323.3020.5580.5580.0000.0000.0000.000
52C110PRO00.0450.01119.820-0.289-0.2890.0000.0000.0000.000
53C111SER0-0.028-0.05421.1870.3620.3620.0000.0000.0000.000
54C112THR0-0.039-0.03921.8250.1620.1620.0000.0000.0000.000
55C113VAL0-0.010-0.00618.6340.1500.1500.0000.0000.0000.000
56C114LEU0-0.028-0.01415.9130.8060.8060.0000.0000.0000.000
57C115LYS10.8360.89517.583-12.594-12.5940.0000.0000.0000.000
58C116ALA00.0300.03620.083-0.235-0.2350.0000.0000.0000.000
59C117GLY0-0.003-0.01617.5790.8790.8790.0000.0000.0000.000
60C118GLY00.0020.00015.4020.8060.8060.0000.0000.0000.000
61C119LYS10.7560.86513.359-17.718-17.7180.0000.0000.0000.000
62C120ALA00.0570.03313.1241.5671.5670.0000.0000.0000.000
63C121GLN00.0380.00413.6471.1411.1410.0000.0000.0000.000
64C122LYS10.8650.9527.062-27.103-27.1030.0000.0000.0000.000
65C123LEU00.0060.0058.5233.2223.2220.0000.0000.0000.000
66C124ALA00.0550.03010.483-0.604-0.6040.0000.0000.0000.000
67C125ASN0-0.057-0.03910.2750.7630.7630.0000.0000.0000.000
68C126PHE00.0050.0125.2851.2451.2450.0000.0000.0000.000
69C127LYS10.8110.89111.426-18.332-18.3320.0000.0000.0000.000
70C128TYR0-0.008-0.00812.986-1.561-1.5610.0000.0000.0000.000
71C129LEU00.0220.01612.4452.5422.5420.0000.0000.0000.000
72C130ARG10.8040.89213.980-18.076-18.0760.0000.0000.0000.000
73C131CYS0-0.028-0.01614.7051.5891.5890.0000.0000.0000.000
74C132ASP-1-0.756-0.84216.96214.89414.8940.0000.0000.0000.000
75C133VAL0-0.011-0.01318.9940.8610.8610.0000.0000.0000.000
76C134GLN0-0.0020.02720.267-1.262-1.2620.0000.0000.0000.000
77C135VAL00.0330.00722.0900.2070.2070.0000.0000.0000.000
78C136LYS10.8460.91724.785-11.961-11.9610.0000.0000.0000.000
79C137LEU0-0.0090.01226.5230.0350.0350.0000.0000.0000.000
80C138VAL0-0.005-0.02228.1550.0110.0110.0000.0000.0000.000
81C139LEU0-0.0450.00631.018-0.062-0.0620.0000.0000.0000.000
82C140ASN0-0.045-0.02934.775-0.013-0.0130.0000.0000.0000.000
83C141ALA00.0420.03236.700-0.178-0.1780.0000.0000.0000.000
84C142ASN00.0020.00240.256-0.147-0.1470.0000.0000.0000.000
85C143PRO00.0280.00143.504-0.023-0.0230.0000.0000.0000.000
86C144PHE0-0.046-0.01046.402-0.125-0.1250.0000.0000.0000.000
87C145VAL0-0.009-0.01044.865-0.111-0.1110.0000.0000.0000.000
88C146ALA00.0090.00945.1830.1280.1280.0000.0000.0000.000
89C147GLY00.0130.00245.059-0.081-0.0810.0000.0000.0000.000
90C148ARG10.7720.86441.396-7.418-7.4180.0000.0000.0000.000
91C149MET0-0.033-0.01038.299-0.042-0.0420.0000.0000.0000.000
92C150TYR00.010-0.01237.1700.0290.0290.0000.0000.0000.000
93C151LEU0-0.0060.00929.694-0.007-0.0070.0000.0000.0000.000
94C152ALA00.0340.00533.4970.0440.0440.0000.0000.0000.000
95C153TYR00.008-0.01529.0420.1720.1720.0000.0000.0000.000
96C154SER0-0.021-0.03831.594-0.200-0.2000.0000.0000.0000.000
97C155PRO00.017-0.00729.2460.1550.1550.0000.0000.0000.000
98C156TYR00.001-0.00726.431-0.209-0.2090.0000.0000.0000.000
99C157ASP-1-0.742-0.79431.2058.6858.6850.0000.0000.0000.000
100C158ASP-1-0.793-0.87231.77910.05010.0500.0000.0000.0000.000
101C159LYS10.7800.87329.301-10.864-10.8640.0000.0000.0000.000
102C160VAL0-0.019-0.00234.041-0.032-0.0320.0000.0000.0000.000
103C161ASP-1-0.818-0.89136.9027.3627.3620.0000.0000.0000.000
104C162THR00.0720.02440.6050.1120.1120.0000.0000.0000.000
105C163ALA0-0.041-0.02242.0920.0050.0050.0000.0000.0000.000
106C164ARG10.8070.87839.656-7.730-7.7300.0000.0000.0000.000
107C165SER00.0060.01037.9160.1170.1170.0000.0000.0000.000
108C166VAL00.013-0.00436.602-0.265-0.2650.0000.0000.0000.000
109C167LEU0-0.056-0.03038.044-0.221-0.2210.0000.0000.0000.000
110C168GLN0-0.041-0.02741.213-0.401-0.4010.0000.0000.0000.000
111C169THR00.0200.01442.735-0.230-0.2300.0000.0000.0000.000
112C170SER0-0.002-0.00545.4460.0060.0060.0000.0000.0000.000
113C171ARG10.9140.95545.323-6.553-6.5530.0000.0000.0000.000
114C172ALA0-0.018-0.01444.8160.1220.1220.0000.0000.0000.000
115C173GLY00.0210.02444.1200.0750.0750.0000.0000.0000.000
116C174VAL0-0.011-0.01040.0390.1780.1780.0000.0000.0000.000
117C175THR0-0.057-0.03339.8610.1980.1980.0000.0000.0000.000
118C176GLY00.0010.01540.5850.0130.0130.0000.0000.0000.000
119C177TYR0-0.036-0.01735.7310.0430.0430.0000.0000.0000.000
120C178PRO0-0.020-0.00532.236-0.081-0.0810.0000.0000.0000.000
121C179GLY00.0470.00433.1090.1600.1600.0000.0000.0000.000
122C180VAL0-0.043-0.00331.888-0.017-0.0170.0000.0000.0000.000
123C181GLU-1-0.869-0.92634.9057.7417.7410.0000.0000.0000.000
124C182LEU00.0100.00334.4430.2610.2610.0000.0000.0000.000
125C183ASP-1-0.821-0.90337.5127.1617.1610.0000.0000.0000.000
126C184PHE00.008-0.03038.6160.0990.0990.0000.0000.0000.000
127C185GLN0-0.043-0.03041.2080.0140.0140.0000.0000.0000.000
128C186LEU0-0.059-0.01940.917-0.126-0.1260.0000.0000.0000.000
129C187ASP-1-0.833-0.90135.9958.5448.5440.0000.0000.0000.000
130C188ASN0-0.015-0.01734.6570.0050.0050.0000.0000.0000.000
131C189SER0-0.033-0.02430.0280.2680.2680.0000.0000.0000.000
132C190VAL00.0020.02331.179-0.065-0.0650.0000.0000.0000.000
133C191GLU-1-0.839-0.93025.14212.40112.4010.0000.0000.0000.000
134C192MET0-0.0200.00326.875-0.451-0.4510.0000.0000.0000.000
135C193THR0-0.017-0.02422.6430.4010.4010.0000.0000.0000.000
136C194ILE0-0.036-0.01724.015-0.612-0.6120.0000.0000.0000.000
137C195PRO0-0.003-0.01122.8860.6630.6630.0000.0000.0000.000
138C196TYR0-0.035-0.04719.3590.0090.0090.0000.0000.0000.000
139C197ALA0-0.0100.00322.157-0.258-0.2580.0000.0000.0000.000
140C198SER00.0010.00622.823-0.502-0.5020.0000.0000.0000.000
141C199PHE0-0.040-0.01424.8100.0790.0790.0000.0000.0000.000
142C200GLN0-0.006-0.02322.936-0.440-0.4400.0000.0000.0000.000
143C201GLU-1-0.796-0.87219.59615.47315.4730.0000.0000.0000.000
144C202ALA0-0.087-0.04716.3761.1071.1070.0000.0000.0000.000
145C203TYR0-0.020-0.00917.678-0.606-0.6060.0000.0000.0000.000
146C204ASP-1-0.726-0.85417.20317.12717.1270.0000.0000.0000.000
147C205LEU0-0.029-0.01512.952-0.595-0.5950.0000.0000.0000.000
148C206VAL0-0.096-0.05317.1130.0080.0080.0000.0000.0000.000
149C207THR0-0.040-0.05219.354-0.666-0.6660.0000.0000.0000.000
150C208GLY0-0.0060.01521.278-0.613-0.6130.0000.0000.0000.000
151C209THR0-0.020-0.02122.518-0.429-0.4290.0000.0000.0000.000
152C210GLU-1-0.836-0.90421.89513.75413.7540.0000.0000.0000.000
153C211ASP-1-0.752-0.82123.94713.52613.5260.0000.0000.0000.000
154C212PHE00.0300.02420.804-0.513-0.5130.0000.0000.0000.000
155C213VAL0-0.037-0.01325.396-0.343-0.3430.0000.0000.0000.000
156C214GLN0-0.0160.00227.8620.2280.2280.0000.0000.0000.000
157C215LEU0-0.017-0.00927.425-0.042-0.0420.0000.0000.0000.000
158C216TYR0-0.018-0.04030.854-0.073-0.0730.0000.0000.0000.000
159C217LEU00.0280.02033.9390.1150.1150.0000.0000.0000.000
160C218PHE00.0250.00035.710-0.208-0.2080.0000.0000.0000.000
161C219PRO00.0570.03139.4810.0580.0580.0000.0000.0000.000
162C220ILE0-0.0010.00241.006-0.157-0.1570.0000.0000.0000.000
163C221THR0-0.054-0.02944.186-0.163-0.1630.0000.0000.0000.000
164C222PRO0-0.015-0.00445.6120.1080.1080.0000.0000.0000.000
165C223VAL00.0340.02343.9030.0290.0290.0000.0000.0000.000
166C224LEU0-0.032-0.01746.602-0.181-0.1810.0000.0000.0000.000
167C225GLY00.0790.02948.4770.1320.1320.0000.0000.0000.000
168C226PRO0-0.049-0.00750.122-0.126-0.1260.0000.0000.0000.000
169C227LYS10.9430.95753.102-5.428-5.4280.0000.0000.0000.000
170C228SER00.002-0.01554.036-0.114-0.1140.0000.0000.0000.000
171C229GLU-1-0.935-0.95954.3215.6765.6760.0000.0000.0000.000
172C230SER0-0.073-0.05554.905-0.002-0.0020.0000.0000.0000.000
173C231GLU-1-0.884-0.90551.3095.8075.8070.0000.0000.0000.000
174C232SER0-0.012-0.00547.0930.0450.0450.0000.0000.0000.000
175C233SER0-0.022-0.00647.0300.0640.0640.0000.0000.0000.000
176C234LYS10.8610.93237.304-8.053-8.0530.0000.0000.0000.000
177C235VAL0-0.021-0.01438.988-0.075-0.0750.0000.0000.0000.000
178C236ASP-1-0.821-0.91235.2598.8798.8790.0000.0000.0000.000
179C237ILE00.0130.01132.259-0.005-0.0050.0000.0000.0000.000
180C238SER0-0.040-0.01328.5760.0350.0350.0000.0000.0000.000
181C239VAL0-0.014-0.00727.0070.0530.0530.0000.0000.0000.000
182C240TYR00.006-0.00522.8730.3580.3580.0000.0000.0000.000
183C241MET00.0010.00421.974-0.082-0.0820.0000.0000.0000.000
184C242TRP0-0.047-0.02016.7450.1740.1740.0000.0000.0000.000
185C243LEU00.0240.01115.093-0.460-0.4600.0000.0000.0000.000
186C244SER00.025-0.00115.4550.1850.1850.0000.0000.0000.000
187C245ASN0-0.037-0.04115.0710.6110.6110.0000.0000.0000.000
188C246ILE0-0.044-0.00311.095-0.057-0.0570.0000.0000.0000.000
189C247SER0-0.0170.00010.5952.0712.0710.0000.0000.0000.000
190C248LEU00.003-0.0037.546-2.181-2.1810.0000.0000.0000.000
191C249VAL0-0.012-0.0107.8574.7214.7210.0000.0000.0000.000
192C250ILE00.0270.0099.800-2.051-2.0510.0000.0000.0000.000
193C251PRO00.0390.0329.623-0.174-0.1740.0000.0000.0000.000
194C252THR0-0.050-0.04311.232-2.658-2.6580.0000.0000.0000.000
195C253TYR00.0110.00313.9660.4840.4840.0000.0000.0000.000
196C254ARG10.9080.96516.189-15.285-15.2850.0000.0000.0000.000
197C255MET00.0410.01714.8381.1621.1620.0000.0000.0000.000
198C256ASN00.0320.01017.493-1.367-1.3670.0000.0000.0000.000
199C257PRO0-0.058-0.01119.4660.3910.3910.0000.0000.0000.000
200C258ASP-1-0.808-0.87020.45713.35013.3500.0000.0000.0000.000