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: 52GZZ

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 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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2209621.854023
FMO2-HF: Nuclear repulsion 2126823.724267
FMO2-HF: Total energy -82798.129756
FMO2-MP2: Total energy -83036.885412


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.
-17.622-17.61714.859-8.04-6.8240.083
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 : -0.878 / q_NPA : -0.931
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].
3H3GLN0-0.083-0.0621.748-30.875-31.13814.863-7.964-6.6370.083
4H4LEU0-0.013-0.0105.375-5.752-5.716-0.001-0.005-0.0300.000
5H5VAL00.0190.0147.686-0.794-0.7940.0000.0000.0000.000
6H6GLU-1-0.795-0.90110.25122.17322.1730.0000.0000.0000.000
7H7SER0-0.057-0.03913.987-0.231-0.2310.0000.0000.0000.000
8H8GLY00.0340.01016.674-0.482-0.4820.0000.0000.0000.000
9H9GLY0-0.0060.00319.531-0.728-0.7280.0000.0000.0000.000
10H10GLY00.0290.00421.282-0.004-0.0040.0000.0000.0000.000
11H11LEU0-0.090-0.04123.843-0.161-0.1610.0000.0000.0000.000
12H12VAL00.0040.00727.600-0.079-0.0790.0000.0000.0000.000
13H13LYS10.9300.97029.795-9.008-9.0080.0000.0000.0000.000
14H14PRO00.0790.01933.2480.0880.0880.0000.0000.0000.000
15H15GLY0-0.074-0.02434.830-0.157-0.1570.0000.0000.0000.000
16H16GLY0-0.0110.00232.888-0.092-0.0920.0000.0000.0000.000
17H17SER0-0.001-0.01630.385-0.079-0.0790.0000.0000.0000.000
18H18LEU0-0.030-0.01424.087-0.002-0.0020.0000.0000.0000.000
19H19LYS10.8240.91122.414-13.238-13.2380.0000.0000.0000.000
20H20LEU00.0040.01519.4530.3600.3600.0000.0000.0000.000
21H21SER0-0.015-0.01817.604-0.181-0.1810.0000.0000.0000.000
22H22CYS0-0.0050.01612.762-0.043-0.0430.0000.0000.0000.000
23H23ALA0-0.0020.02311.116-0.958-0.9580.0000.0000.0000.000
24H24ALA00.0190.0149.9362.6262.6260.0000.0000.0000.000
25H25SER0-0.013-0.0146.9070.9830.9830.0000.0000.0000.000
26H26GLY00.0720.0344.1643.6223.713-0.001-0.054-0.0360.000
27H27PHE00.0060.0004.792-1.340-1.268-0.001-0.012-0.0580.000
28H28THR00.0150.0137.771-0.008-0.0080.0000.0000.0000.000
29H29PHE00.0490.03211.160-1.687-1.6870.0000.0000.0000.000
30H30SER0-0.005-0.01112.759-0.743-0.7430.0000.0000.0000.000
31H31SER0-0.079-0.04114.339-1.243-1.2430.0000.0000.0000.000
32H32TYR0-0.040-0.04411.832-0.054-0.0540.0000.0000.0000.000
33H33ALA0-0.0080.01515.672-0.122-0.1220.0000.0000.0000.000
34H34MET0-0.038-0.00712.1330.9410.9410.0000.0000.0000.000
35H35SER00.076-0.01116.400-1.386-1.3860.0000.0000.0000.000
36H36TRP0-0.051-0.01516.8391.2701.2700.0000.0000.0000.000
37H37VAL0-0.032-0.00917.894-0.988-0.9880.0000.0000.0000.000
38H38ARG10.7940.88419.091-10.923-10.9230.0000.0000.0000.000
39H39GLN0-0.0060.00220.0020.2220.2220.0000.0000.0000.000
40H40SER00.0420.03622.3870.1530.1530.0000.0000.0000.000
41H41PRO00.0460.00625.1200.3060.3060.0000.0000.0000.000
42H42GLU-1-0.987-0.99426.8549.8829.8820.0000.0000.0000.000
43H43LYS10.8780.93422.445-13.276-13.2760.0000.0000.0000.000
44H44ARG10.8760.93724.562-10.490-10.4900.0000.0000.0000.000
45H45LEU0-0.002-0.00319.2650.2060.2060.0000.0000.0000.000
46H46GLU-1-0.766-0.86522.91710.43910.4390.0000.0000.0000.000
47H47TRP00.0010.00020.7930.1310.1310.0000.0000.0000.000
48H48VAL0-0.009-0.02322.192-0.525-0.5250.0000.0000.0000.000
49H49ALA00.004-0.00522.430-0.535-0.5350.0000.0000.0000.000
50H50GLU-1-0.857-0.88920.00115.21015.2100.0000.0000.0000.000
51H51VAL0-0.017-0.00220.253-0.676-0.6760.0000.0000.0000.000
52H52SER00.032-0.01520.5330.7320.7320.0000.0000.0000.000
53H52SER00.0180.01118.6240.0310.0310.0000.0000.0000.000
54H53ASP-1-0.802-0.86119.77412.66112.6610.0000.0000.0000.000
55H54GLY0-0.056-0.04022.480-0.253-0.2530.0000.0000.0000.000
56H55SER0-0.102-0.06723.840-0.400-0.4000.0000.0000.0000.000
57H56TYR00.0150.00625.800-0.631-0.6310.0000.0000.0000.000
58H57ALA0-0.0100.00425.2240.5960.5960.0000.0000.0000.000
59H58TYR0-0.010-0.00424.818-0.658-0.6580.0000.0000.0000.000
60H59TYR00.0420.01825.8580.6650.6650.0000.0000.0000.000
61H60PRO00.0100.01826.600-0.359-0.3590.0000.0000.0000.000
62H61ASP-1-0.845-0.92329.5649.2369.2360.0000.0000.0000.000
63H62THR0-0.064-0.04231.651-0.095-0.0950.0000.0000.0000.000
64H63LEU0-0.056-0.02027.258-0.123-0.1230.0000.0000.0000.000
65H64THR0-0.011-0.00530.4870.2160.2160.0000.0000.0000.000
66H65GLY00.0190.01331.829-0.346-0.3460.0000.0000.0000.000
67H66ARG10.7560.85331.509-9.820-9.8200.0000.0000.0000.000
68H67PHE00.0180.00325.6420.2610.2610.0000.0000.0000.000
69H68THR0-0.004-0.00127.008-0.309-0.3090.0000.0000.0000.000
70H69ILE0-0.0320.00720.0400.3830.3830.0000.0000.0000.000
71H70SER00.0070.00222.523-0.324-0.3240.0000.0000.0000.000
72H71ARG10.8150.90616.373-15.977-15.9770.0000.0000.0000.000
73H72ASP-1-0.800-0.88619.27314.03314.0330.0000.0000.0000.000
74H73ASN00.022-0.00717.5401.6111.6110.0000.0000.0000.000
75H74ALA0-0.0250.01217.2640.5410.5410.0000.0000.0000.000
76H75LYS10.8430.89417.638-13.944-13.9440.0000.0000.0000.000
77H76ASN0-0.040-0.01212.9341.2881.2880.0000.0000.0000.000
78H77THR00.0400.01113.7571.4841.4840.0000.0000.0000.000
79H78LEU0-0.024-0.01415.706-1.202-1.2020.0000.0000.0000.000
80H79TYR0-0.028-0.03617.4260.3820.3820.0000.0000.0000.000
81H80LEU00.0250.00620.322-0.292-0.2920.0000.0000.0000.000
82H81GLU-1-0.879-0.91722.57611.81511.8150.0000.0000.0000.000
83H82MET0-0.0150.00824.148-0.201-0.2010.0000.0000.0000.000
84H82THR00.0260.00027.977-0.154-0.1540.0000.0000.0000.000
85H82SER0-0.015-0.01831.6960.0010.0010.0000.0000.0000.000
86H82LEU0-0.026-0.00127.743-0.085-0.0850.0000.0000.0000.000
87H83ARG10.9020.93431.862-9.082-9.0820.0000.0000.0000.000
88H84SER00.0290.01831.7190.2700.2700.0000.0000.0000.000
89H85GLU-1-0.792-0.90031.2149.3559.3550.0000.0000.0000.000
90H86ASP-1-0.768-0.82328.34610.51910.5190.0000.0000.0000.000
91H87THR0-0.019-0.00226.9720.5490.5490.0000.0000.0000.000
92H88ALA00.003-0.01423.711-0.181-0.1810.0000.0000.0000.000
93H89MET0-0.064-0.00716.280-0.223-0.2230.0000.0000.0000.000
94H90TYR00.004-0.02219.319-0.301-0.3010.0000.0000.0000.000
95H91TYR00.004-0.01614.4950.6460.6460.0000.0000.0000.000
96H93ALA00.009-0.01012.4901.6541.6540.0000.0000.0000.000
97H94SER00.006-0.00210.940-1.646-1.6460.0000.0000.0000.000
98H96PHE00.000-0.02512.9480.4790.4790.0000.0000.0000.000
99H97ASN0-0.060-0.02613.545-1.395-1.3950.0000.0000.0000.000
100H98TRP00.0490.00812.5981.2331.2330.0000.0000.0000.000
101H99ASP-1-0.836-0.89011.40820.55420.5540.0000.0000.0000.000
102H100VAL0-0.029-0.0187.2862.1422.1420.0000.0000.0000.000
103H101ALA0-0.0160.0279.4480.5240.5240.0000.0000.0000.000
104H102TYR00.0210.0004.732-0.591-0.522-0.001-0.005-0.0630.000
105H103TRP0-0.010-0.0199.065-2.482-2.4820.0000.0000.0000.000
106H104GLY00.0780.0549.3062.3042.3040.0000.0000.0000.000
107H105GLN0-0.046-0.0339.905-1.484-1.4840.0000.0000.0000.000
108H106GLY0-0.018-0.00411.826-1.900-1.9000.0000.0000.0000.000
109H107THR0-0.016-0.01014.8630.1570.1570.0000.0000.0000.000
110H108LEU0-0.037-0.02517.347-0.691-0.6910.0000.0000.0000.000
111H109VAL0-0.0270.00420.752-0.089-0.0890.0000.0000.0000.000
112H110THR0-0.025-0.01823.883-0.335-0.3350.0000.0000.0000.000
113H111VAL00.0100.01927.167-0.148-0.1480.0000.0000.0000.000
114H112SER00.0350.00730.253-0.387-0.3870.0000.0000.0000.000
115H113ALA00.009-0.00733.0280.0630.0630.0000.0000.0000.000
116H114ALA0-0.0070.01133.756-0.125-0.1250.0000.0000.0000.000
117H115LYS10.9220.95233.648-8.926-8.9260.0000.0000.0000.000
118H116THR00.0300.00828.403-0.069-0.0690.0000.0000.0000.000
119H117THR0-0.057-0.02431.131-0.292-0.2920.0000.0000.0000.000
120H118PRO00.0280.01329.2180.1880.1880.0000.0000.0000.000
121H119PRO00.0090.01827.113-0.296-0.2960.0000.0000.0000.000
122H120SER0-0.037-0.00430.398-0.166-0.1660.0000.0000.0000.000
123H121VAL00.0100.00028.5080.0060.0060.0000.0000.0000.000
124H122TYR0-0.013-0.00931.645-0.217-0.2170.0000.0000.0000.000
125H123PRO00.0270.01733.2130.2230.2230.0000.0000.0000.000
126H124LEU0-0.052-0.00833.572-0.286-0.2860.0000.0000.0000.000
127H125ALA00.0290.01135.2500.1300.1300.0000.0000.0000.000
128H126PRO00.018-0.00737.143-0.133-0.1330.0000.0000.0000.000
129H127GLY00.0500.02839.6100.0330.0330.0000.0000.0000.000
130H128SER0-0.046-0.02943.024-0.151-0.1510.0000.0000.0000.000
131H129LEU00.0510.03846.1020.0420.0420.0000.0000.0000.000
132H130ALA00.0130.01646.2050.1540.1540.0000.0000.0000.000
133H131GLN0-0.037-0.01945.209-0.149-0.1490.0000.0000.0000.000
134H132THR00.0240.00742.2050.1870.1870.0000.0000.0000.000
135H133ASN0-0.021-0.01239.742-0.096-0.0960.0000.0000.0000.000
136H134SER00.0180.02637.5940.1040.1040.0000.0000.0000.000
137H135MET00.0140.01231.1150.1530.1530.0000.0000.0000.000
138H136VAL0-0.0170.00234.064-0.244-0.2440.0000.0000.0000.000
139H137THR0-0.005-0.01431.7380.2530.2530.0000.0000.0000.000
140H138LEU0-0.067-0.02331.209-0.287-0.2870.0000.0000.0000.000
141H139GLY00.0850.00931.0210.2070.2070.0000.0000.0000.000
142H140CYS0-0.063-0.02325.6800.3520.3520.0000.0000.0000.000
143H141LEU0-0.0250.01230.2010.1850.1850.0000.0000.0000.000
144H142VAL00.0120.02327.078-0.097-0.0970.0000.0000.0000.000
145H143LYS10.9760.96630.321-8.396-8.3960.0000.0000.0000.000
146H144GLY00.0040.00332.9570.0260.0260.0000.0000.0000.000
147H145TYR0-0.012-0.01826.566-0.127-0.1270.0000.0000.0000.000
148H146PHE00.0430.05729.541-0.013-0.0130.0000.0000.0000.000
149H147PRO0-0.007-0.01525.836-0.081-0.0810.0000.0000.0000.000
150H148GLU-1-0.769-0.87324.25612.25912.2590.0000.0000.0000.000
151H149PRO0-0.008-0.01719.6330.0980.0980.0000.0000.0000.000
152H150VAL00.038-0.01022.693-0.156-0.1560.0000.0000.0000.000
153H151THR0-0.0290.00417.2870.2160.2160.0000.0000.0000.000
154H152VAL0-0.025-0.02120.514-0.336-0.3360.0000.0000.0000.000
155H153THR00.0210.01717.9130.5260.5260.0000.0000.0000.000
156H154TRP00.0090.00921.300-0.721-0.7210.0000.0000.0000.000
157H155ASN00.001-0.01822.3190.1840.1840.0000.0000.0000.000
158H156SER00.006-0.01218.7810.2390.2390.0000.0000.0000.000
159H157GLY0-0.0030.00617.9820.9070.9070.0000.0000.0000.000
160H158SER0-0.042-0.00418.849-0.092-0.0920.0000.0000.0000.000
161H159LEU0-0.035-0.01820.213-0.137-0.1370.0000.0000.0000.000
162H160SER00.0170.00917.8360.0570.0570.0000.0000.0000.000
163H163GLY00.0330.00824.3700.0700.0700.0000.0000.0000.000
164H164VAL0-0.024-0.00522.659-0.486-0.4860.0000.0000.0000.000
165H165HIS00.0180.02324.2730.3210.3210.0000.0000.0000.000
166H166THR00.0100.01223.175-0.543-0.5430.0000.0000.0000.000
167H167PHE0-0.0090.00425.2960.2270.2270.0000.0000.0000.000
168H168PRO00.0470.01226.5940.1330.1330.0000.0000.0000.000
169H169ALA00.0010.01027.730-0.384-0.3840.0000.0000.0000.000
170H170VAL0-0.036-0.01829.606-0.092-0.0920.0000.0000.0000.000
171H171LEU0-0.028-0.00932.480-0.010-0.0100.0000.0000.0000.000
172H172GLN0-0.011-0.02134.262-0.341-0.3410.0000.0000.0000.000
173H173SER0-0.026-0.00937.600-0.052-0.0520.0000.0000.0000.000
174H174ASP-1-0.910-0.96135.3218.6658.6650.0000.0000.0000.000
175H175LEU0-0.029-0.00533.5390.1950.1950.0000.0000.0000.000
176H176TYR00.0210.01829.703-0.150-0.1500.0000.0000.0000.000
177H177THR0-0.029-0.02931.630-0.148-0.1480.0000.0000.0000.000
178H178LEU00.0300.03325.312-0.106-0.1060.0000.0000.0000.000
179H179SER0-0.009-0.01129.802-0.307-0.3070.0000.0000.0000.000
180H180SER00.007-0.01525.4150.2910.2910.0000.0000.0000.000
181H181SER00.0170.00228.196-0.282-0.2820.0000.0000.0000.000
182H182VAL00.021-0.00526.2020.4300.4300.0000.0000.0000.000
183H183THR0-0.042-0.00828.154-0.547-0.5470.0000.0000.0000.000
184H184VAL0-0.0020.00528.1020.4220.4220.0000.0000.0000.000
185H185PRO00.0460.01230.234-0.322-0.3220.0000.0000.0000.000
186H186SER0-0.009-0.03633.346-0.009-0.0090.0000.0000.0000.000
187H187SER0-0.0120.00035.793-0.066-0.0660.0000.0000.0000.000
188H188PRO00.0610.04031.323-0.099-0.0990.0000.0000.0000.000
189H189ARG10.9121.03332.793-9.060-9.0600.0000.0000.0000.000
190H190PRO0-0.074-0.07034.679-0.147-0.1470.0000.0000.0000.000
191H191SER0-0.037-0.02235.6870.0540.0540.0000.0000.0000.000
192H192GLU-1-0.868-0.93630.75010.34910.3490.0000.0000.0000.000
193H193THR0-0.002-0.02329.895-0.255-0.2550.0000.0000.0000.000
194H194VAL00.0280.01328.7130.3130.3130.0000.0000.0000.000
195H195THR0-0.014-0.01226.482-0.568-0.5680.0000.0000.0000.000
196H197ASN0-0.023-0.04121.800-0.045-0.0450.0000.0000.0000.000
197H198VAL00.0100.01122.4500.4780.4780.0000.0000.0000.000
198H199ALA00.0240.00620.3670.0320.0320.0000.0000.0000.000
199H200HIS00.0120.02422.437-0.032-0.0320.0000.0000.0000.000
200H201PRO00.0610.02819.343-0.341-0.3410.0000.0000.0000.000
201H202ALA00.0060.01921.485-0.202-0.2020.0000.0000.0000.000
202H203SER0-0.018-0.04824.385-0.413-0.4130.0000.0000.0000.000
203H204SER0-0.042-0.01922.802-0.096-0.0960.0000.0000.0000.000
204H205THR0-0.0150.00023.867-0.201-0.2010.0000.0000.0000.000
205H206LYS10.9250.95820.780-13.590-13.5900.0000.0000.0000.000
206H207VAL0-0.027-0.01224.216-0.504-0.5040.0000.0000.0000.000
207H208ASP-1-0.828-0.90224.46613.50713.5070.0000.0000.0000.000
208H209LYS10.8810.93027.359-10.038-10.0380.0000.0000.0000.000
209H210LYS10.9810.97730.130-9.465-9.4650.0000.0000.0000.000
210H211ILE0-0.024-0.02430.888-0.355-0.3550.0000.0000.0000.000
211H212VAL00.0310.01833.9040.0110.0110.0000.0000.0000.000
212H213PRO0-0.059-0.02237.329-0.003-0.0030.0000.0000.0000.000
213H214ARG10.8550.90939.909-7.954-7.9540.0000.0000.0000.000
214H215ASP-1-0.829-0.89341.8636.9426.9420.0000.0000.0000.000
215H216CYS0-0.073-0.03645.334-0.014-0.0140.0000.0000.0000.000