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: NNL7Q

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 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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2066367.555176
FMO2-HF: Nuclear repulsion 1979963.330489
FMO2-HF: Total energy -86404.224687
FMO2-MP2: Total energy -86658.02368


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.
-3.207-0.795-0.012-1.15-1.250.002
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 : -0.032 / 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].
3B14ASN00.004-0.0043.806-0.5830.953-0.021-0.733-0.7820.004
4B15MET00.0770.0246.8800.4870.4870.0000.0000.0000.000
5B16GLU-1-0.869-0.9448.305-0.072-0.0720.0000.0000.0000.000
6B17VAL0-0.017-0.00310.3110.0470.0470.0000.0000.0000.000
7B18GLU-1-0.911-0.9766.6290.5550.5550.0000.0000.0000.000
8B19HIS0-0.0060.02311.0690.1020.1020.0000.0000.0000.000
9B20TRP00.0300.01313.7060.0590.0590.0000.0000.0000.000
10B21MET00.0170.01513.8200.0410.0410.0000.0000.0000.000
11B22THR0-0.032-0.03313.4970.0470.0470.0000.0000.0000.000
12B23SER00.0270.00816.1070.0010.0010.0000.0000.0000.000
13B24LEU0-0.043-0.01918.862-0.002-0.0020.0000.0000.0000.000
14B25LYS10.9520.96814.386-0.224-0.2240.0000.0000.0000.000
15B26GLU-1-0.958-0.97519.6310.1950.1950.0000.0000.0000.000
16B27VAL0-0.036-0.02421.991-0.005-0.0050.0000.0000.0000.000
17B28GLU-1-0.799-0.87722.6900.0590.0590.0000.0000.0000.000
18B29LYS10.9781.00323.360-0.182-0.1820.0000.0000.0000.000
19B30VAL0-0.039-0.01725.663-0.002-0.0020.0000.0000.0000.000
20B31LEU00.000-0.00227.724-0.004-0.0040.0000.0000.0000.000
21B32ASP-1-0.830-0.92127.2780.0580.0580.0000.0000.0000.000
22B33SER0-0.065-0.01429.9140.0000.0000.0000.0000.0000.000
23B34VAL0-0.014-0.03031.641-0.002-0.0020.0000.0000.0000.000
24B35GLU-1-0.746-0.82733.4200.0240.0240.0000.0000.0000.000
25B36PRO00.0270.00834.052-0.004-0.0040.0000.0000.0000.000
26B37LYS10.8500.91833.906-0.077-0.0770.0000.0000.0000.000
27B38LEU00.0140.00336.667-0.003-0.0030.0000.0000.0000.000
28B39THR0-0.0110.00239.002-0.004-0.0040.0000.0000.0000.000
29B40SER0-0.0340.00041.556-0.001-0.0010.0000.0000.0000.000
30B41SER0-0.006-0.02143.1780.0000.0000.0000.0000.0000.000
31B42GLY00.0930.04644.7690.0000.0000.0000.0000.0000.000
32B43THR0-0.040-0.03546.5960.0000.0000.0000.0000.0000.000
33B44LYS10.8600.92443.815-0.043-0.0430.0000.0000.0000.000
34B45TRP00.0830.02648.8410.0000.0000.0000.0000.0000.000
35B46ARG10.9671.01751.647-0.028-0.0280.0000.0000.0000.000
36B47VAL0-0.057-0.03750.979-0.001-0.0010.0000.0000.0000.000
37B48VAL00.0340.02753.0950.0000.0000.0000.0000.0000.000
38B49ALA00.0390.01955.679-0.001-0.0010.0000.0000.0000.000
39B50GLN0-0.068-0.04557.071-0.002-0.0020.0000.0000.0000.000
40B51HIS00.0200.01557.4640.0000.0000.0000.0000.0000.000
41B52ILE00.007-0.00259.3620.0000.0000.0000.0000.0000.000
42B53LYS10.8020.88460.149-0.020-0.0200.0000.0000.0000.000
43B54ASP-1-0.854-0.91061.1410.0230.0230.0000.0000.0000.000
44B55ILE00.0170.01362.2890.0000.0000.0000.0000.0000.000
45B56CYS0-0.0100.00065.595-0.001-0.0010.0000.0000.0000.000
46B57SER0-0.027-0.02067.323-0.001-0.0010.0000.0000.0000.000
47B58ASP-1-0.912-0.95567.8160.0220.0220.0000.0000.0000.000
48B59LEU0-0.067-0.03469.7530.0000.0000.0000.0000.0000.000
49B60ASN0-0.033-0.02771.693-0.001-0.0010.0000.0000.0000.000
50B61GLN00.0020.02470.587-0.001-0.0010.0000.0000.0000.000
51B62ILE0-0.041-0.02574.773-0.001-0.0010.0000.0000.0000.000
52B63PHE0-0.035-0.00376.8170.0000.0000.0000.0000.0000.000
53B64ASN00.0440.00179.004-0.001-0.0010.0000.0000.0000.000
54B65LYS10.8850.93481.562-0.014-0.0140.0000.0000.0000.000
55B66GLU-1-0.869-0.93482.2280.0120.0120.0000.0000.0000.000
56B67ASP-1-0.863-0.91682.5800.0140.0140.0000.0000.0000.000
57B68PRO00.0420.01782.6260.0000.0000.0000.0000.0000.000
58B69ARG10.9080.94379.362-0.015-0.0150.0000.0000.0000.000
59B70TYR0-0.091-0.04276.6630.0000.0000.0000.0000.0000.000
60B71GLU-1-0.862-0.92377.4300.0130.0130.0000.0000.0000.000
61B72VAL00.0050.01373.7030.0000.0000.0000.0000.0000.000
62B73VAL00.0050.00472.6210.0000.0000.0000.0000.0000.000
63B74GLN0-0.0180.00772.3800.0000.0000.0000.0000.0000.000
64B75ALA00.015-0.00472.6620.0000.0000.0000.0000.0000.000
65B76GLY00.0470.01869.7420.0000.0000.0000.0000.0000.000
66B77ALA0-0.007-0.02168.2410.0000.0000.0000.0000.0000.000
67B78SER0-0.022-0.00868.1820.0000.0000.0000.0000.0000.000
68B79ALA00.0150.00366.9760.0000.0000.0000.0000.0000.000
69B80ALA00.0010.00364.1810.0010.0010.0000.0000.0000.000
70B81HIS0-0.032-0.01863.3660.0010.0010.0000.0000.0000.000
71B82ASP-1-0.848-0.91663.7380.0130.0130.0000.0000.0000.000
72B83PHE0-0.0010.00156.2010.0000.0000.0000.0000.0000.000
73B84ASP-1-0.849-0.93159.2380.0190.0190.0000.0000.0000.000
74B85VAL0-0.008-0.00258.9720.0000.0000.0000.0000.0000.000
75B86ARG10.8520.91659.278-0.014-0.0140.0000.0000.0000.000
76B87TYR0-0.021-0.01151.3480.0000.0000.0000.0000.0000.000
77B88LEU0-0.003-0.01654.7890.0000.0000.0000.0000.0000.000
78B89ASP-1-0.870-0.91155.1330.0080.0080.0000.0000.0000.000
79B90ILE0-0.044-0.01253.144-0.001-0.0010.0000.0000.0000.000
80B91HIS0-0.043-0.01948.5160.0020.0020.0000.0000.0000.000
81B92LYS10.8940.94050.417-0.011-0.0110.0000.0000.0000.000
82B93HIS0-0.069-0.04252.214-0.002-0.0020.0000.0000.0000.000
83B94GLY00.0150.03150.078-0.001-0.0010.0000.0000.0000.000
84B95ARG10.9340.95847.4640.0010.0010.0000.0000.0000.000
85B96GLU-1-0.845-0.93344.8800.0080.0080.0000.0000.0000.000
86B97ILE00.0510.03341.5950.0000.0000.0000.0000.0000.000
87B98ALA00.0550.03541.5240.0000.0000.0000.0000.0000.000
88B99ARG10.8600.91841.576-0.003-0.0030.0000.0000.0000.000
89B100LEU00.0230.02636.748-0.002-0.0020.0000.0000.0000.000
90B101LEU00.016-0.00437.0710.0000.0000.0000.0000.0000.000
91B102GLU-1-0.807-0.88536.343-0.011-0.0110.0000.0000.0000.000
92B103LYS10.7500.85435.7150.0010.0010.0000.0000.0000.000
93B104ILE0-0.013-0.00531.828-0.003-0.0030.0000.0000.0000.000
94B105GLN0-0.029-0.02431.630-0.005-0.0050.0000.0000.0000.000
95B106LYS10.8330.90331.6870.0150.0150.0000.0000.0000.000
96B107TYR0-0.026-0.03626.2890.0010.0010.0000.0000.0000.000
97B108ARG10.8230.88326.960-0.034-0.0340.0000.0000.0000.000
98B109GLN0-0.038-0.01226.4530.0020.0020.0000.0000.0000.000
99B110GLU-1-0.765-0.86226.722-0.058-0.0580.0000.0000.0000.000
100B111ILE00.000-0.01121.618-0.014-0.0140.0000.0000.0000.000
101B112GLU-1-0.847-0.91721.8420.0120.0120.0000.0000.0000.000
102B113GLU-1-0.950-0.97622.191-0.085-0.0850.0000.0000.0000.000
103B114ILE00.0440.01818.911-0.023-0.0230.0000.0000.0000.000
104B115LYS10.7810.85917.808-0.070-0.0700.0000.0000.0000.000
105B116LYS10.7900.88617.2780.0320.0320.0000.0000.0000.000
106B117GLU-1-0.786-0.87018.195-0.253-0.2530.0000.0000.0000.000
107B118TYR00.0070.0109.693-0.029-0.0290.0000.0000.0000.000
108B119LYS10.9310.94913.264-0.052-0.0520.0000.0000.0000.000
109B120GLU-1-0.807-0.87313.588-0.354-0.3540.0000.0000.0000.000
110B121THR00.001-0.00310.557-0.082-0.0820.0000.0000.0000.000
111B122ASP-1-0.828-0.9067.527-0.811-0.8110.0000.0000.0000.000
112B123LYS10.8200.8989.4040.1640.1640.0000.0000.0000.000
113B124TYR0-0.030-0.02411.587-0.077-0.0770.0000.0000.0000.000
114B125ARG10.7670.8583.4713.0123.2490.001-0.058-0.1800.000
115B126GLU-1-0.821-0.9056.883-1.642-1.6420.0000.0000.0000.000
116B127ARG10.8180.9188.9301.0101.0100.0000.0000.0000.000
117B128TYR00.0400.0174.8110.3130.3130.0000.0000.0000.000
118B129ASP-1-0.771-0.8753.509-8.523-7.8840.008-0.359-0.288-0.002
119B130HIS0-0.0320.0036.8190.5620.5620.0000.0000.0000.000
120B131TYR0-0.010-0.03910.3370.1770.1770.0000.0000.0000.000
121B132LYS10.9811.0105.5292.0622.0620.0000.0000.0000.000
122B133VAL00.0450.0328.7030.2550.2550.0000.0000.0000.000
123B134LYS10.8520.91411.2610.8280.8280.0000.0000.0000.000
124B135LEU00.0340.01413.3960.1040.1040.0000.0000.0000.000
125B136ASP-1-0.825-0.87512.301-0.437-0.4370.0000.0000.0000.000
126B137ASN0-0.064-0.06214.2350.2070.2070.0000.0000.0000.000
127B138LEU0-0.095-0.06016.8640.0680.0680.0000.0000.0000.000
128B139GLU-1-0.842-0.90517.472-0.367-0.3670.0000.0000.0000.000
129B140LYS10.8340.93015.3230.4050.4050.0000.0000.0000.000
130B141LYS10.8380.93018.6340.3640.3640.0000.0000.0000.000
131B142ASN00.020-0.00322.844-0.020-0.0200.0000.0000.0000.000
132B143LYS10.9320.96624.5860.1970.1970.0000.0000.0000.000
133B144ASP-1-0.846-0.93025.461-0.232-0.2320.0000.0000.0000.000
134B145GLN00.0610.01824.742-0.032-0.0320.0000.0000.0000.000
135B146GLU-1-0.789-0.89625.141-0.211-0.2110.0000.0000.0000.000
136B147ARG10.8250.92521.9060.2970.2970.0000.0000.0000.000
137B148ILE0-0.039-0.02720.368-0.047-0.0470.0000.0000.0000.000
138B149GLU-1-0.865-0.92120.273-0.293-0.2930.0000.0000.0000.000
139B150ARG10.9160.96021.7940.2510.2510.0000.0000.0000.000
140B151ASN0-0.121-0.08216.968-0.075-0.0750.0000.0000.0000.000
141B152GLN00.0480.03316.598-0.073-0.0730.0000.0000.0000.000
142B153GLN0-0.0210.00117.403-0.011-0.0110.0000.0000.0000.000
143B154LYS10.8800.92916.5900.4430.4430.0000.0000.0000.000
144B155PHE0-0.036-0.0148.868-0.081-0.0810.0000.0000.0000.000
145B156LYS10.9120.93613.0980.4790.4790.0000.0000.0000.000
146B157ASP-1-0.842-0.91115.411-0.510-0.5100.0000.0000.0000.000
147B158ALA0-0.054-0.02911.748-0.001-0.0010.0000.0000.0000.000
148B159GLU-1-0.828-0.91710.740-1.025-1.0250.0000.0000.0000.000
149B160ALA0-0.0080.01211.8420.0300.0300.0000.0000.0000.000
150B161ALA0-0.003-0.00215.1670.0500.0500.0000.0000.0000.000
151B162TYR00.014-0.0047.465-0.157-0.1570.0000.0000.0000.000
152B163SER00.0340.00712.3900.0360.0360.0000.0000.0000.000
153B164SER0-0.0290.00313.1190.1020.1020.0000.0000.0000.000
154B165VAL00.0170.00014.0310.0480.0480.0000.0000.0000.000
155B166CYS0-0.077-0.01711.619-0.018-0.0180.0000.0000.0000.000
156B167ALA00.0240.01214.2810.0920.0920.0000.0000.0000.000
157B168ASP-1-0.893-0.94516.762-0.293-0.2930.0000.0000.0000.000
158B169LEU0-0.018-0.00814.7970.0580.0580.0000.0000.0000.000
159B170ILE00.006-0.01013.2890.0480.0480.0000.0000.0000.000
160B171GLN00.0220.02317.6110.0710.0710.0000.0000.0000.000
161B172LYS10.8290.90120.8510.2470.2470.0000.0000.0000.000
162B173MET0-0.064-0.04014.6570.0410.0410.0000.0000.0000.000
163B174GLU-1-0.851-0.90020.420-0.060-0.0600.0000.0000.0000.000
164B175THR0-0.021-0.02922.1780.0240.0240.0000.0000.0000.000
165B176VAL00.0200.02623.2770.0140.0140.0000.0000.0000.000
166B177TRP00.0580.04322.3450.0190.0190.0000.0000.0000.000
167B178LYS10.8450.91424.3810.0820.0820.0000.0000.0000.000
168B179LYS10.8160.90027.4860.0570.0570.0000.0000.0000.000
169B180HIS10.8490.92626.376-0.027-0.0270.0000.0000.0000.000
170B181VAL00.0150.02129.2280.0060.0060.0000.0000.0000.000
171B182SER00.0450.02031.5880.0020.0020.0000.0000.0000.000
172B183ILE00.0040.00131.4500.0020.0020.0000.0000.0000.000
173B184PHE0-0.015-0.01728.4510.0040.0040.0000.0000.0000.000
174B185ALA00.0190.01734.0720.0030.0030.0000.0000.0000.000
175B186GLU-1-0.813-0.88237.1370.0020.0020.0000.0000.0000.000
176B187ALA00.0230.00736.4310.0010.0010.0000.0000.0000.000
177B188ALA00.0020.00938.1150.0010.0010.0000.0000.0000.000
178B189SER00.002-0.01239.9470.0000.0000.0000.0000.0000.000
179B190ALA0-0.014-0.01141.4990.0000.0000.0000.0000.0000.000
180B191VAL00.0150.01240.4350.0000.0000.0000.0000.0000.000
181B192TRP00.0370.02342.957-0.001-0.0010.0000.0000.0000.000
182B193SER0-0.0170.00745.974-0.001-0.0010.0000.0000.0000.000
183B194THR00.003-0.01346.046-0.001-0.0010.0000.0000.0000.000
184B195GLN0-0.021-0.01446.1480.0010.0010.0000.0000.0000.000
185B196LEU0-0.006-0.00849.0410.0000.0000.0000.0000.0000.000
186B197GLN0-0.078-0.04450.089-0.001-0.0010.0000.0000.0000.000
187B198TYR00.0110.00648.9800.0000.0000.0000.0000.0000.000
188B199ALA00.0180.01253.5240.0000.0000.0000.0000.0000.000
189B200LYS10.9780.98454.400-0.016-0.0160.0000.0000.0000.000
190B201ALA0-0.019-0.00356.796-0.001-0.0010.0000.0000.0000.000
191B202LEU0-0.009-0.00957.5860.0000.0000.0000.0000.0000.000
192B203GLU-1-0.919-0.96259.3560.0200.0200.0000.0000.0000.000
193B204ALA0-0.059-0.02961.381-0.001-0.0010.0000.0000.0000.000
194B205ALA0-0.015-0.00862.559-0.001-0.0010.0000.0000.0000.000
195B206ALA00.0380.02764.1870.0000.0000.0000.0000.0000.000
196B207ASN0-0.077-0.04365.9070.0000.0000.0000.0000.0000.000
197B208PRO0-0.023-0.01168.5560.0000.0000.0000.0000.0000.000
198B209ILE00.0150.00267.4940.0000.0000.0000.0000.0000.000
199B210VAL0-0.0020.01167.8070.0000.0000.0000.0000.0000.000
200B211PRO0-0.007-0.00570.3680.0000.0000.0000.0000.0000.000
201B212TYR0-0.070-0.05073.3530.0000.0000.0000.0000.0000.000
202B213LEU0-0.0030.01267.5010.0000.0000.0000.0000.0000.000
203B214GLN00.0210.01371.6270.0000.0000.0000.0000.0000.000
204B215GLN0-0.105-0.04673.3450.0000.0000.0000.0000.0000.000
205B216GLU-1-0.856-0.92571.8700.0190.0190.0000.0000.0000.000
206B217GLU-1-0.977-0.99768.8340.0210.0210.0000.0000.0000.000
207B218GLN0-0.133-0.07671.2160.0000.0000.0000.0000.0000.000
208B219GLU-1-0.984-0.96574.2700.0200.0200.0000.0000.0000.000
209B220GLU-1-0.965-0.99171.8600.0260.0260.0000.0000.0000.000
210B221GLU-1-1.040-1.01174.9360.0210.0210.0000.0000.0000.000