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: LNJL9

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 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 200
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2175039.581709
FMO2-HF: Nuclear repulsion 2097056.223212
FMO2-HF: Total energy -77983.358497
FMO2-MP2: Total energy -78212.424652


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.
-58.732-51.5890.357-3.527-3.9730.022
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 : -0.799 / q_NPA : -0.890
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].
3C61HIS00.0120.0143.249-18.402-13.4980.057-2.617-2.3430.019
4C62SER0-0.029-0.0212.441-10.700-8.8290.300-0.821-1.3510.003
5C63ILE00.0100.0014.123-6.329-5.9610.000-0.089-0.2790.000
6C64ILE00.0340.0086.370-4.375-4.3750.0000.0000.0000.000
7C65GLN00.0400.0147.157-4.004-4.0040.0000.0000.0000.000
8C66PHE0-0.052-0.0298.311-2.346-2.3460.0000.0000.0000.000
9C67LEU00.0340.00910.216-2.299-2.2990.0000.0000.0000.000
10C68GLN0-0.0080.01211.734-2.470-2.4700.0000.0000.0000.000
11C69ARG10.8910.96311.054-21.838-21.8380.0000.0000.0000.000
12C70PRO00.0420.03315.155-0.027-0.0270.0000.0000.0000.000
13C71VAL0-0.046-0.01517.8610.1180.1180.0000.0000.0000.000
14C72LEU0-0.003-0.00120.588-0.153-0.1530.0000.0000.0000.000
15C73ILE0-0.054-0.03021.7470.1430.1430.0000.0000.0000.000
16C74ASP-1-0.788-0.89725.2019.6009.6000.0000.0000.0000.000
17C75ASN00.0090.00728.8990.3950.3950.0000.0000.0000.000
18C76ILE0-0.051-0.00531.712-0.199-0.1990.0000.0000.0000.000
19C77GLU-1-0.808-0.92234.9947.6087.6080.0000.0000.0000.000
20C78ILE0-0.060-0.03038.310-0.124-0.1240.0000.0000.0000.000
21C79ILE00.026-0.00441.053-0.067-0.0670.0000.0000.0000.000
22C80ALA00.021-0.00344.587-0.056-0.0560.0000.0000.0000.000
23C81GLY00.0140.03247.306-0.111-0.1110.0000.0000.0000.000
24C82THR0-0.028-0.01648.0250.0990.0990.0000.0000.0000.000
25C83THR0-0.034-0.02249.195-0.078-0.0780.0000.0000.0000.000
26C84ALA00.0440.03846.020-0.047-0.0470.0000.0000.0000.000
27C85ASP-1-0.875-0.96244.7906.7906.7900.0000.0000.0000.000
28C86ALA0-0.048-0.04042.5380.1600.1600.0000.0000.0000.000
29C87ALA00.0390.00642.5930.1390.1390.0000.0000.0000.000
30C88LYS10.9110.98145.140-6.677-6.6770.0000.0000.0000.000
31C89PRO0-0.0380.00044.7080.1420.1420.0000.0000.0000.000
32C90LEU0-0.017-0.01741.965-0.123-0.1230.0000.0000.0000.000
33C91SER00.001-0.02245.802-0.217-0.2170.0000.0000.0000.000
34C92ARG10.8970.94348.481-5.754-5.7540.0000.0000.0000.000
35C93TYR0-0.014-0.02750.726-0.023-0.0230.0000.0000.0000.000
36C94VAL00.0640.02846.8180.0150.0150.0000.0000.0000.000
37C95LEU0-0.019-0.00550.2820.0070.0070.0000.0000.0000.000
38C96ASP-1-0.783-0.86951.5736.1336.1330.0000.0000.0000.000
39C97GLN00.0600.02446.8140.1370.1370.0000.0000.0000.000
40C98GLN0-0.082-0.03147.4360.1150.1150.0000.0000.0000.000
41C99ASN0-0.154-0.08349.4440.0310.0310.0000.0000.0000.000
42C100SER00.0130.01343.9390.0590.0590.0000.0000.0000.000
43C101GLN0-0.0040.02642.505-0.200-0.2000.0000.0000.0000.000
44C102LYS10.9150.96542.618-6.796-6.7960.0000.0000.0000.000
45C103TYR00.000-0.00536.863-0.021-0.0210.0000.0000.0000.000
46C104VAL00.0110.01037.268-0.054-0.0540.0000.0000.0000.000
47C105ARG10.8260.89432.697-9.084-9.0840.0000.0000.0000.000
48C106SER0-0.0050.00333.007-0.034-0.0340.0000.0000.0000.000
49C107TRP0-0.009-0.01527.6810.0920.0920.0000.0000.0000.000
50C108THR00.0250.02427.322-0.139-0.1390.0000.0000.0000.000
51C109LEU0-0.0370.01723.2450.5650.5650.0000.0000.0000.000
52C110PRO00.039-0.00120.118-0.294-0.2940.0000.0000.0000.000
53C111SER0-0.012-0.05221.0500.5020.5020.0000.0000.0000.000
54C112THR0-0.035-0.04221.8040.0900.0900.0000.0000.0000.000
55C113VAL0-0.0030.00118.6060.0680.0680.0000.0000.0000.000
56C114LEU0-0.049-0.02315.7990.7770.7770.0000.0000.0000.000
57C115LYS10.8690.91017.660-12.382-12.3820.0000.0000.0000.000
58C116ALA00.0190.03720.050-0.249-0.2490.0000.0000.0000.000
59C117GLY0-0.025-0.03617.6410.7960.7960.0000.0000.0000.000
60C118GLY0-0.017-0.00215.8450.7430.7430.0000.0000.0000.000
61C119LYS10.7630.86613.284-17.142-17.1420.0000.0000.0000.000
62C120ALA00.0680.04712.8821.6281.6280.0000.0000.0000.000
63C121GLN00.013-0.00513.4491.1351.1350.0000.0000.0000.000
64C122LYS10.8670.9507.404-25.333-25.3330.0000.0000.0000.000
65C123LEU0-0.019-0.0048.5812.9332.9330.0000.0000.0000.000
66C124ALA00.0540.02810.477-1.000-1.0000.0000.0000.0000.000
67C125ASN0-0.034-0.0299.9950.7430.7430.0000.0000.0000.000
68C126PHE00.0350.0275.2401.0571.0570.0000.0000.0000.000
69C127LYS10.7940.88011.432-18.036-18.0360.0000.0000.0000.000
70C128TYR0-0.003-0.00513.236-1.247-1.2470.0000.0000.0000.000
71C129LEU00.0260.01212.8212.2562.2560.0000.0000.0000.000
72C130ARG10.8490.92114.463-17.433-17.4330.0000.0000.0000.000
73C131CYS0-0.042-0.01715.3331.3171.3170.0000.0000.0000.000
74C132ASP-1-0.759-0.85917.65314.51014.5100.0000.0000.0000.000
75C133VAL0-0.027-0.03319.2730.7600.7600.0000.0000.0000.000
76C134GLN00.0110.02920.093-1.237-1.2370.0000.0000.0000.000
77C135VAL00.025-0.00522.0400.1220.1220.0000.0000.0000.000
78C136LYS10.8600.92824.921-11.754-11.7540.0000.0000.0000.000
79C137LEU0-0.0190.00526.6510.0780.0780.0000.0000.0000.000
80C138VAL0-0.005-0.01428.118-0.116-0.1160.0000.0000.0000.000
81C139LEU0-0.0100.00330.904-0.063-0.0630.0000.0000.0000.000
82C140ASN0-0.032-0.01634.673-0.060-0.0600.0000.0000.0000.000
83C141ALA00.0410.03936.762-0.112-0.1120.0000.0000.0000.000
84C142ASN0-0.027-0.00940.433-0.165-0.1650.0000.0000.0000.000
85C143PRO00.047-0.00543.749-0.021-0.0210.0000.0000.0000.000
86C144PHE0-0.044-0.01546.256-0.126-0.1260.0000.0000.0000.000
87C145VAL0-0.016-0.00344.675-0.114-0.1140.0000.0000.0000.000
88C146ALA0-0.0030.00345.0630.1290.1290.0000.0000.0000.000
89C147GLY00.004-0.01544.530-0.058-0.0580.0000.0000.0000.000
90C148ARG10.7950.88041.370-7.289-7.2890.0000.0000.0000.000
91C149MET0-0.066-0.03038.351-0.046-0.0460.0000.0000.0000.000
92C150TYR00.007-0.01737.7260.0350.0350.0000.0000.0000.000
93C151LEU0-0.020-0.00129.8910.0150.0150.0000.0000.0000.000
94C152ALA00.0510.02633.6640.0850.0850.0000.0000.0000.000
95C153TYR00.007-0.01129.7880.1610.1610.0000.0000.0000.000
96C154SER0-0.038-0.05232.105-0.173-0.1730.0000.0000.0000.000
97C155PRO00.028-0.00529.5930.1150.1150.0000.0000.0000.000
98C156TYR00.0140.00526.515-0.235-0.2350.0000.0000.0000.000
99C157ASP-1-0.731-0.81031.7028.4738.4730.0000.0000.0000.000
100C158ASP-1-0.810-0.88632.2279.8229.8220.0000.0000.0000.000
101C159LYS10.7890.88029.652-10.592-10.5920.0000.0000.0000.000
102C160VAL0-0.0120.00334.493-0.046-0.0460.0000.0000.0000.000
103C161ASP-1-0.836-0.90637.4247.2577.2570.0000.0000.0000.000
104C162THR00.0750.02841.1060.0970.0970.0000.0000.0000.000
105C163ALA0-0.009-0.00842.5210.0240.0240.0000.0000.0000.000
106C164ARG10.7820.87740.112-7.612-7.6120.0000.0000.0000.000
107C165SER00.0060.01538.5920.1270.1270.0000.0000.0000.000
108C166VAL00.001-0.00936.977-0.237-0.2370.0000.0000.0000.000
109C167LEU0-0.063-0.03738.400-0.211-0.2110.0000.0000.0000.000
110C168GLN0-0.028-0.02741.765-0.382-0.3820.0000.0000.0000.000
111C169THR00.0350.02843.011-0.215-0.2150.0000.0000.0000.000
112C170SER0-0.012-0.00745.7170.0170.0170.0000.0000.0000.000
113C171ARG10.9600.98545.530-6.423-6.4230.0000.0000.0000.000
114C172ALA0-0.034-0.02845.0240.1150.1150.0000.0000.0000.000
115C173GLY00.0390.02544.5380.0910.0910.0000.0000.0000.000
116C174VAL00.0150.01340.0750.1690.1690.0000.0000.0000.000
117C175THR0-0.073-0.03640.0420.1940.1940.0000.0000.0000.000
118C176GLY0-0.015-0.00141.1200.0180.0180.0000.0000.0000.000
119C177TYR0-0.042-0.01636.0630.0370.0370.0000.0000.0000.000
120C178PRO0-0.018-0.00632.734-0.092-0.0920.0000.0000.0000.000
121C179GLY00.0510.00233.4170.1890.1890.0000.0000.0000.000
122C180VAL0-0.047-0.00431.858-0.059-0.0590.0000.0000.0000.000
123C181GLU-1-0.870-0.92734.9077.5767.5760.0000.0000.0000.000
124C182LEU0-0.007-0.00134.6510.2070.2070.0000.0000.0000.000
125C183ASP-1-0.815-0.90537.6427.0217.0210.0000.0000.0000.000
126C184PHE00.014-0.02738.7890.1020.1020.0000.0000.0000.000
127C185GLN0-0.006-0.00240.9140.0890.0890.0000.0000.0000.000
128C186LEU0-0.085-0.03140.910-0.102-0.1020.0000.0000.0000.000
129C187ASP-1-0.848-0.90535.6578.4258.4250.0000.0000.0000.000
130C188ASN00.0200.00034.441-0.142-0.1420.0000.0000.0000.000
131C189SER0-0.029-0.03630.0500.2810.2810.0000.0000.0000.000
132C190VAL0-0.0030.02331.120-0.075-0.0750.0000.0000.0000.000
133C191GLU-1-0.852-0.93124.86912.11412.1140.0000.0000.0000.000
134C192MET0-0.0110.00326.764-0.443-0.4430.0000.0000.0000.000
135C193THR0-0.013-0.02023.0100.3530.3530.0000.0000.0000.000
136C194ILE0-0.046-0.02024.278-0.494-0.4940.0000.0000.0000.000
137C195PRO0-0.002-0.00623.7760.6430.6430.0000.0000.0000.000
138C196TYR0-0.027-0.03719.9430.0300.0300.0000.0000.0000.000
139C197ALA0-0.014-0.00422.718-0.347-0.3470.0000.0000.0000.000
140C198SER00.0070.01223.075-0.670-0.6700.0000.0000.0000.000
141C199PHE0-0.019-0.01125.0600.0610.0610.0000.0000.0000.000
142C200GLN0-0.054-0.03823.171-0.273-0.2730.0000.0000.0000.000
143C201GLU-1-0.831-0.90220.09914.75614.7560.0000.0000.0000.000
144C202ALA0-0.082-0.04516.8820.9810.9810.0000.0000.0000.000
145C203TYR0-0.014-0.00818.051-0.494-0.4940.0000.0000.0000.000
146C204ASP-1-0.755-0.86417.49116.92716.9270.0000.0000.0000.000
147C205LEU0-0.015-0.01413.228-0.496-0.4960.0000.0000.0000.000
148C206VAL0-0.093-0.05116.805-0.351-0.3510.0000.0000.0000.000
149C207THR0-0.059-0.05618.943-0.640-0.6400.0000.0000.0000.000
150C208GLY00.0280.03021.339-0.522-0.5220.0000.0000.0000.000
151C209THR0-0.034-0.02022.721-0.505-0.5050.0000.0000.0000.000
152C210GLU-1-0.837-0.90822.27013.47813.4780.0000.0000.0000.000
153C211ASP-1-0.734-0.80824.32613.16013.1600.0000.0000.0000.000
154C212PHE00.0220.00121.203-0.422-0.4220.0000.0000.0000.000
155C213VAL0-0.045-0.00925.827-0.357-0.3570.0000.0000.0000.000
156C214GLN0-0.0160.00928.1870.2510.2510.0000.0000.0000.000
157C215LEU0-0.022-0.00927.551-0.116-0.1160.0000.0000.0000.000
158C216TYR0-0.009-0.03130.852-0.094-0.0940.0000.0000.0000.000
159C217LEU00.0460.02734.0280.0710.0710.0000.0000.0000.000
160C218PHE00.023-0.00235.745-0.207-0.2070.0000.0000.0000.000
161C219PRO00.0530.03339.4570.0580.0580.0000.0000.0000.000
162C220ILE00.0060.01741.074-0.172-0.1720.0000.0000.0000.000
163C221THR0-0.015-0.01244.157-0.158-0.1580.0000.0000.0000.000
164C222PRO0-0.040-0.01445.6880.1100.1100.0000.0000.0000.000
165C223VAL00.0240.00443.893-0.004-0.0040.0000.0000.0000.000
166C224LEU0-0.020-0.00146.652-0.150-0.1500.0000.0000.0000.000
167C225GLY00.0740.03348.7180.1100.1100.0000.0000.0000.000
168C226PRO0-0.053-0.01550.233-0.117-0.1170.0000.0000.0000.000
169C227LYS10.9390.95653.411-5.344-5.3440.0000.0000.0000.000
170C228SER0-0.002-0.01554.339-0.086-0.0860.0000.0000.0000.000
171C229GLU-1-0.986-0.97455.0275.6045.6040.0000.0000.0000.000
172C230SER0-0.040-0.04455.417-0.004-0.0040.0000.0000.0000.000
173C231GLU-1-0.897-0.92051.8675.7645.7640.0000.0000.0000.000
174C232SER00.0200.01447.7230.0060.0060.0000.0000.0000.000
175C233SER0-0.041-0.01447.2250.0240.0240.0000.0000.0000.000
176C234LYS10.8500.91638.011-7.880-7.8800.0000.0000.0000.000
177C235VAL0-0.041-0.02738.953-0.063-0.0630.0000.0000.0000.000
178C236ASP-1-0.809-0.88435.6038.6738.6730.0000.0000.0000.000
179C237ILE0-0.019-0.00932.513-0.003-0.0030.0000.0000.0000.000
180C238SER0-0.043-0.01828.7490.0310.0310.0000.0000.0000.000
181C239VAL0-0.0080.00326.9750.0990.0990.0000.0000.0000.000
182C240TYR00.0060.00223.0850.4000.4000.0000.0000.0000.000
183C241MET00.0120.00522.014-0.031-0.0310.0000.0000.0000.000
184C242TRP0-0.051-0.02116.7360.2500.2500.0000.0000.0000.000
185C243LEU00.0140.00915.065-0.479-0.4790.0000.0000.0000.000
186C244SER00.0630.02715.4940.3420.3420.0000.0000.0000.000
187C245ASN0-0.051-0.04215.8080.4490.4490.0000.0000.0000.000
188C246ILE0-0.053-0.01411.2230.1110.1110.0000.0000.0000.000
189C247SER0-0.0050.00711.4081.6621.6620.0000.0000.0000.000
190C248LEU0-0.037-0.0167.578-1.769-1.7690.0000.0000.0000.000
191C249VAL0-0.092-0.0608.2753.5723.5720.0000.0000.0000.000
192C250ILE00.0750.0519.516-1.461-1.4610.0000.0000.0000.000
193C251PRO0-0.0140.0419.332-0.522-0.5220.0000.0000.0000.000
194C252THR00.045-0.02111.216-2.217-2.2170.0000.0000.0000.000
195C253TYR00.0200.00713.4500.5780.5780.0000.0000.0000.000
196C254ARG10.9090.96515.633-15.040-15.0400.0000.0000.0000.000
197C255MET00.008-0.01814.7331.1651.1650.0000.0000.0000.000
198C256ASN00.0410.01917.367-1.095-1.0950.0000.0000.0000.000
199C257PRO0-0.070-0.00319.8520.2620.2620.0000.0000.0000.000
200C258ASP-1-0.794-0.88020.67513.08513.0850.0000.0000.0000.000