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: V5691

Calculation Name: 5D0Q-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D0Q

Chain ID: C

ChEMBL ID:

UniProt ID: P0A940

Base Structure: X-ray

Registration Date: 2023-06-26

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 320
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3702743.82736
FMO2-HF: Nuclear repulsion 3581606.677958
FMO2-HF: Total energy -121137.149402
FMO2-MP2: Total energy -121489.311844


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:25:CYS)


Summations of interaction energy for fragment #1(C:25:CYS)
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.
-0.5421.820.073-0.962-1.4730
Interaction energy analysis for fragmet #1(C:25:CYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.012
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].
3C27SER00.0290.0052.784-0.7771.3400.075-0.941-1.2500.000
4C28ASP-1-0.895-0.9465.381-0.435-0.289-0.001-0.010-0.1350.000
5C29SER0-0.038-0.0086.6570.2150.2150.0000.0000.0000.000
6C30ARG10.9570.9808.1390.0430.0430.0000.0000.0000.000
7C31TYR0-0.004-0.0096.2700.2650.2650.0000.0000.0000.000
8C32LYS10.7730.8676.2250.4670.4670.0000.0000.0000.000
9C33ARG10.8200.88511.8380.0830.0830.0000.0000.0000.000
10C34GLN00.0130.03215.0080.0220.0220.0000.0000.0000.000
11C35VAL00.0480.03017.821-0.010-0.0100.0000.0000.0000.000
12C36SER0-0.013-0.01018.374-0.033-0.0330.0000.0000.0000.000
13C37GLY00.0090.00919.9620.0200.0200.0000.0000.0000.000
14C38ASP-1-0.887-0.95521.607-0.143-0.1430.0000.0000.0000.000
15C39GLU-1-0.821-0.93323.421-0.115-0.1150.0000.0000.0000.000
16C40ALA00.0060.01026.3770.0100.0100.0000.0000.0000.000
17C41TYR0-0.036-0.02125.4640.0110.0110.0000.0000.0000.000
18C42LEU0-0.040-0.02627.1570.0080.0080.0000.0000.0000.000
19C43GLU-1-0.942-0.96730.482-0.067-0.0670.0000.0000.0000.000
20C44ALA0-0.055-0.01233.4680.0020.0020.0000.0000.0000.000
21C45ALA00.002-0.00136.0980.0030.0030.0000.0000.0000.000
22C46PRO0-0.006-0.00139.6960.0010.0010.0000.0000.0000.000
23C47LEU00.009-0.00340.9240.0000.0000.0000.0000.0000.000
24C48ALA0-0.037-0.01543.7640.0020.0020.0000.0000.0000.000
25C49GLU-1-0.934-0.95447.160-0.020-0.0200.0000.0000.0000.000
26C50LEU0-0.036-0.02549.9240.0010.0010.0000.0000.0000.000
27C51HIS00.000-0.00453.0590.0010.0010.0000.0000.0000.000
28C52ALA00.0040.00656.346-0.001-0.0010.0000.0000.0000.000
29C53PRO00.0020.00459.3930.0010.0010.0000.0000.0000.000
30C54ALA00.006-0.01662.2670.0010.0010.0000.0000.0000.000
31C55GLY0-0.008-0.00165.8010.0000.0000.0000.0000.0000.000
32C56MET0-0.054-0.02063.3650.0000.0000.0000.0000.0000.000
33C57ILE00.0140.01660.9710.0000.0000.0000.0000.0000.000
34C58LEU00.0490.01356.111-0.001-0.0010.0000.0000.0000.000
35C59PRO0-0.024-0.02156.3300.0010.0010.0000.0000.0000.000
36C60VAL00.0150.01652.860-0.001-0.0010.0000.0000.0000.000
37C61THR00.009-0.00749.964-0.001-0.0010.0000.0000.0000.000
38C62SER0-0.093-0.05151.9660.0010.0010.0000.0000.0000.000
39C63GLY00.0100.01050.0680.0000.0000.0000.0000.0000.000
40C64ASP-1-0.891-0.93744.745-0.021-0.0210.0000.0000.0000.000
41C65TYR0-0.044-0.03341.595-0.001-0.0010.0000.0000.0000.000
42C66ALA00.0170.02643.405-0.001-0.0010.0000.0000.0000.000
43C67ILE0-0.010-0.00639.3680.0000.0000.0000.0000.0000.000
44C68PRO0-0.0180.00940.9940.0010.0010.0000.0000.0000.000
45C69VAL00.0210.00039.399-0.002-0.0020.0000.0000.0000.000
46C70THR00.023-0.00937.5060.0030.0030.0000.0000.0000.000
47C71ASN0-0.0030.00137.6570.0010.0010.0000.0000.0000.000
48C72GLY0-0.0150.02634.460-0.002-0.0020.0000.0000.0000.000
49C73SER0-0.036-0.02532.7530.0030.0030.0000.0000.0000.000
50C74GLY00.000-0.02229.5570.0050.0050.0000.0000.0000.000
51C75ALA0-0.0290.00024.374-0.003-0.0030.0000.0000.0000.000
52C76VAL00.0310.01126.2230.0000.0000.0000.0000.0000.000
53C77GLY00.0610.03924.739-0.002-0.0020.0000.0000.0000.000
54C78LYS10.7840.87818.7780.2000.2000.0000.0000.0000.000
55C79ALA0-0.023-0.00419.687-0.002-0.0020.0000.0000.0000.000
56C80LEU0-0.059-0.02421.6180.0170.0170.0000.0000.0000.000
57C81ASP-1-0.744-0.85917.831-0.004-0.0040.0000.0000.0000.000
58C82ILE0-0.030-0.01118.8170.0160.0160.0000.0000.0000.000
59C83ARG10.7030.80814.335-0.078-0.0780.0000.0000.0000.000
60C84PRO00.0110.00917.5090.0070.0070.0000.0000.0000.000
61C85PRO00.0200.00520.2930.0180.0180.0000.0000.0000.000
62C86ALA0-0.0120.00621.0660.0030.0030.0000.0000.0000.000
63C87GLN00.0400.01822.585-0.012-0.0120.0000.0000.0000.000
64C88PRO0-0.001-0.00724.5670.0130.0130.0000.0000.0000.000
65C89LEU0-0.019-0.00922.241-0.008-0.0080.0000.0000.0000.000
66C90ALA00.017-0.00126.7720.0050.0050.0000.0000.0000.000
67C91LEU0-0.011-0.00124.660-0.003-0.0030.0000.0000.0000.000
68C92VAL0-0.0080.00528.718-0.004-0.0040.0000.0000.0000.000
69C93SER00.0460.00732.364-0.002-0.0020.0000.0000.0000.000
70C94GLY00.0260.02034.839-0.002-0.0020.0000.0000.0000.000
71C95ALA0-0.050-0.01033.263-0.003-0.0030.0000.0000.0000.000
72C96ARG10.8700.91934.618-0.047-0.0470.0000.0000.0000.000
73C97THR0-0.0070.01029.4950.0020.0020.0000.0000.0000.000
74C98GLN0-0.022-0.02132.450-0.006-0.0060.0000.0000.0000.000
75C99PHE00.0330.02028.7800.0060.0060.0000.0000.0000.000
76C100THR00.0050.00532.190-0.007-0.0070.0000.0000.0000.000
77C101GLY00.0380.02233.3450.0040.0040.0000.0000.0000.000
78C102ASP-1-0.756-0.84729.9080.0690.0690.0000.0000.0000.000
79C103THR0-0.052-0.02530.0450.0090.0090.0000.0000.0000.000
80C104ALA00.0380.03028.477-0.005-0.0050.0000.0000.0000.000
81C105SER0-0.029-0.05230.5810.0000.0000.0000.0000.0000.000
82C106LEU00.0060.00530.268-0.002-0.0020.0000.0000.0000.000
83C107LEU0-0.043-0.01533.3310.0000.0000.0000.0000.0000.000
84C108VAL00.0520.01334.7590.0000.0000.0000.0000.0000.000
85C109GLU-1-0.932-0.96637.6880.0460.0460.0000.0000.0000.000
86C110ASN00.0280.00138.1440.0050.0050.0000.0000.0000.000
87C111GLY00.0420.02141.4550.0000.0000.0000.0000.0000.000
88C112ARG10.9090.94042.293-0.059-0.0590.0000.0000.0000.000
89C113GLY00.0350.02541.4140.0030.0030.0000.0000.0000.000
90C114ASN00.0220.00340.6940.0030.0030.0000.0000.0000.000
91C115THR0-0.0070.00740.8560.0000.0000.0000.0000.0000.000
92C116LEU00.0270.02734.9300.0040.0040.0000.0000.0000.000
93C117TRP00.0130.01735.7760.0050.0050.0000.0000.0000.000
94C118PRO00.0320.00635.4360.0050.0050.0000.0000.0000.000
95C119GLN0-0.0010.01233.7490.0010.0010.0000.0000.0000.000
96C120VAL00.0280.01430.8120.0080.0080.0000.0000.0000.000
97C121VAL00.0020.00630.6370.0090.0090.0000.0000.0000.000
98C122SER0-0.050-0.01931.1380.0080.0080.0000.0000.0000.000
99C123VAL0-0.0010.00926.3360.0090.0090.0000.0000.0000.000
100C124LEU0-0.001-0.01326.5330.0140.0140.0000.0000.0000.000
101C125GLN0-0.008-0.01626.6880.0040.0040.0000.0000.0000.000
102C126ALA00.0030.01026.0760.0050.0050.0000.0000.0000.000
103C127LYS10.8680.92618.674-0.263-0.2630.0000.0000.0000.000
104C128ASN0-0.080-0.02622.5650.0050.0050.0000.0000.0000.000
105C129TYR00.0310.02320.5930.0140.0140.0000.0000.0000.000
106C130THR00.0350.01525.161-0.009-0.0090.0000.0000.0000.000
107C131ILE0-0.020-0.00827.656-0.001-0.0010.0000.0000.0000.000
108C132THR0-0.008-0.01630.848-0.001-0.0010.0000.0000.0000.000
109C133GLN0-0.0050.00733.270-0.004-0.0040.0000.0000.0000.000
110C134ARG10.8020.85735.032-0.082-0.0820.0000.0000.0000.000
111C135ASP-1-0.819-0.89737.4020.0570.0570.0000.0000.0000.000
112C136ASP-1-0.750-0.86639.8030.0760.0760.0000.0000.0000.000
113C137ALA0-0.054-0.01141.110-0.001-0.0010.0000.0000.0000.000
114C138GLY00.0290.01343.020-0.002-0.0020.0000.0000.0000.000
115C139GLN0-0.080-0.04539.5450.0000.0000.0000.0000.0000.000
116C140THR0-0.005-0.03536.8360.0030.0030.0000.0000.0000.000
117C141LEU00.0050.01331.0370.0000.0000.0000.0000.0000.000
118C142THR0-0.014-0.01032.493-0.001-0.0010.0000.0000.0000.000
119C143THR0-0.020-0.02427.261-0.001-0.0010.0000.0000.0000.000
120C144ASP-1-0.832-0.91526.8230.1250.1250.0000.0000.0000.000
121C145TRP0-0.053-0.04623.6950.0040.0040.0000.0000.0000.000
122C146VAL0-0.0040.00720.4750.0120.0120.0000.0000.0000.000
123C147GLN0-0.024-0.01315.278-0.034-0.0340.0000.0000.0000.000
124C148TRP0-0.006-0.00716.2410.0240.0240.0000.0000.0000.000
125C149ASN0-0.008-0.0229.2590.0330.0330.0000.0000.0000.000
126C150ARG10.8340.89111.428-0.146-0.1460.0000.0000.0000.000
127C151LEU00.0620.0305.216-0.137-0.038-0.001-0.011-0.0880.000
128C152ASP-1-0.803-0.8597.5730.0240.0240.0000.0000.0000.000
129C153GLU-1-0.788-0.86010.266-0.012-0.0120.0000.0000.0000.000
130C154ASP-1-0.753-0.8589.968-0.024-0.0240.0000.0000.0000.000
131C155GLU-1-0.894-0.93311.1290.1700.1700.0000.0000.0000.000
132C156GLN00.0110.00310.483-0.037-0.0370.0000.0000.0000.000
133C157TYR00.027-0.00614.658-0.027-0.0270.0000.0000.0000.000
134C158ARG10.8490.91718.216-0.136-0.1360.0000.0000.0000.000
135C159GLY00.0180.01221.101-0.019-0.0190.0000.0000.0000.000
136C160ARG10.8580.93723.856-0.089-0.0890.0000.0000.0000.000
137C161TYR00.007-0.02923.277-0.005-0.0050.0000.0000.0000.000
138C162GLN00.0100.03029.371-0.001-0.0010.0000.0000.0000.000
139C163ILE0-0.011-0.01328.1390.0020.0020.0000.0000.0000.000
140C164SER0-0.043-0.01632.579-0.004-0.0040.0000.0000.0000.000
141C165VAL00.0260.02735.4300.0020.0020.0000.0000.0000.000
142C166LYS10.8750.93837.751-0.066-0.0660.0000.0000.0000.000
143C167PRO0-0.0110.00040.8330.0000.0000.0000.0000.0000.000
144C168GLN00.0090.00742.284-0.001-0.0010.0000.0000.0000.000
145C169GLY00.0230.00744.132-0.003-0.0030.0000.0000.0000.000
146C170TYR0-0.028-0.01445.8020.0000.0000.0000.0000.0000.000
147C171GLN00.0290.04241.5780.0020.0020.0000.0000.0000.000
148C172GLN00.013-0.02438.8040.0010.0010.0000.0000.0000.000
149C173ALA00.0180.02937.1040.0020.0020.0000.0000.0000.000
150C174VAL00.0480.01931.6000.0000.0000.0000.0000.0000.000
151C175THR0-0.066-0.04033.450-0.002-0.0020.0000.0000.0000.000
152C176VAL00.0270.00727.4720.0030.0030.0000.0000.0000.000
153C177LYS10.8540.90830.934-0.068-0.0680.0000.0000.0000.000
154C178LEU0-0.0060.00225.0660.0040.0040.0000.0000.0000.000
155C179LEU00.0000.00728.971-0.006-0.0060.0000.0000.0000.000
156C180ASN0-0.023-0.01428.573-0.005-0.0050.0000.0000.0000.000
157C181LEU00.0410.02921.7660.0110.0110.0000.0000.0000.000
158C182GLU-1-0.845-0.90622.8460.1270.1270.0000.0000.0000.000
159C183GLN00.0090.00916.4370.0060.0060.0000.0000.0000.000
160C184ALA0-0.006-0.00616.983-0.013-0.0130.0000.0000.0000.000
161C185GLY00.0310.01919.086-0.012-0.0120.0000.0000.0000.000
162C186LYS10.8260.91219.300-0.120-0.1200.0000.0000.0000.000
163C187PRO0-0.004-0.00823.7760.0060.0060.0000.0000.0000.000
164C188VAL0-0.024-0.00722.412-0.008-0.0080.0000.0000.0000.000
165C189ALA00.022-0.00225.6560.0040.0040.0000.0000.0000.000
166C190ASP-1-0.792-0.84023.2530.0490.0490.0000.0000.0000.000
167C191ALA00.0430.00226.0360.0080.0080.0000.0000.0000.000
168C192ALA00.0200.02522.7260.0060.0060.0000.0000.0000.000
169C193SER0-0.034-0.05821.3450.0170.0170.0000.0000.0000.000
170C194MET0-0.0040.00422.3680.0180.0180.0000.0000.0000.000
171C195GLN0-0.008-0.00925.3930.0020.0020.0000.0000.0000.000
172C196ARG10.8050.90317.703-0.062-0.0620.0000.0000.0000.000
173C197TYR00.040-0.01516.0860.0340.0340.0000.0000.0000.000
174C198SER0-0.036-0.00821.8980.0100.0100.0000.0000.0000.000
175C199THR0-0.069-0.04123.0730.0020.0020.0000.0000.0000.000
176C200GLU-1-0.887-0.92717.3820.2700.2700.0000.0000.0000.000
177C201MET0-0.0300.01121.2990.0160.0160.0000.0000.0000.000
178C202MET00.0080.01723.8050.0000.0000.0000.0000.0000.000
179C203ASN00.0210.01121.787-0.015-0.0150.0000.0000.0000.000
180C204VAL0-0.006-0.00120.2220.0060.0060.0000.0000.0000.000
181C205ILE00.0030.00122.745-0.003-0.0030.0000.0000.0000.000
182C206SER0-0.035-0.03226.145-0.009-0.0090.0000.0000.0000.000
183C207ALA00.0260.00922.855-0.007-0.0070.0000.0000.0000.000
184C208GLY00.0110.01224.8030.0020.0020.0000.0000.0000.000
185C209LEU0-0.032-0.02826.061-0.007-0.0070.0000.0000.0000.000
186C210ASP-1-0.879-0.93526.8560.1150.1150.0000.0000.0000.000
187C211LYS10.8370.92523.687-0.162-0.1620.0000.0000.0000.000
188C212SER0-0.039-0.01027.208-0.007-0.0070.0000.0000.0000.000
189C213ALA00.010-0.00230.436-0.006-0.0060.0000.0000.0000.000
190C214THR0-0.008-0.02728.549-0.003-0.0030.0000.0000.0000.000
191C215ASP-1-0.833-0.91227.4690.1380.1380.0000.0000.0000.000
192C216ALA0-0.023-0.00230.676-0.006-0.0060.0000.0000.0000.000
193C217ALA00.0160.00734.183-0.005-0.0050.0000.0000.0000.000
194C218ASN00.0180.01230.266-0.011-0.0110.0000.0000.0000.000
195C219ALA0-0.004-0.00733.380-0.004-0.0040.0000.0000.0000.000
196C220ALA0-0.012-0.01034.917-0.004-0.0040.0000.0000.0000.000
197C221GLN00.0150.00436.895-0.003-0.0030.0000.0000.0000.000
198C222ASN0-0.035-0.00534.9520.0000.0000.0000.0000.0000.000
199C223ARG10.9100.95137.621-0.069-0.0690.0000.0000.0000.000
200C224ALA00.0190.02240.074-0.002-0.0020.0000.0000.0000.000
201C225SER0-0.0100.01343.1040.0000.0000.0000.0000.0000.000
202C226THR0-0.028-0.01645.505-0.002-0.0020.0000.0000.0000.000
203C227THR00.011-0.01046.8090.0000.0000.0000.0000.0000.000
204C228MET0-0.013-0.01844.2730.0010.0010.0000.0000.0000.000
205C229ASP-1-0.855-0.89445.6190.0360.0360.0000.0000.0000.000
206C230VAL0-0.0230.00445.7100.0010.0010.0000.0000.0000.000
207C231GLN00.0170.00648.230-0.001-0.0010.0000.0000.0000.000
208C232SER00.000-0.01850.1250.0010.0010.0000.0000.0000.000
209C233ALA0-0.048-0.03450.4830.0000.0000.0000.0000.0000.000
210C234ALA00.042-0.00252.591-0.001-0.0010.0000.0000.0000.000
211C235ASP-1-0.776-0.87149.2390.0190.0190.0000.0000.0000.000
212C236ASP-1-0.897-0.92750.4350.0230.0230.0000.0000.0000.000
213C237THR0-0.150-0.09950.844-0.002-0.0020.0000.0000.0000.000
214C238GLY0-0.021-0.00853.711-0.001-0.0010.0000.0000.0000.000
215C239LEU0-0.068-0.01651.646-0.001-0.0010.0000.0000.0000.000
216C240PRO0-0.0250.00452.7090.0010.0010.0000.0000.0000.000
217C241MET0-0.040-0.01047.5670.0010.0010.0000.0000.0000.000
218C242LEU00.0230.01946.6910.0000.0000.0000.0000.0000.000
219C243VAL00.000-0.01045.9720.0010.0010.0000.0000.0000.000
220C244VAL00.0010.00242.248-0.001-0.0010.0000.0000.0000.000
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