FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 7M6ZK

Calculation Name: 2H1S-B-Xray372

Preferred Name: Glyoxylate reductase/hydroxypyruvate reductase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2H1S

Chain ID: B

ChEMBL ID: CHEMBL4295972

UniProt ID: Q9UBQ7

Base Structure: X-ray

Registration Date: 2023-09-27

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 321
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4444802.420726
FMO2-HF: Nuclear repulsion 4322428.429397
FMO2-HF: Total energy -122373.991329
FMO2-MP2: Total energy -122729.708428


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:6:LEU)


Summations of interaction energy for fragment #1(B:6:LEU)
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.
-13.617-4.2513.566-4.784-8.149-0.041
Interaction energy analysis for fragmet #1(B:6:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / q_NPA : -0.020
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].
3B8LYS10.9050.9393.801-0.3231.019-0.004-0.557-0.7800.002
4B9VAL0-0.005-0.0065.5330.6110.6110.0000.0000.0000.000
5B10PHE00.0060.0148.265-0.059-0.0590.0000.0000.0000.000
6B11VAL0-0.031-0.01811.5130.1090.1090.0000.0000.0000.000
7B12THR0-0.028-0.05014.207-0.013-0.0130.0000.0000.0000.000
8B13ARG10.9110.94417.5810.2740.2740.0000.0000.0000.000
9B14ARG10.9371.00317.4700.2650.2650.0000.0000.0000.000
10B15ILE0-0.0150.00315.8200.0390.0390.0000.0000.0000.000
11B16PRO0-0.017-0.02819.342-0.011-0.0110.0000.0000.0000.000
12B17ALA00.023-0.00318.662-0.023-0.0230.0000.0000.0000.000
13B18GLU-1-0.896-0.95217.416-0.216-0.2160.0000.0000.0000.000
14B19GLY00.0370.02516.786-0.007-0.0070.0000.0000.0000.000
15B20ARG10.9310.96613.7660.3530.3530.0000.0000.0000.000
16B21VAL0-0.026-0.01012.670-0.085-0.0850.0000.0000.0000.000
17B22ALA0-0.008-0.00612.835-0.036-0.0360.0000.0000.0000.000
18B23LEU00.001-0.0059.8370.0000.0000.0000.0000.0000.000
19B24ALA0-0.013-0.0038.368-0.201-0.2010.0000.0000.0000.000
20B25ARG10.9000.9509.0610.2790.2790.0000.0000.0000.000
21B26ALA0-0.0180.0136.9200.1800.1800.0000.0000.0000.000
22B27ALA00.0300.0094.979-0.467-0.4670.0000.0000.0000.000
23B28ASP-1-0.832-0.8772.786-1.763-0.3750.857-0.748-1.497-0.008
24B29CYS0-0.064-0.0412.841-2.3960.3140.792-1.520-1.983-0.016
25B30GLU-1-0.897-0.9332.532-9.007-5.1601.894-2.002-3.740-0.019
26B31VAL0-0.040-0.0303.5860.7990.8780.0270.043-0.1490.000
27B32GLU-1-0.836-0.9027.168-0.734-0.7340.0000.0000.0000.000
28B33GLN0-0.078-0.05010.0390.0540.0540.0000.0000.0000.000
29B34TRP00.018-0.00213.3870.0090.0090.0000.0000.0000.000
30B35ASP-1-0.952-0.97217.023-0.414-0.4140.0000.0000.0000.000
31B36SER0-0.016-0.01618.1530.0440.0440.0000.0000.0000.000
32B37ASP-1-0.850-0.93921.457-0.260-0.2600.0000.0000.0000.000
33B38GLU-1-0.923-0.96624.222-0.174-0.1740.0000.0000.0000.000
34B39PRO0-0.0320.00023.705-0.026-0.0260.0000.0000.0000.000
35B40ILE00.0110.02218.7410.0000.0000.0000.0000.0000.000
36B41PRO00.001-0.00822.7250.0180.0180.0000.0000.0000.000
37B42ALA00.0360.01322.832-0.019-0.0190.0000.0000.0000.000
38B43LYS10.9820.97822.5970.1630.1630.0000.0000.0000.000
39B44GLU-1-0.903-0.95120.234-0.335-0.3350.0000.0000.0000.000
40B45LEU0-0.0080.00417.732-0.046-0.0460.0000.0000.0000.000
41B46GLU-1-0.964-0.99617.704-0.217-0.2170.0000.0000.0000.000
42B47ARG10.9300.96315.5200.4260.4260.0000.0000.0000.000
43B48GLY00.0090.00914.403-0.038-0.0380.0000.0000.0000.000
44B49VAL0-0.033-0.01912.849-0.096-0.0960.0000.0000.0000.000
45B50ALA00.0040.02113.3290.0060.0060.0000.0000.0000.000
46B51GLY0-0.039-0.02310.530-0.103-0.1030.0000.0000.0000.000
47B52ALA0-0.049-0.0029.141-0.150-0.1500.0000.0000.0000.000
48B53HIS00.0670.0176.119-0.092-0.0920.0000.0000.0000.000
49B54GLY00.0180.0029.5160.2000.2000.0000.0000.0000.000
50B55LEU0-0.0020.01811.012-0.142-0.1420.0000.0000.0000.000
51B56LEU0-0.022-0.00913.7800.0660.0660.0000.0000.0000.000
52B57CYS0-0.041-0.00215.452-0.015-0.0150.0000.0000.0000.000
53B58LEU0-0.012-0.03418.8100.0210.0210.0000.0000.0000.000
54B59LEU00.0160.01422.4080.0050.0050.0000.0000.0000.000
55B60SER00.0280.00624.8850.0030.0030.0000.0000.0000.000
56B61ASP-1-0.832-0.87521.349-0.260-0.2600.0000.0000.0000.000
57B62HIS00.0500.02023.9090.0080.0080.0000.0000.0000.000
58B63VAL00.002-0.00119.985-0.012-0.0120.0000.0000.0000.000
59B64ASP-1-0.807-0.90822.955-0.112-0.1120.0000.0000.0000.000
60B65LYS10.9160.93123.3890.0410.0410.0000.0000.0000.000
61B66ARG10.9440.97523.5620.1090.1090.0000.0000.0000.000
62B67ILE00.0510.04419.041-0.011-0.0110.0000.0000.0000.000
63B68LEU0-0.006-0.01019.037-0.019-0.0190.0000.0000.0000.000
64B69ASP-1-0.886-0.92919.021-0.067-0.0670.0000.0000.0000.000
65B70ALA0-0.028-0.00918.6390.0030.0030.0000.0000.0000.000
66B71ALA0-0.0020.02815.072-0.023-0.0230.0000.0000.0000.000
67B72GLY00.0490.03613.996-0.055-0.0550.0000.0000.0000.000
68B73ALA0-0.060-0.07214.7240.0030.0030.0000.0000.0000.000
69B74ASN0-0.060-0.0369.1890.2250.2250.0000.0000.0000.000
70B75LEU0-0.0130.02011.6530.0350.0350.0000.0000.0000.000
71B76LYS10.9310.9729.554-0.550-0.5500.0000.0000.0000.000
72B77VAL0-0.063-0.01712.1360.0280.0280.0000.0000.0000.000
73B78ILE00.0390.02014.294-0.080-0.0800.0000.0000.0000.000
74B79SER0-0.058-0.04016.0870.0540.0540.0000.0000.0000.000
75B80THR00.042-0.00317.725-0.031-0.0310.0000.0000.0000.000
76B81MET0-0.038-0.01820.0900.0240.0240.0000.0000.0000.000
77B82SER0-0.068-0.05622.1550.0000.0000.0000.0000.0000.000
78B83VAL00.0030.03525.3690.0050.0050.0000.0000.0000.000
79B84GLY00.013-0.00328.1050.0090.0090.0000.0000.0000.000
80B85ILE00.0600.02225.628-0.010-0.0100.0000.0000.0000.000
81B86ASP-1-0.892-0.94227.463-0.085-0.0850.0000.0000.0000.000
82B87HIS00.0330.03322.8560.0160.0160.0000.0000.0000.000
83B88LEU0-0.018-0.01121.786-0.012-0.0120.0000.0000.0000.000
84B89ALA00.0150.01324.8820.0140.0140.0000.0000.0000.000
85B90LEU0-0.003-0.01625.4480.0070.0070.0000.0000.0000.000
86B91ASP-1-0.889-0.93726.3160.0000.0000.0000.0000.0000.000
87B92GLU-1-0.881-0.95524.779-0.015-0.0150.0000.0000.0000.000
88B93ILE00.0240.01120.9580.0080.0080.0000.0000.0000.000
89B94LYS10.9610.98222.240-0.017-0.0170.0000.0000.0000.000
90B95LYS10.8340.91524.3890.0170.0170.0000.0000.0000.000
91B96ARG10.7640.85420.0370.0650.0650.0000.0000.0000.000
92B97GLY00.0000.01519.7680.0160.0160.0000.0000.0000.000
93B98ILE0-0.070-0.01816.8100.0200.0200.0000.0000.0000.000
94B99ARG10.8150.88915.210-0.153-0.1530.0000.0000.0000.000
95B100VAL00.0480.01718.115-0.035-0.0350.0000.0000.0000.000
96B101GLY0-0.0080.01519.4940.0240.0240.0000.0000.0000.000
97B102TYR0-0.0100.00320.458-0.024-0.0240.0000.0000.0000.000
98B103THR0-0.019-0.06222.6930.0020.0020.0000.0000.0000.000
99B104PRO00.0270.04125.185-0.005-0.0050.0000.0000.0000.000
100B105ASP-1-0.903-0.94528.345-0.035-0.0350.0000.0000.0000.000
101B106VAL0-0.039-0.03426.288-0.001-0.0010.0000.0000.0000.000
102B107LEU00.024-0.00528.361-0.004-0.0040.0000.0000.0000.000
103B108THR0-0.0460.00531.1390.0000.0000.0000.0000.0000.000
104B109ASP-1-0.859-0.95134.386-0.047-0.0470.0000.0000.0000.000
105B110THR0-0.017-0.02632.6050.0030.0030.0000.0000.0000.000
106B111THR00.000-0.00333.640-0.002-0.0020.0000.0000.0000.000
107B112ALA00.001-0.00535.9280.0020.0020.0000.0000.0000.000
108B113GLU-1-0.997-0.99237.885-0.066-0.0660.0000.0000.0000.000
109B114LEU00.0300.02537.1210.0020.0020.0000.0000.0000.000
110B115ALA00.008-0.00139.2150.0020.0020.0000.0000.0000.000
111B116VAL0-0.0080.00341.4530.0020.0020.0000.0000.0000.000
112B117SER0-0.004-0.00941.7520.0020.0020.0000.0000.0000.000
113B118LEU0-0.0170.00341.6270.0010.0010.0000.0000.0000.000
114B119LEU00.0150.00544.0600.0020.0020.0000.0000.0000.000
115B120LEU0-0.003-0.01147.0030.0020.0020.0000.0000.0000.000
116B121THR0-0.025-0.01245.8770.0010.0010.0000.0000.0000.000
117B122THR00.0080.00346.8850.0000.0000.0000.0000.0000.000
118B123CYS0-0.087-0.01549.4770.0010.0010.0000.0000.0000.000
119B124ARG10.9140.93151.7550.0400.0400.0000.0000.0000.000
120B125ARG10.8210.91752.4170.0400.0400.0000.0000.0000.000
121B126LEU00.0010.00148.9310.0000.0000.0000.0000.0000.000
122B127PRO00.0100.01347.5430.0000.0000.0000.0000.0000.000
123B128GLU-1-0.773-0.89349.866-0.045-0.0450.0000.0000.0000.000
124B129ALA00.0100.00253.2940.0010.0010.0000.0000.0000.000
125B130ILE0-0.069-0.04547.8230.0000.0000.0000.0000.0000.000
126B131GLU-1-0.932-0.97651.555-0.059-0.0590.0000.0000.0000.000
127B132GLU-1-0.880-0.93753.012-0.044-0.0440.0000.0000.0000.000
128B133VAL0-0.090-0.03754.1790.0010.0010.0000.0000.0000.000
129B134LYS10.9050.94347.1380.0670.0670.0000.0000.0000.000
130B135ASN00.0090.02054.3710.0010.0010.0000.0000.0000.000
131B136GLY0-0.024-0.01156.9200.0010.0010.0000.0000.0000.000
132B137GLY00.0350.03159.4060.0020.0020.0000.0000.0000.000
133B138TRP0-0.125-0.05557.5240.0020.0020.0000.0000.0000.000
134B139THR00.018-0.00761.4000.0010.0010.0000.0000.0000.000
135B140SER0-0.002-0.01164.4710.0010.0010.0000.0000.0000.000
136B141TRP00.0230.02663.017-0.001-0.0010.0000.0000.0000.000
137B142LYS10.9210.94964.4510.0350.0350.0000.0000.0000.000
138B143PRO00.0380.01464.812-0.001-0.0010.0000.0000.0000.000
139B144LEU0-0.015-0.00966.0280.0000.0000.0000.0000.0000.000
140B145TRP0-0.0040.00759.8710.0000.0000.0000.0000.0000.000
141B146LEU00.005-0.00256.4250.0000.0000.0000.0000.0000.000
142B147CYS0-0.0130.00458.4840.0000.0000.0000.0000.0000.000
143B148GLY00.0470.03356.803-0.001-0.0010.0000.0000.0000.000
144B149TYR00.0180.02056.6080.0020.0020.0000.0000.0000.000
145B150GLY00.004-0.01255.243-0.002-0.0020.0000.0000.0000.000
146B151LEU00.020-0.00350.9370.0010.0010.0000.0000.0000.000
147B152THR00.0050.01555.3910.0010.0010.0000.0000.0000.000
148B153GLN0-0.051-0.03058.5360.0000.0000.0000.0000.0000.000
149B154SER0-0.0060.02155.0660.0000.0000.0000.0000.0000.000
150B155THR0-0.005-0.00854.9150.0020.0020.0000.0000.0000.000
151B156VAL00.0070.01149.144-0.002-0.0020.0000.0000.0000.000
152B157GLY00.0300.01350.5500.0020.0020.0000.0000.0000.000
153B158ILE0-0.048-0.03444.266-0.003-0.0030.0000.0000.0000.000
154B159ILE00.0240.00543.4620.0030.0030.0000.0000.0000.000
155B160GLY00.0150.00541.448-0.003-0.0030.0000.0000.0000.000
156B161LEU00.0030.00541.883-0.003-0.0030.0000.0000.0000.000
157B162GLY00.0330.01238.5420.0030.0030.0000.0000.0000.000
158B163ARG10.9590.97735.1280.0150.0150.0000.0000.0000.000
159B164ILE00.0670.02433.6900.0000.0000.0000.0000.0000.000
160B165GLY00.0870.04438.0130.0000.0000.0000.0000.0000.000
161B166GLN0-0.008-0.00640.6210.0020.0020.0000.0000.0000.000
162B167ALA00.0020.01139.4000.0010.0010.0000.0000.0000.000
163B168ILE0-0.014-0.00540.607-0.002-0.0020.0000.0000.0000.000
164B169ALA00.0160.00343.3340.0010.0010.0000.0000.0000.000
165B170ARG10.8180.88540.9010.0270.0270.0000.0000.0000.000
166B171ARG10.8630.95138.8070.0500.0500.0000.0000.0000.000
167B172LEU00.0450.01845.9960.0000.0000.0000.0000.0000.000
168B173LYS10.9711.01048.9070.0200.0200.0000.0000.0000.000
169B174PRO0-0.035-0.03049.6420.0010.0010.0000.0000.0000.000
170B175PHE0-0.031-0.01348.4500.0000.0000.0000.0000.0000.000
171B176GLY0-0.019-0.00653.4770.0000.0000.0000.0000.0000.000
172B177VAL0-0.042-0.01151.9230.0010.0010.0000.0000.0000.000
173B178GLN0-0.0010.01055.2450.0000.0000.0000.0000.0000.000
174B179ARG10.9170.97056.0870.0190.0190.0000.0000.0000.000
175B180PHE00.0420.01949.235-0.002-0.0020.0000.0000.0000.000
176B181LEU00.0090.01451.7370.0020.0020.0000.0000.0000.000
177B182TYR00.0250.01446.496-0.002-0.0020.0000.0000.0000.000
178B183THR0-0.001-0.03447.2910.0020.0020.0000.0000.0000.000
179B184GLY00.007-0.00844.644-0.002-0.0020.0000.0000.0000.000
180B185ARG10.9290.96342.9030.0130.0130.0000.0000.0000.000
181B186GLN00.0140.00843.4490.0020.0020.0000.0000.0000.000
182B187PRO0-0.0180.00245.682-0.002-0.0020.0000.0000.0000.000
183B188ARG10.8890.94538.7060.0150.0150.0000.0000.0000.000
184B189PRO00.0240.00646.091-0.001-0.0010.0000.0000.0000.000
185B190GLU-1-0.902-0.95645.0370.0030.0030.0000.0000.0000.000
186B191GLU-1-0.892-0.94541.547-0.008-0.0080.0000.0000.0000.000
187B192ALA0-0.017-0.01144.821-0.003-0.0030.0000.0000.0000.000
188B193ALA00.0160.00848.012-0.001-0.0010.0000.0000.0000.000
189B194GLU-1-0.834-0.89145.400-0.021-0.0210.0000.0000.0000.000
190B195PHE0-0.083-0.05944.915-0.001-0.0010.0000.0000.0000.000
191B196GLN0-0.032-0.01350.779-0.001-0.0010.0000.0000.0000.000
192B197ALA0-0.0170.00949.7080.0000.0000.0000.0000.0000.000
193B198GLU-1-0.909-0.95751.737-0.011-0.0110.0000.0000.0000.000
194B199PHE0-0.085-0.04847.766-0.001-0.0010.0000.0000.0000.000
195B200VAL00.0510.03151.3820.0010.0010.0000.0000.0000.000
196B201SER00.0190.03751.390-0.001-0.0010.0000.0000.0000.000
197B202THR00.0850.01748.9570.0000.0000.0000.0000.0000.000
198B203PRO0-0.021-0.01851.589-0.001-0.0010.0000.0000.0000.000
199B204GLU-1-0.843-0.92855.082-0.017-0.0170.0000.0000.0000.000
200B205LEU0-0.065-0.01249.371-0.001-0.0010.0000.0000.0000.000
201B206ALA0-0.006-0.00253.022-0.001-0.0010.0000.0000.0000.000
202B207ALA00.0230.02554.218-0.001-0.0010.0000.0000.0000.000
203B208GLN0-0.066-0.03856.7830.0000.0000.0000.0000.0000.000
204B209SER0-0.066-0.04953.2320.0000.0000.0000.0000.0000.000
205B210ASP-1-0.857-0.93155.288-0.026-0.0260.0000.0000.0000.000
206B211PHE0-0.019-0.02550.471-0.002-0.0020.0000.0000.0000.000
207B212ILE00.0370.01947.9350.0020.0020.0000.0000.0000.000
208B213VAL0-0.018-0.00443.281-0.003-0.0030.0000.0000.0000.000
209B214VAL00.009-0.00241.2570.0030.0030.0000.0000.0000.000
210B215ALA0-0.0160.00539.384-0.005-0.0050.0000.0000.0000.000
211B216CYS0-0.066-0.02838.7130.0030.0030.0000.0000.0000.000
212B217SER00.0380.00434.076-0.003-0.0030.0000.0000.0000.000
213B218LEU00.0260.02334.3570.0040.0040.0000.0000.0000.000
214B219THR0-0.038-0.02934.8790.0010.0010.0000.0000.0000.000
215B220PRO00.0930.02736.7830.0000.0000.0000.0000.0000.000
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