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: JLJ89

Calculation Name: 2PHC-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PHC

Chain ID: B

ChEMBL ID:

UniProt ID: O58715

Base Structure: X-ray

Registration Date: 2023-09-20

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2381654.167888
FMO2-HF: Nuclear repulsion 2299341.793994
FMO2-HF: Total energy -82312.373894
FMO2-MP2: Total energy -82559.940779


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:2:ILE)


Summations of interaction energy for fragment #1(B:2:ILE)
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.
-12.864-7.3517.868-6.042-7.342-0.036
Interaction energy analysis for fragmet #1(B:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / 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].
3B4LYS10.8440.9233.3690.1702.787-0.005-1.127-1.4850.003
4B5PRO00.0500.0136.1220.0950.0950.0000.0000.0000.000
5B6ALA0-0.039-0.0229.507-0.138-0.1380.0000.0000.0000.000
6B7GLY00.0030.00611.719-0.039-0.0390.0000.0000.0000.000
7B8ASP-1-0.900-0.93415.3100.1570.1570.0000.0000.0000.000
8B9SER0-0.021-0.02717.5460.0100.0100.0000.0000.0000.000
9B10ALA00.0170.01714.0910.0370.0370.0000.0000.0000.000
10B11PHE0-0.035-0.0188.9730.0130.0130.0000.0000.0000.000
11B12LEU00.0270.0156.9630.0090.0090.0000.0000.0000.000
12B13ILE0-0.0100.0073.000-1.476-0.5260.484-0.542-0.8930.006
13B14SER0-0.007-0.0252.508-0.7660.7870.196-0.608-1.1420.000
14B15PHE0-0.011-0.0071.979-9.416-9.3147.193-3.726-3.570-0.045
15B16GLY00.015-0.0024.022-0.406-0.1150.000-0.039-0.2520.000
16B17ASP-1-0.878-0.9136.241-0.693-0.6930.0000.0000.0000.000
17B18GLU-1-0.825-0.8969.279-0.796-0.7960.0000.0000.0000.000
18B19ILE0-0.022-0.01211.1540.0240.0240.0000.0000.0000.000
19B20SER00.0270.01312.0870.0770.0770.0000.0000.0000.000
20B21GLU-1-0.764-0.85313.224-0.131-0.1310.0000.0000.0000.000
21B22GLU-1-0.782-0.86510.893-0.456-0.4560.0000.0000.0000.000
22B23ILE00.0260.0087.9200.0620.0620.0000.0000.0000.000
23B24ASN0-0.016-0.0019.7240.1280.1280.0000.0000.0000.000
24B25ASP-1-0.843-0.93212.3480.1790.1790.0000.0000.0000.000
25B26ARG10.8150.9027.5810.3590.3590.0000.0000.0000.000
26B27VAL0-0.028-0.0057.9140.3020.3020.0000.0000.0000.000
27B28HIS0-0.057-0.0279.5490.1550.1550.0000.0000.0000.000
28B29SER0-0.023-0.01612.0530.0400.0400.0000.0000.0000.000
29B30LEU00.0040.0056.4610.0950.0950.0000.0000.0000.000
30B31ALA00.0090.00510.6470.0460.0460.0000.0000.0000.000
31B32LYS10.8450.89612.847-0.261-0.2610.0000.0000.0000.000
32B33ALA0-0.026-0.00412.561-0.033-0.0330.0000.0000.0000.000
33B34ILE0-0.011-0.02210.232-0.016-0.0160.0000.0000.0000.000
34B35GLU-1-0.796-0.88214.5470.2300.2300.0000.0000.0000.000
35B36LYS10.8410.92817.686-0.440-0.4400.0000.0000.0000.000
36B37GLU-1-0.852-0.90415.9700.5150.5150.0000.0000.0000.000
37B38SER0-0.044-0.02219.042-0.030-0.0300.0000.0000.0000.000
38B39PRO0-0.0180.01216.442-0.029-0.0290.0000.0000.0000.000
39B40GLU-1-0.897-0.97019.7880.2390.2390.0000.0000.0000.000
40B41TRP0-0.014-0.01213.597-0.013-0.0130.0000.0000.0000.000
41B42LEU0-0.032-0.02115.6870.0090.0090.0000.0000.0000.000
42B43VAL0-0.029-0.00518.181-0.040-0.0400.0000.0000.0000.000
43B44GLU-1-0.939-0.97817.3570.1060.1060.0000.0000.0000.000
44B45LEU0-0.020-0.01012.7660.0860.0860.0000.0000.0000.000
45B46VAL00.0200.01213.386-0.053-0.0530.0000.0000.0000.000
46B47PRO0-0.009-0.00111.474-0.008-0.0080.0000.0000.0000.000
47B48ALA00.0080.00210.914-0.044-0.0440.0000.0000.0000.000
48B49TYR0-0.057-0.06511.2660.0500.0500.0000.0000.0000.000
49B50SER00.0010.0108.209-0.086-0.0860.0000.0000.0000.000
50B51SER0-0.010-0.0236.226-0.556-0.5560.0000.0000.0000.000
51B52LEU00.0130.0136.9420.1220.1220.0000.0000.0000.000
52B53LEU00.0000.0148.2310.1980.1980.0000.0000.0000.000
53B54VAL0-0.013-0.0179.9330.0670.0670.0000.0000.0000.000
54B55ILE00.0090.01312.478-0.024-0.0240.0000.0000.0000.000
55B56TYR00.002-0.01115.1360.0420.0420.0000.0000.0000.000
56B57ASP-1-0.753-0.86717.8660.1640.1640.0000.0000.0000.000
57B58PRO0-0.020-0.02720.3200.0180.0180.0000.0000.0000.000
58B59LEU0-0.059-0.01921.696-0.008-0.0080.0000.0000.0000.000
59B60LYS10.7920.90321.991-0.216-0.2160.0000.0000.0000.000
60B61ALA00.003-0.00118.5120.0140.0140.0000.0000.0000.000
61B62SER0-0.047-0.05218.733-0.005-0.0050.0000.0000.0000.000
62B63TYR00.009-0.03410.9720.0170.0170.0000.0000.0000.000
63B64GLU-1-0.902-0.94814.0120.4600.4600.0000.0000.0000.000
64B65GLU-1-0.836-0.87613.8770.4550.4550.0000.0000.0000.000
65B66VAL00.0300.02112.5720.1050.1050.0000.0000.0000.000
66B67GLU-1-0.797-0.8678.5580.9930.9930.0000.0000.0000.000
67B68SER0-0.015-0.0279.0680.3570.3570.0000.0000.0000.000
68B69TYR0-0.065-0.01211.0520.0830.0830.0000.0000.0000.000
69B70LEU00.0650.0328.0820.1210.1210.0000.0000.0000.000
70B71LYS10.8860.9405.835-0.581-0.5810.0000.0000.0000.000
71B72ARG10.8990.9307.431-0.744-0.7440.0000.0000.0000.000
72B73ILE0-0.048-0.0019.913-0.155-0.1550.0000.0000.0000.000
73B74SER00.0420.0015.3060.2000.2000.0000.0000.0000.000
74B75ALA0-0.025-0.0097.452-0.330-0.3300.0000.0000.0000.000
75B76ARG10.8160.8838.673-1.021-1.0210.0000.0000.0000.000
76B77GLU-1-0.733-0.8369.0770.4030.4030.0000.0000.0000.000
77B78VAL0-0.023-0.0116.256-0.233-0.2330.0000.0000.0000.000
78B79GLU-1-0.892-0.9339.5960.2070.2070.0000.0000.0000.000
79B80ARG10.7830.86012.872-0.458-0.4580.0000.0000.0000.000
80B81ILE0-0.016-0.00910.308-0.078-0.0780.0000.0000.0000.000
81B82LYS10.8860.94612.508-0.330-0.3300.0000.0000.0000.000
82B83GLY0-0.023-0.01114.270-0.038-0.0380.0000.0000.0000.000
83B84LYS10.8290.91417.163-0.099-0.0990.0000.0000.0000.000
84B85THR0-0.031-0.02115.038-0.039-0.0390.0000.0000.0000.000
85B86ILE0-0.032-0.00817.6050.0050.0050.0000.0000.0000.000
86B87GLU-1-0.900-0.96316.442-0.156-0.1560.0000.0000.0000.000
87B88ILE0-0.077-0.04019.8770.0180.0180.0000.0000.0000.000
88B89PRO00.0160.01822.610-0.016-0.0160.0000.0000.0000.000
89B90VAL0-0.006-0.02524.1410.0110.0110.0000.0000.0000.000
90B91ALA00.0260.02925.699-0.010-0.0100.0000.0000.0000.000
91B92TYR0-0.005-0.05022.8660.0040.0040.0000.0000.0000.000
92B93GLY00.0240.00828.1500.0010.0010.0000.0000.0000.000
93B94GLY00.0140.01031.1730.0060.0060.0000.0000.0000.000
94B95GLU-1-0.930-0.97534.709-0.064-0.0640.0000.0000.0000.000
95B96PHE0-0.052-0.02732.1870.0050.0050.0000.0000.0000.000
96B97GLY0-0.036-0.01831.918-0.001-0.0010.0000.0000.0000.000
97B98PRO00.0080.01032.920-0.005-0.0050.0000.0000.0000.000
98B99ASP-1-0.779-0.84233.897-0.078-0.0780.0000.0000.0000.000
99B100ILE00.0050.01127.092-0.004-0.0040.0000.0000.0000.000
100B101GLU-1-0.846-0.92630.834-0.118-0.1180.0000.0000.0000.000
101B102PHE0-0.027-0.01233.254-0.001-0.0010.0000.0000.0000.000
102B103VAL0-0.027-0.02428.104-0.001-0.0010.0000.0000.0000.000
103B104ALA00.0270.02228.711-0.008-0.0080.0000.0000.0000.000
104B105GLN0-0.011-0.00729.741-0.003-0.0030.0000.0000.0000.000
105B106TYR0-0.076-0.05431.0430.0060.0060.0000.0000.0000.000
106B107ASN0-0.059-0.04327.182-0.003-0.0030.0000.0000.0000.000
107B108GLY0-0.0440.00228.179-0.011-0.0110.0000.0000.0000.000
108B109LEU0-0.064-0.02324.431-0.012-0.0120.0000.0000.0000.000
109B110SER0-0.032-0.04725.8080.0180.0180.0000.0000.0000.000
110B111VAL00.037-0.01527.078-0.005-0.0050.0000.0000.0000.000
111B112ASP-1-0.889-0.94824.129-0.184-0.1840.0000.0000.0000.000
112B113ASP-1-0.822-0.87322.209-0.264-0.2640.0000.0000.0000.000
113B114VAL0-0.017-0.01122.113-0.018-0.0180.0000.0000.0000.000
114B115ILE0-0.020-0.00121.913-0.001-0.0010.0000.0000.0000.000
115B116GLU-1-0.896-0.92615.500-0.458-0.4580.0000.0000.0000.000
116B117ILE0-0.039-0.02818.422-0.021-0.0210.0000.0000.0000.000
117B118HIS00.0060.01419.340-0.005-0.0050.0000.0000.0000.000
118B119SER0-0.048-0.03019.0850.0080.0080.0000.0000.0000.000
119B120LYS10.8600.92710.3960.8130.8130.0000.0000.0000.000
120B121PRO0-0.044-0.02014.153-0.040-0.0400.0000.0000.0000.000
121B122LEU0-0.057-0.01813.1730.0430.0430.0000.0000.0000.000
122B123TYR0-0.053-0.04815.4360.0180.0180.0000.0000.0000.000
123B124ARG10.8050.86118.7980.1120.1120.0000.0000.0000.000
124B125VAL00.013-0.00120.617-0.012-0.0120.0000.0000.0000.000
125B126TYR0-0.059-0.04424.2210.0190.0190.0000.0000.0000.000
126B127PHE0-0.008-0.00925.9950.0090.0090.0000.0000.0000.000
127B128LEU0-0.0090.00428.748-0.006-0.0060.0000.0000.0000.000
128B129GLY00.0020.01831.8190.0040.0040.0000.0000.0000.000
129B130PHE00.004-0.02333.950-0.001-0.0010.0000.0000.0000.000
130B131LEU0-0.053-0.00438.1160.0000.0000.0000.0000.0000.000
131B132PRO00.0500.02139.0700.0010.0010.0000.0000.0000.000
132B133GLY0-0.006-0.01436.1200.0010.0010.0000.0000.0000.000
133B134PHE0-0.026-0.01230.937-0.004-0.0040.0000.0000.0000.000
134B135ALA00.0210.02128.1150.0080.0080.0000.0000.0000.000
135B136TYR0-0.014-0.00728.554-0.008-0.0080.0000.0000.0000.000
136B137LEU00.0170.01123.1920.0090.0090.0000.0000.0000.000
137B138GLY0-0.027-0.01422.726-0.002-0.0020.0000.0000.0000.000
138B139GLY00.0620.01718.7780.0060.0060.0000.0000.0000.000
139B140MET0-0.070-0.01118.527-0.022-0.0220.0000.0000.0000.000
140B141ASP-1-0.757-0.84818.135-0.340-0.3400.0000.0000.0000.000
141B142GLU-1-0.810-0.91820.147-0.145-0.1450.0000.0000.0000.000
142B143ARG10.8490.90117.2640.3890.3890.0000.0000.0000.000
143B144ILE00.0570.03622.6150.0070.0070.0000.0000.0000.000
144B145ALA0-0.0030.00325.4960.0170.0170.0000.0000.0000.000
145B146THR00.0020.00527.6260.0020.0020.0000.0000.0000.000
146B147PRO0-0.0170.01331.2380.0050.0050.0000.0000.0000.000
147B148ARG10.9590.97833.7900.0660.0660.0000.0000.0000.000
148B149LEU0-0.0120.01036.465-0.002-0.0020.0000.0000.0000.000
149B150GLU-1-0.901-0.95839.534-0.064-0.0640.0000.0000.0000.000
150B151LYS10.9090.95642.8180.0450.0450.0000.0000.0000.000
151B152PRO0-0.021-0.01541.458-0.002-0.0020.0000.0000.0000.000
152B153ARG10.8480.90037.3000.0720.0720.0000.0000.0000.000
153B154LEU0-0.006-0.02542.8480.0010.0010.0000.0000.0000.000
154B155LYS10.8030.88342.9520.0340.0340.0000.0000.0000.000
155B156VAL00.0260.02836.411-0.003-0.0030.0000.0000.0000.000
156B157PRO00.0370.02236.8050.0040.0040.0000.0000.0000.000
157B158ALA00.0010.01036.154-0.003-0.0030.0000.0000.0000.000
158B159GLY00.0520.03932.0390.0000.0000.0000.0000.0000.000
159B160SER0-0.040-0.02231.032-0.008-0.0080.0000.0000.0000.000
160B161VAL00.0480.01626.2130.0050.0050.0000.0000.0000.000
161B162GLY00.0260.00829.590-0.002-0.0020.0000.0000.0000.000
162B163ILE00.0010.02126.0020.0000.0000.0000.0000.0000.000
163B164ALA0-0.041-0.03229.5320.0090.0090.0000.0000.0000.000
164B165GLY0-0.034-0.01030.4110.0030.0030.0000.0000.0000.000
165B166LYS10.8450.89625.6640.1360.1360.0000.0000.0000.000
166B167GLN00.0310.04325.4310.0010.0010.0000.0000.0000.000
167B168THR00.031-0.00423.723-0.003-0.0030.0000.0000.0000.000
168B169GLY00.0270.00626.9250.0070.0070.0000.0000.0000.000
169B170TRP0-0.010-0.01125.171-0.007-0.0070.0000.0000.0000.000
170B171TYR00.0500.02830.6260.0080.0080.0000.0000.0000.000
171B172ALA0-0.0110.00832.895-0.001-0.0010.0000.0000.0000.000
172B173ILE0-0.047-0.03434.1440.0030.0030.0000.0000.0000.000
173B174GLU-1-0.830-0.88737.875-0.035-0.0350.0000.0000.0000.000
174B175SER0-0.003-0.01138.8820.0030.0030.0000.0000.0000.000
175B176PRO00.0080.00940.790-0.003-0.0030.0000.0000.0000.000
176B177GLY00.0400.00338.5420.0010.0010.0000.0000.0000.000
177B178GLY00.0070.00338.2970.0000.0000.0000.0000.0000.000
178B179TRP0-0.048-0.01429.546-0.001-0.0010.0000.0000.0000.000
179B180ARG10.8770.93732.1330.0900.0900.0000.0000.0000.000
180B181ILE0-0.011-0.01731.731-0.005-0.0050.0000.0000.0000.000
181B182ILE00.011-0.00326.3230.0000.0000.0000.0000.0000.000
182B183GLY00.1100.04628.719-0.009-0.0090.0000.0000.0000.000
183B184ARG10.7840.91329.7760.0600.0600.0000.0000.0000.000
184B185ILE0-0.0010.01126.869-0.003-0.0030.0000.0000.0000.000
185B186PRO00.0040.01828.2440.0060.0060.0000.0000.0000.000
186B187LEU00.0120.00626.4090.0080.0080.0000.0000.0000.000
187B188ARG10.9270.95430.8020.0120.0120.0000.0000.0000.000
188B189THR00.0270.00928.9640.0070.0070.0000.0000.0000.000
189B190PHE00.0370.02131.0010.0050.0050.0000.0000.0000.000
190B191ASN0-0.063-0.04334.258-0.002-0.0020.0000.0000.0000.000
191B192PRO00.0380.02136.7050.0040.0040.0000.0000.0000.000
192B193GLY00.0480.02539.545-0.001-0.0010.0000.0000.0000.000
193B194LYS10.8350.91835.046-0.007-0.0070.0000.0000.0000.000
194B195VAL00.0160.02535.093-0.001-0.0010.0000.0000.0000.000
195B196PRO00.0700.03030.1180.0040.0040.0000.0000.0000.000
196B197PRO0-0.022-0.01333.416-0.003-0.0030.0000.0000.0000.000
197B198SER0-0.003-0.01830.595-0.005-0.0050.0000.0000.0000.000
198B199ILE0-0.042-0.02026.3400.0060.0060.0000.0000.0000.000
199B200VAL00.0360.02924.1420.0000.0000.0000.0000.0000.000
200B201LEU0-0.023-0.01226.117-0.002-0.0020.0000.0000.0000.000
201B202PRO0-0.004-0.01525.689-0.003-0.0030.0000.0000.0000.000
202B203GLY00.0170.01422.9580.0110.0110.0000.0000.0000.000
203B204ASP-1-0.868-0.92321.3820.0630.0630.0000.0000.0000.000
204B205TYR00.0160.00215.8250.0070.0070.0000.0000.0000.000
205B206VAL0-0.015-0.00919.2010.0110.0110.0000.0000.0000.000
206B207LYS10.8910.96513.9940.2600.2600.0000.0000.0000.000
207B208PHE00.0220.01118.0080.0250.0250.0000.0000.0000.000
208B209VAL00.0050.00118.184-0.031-0.0310.0000.0000.0000.000
209B210PRO00.019-0.00119.6880.0220.0220.0000.0000.0000.000
210B211ILE0-0.0410.00122.5980.0010.0010.0000.0000.0000.000
211B212ASP-1-0.816-0.91825.464-0.091-0.0910.0000.0000.0000.000
212B213GLU-1-0.810-0.90328.830-0.060-0.0600.0000.0000.0000.000
213B214LYS10.7570.84331.8260.0750.0750.0000.0000.0000.000
214B215GLU-1-0.852-0.88828.419-0.043-0.0430.0000.0000.0000.000
215B216PHE0-0.083-0.02429.3870.0000.0000.0000.0000.0000.000
216B217TRP0-0.100-0.08531.4030.0090.0090.0000.0000.0000.000