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: 8531Y

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2379583.357005
FMO2-HF: Nuclear repulsion 2297275.063681
FMO2-HF: Total energy -82308.293324
FMO2-MP2: Total energy -82555.841959


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.
-10.712-3.7362.254-2.961-6.267-0.015
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 : 0.029 / 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].
3B4LYS10.8890.9502.3530.0991.2730.566-0.117-1.6220.006
4B5PRO00.0520.0175.9060.0570.0570.0000.0000.0000.000
5B6ALA0-0.043-0.0299.536-0.126-0.1260.0000.0000.0000.000
6B7GLY0-0.0130.00911.344-0.038-0.0380.0000.0000.0000.000
7B8ASP-1-0.920-0.97314.8780.1900.1900.0000.0000.0000.000
8B9SER00.0020.00716.9610.0100.0100.0000.0000.0000.000
9B10ALA00.0340.01313.7460.0210.0210.0000.0000.0000.000
10B11PHE0-0.057-0.0348.4490.0550.0550.0000.0000.0000.000
11B12LEU00.0300.0217.047-0.068-0.0680.0000.0000.0000.000
12B13ILE0-0.058-0.0142.777-1.136-0.1980.297-0.447-0.7880.004
13B14SER00.0710.0572.897-1.033-0.0230.095-0.269-0.8360.001
14B15PHE0-0.036-0.0412.684-7.523-3.8811.297-2.141-2.797-0.026
15B16GLY0-0.022-0.0463.911-0.2110.001-0.0010.013-0.2240.000
16B17ASP-1-0.976-1.0025.841-0.652-0.6520.0000.0000.0000.000
17B18GLU-1-0.878-0.8848.953-1.080-1.0800.0000.0000.0000.000
18B19ILE0-0.008-0.01711.050-0.041-0.0410.0000.0000.0000.000
19B20SER00.016-0.01311.9210.0560.0560.0000.0000.0000.000
20B21GLU-1-0.774-0.83613.430-0.282-0.2820.0000.0000.0000.000
21B22GLU-1-0.798-0.90310.645-0.763-0.7630.0000.0000.0000.000
22B23ILE0-0.030-0.0107.1710.0030.0030.0000.0000.0000.000
23B24ASN00.0030.01310.0430.0170.0170.0000.0000.0000.000
24B25ASP-1-0.865-0.95112.649-0.124-0.1240.0000.0000.0000.000
25B26ARG10.8400.9427.3290.8990.8990.0000.0000.0000.000
26B27VAL0-0.0140.0228.3060.2120.2120.0000.0000.0000.000
27B28HIS00.005-0.0099.5090.2250.2250.0000.0000.0000.000
28B29SER0-0.053-0.04911.6100.0930.0930.0000.0000.0000.000
29B30LEU00.0150.0065.9710.1170.1170.0000.0000.0000.000
30B31ALA0-0.022-0.01210.1900.1250.1250.0000.0000.0000.000
31B32LYS10.9590.96512.376-0.060-0.0600.0000.0000.0000.000
32B33ALA0-0.0230.02711.9070.0000.0000.0000.0000.0000.000
33B34ILE0-0.005-0.0459.7930.0320.0320.0000.0000.0000.000
34B35GLU-1-0.915-0.95613.9080.1910.1910.0000.0000.0000.000
35B36LYS10.8430.93016.839-0.283-0.2830.0000.0000.0000.000
36B37GLU-1-0.984-1.01215.5860.4600.4600.0000.0000.0000.000
37B38SER0-0.0210.01218.613-0.028-0.0280.0000.0000.0000.000
38B39PRO0-0.0200.01415.753-0.019-0.0190.0000.0000.0000.000
39B40GLU-1-0.898-0.96619.0030.2170.2170.0000.0000.0000.000
40B41TRP0-0.036-0.02513.051-0.011-0.0110.0000.0000.0000.000
41B42LEU0-0.031-0.00315.1760.0210.0210.0000.0000.0000.000
42B43VAL0-0.011-0.02317.656-0.041-0.0410.0000.0000.0000.000
43B44GLU-1-0.954-0.97117.0970.0450.0450.0000.0000.0000.000
44B45LEU0-0.032-0.02311.9800.0800.0800.0000.0000.0000.000
45B46VAL00.0160.02013.260-0.047-0.0470.0000.0000.0000.000
46B47PRO0-0.003-0.00811.587-0.031-0.0310.0000.0000.0000.000
47B48ALA00.0090.01111.2040.0090.0090.0000.0000.0000.000
48B49TYR0-0.025-0.03811.496-0.016-0.0160.0000.0000.0000.000
49B50SER00.0270.0117.806-0.057-0.0570.0000.0000.0000.000
50B51SER0-0.038-0.0386.713-0.448-0.4480.0000.0000.0000.000
51B52LEU0-0.018-0.0086.9160.1730.1730.0000.0000.0000.000
52B53LEU00.0050.0048.2900.1550.1550.0000.0000.0000.000
53B54VAL0-0.004-0.0029.3270.0490.0490.0000.0000.0000.000
54B55ILE00.0530.04612.0160.0140.0140.0000.0000.0000.000
55B56TYR00.0020.00114.4790.0150.0150.0000.0000.0000.000
56B57ASP-1-0.794-0.90117.4200.1760.1760.0000.0000.0000.000
57B58PRO00.000-0.01920.2270.0200.0200.0000.0000.0000.000
58B59LEU0-0.074-0.03021.166-0.005-0.0050.0000.0000.0000.000
59B60LYS10.8420.93221.925-0.217-0.2170.0000.0000.0000.000
60B61ALA00.0240.02118.0710.0170.0170.0000.0000.0000.000
61B62SER00.0020.01918.637-0.006-0.0060.0000.0000.0000.000
62B63TYR00.0750.01311.9190.0310.0310.0000.0000.0000.000
63B64GLU-1-0.980-0.97113.9810.5430.5430.0000.0000.0000.000
64B65GLU-1-0.870-0.96813.7320.5090.5090.0000.0000.0000.000
65B66VAL0-0.027-0.00312.1490.1210.1210.0000.0000.0000.000
66B67GLU-1-0.873-0.9348.5631.1971.1970.0000.0000.0000.000
67B68SER0-0.066-0.0449.0680.4470.4470.0000.0000.0000.000
68B69TYR00.008-0.01610.6390.1910.1910.0000.0000.0000.000
69B70LEU00.0450.0377.4810.0890.0890.0000.0000.0000.000
70B71LYS10.9781.0265.879-0.814-0.8140.0000.0000.0000.000
71B72ARG10.8680.9487.391-0.943-0.9430.0000.0000.0000.000
72B73ILE0-0.0150.0069.459-0.135-0.1350.0000.0000.0000.000
73B74SER00.025-0.0454.8390.0760.0760.0000.0000.0000.000
74B75ALA0-0.071-0.0246.898-0.528-0.5280.0000.0000.0000.000
75B76ARG11.0040.9928.459-0.967-0.9670.0000.0000.0000.000
76B77GLU-1-0.779-0.8528.6860.1110.1110.0000.0000.0000.000
77B78VAL0-0.015-0.0095.521-0.259-0.2590.0000.0000.0000.000
78B79GLU-1-0.965-0.9858.8720.2480.2480.0000.0000.0000.000
79B80ARG10.8240.89712.148-0.205-0.2050.0000.0000.0000.000
80B81ILE0-0.052-0.0299.893-0.060-0.0600.0000.0000.0000.000
81B82LYS11.0031.00712.361-0.103-0.1030.0000.0000.0000.000
82B83GLY0-0.023-0.00113.821-0.015-0.0150.0000.0000.0000.000
83B84LYS10.8770.94216.3820.0160.0160.0000.0000.0000.000
84B85THR0-0.011-0.01115.030-0.042-0.0420.0000.0000.0000.000
85B86ILE0-0.049-0.01117.4720.0160.0160.0000.0000.0000.000
86B87GLU-1-0.944-0.97516.631-0.195-0.1950.0000.0000.0000.000
87B88ILE0-0.056-0.04420.2420.0210.0210.0000.0000.0000.000
88B89PRO00.0240.02622.915-0.017-0.0170.0000.0000.0000.000
89B90VAL0-0.011-0.01424.1320.0130.0130.0000.0000.0000.000
90B91ALA00.0240.02025.752-0.009-0.0090.0000.0000.0000.000
91B92TYR0-0.002-0.04722.7620.0030.0030.0000.0000.0000.000
92B93GLY00.0190.01128.2310.0030.0030.0000.0000.0000.000
93B94GLY00.0040.00731.1490.0050.0050.0000.0000.0000.000
94B95GLU-1-0.906-0.96334.708-0.076-0.0760.0000.0000.0000.000
95B96PHE0-0.059-0.03632.3050.0040.0040.0000.0000.0000.000
96B97GLY0-0.014-0.01432.183-0.002-0.0020.0000.0000.0000.000
97B98PRO0-0.0150.00333.206-0.002-0.0020.0000.0000.0000.000
98B99ASP-1-0.813-0.87634.068-0.100-0.1000.0000.0000.0000.000
99B100ILE00.0130.00227.562-0.006-0.0060.0000.0000.0000.000
100B101GLU-1-0.863-0.92631.146-0.123-0.1230.0000.0000.0000.000
101B102PHE0-0.003-0.01133.351-0.001-0.0010.0000.0000.0000.000
102B103VAL0-0.044-0.01928.228-0.001-0.0010.0000.0000.0000.000
103B104ALA00.0510.03228.705-0.008-0.0080.0000.0000.0000.000
104B105GLN0-0.0130.00729.766-0.002-0.0020.0000.0000.0000.000
105B106TYR0-0.094-0.06431.3420.0070.0070.0000.0000.0000.000
106B107ASN0-0.040-0.04227.394-0.001-0.0010.0000.0000.0000.000
107B108GLY0-0.0650.00228.229-0.009-0.0090.0000.0000.0000.000
108B109LEU0-0.032-0.02123.723-0.011-0.0110.0000.0000.0000.000
109B110SER0-0.024-0.00725.7640.0170.0170.0000.0000.0000.000
110B111VAL00.0730.00626.816-0.009-0.0090.0000.0000.0000.000
111B112ASP-1-0.891-0.95124.232-0.192-0.1920.0000.0000.0000.000
112B113ASP-1-0.860-0.92822.247-0.273-0.2730.0000.0000.0000.000
113B114VAL0-0.026-0.01722.184-0.020-0.0200.0000.0000.0000.000
114B115ILE0-0.011-0.00822.223-0.012-0.0120.0000.0000.0000.000
115B116GLU-1-0.933-0.93615.694-0.469-0.4690.0000.0000.0000.000
116B117ILE0-0.026-0.02818.191-0.037-0.0370.0000.0000.0000.000
117B118HIS00.0080.00619.199-0.022-0.0220.0000.0000.0000.000
118B119SER0-0.052-0.00619.142-0.007-0.0070.0000.0000.0000.000
119B120LYS10.9600.99910.5610.8630.8630.0000.0000.0000.000
120B121PRO0-0.049-0.03314.313-0.056-0.0560.0000.0000.0000.000
121B122LEU0-0.0360.00312.0890.0560.0560.0000.0000.0000.000
122B123TYR0-0.090-0.07315.2730.0050.0050.0000.0000.0000.000
123B124ARG10.8520.88618.7350.2320.2320.0000.0000.0000.000
124B125VAL00.0220.00320.3620.0000.0000.0000.0000.0000.000
125B126TYR0-0.104-0.11423.8380.0160.0160.0000.0000.0000.000
126B127PHE0-0.008-0.00725.9240.0120.0120.0000.0000.0000.000
127B128LEU00.0080.01028.216-0.006-0.0060.0000.0000.0000.000
128B129GLY0-0.0150.00531.4530.0060.0060.0000.0000.0000.000
129B130PHE0-0.029-0.01133.379-0.002-0.0020.0000.0000.0000.000
130B131LEU0-0.0120.02537.4740.0010.0010.0000.0000.0000.000
131B132PRO0-0.005-0.01139.0350.0020.0020.0000.0000.0000.000
132B133GLY00.061-0.02035.5350.0000.0000.0000.0000.0000.000
133B134PHE0-0.027-0.00230.942-0.003-0.0030.0000.0000.0000.000
134B135ALA00.0070.00827.7140.0060.0060.0000.0000.0000.000
135B136TYR0-0.0120.01528.415-0.006-0.0060.0000.0000.0000.000
136B137LEU00.0320.00822.7590.0060.0060.0000.0000.0000.000
137B138GLY0-0.039-0.02922.6140.0060.0060.0000.0000.0000.000
138B139GLY00.0510.00518.931-0.005-0.0050.0000.0000.0000.000
139B140MET0-0.0540.01718.620-0.023-0.0230.0000.0000.0000.000
140B141ASP-1-0.770-0.87317.913-0.405-0.4050.0000.0000.0000.000
141B142GLU-1-0.927-0.98619.971-0.208-0.2080.0000.0000.0000.000
142B143ARG10.8500.90617.1830.4280.4280.0000.0000.0000.000
143B144ILE00.0240.01622.8370.0150.0150.0000.0000.0000.000
144B145ALA00.0010.01425.3820.0170.0170.0000.0000.0000.000
145B146THR0-0.010-0.00527.4430.0070.0070.0000.0000.0000.000
146B147PRO0-0.052-0.00731.0920.0030.0030.0000.0000.0000.000
147B148ARG11.0170.98633.8740.1000.1000.0000.0000.0000.000
148B149LEU0-0.049-0.03436.2880.0010.0010.0000.0000.0000.000
149B150GLU-1-0.917-0.95239.340-0.078-0.0780.0000.0000.0000.000
150B151LYS10.9330.96342.4260.0590.0590.0000.0000.0000.000
151B152PRO0-0.016-0.02141.392-0.002-0.0020.0000.0000.0000.000
152B153ARG10.8870.93437.4440.0910.0910.0000.0000.0000.000
153B154LEU0-0.008-0.02642.8340.0000.0000.0000.0000.0000.000
154B155LYS10.8960.95342.8940.0500.0500.0000.0000.0000.000
155B156VAL0-0.0380.00936.365-0.002-0.0020.0000.0000.0000.000
156B157PRO00.0570.03237.0520.0040.0040.0000.0000.0000.000
157B158ALA00.0070.01136.207-0.005-0.0050.0000.0000.0000.000
158B159GLY00.0050.00332.0040.0000.0000.0000.0000.0000.000
159B160SER0-0.046-0.03231.054-0.008-0.0080.0000.0000.0000.000
160B161VAL00.0560.04126.2970.0030.0030.0000.0000.0000.000
161B162GLY00.003-0.00829.5480.0020.0020.0000.0000.0000.000
162B163ILE00.0050.01826.728-0.005-0.0050.0000.0000.0000.000
163B164ALA0-0.021-0.01729.5210.0130.0130.0000.0000.0000.000
164B165GLY0-0.064-0.03430.3270.0010.0010.0000.0000.0000.000
165B166LYS10.9920.97525.2140.1720.1720.0000.0000.0000.000
166B167GLN00.0700.13425.191-0.004-0.0040.0000.0000.0000.000
167B168THR00.0580.00923.4930.0040.0040.0000.0000.0000.000
168B169GLY00.010-0.00326.6510.0040.0040.0000.0000.0000.000
169B170TRP0-0.027-0.03124.912-0.006-0.0060.0000.0000.0000.000
170B171TYR00.0460.02130.3630.0080.0080.0000.0000.0000.000
171B172ALA0-0.0090.02233.046-0.001-0.0010.0000.0000.0000.000
172B173ILE0-0.017-0.03134.0690.0040.0040.0000.0000.0000.000
173B174GLU-1-0.878-0.93937.707-0.054-0.0540.0000.0000.0000.000
174B175SER0-0.045-0.04038.8230.0030.0030.0000.0000.0000.000
175B176PRO00.0350.02540.724-0.003-0.0030.0000.0000.0000.000
176B177GLY00.0330.00238.483-0.001-0.0010.0000.0000.0000.000
177B178GLY0-0.016-0.01138.6360.0010.0010.0000.0000.0000.000
178B179TRP0-0.0500.01829.293-0.001-0.0010.0000.0000.0000.000
179B180ARG10.9040.96332.0510.1130.1130.0000.0000.0000.000
180B181ILE00.015-0.01631.835-0.008-0.0080.0000.0000.0000.000
181B182ILE00.0070.00625.9290.0040.0040.0000.0000.0000.000
182B183GLY00.0990.04228.687-0.007-0.0070.0000.0000.0000.000
183B184ARG10.8810.96329.7730.0820.0820.0000.0000.0000.000
184B185ILE0-0.030-0.00326.971-0.003-0.0030.0000.0000.0000.000
185B186PRO0-0.0130.00428.4810.0070.0070.0000.0000.0000.000
186B187LEU00.0360.01826.3990.0080.0080.0000.0000.0000.000
187B188ARG10.9170.96130.9440.0360.0360.0000.0000.0000.000
188B189THR00.0380.01828.6450.0060.0060.0000.0000.0000.000
189B190PHE00.0310.02430.3030.0040.0040.0000.0000.0000.000
190B191ASN0-0.091-0.06433.9690.0020.0020.0000.0000.0000.000
191B192PRO00.0640.03936.6350.0020.0020.0000.0000.0000.000
192B193GLY00.006-0.01739.1830.0000.0000.0000.0000.0000.000
193B194LYS10.8980.96834.2010.0210.0210.0000.0000.0000.000
194B195VAL0-0.0100.01934.633-0.001-0.0010.0000.0000.0000.000
195B196PRO00.021-0.00529.9130.0040.0040.0000.0000.0000.000
196B197PRO00.0400.00133.161-0.002-0.0020.0000.0000.0000.000
197B198SER00.0100.02329.992-0.002-0.0020.0000.0000.0000.000
198B199ILE0-0.032-0.00426.7940.0050.0050.0000.0000.0000.000
199B200VAL0-0.0230.00524.089-0.002-0.0020.0000.0000.0000.000
200B201LEU0-0.034-0.04925.2910.0040.0040.0000.0000.0000.000
201B202PRO00.0240.00724.927-0.007-0.0070.0000.0000.0000.000
202B203GLY0-0.047-0.01322.4090.0140.0140.0000.0000.0000.000
203B204ASP-1-0.852-0.92720.657-0.042-0.0420.0000.0000.0000.000
204B205TYR0-0.019-0.03415.292-0.003-0.0030.0000.0000.0000.000
205B206VAL0-0.004-0.00618.6960.0220.0220.0000.0000.0000.000
206B207LYS10.9501.00213.7610.3420.3420.0000.0000.0000.000
207B208PHE0-0.010-0.00517.9810.0340.0340.0000.0000.0000.000
208B209VAL00.006-0.00218.692-0.032-0.0320.0000.0000.0000.000
209B210PRO00.026-0.00420.0380.0230.0230.0000.0000.0000.000
210B211ILE0-0.0190.01822.9220.0010.0010.0000.0000.0000.000
211B212ASP-1-0.812-0.92025.730-0.106-0.1060.0000.0000.0000.000
212B213GLU-1-0.976-1.02229.069-0.076-0.0760.0000.0000.0000.000
213B214LYS10.8720.93931.8250.0810.0810.0000.0000.0000.000
214B215GLU-1-0.870-0.91428.287-0.059-0.0590.0000.0000.0000.000
215B216PHE0-0.134-0.06029.398-0.002-0.0020.0000.0000.0000.000
216B217TRP0-0.022-0.01631.5730.0080.0080.0000.0000.0000.000