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: 6NRVZ

Calculation Name: 5D1Q-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5D1Q

Chain ID: C

ChEMBL ID:

UniProt ID: Q2FZF0

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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2321219.830316
FMO2-HF: Nuclear repulsion 2234823.387424
FMO2-HF: Total energy -86396.442893
FMO2-MP2: Total energy -86648.78094


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:1:GLU)


Summations of interaction energy for fragment #1(C:1:GLU)
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.
3.8695.855-0.008-0.885-1.0930.003
Interaction energy analysis for fragmet #1(C:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.967 / q_NPA : -0.998
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].
3C3GLN0-0.027-0.0173.479-1.5800.329-0.006-0.836-1.0670.003
4C4LEU0-0.010-0.0075.717-1.354-1.3540.0000.0000.0000.000
5C5VAL0-0.0010.0019.490-0.495-0.4950.0000.0000.0000.000
6C6GLU-1-0.779-0.88911.86616.88516.8850.0000.0000.0000.000
7C7SER0-0.055-0.03315.392-0.377-0.3770.0000.0000.0000.000
8C8GLY00.0500.01018.431-0.088-0.0880.0000.0000.0000.000
9C9GLY00.0100.02321.665-0.397-0.3970.0000.0000.0000.000
10C10GLY00.011-0.00723.427-0.093-0.0930.0000.0000.0000.000
11C11LEU0-0.032-0.00726.691-0.004-0.0040.0000.0000.0000.000
12C12VAL00.0000.00030.182-0.124-0.1240.0000.0000.0000.000
13C13GLN00.023-0.00332.693-0.230-0.2300.0000.0000.0000.000
14C14PRO00.015-0.00235.2490.1580.1580.0000.0000.0000.000
15C15GLY0-0.031-0.01336.856-0.175-0.1750.0000.0000.0000.000
16C16GLY0-0.0220.00134.763-0.053-0.0530.0000.0000.0000.000
17C17SER0-0.070-0.06631.6450.0190.0190.0000.0000.0000.000
18C18LEU0-0.012-0.00925.109-0.083-0.0830.0000.0000.0000.000
19C19THR00.0310.02324.062-0.018-0.0180.0000.0000.0000.000
20C20LEU0-0.0320.01020.5870.1380.1380.0000.0000.0000.000
21C21SER0-0.015-0.01919.340-0.039-0.0390.0000.0000.0000.000
22C22CYS0-0.051-0.01513.7590.0530.0530.0000.0000.0000.000
23C23ALA00.0290.01512.766-0.182-0.1820.0000.0000.0000.000
24C24ALA0-0.007-0.00210.2401.1531.1530.0000.0000.0000.000
25C25SER00.0340.0096.372-1.374-1.3740.0000.0000.0000.000
26C26GLY00.0590.0274.2851.1001.016-0.001-0.0400.1250.000
27C27LEU0-0.036-0.0084.6804.5584.719-0.001-0.009-0.1510.000
28C28ILE00.0100.0077.419-1.359-1.3590.0000.0000.0000.000
29C29PHE00.0320.01610.970-1.361-1.3610.0000.0000.0000.000
30C30SER00.016-0.00212.770-0.681-0.6810.0000.0000.0000.000
31C31ASP-1-0.927-0.97314.41417.80917.8090.0000.0000.0000.000
32C32SER0-0.0320.00212.1870.0040.0040.0000.0000.0000.000
33C33THR0-0.024-0.00114.569-1.083-1.0830.0000.0000.0000.000
34C34MET0-0.0190.00312.7431.1601.1600.0000.0000.0000.000
35C35HIS00.011-0.01516.643-1.641-1.6410.0000.0000.0000.000
36C36TRP00.0490.02817.4720.4940.4940.0000.0000.0000.000
37C37VAL0-0.013-0.01118.778-0.683-0.6830.0000.0000.0000.000
38C38ARG10.8050.91019.886-9.951-9.9510.0000.0000.0000.000
39C39GLN00.000-0.00121.2190.3140.3140.0000.0000.0000.000
40C40ALA00.0470.03823.785-0.009-0.0090.0000.0000.0000.000
41C41SER00.016-0.01726.0300.3130.3130.0000.0000.0000.000
42C42GLY00.0080.01226.643-0.324-0.3240.0000.0000.0000.000
43C43ARG10.8910.95126.955-9.461-9.4610.0000.0000.0000.000
44C44GLY00.0360.01225.8590.3460.3460.0000.0000.0000.000
45C45LEU0-0.0010.00220.270-0.109-0.1090.0000.0000.0000.000
46C46GLU-1-0.877-0.94823.7779.7289.7280.0000.0000.0000.000
47C47TRP00.0110.01121.505-0.023-0.0230.0000.0000.0000.000
48C48VAL0-0.031-0.00923.082-0.568-0.5680.0000.0000.0000.000
49C49ALA0-0.001-0.02523.098-0.538-0.5380.0000.0000.0000.000
50C50ARG10.8260.91121.241-11.464-11.4640.0000.0000.0000.000
51C51ILE0-0.027-0.01120.324-0.739-0.7390.0000.0000.0000.000
52C52ARG10.8150.92020.176-11.785-11.7850.0000.0000.0000.000
53C52SER00.0800.04318.958-0.376-0.3760.0000.0000.0000.000
54C52LYS10.9580.95720.686-11.843-11.8430.0000.0000.0000.000
55C52ALA00.0000.00622.225-0.513-0.5130.0000.0000.0000.000
56C52ASN0-0.022-0.00623.290-0.111-0.1110.0000.0000.0000.000
57C52ASN00.0080.00322.309-0.151-0.1510.0000.0000.0000.000
58C52TYR00.004-0.00822.9490.2310.2310.0000.0000.0000.000
59C52ALA00.0860.05222.4270.0270.0270.0000.0000.0000.000
60C52THR00.0280.00324.154-0.331-0.3310.0000.0000.0000.000
61C52SER0-0.048-0.03527.800-0.058-0.0580.0000.0000.0000.000
62C52SER0-0.009-0.01231.057-0.341-0.3410.0000.0000.0000.000
63C53ASP-1-0.837-0.89327.06310.91010.9100.0000.0000.0000.000
64C54LYS10.9420.96827.861-9.309-9.3090.0000.0000.0000.000
65C55SER00.0040.00828.3750.1020.1020.0000.0000.0000.000
66C56ALA00.0650.05025.5720.3000.3000.0000.0000.0000.000
67C57THR0-0.0020.00224.6630.3900.3900.0000.0000.0000.000
68C58ALA0-0.023-0.01026.124-0.344-0.3440.0000.0000.0000.000
69C59TYR00.0010.01626.3730.3440.3440.0000.0000.0000.000
70C60LEU00.0250.03127.939-0.289-0.2890.0000.0000.0000.000
71C61ALA00.003-0.01529.597-0.200-0.2000.0000.0000.0000.000
72C62SER0-0.006-0.00731.838-0.143-0.1430.0000.0000.0000.000
73C63VAL0-0.0010.00228.345-0.192-0.1920.0000.0000.0000.000
74C64LYS10.9810.99031.681-8.906-8.9060.0000.0000.0000.000
75C65GLY0-0.029-0.01833.369-0.196-0.1960.0000.0000.0000.000
76C66ARG10.8110.92132.377-9.013-9.0130.0000.0000.0000.000
77C67PHE00.004-0.00527.0690.0940.0940.0000.0000.0000.000
78C68THR0-0.0040.00128.008-0.184-0.1840.0000.0000.0000.000
79C69ILE0-0.028-0.00520.7280.1130.1130.0000.0000.0000.000
80C70SER0-0.027-0.02223.129-0.280-0.2800.0000.0000.0000.000
81C71ARG10.7990.88217.143-15.383-15.3830.0000.0000.0000.000
82C72ASP-1-0.827-0.90419.39712.56212.5620.0000.0000.0000.000
83C73ASP-1-0.818-0.91717.68915.86715.8670.0000.0000.0000.000
84C74SER0-0.090-0.03417.5190.5080.5080.0000.0000.0000.000
85C75LYS10.8600.90817.454-13.061-13.0610.0000.0000.0000.000
86C76ASP-1-0.861-0.91012.59020.38920.3890.0000.0000.0000.000
87C77THR0-0.0140.00514.1390.4340.4340.0000.0000.0000.000
88C78THR0-0.068-0.05416.042-0.625-0.6250.0000.0000.0000.000
89C79PHE0-0.007-0.01918.5780.1200.1200.0000.0000.0000.000
90C80LEU0-0.009-0.01621.695-0.044-0.0440.0000.0000.0000.000
91C81GLU-1-0.903-0.94823.8059.5829.5820.0000.0000.0000.000
92C82MET0-0.036-0.00726.029-0.130-0.1300.0000.0000.0000.000
93C82SER00.0870.03128.829-0.259-0.2590.0000.0000.0000.000
94C82SER0-0.021-0.01732.607-0.073-0.0730.0000.0000.0000.000
95C82LEU0-0.065-0.01029.395-0.039-0.0390.0000.0000.0000.000
96C83LYS10.9720.99233.169-8.401-8.4010.0000.0000.0000.000
97C84ILE00.0440.01833.1170.2120.2120.0000.0000.0000.000
98C85GLU-1-0.899-0.94932.9868.2498.2490.0000.0000.0000.000
99C86ASP-1-0.813-0.88029.1489.3849.3840.0000.0000.0000.000
100C87THR0-0.027-0.01928.0390.3590.3590.0000.0000.0000.000
101C88ALA0-0.039-0.01624.662-0.061-0.0610.0000.0000.0000.000
102C89VAL00.0040.01519.400-0.015-0.0150.0000.0000.0000.000
103C90TYR0-0.028-0.03920.428-0.115-0.1150.0000.0000.0000.000
104C91TYR00.0180.00214.8870.2530.2530.0000.0000.0000.000
105C93ILE0-0.024-0.00713.2780.7910.7910.0000.0000.0000.000
106C94ALA00.0310.01110.856-0.839-0.8390.0000.0000.0000.000
107C95SER0-0.052-0.03912.4700.3500.3500.0000.0000.0000.000
108C96SER0-0.0270.0159.808-0.140-0.1400.0000.0000.0000.000
109C97THR00.0200.00811.996-0.714-0.7140.0000.0000.0000.000
110C98THR0-0.032-0.01510.088-0.969-0.9690.0000.0000.0000.000
111C99GLY00.037-0.00113.293-0.577-0.5770.0000.0000.0000.000
112C100TRP0-0.0060.00316.756-0.185-0.1850.0000.0000.0000.000
113C100TYR0-0.036-0.02019.909-0.752-0.7520.0000.0000.0000.000
114C100VAL00.0050.00519.4400.8020.8020.0000.0000.0000.000
115C100ARG10.8020.91813.252-20.571-20.5710.0000.0000.0000.000
116C100GLU-1-0.876-0.94217.38014.13714.1370.0000.0000.0000.000
117C100ASP-1-0.855-0.91816.10015.45115.4510.0000.0000.0000.000
118C100PHE0-0.027-0.02315.2610.3950.3950.0000.0000.0000.000
119C101ASP-1-0.802-0.90710.59521.90521.9050.0000.0000.0000.000
120C102TYR00.0350.0095.9570.2620.2620.0000.0000.0000.000
121C103TRP0-0.037-0.0299.867-2.505-2.5050.0000.0000.0000.000
122C104GLY00.0490.0369.6851.5481.5480.0000.0000.0000.000
123C105HIS0-0.048-0.03311.3060.1010.1010.0000.0000.0000.000
124C106GLY00.0100.00913.462-0.233-0.2330.0000.0000.0000.000
125C107THR0-0.0160.00116.924-0.481-0.4810.0000.0000.0000.000
126C108LEU0-0.027-0.02419.231-0.157-0.1570.0000.0000.0000.000
127C109VAL00.0000.00922.772-0.143-0.1430.0000.0000.0000.000
128C110THR0-0.030-0.03325.790-0.136-0.1360.0000.0000.0000.000
129C111VAL00.0140.02229.293-0.081-0.0810.0000.0000.0000.000
130C112SER0-0.014-0.02932.497-0.191-0.1910.0000.0000.0000.000
131C113SER00.0180.00335.6190.0460.0460.0000.0000.0000.000
132C114ALA00.005-0.04037.699-0.206-0.2060.0000.0000.0000.000
133C119SER00.0740.13339.7590.1490.1490.0000.0000.0000.000
134C120THR0-0.130-0.10335.811-0.010-0.0100.0000.0000.0000.000
135C121LYS10.8630.92837.796-6.946-6.9460.0000.0000.0000.000
136C122GLY00.0190.01238.5520.1710.1710.0000.0000.0000.000
137C123PRO0-0.045-0.01038.213-0.099-0.0990.0000.0000.0000.000
138C124SER0-0.005-0.01440.822-0.144-0.1440.0000.0000.0000.000
139C125VAL0-0.0010.00541.5160.0860.0860.0000.0000.0000.000
140C126PHE00.0150.00444.038-0.124-0.1240.0000.0000.0000.000
141C127PRO00.0100.00245.6880.1280.1280.0000.0000.0000.000
142C128LEU0-0.031-0.02543.878-0.048-0.0480.0000.0000.0000.000
143C129ALA00.0210.00947.9040.0350.0350.0000.0000.0000.000
144C130PRO00.0020.00450.2540.0160.0160.0000.0000.0000.000
145C131SER0-0.035-0.01751.555-0.133-0.1330.0000.0000.0000.000
146C132SER00.0300.00853.709-0.024-0.0240.0000.0000.0000.000
147C133LYS10.9110.96455.860-5.442-5.4420.0000.0000.0000.000
148C134SER00.0880.04454.4800.0740.0740.0000.0000.0000.000
149C135THR00.0300.02855.3110.0310.0310.0000.0000.0000.000
150C136SER00.1160.05052.2200.0310.0310.0000.0000.0000.000
151C137GLY00.1660.26052.1450.0300.0300.0000.0000.0000.000
152C138GLY0-0.241-0.27752.368-0.089-0.0890.0000.0000.0000.000
153C139THR0-0.096-0.06646.9650.0070.0070.0000.0000.0000.000
154C140ALA0-0.0040.00648.980-0.049-0.0490.0000.0000.0000.000
155C141ALA00.012-0.00245.7260.1250.1250.0000.0000.0000.000
156C142LEU0-0.0120.01145.055-0.149-0.1490.0000.0000.0000.000
157C143GLY00.0550.01343.3540.1800.1800.0000.0000.0000.000
158C144CYS0-0.080-0.00140.427-0.015-0.0150.0000.0000.0000.000
159C145LEU00.0210.02441.5470.1690.1690.0000.0000.0000.000
160C146VAL0-0.026-0.02138.015-0.055-0.0550.0000.0000.0000.000
161C147LYS10.9470.97039.861-6.395-6.3950.0000.0000.0000.000
162C148ASP-1-0.834-0.91441.3136.5966.5960.0000.0000.0000.000
163C149TYR0-0.028-0.02333.380-0.170-0.1700.0000.0000.0000.000
164C150PHE00.0940.05333.8430.1330.1330.0000.0000.0000.000
165C151PRO00.0010.01831.136-0.192-0.1920.0000.0000.0000.000
166C152GLU-1-0.775-0.87429.3978.8528.8520.0000.0000.0000.000
167C153PRO0-0.024-0.01227.6610.0840.0840.0000.0000.0000.000
168C154VAL0-0.017-0.02730.018-0.278-0.2780.0000.0000.0000.000
169C155THR0-0.026-0.00430.2450.2530.2530.0000.0000.0000.000
170C156VAL00.006-0.00532.542-0.235-0.2350.0000.0000.0000.000
171C157SER00.0200.00633.8910.2440.2440.0000.0000.0000.000
172C158TRP00.0150.00736.178-0.272-0.2720.0000.0000.0000.000
173C159ASN00.0620.03339.3430.0420.0420.0000.0000.0000.000
174C160SER0-0.076-0.04038.4080.0270.0270.0000.0000.0000.000
175C161GLY00.0230.00535.6280.1130.1130.0000.0000.0000.000
176C162ALA0-0.019-0.00536.3930.1070.1070.0000.0000.0000.000
177C163LEU0-0.0210.00338.7460.0060.0060.0000.0000.0000.000
178C164THR00.000-0.01134.2460.1040.1040.0000.0000.0000.000
179C165SER00.006-0.00736.4480.0260.0260.0000.0000.0000.000
180C166GLY00.0220.01337.703-0.166-0.1660.0000.0000.0000.000
181C167VAL00.0170.01235.756-0.170-0.1700.0000.0000.0000.000
182C168HIS0-0.033-0.01034.8020.2900.2900.0000.0000.0000.000
183C169THR00.016-0.00333.103-0.309-0.3090.0000.0000.0000.000
184C170PHE0-0.0070.00933.2450.2530.2530.0000.0000.0000.000
185C171PRO00.0130.00431.0780.0490.0490.0000.0000.0000.000
186C172ALA0-0.006-0.00632.631-0.265-0.2650.0000.0000.0000.000
187C173VAL0-0.003-0.00433.9740.1510.1510.0000.0000.0000.000
188C174LEU0-0.039-0.02033.962-0.150-0.1500.0000.0000.0000.000
189C175GLN0-0.062-0.04836.724-0.182-0.1820.0000.0000.0000.000
190C176SER00.0310.00140.0330.0910.0910.0000.0000.0000.000
191C177SER0-0.011-0.00542.492-0.007-0.0070.0000.0000.0000.000
192C178GLY00.0410.03238.822-0.018-0.0180.0000.0000.0000.000
193C179LEU0-0.052-0.01838.2960.1080.1080.0000.0000.0000.000
194C180TYR00.0370.02131.478-0.041-0.0410.0000.0000.0000.000
195C181SER0-0.003-0.00437.073-0.221-0.2210.0000.0000.0000.000
196C182LEU0-0.0050.02033.5300.0810.0810.0000.0000.0000.000
197C183SER00.007-0.01937.369-0.237-0.2370.0000.0000.0000.000
198C184SER00.0310.03936.7440.1220.1220.0000.0000.0000.000
199C185VAL00.016-0.00738.573-0.227-0.2270.0000.0000.0000.000
200C186VAL00.0360.01839.4890.1940.1940.0000.0000.0000.000
201C187THR0-0.045-0.01941.762-0.167-0.1670.0000.0000.0000.000
202C188VAL00.0420.02843.6200.1110.1110.0000.0000.0000.000
203C189PRO00.036-0.00846.188-0.104-0.1040.0000.0000.0000.000
204C190SER0-0.008-0.00249.341-0.023-0.0230.0000.0000.0000.000
205C191SER00.0020.00452.458-0.066-0.0660.0000.0000.0000.000
206C192SER0-0.060-0.02850.073-0.053-0.0530.0000.0000.0000.000
207C193LEU00.0230.01050.7980.1040.1040.0000.0000.0000.000
208C194GLY00.0130.00452.7900.0220.0220.0000.0000.0000.000
209C195THR0-0.014-0.00951.598-0.044-0.0440.0000.0000.0000.000
210C196GLN0-0.024-0.00246.9440.0400.0400.0000.0000.0000.000
211C197THR00.0390.03548.675-0.077-0.0770.0000.0000.0000.000
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