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: 49GRN

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2210931.828582
FMO2-HF: Nuclear repulsion 2128135.040377
FMO2-HF: Total energy -82796.788205
FMO2-MP2: Total energy -83035.703627


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.
-9.956-3.32.382-4.085-4.9540.038
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 : -0.960 / q_NPA : -0.999
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].
3H3GLN0-0.040-0.0232.328-23.291-16.8742.385-4.018-4.7840.038
4H4LEU0-0.016-0.0104.869-5.843-5.811-0.001-0.011-0.0200.000
5H5VAL00.0220.0207.698-1.090-1.0900.0000.0000.0000.000
6H6GLU-1-0.786-0.89510.05522.29222.2920.0000.0000.0000.000
7H7SER0-0.063-0.04313.790-0.282-0.2820.0000.0000.0000.000
8H8GLY00.0290.00816.562-0.476-0.4760.0000.0000.0000.000
9H9GLY0-0.0120.00019.493-0.714-0.7140.0000.0000.0000.000
10H10GLY00.0260.00521.229-0.016-0.0160.0000.0000.0000.000
11H11LEU0-0.087-0.04023.879-0.153-0.1530.0000.0000.0000.000
12H12VAL0-0.0010.01227.643-0.066-0.0660.0000.0000.0000.000
13H13LYS10.9440.96829.757-8.931-8.9310.0000.0000.0000.000
14H14PRO00.0840.02133.1510.1000.1000.0000.0000.0000.000
15H15GLY0-0.077-0.02334.737-0.159-0.1590.0000.0000.0000.000
16H16GLY0-0.017-0.00232.747-0.087-0.0870.0000.0000.0000.000
17H17SER0-0.027-0.02630.1940.0150.0150.0000.0000.0000.000
18H18LEU0-0.027-0.00323.585-0.015-0.0150.0000.0000.0000.000
19H19LYS10.8770.94122.511-13.169-13.1690.0000.0000.0000.000
20H20LEU0-0.0080.00919.2250.3590.3590.0000.0000.0000.000
21H21SER0-0.032-0.02416.8180.0380.0380.0000.0000.0000.000
22H22CYS00.0090.03312.285-0.068-0.0680.0000.0000.0000.000
23H23ALA0-0.0020.01610.746-0.941-0.9410.0000.0000.0000.000
24H24ALA00.0250.0169.3732.7252.7250.0000.0000.0000.000
25H25SER0-0.049-0.0255.4540.7350.7350.0000.0000.0000.000
26H26GLY00.0980.0384.4044.1444.265-0.001-0.046-0.0750.000
27H27PHE00.0090.0035.118-1.474-1.388-0.001-0.010-0.0750.000
28H28THR00.0160.0128.159-0.098-0.0980.0000.0000.0000.000
29H29PHE00.0390.02711.562-1.939-1.9390.0000.0000.0000.000
30H30SER00.002-0.00912.958-0.879-0.8790.0000.0000.0000.000
31H31SER0-0.056-0.03414.536-1.313-1.3130.0000.0000.0000.000
32H32TYR0-0.065-0.03212.099-0.004-0.0040.0000.0000.0000.000
33H33ALA0-0.0010.01915.709-0.108-0.1080.0000.0000.0000.000
34H34MET0-0.033-0.00612.2501.0371.0370.0000.0000.0000.000
35H35SER00.0650.01216.380-1.467-1.4670.0000.0000.0000.000
36H36TRP0-0.048-0.01916.4971.3151.3150.0000.0000.0000.000
37H37VAL0-0.018-0.00617.888-1.000-1.0000.0000.0000.0000.000
38H38ARG10.7950.88319.054-10.999-10.9990.0000.0000.0000.000
39H39GLN0-0.003-0.00320.2440.0960.0960.0000.0000.0000.000
40H40SER00.0270.03222.3690.1380.1380.0000.0000.0000.000
41H41PRO00.0530.00925.1020.3010.3010.0000.0000.0000.000
42H42GLU-1-0.972-0.98426.8249.7209.7200.0000.0000.0000.000
43H43LYS10.8670.92622.179-13.237-13.2370.0000.0000.0000.000
44H44ARG10.9631.00824.591-10.539-10.5390.0000.0000.0000.000
45H45LEU0-0.006-0.00619.3540.1910.1910.0000.0000.0000.000
46H46GLU-1-0.853-0.92222.93010.67310.6730.0000.0000.0000.000
47H47TRP00.0110.01220.8190.1950.1950.0000.0000.0000.000
48H48VAL00.007-0.03521.966-0.534-0.5340.0000.0000.0000.000
49H49ALA00.016-0.00722.406-0.537-0.5370.0000.0000.0000.000
50H50GLU-1-0.908-0.94220.07615.28215.2820.0000.0000.0000.000
51H51VAL0-0.0110.01320.155-0.716-0.7160.0000.0000.0000.000
52H52SER00.0490.00320.5550.7980.7980.0000.0000.0000.000
53H52SER00.0100.01218.8750.0430.0430.0000.0000.0000.000
54H53ASP-1-0.818-0.90419.81512.90612.9060.0000.0000.0000.000
55H54GLY0-0.054-0.04922.532-0.246-0.2460.0000.0000.0000.000
56H55SER0-0.111-0.04323.879-0.487-0.4870.0000.0000.0000.000
57H56TYR00.0230.00825.833-0.660-0.6600.0000.0000.0000.000
58H57ALA0-0.0050.00725.2480.6240.6240.0000.0000.0000.000
59H58TYR0-0.014-0.00524.975-0.472-0.4720.0000.0000.0000.000
60H59TYR00.0300.02525.8380.6950.6950.0000.0000.0000.000
61H60PRO00.0010.01826.707-0.363-0.3630.0000.0000.0000.000
62H61ASP-1-0.866-0.94929.5609.2739.2730.0000.0000.0000.000
63H62THR0-0.040-0.01931.517-0.031-0.0310.0000.0000.0000.000
64H63LEU0-0.065-0.00826.621-0.121-0.1210.0000.0000.0000.000
65H64THR0-0.0070.00530.4470.2210.2210.0000.0000.0000.000
66H65GLY00.0180.00831.615-0.355-0.3550.0000.0000.0000.000
67H66ARG10.7740.87331.056-9.896-9.8960.0000.0000.0000.000
68H67PHE00.0120.00225.4530.2610.2610.0000.0000.0000.000
69H68THR00.0230.00926.553-0.290-0.2900.0000.0000.0000.000
70H69ILE0-0.043-0.00919.9390.3730.3730.0000.0000.0000.000
71H70SER00.0050.00422.011-0.309-0.3090.0000.0000.0000.000
72H71ARG10.8270.91216.371-16.444-16.4440.0000.0000.0000.000
73H72ASP-1-0.841-0.92218.68314.34414.3440.0000.0000.0000.000
74H73ASN00.016-0.01717.7551.7331.7330.0000.0000.0000.000
75H74ALA0-0.0250.01617.5010.5490.5490.0000.0000.0000.000
76H75LYS10.8830.93417.452-14.628-14.6280.0000.0000.0000.000
77H76ASN00.0020.00712.7440.2690.2690.0000.0000.0000.000
78H77THR00.0250.01713.1881.2901.2900.0000.0000.0000.000
79H78LEU0-0.023-0.02015.209-1.220-1.2200.0000.0000.0000.000
80H79TYR0-0.055-0.05916.9110.0530.0530.0000.0000.0000.000
81H80LEU00.0170.00919.881-0.271-0.2710.0000.0000.0000.000
82H81GLU-1-0.884-0.94322.18811.81611.8160.0000.0000.0000.000
83H82MET0-0.0290.00723.686-0.203-0.2030.0000.0000.0000.000
84H82THR00.0360.00427.681-0.182-0.1820.0000.0000.0000.000
85H82SER0-0.037-0.03431.4110.0160.0160.0000.0000.0000.000
86H82LEU0-0.023-0.00227.611-0.095-0.0950.0000.0000.0000.000
87H83ARG11.0071.00531.677-9.204-9.2040.0000.0000.0000.000
88H84SER00.0560.02431.6050.3420.3420.0000.0000.0000.000
89H85GLU-1-0.903-0.96631.1569.3329.3320.0000.0000.0000.000
90H86ASP-1-0.776-0.84228.23210.54110.5410.0000.0000.0000.000
91H87THR0-0.023-0.00926.8530.5410.5410.0000.0000.0000.000
92H88ALA00.008-0.02323.682-0.194-0.1940.0000.0000.0000.000
93H89MET0-0.0440.01517.5830.1390.1390.0000.0000.0000.000
94H90TYR0-0.033-0.04319.168-0.285-0.2850.0000.0000.0000.000
95H91TYR00.017-0.01014.1340.5840.5840.0000.0000.0000.000
96H93ALA0-0.001-0.01512.4481.6421.6420.0000.0000.0000.000
97H94SER0-0.001-0.00810.980-1.650-1.6500.0000.0000.0000.000
98H96PHE00.009-0.02813.0100.3200.3200.0000.0000.0000.000
99H97ASN0-0.066-0.02713.482-1.562-1.5620.0000.0000.0000.000
100H98TRP00.040-0.00512.5921.3641.3640.0000.0000.0000.000
101H99ASP-1-0.812-0.88411.36721.01921.0190.0000.0000.0000.000
102H100VAL0-0.031-0.0177.5452.2272.2270.0000.0000.0000.000
103H101ALA0-0.0170.0299.4510.5830.5830.0000.0000.0000.000
104H102TYR00.015-0.0055.7671.9591.9590.0000.0000.0000.000
105H103TRP0-0.006-0.0159.129-2.421-2.4210.0000.0000.0000.000
106H104GLY00.0700.0499.2902.2312.2310.0000.0000.0000.000
107H105GLN0-0.051-0.04110.359-2.015-2.0150.0000.0000.0000.000
108H106GLY0-0.026-0.00111.897-1.822-1.8220.0000.0000.0000.000
109H107THR0-0.037-0.01314.8340.0290.0290.0000.0000.0000.000
110H108LEU00.002-0.01817.333-0.668-0.6680.0000.0000.0000.000
111H109VAL0-0.0060.01620.794-0.092-0.0920.0000.0000.0000.000
112H110THR0-0.030-0.02223.860-0.352-0.3520.0000.0000.0000.000
113H111VAL00.0010.02027.198-0.141-0.1410.0000.0000.0000.000
114H112SER00.0330.01230.226-0.355-0.3550.0000.0000.0000.000
115H113ALA00.003-0.01133.0590.0640.0640.0000.0000.0000.000
116H114ALA0-0.0080.01133.780-0.131-0.1310.0000.0000.0000.000
117H115LYS10.9470.96833.821-8.711-8.7110.0000.0000.0000.000
118H116THR00.0260.00228.814-0.013-0.0130.0000.0000.0000.000
119H117THR0-0.066-0.02531.355-0.264-0.2640.0000.0000.0000.000
120H118PRO00.0050.00229.5640.1960.1960.0000.0000.0000.000
121H119PRO00.0200.01427.538-0.299-0.2990.0000.0000.0000.000
122H120SER0-0.0350.00030.803-0.156-0.1560.0000.0000.0000.000
123H121VAL0-0.008-0.01229.0910.0200.0200.0000.0000.0000.000
124H122TYR0-0.033-0.02132.164-0.224-0.2240.0000.0000.0000.000
125H123PRO00.0320.00833.4360.2180.2180.0000.0000.0000.000
126H124LEU0-0.0710.01933.184-0.279-0.2790.0000.0000.0000.000
127H125ALA00.0360.01335.3430.1270.1270.0000.0000.0000.000
128H126PRO00.003-0.02237.424-0.118-0.1180.0000.0000.0000.000
129H127GLY00.0520.03439.7090.0230.0230.0000.0000.0000.000
130H128SER0-0.040-0.02843.126-0.149-0.1490.0000.0000.0000.000
131H129LEU00.0510.03946.2140.0370.0370.0000.0000.0000.000
132H130ALA00.0080.01546.2130.1520.1520.0000.0000.0000.000
133H131GLN0-0.033-0.01745.513-0.160-0.1600.0000.0000.0000.000
134H132THR00.0230.00842.2630.1730.1730.0000.0000.0000.000
135H133ASN0-0.020-0.01139.821-0.073-0.0730.0000.0000.0000.000
136H134SER00.0290.02837.6350.1020.1020.0000.0000.0000.000
137H135MET00.0000.00931.0170.1670.1670.0000.0000.0000.000
138H136VAL0-0.0260.00834.167-0.236-0.2360.0000.0000.0000.000
139H137THR00.0270.00932.0100.2450.2450.0000.0000.0000.000
140H138LEU0-0.080-0.02931.224-0.301-0.3010.0000.0000.0000.000
141H139GLY00.091-0.00731.1210.2010.2010.0000.0000.0000.000
142H140CYS0-0.017-0.01125.7780.3080.3080.0000.0000.0000.000
143H141LEU0-0.0200.00730.4700.1800.1800.0000.0000.0000.000
144H142VAL00.0210.03327.541-0.087-0.0870.0000.0000.0000.000
145H143LYS10.9820.95930.802-8.305-8.3050.0000.0000.0000.000
146H144GLY0-0.020-0.01433.3710.0240.0240.0000.0000.0000.000
147H145TYR00.0070.01126.962-0.103-0.1030.0000.0000.0000.000
148H146PHE00.0190.04329.762-0.026-0.0260.0000.0000.0000.000
149H147PRO0-0.004-0.01626.215-0.075-0.0750.0000.0000.0000.000
150H148GLU-1-0.788-0.89924.47512.20212.2020.0000.0000.0000.000
151H149PRO0-0.016-0.02220.0300.1370.1370.0000.0000.0000.000
152H150VAL00.030-0.01023.068-0.133-0.1330.0000.0000.0000.000
153H151THR0-0.040-0.01717.9680.2790.2790.0000.0000.0000.000
154H152VAL0-0.021-0.00620.986-0.307-0.3070.0000.0000.0000.000
155H153THR0-0.008-0.01918.1470.4460.4460.0000.0000.0000.000
156H154TRP00.013-0.00221.382-0.703-0.7030.0000.0000.0000.000
157H155ASN0-0.006-0.01422.3740.1670.1670.0000.0000.0000.000
158H156SER00.014-0.01018.7880.2730.2730.0000.0000.0000.000
159H157GLY0-0.0090.01018.0320.9040.9040.0000.0000.0000.000
160H158SER0-0.035-0.00718.9260.1610.1610.0000.0000.0000.000
161H159LEU0-0.048-0.02020.263-0.184-0.1840.0000.0000.0000.000
162H160SER00.0250.01317.827-0.030-0.0300.0000.0000.0000.000
163H163GLY00.0290.00824.5780.0790.0790.0000.0000.0000.000
164H164VAL0-0.015-0.00422.823-0.476-0.4760.0000.0000.0000.000
165H165HIS00.0240.02724.4510.3840.3840.0000.0000.0000.000
166H166THR00.001-0.00223.101-0.519-0.5190.0000.0000.0000.000
167H167PHE0-0.013-0.00325.4660.2170.2170.0000.0000.0000.000
168H168PRO00.0420.01026.7970.1340.1340.0000.0000.0000.000
169H169ALA00.0020.01527.996-0.380-0.3800.0000.0000.0000.000
170H170VAL0-0.032-0.01429.967-0.089-0.0890.0000.0000.0000.000
171H171LEU0-0.027-0.01632.669-0.015-0.0150.0000.0000.0000.000
172H172GLN0-0.025-0.02734.533-0.368-0.3680.0000.0000.0000.000
173H173SER0-0.027-0.00937.887-0.052-0.0520.0000.0000.0000.000
174H174ASP-1-0.920-0.96035.5418.5798.5790.0000.0000.0000.000
175H175LEU0-0.0190.00433.7770.1940.1940.0000.0000.0000.000
176H176TYR00.0320.02130.057-0.162-0.1620.0000.0000.0000.000
177H177THR0-0.019-0.02431.997-0.151-0.1510.0000.0000.0000.000
178H178LEU00.0410.04125.754-0.113-0.1130.0000.0000.0000.000
179H179SER00.000-0.01230.018-0.279-0.2790.0000.0000.0000.000
180H180SER00.0000.00425.6740.2850.2850.0000.0000.0000.000
181H181SER00.0230.00228.323-0.252-0.2520.0000.0000.0000.000
182H182VAL00.017-0.00326.4090.4030.4030.0000.0000.0000.000
183H183THR0-0.053-0.02528.286-0.514-0.5140.0000.0000.0000.000
184H184VAL0-0.0140.00328.2600.4070.4070.0000.0000.0000.000
185H185PRO00.0680.01830.309-0.317-0.3170.0000.0000.0000.000
186H186SER0-0.013-0.04833.464-0.001-0.0010.0000.0000.0000.000
187H187SER0-0.020-0.00735.371-0.091-0.0910.0000.0000.0000.000
188H188PRO00.0590.03631.363-0.095-0.0950.0000.0000.0000.000
189H189ARG10.9451.03832.544-9.049-9.0490.0000.0000.0000.000
190H190PRO0-0.085-0.07734.742-0.144-0.1440.0000.0000.0000.000
191H191SER0-0.030-0.01435.1520.0450.0450.0000.0000.0000.000
192H192GLU-1-0.906-0.93830.94910.12610.1260.0000.0000.0000.000
193H193THR0-0.014-0.03329.942-0.258-0.2580.0000.0000.0000.000
194H194VAL00.0250.00828.7380.3110.3110.0000.0000.0000.000
195H195THR0-0.043-0.02327.230-0.381-0.3810.0000.0000.0000.000
196H197ASN00.0520.02622.1960.2360.2360.0000.0000.0000.000
197H198VAL0-0.0140.00522.9450.4540.4540.0000.0000.0000.000
198H199ALA00.0170.00320.9030.0550.0550.0000.0000.0000.000
199H200HIS00.0180.03422.898-0.044-0.0440.0000.0000.0000.000
200H201PRO00.0560.02119.664-0.314-0.3140.0000.0000.0000.000
201H202ALA00.0090.02321.765-0.168-0.1680.0000.0000.0000.000
202H203SER0-0.020-0.03124.590-0.379-0.3790.0000.0000.0000.000
203H204SER0-0.035-0.01823.093-0.076-0.0760.0000.0000.0000.000
204H205THR0-0.016-0.01324.168-0.211-0.2110.0000.0000.0000.000
205H206LYS10.9590.97619.766-15.178-15.1780.0000.0000.0000.000
206H207VAL0-0.016-0.01324.684-0.488-0.4880.0000.0000.0000.000
207H208ASP-1-0.813-0.89225.28713.18013.1800.0000.0000.0000.000
208H209LYS10.9000.94227.942-10.024-10.0240.0000.0000.0000.000
209H210LYS10.9650.97630.365-9.215-9.2150.0000.0000.0000.000
210H211ILE0-0.039-0.02530.886-0.335-0.3350.0000.0000.0000.000
211H212VAL00.0250.00733.9460.0160.0160.0000.0000.0000.000
212H213PRO0-0.040-0.01337.361-0.008-0.0080.0000.0000.0000.000
213H214ARG10.8460.90739.958-7.920-7.9200.0000.0000.0000.000
214H215ASP-1-0.841-0.91941.9136.9916.9910.0000.0000.0000.000
215H216CYS0-0.061-0.01445.388-0.019-0.0190.0000.0000.0000.000