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: YZM42

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 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 320
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3694361.470139
FMO2-HF: Nuclear repulsion 3573225.786788
FMO2-HF: Total energy -121135.683351
FMO2-MP2: Total energy -121487.9028


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.
-3.645-0.1970.746-1.588-2.606-0.007
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 : -0.015 / q_NPA : -0.026
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].
3C27SER0-0.0060.0012.656-3.310-0.1910.744-1.538-2.325-0.007
4C28ASP-1-0.864-0.9214.535-0.538-0.354-0.001-0.023-0.1590.000
5C29SER0-0.064-0.0306.5530.2620.2620.0000.0000.0000.000
6C30ARG11.0081.0087.960-0.014-0.0140.0000.0000.0000.000
7C31TYR00.005-0.0035.7760.2650.2650.0000.0000.0000.000
8C32LYS10.7850.8806.655-0.150-0.1500.0000.0000.0000.000
9C33ARG10.8090.89011.663-0.108-0.1080.0000.0000.0000.000
10C34GLN00.0430.04914.7610.0000.0000.0000.0000.0000.000
11C35VAL00.0440.02517.276-0.015-0.0150.0000.0000.0000.000
12C36SER0-0.021-0.01618.179-0.034-0.0340.0000.0000.0000.000
13C37GLY00.0060.00219.6470.0170.0170.0000.0000.0000.000
14C38ASP-1-0.906-0.95221.859-0.115-0.1150.0000.0000.0000.000
15C39GLU-1-0.810-0.92723.254-0.075-0.0750.0000.0000.0000.000
16C40ALA00.0300.01925.8510.0100.0100.0000.0000.0000.000
17C41TYR0-0.021-0.01625.5720.0110.0110.0000.0000.0000.000
18C42LEU0-0.044-0.02726.8050.0080.0080.0000.0000.0000.000
19C43GLU-1-0.952-0.97429.708-0.055-0.0550.0000.0000.0000.000
20C44ALA0-0.083-0.02432.9800.0030.0030.0000.0000.0000.000
21C45ALA0-0.005-0.00135.6400.0030.0030.0000.0000.0000.000
22C46PRO0-0.0030.00139.2550.0010.0010.0000.0000.0000.000
23C47LEU00.005-0.01240.9190.0000.0000.0000.0000.0000.000
24C48ALA0-0.0230.00643.3220.0020.0020.0000.0000.0000.000
25C49GLU-1-0.942-0.96646.717-0.011-0.0110.0000.0000.0000.000
26C50LEU0-0.049-0.02949.6360.0000.0000.0000.0000.0000.000
27C51HIS00.0210.00352.8440.0010.0010.0000.0000.0000.000
28C52ALA0-0.0070.00256.100-0.001-0.0010.0000.0000.0000.000
29C53PRO00.0150.00759.1040.0000.0000.0000.0000.0000.000
30C54ALA00.000-0.01162.0060.0010.0010.0000.0000.0000.000
31C55GLY0-0.0090.00065.4920.0000.0000.0000.0000.0000.000
32C56MET0-0.035-0.02063.0970.0000.0000.0000.0000.0000.000
33C57ILE0-0.0060.01260.4010.0000.0000.0000.0000.0000.000
34C58LEU00.0420.01355.630-0.001-0.0010.0000.0000.0000.000
35C59PRO0-0.016-0.02156.1280.0010.0010.0000.0000.0000.000
36C60VAL00.0190.01952.826-0.001-0.0010.0000.0000.0000.000
37C61THR00.001-0.01149.600-0.001-0.0010.0000.0000.0000.000
38C62SER0-0.091-0.04251.8220.0010.0010.0000.0000.0000.000
39C63GLY00.0100.00849.4580.0010.0010.0000.0000.0000.000
40C64ASP-1-0.880-0.93844.908-0.008-0.0080.0000.0000.0000.000
41C65TYR0-0.060-0.04041.525-0.001-0.0010.0000.0000.0000.000
42C66ALA00.0340.03643.474-0.001-0.0010.0000.0000.0000.000
43C67ILE0-0.001-0.01539.1500.0010.0010.0000.0000.0000.000
44C68PRO0-0.0310.00840.6230.0000.0000.0000.0000.0000.000
45C69VAL00.0270.00738.9980.0000.0000.0000.0000.0000.000
46C70THR00.024-0.00936.8750.0020.0020.0000.0000.0000.000
47C71ASN0-0.024-0.01437.5950.0010.0010.0000.0000.0000.000
48C72GLY0-0.0310.04034.1430.0000.0000.0000.0000.0000.000
49C73SER0-0.021-0.02432.4290.0010.0010.0000.0000.0000.000
50C74GLY00.021-0.01429.6150.0060.0060.0000.0000.0000.000
51C75ALA0-0.033-0.01024.539-0.005-0.0050.0000.0000.0000.000
52C76VAL00.0360.01126.439-0.001-0.0010.0000.0000.0000.000
53C77GLY00.0240.02124.558-0.001-0.0010.0000.0000.0000.000
54C78LYS10.7920.87418.0900.1650.1650.0000.0000.0000.000
55C79ALA0-0.018-0.00419.8750.0090.0090.0000.0000.0000.000
56C80LEU0-0.048-0.01521.0090.0200.0200.0000.0000.0000.000
57C81ASP-1-0.751-0.86517.8320.1080.1080.0000.0000.0000.000
58C82ILE0-0.040-0.02418.2410.0050.0050.0000.0000.0000.000
59C83ARG10.7170.82514.316-0.224-0.2240.0000.0000.0000.000
60C84PRO0-0.0060.00017.086-0.004-0.0040.0000.0000.0000.000
61C85PRO0-0.013-0.01220.1220.0270.0270.0000.0000.0000.000
62C86ALA00.0060.01620.9220.0020.0020.0000.0000.0000.000
63C87GLN00.0370.01622.356-0.023-0.0230.0000.0000.0000.000
64C88PRO0-0.012-0.01124.6510.0150.0150.0000.0000.0000.000
65C89LEU0-0.014-0.00522.079-0.009-0.0090.0000.0000.0000.000
66C90ALA00.005-0.01126.5830.0040.0040.0000.0000.0000.000
67C91LEU0-0.028-0.00324.807-0.005-0.0050.0000.0000.0000.000
68C92VAL0-0.0220.00028.832-0.005-0.0050.0000.0000.0000.000
69C93SER00.0520.01432.4720.0000.0000.0000.0000.0000.000
70C94GLY00.0090.01534.970-0.003-0.0030.0000.0000.0000.000
71C95ALA0-0.0120.00233.025-0.002-0.0020.0000.0000.0000.000
72C96ARG10.8940.93333.977-0.067-0.0670.0000.0000.0000.000
73C97THR00.0300.02529.4040.0030.0030.0000.0000.0000.000
74C98GLN0-0.031-0.02032.305-0.006-0.0060.0000.0000.0000.000
75C99PHE00.0340.00828.6820.0070.0070.0000.0000.0000.000
76C100THR00.001-0.00132.032-0.008-0.0080.0000.0000.0000.000
77C101GLY00.0440.03333.6780.0030.0030.0000.0000.0000.000
78C102ASP-1-0.777-0.87130.3380.1050.1050.0000.0000.0000.000
79C103THR0-0.042-0.03630.5460.0090.0090.0000.0000.0000.000
80C104ALA00.0080.02428.446-0.004-0.0040.0000.0000.0000.000
81C105SER0-0.010-0.03530.569-0.001-0.0010.0000.0000.0000.000
82C106LEU00.0060.01430.172-0.002-0.0020.0000.0000.0000.000
83C107LEU0-0.064-0.02533.196-0.002-0.0020.0000.0000.0000.000
84C108VAL00.0490.00834.4510.0010.0010.0000.0000.0000.000
85C109GLU-1-0.941-0.97037.4230.0630.0630.0000.0000.0000.000
86C110ASN0-0.033-0.02038.2140.0050.0050.0000.0000.0000.000
87C111GLY00.0410.02541.759-0.002-0.0020.0000.0000.0000.000
88C112ARG10.9500.95142.414-0.074-0.0740.0000.0000.0000.000
89C113GLY00.0390.00941.3430.0030.0030.0000.0000.0000.000
90C114ASN00.0190.00840.6380.0040.0040.0000.0000.0000.000
91C115THR0-0.0060.00841.0760.0000.0000.0000.0000.0000.000
92C116LEU00.0170.02134.6450.0030.0030.0000.0000.0000.000
93C117TRP00.0110.01236.0590.0060.0060.0000.0000.0000.000
94C118PRO00.037-0.00335.6060.0070.0070.0000.0000.0000.000
95C119GLN00.0010.01134.0060.0000.0000.0000.0000.0000.000
96C120VAL00.0310.01330.7820.0100.0100.0000.0000.0000.000
97C121VAL0-0.0200.00230.7990.0110.0110.0000.0000.0000.000
98C122SER0-0.032-0.01231.4390.0080.0080.0000.0000.0000.000
99C123VAL00.0000.01026.3770.0100.0100.0000.0000.0000.000
100C124LEU0-0.007-0.01626.5120.0160.0160.0000.0000.0000.000
101C125GLN0-0.028-0.02626.9930.0030.0030.0000.0000.0000.000
102C126ALA0-0.0100.01426.0460.0020.0020.0000.0000.0000.000
103C127LYS10.8610.92818.817-0.326-0.3260.0000.0000.0000.000
104C128ASN0-0.064-0.01822.7480.0040.0040.0000.0000.0000.000
105C129TYR00.0440.02720.8650.0100.0100.0000.0000.0000.000
106C130THR00.0430.01925.395-0.011-0.0110.0000.0000.0000.000
107C131ILE0-0.0050.00128.008-0.001-0.0010.0000.0000.0000.000
108C132THR00.005-0.00131.178-0.004-0.0040.0000.0000.0000.000
109C133GLN0-0.0070.00533.483-0.004-0.0040.0000.0000.0000.000
110C134ARG10.8370.87935.113-0.099-0.0990.0000.0000.0000.000
111C135ASP-1-0.809-0.90437.3320.0730.0730.0000.0000.0000.000
112C136ASP-1-0.752-0.86439.9850.0950.0950.0000.0000.0000.000
113C137ALA0-0.048-0.00941.363-0.001-0.0010.0000.0000.0000.000
114C138GLY00.0190.00942.842-0.002-0.0020.0000.0000.0000.000
115C139GLN0-0.086-0.05139.6720.0000.0000.0000.0000.0000.000
116C140THR0-0.028-0.03737.0690.0060.0060.0000.0000.0000.000
117C141LEU0-0.030-0.00431.321-0.002-0.0020.0000.0000.0000.000
118C142THR0-0.018-0.01632.9610.0020.0020.0000.0000.0000.000
119C143THR0-0.005-0.00527.565-0.002-0.0020.0000.0000.0000.000
120C144ASP-1-0.885-0.95127.4280.1550.1550.0000.0000.0000.000
121C145TRP0-0.047-0.04323.8380.0090.0090.0000.0000.0000.000
122C146VAL0-0.040-0.00620.8340.0080.0080.0000.0000.0000.000
123C147GLN00.0220.00916.040-0.029-0.0290.0000.0000.0000.000
124C148TRP0-0.020-0.01116.1250.0340.0340.0000.0000.0000.000
125C149ASN0-0.013-0.0209.5540.0820.0820.0000.0000.0000.000
126C150ARG10.8170.87611.382-0.305-0.3050.0000.0000.0000.000
127C151LEU00.0820.0354.825-0.1330.0120.003-0.027-0.1220.000
128C152ASP-1-0.841-0.8857.8790.2530.2530.0000.0000.0000.000
129C153GLU-1-0.792-0.87810.2350.0700.0700.0000.0000.0000.000
130C154ASP-1-0.749-0.8639.9210.2470.2470.0000.0000.0000.000
131C155GLU-1-0.894-0.94110.9400.2280.2280.0000.0000.0000.000
132C156GLN0-0.008-0.01210.669-0.074-0.0740.0000.0000.0000.000
133C157TYR00.010-0.00915.040-0.047-0.0470.0000.0000.0000.000
134C158ARG10.8520.91618.514-0.188-0.1880.0000.0000.0000.000
135C159GLY00.0150.00421.530-0.020-0.0200.0000.0000.0000.000
136C160ARG10.8850.95524.129-0.121-0.1210.0000.0000.0000.000
137C161TYR00.025-0.03023.137-0.001-0.0010.0000.0000.0000.000
138C162GLN00.0000.02029.155-0.005-0.0050.0000.0000.0000.000
139C163ILE0-0.015-0.01128.1550.0010.0010.0000.0000.0000.000
140C164SER0-0.057-0.02232.617-0.008-0.0080.0000.0000.0000.000
141C165VAL00.0400.02735.6580.0020.0020.0000.0000.0000.000
142C166LYS10.8970.94737.852-0.089-0.0890.0000.0000.0000.000
143C167PRO0-0.0170.00340.5650.0010.0010.0000.0000.0000.000
144C168GLN00.0280.02442.401-0.001-0.0010.0000.0000.0000.000
145C169GLY00.0160.00443.444-0.003-0.0030.0000.0000.0000.000
146C170TYR0-0.042-0.02445.120-0.001-0.0010.0000.0000.0000.000
147C171GLN00.0270.05341.1760.0020.0020.0000.0000.0000.000
148C172GLN00.063-0.01338.7100.0010.0010.0000.0000.0000.000
149C173ALA00.0140.01137.0200.0020.0020.0000.0000.0000.000
150C174VAL00.0120.01731.457-0.001-0.0010.0000.0000.0000.000
151C175THR0-0.023-0.01433.320-0.001-0.0010.0000.0000.0000.000
152C176VAL0-0.006-0.00627.4060.0010.0010.0000.0000.0000.000
153C177LYS10.8790.92230.783-0.098-0.0980.0000.0000.0000.000
154C178LEU0-0.011-0.00224.9430.0040.0040.0000.0000.0000.000
155C179LEU0-0.0160.00029.003-0.007-0.0070.0000.0000.0000.000
156C180ASN0-0.019-0.01728.683-0.008-0.0080.0000.0000.0000.000
157C181LEU00.0670.04322.2520.0130.0130.0000.0000.0000.000
158C182GLU-1-0.901-0.93823.0120.1590.1590.0000.0000.0000.000
159C183GLN00.0490.04317.0580.0080.0080.0000.0000.0000.000
160C184ALA00.004-0.00117.504-0.018-0.0180.0000.0000.0000.000
161C185GLY00.0010.00419.596-0.018-0.0180.0000.0000.0000.000
162C186LYS10.8820.93619.740-0.167-0.1670.0000.0000.0000.000
163C187PRO0-0.002-0.00624.0030.0100.0100.0000.0000.0000.000
164C188VAL0-0.0130.00422.306-0.011-0.0110.0000.0000.0000.000
165C189ALA00.006-0.01225.5960.0020.0020.0000.0000.0000.000
166C190ASP-1-0.833-0.87123.2350.1130.1130.0000.0000.0000.000
167C191ALA00.015-0.00226.2460.0090.0090.0000.0000.0000.000
168C192ALA00.0530.02222.7290.0080.0080.0000.0000.0000.000
169C193SER0-0.023-0.03521.4360.0210.0210.0000.0000.0000.000
170C194MET00.0390.01922.3890.0210.0210.0000.0000.0000.000
171C195GLN0-0.012-0.00325.166-0.002-0.0020.0000.0000.0000.000
172C196ARG10.8330.92017.564-0.164-0.1640.0000.0000.0000.000
173C197TYR00.028-0.01516.2970.0420.0420.0000.0000.0000.000
174C198SER0-0.0050.02521.9690.0060.0060.0000.0000.0000.000
175C199THR0-0.074-0.04722.766-0.002-0.0020.0000.0000.0000.000
176C200GLU-1-0.879-0.90117.1650.3930.3930.0000.0000.0000.000
177C201MET0-0.0250.00321.1430.0140.0140.0000.0000.0000.000
178C202MET0-0.0030.00423.736-0.005-0.0050.0000.0000.0000.000
179C203ASN00.022-0.00521.231-0.025-0.0250.0000.0000.0000.000
180C204VAL0-0.015-0.00120.3380.0090.0090.0000.0000.0000.000
181C205ILE0-0.003-0.00322.718-0.005-0.0050.0000.0000.0000.000
182C206SER0-0.008-0.01825.978-0.012-0.0120.0000.0000.0000.000
183C207ALA00.0130.01422.691-0.009-0.0090.0000.0000.0000.000
184C208GLY00.0060.00324.643-0.004-0.0040.0000.0000.0000.000
185C209LEU0-0.028-0.02726.061-0.010-0.0100.0000.0000.0000.000
186C210ASP-1-0.867-0.93026.5250.1450.1450.0000.0000.0000.000
187C211LYS10.8400.92623.931-0.195-0.1950.0000.0000.0000.000
188C212SER0-0.049-0.01127.335-0.010-0.0100.0000.0000.0000.000
189C213ALA00.0220.00330.562-0.008-0.0080.0000.0000.0000.000
190C214THR0-0.002-0.02128.592-0.005-0.0050.0000.0000.0000.000
191C215ASP-1-0.839-0.92027.6510.1600.1600.0000.0000.0000.000
192C216ALA0-0.025-0.00730.783-0.007-0.0070.0000.0000.0000.000
193C217ALA00.0130.00634.166-0.007-0.0070.0000.0000.0000.000
194C218ASN00.0290.02030.596-0.013-0.0130.0000.0000.0000.000
195C219ALA0-0.011-0.00333.651-0.005-0.0050.0000.0000.0000.000
196C220ALA0-0.019-0.00935.157-0.005-0.0050.0000.0000.0000.000
197C221GLN00.0130.01037.031-0.004-0.0040.0000.0000.0000.000
198C222ASN0-0.054-0.02435.2020.0000.0000.0000.0000.0000.000
199C223ARG10.9120.94337.632-0.080-0.0800.0000.0000.0000.000
200C224ALA00.0000.02339.971-0.003-0.0030.0000.0000.0000.000
201C225SER0-0.0110.00342.979-0.001-0.0010.0000.0000.0000.000
202C226THR0-0.024-0.02245.620-0.002-0.0020.0000.0000.0000.000
203C227THR00.010-0.01047.0170.0000.0000.0000.0000.0000.000
204C228MET00.014-0.01744.8860.0010.0010.0000.0000.0000.000
205C229ASP-1-0.894-0.89845.7940.0440.0440.0000.0000.0000.000
206C230VAL0-0.018-0.00245.9560.0010.0010.0000.0000.0000.000
207C231GLN00.0050.00348.3060.0000.0000.0000.0000.0000.000
208C232SER00.000-0.00550.3790.0010.0010.0000.0000.0000.000
209C233ALA0-0.047-0.02950.4200.0010.0010.0000.0000.0000.000
210C234ALA0-0.006-0.00852.534-0.001-0.0010.0000.0000.0000.000
211C235ASP-1-0.736-0.87849.1700.0270.0270.0000.0000.0000.000
212C236ASP-1-0.931-0.95550.3300.0320.0320.0000.0000.0000.000
213C237THR0-0.117-0.07650.997-0.002-0.0020.0000.0000.0000.000
214C238GLY0-0.059-0.02353.732-0.002-0.0020.0000.0000.0000.000
215C239LEU0-0.070-0.01651.094-0.001-0.0010.0000.0000.0000.000
216C240PRO00.0070.02452.7260.0010.0010.0000.0000.0000.000
217C241MET0-0.034-0.01347.4010.0010.0010.0000.0000.0000.000
218C242LEU00.0160.00946.9520.0000.0000.0000.0000.0000.000
219C243VAL0-0.001-0.00245.8450.0020.0020.0000.0000.0000.000
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