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: N95RQ

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 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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2380769.954951
FMO2-HF: Nuclear repulsion 2298459.471627
FMO2-HF: Total energy -82310.483324
FMO2-MP2: Total energy -82557.978781


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.
-8.13-1.8581.344-2.487-5.129-0.011
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 : 0.034 / q_NPA : -0.004
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].
3B4LYS10.8760.9352.3890.7422.0620.370-0.144-1.5460.004
4B5PRO00.0600.0236.2130.0480.0480.0000.0000.0000.000
5B6ALA0-0.042-0.0269.926-0.117-0.1170.0000.0000.0000.000
6B7GLY0-0.0120.01011.769-0.027-0.0270.0000.0000.0000.000
7B8ASP-1-0.899-0.94415.2800.1610.1610.0000.0000.0000.000
8B9SER0-0.019-0.02716.9730.0070.0070.0000.0000.0000.000
9B10ALA00.0320.00913.7540.0200.0200.0000.0000.0000.000
10B11PHE0-0.056-0.0358.4800.0500.0500.0000.0000.0000.000
11B12LEU00.0270.0227.288-0.044-0.0440.0000.0000.0000.000
12B13ILE0-0.053-0.0102.562-1.309-0.4330.417-0.475-0.8180.003
13B14SER00.0740.0573.026-0.7080.0780.017-0.201-0.6020.000
14B15PHE0-0.020-0.0282.862-5.878-2.7840.541-1.662-1.974-0.018
15B16GLY0-0.030-0.0454.458-0.284-0.088-0.001-0.005-0.1890.000
16B17ASP-1-0.965-0.9816.096-0.606-0.6060.0000.0000.0000.000
17B18GLU-1-0.770-0.8289.531-0.931-0.9310.0000.0000.0000.000
18B19ILE00.002-0.00511.523-0.033-0.0330.0000.0000.0000.000
19B20SER00.021-0.00812.2720.0470.0470.0000.0000.0000.000
20B21GLU-1-0.774-0.85513.824-0.244-0.2440.0000.0000.0000.000
21B22GLU-1-0.782-0.87410.786-0.681-0.6810.0000.0000.0000.000
22B23ILE0-0.006-0.0057.9770.0100.0100.0000.0000.0000.000
23B24ASN00.0080.01810.1030.0230.0230.0000.0000.0000.000
24B25ASP-1-0.865-0.95212.645-0.086-0.0860.0000.0000.0000.000
25B26ARG10.8330.9117.4600.7950.7950.0000.0000.0000.000
26B27VAL0-0.0150.0178.1350.1970.1970.0000.0000.0000.000
27B28HIS0-0.028-0.0189.4950.2010.2010.0000.0000.0000.000
28B29SER0-0.032-0.02211.7450.0780.0780.0000.0000.0000.000
29B30LEU00.0180.0105.9490.1150.1150.0000.0000.0000.000
30B31ALA0-0.036-0.01510.1640.1150.1150.0000.0000.0000.000
31B32LYS10.8900.91212.342-0.086-0.0860.0000.0000.0000.000
32B33ALA0-0.0260.02011.9020.0020.0020.0000.0000.0000.000
33B34ILE0-0.017-0.0499.5010.0220.0220.0000.0000.0000.000
34B35GLU-1-0.835-0.90013.8680.1300.1300.0000.0000.0000.000
35B36LYS10.8620.94116.811-0.287-0.2870.0000.0000.0000.000
36B37GLU-1-0.856-0.93315.5250.4770.4770.0000.0000.0000.000
37B38SER0-0.0360.01118.596-0.026-0.0260.0000.0000.0000.000
38B39PRO0-0.0130.01215.669-0.017-0.0170.0000.0000.0000.000
39B40GLU-1-0.895-0.96519.0030.2070.2070.0000.0000.0000.000
40B41TRP0-0.035-0.02312.921-0.014-0.0140.0000.0000.0000.000
41B42LEU0-0.036-0.01215.1150.0150.0150.0000.0000.0000.000
42B43VAL0-0.005-0.01117.612-0.037-0.0370.0000.0000.0000.000
43B44GLU-1-0.945-0.97517.0870.0370.0370.0000.0000.0000.000
44B45LEU0-0.032-0.01912.1390.0680.0680.0000.0000.0000.000
45B46VAL00.0240.01813.211-0.039-0.0390.0000.0000.0000.000
46B47PRO0-0.003-0.00411.558-0.030-0.0300.0000.0000.0000.000
47B48ALA00.0060.00411.1750.0070.0070.0000.0000.0000.000
48B49TYR0-0.052-0.06011.4840.0020.0020.0000.0000.0000.000
49B50SER00.0110.0028.411-0.070-0.0700.0000.0000.0000.000
50B51SER0-0.020-0.0276.704-0.384-0.3840.0000.0000.0000.000
51B52LEU0-0.035-0.0126.8930.1660.1660.0000.0000.0000.000
52B53LEU00.0210.0118.2470.1140.1140.0000.0000.0000.000
53B54VAL0-0.003-0.0079.3810.0530.0530.0000.0000.0000.000
54B55ILE00.0340.03311.9660.0060.0060.0000.0000.0000.000
55B56TYR00.0150.01314.5110.0320.0320.0000.0000.0000.000
56B57ASP-1-0.748-0.86717.3670.1560.1560.0000.0000.0000.000
57B58PRO00.009-0.01719.9130.0200.0200.0000.0000.0000.000
58B59LEU0-0.071-0.02621.166-0.004-0.0040.0000.0000.0000.000
59B60LYS10.7900.89921.677-0.197-0.1970.0000.0000.0000.000
60B61ALA00.0110.01317.9490.0160.0160.0000.0000.0000.000
61B62SER0-0.048-0.04918.610-0.003-0.0030.0000.0000.0000.000
62B63TYR00.008-0.03011.4830.0160.0160.0000.0000.0000.000
63B64GLU-1-0.941-0.96213.9040.5010.5010.0000.0000.0000.000
64B65GLU-1-0.815-0.88713.6480.4830.4830.0000.0000.0000.000
65B66VAL0-0.033-0.00112.2500.1140.1140.0000.0000.0000.000
66B67GLU-1-0.774-0.8618.6801.0991.0990.0000.0000.0000.000
67B68SER0-0.078-0.0598.9680.4260.4260.0000.0000.0000.000
68B69TYR00.018-0.01210.5350.1800.1800.0000.0000.0000.000
69B70LEU00.0110.0277.5220.0860.0860.0000.0000.0000.000
70B71LYS10.9030.9395.501-0.682-0.6820.0000.0000.0000.000
71B72ARG10.9000.9607.282-0.846-0.8460.0000.0000.0000.000
72B73ILE0-0.031-0.0059.190-0.133-0.1330.0000.0000.0000.000
73B74SER00.0420.0044.8300.0920.0920.0000.0000.0000.000
74B75ALA0-0.068-0.0276.947-0.495-0.4950.0000.0000.0000.000
75B76ARG10.8730.9138.510-0.956-0.9560.0000.0000.0000.000
76B77GLU-1-0.757-0.8388.7880.1240.1240.0000.0000.0000.000
77B78VAL0-0.019-0.0156.105-0.249-0.2490.0000.0000.0000.000
78B79GLU-1-0.970-0.9809.4170.2450.2450.0000.0000.0000.000
79B80ARG10.8050.88012.615-0.209-0.2090.0000.0000.0000.000
80B81ILE0-0.046-0.02710.449-0.061-0.0610.0000.0000.0000.000
81B82LYS10.9821.00312.269-0.123-0.1230.0000.0000.0000.000
82B83GLY0-0.0120.00114.013-0.016-0.0160.0000.0000.0000.000
83B84LYS10.8540.93316.7870.0120.0120.0000.0000.0000.000
84B85THR0-0.033-0.02315.097-0.039-0.0390.0000.0000.0000.000
85B86ILE0-0.047-0.01217.6050.0140.0140.0000.0000.0000.000
86B87GLU-1-0.926-0.97016.472-0.206-0.2060.0000.0000.0000.000
87B88ILE0-0.063-0.04719.9990.0210.0210.0000.0000.0000.000
88B89PRO00.0240.02622.735-0.016-0.0160.0000.0000.0000.000
89B90VAL0-0.023-0.02424.3420.0120.0120.0000.0000.0000.000
90B91ALA00.0240.02925.614-0.009-0.0090.0000.0000.0000.000
91B92TYR00.006-0.05622.8090.0040.0040.0000.0000.0000.000
92B93GLY00.0260.01428.1510.0020.0020.0000.0000.0000.000
93B94GLY0-0.0050.00331.1010.0050.0050.0000.0000.0000.000
94B95GLU-1-0.925-0.97034.649-0.071-0.0710.0000.0000.0000.000
95B96PHE0-0.058-0.03332.2320.0040.0040.0000.0000.0000.000
96B97GLY0-0.006-0.00932.132-0.001-0.0010.0000.0000.0000.000
97B98PRO0-0.0190.00633.151-0.002-0.0020.0000.0000.0000.000
98B99ASP-1-0.790-0.84934.066-0.091-0.0910.0000.0000.0000.000
99B100ILE00.0040.00027.445-0.005-0.0050.0000.0000.0000.000
100B101GLU-1-0.839-0.91731.090-0.120-0.1200.0000.0000.0000.000
101B102PHE0-0.011-0.01333.310-0.001-0.0010.0000.0000.0000.000
102B103VAL0-0.042-0.02228.271-0.001-0.0010.0000.0000.0000.000
103B104ALA00.0620.03828.688-0.007-0.0070.0000.0000.0000.000
104B105GLN0-0.0050.01029.734-0.002-0.0020.0000.0000.0000.000
105B106TYR0-0.096-0.06431.3870.0070.0070.0000.0000.0000.000
106B107ASN0-0.049-0.04927.394-0.002-0.0020.0000.0000.0000.000
107B108GLY0-0.0680.00228.244-0.008-0.0080.0000.0000.0000.000
108B109LEU0-0.052-0.03124.025-0.011-0.0110.0000.0000.0000.000
109B110SER0-0.045-0.05025.7150.0170.0170.0000.0000.0000.000
110B111VAL00.0770.00626.770-0.008-0.0080.0000.0000.0000.000
111B112ASP-1-0.903-0.95624.265-0.179-0.1790.0000.0000.0000.000
112B113ASP-1-0.829-0.88022.197-0.251-0.2510.0000.0000.0000.000
113B114VAL0-0.015-0.01322.133-0.019-0.0190.0000.0000.0000.000
114B115ILE0-0.015-0.00522.285-0.010-0.0100.0000.0000.0000.000
115B116GLU-1-0.929-0.93115.739-0.439-0.4390.0000.0000.0000.000
116B117ILE0-0.020-0.02418.166-0.035-0.0350.0000.0000.0000.000
117B118HIS00.0180.01019.243-0.019-0.0190.0000.0000.0000.000
118B119SER0-0.047-0.01819.171-0.005-0.0050.0000.0000.0000.000
119B120LYS10.8570.93910.6240.8350.8350.0000.0000.0000.000
120B121PRO0-0.058-0.02714.279-0.046-0.0460.0000.0000.0000.000
121B122LEU0-0.045-0.00812.6760.0490.0490.0000.0000.0000.000
122B123TYR0-0.077-0.05115.3800.0120.0120.0000.0000.0000.000
123B124ARG10.8470.89318.8790.2080.2080.0000.0000.0000.000
124B125VAL00.005-0.00620.618-0.001-0.0010.0000.0000.0000.000
125B126TYR0-0.053-0.03524.1940.0160.0160.0000.0000.0000.000
126B127PHE0-0.005-0.00926.1760.0110.0110.0000.0000.0000.000
127B128LEU0-0.0110.00728.465-0.006-0.0060.0000.0000.0000.000
128B129GLY0-0.0120.00631.8580.0060.0060.0000.0000.0000.000
129B130PHE0-0.035-0.01233.560-0.002-0.0020.0000.0000.0000.000
130B131LEU0-0.0090.02637.7530.0010.0010.0000.0000.0000.000
131B132PRO00.0170.00338.9080.0020.0020.0000.0000.0000.000
132B133GLY00.048-0.03135.6340.0000.0000.0000.0000.0000.000
133B134PHE0-0.033-0.00730.765-0.003-0.0030.0000.0000.0000.000
134B135ALA00.0040.01427.8880.0060.0060.0000.0000.0000.000
135B136TYR00.0010.01128.553-0.006-0.0060.0000.0000.0000.000
136B137LEU00.0210.00423.2370.0060.0060.0000.0000.0000.000
137B138GLY0-0.033-0.02122.6660.0050.0050.0000.0000.0000.000
138B139GLY00.0570.00419.062-0.004-0.0040.0000.0000.0000.000
139B140MET0-0.0610.01218.803-0.020-0.0200.0000.0000.0000.000
140B141ASP-1-0.762-0.85618.279-0.358-0.3580.0000.0000.0000.000
141B142GLU-1-0.802-0.91920.239-0.177-0.1770.0000.0000.0000.000
142B143ARG10.8570.90917.2730.3900.3900.0000.0000.0000.000
143B144ILE00.0240.01922.8630.0140.0140.0000.0000.0000.000
144B145ALA00.0020.01225.5440.0150.0150.0000.0000.0000.000
145B146THR0-0.011-0.00827.7170.0060.0060.0000.0000.0000.000
146B147PRO0-0.0340.00731.3380.0030.0030.0000.0000.0000.000
147B148ARG11.0150.99933.9540.0900.0900.0000.0000.0000.000
148B149LEU0-0.040-0.01836.4750.0010.0010.0000.0000.0000.000
149B150GLU-1-0.908-0.94939.506-0.072-0.0720.0000.0000.0000.000
150B151LYS10.9270.95742.6250.0540.0540.0000.0000.0000.000
151B152PRO0-0.022-0.02141.502-0.002-0.0020.0000.0000.0000.000
152B153ARG10.8660.90537.4610.0840.0840.0000.0000.0000.000
153B154LEU0-0.004-0.02342.7950.0010.0010.0000.0000.0000.000
154B155LYS10.8130.88542.8020.0470.0470.0000.0000.0000.000
155B156VAL0-0.0290.01336.260-0.002-0.0020.0000.0000.0000.000
156B157PRO00.0470.02936.5400.0040.0040.0000.0000.0000.000
157B158ALA00.0170.01036.081-0.004-0.0040.0000.0000.0000.000
158B159GLY00.0210.01331.8480.0000.0000.0000.0000.0000.000
159B160SER0-0.038-0.01930.920-0.008-0.0080.0000.0000.0000.000
160B161VAL00.0560.04126.1750.0030.0030.0000.0000.0000.000
161B162GLY00.008-0.00429.4670.0010.0010.0000.0000.0000.000
162B163ILE00.0030.01726.408-0.005-0.0050.0000.0000.0000.000
163B164ALA0-0.027-0.02229.6440.0120.0120.0000.0000.0000.000
164B165GLY0-0.050-0.02430.5210.0010.0010.0000.0000.0000.000
165B166LYS10.8430.89125.5650.1700.1700.0000.0000.0000.000
166B167GLN00.0300.05625.408-0.003-0.0030.0000.0000.0000.000
167B168THR00.0580.01123.6240.0030.0030.0000.0000.0000.000
168B169GLY00.012-0.00426.7330.0040.0040.0000.0000.0000.000
169B170TRP0-0.025-0.02024.827-0.005-0.0050.0000.0000.0000.000
170B171TYR00.0380.01730.2620.0070.0070.0000.0000.0000.000
171B172ALA0-0.0090.02133.089-0.001-0.0010.0000.0000.0000.000
172B173ILE0-0.017-0.03233.9660.0040.0040.0000.0000.0000.000
173B174GLU-1-0.821-0.88837.548-0.049-0.0490.0000.0000.0000.000
174B175SER0-0.028-0.02738.6290.0020.0020.0000.0000.0000.000
175B176PRO00.0370.02640.633-0.003-0.0030.0000.0000.0000.000
176B177GLY00.031-0.00138.477-0.001-0.0010.0000.0000.0000.000
177B178GLY0-0.017-0.01238.7370.0010.0010.0000.0000.0000.000
178B179TRP0-0.0410.01629.488-0.001-0.0010.0000.0000.0000.000
179B180ARG10.8610.92932.1550.1040.1040.0000.0000.0000.000
180B181ILE00.007-0.01831.856-0.007-0.0070.0000.0000.0000.000
181B182ILE00.0160.00526.2290.0030.0030.0000.0000.0000.000
182B183GLY00.1050.04428.602-0.007-0.0070.0000.0000.0000.000
183B184ARG10.8230.92829.6900.0760.0760.0000.0000.0000.000
184B185ILE0-0.0190.00326.894-0.003-0.0030.0000.0000.0000.000
185B186PRO0-0.0070.01128.3300.0060.0060.0000.0000.0000.000
186B187LEU00.0310.01626.2240.0080.0080.0000.0000.0000.000
187B188ARG10.9140.96030.7100.0330.0330.0000.0000.0000.000
188B189THR00.0360.01228.7240.0060.0060.0000.0000.0000.000
189B190PHE00.0390.02630.7800.0040.0040.0000.0000.0000.000
190B191ASN0-0.084-0.06533.9450.0010.0010.0000.0000.0000.000
191B192PRO00.0770.04736.5800.0020.0020.0000.0000.0000.000
192B193GLY00.010-0.00939.2510.0000.0000.0000.0000.0000.000
193B194LYS10.8570.94134.5570.0160.0160.0000.0000.0000.000
194B195VAL0-0.0030.02234.903-0.001-0.0010.0000.0000.0000.000
195B196PRO00.0380.00430.2080.0030.0030.0000.0000.0000.000
196B197PRO00.025-0.00333.287-0.002-0.0020.0000.0000.0000.000
197B198SER0-0.0010.01029.994-0.002-0.0020.0000.0000.0000.000
198B199ILE0-0.0110.00926.1680.0050.0050.0000.0000.0000.000
199B200VAL0-0.0100.00423.681-0.002-0.0020.0000.0000.0000.000
200B201LEU0-0.015-0.02725.6630.0040.0040.0000.0000.0000.000
201B202PRO00.0280.00825.424-0.006-0.0060.0000.0000.0000.000
202B203GLY0-0.027-0.00122.9310.0130.0130.0000.0000.0000.000
203B204ASP-1-0.878-0.95421.156-0.026-0.0260.0000.0000.0000.000
204B205TYR00.007-0.01516.205-0.001-0.0010.0000.0000.0000.000
205B206VAL0-0.012-0.00718.9800.0200.0200.0000.0000.0000.000
206B207LYS10.9300.97114.2200.3100.3100.0000.0000.0000.000
207B208PHE0-0.0080.00117.8150.0320.0320.0000.0000.0000.000
208B209VAL00.015-0.00418.304-0.031-0.0310.0000.0000.0000.000
209B210PRO00.023-0.00219.9020.0220.0220.0000.0000.0000.000
210B211ILE0-0.0280.01522.7590.0000.0000.0000.0000.0000.000
211B212ASP-1-0.816-0.92725.560-0.097-0.0970.0000.0000.0000.000
212B213GLU-1-0.872-0.95328.913-0.069-0.0690.0000.0000.0000.000
213B214LYS10.7890.88031.7320.0790.0790.0000.0000.0000.000
214B215GLU-1-0.876-0.92428.127-0.056-0.0560.0000.0000.0000.000
215B216PHE0-0.121-0.05528.899-0.004-0.0040.0000.0000.0000.000
216B217TRP0-0.025-0.01031.3680.0080.0080.0000.0000.0000.000