Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 5N9RZ

Calculation Name: 1HDM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1HDM

Chain ID: B

ChEMBL ID:

UniProt ID: P28067

Base Structure: X-ray

Registration Date: 2023-09-26

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1639269.286724
FMO2-HF: Nuclear repulsion 1565342.987121
FMO2-HF: Total energy -73926.299602
FMO2-MP2: Total energy -74136.578417


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:3:PHE)


Summations of interaction energy for fragment #1(B:3:PHE)
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.
-9.595-1.9563.957-3.626-7.97-0.011
Interaction energy analysis for fragmet #1(B:3:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.022 / q_NPA : -0.021
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].
3B5ALA0-0.030-0.0233.836-1.1440.469-0.009-0.752-0.8520.001
4B6HIS0-0.0030.0065.8350.0210.0210.0000.0000.0000.000
5B7VAL00.002-0.0139.6680.0180.0180.0000.0000.0000.000
6B8GLU-1-0.924-0.94712.889-0.189-0.1890.0000.0000.0000.000
7B9SER0-0.017-0.02115.1570.0170.0170.0000.0000.0000.000
8B10THR0-0.026-0.01218.9680.0070.0070.0000.0000.0000.000
9B11CYS00.0080.01121.684-0.002-0.0020.0000.0000.0000.000
10B12LEU00.0080.02825.4870.0040.0040.0000.0000.0000.000
11B13LEU00.004-0.00828.153-0.001-0.0010.0000.0000.0000.000
12B14ASP-1-0.759-0.84231.571-0.032-0.0320.0000.0000.0000.000
13B15ASP-1-0.872-0.94834.831-0.024-0.0240.0000.0000.0000.000
14B16ALA0-0.051-0.01637.1220.0010.0010.0000.0000.0000.000
15B17GLY0-0.008-0.00234.410-0.001-0.0010.0000.0000.0000.000
16B18THR0-0.078-0.05834.711-0.003-0.0030.0000.0000.0000.000
17B19PRO0-0.048-0.01831.2540.0000.0000.0000.0000.0000.000
18B20LYS10.8240.86831.1400.0390.0390.0000.0000.0000.000
19B21ASP-1-0.828-0.90425.197-0.080-0.0800.0000.0000.0000.000
20B22PHE0-0.057-0.03222.541-0.002-0.0020.0000.0000.0000.000
21B23THR00.0310.02719.625-0.002-0.0020.0000.0000.0000.000
22B24TYR0-0.004-0.01517.019-0.011-0.0110.0000.0000.0000.000
23B25CYS00.0280.01214.933-0.013-0.0130.0000.0000.0000.000
24B26ILE0-0.030-0.01510.089-0.037-0.0370.0000.0000.0000.000
25B27SER0-0.0060.0029.1170.0850.0850.0000.0000.0000.000
26B28PHE00.005-0.0142.971-4.470-1.5852.799-1.315-4.3690.004
27B29ASN0-0.020-0.0082.573-4.167-1.2131.163-1.522-2.595-0.016
28B30LYS10.9180.9613.8650.3550.5420.004-0.037-0.1540.000
29B31ASP-1-0.876-0.9317.266-0.085-0.0850.0000.0000.0000.000
30B32LEU00.0250.0079.230-0.060-0.0600.0000.0000.0000.000
31B33LEU0-0.015-0.0148.3560.0490.0490.0000.0000.0000.000
32B34THR0-0.051-0.05112.2850.0280.0280.0000.0000.0000.000
33B36TRP00.0650.00817.8620.0030.0030.0000.0000.0000.000
34B37ASP-1-0.803-0.88921.058-0.078-0.0780.0000.0000.0000.000
35B38PRO0-0.015-0.03024.1830.0020.0020.0000.0000.0000.000
36B39GLU-1-0.912-0.93427.294-0.055-0.0550.0000.0000.0000.000
37B40GLU-1-0.944-0.97627.047-0.065-0.0650.0000.0000.0000.000
38B41ASN0-0.115-0.04426.961-0.003-0.0030.0000.0000.0000.000
39B42LYS10.7840.88523.5110.0810.0810.0000.0000.0000.000
40B43MET0-0.043-0.00916.430-0.003-0.0030.0000.0000.0000.000
41B44ALA00.0390.01719.6180.0100.0100.0000.0000.0000.000
42B45PRO0-0.0050.00416.873-0.013-0.0130.0000.0000.0000.000
43B46CYS0-0.0300.00714.7760.0120.0120.0000.0000.0000.000
44B47ASN00.0990.02712.562-0.001-0.0010.0000.0000.0000.000
45B48SER00.0110.01812.5320.0000.0000.0000.0000.0000.000
46B49LEU00.0430.0127.750-0.009-0.0090.0000.0000.0000.000
47B50ALA00.0500.04112.185-0.029-0.0290.0000.0000.0000.000
48B51ASN0-0.015-0.00413.876-0.012-0.0120.0000.0000.0000.000
49B52VAL00.0050.00413.839-0.006-0.0060.0000.0000.0000.000
50B53LEU0-0.008-0.0079.553-0.016-0.0160.0000.0000.0000.000
51B54SER00.012-0.00314.126-0.010-0.0100.0000.0000.0000.000
52B55GLN0-0.045-0.03217.4780.0010.0010.0000.0000.0000.000
53B56HIS00.0300.01115.954-0.012-0.0120.0000.0000.0000.000
54B57LEU0-0.001-0.01414.606-0.005-0.0050.0000.0000.0000.000
55B58ASN00.0440.01918.5220.0020.0020.0000.0000.0000.000
56B59GLN0-0.023-0.00221.2800.0110.0110.0000.0000.0000.000
57B60LYS10.8130.91818.5800.1800.1800.0000.0000.0000.000
58B61ASP-1-0.818-0.90322.972-0.095-0.0950.0000.0000.0000.000
59B62THR00.005-0.00824.3330.0000.0000.0000.0000.0000.000
60B63LEU0-0.057-0.01818.806-0.003-0.0030.0000.0000.0000.000
61B64MET00.0020.01221.3570.0040.0040.0000.0000.0000.000
62B65GLN0-0.0140.00525.1770.0080.0080.0000.0000.0000.000
63B66ARG10.9130.97419.6400.1680.1680.0000.0000.0000.000
64B67LEU00.0040.01020.3910.0060.0060.0000.0000.0000.000
65B68ASN0-0.046-0.04528.0420.0060.0060.0000.0000.0000.000
66B69GLY00.0640.03726.1940.0030.0030.0000.0000.0000.000
67B70LEU00.0330.01026.9240.0010.0010.0000.0000.0000.000
68B71GLN00.0490.02329.6340.0050.0050.0000.0000.0000.000
69B72ASN0-0.043-0.00727.140-0.002-0.0020.0000.0000.0000.000
70B74ALA00.0500.04428.6030.0040.0040.0000.0000.0000.000
71B75THR0-0.060-0.06431.8530.0010.0010.0000.0000.0000.000
72B76HIS0-0.0180.00226.3160.0000.0000.0000.0000.0000.000
73B77THR0-0.013-0.02728.8180.0040.0040.0000.0000.0000.000
74B78GLN00.0070.01231.1550.0040.0040.0000.0000.0000.000
75B79PRO0-0.039-0.02133.1710.0040.0040.0000.0000.0000.000
76B80PHE0-0.015-0.00828.3940.0030.0030.0000.0000.0000.000
77B81TRP0-0.0040.00129.0270.0020.0020.0000.0000.0000.000
78B82GLY00.0800.04834.1230.0030.0030.0000.0000.0000.000
79B83SER0-0.077-0.05535.6450.0030.0030.0000.0000.0000.000
80B84LEU0-0.076-0.04130.3400.0030.0030.0000.0000.0000.000
81B85THR00.0370.01434.4010.0020.0020.0000.0000.0000.000
82B86ASN0-0.0160.00236.0470.0020.0020.0000.0000.0000.000
83B87ARG10.7960.92633.7130.0070.0070.0000.0000.0000.000
84B88THR00.0380.01537.0350.0010.0010.0000.0000.0000.000
85B89ARG10.8770.92537.6460.0010.0010.0000.0000.0000.000
86B90PRO00.0670.04439.7900.0010.0010.0000.0000.0000.000
87B91PRO0-0.029-0.00140.7740.0010.0010.0000.0000.0000.000
88B92SER0-0.0070.00541.403-0.001-0.0010.0000.0000.0000.000
89B93VAL00.024-0.00742.2270.0020.0020.0000.0000.0000.000
90B94GLN0-0.002-0.00544.622-0.001-0.0010.0000.0000.0000.000
91B95VAL0-0.0040.01045.5670.0010.0010.0000.0000.0000.000
92B96ALA0-0.0030.01346.624-0.001-0.0010.0000.0000.0000.000
93B97LYS10.9560.97547.670-0.028-0.0280.0000.0000.0000.000
94B98THR0-0.011-0.00342.5430.0020.0020.0000.0000.0000.000
95B99THR00.0120.00443.364-0.002-0.0020.0000.0000.0000.000
96B100PRO00.005-0.00344.1850.0010.0010.0000.0000.0000.000
97B101PHE00.0190.00439.3790.0020.0020.0000.0000.0000.000
98B102ASN0-0.013-0.01541.595-0.001-0.0010.0000.0000.0000.000
99B103THR00.0010.00143.739-0.003-0.0030.0000.0000.0000.000
100B104ARG10.8810.91747.512-0.025-0.0250.0000.0000.0000.000
101B105GLU-1-0.832-0.86550.6690.0230.0230.0000.0000.0000.000
102B106PRO0-0.0030.00451.2200.0010.0010.0000.0000.0000.000
103B107VAL0-0.038-0.02651.3700.0010.0010.0000.0000.0000.000
104B108MET0-0.0190.01444.2120.0000.0000.0000.0000.0000.000
105B109LEU0-0.0230.00147.9320.0010.0010.0000.0000.0000.000
106B110ALA00.0180.00242.7380.0010.0010.0000.0000.0000.000
107B111CYS0-0.079-0.02844.377-0.001-0.0010.0000.0000.0000.000
108B112TYR00.0090.00139.8180.0020.0020.0000.0000.0000.000
109B113VAL00.0510.00239.737-0.002-0.0020.0000.0000.0000.000
110B114TRP00.017-0.00637.2700.0030.0030.0000.0000.0000.000
111B115GLY00.0390.01936.604-0.002-0.0020.0000.0000.0000.000
112B116PHE0-0.041-0.00235.571-0.002-0.0020.0000.0000.0000.000
113B117TYR00.046-0.00830.6460.0010.0010.0000.0000.0000.000
114B118PRO00.0570.02833.978-0.001-0.0010.0000.0000.0000.000
115B119ALA00.0250.02431.7060.0030.0030.0000.0000.0000.000
116B120GLU-1-0.887-0.95333.4330.0050.0050.0000.0000.0000.000
117B121VAL0-0.024-0.00436.633-0.001-0.0010.0000.0000.0000.000
118B122THR0-0.043-0.05539.2770.0010.0010.0000.0000.0000.000
119B123ILE0-0.019-0.02340.3010.0010.0010.0000.0000.0000.000
120B124THR0-0.025-0.00543.8360.0010.0010.0000.0000.0000.000
121B125TRP00.0370.00245.8530.0000.0000.0000.0000.0000.000
122B126ARG10.9410.96449.955-0.011-0.0110.0000.0000.0000.000
123B127LYS10.8540.94153.785-0.016-0.0160.0000.0000.0000.000
124B128ASN0-0.002-0.02856.257-0.001-0.0010.0000.0000.0000.000
125B129GLY00.0320.02057.809-0.001-0.0010.0000.0000.0000.000
126B130LYS10.9100.95957.460-0.011-0.0110.0000.0000.0000.000
127B131LEU00.0330.00550.4790.0010.0010.0000.0000.0000.000
128B132VAL0-0.040-0.01450.7070.0000.0000.0000.0000.0000.000
129B133MET0-0.009-0.01147.9390.0010.0010.0000.0000.0000.000
130B134HIS00.0230.02246.9460.0000.0000.0000.0000.0000.000
131B135SER00.006-0.00243.8820.0010.0010.0000.0000.0000.000
132B136SER0-0.014-0.00739.051-0.002-0.0020.0000.0000.0000.000
133B137ALA00.0470.03841.6790.0010.0010.0000.0000.0000.000
134B138HIS00.0710.03837.6030.0000.0000.0000.0000.0000.000
135B139LYS10.7960.89537.415-0.020-0.0200.0000.0000.0000.000
136B140THR00.0430.03231.788-0.002-0.0020.0000.0000.0000.000
137B141ALA0-0.013-0.00632.0100.0010.0010.0000.0000.0000.000
138B142GLN0-0.031-0.00726.3780.0030.0030.0000.0000.0000.000
139B143PRO00.0170.00126.067-0.004-0.0040.0000.0000.0000.000
140B144ASN0-0.017-0.01828.0050.0130.0130.0000.0000.0000.000
141B145GLY0-0.0090.00926.3060.0050.0050.0000.0000.0000.000
142B146ASP-1-0.840-0.91127.0670.0150.0150.0000.0000.0000.000
143B147TRP0-0.040-0.02226.846-0.005-0.0050.0000.0000.0000.000
144B148THR0-0.031-0.00230.689-0.002-0.0020.0000.0000.0000.000
145B149TYR00.0230.01628.7020.0020.0020.0000.0000.0000.000
146B150GLN0-0.071-0.04432.6300.0000.0000.0000.0000.0000.000
147B151THR0-0.002-0.01333.9350.0020.0020.0000.0000.0000.000
148B152LEU0-0.009-0.00236.489-0.001-0.0010.0000.0000.0000.000
149B153SER00.0090.00339.1640.0000.0000.0000.0000.0000.000
150B154HIS00.0480.01439.253-0.003-0.0030.0000.0000.0000.000
151B155LEU00.0040.00643.959-0.002-0.0020.0000.0000.0000.000
152B156ALA0-0.031-0.00147.5260.0000.0000.0000.0000.0000.000
153B157LEU0-0.010-0.01349.043-0.001-0.0010.0000.0000.0000.000
154B158THR00.0560.00452.8810.0010.0010.0000.0000.0000.000
155B159PRO0-0.070-0.02555.724-0.001-0.0010.0000.0000.0000.000
156B160SER00.0420.01057.7590.0000.0000.0000.0000.0000.000
157B161TYR00.006-0.00860.9050.0000.0000.0000.0000.0000.000
158B162GLY00.0160.02762.7950.0000.0000.0000.0000.0000.000
159B163ASP-1-0.818-0.87558.4710.0160.0160.0000.0000.0000.000
160B164THR0-0.045-0.02157.2020.0000.0000.0000.0000.0000.000
161B165TYR0-0.043-0.03752.8180.0000.0000.0000.0000.0000.000
162B166THR00.007-0.01752.4970.0010.0010.0000.0000.0000.000
163B168VAL0-0.013-0.01548.270-0.001-0.0010.0000.0000.0000.000
164B169VAL00.0060.00342.8460.0010.0010.0000.0000.0000.000
165B170GLU-1-0.856-0.89844.2510.0070.0070.0000.0000.0000.000
166B171HIS0-0.014-0.02137.5910.0010.0010.0000.0000.0000.000
167B172ILE00.0550.02838.4760.0000.0000.0000.0000.0000.000
168B173GLY00.0080.00241.660-0.002-0.0020.0000.0000.0000.000
169B174ALA0-0.076-0.04442.4530.0000.0000.0000.0000.0000.000
170B175PRO0-0.030-0.00545.9370.0000.0000.0000.0000.0000.000
171B176GLU-1-0.890-0.94849.1490.0030.0030.0000.0000.0000.000
172B177PRO0-0.036-0.01448.5010.0010.0010.0000.0000.0000.000
173B178ILE0-0.025-0.00645.8470.0000.0000.0000.0000.0000.000
174B179LEU00.0020.00048.7720.0010.0010.0000.0000.0000.000
175B180ARG10.8560.91348.279-0.015-0.0150.0000.0000.0000.000
176B181ASP-1-0.826-0.88051.0430.0140.0140.0000.0000.0000.000
177B182TRP00.0330.01852.1600.0010.0010.0000.0000.0000.000
178B183THR00.022-0.00754.234-0.001-0.0010.0000.0000.0000.000
179B184PRO0-0.036-0.02456.7000.0010.0010.0000.0000.0000.000
180B185GLY0-0.0110.01256.9130.0000.0000.0000.0000.0000.000