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: 89Q6Y

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2064832.212451
FMO2-HF: Nuclear repulsion 1978429.948487
FMO2-HF: Total energy -86402.263964
FMO2-MP2: Total energy -86656.040185


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.
-6.85-3.158-0.003-1.968-1.720.005
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 : -0.002 / q_NPA : 0.000
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].
3B14ASN00.0350.0193.806-0.4622.143-0.024-1.404-1.1770.008
4B15MET00.0650.0186.9250.3900.3900.0000.0000.0000.000
5B16GLU-1-0.901-0.9588.282-0.316-0.3160.0000.0000.0000.000
6B17VAL0-0.013-0.00210.3290.0760.0760.0000.0000.0000.000
7B18GLU-1-0.924-0.9777.035-1.112-1.1120.0000.0000.0000.000
8B19HIS0-0.0230.00711.0400.1890.1890.0000.0000.0000.000
9B20TRP00.0440.01413.6800.0860.0860.0000.0000.0000.000
10B21MET00.0050.01013.7640.0660.0660.0000.0000.0000.000
11B22THR0-0.016-0.01813.4330.0680.0680.0000.0000.0000.000
12B23SER00.0420.01816.0810.0520.0520.0000.0000.0000.000
13B24LEU0-0.039-0.01518.8300.0390.0390.0000.0000.0000.000
14B25LYS10.9580.97315.0250.4780.4780.0000.0000.0000.000
15B26GLU-1-0.970-0.98119.486-0.067-0.0670.0000.0000.0000.000
16B27VAL0-0.028-0.02021.9670.0240.0240.0000.0000.0000.000
17B28GLU-1-0.875-0.93923.019-0.261-0.2610.0000.0000.0000.000
18B29LYS10.9691.00023.6180.0940.0940.0000.0000.0000.000
19B30VAL0-0.041-0.01725.6400.0200.0200.0000.0000.0000.000
20B31LEU0-0.001-0.00628.0550.0140.0140.0000.0000.0000.000
21B32ASP-1-0.838-0.92326.908-0.171-0.1710.0000.0000.0000.000
22B33SER0-0.081-0.03129.8900.0140.0140.0000.0000.0000.000
23B34VAL0-0.044-0.04231.6190.0110.0110.0000.0000.0000.000
24B35GLU-1-0.827-0.89633.318-0.126-0.1260.0000.0000.0000.000
25B36PRO00.0480.03134.0330.0050.0050.0000.0000.0000.000
26B37LYS10.8990.94234.3720.0610.0610.0000.0000.0000.000
27B38LEU0-0.008-0.00636.5610.0050.0050.0000.0000.0000.000
28B39THR00.0130.00939.3760.0040.0040.0000.0000.0000.000
29B40SER0-0.055-0.01241.2300.0050.0050.0000.0000.0000.000
30B41SER0-0.004-0.01243.1210.0070.0070.0000.0000.0000.000
31B42GLY00.1100.05144.7450.0040.0040.0000.0000.0000.000
32B43THR0-0.050-0.03546.4820.0010.0010.0000.0000.0000.000
33B44LYS10.8980.94243.9950.0430.0430.0000.0000.0000.000
34B45TRP00.0840.02948.8190.0030.0030.0000.0000.0000.000
35B46ARG10.9671.01651.6190.0410.0410.0000.0000.0000.000
36B47VAL0-0.065-0.04150.8100.0010.0010.0000.0000.0000.000
37B48VAL00.0380.03053.1000.0020.0020.0000.0000.0000.000
38B49ALA00.0460.02055.6580.0020.0020.0000.0000.0000.000
39B50GLN0-0.063-0.04557.112-0.001-0.0010.0000.0000.0000.000
40B51HIS00.0160.01657.4140.0000.0000.0000.0000.0000.000
41B52ILE00.0150.00559.3420.0010.0010.0000.0000.0000.000
42B53LYS10.8810.93760.4530.0320.0320.0000.0000.0000.000
43B54ASP-1-0.881-0.93561.157-0.023-0.0230.0000.0000.0000.000
44B55ILE00.0200.01662.2630.0010.0010.0000.0000.0000.000
45B56CYS0-0.017-0.00365.5760.0010.0010.0000.0000.0000.000
46B57SER0-0.096-0.04566.8580.0010.0010.0000.0000.0000.000
47B58ASP-1-0.858-0.92467.693-0.016-0.0160.0000.0000.0000.000
48B59LEU0-0.087-0.05169.5980.0010.0010.0000.0000.0000.000
49B60ASN0-0.040-0.03171.6730.0010.0010.0000.0000.0000.000
50B61GLN00.0090.02671.966-0.001-0.0010.0000.0000.0000.000
51B62ILE0-0.045-0.02474.7530.0000.0000.0000.0000.0000.000
52B63PHE0-0.043-0.00177.0190.0010.0010.0000.0000.0000.000
53B64ASN00.0530.00278.984-0.001-0.0010.0000.0000.0000.000
54B65LYS10.8730.92681.5420.0100.0100.0000.0000.0000.000
55B66GLU-1-0.869-0.93682.098-0.015-0.0150.0000.0000.0000.000
56B67ASP-1-0.912-0.95482.525-0.009-0.0090.0000.0000.0000.000
57B68PRO00.0380.02182.605-0.001-0.0010.0000.0000.0000.000
58B69ARG10.9590.97479.3720.0080.0080.0000.0000.0000.000
59B70TYR0-0.080-0.02776.9990.0000.0000.0000.0000.0000.000
60B71GLU-1-0.884-0.94377.409-0.015-0.0150.0000.0000.0000.000
61B72VAL00.0020.01473.725-0.001-0.0010.0000.0000.0000.000
62B73VAL00.0120.00772.589-0.001-0.0010.0000.0000.0000.000
63B74GLN0-0.0010.01372.358-0.001-0.0010.0000.0000.0000.000
64B75ALA0-0.010-0.02272.640-0.001-0.0010.0000.0000.0000.000
65B76GLY00.0660.01469.769-0.001-0.0010.0000.0000.0000.000
66B77ALA0-0.004-0.02568.219-0.001-0.0010.0000.0000.0000.000
67B78SER0-0.071-0.02568.159-0.002-0.0020.0000.0000.0000.000
68B79ALA00.0820.03166.948-0.002-0.0020.0000.0000.0000.000
69B80ALA00.0010.00064.159-0.001-0.0010.0000.0000.0000.000
70B81HIS0-0.042-0.02563.343-0.002-0.0020.0000.0000.0000.000
71B82ASP-1-0.885-0.94663.713-0.031-0.0310.0000.0000.0000.000
72B83PHE0-0.013-0.00856.169-0.002-0.0020.0000.0000.0000.000
73B84ASP-1-0.883-0.95558.929-0.037-0.0370.0000.0000.0000.000
74B85VAL0-0.0110.00158.947-0.003-0.0030.0000.0000.0000.000
75B86ARG10.8920.95959.2520.0290.0290.0000.0000.0000.000
76B87TYR0-0.004-0.00551.537-0.002-0.0020.0000.0000.0000.000
77B88LEU0-0.019-0.02154.763-0.003-0.0030.0000.0000.0000.000
78B89ASP-1-0.926-0.95455.107-0.051-0.0510.0000.0000.0000.000
79B90ILE0-0.032-0.00952.951-0.003-0.0030.0000.0000.0000.000
80B91HIS0-0.046-0.02048.178-0.001-0.0010.0000.0000.0000.000
81B92LYS10.8790.93150.3910.0490.0490.0000.0000.0000.000
82B93HIS0-0.030-0.00652.187-0.004-0.0040.0000.0000.0000.000
83B94GLY00.0230.03750.048-0.001-0.0010.0000.0000.0000.000
84B95ARG10.9340.95347.3470.0690.0690.0000.0000.0000.000
85B96GLU-1-0.941-0.99244.881-0.070-0.0700.0000.0000.0000.000
86B97ILE00.0680.03841.710-0.005-0.0050.0000.0000.0000.000
87B98ALA00.0460.03241.496-0.006-0.0060.0000.0000.0000.000
88B99ARG10.9360.96741.5470.0780.0780.0000.0000.0000.000
89B100LEU00.0300.03436.805-0.008-0.0080.0000.0000.0000.000
90B101LEU0-0.001-0.01137.042-0.008-0.0080.0000.0000.0000.000
91B102GLU-1-0.900-0.93436.315-0.137-0.1370.0000.0000.0000.000
92B103LYS10.7920.89335.6630.1050.1050.0000.0000.0000.000
93B104ILE0-0.007-0.00131.806-0.012-0.0120.0000.0000.0000.000
94B105GLN0-0.001-0.00731.601-0.015-0.0150.0000.0000.0000.000
95B106LYS10.9330.96231.5870.1420.1420.0000.0000.0000.000
96B107TYR0-0.008-0.01126.196-0.009-0.0090.0000.0000.0000.000
97B108ARG10.8530.91127.0940.1600.1600.0000.0000.0000.000
98B109GLN00.002-0.00226.399-0.009-0.0090.0000.0000.0000.000
99B110GLU-1-0.836-0.92026.471-0.280-0.2800.0000.0000.0000.000
100B111ILE00.004-0.00622.203-0.030-0.0300.0000.0000.0000.000
101B112GLU-1-0.911-0.96021.756-0.398-0.3980.0000.0000.0000.000
102B113GLU-1-0.989-0.99721.698-0.395-0.3950.0000.0000.0000.000
103B114ILE00.0410.01918.752-0.056-0.0560.0000.0000.0000.000
104B115LYS10.8730.94417.5220.2810.2810.0000.0000.0000.000
105B116LYS10.8660.92316.6800.3250.3250.0000.0000.0000.000
106B117GLU-1-0.891-0.93517.598-0.646-0.6460.0000.0000.0000.000
107B118TYR00.0070.01510.193-0.154-0.1540.0000.0000.0000.000
108B119LYS10.9250.93812.6640.4930.4930.0000.0000.0000.000
109B120GLU-1-0.904-0.94713.069-0.998-0.9980.0000.0000.0000.000
110B121THR00.0200.01210.461-0.038-0.0380.0000.0000.0000.000
111B122ASP-1-0.838-0.9097.023-3.865-3.8650.0000.0000.0000.000
112B123LYS10.9100.9679.4180.7900.7900.0000.0000.0000.000
113B124TYR0-0.030-0.02211.7000.0570.0570.0000.0000.0000.000
114B125ARG10.8110.8913.3747.0477.3910.005-0.116-0.2330.000
115B126GLU-1-0.859-0.9366.968-2.862-2.8620.0000.0000.0000.000
116B127ARG10.8090.9179.0291.6231.6230.0000.0000.0000.000
117B128TYR00.0160.0005.2510.5460.5460.0000.0000.0000.000
118B129ASP-1-0.778-0.8883.373-9.598-8.8550.016-0.448-0.310-0.003
119B130HIS0-0.082-0.0256.8220.7860.7860.0000.0000.0000.000
120B131TYR0-0.022-0.04810.3490.2830.2830.0000.0000.0000.000
121B132LYS11.0261.0326.110-0.042-0.0420.0000.0000.0000.000
122B133VAL00.0560.0438.6610.2970.2970.0000.0000.0000.000
123B134LYS10.8670.92611.1910.5960.5960.0000.0000.0000.000
124B135LEU00.0310.00713.6970.0790.0790.0000.0000.0000.000
125B136ASP-1-0.830-0.88211.2280.2770.2770.0000.0000.0000.000
126B137ASN0-0.119-0.08114.4680.1060.1060.0000.0000.0000.000
127B138LEU0-0.123-0.07417.0920.0200.0200.0000.0000.0000.000
128B139GLU-1-0.871-0.92116.872-0.014-0.0140.0000.0000.0000.000
129B140LYS10.9430.99118.006-0.161-0.1610.0000.0000.0000.000
130B141LYS10.8300.92419.2720.0250.0250.0000.0000.0000.000
131B142ASN00.0350.00323.131-0.043-0.0430.0000.0000.0000.000
132B143LYS10.9180.95824.6440.0150.0150.0000.0000.0000.000
133B144ASP-1-0.852-0.93825.450-0.126-0.1260.0000.0000.0000.000
134B145GLN00.0660.01724.675-0.022-0.0220.0000.0000.0000.000
135B146GLU-1-0.778-0.89525.181-0.109-0.1090.0000.0000.0000.000
136B147ARG10.8220.93121.1670.1830.1830.0000.0000.0000.000
137B148ILE0-0.051-0.05020.396-0.048-0.0480.0000.0000.0000.000
138B149GLU-1-0.835-0.89820.323-0.155-0.1550.0000.0000.0000.000
139B150ARG10.8770.94321.8770.1810.1810.0000.0000.0000.000
140B151ASN0-0.111-0.06816.938-0.092-0.0920.0000.0000.0000.000
141B152GLN00.1160.06316.682-0.081-0.0810.0000.0000.0000.000
142B153GLN0-0.0250.00217.5080.0020.0020.0000.0000.0000.000
143B154LYS10.9570.97516.4840.3980.3980.0000.0000.0000.000
144B155PHE0-0.022-0.0029.091-0.118-0.1180.0000.0000.0000.000
145B156LYS10.9810.97813.2340.2160.2160.0000.0000.0000.000
146B157ASP-1-0.916-0.95015.550-0.537-0.5370.0000.0000.0000.000
147B158ALA0-0.068-0.03911.798-0.050-0.0500.0000.0000.0000.000
148B159GLU-1-0.896-0.96111.057-0.842-0.8420.0000.0000.0000.000
149B160ALA0-0.0180.00912.016-0.007-0.0070.0000.0000.0000.000
150B161ALA0-0.008-0.00515.3660.0240.0240.0000.0000.0000.000
151B162TYR00.013-0.0067.695-0.197-0.1970.0000.0000.0000.000
152B163SER00.010-0.00412.499-0.024-0.0240.0000.0000.0000.000
153B164SER00.0060.01813.2790.1040.1040.0000.0000.0000.000
154B165VAL00.004-0.00514.0100.0430.0430.0000.0000.0000.000
155B166CYS0-0.070-0.02011.590-0.103-0.1030.0000.0000.0000.000
156B167ALA00.0250.01814.2960.0990.0990.0000.0000.0000.000
157B168ASP-1-0.923-0.96016.787-0.493-0.4930.0000.0000.0000.000
158B169LEU0-0.005-0.00814.6980.0700.0700.0000.0000.0000.000
159B170ILE00.004-0.00813.3880.0440.0440.0000.0000.0000.000
160B171GLN00.0080.02217.5870.1050.1050.0000.0000.0000.000
161B172LYS10.9730.97020.8100.5300.5300.0000.0000.0000.000
162B173MET0-0.056-0.02114.7550.0320.0320.0000.0000.0000.000
163B174GLU-1-0.863-0.91520.412-0.209-0.2090.0000.0000.0000.000
164B175THR0-0.070-0.05022.1470.0490.0490.0000.0000.0000.000
165B176VAL00.0700.04723.3160.0300.0300.0000.0000.0000.000
166B177TRP00.0360.01922.3150.0300.0300.0000.0000.0000.000
167B178LYS10.8420.92224.3510.2580.2580.0000.0000.0000.000
168B179LYS10.8750.95027.4560.2510.2510.0000.0000.0000.000
169B180HIS10.8690.92926.3850.1670.1670.0000.0000.0000.000
170B181VAL00.0110.01829.2290.0150.0150.0000.0000.0000.000
171B182SER00.0030.00331.5600.0130.0130.0000.0000.0000.000
172B183ILE00.0570.01831.3470.0080.0080.0000.0000.0000.000
173B184PHE0-0.024-0.01728.6200.0060.0060.0000.0000.0000.000
174B185ALA00.0120.01434.0440.0090.0090.0000.0000.0000.000
175B186GLU-1-0.866-0.92437.110-0.099-0.0990.0000.0000.0000.000
176B187ALA00.0250.00136.4040.0060.0060.0000.0000.0000.000
177B188ALA0-0.0080.00638.0970.0060.0060.0000.0000.0000.000
178B189SER0-0.004-0.02139.9210.0060.0060.0000.0000.0000.000
179B190ALA0-0.019-0.01641.5300.0040.0040.0000.0000.0000.000
180B191VAL00.0150.00340.4800.0030.0030.0000.0000.0000.000
181B192TRP00.0390.02243.0880.0030.0030.0000.0000.0000.000
182B193SER0-0.035-0.00145.9490.0040.0040.0000.0000.0000.000
183B194THR00.0240.01346.3810.0020.0020.0000.0000.0000.000
184B195GLN0-0.016-0.01646.2080.0050.0050.0000.0000.0000.000
185B196LEU00.000-0.00749.0160.0030.0030.0000.0000.0000.000
186B197GLN0-0.067-0.03850.0800.0030.0030.0000.0000.0000.000
187B198TYR00.0140.00649.1770.0000.0000.0000.0000.0000.000
188B199ALA00.0190.01353.4990.0020.0020.0000.0000.0000.000
189B200LYS10.9560.97354.5330.0390.0390.0000.0000.0000.000
190B201ALA0-0.0040.00356.7500.0010.0010.0000.0000.0000.000
191B202LEU0-0.010-0.01257.7390.0010.0010.0000.0000.0000.000
192B203GLU-1-0.933-0.96759.403-0.021-0.0210.0000.0000.0000.000
193B204ALA0-0.057-0.02661.3590.0010.0010.0000.0000.0000.000
194B205ALA0-0.048-0.03762.5360.0000.0000.0000.0000.0000.000
195B206ALA00.0410.03364.1600.0010.0010.0000.0000.0000.000
196B207ASN0-0.023-0.01665.8840.0020.0020.0000.0000.0000.000
197B208PRO0-0.040-0.01868.4410.0010.0010.0000.0000.0000.000
198B209ILE00.0000.00867.7540.0010.0010.0000.0000.0000.000
199B210VAL00.0080.01167.7640.0010.0010.0000.0000.0000.000
200B211PRO0-0.016-0.00470.3450.0010.0010.0000.0000.0000.000
201B212TYR0-0.058-0.04273.1930.0010.0010.0000.0000.0000.000
202B213LEU0-0.0010.01667.5550.0010.0010.0000.0000.0000.000
203B214GLN00.0300.01971.6060.0000.0000.0000.0000.0000.000
204B215GLN0-0.129-0.05673.3240.0010.0010.0000.0000.0000.000
205B216GLU-1-0.833-0.91371.804-0.008-0.0080.0000.0000.0000.000
206B217GLU-1-0.965-0.99668.769-0.009-0.0090.0000.0000.0000.000
207B218GLN0-0.127-0.06771.1970.0010.0010.0000.0000.0000.000
208B219GLU-1-0.982-0.96874.251-0.003-0.0030.0000.0000.0000.000
209B220GLU-1-0.978-0.98572.0530.0030.0030.0000.0000.0000.000
210B221GLU-1-1.041-1.02174.9190.0000.0000.0000.0000.0000.000