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: JQVR9

Calculation Name: 3CAZ-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CAZ

Chain ID: B

ChEMBL ID:

UniProt ID: D0VWT4

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 OptAll
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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2072360.406855
FMO2-HF: Nuclear repulsion 1985955.192823
FMO2-HF: Total energy -86405.214032
FMO2-MP2: Total energy -86658.929424


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:12:SER)


Summations of interaction energy for fragment #1(B:12: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.
-5.165-1.5120.051-1.716-1.987-0.004
Interaction energy analysis for fragmet #1(B:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.027
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].
3B14ASN00.009-0.0063.872-0.2541.191-0.016-0.710-0.7180.003
4B15MET00.0790.0296.7710.4680.4680.0000.0000.0000.000
5B16GLU-1-0.834-0.9118.223-0.072-0.0720.0000.0000.0000.000
6B17VAL0-0.018-0.01110.3150.0800.0800.0000.0000.0000.000
7B18GLU-1-0.908-0.9696.4920.4690.4690.0000.0000.0000.000
8B19HIS0-0.0100.01911.0900.1020.1020.0000.0000.0000.000
9B20TRP0-0.008-0.01113.6810.0490.0490.0000.0000.0000.000
10B21MET00.0180.01314.1480.0410.0410.0000.0000.0000.000
11B22THR0-0.035-0.04113.6850.0390.0390.0000.0000.0000.000
12B23SER00.0350.01216.3610.0050.0050.0000.0000.0000.000
13B24LEU0-0.033-0.01719.011-0.002-0.0020.0000.0000.0000.000
14B25LYS10.9260.96514.328-0.194-0.1940.0000.0000.0000.000
15B26GLU-1-0.958-0.97419.8950.1660.1660.0000.0000.0000.000
16B27VAL0-0.024-0.01522.319-0.004-0.0040.0000.0000.0000.000
17B28GLU-1-0.790-0.88722.7550.0450.0450.0000.0000.0000.000
18B29LYS10.9580.98323.430-0.155-0.1550.0000.0000.0000.000
19B30VAL0-0.037-0.01325.9100.0010.0010.0000.0000.0000.000
20B31LEU0-0.019-0.01327.774-0.004-0.0040.0000.0000.0000.000
21B32ASP-1-0.801-0.89627.9730.0420.0420.0000.0000.0000.000
22B33SER0-0.043-0.00230.2280.0000.0000.0000.0000.0000.000
23B34VAL0-0.001-0.01431.907-0.002-0.0020.0000.0000.0000.000
24B35GLU-1-0.742-0.84133.3660.0150.0150.0000.0000.0000.000
25B36PRO00.0280.01834.592-0.004-0.0040.0000.0000.0000.000
26B37LYS10.8600.92334.060-0.063-0.0630.0000.0000.0000.000
27B38LEU00.0350.01737.020-0.002-0.0020.0000.0000.0000.000
28B39THR00.0000.00739.250-0.003-0.0030.0000.0000.0000.000
29B40SER0-0.062-0.02341.594-0.001-0.0010.0000.0000.0000.000
30B41SER0-0.009-0.01043.4200.0000.0000.0000.0000.0000.000
31B42GLY00.1000.04545.0270.0000.0000.0000.0000.0000.000
32B43THR0-0.018-0.02746.8990.0000.0000.0000.0000.0000.000
33B44LYS10.8200.90444.185-0.033-0.0330.0000.0000.0000.000
34B45TRP00.0720.02249.0560.0000.0000.0000.0000.0000.000
35B46ARG10.9581.00051.732-0.021-0.0210.0000.0000.0000.000
36B47VAL0-0.056-0.02851.263-0.001-0.0010.0000.0000.0000.000
37B48VAL00.0160.01653.1810.0000.0000.0000.0000.0000.000
38B49ALA00.0370.01355.8040.0000.0000.0000.0000.0000.000
39B50GLN0-0.073-0.04357.231-0.001-0.0010.0000.0000.0000.000
40B51HIS00.0200.01057.7500.0000.0000.0000.0000.0000.000
41B52ILE00.0250.00959.4300.0000.0000.0000.0000.0000.000
42B53LYS10.8460.91760.058-0.015-0.0150.0000.0000.0000.000
43B54ASP-1-0.837-0.89061.4590.0180.0180.0000.0000.0000.000
44B55ILE0-0.007-0.00262.3990.0000.0000.0000.0000.0000.000
45B56CYS0-0.035-0.01565.6220.0000.0000.0000.0000.0000.000
46B57SER0-0.058-0.05066.687-0.001-0.0010.0000.0000.0000.000
47B58ASP-1-0.870-0.94467.9570.0170.0170.0000.0000.0000.000
48B59LEU0-0.020-0.01469.7380.0000.0000.0000.0000.0000.000
49B60ASN0-0.016-0.00671.912-0.001-0.0010.0000.0000.0000.000
50B61GLN0-0.080-0.00370.586-0.001-0.0010.0000.0000.0000.000
51B62ILE00.033-0.01274.865-0.001-0.0010.0000.0000.0000.000
52B63PHE0-0.0180.01276.8370.0000.0000.0000.0000.0000.000
53B64ASN0-0.033-0.00779.319-0.001-0.0010.0000.0000.0000.000
54B65LYS10.8820.90681.885-0.011-0.0110.0000.0000.0000.000
55B66GLU-1-0.880-0.93282.3860.0090.0090.0000.0000.0000.000
56B67ASP-1-0.841-0.90083.2090.0110.0110.0000.0000.0000.000
57B68PRO00.0350.00482.6800.0000.0000.0000.0000.0000.000
58B69ARG10.8980.93579.535-0.012-0.0120.0000.0000.0000.000
59B70TYR0-0.081-0.03876.6540.0000.0000.0000.0000.0000.000
60B71GLU-1-0.866-0.90677.4380.0100.0100.0000.0000.0000.000
61B72VAL00.0170.01473.5730.0000.0000.0000.0000.0000.000
62B73VAL0-0.0150.00072.9310.0000.0000.0000.0000.0000.000
63B74GLN0-0.0180.00072.6270.0000.0000.0000.0000.0000.000
64B75ALA00.0190.00372.9280.0000.0000.0000.0000.0000.000
65B76GLY00.0430.01869.6220.0000.0000.0000.0000.0000.000
66B77ALA0-0.008-0.01568.3050.0000.0000.0000.0000.0000.000
67B78SER0-0.022-0.01368.2660.0000.0000.0000.0000.0000.000
68B79ALA00.0140.01166.8990.0000.0000.0000.0000.0000.000
69B80ALA00.0100.00364.1330.0000.0000.0000.0000.0000.000
70B81HIS0-0.029-0.01163.4410.0010.0010.0000.0000.0000.000
71B82ASP-1-0.834-0.90363.9800.0090.0090.0000.0000.0000.000
72B83PHE0-0.008-0.00356.5630.0000.0000.0000.0000.0000.000
73B84ASP-1-0.845-0.92559.2720.0140.0140.0000.0000.0000.000
74B85VAL0-0.005-0.00459.1470.0000.0000.0000.0000.0000.000
75B86ARG10.8380.89859.733-0.010-0.0100.0000.0000.0000.000
76B87TYR0-0.027-0.02251.7250.0000.0000.0000.0000.0000.000
77B88LEU0-0.035-0.03255.0620.0000.0000.0000.0000.0000.000
78B89ASP-1-0.878-0.92855.5230.0040.0040.0000.0000.0000.000
79B90ILE00.0190.01553.318-0.001-0.0010.0000.0000.0000.000
80B91HIS0-0.039-0.00449.0080.0010.0010.0000.0000.0000.000
81B92LYS10.8900.95450.671-0.006-0.0060.0000.0000.0000.000
82B93HIS0-0.088-0.05352.111-0.002-0.0020.0000.0000.0000.000
83B94GLY00.0260.03650.433-0.001-0.0010.0000.0000.0000.000
84B95ARG10.9300.94547.4690.0040.0040.0000.0000.0000.000
85B96GLU-1-0.843-0.91045.0860.0020.0020.0000.0000.0000.000
86B97ILE00.0570.01841.383-0.001-0.0010.0000.0000.0000.000
87B98ALA00.0250.02641.5120.0000.0000.0000.0000.0000.000
88B99ARG10.8520.90641.5510.0010.0010.0000.0000.0000.000
89B100LEU00.0000.01736.846-0.002-0.0020.0000.0000.0000.000
90B101LEU00.0130.00537.0780.0000.0000.0000.0000.0000.000
91B102GLU-1-0.820-0.89436.408-0.016-0.0160.0000.0000.0000.000
92B103LYS10.7620.86135.5420.0060.0060.0000.0000.0000.000
93B104ILE0-0.008-0.00432.010-0.003-0.0030.0000.0000.0000.000
94B105GLN0-0.034-0.02231.543-0.005-0.0050.0000.0000.0000.000
95B106LYS10.8470.91031.4530.0200.0200.0000.0000.0000.000
96B107TYR0-0.058-0.04726.3570.0000.0000.0000.0000.0000.000
97B108ARG10.8310.87126.898-0.024-0.0240.0000.0000.0000.000
98B109GLN0-0.081-0.04326.4160.0050.0050.0000.0000.0000.000
99B110GLU-1-0.741-0.85126.240-0.063-0.0630.0000.0000.0000.000
100B111ILE0-0.020-0.00721.762-0.014-0.0140.0000.0000.0000.000
101B112GLU-1-0.790-0.89221.786-0.008-0.0080.0000.0000.0000.000
102B113GLU-1-0.929-0.94722.316-0.086-0.0860.0000.0000.0000.000
103B114ILE00.0520.03118.882-0.021-0.0210.0000.0000.0000.000
104B115LYS10.7470.84217.689-0.058-0.0580.0000.0000.0000.000
105B116LYS10.7810.87117.3730.0620.0620.0000.0000.0000.000
106B117GLU-1-0.756-0.85717.287-0.251-0.2510.0000.0000.0000.000
107B118TYR00.0090.00910.145-0.050-0.0500.0000.0000.0000.000
108B119LYS10.9230.96312.711-0.017-0.0170.0000.0000.0000.000
109B120GLU-1-0.813-0.88413.027-0.346-0.3460.0000.0000.0000.000
110B121THR0-0.006-0.01610.531-0.092-0.0920.0000.0000.0000.000
111B122ASP-1-0.847-0.9137.080-0.774-0.7740.0000.0000.0000.000
112B123LYS10.8050.8858.8340.1020.1020.0000.0000.0000.000
113B124TYR00.001-0.00110.966-0.053-0.0530.0000.0000.0000.000
114B125ARG10.7890.8733.0992.8693.3940.023-0.160-0.3890.000
115B126GLU-1-0.852-0.9096.549-1.791-1.7910.0000.0000.0000.000
116B127ARG10.7830.8898.3361.2081.2080.0000.0000.0000.000
117B128TYR00.0460.0274.0560.1970.336-0.001-0.011-0.1270.000
118B129ASP-1-0.759-0.8833.191-10.203-8.7030.046-0.835-0.711-0.007
119B130HIS00.0120.0206.5040.7060.7060.0000.0000.0000.000
120B131TYR00.019-0.0159.9130.2460.2460.0000.0000.0000.000
121B132LYS10.9420.9944.6521.6691.713-0.0010.000-0.0420.000
122B133VAL00.0240.0118.3870.2720.2720.0000.0000.0000.000
123B134LYS10.8710.92810.8840.8300.8300.0000.0000.0000.000
124B135LEU00.0170.01512.6370.1060.1060.0000.0000.0000.000
125B136ASP-1-0.788-0.87611.942-0.266-0.2660.0000.0000.0000.000
126B137ASN0-0.051-0.03813.6430.1850.1850.0000.0000.0000.000
127B138LEU0-0.051-0.03116.3060.0650.0650.0000.0000.0000.000
128B139GLU-1-0.829-0.90916.931-0.302-0.3020.0000.0000.0000.000
129B140LYS10.7770.88314.8160.3100.3100.0000.0000.0000.000
130B141LYS10.8140.91118.1560.3140.3140.0000.0000.0000.000
131B142ASN00.0120.00022.325-0.012-0.0120.0000.0000.0000.000
132B143LYS10.9550.97724.2110.1630.1630.0000.0000.0000.000
133B144ASP-1-0.817-0.90124.966-0.217-0.2170.0000.0000.0000.000
134B145GLN00.0430.02424.355-0.023-0.0230.0000.0000.0000.000
135B146GLU-1-0.753-0.89424.260-0.199-0.1990.0000.0000.0000.000
136B147ARG10.7890.92121.6640.2550.2550.0000.0000.0000.000
137B148ILE0-0.0100.00119.874-0.047-0.0470.0000.0000.0000.000
138B149GLU-1-0.894-0.92919.543-0.270-0.2700.0000.0000.0000.000
139B150ARG10.8910.92320.7190.2210.2210.0000.0000.0000.000
140B151ASN0-0.097-0.06816.457-0.085-0.0850.0000.0000.0000.000
141B152GLN0-0.002-0.00415.995-0.076-0.0760.0000.0000.0000.000
142B153GLN0-0.022-0.00816.443-0.021-0.0210.0000.0000.0000.000
143B154LYS10.8610.92816.2360.4070.4070.0000.0000.0000.000
144B155PHE0-0.027-0.0118.229-0.082-0.0820.0000.0000.0000.000
145B156LYS10.8930.93912.4700.4270.4270.0000.0000.0000.000
146B157ASP-1-0.822-0.91514.818-0.510-0.5100.0000.0000.0000.000
147B158ALA0-0.028-0.01111.426-0.001-0.0010.0000.0000.0000.000
148B159GLU-1-0.837-0.9209.971-1.009-1.0090.0000.0000.0000.000
149B160ALA00.0020.01211.1650.0120.0120.0000.0000.0000.000
150B161ALA0-0.006-0.00414.3580.0360.0360.0000.0000.0000.000
151B162TYR00.015-0.0076.611-0.238-0.2380.0000.0000.0000.000
152B163SER00.0260.00711.7430.0370.0370.0000.0000.0000.000
153B164SER0-0.054-0.01612.8350.0950.0950.0000.0000.0000.000
154B165VAL00.0190.00613.2460.0380.0380.0000.0000.0000.000
155B166CYS0-0.072-0.02410.893-0.017-0.0170.0000.0000.0000.000
156B167ALA00.0370.02513.5850.0930.0930.0000.0000.0000.000
157B168ASP-1-0.870-0.93116.384-0.301-0.3010.0000.0000.0000.000
158B169LEU0-0.019-0.01514.3740.0600.0600.0000.0000.0000.000
159B170ILE00.002-0.00213.1300.0470.0470.0000.0000.0000.000
160B171GLN00.0210.01817.4220.0690.0690.0000.0000.0000.000
161B172LYS10.8000.88220.3710.2420.2420.0000.0000.0000.000
162B173MET0-0.047-0.01714.5970.0430.0430.0000.0000.0000.000
163B174GLU-1-0.829-0.89520.323-0.068-0.0680.0000.0000.0000.000
164B175THR0-0.005-0.02921.9280.0260.0260.0000.0000.0000.000
165B176VAL0-0.0120.00923.1780.0130.0130.0000.0000.0000.000
166B177TRP00.0500.03422.4030.0200.0200.0000.0000.0000.000
167B178LYS10.8250.91824.4420.0880.0880.0000.0000.0000.000
168B179LYS10.8340.89827.7570.0630.0630.0000.0000.0000.000
169B180HIS10.8530.93126.164-0.016-0.0160.0000.0000.0000.000
170B181VAL00.0120.01329.2340.0060.0060.0000.0000.0000.000
171B182SER00.0350.01831.6080.0020.0020.0000.0000.0000.000
172B183ILE00.0150.00330.9720.0020.0020.0000.0000.0000.000
173B184PHE00.0010.00228.7660.0040.0040.0000.0000.0000.000
174B185ALA00.0280.02234.3870.0030.0030.0000.0000.0000.000
175B186GLU-1-0.814-0.87637.362-0.004-0.0040.0000.0000.0000.000
176B187ALA00.012-0.00636.4300.0010.0010.0000.0000.0000.000
177B188ALA00.0000.00238.3810.0010.0010.0000.0000.0000.000
178B189SER0-0.005-0.01540.1500.0000.0000.0000.0000.0000.000
179B190ALA0-0.020-0.01241.582-0.001-0.0010.0000.0000.0000.000
180B191VAL00.0140.01740.6400.0000.0000.0000.0000.0000.000
181B192TRP00.0300.01043.0200.0000.0000.0000.0000.0000.000
182B193SER0-0.0190.00246.0510.0000.0000.0000.0000.0000.000
183B194THR00.003-0.01946.059-0.001-0.0010.0000.0000.0000.000
184B195GLN0-0.012-0.00646.3550.0010.0010.0000.0000.0000.000
185B196LEU00.0150.01249.2460.0000.0000.0000.0000.0000.000
186B197GLN0-0.069-0.03250.289-0.001-0.0010.0000.0000.0000.000
187B198TYR00.0250.00149.0110.0000.0000.0000.0000.0000.000
188B199ALA00.0040.00553.4690.0000.0000.0000.0000.0000.000
189B200LYS10.9960.99454.651-0.012-0.0120.0000.0000.0000.000
190B201ALA0-0.032-0.00756.917-0.001-0.0010.0000.0000.0000.000
191B202LEU00.0070.00158.0370.0000.0000.0000.0000.0000.000
192B203GLU-1-0.931-0.97258.9420.0160.0160.0000.0000.0000.000
193B204ALA0-0.063-0.03561.411-0.001-0.0010.0000.0000.0000.000
194B205ALA00.0080.01162.670-0.001-0.0010.0000.0000.0000.000
195B206ALA00.0080.01064.1870.0000.0000.0000.0000.0000.000
196B207ASN0-0.053-0.03665.9060.0000.0000.0000.0000.0000.000
197B208PRO0-0.020-0.01368.7250.0000.0000.0000.0000.0000.000
198B209ILE00.0140.00767.3980.0000.0000.0000.0000.0000.000
199B210VAL0-0.0030.00268.0210.0000.0000.0000.0000.0000.000
200B211PRO0-0.013-0.00770.5980.0000.0000.0000.0000.0000.000
201B212TYR0-0.072-0.05773.8430.0000.0000.0000.0000.0000.000
202B213LEU00.0000.00167.8660.0000.0000.0000.0000.0000.000
203B214GLN00.0030.00972.0140.0000.0000.0000.0000.0000.000
204B215GLN0-0.105-0.03273.632-0.001-0.0010.0000.0000.0000.000
205B216GLU-1-0.819-0.92972.2180.0160.0160.0000.0000.0000.000
206B217GLU-1-1.007-1.00969.3070.0170.0170.0000.0000.0000.000
207B218GLN0-0.132-0.07571.6830.0000.0000.0000.0000.0000.000
208B219GLU-1-0.974-0.95374.6010.0160.0160.0000.0000.0000.000
209B220GLU-1-0.978-0.99671.9570.0220.0220.0000.0000.0000.000
210B221GLU-1-1.034-1.01475.1400.0180.0180.0000.0000.0000.000