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: GYQY1

Calculation Name: 1H7S-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1H7S

Chain ID: B

ChEMBL ID:

UniProt ID: P54278

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 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 302
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4112303.363919
FMO2-HF: Nuclear repulsion 3993324.895862
FMO2-HF: Total energy -118978.468058
FMO2-MP2: Total energy -119319.134175


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:33:LEU)


Summations of interaction energy for fragment #1(B:33: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.
-17.5-12.81714.967-7.862-11.789-0.012
Interaction energy analysis for fragmet #1(B:33:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / 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].
3B35LEU00.0700.0343.659-2.1160.524-0.010-1.397-1.2330.006
4B36SER0-0.037-0.0356.070-0.100-0.1000.0000.0000.0000.000
5B37THR00.0530.0271.618-0.017-2.3129.394-3.737-3.362-0.007
6B38ALA00.0470.0402.936-2.107-0.7520.326-0.435-1.246-0.002
7B39VAL00.002-0.0143.613-0.596-0.5470.0280.127-0.2040.000
8B40LYS10.8600.9376.323-0.731-0.7310.0000.0000.0000.000
9B41GLU-1-0.864-0.9293.252-6.750-4.7360.138-1.062-1.090-0.009
10B42LEU0-0.031-0.0156.4210.0220.0220.0000.0000.0000.000
11B43VAL0-0.022-0.0098.4510.0710.0710.0000.0000.0000.000
12B44GLU-1-0.906-0.9669.381-0.005-0.0050.0000.0000.0000.000
13B45ASN00.0550.0278.2060.0670.0670.0000.0000.0000.000
14B46SER0-0.061-0.04411.8070.0330.0330.0000.0000.0000.000
15B47LEU0-0.089-0.05514.2600.0390.0390.0000.0000.0000.000
16B48ASP-1-0.877-0.92813.985-0.251-0.2510.0000.0000.0000.000
17B49ALA0-0.066-0.01516.3530.0090.0090.0000.0000.0000.000
18B50GLY00.0230.00718.0540.0180.0180.0000.0000.0000.000
19B51ALA0-0.051-0.01218.1720.0160.0160.0000.0000.0000.000
20B52THR00.014-0.00220.1020.0150.0150.0000.0000.0000.000
21B53ASN0-0.072-0.03821.0320.0270.0270.0000.0000.0000.000
22B54ILE00.0710.02914.775-0.022-0.0220.0000.0000.0000.000
23B55ASP-1-0.842-0.89217.337-0.031-0.0310.0000.0000.0000.000
24B56LEU00.0270.01511.540-0.037-0.0370.0000.0000.0000.000
25B57LYS10.8820.93315.0500.1820.1820.0000.0000.0000.000
26B58LEU00.010-0.00412.069-0.027-0.0270.0000.0000.0000.000
27B59LYS10.9750.98714.5760.1210.1210.0000.0000.0000.000
28B60ASP-1-0.763-0.89614.8240.0180.0180.0000.0000.0000.000
29B61TYR0-0.108-0.06514.2280.0210.0210.0000.0000.0000.000
30B62GLY00.0320.00810.8200.0710.0710.0000.0000.0000.000
31B63VAL0-0.058-0.02510.300-0.049-0.0490.0000.0000.0000.000
32B64ASP-1-0.894-0.95411.872-0.174-0.1740.0000.0000.0000.000
33B65LEU0-0.036-0.02212.419-0.051-0.0510.0000.0000.0000.000
34B66ILE00.0100.0147.1630.1140.1140.0000.0000.0000.000
35B67GLU-1-0.902-0.94810.790-0.328-0.3280.0000.0000.0000.000
36B68VAL00.0230.02610.5440.0870.0870.0000.0000.0000.000
37B69SER0-0.032-0.00813.224-0.055-0.0550.0000.0000.0000.000
38B70ASP-1-0.765-0.86215.699-0.254-0.2540.0000.0000.0000.000
39B71ASN0-0.001-0.02018.102-0.012-0.0120.0000.0000.0000.000
40B72GLY00.0420.01619.2900.0200.0200.0000.0000.0000.000
41B73CYS0-0.054-0.04320.2980.0050.0050.0000.0000.0000.000
42B74GLY0-0.025-0.00419.2950.0100.0100.0000.0000.0000.000
43B75VAL00.012-0.00516.745-0.008-0.0080.0000.0000.0000.000
44B76GLU-1-0.902-0.94719.936-0.221-0.2210.0000.0000.0000.000
45B77GLU-1-0.923-1.01422.300-0.231-0.2310.0000.0000.0000.000
46B78GLU-1-0.948-0.96823.609-0.214-0.2140.0000.0000.0000.000
47B79ASN00.010-0.00819.658-0.015-0.0150.0000.0000.0000.000
48B80PHE0-0.0260.01618.576-0.044-0.0440.0000.0000.0000.000
49B81GLU-1-0.923-0.96917.298-0.380-0.3800.0000.0000.0000.000
50B82GLY0-0.034-0.01417.057-0.020-0.0200.0000.0000.0000.000
51B83LEU0-0.054-0.05513.508-0.076-0.0760.0000.0000.0000.000
52B84THR0-0.051-0.07010.665-0.086-0.0860.0000.0000.0000.000
53B85LEU0-0.0100.02412.2210.0110.0110.0000.0000.0000.000
54B108GLY00.0030.00611.806-0.016-0.0160.0000.0000.0000.000
55B109GLU-1-0.868-0.9439.054-0.978-0.9780.0000.0000.0000.000
56B110ALA00.0310.0255.778-0.359-0.3590.0000.0000.0000.000
57B111LEU00.0310.0045.289-0.764-0.7640.0000.0000.0000.000
58B112SER00.0420.0417.3190.0200.0200.0000.0000.0000.000
59B113SER0-0.050-0.0303.003-1.282-0.6770.076-0.218-0.464-0.001
60B114LEU0-0.007-0.0172.423-0.4850.3370.493-0.225-1.090-0.001
61B115CYS0-0.0190.0084.2770.5560.579-0.001-0.009-0.0130.000
62B116ALA00.0290.0406.2840.2420.2420.0000.0000.0000.000
63B117LEU0-0.062-0.0252.1261.207-0.9074.404-0.505-1.7850.001
64B118SER0-0.071-0.0316.1820.1750.1750.0000.0000.0000.000
65B119ASP-1-0.890-0.9388.253-0.443-0.4430.0000.0000.0000.000
66B120VAL00.0410.0167.9700.0150.0150.0000.0000.0000.000
67B121THR0-0.041-0.02210.9090.0750.0750.0000.0000.0000.000
68B122ILE00.0190.00511.767-0.021-0.0210.0000.0000.0000.000
69B123SER0-0.052-0.00915.3250.0480.0480.0000.0000.0000.000
70B124THR00.0310.01318.204-0.011-0.0110.0000.0000.0000.000
71B125CYS0-0.012-0.00320.2210.0190.0190.0000.0000.0000.000
72B126HIS00.1390.09123.3430.0010.0010.0000.0000.0000.000
73B127ALA0-0.018-0.02824.6570.0120.0120.0000.0000.0000.000
74B128SER0-0.039-0.00427.7630.0080.0080.0000.0000.0000.000
75B129ALA00.0050.00927.2960.0030.0030.0000.0000.0000.000
76B130LYS10.9150.95229.2210.1200.1200.0000.0000.0000.000
77B131VAL0-0.027-0.01128.0470.0080.0080.0000.0000.0000.000
78B132GLY00.0620.02424.711-0.007-0.0070.0000.0000.0000.000
79B133THR0-0.033-0.00421.9010.0130.0130.0000.0000.0000.000
80B134ARG10.8930.93619.5000.2370.2370.0000.0000.0000.000
81B135LEU00.0080.00016.7260.0220.0220.0000.0000.0000.000
82B136MET0-0.0090.01015.794-0.006-0.0060.0000.0000.0000.000
83B137PHE00.0620.02412.2860.0200.0200.0000.0000.0000.000
84B138ASP-1-0.796-0.88413.618-0.490-0.4900.0000.0000.0000.000
85B139HIS10.8450.88410.0910.5290.5290.0000.0000.0000.000
86B140ASN0-0.042-0.01010.748-0.121-0.1210.0000.0000.0000.000
87B141GLY00.0520.02111.931-0.039-0.0390.0000.0000.0000.000
88B142LYS10.9611.02512.5070.3560.3560.0000.0000.0000.000
89B143ILE00.0120.00416.1830.0030.0030.0000.0000.0000.000
90B144ILE0-0.055-0.01716.5620.0350.0350.0000.0000.0000.000
91B145GLN0-0.044-0.03419.4090.0350.0350.0000.0000.0000.000
92B146LYS10.9520.98720.1690.2120.2120.0000.0000.0000.000
93B147THR0-0.035-0.00922.5340.0160.0160.0000.0000.0000.000
94B148PRO00.0190.01124.257-0.013-0.0130.0000.0000.0000.000
95B149TYR0-0.034-0.03722.7330.0010.0010.0000.0000.0000.000
96B150PRO00.0410.02625.720-0.002-0.0020.0000.0000.0000.000
97B151ARG10.8570.92519.6860.2170.2170.0000.0000.0000.000
98B152PRO00.0310.01824.5680.0000.0000.0000.0000.0000.000
99B153ARG10.9170.95723.6090.1270.1270.0000.0000.0000.000
100B154GLY00.0020.01920.5810.0150.0150.0000.0000.0000.000
101B155THR00.009-0.01015.203-0.010-0.0100.0000.0000.0000.000
102B156THR0-0.040-0.00815.7860.0350.0350.0000.0000.0000.000
103B157VAL00.0330.0269.641-0.014-0.0140.0000.0000.0000.000
104B158SER0-0.040-0.04112.2520.0370.0370.0000.0000.0000.000
105B159VAL00.0370.0186.249-0.043-0.0430.0000.0000.0000.000
106B160GLN0-0.008-0.0209.3220.0850.0850.0000.0000.0000.000
107B161GLN0-0.002-0.00310.493-0.019-0.0190.0000.0000.0000.000
108B162LEU00.0430.0223.592-0.422-0.0500.009-0.067-0.3140.000
109B163PHE0-0.013-0.0332.849-0.9560.1350.111-0.313-0.8890.001
110B164SER00.0060.0197.5710.0380.0380.0000.0000.0000.000
111B165THR0-0.018-0.0158.3650.0630.0630.0000.0000.0000.000
112B166LEU0-0.014-0.0066.7720.0260.0260.0000.0000.0000.000
113B167PRO00.0600.02310.2050.0590.0590.0000.0000.0000.000
114B168VAL00.0290.02111.2890.0420.0420.0000.0000.0000.000
115B169ARG10.9180.9634.656-0.336-0.215-0.001-0.021-0.0990.000
116B170HIS00.0210.0148.9420.1200.1200.0000.0000.0000.000
117B171LYS10.9310.95610.6250.0080.0080.0000.0000.0000.000
118B172GLU-1-0.797-0.88810.1740.3710.3710.0000.0000.0000.000
119B173PHE0-0.047-0.0138.8270.1440.1440.0000.0000.0000.000
120B174GLN00.0520.01610.6480.0480.0480.0000.0000.0000.000
121B175ARG10.8230.89213.993-0.288-0.2880.0000.0000.0000.000
122B176ASN0-0.082-0.02311.769-0.021-0.0210.0000.0000.0000.000
123B177ILE00.0920.05012.2010.1040.1040.0000.0000.0000.000
124B178LYS10.9820.99713.948-0.309-0.3090.0000.0000.0000.000
125B179LYS10.9440.96112.850-0.814-0.8140.0000.0000.0000.000
126B180GLU-1-0.891-0.9578.2041.6031.6030.0000.0000.0000.000
127B181TYR00.0450.01710.9420.0650.0650.0000.0000.0000.000
128B182ALA0-0.019-0.00713.181-0.016-0.0160.0000.0000.0000.000
129B183LYS10.9410.9738.466-1.985-1.9850.0000.0000.0000.000
130B184MET00.0140.0139.214-0.010-0.0100.0000.0000.0000.000
131B185VAL0-0.031-0.00910.855-0.086-0.0860.0000.0000.0000.000
132B186GLN0-0.0140.00313.774-0.061-0.0610.0000.0000.0000.000
133B187VAL00.004-0.0059.143-0.050-0.0500.0000.0000.0000.000
134B188LEU00.0100.00412.341-0.088-0.0880.0000.0000.0000.000
135B189HIS00.0410.00414.071-0.061-0.0610.0000.0000.0000.000
136B190ALA00.0020.01114.844-0.040-0.0400.0000.0000.0000.000
137B191TYR00.0650.01311.0520.0010.0010.0000.0000.0000.000
138B192CYS0-0.058-0.01216.375-0.046-0.0460.0000.0000.0000.000
139B193ILE0-0.035-0.02119.204-0.025-0.0250.0000.0000.0000.000
140B194ILE0-0.048-0.01617.965-0.024-0.0240.0000.0000.0000.000
141B195SER0-0.006-0.01318.073-0.026-0.0260.0000.0000.0000.000
142B196ALA0-0.049-0.00920.756-0.008-0.0080.0000.0000.0000.000
143B197GLY0-0.026-0.01224.322-0.010-0.0100.0000.0000.0000.000
144B198ILE0-0.009-0.00219.457-0.014-0.0140.0000.0000.0000.000
145B199ARG10.7590.87321.3810.0500.0500.0000.0000.0000.000
146B200VAL00.006-0.00116.800-0.017-0.0170.0000.0000.0000.000
147B201SER0-0.023-0.01918.7390.0210.0210.0000.0000.0000.000
148B202CYS0-0.0010.01615.5390.0020.0020.0000.0000.0000.000
149B203THR00.0060.01317.8100.0040.0040.0000.0000.0000.000
150B204ASN00.0380.00717.136-0.020-0.0200.0000.0000.0000.000
151B205GLN0-0.076-0.06718.648-0.011-0.0110.0000.0000.0000.000
152B206LEU00.0180.03819.217-0.002-0.0020.0000.0000.0000.000
153B207GLY00.0510.01820.4930.0000.0000.0000.0000.0000.000
154B208GLN0-0.0220.00422.433-0.019-0.0190.0000.0000.0000.000
155B209GLY0-0.0080.01424.774-0.001-0.0010.0000.0000.0000.000
156B210LYS10.9790.99125.386-0.028-0.0280.0000.0000.0000.000
157B211ARG10.8500.91718.7320.0390.0390.0000.0000.0000.000
158B212GLN0-0.037-0.02122.845-0.007-0.0070.0000.0000.0000.000
159B213PRO00.0300.00222.2730.0010.0010.0000.0000.0000.000
160B214VAL0-0.053-0.01518.0110.0090.0090.0000.0000.0000.000
161B215VAL00.0260.00218.5720.0130.0130.0000.0000.0000.000
162B216CYS0-0.026-0.03121.159-0.023-0.0230.0000.0000.0000.000
163B217THR00.0280.04221.5030.0010.0010.0000.0000.0000.000
164B218GLY00.022-0.00524.061-0.012-0.0120.0000.0000.0000.000
165B219GLY00.0080.01425.214-0.007-0.0070.0000.0000.0000.000
166B220SER0-0.053-0.08426.210-0.003-0.0030.0000.0000.0000.000
167B221PRO00.0480.01726.9840.0040.0040.0000.0000.0000.000
168B222SER00.0250.01328.8320.0090.0090.0000.0000.0000.000
169B223ILE00.0710.02524.8480.0020.0020.0000.0000.0000.000
170B224LYS10.9570.98226.594-0.069-0.0690.0000.0000.0000.000
171B225GLU-1-0.830-0.84929.1210.0450.0450.0000.0000.0000.000
172B226ASN00.0150.00823.658-0.005-0.0050.0000.0000.0000.000
173B227ILE0-0.015-0.00324.8510.0100.0100.0000.0000.0000.000
174B228GLY0-0.0080.00425.9150.0080.0080.0000.0000.0000.000
175B229SER0-0.082-0.03525.372-0.004-0.0040.0000.0000.0000.000
176B230VAL0-0.038-0.00521.293-0.001-0.0010.0000.0000.0000.000
177B231PHE0-0.053-0.03821.3060.0090.0090.0000.0000.0000.000
178B232GLY00.0360.02826.309-0.002-0.0020.0000.0000.0000.000
179B233GLN00.046-0.01529.7460.0100.0100.0000.0000.0000.000
180B234LYS10.9020.96832.458-0.091-0.0910.0000.0000.0000.000
181B235GLN0-0.013-0.01627.7420.0130.0130.0000.0000.0000.000
182B236LEU00.0150.00229.6450.0040.0040.0000.0000.0000.000
183B237GLN00.0030.01632.550-0.002-0.0020.0000.0000.0000.000
184B238SER0-0.0150.00633.351-0.003-0.0030.0000.0000.0000.000
185B239LEU0-0.051-0.02029.1850.0080.0080.0000.0000.0000.000
186B240ILE00.0180.00733.333-0.010-0.0100.0000.0000.0000.000
187B241PRO0-0.023-0.01432.4290.0090.0090.0000.0000.0000.000
188B242PHE00.031-0.00628.0720.0000.0000.0000.0000.0000.000
189B243VAL0-0.022-0.02932.758-0.007-0.0070.0000.0000.0000.000
190B244GLN0-0.002-0.01233.0110.0050.0050.0000.0000.0000.000
191B245LEU0-0.0160.00035.538-0.007-0.0070.0000.0000.0000.000
192B246PRO0-0.007-0.00637.2210.0050.0050.0000.0000.0000.000
193B247PRO0-0.019-0.00936.6330.0020.0020.0000.0000.0000.000
194B248SER00.0410.01138.535-0.005-0.0050.0000.0000.0000.000
195B249ASP-1-0.823-0.92341.0280.0680.0680.0000.0000.0000.000
196B250SER00.0530.02642.2110.0010.0010.0000.0000.0000.000
197B251VAL0-0.0270.00136.5960.0050.0050.0000.0000.0000.000
198B252CYS0-0.046-0.03038.1090.0070.0070.0000.0000.0000.000
199B253GLU-1-0.915-0.95339.0230.0770.0770.0000.0000.0000.000
200B254GLU-1-0.918-0.94337.8320.1180.1180.0000.0000.0000.000
201B255TYR0-0.125-0.06331.4740.0170.0170.0000.0000.0000.000
202B256GLY0-0.042-0.01935.8640.0030.0030.0000.0000.0000.000
203B257LEU0-0.083-0.03834.597-0.001-0.0010.0000.0000.0000.000
204B258SER00.002-0.02738.752-0.004-0.0040.0000.0000.0000.000
205B259CYS00.0490.00541.1100.0010.0010.0000.0000.0000.000
206B260SER00.0170.00942.924-0.002-0.0020.0000.0000.0000.000
207B261ASP-1-0.809-0.88037.6440.0720.0720.0000.0000.0000.000
208B262ALA0-0.027-0.01737.8410.0010.0010.0000.0000.0000.000
209B263LEU0-0.026-0.02038.792-0.001-0.0010.0000.0000.0000.000
210B264HIS10.8420.94634.930-0.076-0.0760.0000.0000.0000.000
211B265ASN00.003-0.00633.5900.0090.0090.0000.0000.0000.000
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