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: 52QVZ

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 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 320
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3693932.015521
FMO2-HF: Nuclear repulsion 3572798.619812
FMO2-HF: Total energy -121133.395709
FMO2-MP2: Total energy -121485.882054


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.
-4.637-0.6130.514-1.766-2.772-0.01
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 : -0.038 / q_NPA : -0.038
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].
3C27SER00.0110.0292.783-4.646-1.0900.472-1.692-2.336-0.010
4C28ASP-1-0.881-0.9254.382-0.605-0.4270.000-0.021-0.1560.000
5C29SER0-0.064-0.0396.5980.0680.0680.0000.0000.0000.000
6C30ARG10.9960.9908.0200.3460.3460.0000.0000.0000.000
7C31TYR00.0030.0066.433-0.082-0.0820.0000.0000.0000.000
8C32LYS10.8500.9246.3781.4431.4430.0000.0000.0000.000
9C33ARG10.8630.96411.7380.3820.3820.0000.0000.0000.000
10C34GLN00.0080.02414.6970.0640.0640.0000.0000.0000.000
11C35VAL00.0400.02617.212-0.029-0.0290.0000.0000.0000.000
12C36SER0-0.044-0.03117.942-0.025-0.0250.0000.0000.0000.000
13C37GLY00.0160.00719.5900.0260.0260.0000.0000.0000.000
14C38ASP-1-0.939-0.96921.769-0.197-0.1970.0000.0000.0000.000
15C39GLU-1-0.783-0.89923.150-0.185-0.1850.0000.0000.0000.000
16C40ALA00.0340.02325.7430.0140.0140.0000.0000.0000.000
17C41TYR0-0.007-0.01025.9270.0070.0070.0000.0000.0000.000
18C42LEU0-0.058-0.03326.3010.0090.0090.0000.0000.0000.000
19C43GLU-1-0.938-0.96729.247-0.114-0.1140.0000.0000.0000.000
20C44ALA0-0.083-0.02332.8600.0070.0070.0000.0000.0000.000
21C45ALA0-0.007-0.00335.5320.0040.0040.0000.0000.0000.000
22C46PRO0-0.0070.00239.1420.0000.0000.0000.0000.0000.000
23C47LEU00.008-0.01340.6990.0020.0020.0000.0000.0000.000
24C48ALA0-0.0210.00843.2220.0030.0030.0000.0000.0000.000
25C49GLU-1-0.939-0.96346.610-0.044-0.0440.0000.0000.0000.000
26C50LEU0-0.049-0.03049.5380.0020.0020.0000.0000.0000.000
27C51HIS00.0150.00052.7430.0010.0010.0000.0000.0000.000
28C52ALA0-0.0040.00055.9980.0000.0000.0000.0000.0000.000
29C53PRO00.0110.00959.0080.0010.0010.0000.0000.0000.000
30C54ALA00.008-0.01061.9070.0010.0010.0000.0000.0000.000
31C55GLY0-0.0110.00165.3930.0000.0000.0000.0000.0000.000
32C56MET0-0.031-0.02262.7960.0000.0000.0000.0000.0000.000
33C57ILE0-0.0090.01860.2460.0000.0000.0000.0000.0000.000
34C58LEU00.0320.00255.6910.0000.0000.0000.0000.0000.000
35C59PRO0-0.012-0.01556.0000.0010.0010.0000.0000.0000.000
36C60VAL00.0200.02252.817-0.001-0.0010.0000.0000.0000.000
37C61THR0-0.009-0.02049.333-0.003-0.0030.0000.0000.0000.000
38C62SER0-0.086-0.03751.7460.0020.0020.0000.0000.0000.000
39C63GLY00.0010.00349.4180.0010.0010.0000.0000.0000.000
40C64ASP-1-0.846-0.92444.694-0.052-0.0520.0000.0000.0000.000
41C65TYR0-0.075-0.04441.512-0.001-0.0010.0000.0000.0000.000
42C66ALA00.0320.03443.414-0.001-0.0010.0000.0000.0000.000
43C67ILE00.002-0.01338.821-0.002-0.0020.0000.0000.0000.000
44C68PRO0-0.0340.00640.4850.0020.0020.0000.0000.0000.000
45C69VAL00.0330.01339.026-0.004-0.0040.0000.0000.0000.000
46C70THR00.031-0.00736.7100.0040.0040.0000.0000.0000.000
47C71ASN0-0.009-0.01237.5120.0000.0000.0000.0000.0000.000
48C72GLY0-0.0560.03834.023-0.002-0.0020.0000.0000.0000.000
49C73SER0-0.022-0.03132.4100.0050.0050.0000.0000.0000.000
50C74GLY00.016-0.01629.4340.0040.0040.0000.0000.0000.000
51C75ALA0-0.031-0.00724.5140.0000.0000.0000.0000.0000.000
52C76VAL00.0210.00626.343-0.001-0.0010.0000.0000.0000.000
53C77GLY00.0400.01924.453-0.003-0.0030.0000.0000.0000.000
54C78LYS10.8290.88517.7560.3150.3150.0000.0000.0000.000
55C79ALA0-0.023-0.00319.768-0.012-0.0120.0000.0000.0000.000
56C80LEU0-0.044-0.01620.9870.0070.0070.0000.0000.0000.000
57C81ASP-1-0.754-0.88817.505-0.239-0.2390.0000.0000.0000.000
58C82ILE0-0.042-0.01717.9560.0260.0260.0000.0000.0000.000
59C83ARG10.7420.86213.4400.1900.1900.0000.0000.0000.000
60C84PRO0-0.0050.00516.3770.0240.0240.0000.0000.0000.000
61C85PRO0-0.003-0.00919.1180.0060.0060.0000.0000.0000.000
62C86ALA00.0050.01619.4920.0030.0030.0000.0000.0000.000
63C87GLN00.0600.01620.9690.0030.0030.0000.0000.0000.000
64C88PRO0-0.028-0.01523.3170.0060.0060.0000.0000.0000.000
65C89LEU0-0.016-0.00420.747-0.004-0.0040.0000.0000.0000.000
66C90ALA00.008-0.00925.3660.0080.0080.0000.0000.0000.000
67C91LEU0-0.039-0.00523.863-0.003-0.0030.0000.0000.0000.000
68C92VAL0-0.0150.00427.8330.0000.0000.0000.0000.0000.000
69C93SER00.0470.01131.499-0.004-0.0040.0000.0000.0000.000
70C94GLY00.0120.01734.0060.0010.0010.0000.0000.0000.000
71C95ALA0-0.0130.00531.8920.0010.0010.0000.0000.0000.000
72C96ARG10.9240.95532.805-0.007-0.0070.0000.0000.0000.000
73C97THR00.0320.02028.2220.0030.0030.0000.0000.0000.000
74C98GLN0-0.024-0.01131.008-0.002-0.0020.0000.0000.0000.000
75C99PHE00.0100.00026.4930.0040.0040.0000.0000.0000.000
76C100THR0-0.013-0.00730.602-0.005-0.0050.0000.0000.0000.000
77C101GLY00.0410.03132.3060.0050.0050.0000.0000.0000.000
78C102ASP-1-0.849-0.93228.9530.0100.0100.0000.0000.0000.000
79C103THR0-0.037-0.03329.1270.0080.0080.0000.0000.0000.000
80C104ALA0-0.0020.01627.061-0.006-0.0060.0000.0000.0000.000
81C105SER0-0.008-0.03229.1900.0060.0060.0000.0000.0000.000
82C106LEU00.0110.01728.995-0.004-0.0040.0000.0000.0000.000
83C107LEU0-0.073-0.03231.9490.0030.0030.0000.0000.0000.000
84C108VAL00.0330.00333.331-0.001-0.0010.0000.0000.0000.000
85C109GLU-1-0.938-0.97836.3060.0170.0170.0000.0000.0000.000
86C110ASN00.0290.01337.1100.0000.0000.0000.0000.0000.000
87C111GLY00.0120.00640.747-0.001-0.0010.0000.0000.0000.000
88C112ARG10.9560.95541.410-0.036-0.0360.0000.0000.0000.000
89C113GLY00.0260.00340.3090.0010.0010.0000.0000.0000.000
90C114ASN00.0590.02739.6230.0020.0020.0000.0000.0000.000
91C115THR0-0.029-0.01539.7760.0010.0010.0000.0000.0000.000
92C116LEU00.0130.02133.4770.0030.0030.0000.0000.0000.000
93C117TRP0-0.0140.00835.1090.0050.0050.0000.0000.0000.000
94C118PRO00.024-0.01234.6530.0040.0040.0000.0000.0000.000
95C119GLN0-0.0070.00933.2820.0020.0020.0000.0000.0000.000
96C120VAL00.0400.01729.8890.0070.0070.0000.0000.0000.000
97C121VAL0-0.0150.00229.9240.0070.0070.0000.0000.0000.000
98C122SER0-0.045-0.01730.8110.0100.0100.0000.0000.0000.000
99C123VAL00.0150.01525.5790.0090.0090.0000.0000.0000.000
100C124LEU0-0.021-0.02625.7890.0130.0130.0000.0000.0000.000
101C125GLN0-0.042-0.03126.4510.0060.0060.0000.0000.0000.000
102C126ALA0-0.0110.01825.6470.0070.0070.0000.0000.0000.000
103C127LYS10.8890.94317.955-0.168-0.1680.0000.0000.0000.000
104C128ASN0-0.042-0.00622.3850.0010.0010.0000.0000.0000.000
105C129TYR00.0260.01119.9110.0040.0040.0000.0000.0000.000
106C130THR00.0340.01724.918-0.004-0.0040.0000.0000.0000.000
107C131ILE0-0.007-0.00227.631-0.007-0.0070.0000.0000.0000.000
108C132THR00.006-0.02230.625-0.001-0.0010.0000.0000.0000.000
109C133GLN00.0000.02832.964-0.002-0.0020.0000.0000.0000.000
110C134ARG10.9130.94934.389-0.071-0.0710.0000.0000.0000.000
111C135ASP-1-0.816-0.91736.6110.0410.0410.0000.0000.0000.000
112C136ASP-1-0.809-0.91739.2230.0570.0570.0000.0000.0000.000
113C137ALA0-0.062-0.01740.523-0.002-0.0020.0000.0000.0000.000
114C138GLY00.0070.00941.775-0.002-0.0020.0000.0000.0000.000
115C139GLN0-0.047-0.02938.541-0.001-0.0010.0000.0000.0000.000
116C140THR0-0.059-0.04835.9480.0000.0000.0000.0000.0000.000
117C141LEU0-0.0010.00430.4690.0020.0020.0000.0000.0000.000
118C142THR0-0.019-0.01332.033-0.004-0.0040.0000.0000.0000.000
119C143THR00.0060.00326.8250.0010.0010.0000.0000.0000.000
120C144ASP-1-0.900-0.96526.9690.1070.1070.0000.0000.0000.000
121C145TRP0-0.026-0.03323.234-0.001-0.0010.0000.0000.0000.000
122C146VAL0-0.035-0.00319.8250.0140.0140.0000.0000.0000.000
123C147GLN00.0180.00515.710-0.040-0.0400.0000.0000.0000.000
124C148TRP0-0.030-0.01014.8210.0260.0260.0000.0000.0000.000
125C149ASN0-0.020-0.0279.181-0.005-0.0050.0000.0000.0000.000
126C150ARG10.8310.88210.0490.1160.1160.0000.0000.0000.000
127C151LEU00.0840.0303.177-0.375-0.0850.042-0.053-0.2800.000
128C152ASP-1-0.903-0.9276.783-0.542-0.5420.0000.0000.0000.000
129C153GLU-1-0.772-0.8929.236-0.130-0.1300.0000.0000.0000.000
130C154ASP-1-0.786-0.9039.607-0.379-0.3790.0000.0000.0000.000
131C155GLU-1-0.975-0.98510.9610.1140.1140.0000.0000.0000.000
132C156GLN00.0060.0149.927-0.084-0.0840.0000.0000.0000.000
133C157TYR0-0.002-0.00714.4210.0000.0000.0000.0000.0000.000
134C158ARG10.9160.95717.656-0.121-0.1210.0000.0000.0000.000
135C159GLY00.009-0.00220.595-0.019-0.0190.0000.0000.0000.000
136C160ARG10.8760.95723.031-0.051-0.0510.0000.0000.0000.000
137C161TYR00.0490.00221.618-0.005-0.0050.0000.0000.0000.000
138C162GLN0-0.0040.01927.9940.0050.0050.0000.0000.0000.000
139C163ILE0-0.003-0.00227.300-0.004-0.0040.0000.0000.0000.000
140C164SER0-0.063-0.03531.4220.0000.0000.0000.0000.0000.000
141C165VAL00.0260.01634.453-0.002-0.0020.0000.0000.0000.000
142C166LYS10.9190.95736.688-0.032-0.0320.0000.0000.0000.000
143C167PRO0-0.0170.00539.332-0.001-0.0010.0000.0000.0000.000
144C168GLN00.0330.02441.1650.0010.0010.0000.0000.0000.000
145C169GLY00.0080.01042.199-0.002-0.0020.0000.0000.0000.000
146C170TYR0-0.051-0.02943.8810.0000.0000.0000.0000.0000.000
147C171GLN00.0060.03239.905-0.001-0.0010.0000.0000.0000.000
148C172GLN00.062-0.00737.6430.0010.0010.0000.0000.0000.000
149C173ALA00.0110.01635.798-0.001-0.0010.0000.0000.0000.000
150C174VAL00.0100.01530.2210.0030.0030.0000.0000.0000.000
151C175THR0-0.029-0.01231.997-0.003-0.0030.0000.0000.0000.000
152C176VAL00.0080.00026.1010.0060.0060.0000.0000.0000.000
153C177LYS10.9570.99529.448-0.027-0.0270.0000.0000.0000.000
154C178LEU0-0.008-0.00923.7480.0080.0080.0000.0000.0000.000
155C179LEU0-0.035-0.01127.640-0.006-0.0060.0000.0000.0000.000
156C180ASN0-0.013-0.01227.8040.0000.0000.0000.0000.0000.000
157C181LEU00.0610.03721.3210.0090.0090.0000.0000.0000.000
158C182GLU-1-0.957-0.98322.5230.0740.0740.0000.0000.0000.000
159C183GLN00.0420.03917.0580.0240.0240.0000.0000.0000.000
160C184ALA00.0490.02617.619-0.001-0.0010.0000.0000.0000.000
161C185GLY0-0.046-0.02419.581-0.005-0.0050.0000.0000.0000.000
162C186LYS10.9170.95821.255-0.061-0.0610.0000.0000.0000.000
163C187PRO00.0210.00923.794-0.002-0.0020.0000.0000.0000.000
164C188VAL0-0.0150.00621.871-0.008-0.0080.0000.0000.0000.000
165C189ALA00.006-0.01525.1560.0050.0050.0000.0000.0000.000
166C190ASP-1-0.880-0.90922.755-0.060-0.0600.0000.0000.0000.000
167C191ALA00.0250.00125.4490.0050.0050.0000.0000.0000.000
168C192ALA00.0490.01621.7510.0050.0050.0000.0000.0000.000
169C193SER00.000-0.02020.3750.0000.0000.0000.0000.0000.000
170C194MET00.0440.02921.3450.0130.0130.0000.0000.0000.000
171C195GLN00.0110.00723.3770.0060.0060.0000.0000.0000.000
172C196ARG10.8510.94216.0910.1260.1260.0000.0000.0000.000
173C197TYR0-0.041-0.06815.3960.0030.0030.0000.0000.0000.000
174C198SER00.0430.02720.5440.0180.0180.0000.0000.0000.000
175C199THR0-0.102-0.06121.6420.0080.0080.0000.0000.0000.000
176C200GLU-1-0.892-0.89716.0920.0250.0250.0000.0000.0000.000
177C201MET0-0.0180.00519.8140.0180.0180.0000.0000.0000.000
178C202MET00.003-0.00322.5320.0070.0070.0000.0000.0000.000
179C203ASN00.0460.00719.6380.0030.0030.0000.0000.0000.000
180C204VAL0-0.0170.00119.3000.0120.0120.0000.0000.0000.000
181C205ILE00.0030.00021.6330.0070.0070.0000.0000.0000.000
182C206SER0-0.024-0.03524.7850.0000.0000.0000.0000.0000.000
183C207ALA00.0170.01421.763-0.001-0.0010.0000.0000.0000.000
184C208GLY00.0030.00323.7060.0050.0050.0000.0000.0000.000
185C209LEU0-0.037-0.03025.2130.0010.0010.0000.0000.0000.000
186C210ASP-1-0.869-0.93025.6850.0540.0540.0000.0000.0000.000
187C211LYS10.8930.95823.432-0.122-0.1220.0000.0000.0000.000
188C212SER0-0.043-0.00526.677-0.001-0.0010.0000.0000.0000.000
189C213ALA00.0140.00029.902-0.002-0.0020.0000.0000.0000.000
190C214THR0-0.010-0.02728.0300.0010.0010.0000.0000.0000.000
191C215ASP-1-0.862-0.93727.3720.1070.1070.0000.0000.0000.000
192C216ALA0-0.030-0.01330.342-0.001-0.0010.0000.0000.0000.000
193C217ALA00.0040.00233.644-0.003-0.0030.0000.0000.0000.000
194C218ASN00.0220.01330.159-0.007-0.0070.0000.0000.0000.000
195C219ALA0-0.005-0.00133.384-0.001-0.0010.0000.0000.0000.000
196C220ALA0-0.022-0.01334.880-0.002-0.0020.0000.0000.0000.000
197C221GLN00.0210.01536.794-0.002-0.0020.0000.0000.0000.000
198C222ASN0-0.075-0.05335.1880.0030.0030.0000.0000.0000.000
199C223ARG10.8950.94037.449-0.066-0.0660.0000.0000.0000.000
200C224ALA00.0060.02839.821-0.001-0.0010.0000.0000.0000.000
201C225SER0-0.007-0.00342.776-0.001-0.0010.0000.0000.0000.000
202C226THR0-0.036-0.02345.604-0.002-0.0020.0000.0000.0000.000
203C227THR00.0240.00447.0230.0010.0010.0000.0000.0000.000
204C228MET00.015-0.01544.7480.0000.0000.0000.0000.0000.000
205C229ASP-1-0.956-0.94745.6080.0250.0250.0000.0000.0000.000
206C230VAL0-0.036-0.00545.841-0.001-0.0010.0000.0000.0000.000
207C231GLN00.0150.00248.1080.0000.0000.0000.0000.0000.000
208C232SER00.0220.01750.1060.0000.0000.0000.0000.0000.000
209C233ALA0-0.031-0.02550.0830.0000.0000.0000.0000.0000.000
210C234ALA0-0.007-0.00852.182-0.001-0.0010.0000.0000.0000.000
211C235ASP-1-0.761-0.89548.7160.0030.0030.0000.0000.0000.000
212C236ASP-1-0.903-0.94949.8550.0030.0030.0000.0000.0000.000
213C237THR0-0.134-0.07450.921-0.002-0.0020.0000.0000.0000.000
214C238GLY0-0.069-0.02553.271-0.001-0.0010.0000.0000.0000.000
215C239LEU0-0.075-0.02750.4600.0000.0000.0000.0000.0000.000
216C240PRO00.0240.03752.4410.0010.0010.0000.0000.0000.000
217C241MET0-0.033-0.01546.8370.0010.0010.0000.0000.0000.000
218C242LEU00.0070.00446.8240.0010.0010.0000.0000.0000.000
219C243VAL0-0.002-0.00245.4730.0010.0010.0000.0000.0000.000
220C244VAL00.0070.00242.1340.0010.0010.0000.0000.0000.000
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