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: 94VN2

Calculation Name: 1CAX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CAX

Chain ID: B

ChEMBL ID:

UniProt ID: P50477

Base Structure: X-ray

Registration Date: 2023-09-19

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 184
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1838272.989997
FMO2-HF: Nuclear repulsion 1766096.342181
FMO2-HF: Total energy -72176.647816
FMO2-MP2: Total energy -72388.201213


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:241:THR)


Summations of interaction energy for fragment #1(B:241:THR)
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.
0.5041.842-0.014-0.655-0.6690.001
Interaction energy analysis for fragmet #1(B:241:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.014
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].
3B243SER00.0220.0203.8722.1733.511-0.014-0.655-0.6690.001
4B244SER0-0.015-0.0177.1010.2360.2360.0000.0000.0000.000
5B245GLN0-0.025-0.0234.826-0.875-0.8750.0000.0000.0000.000
6B246ASP-1-0.887-0.9256.546-0.233-0.2330.0000.0000.0000.000
7B247LYS10.8740.9238.5420.4820.4820.0000.0000.0000.000
8B248PRO00.0630.0359.8110.0320.0320.0000.0000.0000.000
9B249PHE0-0.0170.0086.275-0.172-0.1720.0000.0000.0000.000
10B250ASN0-0.0040.0015.322-0.430-0.4300.0000.0000.0000.000
11B251LEU00.0440.0248.2330.0860.0860.0000.0000.0000.000
12B252ARG10.9350.9457.167-0.960-0.9600.0000.0000.0000.000
13B253SER00.0510.02712.142-0.055-0.0550.0000.0000.0000.000
14B254ARG10.7400.83013.134-0.301-0.3010.0000.0000.0000.000
15B255ASP-1-0.767-0.84216.4080.2590.2590.0000.0000.0000.000
16B256PRO0-0.0380.00020.071-0.015-0.0150.0000.0000.0000.000
17B257ILE0-0.011-0.00922.913-0.001-0.0010.0000.0000.0000.000
18B258TYR00.0250.02225.642-0.011-0.0110.0000.0000.0000.000
19B259SER00.018-0.00926.1960.0130.0130.0000.0000.0000.000
20B260ASN0-0.039-0.01428.2770.0020.0020.0000.0000.0000.000
21B261ASN0-0.020-0.01329.8030.0080.0080.0000.0000.0000.000
22B262TYR0-0.024-0.02232.0910.0000.0000.0000.0000.0000.000
23B263GLY00.0460.01228.811-0.002-0.0020.0000.0000.0000.000
24B264LYS10.8810.93723.486-0.166-0.1660.0000.0000.0000.000
25B265LEU00.0330.02324.409-0.007-0.0070.0000.0000.0000.000
26B266TYR0-0.018-0.00619.4120.0180.0180.0000.0000.0000.000
27B267GLU-1-0.724-0.83721.0780.0320.0320.0000.0000.0000.000
28B268ILE0-0.088-0.02816.1710.0170.0170.0000.0000.0000.000
29B269THR00.057-0.00119.532-0.015-0.0150.0000.0000.0000.000
30B270PRO00.0560.03521.1110.0030.0030.0000.0000.0000.000
31B271GLU-1-0.812-0.90022.2930.0010.0010.0000.0000.0000.000
32B272LYS10.8120.91619.613-0.075-0.0750.0000.0000.0000.000
33B273ASN0-0.011-0.02313.946-0.002-0.0020.0000.0000.0000.000
34B274SER00.0400.02915.203-0.002-0.0020.0000.0000.0000.000
35B275GLN00.0260.00411.4200.0760.0760.0000.0000.0000.000
36B276LEU0-0.007-0.00315.935-0.002-0.0020.0000.0000.0000.000
37B277ARG10.8400.90518.9420.0530.0530.0000.0000.0000.000
38B278ASP-1-0.972-0.98019.471-0.160-0.1600.0000.0000.0000.000
39B279LEU0-0.075-0.04519.044-0.011-0.0110.0000.0000.0000.000
40B280ASP-1-0.844-0.92322.734-0.031-0.0310.0000.0000.0000.000
41B281ILE0-0.028-0.01820.7180.0080.0080.0000.0000.0000.000
42B282LEU0-0.058-0.01421.4650.0010.0010.0000.0000.0000.000
43B283LEU0-0.016-0.00416.337-0.009-0.0090.0000.0000.0000.000
44B284ASN0-0.074-0.06020.2100.0070.0070.0000.0000.0000.000
45B285CYM-1-0.776-0.81818.8410.1540.1540.0000.0000.0000.000
46B286LEU00.0060.00120.9700.0070.0070.0000.0000.0000.000
47B287GLN0-0.087-0.08619.5120.0110.0110.0000.0000.0000.000
48B288MET0-0.064-0.02824.961-0.003-0.0030.0000.0000.0000.000
49B289ASN00.0120.01628.6800.0070.0070.0000.0000.0000.000
50B290GLU-1-0.891-0.95330.8830.0640.0640.0000.0000.0000.000
51B291GLY0-0.033-0.01333.7940.0000.0000.0000.0000.0000.000
52B292ALA0-0.024-0.00132.825-0.004-0.0040.0000.0000.0000.000
53B293LEU0-0.031-0.02234.949-0.005-0.0050.0000.0000.0000.000
54B294PHE00.000-0.00429.6190.0030.0030.0000.0000.0000.000
55B295VAL00.0200.00233.811-0.006-0.0060.0000.0000.0000.000
56B296PRO0-0.0030.00135.966-0.001-0.0010.0000.0000.0000.000
57B297HIS10.8320.93132.310-0.042-0.0420.0000.0000.0000.000
58B298TYR00.0240.02635.688-0.002-0.0020.0000.0000.0000.000
59B299ASN00.0130.00430.8080.0090.0090.0000.0000.0000.000
60B300SER0-0.038-0.02333.602-0.005-0.0050.0000.0000.0000.000
61B301ARG10.8720.92531.9710.0070.0070.0000.0000.0000.000
62B302ALA00.0050.02728.261-0.005-0.0050.0000.0000.0000.000
63B303THR0-0.002-0.00530.3170.0050.0050.0000.0000.0000.000
64B304VAL0-0.029-0.02226.440-0.006-0.0060.0000.0000.0000.000
65B305ILE0-0.0050.01025.8960.0030.0030.0000.0000.0000.000
66B306LEU0-0.002-0.01125.8680.0040.0040.0000.0000.0000.000
67B307VAL00.0220.00523.485-0.007-0.0070.0000.0000.0000.000
68B308ALA00.0060.01124.8110.0120.0120.0000.0000.0000.000
69B309ASN0-0.089-0.06019.806-0.015-0.0150.0000.0000.0000.000
70B310GLU-1-0.838-0.91523.2120.1110.1110.0000.0000.0000.000
71B311GLY00.0410.02825.325-0.001-0.0010.0000.0000.0000.000
72B312ARG10.8690.93229.092-0.045-0.0450.0000.0000.0000.000
73B313ALA0-0.003-0.00131.0580.0050.0050.0000.0000.0000.000
74B314GLU-1-0.847-0.91733.0700.0370.0370.0000.0000.0000.000
75B315VAL0-0.0090.00333.1000.0020.0020.0000.0000.0000.000
76B316GLU-1-0.849-0.92235.9230.0210.0210.0000.0000.0000.000
77B317LEU00.009-0.00435.6310.0020.0020.0000.0000.0000.000
78B318VAL0-0.026-0.02238.981-0.002-0.0020.0000.0000.0000.000
79B319GLY00.0650.03341.2610.0000.0000.0000.0000.0000.000
80B320LEU0-0.017-0.00143.2350.0000.0000.0000.0000.0000.000
81B321GLU-1-0.856-0.90341.766-0.007-0.0070.0000.0000.0000.000
82B322GLN00.0480.01844.7490.0000.0000.0000.0000.0000.000
83B323GLN00.0500.03346.3810.0010.0010.0000.0000.0000.000
84B324GLN00.032-0.00145.7520.0020.0020.0000.0000.0000.000
85B325GLN0-0.131-0.04350.0800.0010.0010.0000.0000.0000.000
86B326GLN0-0.007-0.01851.0690.0000.0000.0000.0000.0000.000
87B327GLY0-0.007-0.01353.8630.0000.0000.0000.0000.0000.000
88B328LEU00.001-0.00353.3890.0010.0010.0000.0000.0000.000
89B329GLU-1-0.880-0.91254.6750.0000.0000.0000.0000.0000.000
90B330SER0-0.038-0.03756.1710.0000.0000.0000.0000.0000.000
91B331MET0-0.102-0.03547.251-0.001-0.0010.0000.0000.0000.000
92B332GLN00.0150.01246.8290.0010.0010.0000.0000.0000.000
93B333LEU00.0440.01546.6320.0000.0000.0000.0000.0000.000
94B334ARG10.8770.95545.0090.0010.0010.0000.0000.0000.000
95B335ARG10.8660.93143.014-0.019-0.0190.0000.0000.0000.000
96B336TYR0-0.121-0.10540.086-0.002-0.0020.0000.0000.0000.000
97B337ALA00.0260.00039.4810.0030.0030.0000.0000.0000.000
98B338ALA0-0.0100.00136.060-0.003-0.0030.0000.0000.0000.000
99B339THR0-0.036-0.00336.3170.0020.0020.0000.0000.0000.000
100B340LEU0-0.013-0.00330.4170.0000.0000.0000.0000.0000.000
101B341SER0-0.019-0.03331.1080.0080.0080.0000.0000.0000.000
102B342GLU-1-0.891-0.95325.0860.0500.0500.0000.0000.0000.000
103B343GLY0-0.041-0.01026.213-0.007-0.0070.0000.0000.0000.000
104B344ASP-1-0.871-0.91527.1900.0010.0010.0000.0000.0000.000
105B345ILE0-0.056-0.04326.3290.0030.0030.0000.0000.0000.000
106B346ILE0-0.037-0.00729.625-0.001-0.0010.0000.0000.0000.000
107B347VAL00.012-0.00830.028-0.002-0.0020.0000.0000.0000.000
108B348ILE0-0.011-0.00230.5670.0020.0020.0000.0000.0000.000
109B349PRO00.0220.00632.704-0.002-0.0020.0000.0000.0000.000
110B350SER0-0.012-0.01233.6020.0030.0030.0000.0000.0000.000
111B351SER00.0240.00434.7550.0030.0030.0000.0000.0000.000
112B352PHE0-0.037-0.00837.3890.0020.0020.0000.0000.0000.000
113B353PRO0-0.032-0.00337.1800.0020.0020.0000.0000.0000.000
114B354VAL00.011-0.00433.704-0.002-0.0020.0000.0000.0000.000
115B355ALA00.001-0.00336.0810.0040.0040.0000.0000.0000.000
116B356LEU0-0.007-0.00430.579-0.004-0.0040.0000.0000.0000.000
117B357LYS10.8530.91134.404-0.041-0.0410.0000.0000.0000.000
118B358ALA00.0310.01531.898-0.003-0.0030.0000.0000.0000.000
119B359ALA0-0.033-0.02333.4140.0010.0010.0000.0000.0000.000
120B360SER0-0.029-0.01930.573-0.005-0.0050.0000.0000.0000.000
121B361ASP-1-0.842-0.91528.2980.1080.1080.0000.0000.0000.000
122B362LEU0-0.039-0.00127.628-0.005-0.0050.0000.0000.0000.000
123B363ASN0-0.040-0.05520.9550.0120.0120.0000.0000.0000.000
124B364MET00.0040.00323.969-0.013-0.0130.0000.0000.0000.000
125B365VAL00.0250.02918.8880.0100.0100.0000.0000.0000.000
126B366GLY0-0.003-0.01021.717-0.011-0.0110.0000.0000.0000.000
127B367ILE0-0.006-0.01220.844-0.003-0.0030.0000.0000.0000.000
128B368GLY00.0080.01123.2140.0010.0010.0000.0000.0000.000
129B369VAL00.0330.00424.805-0.010-0.0100.0000.0000.0000.000
130B370ASN0-0.046-0.02227.2220.0050.0050.0000.0000.0000.000
131B371ALA0-0.0190.00325.2370.0090.0090.0000.0000.0000.000
132B372GLU-1-0.804-0.89127.186-0.016-0.0160.0000.0000.0000.000
133B373ASN0-0.079-0.05228.1830.0000.0000.0000.0000.0000.000
134B374ASN00.0120.02528.5800.0000.0000.0000.0000.0000.000
135B375GLU-1-0.845-0.90229.7140.0310.0310.0000.0000.0000.000
136B376ARG10.7730.83326.948-0.052-0.0520.0000.0000.0000.000
137B377ASN0-0.0390.00133.2950.0060.0060.0000.0000.0000.000
138B378PHE0-0.011-0.01532.283-0.001-0.0010.0000.0000.0000.000
139B379LEU0-0.003-0.01737.827-0.002-0.0020.0000.0000.0000.000
140B380ALA0-0.0010.00140.160-0.001-0.0010.0000.0000.0000.000
141B381GLY00.0270.01739.1230.0020.0020.0000.0000.0000.000
142B382HIS00.0530.02239.557-0.002-0.0020.0000.0000.0000.000
143B383LYS10.8380.89333.680-0.079-0.0790.0000.0000.0000.000
144B384GLU-1-0.779-0.86833.9760.0680.0680.0000.0000.0000.000
145B385ASN0-0.0190.00237.485-0.006-0.0060.0000.0000.0000.000
146B386VAL00.0430.01540.389-0.001-0.0010.0000.0000.0000.000
147B387ILE00.001-0.00742.042-0.002-0.0020.0000.0000.0000.000
148B388ARG10.7600.84641.822-0.049-0.0490.0000.0000.0000.000
149B389GLN0-0.054-0.02042.8890.0020.0020.0000.0000.0000.000
150B390ILE0-0.0290.00546.197-0.002-0.0020.0000.0000.0000.000
151B391PRO0-0.0060.00149.3820.0010.0010.0000.0000.0000.000
152B392ARG10.8070.85552.324-0.030-0.0300.0000.0000.0000.000
153B393GLN0-0.035-0.01855.279-0.001-0.0010.0000.0000.0000.000
154B394VAL00.0110.00552.945-0.001-0.0010.0000.0000.0000.000
155B395SER00.0320.02452.049-0.001-0.0010.0000.0000.0000.000
156B396ASP-1-0.791-0.89053.8020.0190.0190.0000.0000.0000.000
157B397LEU0-0.068-0.01657.085-0.001-0.0010.0000.0000.0000.000
158B398THR0-0.083-0.04551.310-0.001-0.0010.0000.0000.0000.000
159B399PHE0-0.025-0.02249.1110.0000.0000.0000.0000.0000.000
160B400PRO0-0.050-0.03255.0530.0000.0000.0000.0000.0000.000
161B401GLY0-0.0160.01457.4240.0000.0000.0000.0000.0000.000
162B402SER0-0.030-0.03958.008-0.001-0.0010.0000.0000.0000.000
163B403GLY0-0.010-0.02355.7540.0010.0010.0000.0000.0000.000
164B404GLU-1-0.919-0.95154.7750.0280.0280.0000.0000.0000.000
165B405GLU-1-0.863-0.92755.1930.0250.0250.0000.0000.0000.000
166B406VAL00.0150.00251.4990.0010.0010.0000.0000.0000.000
167B407GLU-1-0.860-0.89850.9070.0340.0340.0000.0000.0000.000
168B408GLU-1-0.905-0.95550.3360.0360.0360.0000.0000.0000.000
169B409LEU00.0010.00349.0700.0020.0020.0000.0000.0000.000
170B410LEU0-0.066-0.02945.8540.0020.0020.0000.0000.0000.000
171B411GLU-1-0.793-0.86245.7530.0480.0480.0000.0000.0000.000
172B412ASN0-0.074-0.03346.5370.0040.0040.0000.0000.0000.000
173B413GLN0-0.108-0.03241.2850.0040.0040.0000.0000.0000.000
174B414LYS10.8940.92541.395-0.059-0.0590.0000.0000.0000.000
175B415GLU-1-0.832-0.90535.9080.0910.0910.0000.0000.0000.000
176B416SER0-0.050-0.02135.126-0.005-0.0050.0000.0000.0000.000
177B417TYR0-0.018-0.04031.7090.0010.0010.0000.0000.0000.000
178B418PHE0-0.010-0.00528.203-0.004-0.0040.0000.0000.0000.000
179B419VAL00.0160.01834.0610.0030.0030.0000.0000.0000.000
180B420ASP-1-0.787-0.87436.7190.0650.0650.0000.0000.0000.000
181B421GLY0-0.0030.00338.581-0.003-0.0030.0000.0000.0000.000
182B422GLN0-0.043-0.03040.1800.0000.0000.0000.0000.0000.000
183B423PRO0-0.003-0.00542.777-0.002-0.0020.0000.0000.0000.000
184B424ARG10.9861.00645.731-0.030-0.0300.0000.0000.0000.000