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: 8947Y

Calculation Name: 3CRM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CRM

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HUL9

Base Structure: X-ray

Registration Date: 2023-09-23

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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2934220.68912
FMO2-HF: Nuclear repulsion 2842375.138501
FMO2-HF: Total energy -91845.550619
FMO2-MP2: Total energy -92113.632509


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(A:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
0.9242.466-0.02-0.622-0.90.003
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.018
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].
3A5PRO00.0390.0273.800-0.4351.107-0.020-0.622-0.9000.003
4A6PRO00.0410.0186.0140.5180.5180.0000.0000.0000.000
5A7ALA00.0310.0158.4340.0690.0690.0000.0000.0000.000
6A8ILE00.0010.01011.9830.0630.0630.0000.0000.0000.000
7A9PHE0-0.021-0.00615.1080.0160.0160.0000.0000.0000.000
8A10LEU00.0290.00818.1450.0210.0210.0000.0000.0000.000
9A11MET00.0190.01820.2260.0160.0160.0000.0000.0000.000
10A12GLY00.0380.00124.0860.0080.0080.0000.0000.0000.000
11A13PRO0-0.058-0.01927.538-0.003-0.0030.0000.0000.0000.000
12A14THR00.0160.00031.111-0.004-0.0040.0000.0000.0000.000
13A15ALA0-0.033-0.03733.3760.0050.0050.0000.0000.0000.000
14A16ALA0-0.0070.00930.2310.0040.0040.0000.0000.0000.000
15A17GLY00.0660.05331.1740.0010.0010.0000.0000.0000.000
16A18LYS10.8870.95026.1120.1380.1380.0000.0000.0000.000
17A19THR00.0340.00426.276-0.012-0.0120.0000.0000.0000.000
18A20ASP-1-0.849-0.90727.496-0.113-0.1130.0000.0000.0000.000
19A21LEU0-0.034-0.01523.117-0.002-0.0020.0000.0000.0000.000
20A22ALA00.001-0.01422.757-0.012-0.0120.0000.0000.0000.000
21A23MET0-0.0080.00523.080-0.013-0.0130.0000.0000.0000.000
22A24ALA00.0350.03024.831-0.003-0.0030.0000.0000.0000.000
23A25LEU0-0.034-0.03618.693-0.003-0.0030.0000.0000.0000.000
24A26ALA0-0.041-0.02120.188-0.016-0.0160.0000.0000.0000.000
25A27ASP-1-0.842-0.88021.620-0.152-0.1520.0000.0000.0000.000
26A28ALA0-0.073-0.02420.5640.0110.0110.0000.0000.0000.000
27A29LEU0-0.044-0.03214.760-0.005-0.0050.0000.0000.0000.000
28A30PRO00.0410.03714.8120.0080.0080.0000.0000.0000.000
29A31CYS0-0.020-0.00115.809-0.077-0.0770.0000.0000.0000.000
30A32GLU-1-0.890-0.95117.329-0.317-0.3170.0000.0000.0000.000
31A33LEU0-0.0150.01118.835-0.028-0.0280.0000.0000.0000.000
32A34ILE0-0.018-0.00617.9220.0090.0090.0000.0000.0000.000
33A35SER00.0190.01821.9170.0030.0030.0000.0000.0000.000
34A36VAL0-0.005-0.00521.768-0.006-0.0060.0000.0000.0000.000
35A37ASP-1-0.871-0.95224.991-0.112-0.1120.0000.0000.0000.000
36A38SER0-0.032-0.02728.7590.0010.0010.0000.0000.0000.000
37A39ALA00.0000.00131.1130.0060.0060.0000.0000.0000.000
38A40LEU0-0.005-0.02029.7880.0020.0020.0000.0000.0000.000
39A41ILE0-0.0180.00429.232-0.004-0.0040.0000.0000.0000.000
40A42TYR0-0.066-0.02731.7480.0000.0000.0000.0000.0000.000
41A43ARG10.9500.98534.5540.1120.1120.0000.0000.0000.000
42A44GLY00.0040.00037.2710.0040.0040.0000.0000.0000.000
43A45MET0-0.062-0.00938.0500.0040.0040.0000.0000.0000.000
44A46ASP-1-0.836-0.90337.478-0.103-0.1030.0000.0000.0000.000
45A47ILE0-0.018-0.01238.171-0.002-0.0020.0000.0000.0000.000
46A48GLY00.019-0.01440.2530.0000.0000.0000.0000.0000.000
47A49THR0-0.077-0.05935.4990.0000.0000.0000.0000.0000.000
48A50ALA0-0.124-0.06235.277-0.005-0.0050.0000.0000.0000.000
49A51LYS10.7780.88033.0690.1050.1050.0000.0000.0000.000
50A52PRO0-0.043-0.02330.1470.0050.0050.0000.0000.0000.000
51A53SER00.0820.04133.380-0.002-0.0020.0000.0000.0000.000
52A54ARG11.0411.01634.2800.0840.0840.0000.0000.0000.000
53A55GLU-1-0.880-0.95034.762-0.095-0.0950.0000.0000.0000.000
54A56LEU0-0.033-0.02129.835-0.005-0.0050.0000.0000.0000.000
55A57LEU00.000-0.01729.737-0.010-0.0100.0000.0000.0000.000
56A58ALA0-0.033-0.00429.820-0.010-0.0100.0000.0000.0000.000
57A59ARG10.9050.96629.9500.1130.1130.0000.0000.0000.000
58A60TYR0-0.074-0.06725.397-0.005-0.0050.0000.0000.0000.000
59A61PRO00.0170.01625.158-0.002-0.0020.0000.0000.0000.000
60A62HIS0-0.025-0.02024.697-0.019-0.0190.0000.0000.0000.000
61A63ARG10.8660.92121.2660.2870.2870.0000.0000.0000.000
62A64LEU00.010-0.01222.870-0.002-0.0020.0000.0000.0000.000
63A65ILE00.0220.02326.5310.0070.0070.0000.0000.0000.000
64A66ASP-1-0.849-0.90829.714-0.122-0.1220.0000.0000.0000.000
65A67ILE0-0.057-0.03527.8340.0000.0000.0000.0000.0000.000
66A68ARG10.8830.93929.4390.1410.1410.0000.0000.0000.000
67A69ASP-1-0.783-0.87534.430-0.080-0.0800.0000.0000.0000.000
68A70PRO00.013-0.00438.022-0.001-0.0010.0000.0000.0000.000
69A71ALA00.0260.02439.8640.0020.0020.0000.0000.0000.000
70A72GLU-1-0.899-0.93236.235-0.104-0.1040.0000.0000.0000.000
71A73SER0-0.033-0.03035.9500.0000.0000.0000.0000.0000.000
72A74TYR0-0.007-0.04326.521-0.008-0.0080.0000.0000.0000.000
73A75SER0-0.050-0.02129.8460.0010.0010.0000.0000.0000.000
74A76ALA00.008-0.01426.256-0.011-0.0110.0000.0000.0000.000
75A77ALA00.0070.00225.191-0.016-0.0160.0000.0000.0000.000
76A78GLU-1-0.790-0.90124.969-0.143-0.1430.0000.0000.0000.000
77A79PHE00.0390.02921.588-0.021-0.0210.0000.0000.0000.000
78A80ARG10.9060.96517.1290.1970.1970.0000.0000.0000.000
79A81ALA0-0.012-0.00620.416-0.041-0.0410.0000.0000.0000.000
80A82ASP-1-0.792-0.87520.832-0.242-0.2420.0000.0000.0000.000
81A83ALA0-0.014-0.01819.644-0.030-0.0300.0000.0000.0000.000
82A84LEU0-0.019-0.02715.275-0.064-0.0640.0000.0000.0000.000
83A85ALA00.0110.01916.014-0.080-0.0800.0000.0000.0000.000
84A86ALA0-0.038-0.02117.621-0.030-0.0300.0000.0000.0000.000
85A87MET0-0.0160.00613.758-0.034-0.0340.0000.0000.0000.000
86A88ALA00.0220.02912.689-0.124-0.1240.0000.0000.0000.000
87A89LYS10.9560.97713.5470.2680.2680.0000.0000.0000.000
88A90ALA0-0.004-0.01014.9020.0210.0210.0000.0000.0000.000
89A91THR00.0430.0108.725-0.058-0.0580.0000.0000.0000.000
90A92ALA0-0.041-0.00911.106-0.031-0.0310.0000.0000.0000.000
91A93ARG10.8190.89212.7020.4120.4120.0000.0000.0000.000
92A94GLY00.0200.01411.4840.0820.0820.0000.0000.0000.000
93A95ARG10.8910.97712.5720.3900.3900.0000.0000.0000.000
94A96ILE00.016-0.00611.381-0.120-0.1200.0000.0000.0000.000
95A97PRO0-0.024-0.00712.3880.1220.1220.0000.0000.0000.000
96A98LEU00.0220.01415.018-0.019-0.0190.0000.0000.0000.000
97A99LEU00.002-0.00516.6820.0390.0390.0000.0000.0000.000
98A100VAL00.0320.02919.7850.0190.0190.0000.0000.0000.000
99A101GLY00.0220.01123.0870.0080.0080.0000.0000.0000.000
100A102GLY00.0440.00325.7900.0030.0030.0000.0000.0000.000
101A103THR0-0.0090.01527.2040.0170.0170.0000.0000.0000.000
102A104MET00.0190.00525.117-0.014-0.0140.0000.0000.0000.000
103A105LEU00.0240.01424.641-0.005-0.0050.0000.0000.0000.000
104A106TYR00.0240.01324.0410.0000.0000.0000.0000.0000.000
105A107TYR00.008-0.00919.690-0.001-0.0010.0000.0000.0000.000
106A108LYS10.8990.96220.0150.0670.0670.0000.0000.0000.000
107A109ALA00.0040.01120.8800.0010.0010.0000.0000.0000.000
108A110LEU0-0.033-0.02516.798-0.005-0.0050.0000.0000.0000.000
109A111LEU0-0.041-0.02415.234-0.029-0.0290.0000.0000.0000.000
110A112GLU-1-0.916-0.95316.729-0.049-0.0490.0000.0000.0000.000
111A113GLY0-0.025-0.00619.044-0.017-0.0170.0000.0000.0000.000
112A199LEU00.005-0.02212.0340.0060.0060.0000.0000.0000.000
113A200PRO0-0.0210.0158.4970.0860.0860.0000.0000.0000.000
114A201TYR0-0.002-0.0317.731-0.494-0.4940.0000.0000.0000.000
115A202THR00.0030.0165.0060.6820.6820.0000.0000.0000.000
116A203VAL0-0.025-0.0327.658-0.010-0.0100.0000.0000.0000.000
117A204ALA00.0100.02911.4290.1120.1120.0000.0000.0000.000
118A205GLN00.0380.00813.9780.0010.0010.0000.0000.0000.000
119A206LEU00.001-0.00217.2660.0340.0340.0000.0000.0000.000
120A207ALA00.0030.00720.489-0.006-0.0060.0000.0000.0000.000
121A208ILE0-0.014-0.00124.0600.0070.0070.0000.0000.0000.000
122A209ALA0-0.027-0.04527.1970.0000.0000.0000.0000.0000.000
123A210PRO0-0.0140.01130.8590.0020.0020.0000.0000.0000.000
124A211GLU-1-0.897-0.92633.443-0.045-0.0450.0000.0000.0000.000
125A212GLN00.0150.01434.6780.0030.0030.0000.0000.0000.000
126A213ARG10.9680.96735.5990.0470.0470.0000.0000.0000.000
127A214GLN00.010-0.00537.957-0.002-0.0020.0000.0000.0000.000
128A215VAL00.0740.04338.3370.0000.0000.0000.0000.0000.000
129A216LEU00.0100.01334.617-0.001-0.0010.0000.0000.0000.000
130A217HIS0-0.044-0.04438.176-0.003-0.0030.0000.0000.0000.000
131A218ALA00.0260.03041.2310.0000.0000.0000.0000.0000.000
132A219ARG10.9790.98737.3730.0710.0710.0000.0000.0000.000
133A220ILE0-0.024-0.01937.372-0.001-0.0010.0000.0000.0000.000
134A221ALA0-0.011-0.00840.8760.0000.0000.0000.0000.0000.000
135A222GLN00.0480.03042.855-0.002-0.0020.0000.0000.0000.000
136A223ARG10.9100.93935.4060.0810.0810.0000.0000.0000.000
137A224PHE00.0390.01742.333-0.001-0.0010.0000.0000.0000.000
138A225ARG10.9740.97043.9990.0430.0430.0000.0000.0000.000
139A226GLN00.0100.02144.0300.0000.0000.0000.0000.0000.000
140A227MET0-0.0280.00739.3160.0010.0010.0000.0000.0000.000
141A228LEU0-0.032-0.03144.5760.0000.0000.0000.0000.0000.000
142A229GLU-1-0.960-0.96848.132-0.044-0.0440.0000.0000.0000.000
143A230GLN0-0.067-0.03544.362-0.001-0.0010.0000.0000.0000.000
144A231GLY00.0550.03846.364-0.002-0.0020.0000.0000.0000.000
145A232PHE0-0.056-0.01943.339-0.001-0.0010.0000.0000.0000.000
146A233ILE00.025-0.00346.153-0.001-0.0010.0000.0000.0000.000
147A234ALA00.0890.05549.3320.0000.0000.0000.0000.0000.000
148A235GLU-1-0.776-0.85242.007-0.078-0.0780.0000.0000.0000.000
149A236VAL0-0.035-0.03945.288-0.001-0.0010.0000.0000.0000.000
150A237GLU-1-0.898-0.95047.190-0.046-0.0460.0000.0000.0000.000
151A238ALA0-0.0190.00046.9620.0010.0010.0000.0000.0000.000
152A239LEU0-0.077-0.04743.052-0.001-0.0010.0000.0000.0000.000
153A240HIS0-0.042-0.04546.9610.0000.0000.0000.0000.0000.000
154A241ALA00.0080.01450.1300.0020.0020.0000.0000.0000.000
155A242ARG10.6990.81842.8080.0700.0700.0000.0000.0000.000
156A243SER00.0180.00749.8270.0000.0000.0000.0000.0000.000
157A244ASP-1-0.834-0.88145.767-0.062-0.0620.0000.0000.0000.000
158A245LEU0-0.052-0.02343.454-0.004-0.0040.0000.0000.0000.000
159A246HIS00.0600.02645.9050.0040.0040.0000.0000.0000.000
160A247ALA00.0330.00346.042-0.003-0.0030.0000.0000.0000.000
161A248GLY0-0.038-0.01745.353-0.001-0.0010.0000.0000.0000.000
162A249LEU0-0.0160.00541.815-0.001-0.0010.0000.0000.0000.000
163A250PRO0-0.041-0.04037.0540.0000.0000.0000.0000.0000.000
164A251SER00.0490.02337.9740.0000.0000.0000.0000.0000.000
165A252ILE00.0120.02439.001-0.001-0.0010.0000.0000.0000.000
166A253ARG10.8860.94437.8290.0710.0710.0000.0000.0000.000
167A254ALA0-0.0230.00737.4350.0000.0000.0000.0000.0000.000
168A255VAL0-0.027-0.04037.3340.0040.0040.0000.0000.0000.000
169A256GLY00.0140.00939.832-0.002-0.0020.0000.0000.0000.000
170A257TYR00.023-0.01139.9260.0020.0020.0000.0000.0000.000
171A258ARG10.9060.97044.0000.0500.0500.0000.0000.0000.000
172A259GLN0-0.017-0.01545.1050.0000.0000.0000.0000.0000.000
173A260VAL00.0490.02046.7270.0030.0030.0000.0000.0000.000
174A261TRP00.0390.02546.5640.0000.0000.0000.0000.0000.000
175A262ASP-1-0.873-0.95049.650-0.042-0.0420.0000.0000.0000.000
176A263TYR0-0.088-0.04651.7720.0030.0030.0000.0000.0000.000
177A264LEU00.0210.00950.7700.0020.0020.0000.0000.0000.000
178A265ASP-1-0.887-0.91953.459-0.041-0.0410.0000.0000.0000.000
179A266GLY0-0.036-0.01455.8490.0020.0020.0000.0000.0000.000
180A267LYS10.8950.94453.3880.0390.0390.0000.0000.0000.000
181A268LEU0-0.051-0.02551.6570.0010.0010.0000.0000.0000.000
182A269SER00.0480.03656.014-0.001-0.0010.0000.0000.0000.000
183A270TYR00.1060.02652.517-0.001-0.0010.0000.0000.0000.000
184A271ALA00.0100.00553.606-0.002-0.0020.0000.0000.0000.000
185A272GLU-1-0.869-0.93553.275-0.033-0.0330.0000.0000.0000.000
186A273MET0-0.0010.02249.681-0.002-0.0020.0000.0000.0000.000
187A274THR0-0.005-0.01449.206-0.003-0.0030.0000.0000.0000.000
188A275GLU-1-0.992-0.99248.331-0.037-0.0370.0000.0000.0000.000
189A276ARG10.9830.97447.9810.0340.0340.0000.0000.0000.000
190A277GLY00.0670.05345.194-0.002-0.0020.0000.0000.0000.000
191A278ILE0-0.0240.00243.593-0.003-0.0030.0000.0000.0000.000
192A279ILE0-0.050-0.02843.225-0.002-0.0020.0000.0000.0000.000
193A280ALA00.0240.01042.261-0.001-0.0010.0000.0000.0000.000
194A281THR00.007-0.01538.351-0.004-0.0040.0000.0000.0000.000
195A282ARG10.9230.95838.4020.0410.0410.0000.0000.0000.000
196A283GLN0-0.042-0.02338.7730.0010.0010.0000.0000.0000.000
197A284LEU0-0.0210.00833.3310.0000.0000.0000.0000.0000.000
198A285ALA00.0660.03534.238-0.003-0.0030.0000.0000.0000.000
199A286LYS10.9080.95634.1160.0390.0390.0000.0000.0000.000
200A287ARG10.9780.98533.8730.0660.0660.0000.0000.0000.000
201A288GLN00.0520.02630.3840.0060.0060.0000.0000.0000.000
202A289PHE00.0430.00529.670-0.003-0.0030.0000.0000.0000.000
203A290THR0-0.070-0.02230.5340.0040.0040.0000.0000.0000.000
204A291TRP00.010-0.01026.0220.0020.0020.0000.0000.0000.000
205A292LEU00.0160.00125.0840.0010.0010.0000.0000.0000.000
206A293ARG10.9300.97326.1340.0330.0330.0000.0000.0000.000
207A294SER0-0.079-0.02826.8770.0060.0060.0000.0000.0000.000
208A295TRP0-0.044-0.02619.4340.0150.0150.0000.0000.0000.000
209A296SER00.0120.01019.1160.0070.0070.0000.0000.0000.000
210A297HIS00.000-0.01316.149-0.026-0.0260.0000.0000.0000.000
211A298LEU00.0170.01117.832-0.031-0.0310.0000.0000.0000.000
212A299HIS0-0.019-0.00119.3660.0200.0200.0000.0000.0000.000
213A300TRP00.007-0.02121.281-0.016-0.0160.0000.0000.0000.000
214A301MET0-0.055-0.01622.3560.0000.0000.0000.0000.0000.000
215A302ASP-1-0.742-0.88626.405-0.063-0.0630.0000.0000.0000.000
216A303SER0-0.068-0.07030.156-0.002-0.0020.0000.0000.0000.000
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