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

tag_button

FMODB ID: YZR22

Calculation Name: 1H3P-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1H3P

Chain ID: H

ChEMBL ID:

UniProt ID: Q52L64

Base Structure: X-ray

Registration Date: 2023-06-26

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2204373.204447
FMO2-HF: Nuclear repulsion 2121574.224131
FMO2-HF: Total energy -82798.980317
FMO2-MP2: Total energy -83037.574401


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(H:1:GLU)


Summations of interaction energy for fragment #1(H:1:GLU)
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.
-17.524-17.37814.049-7.234-6.9610.072
Interaction energy analysis for fragmet #1(H:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.870 / q_NPA : -0.927
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].
3H3GLN0-0.074-0.0531.834-29.795-30.02114.053-7.097-6.7300.072
4H4LEU0-0.002-0.0075.219-6.523-6.496-0.001-0.006-0.0200.000
5H5VAL00.0160.0067.6150.4510.4510.0000.0000.0000.000
6H6GLU-1-0.808-0.89110.12722.51622.5160.0000.0000.0000.000
7H7SER0-0.064-0.04113.832-0.185-0.1850.0000.0000.0000.000
8H8GLY00.0430.00816.698-0.446-0.4460.0000.0000.0000.000
9H9GLY00.0230.02219.516-0.749-0.7490.0000.0000.0000.000
10H10GLY00.012-0.00721.2320.0950.0950.0000.0000.0000.000
11H11LEU0-0.082-0.02723.980-0.164-0.1640.0000.0000.0000.000
12H12VAL00.0060.00927.706-0.063-0.0630.0000.0000.0000.000
13H13LYS10.8730.93529.825-9.200-9.2000.0000.0000.0000.000
14H14PRO00.031-0.00233.4030.0790.0790.0000.0000.0000.000
15H15GLY0-0.039-0.00835.045-0.207-0.2070.0000.0000.0000.000
16H16GLY0-0.0080.00533.169-0.077-0.0770.0000.0000.0000.000
17H17SER00.002-0.01830.507-0.091-0.0910.0000.0000.0000.000
18H18LEU0-0.051-0.02224.198-0.037-0.0370.0000.0000.0000.000
19H19LYS10.8280.91622.491-13.487-13.4870.0000.0000.0000.000
20H20LEU00.0180.02419.4690.3860.3860.0000.0000.0000.000
21H21SER0-0.016-0.02018.007-0.258-0.2580.0000.0000.0000.000
22H22CYS0-0.0250.00212.9340.0040.0040.0000.0000.0000.000
23H23ALA00.0130.02611.262-1.082-1.0820.0000.0000.0000.000
24H24ALA00.0220.0109.8642.1692.1690.0000.0000.0000.000
25H25SER0-0.014-0.0107.1620.4390.4390.0000.0000.0000.000
26H26GLY00.0610.0214.0162.7722.931-0.001-0.098-0.0600.000
27H27PHE0-0.002-0.0024.683-1.156-1.075-0.001-0.014-0.0660.000
28H28THR00.0090.0077.7830.0370.0370.0000.0000.0000.000
29H29PHE00.0450.02311.296-1.589-1.5890.0000.0000.0000.000
30H30SER0-0.002-0.00612.911-0.767-0.7670.0000.0000.0000.000
31H31SER0-0.054-0.02314.484-1.208-1.2080.0000.0000.0000.000
32H32TYR0-0.054-0.04711.833-0.298-0.2980.0000.0000.0000.000
33H33ALA0-0.0180.00316.023-0.119-0.1190.0000.0000.0000.000
34H34MET0-0.053-0.01812.6091.2321.2320.0000.0000.0000.000
35H35SER00.047-0.02616.479-1.315-1.3150.0000.0000.0000.000
36H36TRP0-0.033-0.01316.8661.3831.3830.0000.0000.0000.000
37H37VAL0-0.014-0.00218.226-0.986-0.9860.0000.0000.0000.000
38H38ARG10.7680.87219.501-11.094-11.0940.0000.0000.0000.000
39H39GLN0-0.017-0.01120.1250.4090.4090.0000.0000.0000.000
40H40SER00.008-0.01222.7620.2420.2420.0000.0000.0000.000
41H41PRO00.022-0.01125.2090.3150.3150.0000.0000.0000.000
42H42GLU-1-0.909-0.92026.94110.28210.2820.0000.0000.0000.000
43H43LYS10.8850.93922.405-13.258-13.2580.0000.0000.0000.000
44H44ARG10.8850.94524.394-10.396-10.3960.0000.0000.0000.000
45H45LEU00.0080.00119.6970.1560.1560.0000.0000.0000.000
46H46GLU-1-0.765-0.86023.12710.47610.4760.0000.0000.0000.000
47H47TRP00.0130.01020.8910.1030.1030.0000.0000.0000.000
48H48VAL0-0.025-0.02222.602-0.578-0.5780.0000.0000.0000.000
49H49ALA00.011-0.00622.843-0.517-0.5170.0000.0000.0000.000
50H50GLU-1-0.877-0.89820.13415.35715.3570.0000.0000.0000.000
51H51VAL0-0.011-0.00220.440-0.702-0.7020.0000.0000.0000.000
52H52SER00.014-0.02120.7310.7050.7050.0000.0000.0000.000
53H52SER00.0110.01118.7930.1110.1110.0000.0000.0000.000
54H53ASP-1-0.771-0.84019.86312.61312.6130.0000.0000.0000.000
55H54GLY0-0.032-0.01722.6940.0150.0150.0000.0000.0000.000
56H55SER0-0.101-0.06924.111-0.357-0.3570.0000.0000.0000.000
57H56TYR0-0.0060.00426.262-0.598-0.5980.0000.0000.0000.000
58H57ALA0-0.006-0.00625.4910.5960.5960.0000.0000.0000.000
59H58TYR0-0.018-0.00724.654-0.689-0.6890.0000.0000.0000.000
60H59TYR00.0520.02225.9340.6490.6490.0000.0000.0000.000
61H60PRO00.0180.02626.704-0.336-0.3360.0000.0000.0000.000
62H61ASP-1-0.822-0.89129.8979.3209.3200.0000.0000.0000.000
63H62THR0-0.053-0.05132.345-0.105-0.1050.0000.0000.0000.000
64H63LEU0-0.061-0.02627.966-0.052-0.0520.0000.0000.0000.000
65H64THR0-0.004-0.01230.9330.1590.1590.0000.0000.0000.000
66H65GLY0-0.0120.00432.119-0.299-0.2990.0000.0000.0000.000
67H66ARG10.7750.86831.516-9.861-9.8610.0000.0000.0000.000
68H67PHE0-0.009-0.01125.7370.2510.2510.0000.0000.0000.000
69H68THR0-0.023-0.01727.060-0.386-0.3860.0000.0000.0000.000
70H69ILE0-0.0330.00920.2030.3510.3510.0000.0000.0000.000
71H70SER0-0.0040.00122.601-0.240-0.2400.0000.0000.0000.000
72H71ARG10.8180.89116.520-15.909-15.9090.0000.0000.0000.000
73H72ASP-1-0.825-0.89519.46114.07414.0740.0000.0000.0000.000
74H73ASN00.0300.00117.6171.7681.7680.0000.0000.0000.000
75H74ALA0-0.0250.00417.5390.3370.3370.0000.0000.0000.000
76H75LYS10.8320.88617.081-13.820-13.8200.0000.0000.0000.000
77H76ASN0-0.037-0.00712.8511.4041.4040.0000.0000.0000.000
78H77THR00.0360.01413.9261.5151.5150.0000.0000.0000.000
79H78LEU00.0080.00815.980-1.105-1.1050.0000.0000.0000.000
80H79TYR0-0.013-0.03117.5520.5310.5310.0000.0000.0000.000
81H80LEU00.0140.00520.204-0.268-0.2680.0000.0000.0000.000
82H81GLU-1-0.857-0.90922.55511.95811.9580.0000.0000.0000.000
83H82MET0-0.0140.00224.401-0.049-0.0490.0000.0000.0000.000
84H82THR00.0520.01727.994-0.134-0.1340.0000.0000.0000.000
85H82SER0-0.026-0.00931.747-0.072-0.0720.0000.0000.0000.000
86H82LEU0-0.038-0.00327.997-0.085-0.0850.0000.0000.0000.000
87H83ARG10.8970.92332.046-9.075-9.0750.0000.0000.0000.000
88H84SER00.0080.00331.8760.2840.2840.0000.0000.0000.000
89H85GLU-1-0.785-0.89231.2489.3689.3680.0000.0000.0000.000
90H86ASP-1-0.754-0.82528.24910.60210.6020.0000.0000.0000.000
91H87THR0-0.039-0.01526.8020.5760.5760.0000.0000.0000.000
92H88ALA00.001-0.00223.621-0.179-0.1790.0000.0000.0000.000
93H89MET0-0.0490.00316.046-0.206-0.2060.0000.0000.0000.000
94H90TYR0-0.002-0.02519.215-0.357-0.3570.0000.0000.0000.000
95H91TYR0-0.001-0.02014.3630.6830.6830.0000.0000.0000.000
96H93ALA00.005-0.01012.9641.7671.7670.0000.0000.0000.000
97H94SER00.015-0.00111.311-1.620-1.6200.0000.0000.0000.000
98H96PHE0-0.014-0.02513.2440.5030.5030.0000.0000.0000.000
99H97ASN0-0.058-0.02514.043-1.445-1.4450.0000.0000.0000.000
100H98TRP00.0400.00213.3021.1381.1380.0000.0000.0000.000
101H99ASP-1-0.841-0.89211.71020.43220.4320.0000.0000.0000.000
102H100VAL0-0.027-0.0127.4782.2192.2190.0000.0000.0000.000
103H101ALA00.0010.0279.821-0.055-0.0550.0000.0000.0000.000
104H102TYR00.0120.0044.325-2.496-2.391-0.001-0.019-0.0850.000
105H103TRP0-0.007-0.0249.276-2.760-2.7600.0000.0000.0000.000
106H104GLY00.0700.0469.2722.5992.5990.0000.0000.0000.000
107H105GLN0-0.061-0.0439.380-1.112-1.1120.0000.0000.0000.000
108H106GLY0-0.005-0.00111.329-1.861-1.8610.0000.0000.0000.000
109H107THR0-0.050-0.03014.690-0.233-0.2330.0000.0000.0000.000
110H108LEU00.000-0.01017.349-0.596-0.5960.0000.0000.0000.000
111H109VAL0-0.0320.00020.787-0.151-0.1510.0000.0000.0000.000
112H110THR0-0.014-0.01523.996-0.285-0.2850.0000.0000.0000.000
113H111VAL00.0090.01127.334-0.136-0.1360.0000.0000.0000.000
114H112SER00.0530.02130.494-0.404-0.4040.0000.0000.0000.000
115H113ALA00.0320.00633.2970.0750.0750.0000.0000.0000.000
116H114ALA00.0230.03533.713-0.156-0.1560.0000.0000.0000.000
117H115LYS10.8800.91633.447-8.983-8.9830.0000.0000.0000.000
118H116THR00.0480.02628.458-0.074-0.0740.0000.0000.0000.000
119H117THR0-0.075-0.04430.732-0.336-0.3360.0000.0000.0000.000
120H118PRO00.0650.02529.0530.2580.2580.0000.0000.0000.000
121H119PRO0-0.0220.01426.829-0.332-0.3320.0000.0000.0000.000
122H120SER0-0.0030.00730.121-0.131-0.1310.0000.0000.0000.000
123H121VAL00.009-0.00128.5960.0850.0850.0000.0000.0000.000
124H122TYR0-0.018-0.01131.782-0.200-0.2000.0000.0000.0000.000
125H123PRO00.0170.01333.1770.1930.1930.0000.0000.0000.000
126H124LEU0-0.030-0.01633.125-0.326-0.3260.0000.0000.0000.000
127H125ALA00.0220.00535.3640.1240.1240.0000.0000.0000.000
128H126PRO00.0010.00137.349-0.179-0.1790.0000.0000.0000.000
129H127GLY00.0480.02239.4820.0040.0040.0000.0000.0000.000
130H128SER0-0.050-0.03442.918-0.158-0.1580.0000.0000.0000.000
131H129LEU00.0440.03346.0140.0430.0430.0000.0000.0000.000
132H130ALA00.0170.01846.0140.1590.1590.0000.0000.0000.000
133H131GLN0-0.038-0.01944.990-0.157-0.1570.0000.0000.0000.000
134H132THR00.0240.00642.2860.2000.2000.0000.0000.0000.000
135H133ASN0-0.027-0.01139.645-0.102-0.1020.0000.0000.0000.000
136H134SER00.0170.02237.6680.0900.0900.0000.0000.0000.000
137H135MET0-0.0040.00231.3210.1650.1650.0000.0000.0000.000
138H136VAL0-0.0170.00134.454-0.273-0.2730.0000.0000.0000.000
139H137THR00.0260.01631.9550.3840.3840.0000.0000.0000.000
140H138LEU0-0.043-0.00731.538-0.317-0.3170.0000.0000.0000.000
141H139GLY00.0920.01830.4750.2650.2650.0000.0000.0000.000
142H140CYS0-0.086-0.00125.7040.1580.1580.0000.0000.0000.000
143H141LEU00.0320.03830.1600.1890.1890.0000.0000.0000.000
144H142VAL0-0.028-0.01627.165-0.027-0.0270.0000.0000.0000.000
145H143LYS11.0000.98530.419-8.461-8.4610.0000.0000.0000.000
146H144GLY00.0210.01432.947-0.007-0.0070.0000.0000.0000.000
147H145TYR0-0.014-0.00726.386-0.243-0.2430.0000.0000.0000.000
148H146PHE00.0660.03629.549-0.022-0.0220.0000.0000.0000.000
149H147PRO00.0010.00425.716-0.089-0.0890.0000.0000.0000.000
150H148GLU-1-0.783-0.88024.24312.63912.6390.0000.0000.0000.000
151H149PRO0-0.003-0.00219.4890.0040.0040.0000.0000.0000.000
152H150VAL00.000-0.01822.491-0.024-0.0240.0000.0000.0000.000
153H151THR0-0.0190.00617.3420.2930.2930.0000.0000.0000.000
154H152VAL0-0.033-0.03620.513-0.417-0.4170.0000.0000.0000.000
155H153THR00.0190.01717.7920.5500.5500.0000.0000.0000.000
156H154TRP0-0.006-0.01021.155-0.926-0.9260.0000.0000.0000.000
157H155ASN00.020-0.00722.2860.3110.3110.0000.0000.0000.000
158H156SER0-0.003-0.01318.4430.2260.2260.0000.0000.0000.000
159H157GLY00.0210.02017.7871.0351.0350.0000.0000.0000.000
160H158SER0-0.045-0.00418.693-0.044-0.0440.0000.0000.0000.000
161H159LEU0-0.031-0.01920.321-0.303-0.3030.0000.0000.0000.000
162H160SER0-0.007-0.03518.1040.0690.0690.0000.0000.0000.000
163H163GLY00.0420.03624.7590.2410.2410.0000.0000.0000.000
164H164VAL0-0.015-0.00322.647-0.518-0.5180.0000.0000.0000.000
165H165HIS0-0.0010.01224.3550.2310.2310.0000.0000.0000.000
166H166THR00.004-0.00823.107-0.438-0.4380.0000.0000.0000.000
167H167PHE0-0.0050.00925.2700.2360.2360.0000.0000.0000.000
168H168PRO00.023-0.00526.3980.1160.1160.0000.0000.0000.000
169H169ALA00.0050.02027.185-0.402-0.4020.0000.0000.0000.000
170H170VAL0-0.031-0.01229.047-0.108-0.1080.0000.0000.0000.000
171H171LEU0-0.013-0.00632.2150.0510.0510.0000.0000.0000.000
172H172GLN0-0.009-0.02233.971-0.349-0.3490.0000.0000.0000.000
173H173SER0-0.017-0.00637.328-0.023-0.0230.0000.0000.0000.000
174H174ASP-1-0.893-0.95635.2668.7848.7840.0000.0000.0000.000
175H175LEU0-0.058-0.01133.5370.2350.2350.0000.0000.0000.000
176H176TYR00.0450.02129.100-0.127-0.1270.0000.0000.0000.000
177H177THR0-0.086-0.05531.681-0.227-0.2270.0000.0000.0000.000
178H178LEU00.0710.05725.009-0.057-0.0570.0000.0000.0000.000
179H179SER0-0.032-0.03729.138-0.455-0.4550.0000.0000.0000.000
180H180SER00.0040.01425.2830.2680.2680.0000.0000.0000.000
181H181SER00.024-0.00227.863-0.492-0.4920.0000.0000.0000.000
182H182VAL00.0030.00226.1260.4480.4480.0000.0000.0000.000
183H183THR0-0.009-0.01128.203-0.374-0.3740.0000.0000.0000.000
184H184VAL0-0.0080.00128.3290.3960.3960.0000.0000.0000.000
185H185PRO00.0610.00430.429-0.332-0.3320.0000.0000.0000.000
186H186SER0-0.027-0.03233.6180.0130.0130.0000.0000.0000.000
187H187SER0-0.0010.01436.088-0.111-0.1110.0000.0000.0000.000
188H188PRO00.0620.03131.747-0.127-0.1270.0000.0000.0000.000
189H189ARG10.9090.98932.984-9.061-9.0610.0000.0000.0000.000
190H190PRO0-0.070-0.05334.730-0.177-0.1770.0000.0000.0000.000
191H191SER0-0.021-0.00636.4590.0410.0410.0000.0000.0000.000
192H192GLU-1-0.882-0.92830.60610.44710.4470.0000.0000.0000.000
193H193THR0-0.013-0.02129.897-0.212-0.2120.0000.0000.0000.000
194H194VAL00.0270.01128.8460.3270.3270.0000.0000.0000.000
195H195THR0-0.034-0.03226.104-0.578-0.5780.0000.0000.0000.000
196H197ASN00.000-0.02421.808-0.010-0.0100.0000.0000.0000.000
197H198VAL0-0.0020.00122.6360.3860.3860.0000.0000.0000.000
198H199ALA00.0230.00720.113-0.129-0.1290.0000.0000.0000.000
199H200HIS00.0320.03022.2500.0010.0010.0000.0000.0000.000
200H201PRO00.0520.02919.019-0.396-0.3960.0000.0000.0000.000
201H202ALA00.0260.01821.277-0.182-0.1820.0000.0000.0000.000
202H203SER0-0.043-0.05124.219-0.512-0.5120.0000.0000.0000.000
203H204SER0-0.024-0.00822.715-0.082-0.0820.0000.0000.0000.000
204H205THR0-0.026-0.00223.776-0.094-0.0940.0000.0000.0000.000
205H206LYS10.8540.90221.038-13.346-13.3460.0000.0000.0000.000
206H207VAL0-0.012-0.00524.097-0.439-0.4390.0000.0000.0000.000
207H208ASP-1-0.789-0.86724.63613.66413.6640.0000.0000.0000.000
208H209LYS10.8610.91427.327-10.113-10.1130.0000.0000.0000.000
209H210LYS10.9730.98230.213-9.589-9.5890.0000.0000.0000.000
210H211ILE0-0.011-0.00130.851-0.331-0.3310.0000.0000.0000.000
211H212VAL00.0420.01733.903-0.035-0.0350.0000.0000.0000.000
212H213PRO0-0.041-0.03337.2730.0390.0390.0000.0000.0000.000
213H214ARG10.8520.92739.817-7.943-7.9430.0000.0000.0000.000
214H215ASP-1-0.837-0.89541.6696.9566.9560.0000.0000.0000.000
215H216CYS0-0.076-0.04145.145-0.015-0.0150.0000.0000.0000.000