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: 2LN5R

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 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 321
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4447502.386674
FMO2-HF: Nuclear repulsion 4325126.608997
FMO2-HF: Total energy -122375.777676
FMO2-MP2: Total energy -122731.410166


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.
-12.078-3.6113.345-4.254-7.557-0.033
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 : -0.036 / q_NPA : -0.018
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].
3B8LYS10.9230.9693.838-0.5140.799-0.009-0.539-0.7650.003
4B9VAL0-0.015-0.0165.6190.5970.5970.0000.0000.0000.000
5B10PHE00.0050.0168.323-0.061-0.0610.0000.0000.0000.000
6B11VAL0-0.022-0.02111.5670.1040.1040.0000.0000.0000.000
7B12THR0-0.020-0.04514.242-0.015-0.0150.0000.0000.0000.000
8B13ARG10.8670.91117.7110.2440.2440.0000.0000.0000.000
9B14ARG10.8200.91217.8380.2450.2450.0000.0000.0000.000
10B15ILE0-0.0050.00915.9580.0360.0360.0000.0000.0000.000
11B16PRO0-0.016-0.02519.751-0.012-0.0120.0000.0000.0000.000
12B17ALA00.0300.00419.054-0.021-0.0210.0000.0000.0000.000
13B18GLU-1-0.902-0.95517.864-0.204-0.2040.0000.0000.0000.000
14B19GLY00.0350.02216.865-0.008-0.0080.0000.0000.0000.000
15B20ARG10.9340.96014.2380.3260.3260.0000.0000.0000.000
16B21VAL0-0.012-0.00913.114-0.079-0.0790.0000.0000.0000.000
17B22ALA0-0.016-0.00512.922-0.037-0.0370.0000.0000.0000.000
18B23LEU00.001-0.00810.110-0.006-0.0060.0000.0000.0000.000
19B24ALA0-0.0080.0008.586-0.192-0.1920.0000.0000.0000.000
20B25ARG10.9040.9529.3810.2640.2640.0000.0000.0000.000
21B26ALA0-0.0260.0056.9340.1530.1530.0000.0000.0000.000
22B27ALA00.0350.0124.822-0.455-0.4550.0000.0000.0000.000
23B28ASP-1-0.803-0.8662.786-1.864-0.5401.357-0.878-1.803-0.010
24B29CYS0-0.083-0.0442.857-2.2410.3391.006-1.477-2.108-0.016
25B30GLU-1-0.909-0.9402.513-7.376-4.2580.981-1.339-2.760-0.010
26B31VAL0-0.022-0.0203.9030.7110.8430.010-0.021-0.1210.000
27B32GLU-1-0.813-0.8897.521-0.661-0.6610.0000.0000.0000.000
28B33GLN0-0.069-0.05510.2300.0620.0620.0000.0000.0000.000
29B34TRP00.0310.01213.6240.0080.0080.0000.0000.0000.000
30B35ASP-1-0.931-0.96016.954-0.378-0.3780.0000.0000.0000.000
31B36SER00.010-0.01018.3140.0400.0400.0000.0000.0000.000
32B37ASP-1-0.795-0.87921.732-0.248-0.2480.0000.0000.0000.000
33B38GLU-1-0.890-0.93724.501-0.158-0.1580.0000.0000.0000.000
34B39PRO0-0.035-0.00923.937-0.023-0.0230.0000.0000.0000.000
35B40ILE0-0.0010.01518.7150.0000.0000.0000.0000.0000.000
36B41PRO00.0100.00222.7720.0170.0170.0000.0000.0000.000
37B42ALA00.0360.00822.894-0.017-0.0170.0000.0000.0000.000
38B43LYS10.8960.93922.6710.1530.1530.0000.0000.0000.000
39B44GLU-1-0.878-0.94720.409-0.296-0.2960.0000.0000.0000.000
40B45LEU0-0.0070.00217.757-0.043-0.0430.0000.0000.0000.000
41B46GLU-1-0.911-0.96217.779-0.186-0.1860.0000.0000.0000.000
42B47ARG10.8800.93414.6800.4610.4610.0000.0000.0000.000
43B48GLY0-0.0140.00014.469-0.036-0.0360.0000.0000.0000.000
44B49VAL0-0.026-0.02012.922-0.090-0.0900.0000.0000.0000.000
45B50ALA00.0000.02413.4230.0110.0110.0000.0000.0000.000
46B51GLY0-0.031-0.02410.587-0.100-0.1000.0000.0000.0000.000
47B52ALA0-0.055-0.0199.236-0.117-0.1170.0000.0000.0000.000
48B53HIS00.0520.0175.928-0.158-0.1580.0000.0000.0000.000
49B54GLY00.0200.0019.6080.1770.1770.0000.0000.0000.000
50B55LEU0-0.0110.01211.083-0.136-0.1360.0000.0000.0000.000
51B56LEU0-0.021-0.01113.8470.0630.0630.0000.0000.0000.000
52B57CYS0-0.036-0.00115.498-0.011-0.0110.0000.0000.0000.000
53B58LEU0-0.006-0.02918.8590.0170.0170.0000.0000.0000.000
54B59LEU00.0220.01122.4520.0040.0040.0000.0000.0000.000
55B60SER00.003-0.00124.3370.0060.0060.0000.0000.0000.000
56B61ASP-1-0.801-0.85821.028-0.231-0.2310.0000.0000.0000.000
57B62HIS00.0360.02123.9690.0080.0080.0000.0000.0000.000
58B63VAL0-0.012-0.00720.205-0.009-0.0090.0000.0000.0000.000
59B64ASP-1-0.811-0.91623.035-0.081-0.0810.0000.0000.0000.000
60B65LYS10.8410.89323.4800.0200.0200.0000.0000.0000.000
61B66ARG10.9600.98123.6600.0910.0910.0000.0000.0000.000
62B67ILE00.0250.02919.032-0.009-0.0090.0000.0000.0000.000
63B68LEU00.002-0.00219.138-0.015-0.0150.0000.0000.0000.000
64B69ASP-1-0.839-0.91519.054-0.037-0.0370.0000.0000.0000.000
65B70ALA0-0.029-0.00918.7680.0050.0050.0000.0000.0000.000
66B71ALA00.0050.02115.076-0.019-0.0190.0000.0000.0000.000
67B72GLY00.0530.04614.054-0.047-0.0470.0000.0000.0000.000
68B73ALA0-0.056-0.06714.7520.0040.0040.0000.0000.0000.000
69B74ASN0-0.058-0.0289.0530.2150.2150.0000.0000.0000.000
70B75LEU0-0.0050.02211.6530.0400.0400.0000.0000.0000.000
71B76LYS10.8760.9349.841-0.594-0.5940.0000.0000.0000.000
72B77VAL0-0.057-0.01712.1210.0180.0180.0000.0000.0000.000
73B78ILE00.0300.02114.368-0.074-0.0740.0000.0000.0000.000
74B79SER0-0.060-0.04016.1510.0490.0490.0000.0000.0000.000
75B80THR00.0510.00017.775-0.029-0.0290.0000.0000.0000.000
76B81MET0-0.053-0.01620.2780.0210.0210.0000.0000.0000.000
77B82SER0-0.033-0.02922.186-0.002-0.0020.0000.0000.0000.000
78B83VAL0-0.0100.02525.4090.0050.0050.0000.0000.0000.000
79B84GLY00.004-0.00728.1440.0090.0090.0000.0000.0000.000
80B85ILE00.0430.00125.830-0.009-0.0090.0000.0000.0000.000
81B86ASP-1-0.808-0.88127.531-0.072-0.0720.0000.0000.0000.000
82B87HIS00.0340.03823.1410.0130.0130.0000.0000.0000.000
83B88LEU0-0.024-0.01122.093-0.010-0.0100.0000.0000.0000.000
84B89ALA00.0200.01324.9580.0120.0120.0000.0000.0000.000
85B90LEU00.002-0.01125.4950.0080.0080.0000.0000.0000.000
86B91ASP-1-0.903-0.94326.3140.0100.0100.0000.0000.0000.000
87B92GLU-1-0.787-0.89524.7760.0030.0030.0000.0000.0000.000
88B93ILE00.0320.01321.0680.0100.0100.0000.0000.0000.000
89B94LYS10.9730.98922.238-0.028-0.0280.0000.0000.0000.000
90B95LYS10.8130.91024.3780.0000.0000.0000.0000.0000.000
91B96ARG10.7200.82920.0510.0360.0360.0000.0000.0000.000
92B97GLY00.0010.01219.7680.0180.0180.0000.0000.0000.000
93B98ILE0-0.073-0.02216.9770.0210.0210.0000.0000.0000.000
94B99ARG10.7950.88715.051-0.175-0.1750.0000.0000.0000.000
95B100VAL00.0450.01418.116-0.031-0.0310.0000.0000.0000.000
96B101GLY0-0.0010.01819.4770.0210.0210.0000.0000.0000.000
97B102TYR0-0.019-0.00120.468-0.023-0.0230.0000.0000.0000.000
98B103THR0-0.010-0.04422.7620.0000.0000.0000.0000.0000.000
99B104PRO00.0260.02325.213-0.004-0.0040.0000.0000.0000.000
100B105ASP-1-0.882-0.94128.200-0.030-0.0300.0000.0000.0000.000
101B106VAL0-0.048-0.03125.997-0.001-0.0010.0000.0000.0000.000
102B107LEU00.014-0.01328.388-0.005-0.0050.0000.0000.0000.000
103B108THR0-0.035-0.00131.091-0.001-0.0010.0000.0000.0000.000
104B109ASP-1-0.822-0.90734.300-0.041-0.0410.0000.0000.0000.000
105B110THR0-0.016-0.02132.7040.0030.0030.0000.0000.0000.000
106B111THR00.0020.00733.585-0.002-0.0020.0000.0000.0000.000
107B112ALA00.002-0.00135.9950.0020.0020.0000.0000.0000.000
108B113GLU-1-0.923-0.93738.356-0.057-0.0570.0000.0000.0000.000
109B114LEU00.0050.00736.9240.0020.0020.0000.0000.0000.000
110B115ALA00.0120.00339.4390.0010.0010.0000.0000.0000.000
111B116VAL00.0010.00141.5050.0020.0020.0000.0000.0000.000
112B117SER00.001-0.00242.1330.0020.0020.0000.0000.0000.000
113B118LEU0-0.0070.01441.4010.0010.0010.0000.0000.0000.000
114B119LEU00.0270.02044.2380.0020.0020.0000.0000.0000.000
115B120LEU00.002-0.00147.1990.0020.0020.0000.0000.0000.000
116B121THR0-0.032-0.02846.0240.0010.0010.0000.0000.0000.000
117B122THR00.010-0.00447.0980.0000.0000.0000.0000.0000.000
118B123CYS0-0.097-0.02749.6510.0020.0020.0000.0000.0000.000
119B124ARG10.9250.94152.0040.0360.0360.0000.0000.0000.000
120B125ARG10.8080.88752.6610.0360.0360.0000.0000.0000.000
121B126LEU00.0050.00848.9990.0000.0000.0000.0000.0000.000
122B127PRO00.0120.01447.8480.0000.0000.0000.0000.0000.000
123B128GLU-1-0.736-0.84050.290-0.039-0.0390.0000.0000.0000.000
124B129ALA00.0150.00653.7790.0000.0000.0000.0000.0000.000
125B130ILE0-0.047-0.03748.1570.0000.0000.0000.0000.0000.000
126B131GLU-1-0.847-0.91451.097-0.056-0.0560.0000.0000.0000.000
127B132GLU-1-0.856-0.93053.384-0.039-0.0390.0000.0000.0000.000
128B133VAL0-0.094-0.04654.5780.0010.0010.0000.0000.0000.000
129B134LYS10.8110.89448.4280.0600.0600.0000.0000.0000.000
130B135ASN0-0.019-0.00254.7100.0010.0010.0000.0000.0000.000
131B136GLY0-0.008-0.00257.2480.0010.0010.0000.0000.0000.000
132B137GLY00.0340.03259.7650.0020.0020.0000.0000.0000.000
133B138TRP0-0.109-0.05258.4690.0020.0020.0000.0000.0000.000
134B139THR00.0330.00461.7810.0010.0010.0000.0000.0000.000
135B140SER0-0.006-0.00864.8600.0010.0010.0000.0000.0000.000
136B141TRP00.0320.02963.501-0.001-0.0010.0000.0000.0000.000
137B142LYS10.9050.94264.8930.0330.0330.0000.0000.0000.000
138B143PRO00.0210.00965.266-0.001-0.0010.0000.0000.0000.000
139B144LEU0-0.021-0.01366.4310.0000.0000.0000.0000.0000.000
140B145TRP0-0.0110.00060.2000.0000.0000.0000.0000.0000.000
141B146LEU00.003-0.00257.0740.0000.0000.0000.0000.0000.000
142B147CYS0-0.0130.01058.8430.0000.0000.0000.0000.0000.000
143B148GLY00.0460.02457.019-0.001-0.0010.0000.0000.0000.000
144B149TYR00.0050.01756.7450.0020.0020.0000.0000.0000.000
145B150GLY0-0.002-0.01755.392-0.002-0.0020.0000.0000.0000.000
146B151LEU00.019-0.00150.9210.0010.0010.0000.0000.0000.000
147B152THR00.0210.02855.4620.0010.0010.0000.0000.0000.000
148B153GLN0-0.060-0.02658.6300.0000.0000.0000.0000.0000.000
149B154SER0-0.014-0.00155.2130.0000.0000.0000.0000.0000.000
150B155THR0-0.023-0.01655.0850.0020.0020.0000.0000.0000.000
151B156VAL00.0060.01049.198-0.001-0.0010.0000.0000.0000.000
152B157GLY00.0340.01350.5900.0020.0020.0000.0000.0000.000
153B158ILE0-0.051-0.03444.411-0.002-0.0020.0000.0000.0000.000
154B159ILE00.0190.00143.6050.0030.0030.0000.0000.0000.000
155B160GLY00.0120.00541.496-0.003-0.0030.0000.0000.0000.000
156B161LEU0-0.0040.00141.925-0.002-0.0020.0000.0000.0000.000
157B162GLY00.0300.01338.5820.0030.0030.0000.0000.0000.000
158B163ARG10.9460.97235.0650.0120.0120.0000.0000.0000.000
159B164ILE00.0570.01533.7380.0000.0000.0000.0000.0000.000
160B165GLY00.0820.04038.0410.0000.0000.0000.0000.0000.000
161B166GLN0-0.007-0.00140.5640.0000.0000.0000.0000.0000.000
162B167ALA00.0130.01939.3280.0010.0010.0000.0000.0000.000
163B168ILE0-0.018-0.00740.476-0.002-0.0020.0000.0000.0000.000
164B169ALA00.0140.00243.3560.0000.0000.0000.0000.0000.000
165B170ARG10.7880.84640.6610.0230.0230.0000.0000.0000.000
166B171ARG10.7760.86538.9920.0470.0470.0000.0000.0000.000
167B172LEU00.0340.01245.9020.0000.0000.0000.0000.0000.000
168B173LYS10.9120.97048.8780.0170.0170.0000.0000.0000.000
169B174PRO0-0.024-0.01949.4210.0010.0010.0000.0000.0000.000
170B175PHE0-0.032-0.01348.3660.0000.0000.0000.0000.0000.000
171B176GLY0-0.016-0.00653.4960.0000.0000.0000.0000.0000.000
172B177VAL0-0.041-0.01051.9180.0010.0010.0000.0000.0000.000
173B178GLN0-0.0050.00655.2570.0010.0010.0000.0000.0000.000
174B179ARG10.8440.91156.0130.0150.0150.0000.0000.0000.000
175B180PHE00.0330.02049.318-0.002-0.0020.0000.0000.0000.000
176B181LEU00.0060.01951.7920.0020.0020.0000.0000.0000.000
177B182TYR00.0260.00746.375-0.002-0.0020.0000.0000.0000.000
178B183THR0-0.009-0.00947.1090.0020.0020.0000.0000.0000.000
179B184GLY00.019-0.00944.701-0.002-0.0020.0000.0000.0000.000
180B185ARG10.9220.96043.1270.0080.0080.0000.0000.0000.000
181B186GLN00.0070.00143.3110.0020.0020.0000.0000.0000.000
182B187PRO0-0.0130.00945.688-0.002-0.0020.0000.0000.0000.000
183B188ARG10.8720.91938.8520.0090.0090.0000.0000.0000.000
184B189PRO00.0270.01246.098-0.001-0.0010.0000.0000.0000.000
185B190GLU-1-0.898-0.95345.0920.0060.0060.0000.0000.0000.000
186B191GLU-1-0.854-0.92041.599-0.004-0.0040.0000.0000.0000.000
187B192ALA0-0.016-0.01444.830-0.003-0.0030.0000.0000.0000.000
188B193ALA00.0260.01548.022-0.001-0.0010.0000.0000.0000.000
189B194GLU-1-0.787-0.83845.120-0.017-0.0170.0000.0000.0000.000
190B195PHE0-0.075-0.05844.720-0.001-0.0010.0000.0000.0000.000
191B196GLN0-0.032-0.01150.667-0.001-0.0010.0000.0000.0000.000
192B197ALA0-0.0080.01549.6370.0000.0000.0000.0000.0000.000
193B198GLU-1-0.845-0.92251.765-0.009-0.0090.0000.0000.0000.000
194B199PHE0-0.062-0.04147.423-0.001-0.0010.0000.0000.0000.000
195B200VAL00.0480.02851.4240.0010.0010.0000.0000.0000.000
196B201SER00.0120.01751.444-0.001-0.0010.0000.0000.0000.000
197B202THR00.0740.01649.2100.0000.0000.0000.0000.0000.000
198B203PRO0-0.012-0.01551.646-0.001-0.0010.0000.0000.0000.000
199B204GLU-1-0.813-0.89755.140-0.013-0.0130.0000.0000.0000.000
200B205LEU0-0.059-0.01049.160-0.001-0.0010.0000.0000.0000.000
201B206ALA0-0.008-0.00653.093-0.001-0.0010.0000.0000.0000.000
202B207ALA00.0220.02354.267-0.001-0.0010.0000.0000.0000.000
203B208GLN0-0.034-0.02356.6310.0000.0000.0000.0000.0000.000
204B209SER0-0.056-0.04753.2790.0000.0000.0000.0000.0000.000
205B210ASP-1-0.836-0.90155.328-0.022-0.0220.0000.0000.0000.000
206B211PHE0-0.009-0.01650.493-0.002-0.0020.0000.0000.0000.000
207B212ILE00.0350.01847.8730.0020.0020.0000.0000.0000.000
208B213VAL0-0.013-0.00643.315-0.003-0.0030.0000.0000.0000.000
209B214VAL0-0.0010.00141.5470.0030.0030.0000.0000.0000.000
210B215ALA0-0.0070.00539.424-0.005-0.0050.0000.0000.0000.000
211B216CYS0-0.049-0.02238.7760.0030.0030.0000.0000.0000.000
212B217SER00.0200.00334.387-0.005-0.0050.0000.0000.0000.000
213B218LEU00.0340.02934.4180.0030.0030.0000.0000.0000.000
214B219THR0-0.042-0.03034.9460.0020.0020.0000.0000.0000.000
215B220PRO00.1130.03836.660-0.001-0.0010.0000.0000.0000.000
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