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: V5V51

Calculation Name: 5CY1-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CY1

Chain ID: B

ChEMBL ID:

UniProt ID: P0ADI2

Base Structure: X-ray

Registration Date: 2023-06-22

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1607999.650025
FMO2-HF: Nuclear repulsion 1535779.982942
FMO2-HF: Total energy -72219.667082
FMO2-MP2: Total energy -72430.455162


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(B:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-17.744-9.8641.595-4.177-5.295-0.026
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.001
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].
3B3ILE00.0230.0043.806-1.2030.710-0.015-0.853-1.0440.005
4B4PHE0-0.016-0.0146.4230.0480.0480.0000.0000.0000.000
5B5GLY00.0340.0289.4800.1350.1350.0000.0000.0000.000
6B6TYR0-0.089-0.06012.833-0.040-0.0400.0000.0000.0000.000
7B7ALA00.0060.00216.1010.0260.0260.0000.0000.0000.000
8B8ARG10.9510.98919.7390.0020.0020.0000.0000.0000.000
9B9VAL0-0.026-0.01122.9290.0090.0090.0000.0000.0000.000
10B10SER0-0.0020.00126.611-0.007-0.0070.0000.0000.0000.000
11B11THR00.0420.00229.950-0.001-0.0010.0000.0000.0000.000
12B12SER0-0.008-0.00530.8140.0030.0030.0000.0000.0000.000
13B13GLN00.0620.01226.200-0.006-0.0060.0000.0000.0000.000
14B14GLN00.0220.01627.7070.0050.0050.0000.0000.0000.000
15B15SER0-0.013-0.01427.2290.0050.0050.0000.0000.0000.000
16B16LEU00.0180.00422.5540.0060.0060.0000.0000.0000.000
17B17ASP-1-0.798-0.90222.9680.0620.0620.0000.0000.0000.000
18B18ILE0-0.043-0.01623.1320.0120.0120.0000.0000.0000.000
19B19GLN0-0.024-0.01820.1420.0120.0120.0000.0000.0000.000
20B20ILE00.0320.02018.6890.0200.0200.0000.0000.0000.000
21B21ARG10.9220.95918.259-0.101-0.1010.0000.0000.0000.000
22B22ALA00.0180.00618.8070.0130.0130.0000.0000.0000.000
23B23LEU0-0.025-0.01213.9430.0290.0290.0000.0000.0000.000
24B24LYS10.8970.94513.827-0.088-0.0880.0000.0000.0000.000
25B25ASP-1-0.913-0.94615.2510.1920.1920.0000.0000.0000.000
26B26ALA0-0.051-0.01312.5070.0190.0190.0000.0000.0000.000
27B27GLY0-0.0090.00710.8800.0850.0850.0000.0000.0000.000
28B28VAL0-0.0250.0009.5570.0200.0200.0000.0000.0000.000
29B29LYS10.9580.9638.922-0.384-0.3840.0000.0000.0000.000
30B30ALA00.040-0.00212.774-0.023-0.0230.0000.0000.0000.000
31B31ASN0-0.006-0.00613.458-0.008-0.0080.0000.0000.0000.000
32B32ARG10.8500.9496.734-0.104-0.1040.0000.0000.0000.000
33B33ILE0-0.0020.00412.479-0.022-0.0220.0000.0000.0000.000
34B34PHE00.0200.02212.511-0.010-0.0100.0000.0000.0000.000
35B35THR0-0.023-0.02417.2490.0140.0140.0000.0000.0000.000
36B36ASP-1-0.751-0.84720.628-0.060-0.0600.0000.0000.0000.000
37B37LYS10.9080.94123.5170.0050.0050.0000.0000.0000.000
38B38ALA00.0230.02827.180-0.006-0.0060.0000.0000.0000.000
39B39SER00.001-0.04030.3150.0010.0010.0000.0000.0000.000
40B40GLY0-0.014-0.01133.4960.0000.0000.0000.0000.0000.000
41B41SER0-0.033-0.02634.720-0.001-0.0010.0000.0000.0000.000
42B42SER0-0.077-0.03430.059-0.002-0.0020.0000.0000.0000.000
43B43THR00.007-0.01829.914-0.003-0.0030.0000.0000.0000.000
44B44ASP-1-0.848-0.85927.377-0.037-0.0370.0000.0000.0000.000
45B45ARG10.8380.89622.6000.0830.0830.0000.0000.0000.000
46B46GLU-1-0.876-0.93721.819-0.057-0.0570.0000.0000.0000.000
47B47GLY00.0080.00519.637-0.011-0.0110.0000.0000.0000.000
48B48LEU0-0.035-0.02716.926-0.015-0.0150.0000.0000.0000.000
49B49ASP-1-0.859-0.93417.396-0.159-0.1590.0000.0000.0000.000
50B50LEU0-0.028-0.02116.677-0.026-0.0260.0000.0000.0000.000
51B51LEU0-0.066-0.02411.405-0.024-0.0240.0000.0000.0000.000
52B52ARG10.7740.84012.7310.1120.1120.0000.0000.0000.000
53B53MET0-0.039-0.00313.880-0.050-0.0500.0000.0000.0000.000
54B54LYS10.8740.93810.5620.1450.1450.0000.0000.0000.000
55B55VAL0-0.053-0.0068.285-0.078-0.0780.0000.0000.0000.000
56B56GLU-1-0.775-0.8616.060-0.541-0.5410.0000.0000.0000.000
57B57GLU-1-0.911-0.9596.686-1.554-1.5540.0000.0000.0000.000
58B58GLY0-0.020-0.0053.758-0.776-0.5530.006-0.044-0.1850.000
59B59ASP-1-0.832-0.9232.836-11.140-6.1651.275-3.072-3.177-0.031
60B60VAL00.0090.0003.442-0.2920.4110.331-0.192-0.8410.000
61B61ILE0-0.049-0.0276.201-0.119-0.146-0.001-0.0030.0310.000
62B62LEU0-0.006-0.0058.7200.0500.0500.0000.0000.0000.000
63B63VAL00.008-0.00311.674-0.076-0.0760.0000.0000.0000.000
64B64LYS10.9120.98115.344-0.081-0.0810.0000.0000.0000.000
65B65LYS10.9700.99118.225-0.062-0.0620.0000.0000.0000.000
66B66LEU00.0680.03018.649-0.011-0.0110.0000.0000.0000.000
67B67ASP-1-0.852-0.91520.6470.0180.0180.0000.0000.0000.000
68B68ARG10.7590.88020.350-0.038-0.0380.0000.0000.0000.000
69B69LEU00.0120.01517.088-0.002-0.0020.0000.0000.0000.000
70B70GLY00.0280.00720.468-0.012-0.0120.0000.0000.0000.000
71B71ARG10.8190.91023.2470.0790.0790.0000.0000.0000.000
72B72ASP-1-0.834-0.92526.223-0.053-0.0530.0000.0000.0000.000
73B73THR00.0390.00525.206-0.002-0.0020.0000.0000.0000.000
74B74ALA00.0270.01624.408-0.009-0.0090.0000.0000.0000.000
75B75ASP-1-0.807-0.88024.191-0.096-0.0960.0000.0000.0000.000
76B76MET00.0140.01220.247-0.010-0.0100.0000.0000.0000.000
77B77ILE0-0.007-0.01019.704-0.016-0.0160.0000.0000.0000.000
78B78GLN0-0.060-0.02319.705-0.016-0.0160.0000.0000.0000.000
79B79LEU00.0070.00217.987-0.023-0.0230.0000.0000.0000.000
80B80ILE00.004-0.00114.631-0.034-0.0340.0000.0000.0000.000
81B81LYS10.9010.94814.8570.1420.1420.0000.0000.0000.000
82B82GLU-1-0.811-0.86716.151-0.262-0.2620.0000.0000.0000.000
83B83PHE0-0.015-0.01511.819-0.018-0.0180.0000.0000.0000.000
84B84ASP-1-0.849-0.93411.447-0.558-0.5580.0000.0000.0000.000
85B85ALA0-0.060-0.02312.411-0.064-0.0640.0000.0000.0000.000
86B86GLN0-0.085-0.04211.670-0.045-0.0450.0000.0000.0000.000
87B87GLY00.0630.0348.990-0.171-0.1710.0000.0000.0000.000
88B88VAL0-0.089-0.0317.192-0.285-0.2850.0000.0000.0000.000
89B89ALA00.0170.0196.3050.1770.1770.0000.0000.0000.000
90B90VAL0-0.029-0.0268.1700.1670.1670.0000.0000.0000.000
91B91ARG10.8460.8765.172-1.918-1.825-0.001-0.013-0.0790.000
92B92PHE0-0.013-0.01511.412-0.001-0.0010.0000.0000.0000.000
93B93ILE0-0.001-0.02013.9980.0120.0120.0000.0000.0000.000
94B94ASP-1-0.876-0.96215.8690.1250.1250.0000.0000.0000.000
95B95ASP-1-0.901-0.96718.6990.0700.0700.0000.0000.0000.000
96B96GLY00.0020.02216.395-0.011-0.0110.0000.0000.0000.000
97B97ILE0-0.039-0.01415.357-0.019-0.0190.0000.0000.0000.000
98B98SER0-0.005-0.01310.2810.1010.1010.0000.0000.0000.000
99B99THR0-0.010-0.00710.836-0.062-0.0620.0000.0000.0000.000
100B100ASP-1-0.758-0.8475.7910.5950.5950.0000.0000.0000.000
101B101GLY0-0.039-0.0217.6300.1530.1530.0000.0000.0000.000
102B102ASP-1-0.915-0.9539.161-0.139-0.1390.0000.0000.0000.000
103B103MET0-0.012-0.00912.923-0.036-0.0360.0000.0000.0000.000
104B104GLY00.0610.03411.515-0.003-0.0030.0000.0000.0000.000
105B105GLN00.0750.02912.462-0.012-0.0120.0000.0000.0000.000
106B106MET00.0040.01215.1100.0110.0110.0000.0000.0000.000
107B107VAL00.0120.00914.9940.0110.0110.0000.0000.0000.000
108B108VAL00.0600.03814.1320.0240.0240.0000.0000.0000.000
109B109THR0-0.042-0.01817.1290.0070.0070.0000.0000.0000.000
110B110ILE00.0020.00120.0440.0090.0090.0000.0000.0000.000
111B111LEU00.0360.01518.3220.0080.0080.0000.0000.0000.000
112B112SER0-0.046-0.04620.258-0.004-0.0040.0000.0000.0000.000
113B113ALA0-0.049-0.01822.6790.0050.0050.0000.0000.0000.000
114B114VAL00.0030.00224.7790.0070.0070.0000.0000.0000.000
115B115ALA00.0430.02524.7310.0040.0040.0000.0000.0000.000
116B116GLN0-0.061-0.03526.6200.0100.0100.0000.0000.0000.000
117B117ALA0-0.0060.00228.5430.0040.0040.0000.0000.0000.000
118B118GLU-1-0.912-0.96328.518-0.054-0.0540.0000.0000.0000.000
119B119ARG10.9780.98626.1980.1000.1000.0000.0000.0000.000
120B120ARG10.8690.92531.8330.0760.0760.0000.0000.0000.000
121B121ARG11.0221.01231.8610.0460.0460.0000.0000.0000.000
122B122ILE0-0.0180.01034.6040.0030.0030.0000.0000.0000.000
123B123LEU0-0.074-0.03635.2120.0010.0010.0000.0000.0000.000
124B124GLU-1-0.867-0.92438.708-0.040-0.0400.0000.0000.0000.000
125B125ARG11.0451.01040.4970.0350.0350.0000.0000.0000.000
126B126THR0-0.018-0.00241.0270.0010.0010.0000.0000.0000.000
127B127ASN0-0.050-0.06237.946-0.002-0.0020.0000.0000.0000.000
128B128GLU-1-0.884-0.92341.499-0.038-0.0380.0000.0000.0000.000
129B129GLY00.0420.02444.2380.0010.0010.0000.0000.0000.000
130B130ARG10.8470.93338.1500.0640.0640.0000.0000.0000.000
131B131GLN0-0.005-0.01641.3130.0000.0000.0000.0000.0000.000
132B132GLU-1-0.802-0.89045.474-0.032-0.0320.0000.0000.0000.000
133B133ALA0-0.048-0.01947.5020.0010.0010.0000.0000.0000.000
134B134LYS10.9210.95042.5000.0540.0540.0000.0000.0000.000
135B135LEU0-0.0180.00147.9020.0000.0000.0000.0000.0000.000
136B136LYS10.8640.92750.5090.0350.0350.0000.0000.0000.000
137B137GLY00.0350.03751.4280.0010.0010.0000.0000.0000.000
138B138ILE0-0.073-0.03149.161-0.001-0.0010.0000.0000.0000.000
139B139LYS10.9520.97548.9470.0390.0390.0000.0000.0000.000
140B140PHE00.0290.00843.494-0.001-0.0010.0000.0000.0000.000
141B141GLY0-0.0010.00042.5720.0000.0000.0000.0000.0000.000
142B142ARG10.9580.97742.1460.0700.0700.0000.0000.0000.000
143B143ARG11.0071.00344.8010.0490.0490.0000.0000.0000.000
144B144ARG10.9270.95948.2690.0480.0480.0000.0000.0000.000
145B145THR00.0420.01449.1550.0010.0010.0000.0000.0000.000
146B146VAL0-0.032-0.00149.3120.0010.0010.0000.0000.0000.000
147B147ASP-1-0.807-0.91052.185-0.039-0.0390.0000.0000.0000.000
148B148ARG10.7230.81348.7990.0500.0500.0000.0000.0000.000
149B149ASN00.0630.03555.2640.0000.0000.0000.0000.0000.000
150B150VAL00.0230.02457.5510.0000.0000.0000.0000.0000.000
151B151VAL0-0.006-0.00652.5540.0000.0000.0000.0000.0000.000
152B152LEU00.0150.00155.1350.0000.0000.0000.0000.0000.000
153B153THR0-0.011-0.00557.5970.0010.0010.0000.0000.0000.000
154B154LEU0-0.036-0.02657.7290.0010.0010.0000.0000.0000.000
155B155HIS00.0550.03655.0660.0000.0000.0000.0000.0000.000
156B156GLN0-0.040-0.00258.1290.0000.0000.0000.0000.0000.000
157B157LYS10.9070.95161.2270.0340.0340.0000.0000.0000.000
158B158GLY00.0170.02060.1850.0010.0010.0000.0000.0000.000
159B159THR0-0.085-0.04557.5810.0000.0000.0000.0000.0000.000
160B160GLY00.0620.03855.555-0.001-0.0010.0000.0000.0000.000
161B161ALA00.015-0.01150.2960.0000.0000.0000.0000.0000.000
162B162THR0-0.019-0.03749.370-0.001-0.0010.0000.0000.0000.000
163B163GLU-1-0.885-0.93351.468-0.041-0.0410.0000.0000.0000.000
164B164ILE00.0260.01153.4190.0000.0000.0000.0000.0000.000
165B165ALA0-0.059-0.03149.2300.0000.0000.0000.0000.0000.000
166B166HIS00.007-0.00251.300-0.001-0.0010.0000.0000.0000.000
167B167GLN0-0.0130.01452.8720.0000.0000.0000.0000.0000.000
168B168LEU0-0.054-0.03953.2270.0010.0010.0000.0000.0000.000
169B169SER0-0.0080.01351.052-0.001-0.0010.0000.0000.0000.000
170B170ILE0-0.049-0.00848.337-0.003-0.0030.0000.0000.0000.000
171B171ALA00.0300.01143.9510.0000.0000.0000.0000.0000.000
172B172ARG11.0160.98643.8340.0680.0680.0000.0000.0000.000
173B173SER0-0.003-0.00941.6060.0030.0030.0000.0000.0000.000
174B174THR00.003-0.00544.403-0.001-0.0010.0000.0000.0000.000
175B175VAL00.0360.02846.1210.0010.0010.0000.0000.0000.000
176B176TYR00.0350.00445.8290.0010.0010.0000.0000.0000.000
177B177LYS11.0001.00641.2350.0730.0730.0000.0000.0000.000
178B178ILE0-0.027-0.00846.4280.0010.0010.0000.0000.0000.000
179B179LEU00.000-0.00749.7940.0020.0020.0000.0000.0000.000
180B180GLU-1-0.932-0.94644.832-0.061-0.0610.0000.0000.0000.000
181B181ASP-1-0.854-0.91647.159-0.057-0.0570.0000.0000.0000.000
182B182GLU-1-0.839-0.91949.761-0.044-0.0440.0000.0000.0000.000
183B183ARG10.8550.94247.9560.0540.0540.0000.0000.0000.000
184B184ALA0-0.052-0.02149.5950.0010.0010.0000.0000.0000.000
185B185SER0-0.0260.00151.6290.0010.0010.0000.0000.0000.000