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: 8NJNY

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 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 302
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4112540.436554
FMO2-HF: Nuclear repulsion 3993560.531194
FMO2-HF: Total energy -118979.905359
FMO2-MP2: Total energy -119320.437596


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.
-21.911-11.8429.004-6.671-12.402-0.032
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 : 0.022 / q_NPA : 0.013
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].
3B35LEU00.0720.0323.078-2.5390.4990.124-1.564-1.5970.002
4B36SER0-0.035-0.0325.600-0.172-0.1720.0000.0000.0000.000
5B37THR00.0520.0211.930-1.723-0.7433.847-2.467-2.359-0.014
6B38ALA00.0680.0492.450-2.006-0.8691.526-0.753-1.910-0.001
7B39VAL0-0.002-0.0173.1200.547-0.2720.1280.960-0.2680.000
8B40LYS10.7770.8846.2510.6170.6170.0000.0000.0000.000
9B41GLU-1-0.861-0.9322.790-8.678-5.9990.435-1.487-1.627-0.017
10B42LEU0-0.0130.0046.1420.1950.1950.0000.0000.0000.000
11B43VAL0-0.015-0.0068.2780.1320.1320.0000.0000.0000.000
12B44GLU-1-0.786-0.8879.513-0.674-0.6740.0000.0000.0000.000
13B45ASN00.006-0.0108.7830.1200.1200.0000.0000.0000.000
14B46SER0-0.041-0.04311.9110.0650.0650.0000.0000.0000.000
15B47LEU0-0.086-0.05414.2120.0600.0600.0000.0000.0000.000
16B48ASP-1-0.878-0.93114.391-0.494-0.4940.0000.0000.0000.000
17B49ALA0-0.063-0.01316.4450.0350.0350.0000.0000.0000.000
18B50GLY00.0240.00818.1650.0380.0380.0000.0000.0000.000
19B51ALA0-0.053-0.01618.0180.0280.0280.0000.0000.0000.000
20B52THR00.0240.00819.9940.0030.0030.0000.0000.0000.000
21B53ASN0-0.061-0.03320.8070.0310.0310.0000.0000.0000.000
22B54ILE00.0690.03314.481-0.024-0.0240.0000.0000.0000.000
23B55ASP-1-0.813-0.85116.915-0.138-0.1380.0000.0000.0000.000
24B56LEU00.0310.01510.858-0.023-0.0230.0000.0000.0000.000
25B57LYS10.8140.88014.4420.1850.1850.0000.0000.0000.000
26B58LEU00.0120.00011.567-0.008-0.0080.0000.0000.0000.000
27B59LYS10.9300.97014.602-0.003-0.0030.0000.0000.0000.000
28B60ASP-1-0.803-0.91814.8110.1190.1190.0000.0000.0000.000
29B61TYR0-0.083-0.05714.2230.0320.0320.0000.0000.0000.000
30B62GLY00.0390.01210.8490.0150.0150.0000.0000.0000.000
31B63VAL0-0.054-0.02310.2730.0300.0300.0000.0000.0000.000
32B64ASP-1-0.845-0.93111.7750.0770.0770.0000.0000.0000.000
33B65LEU0-0.041-0.02012.476-0.023-0.0230.0000.0000.0000.000
34B66ILE00.0180.0167.0680.0370.0370.0000.0000.0000.000
35B67GLU-1-0.806-0.87310.427-0.245-0.2450.0000.0000.0000.000
36B68VAL00.0220.02710.1700.0470.0470.0000.0000.0000.000
37B69SER0-0.021-0.00412.786-0.019-0.0190.0000.0000.0000.000
38B70ASP-1-0.765-0.85815.486-0.364-0.3640.0000.0000.0000.000
39B71ASN0-0.005-0.01817.848-0.003-0.0030.0000.0000.0000.000
40B72GLY00.0550.03119.2580.0190.0190.0000.0000.0000.000
41B73CYS0-0.048-0.03820.2490.0140.0140.0000.0000.0000.000
42B74GLY0-0.023-0.00319.3190.0210.0210.0000.0000.0000.000
43B75VAL00.012-0.00216.763-0.011-0.0110.0000.0000.0000.000
44B76GLU-1-0.850-0.91320.033-0.226-0.2260.0000.0000.0000.000
45B77GLU-1-0.874-0.95922.089-0.171-0.1710.0000.0000.0000.000
46B78GLU-1-0.950-0.96923.406-0.179-0.1790.0000.0000.0000.000
47B79ASN0-0.028-0.03519.493-0.021-0.0210.0000.0000.0000.000
48B80PHE0-0.0080.00418.424-0.032-0.0320.0000.0000.0000.000
49B81GLU-1-0.929-0.97517.129-0.236-0.2360.0000.0000.0000.000
50B82GLY0-0.028-0.01217.081-0.008-0.0080.0000.0000.0000.000
51B83LEU0-0.050-0.04913.277-0.071-0.0710.0000.0000.0000.000
52B84THR0-0.032-0.02410.498-0.071-0.0710.0000.0000.0000.000
53B85LEU0-0.0140.02412.2660.0320.0320.0000.0000.0000.000
54B108GLY00.0070.00611.772-0.021-0.0210.0000.0000.0000.000
55B109GLU-1-0.863-0.9399.052-0.872-0.8720.0000.0000.0000.000
56B110ALA00.0120.0105.610-0.265-0.2650.0000.0000.0000.000
57B111LEU00.0360.0005.229-0.507-0.5070.0000.0000.0000.000
58B112SER00.0510.0477.2250.1390.1390.0000.0000.0000.000
59B113SER0-0.048-0.0173.110-1.582-0.6640.145-0.415-0.648-0.003
60B114LEU00.009-0.0092.463-0.3350.5150.619-0.238-1.2310.000
61B115CYS0-0.0240.0034.3280.5230.544-0.001-0.011-0.0100.000
62B116ALA00.0290.0396.2940.2110.2110.0000.0000.0000.000
63B117LEU0-0.054-0.0202.2290.299-0.0552.019-0.315-1.3510.000
64B118SER0-0.068-0.0396.3180.1320.1320.0000.0000.0000.000
65B119ASP-1-0.870-0.9378.560-0.054-0.0540.0000.0000.0000.000
66B120VAL00.0200.0087.876-0.013-0.0130.0000.0000.0000.000
67B121THR0-0.022-0.01410.9710.0450.0450.0000.0000.0000.000
68B122ILE00.010-0.00211.468-0.035-0.0350.0000.0000.0000.000
69B123SER0-0.0310.00515.2080.0410.0410.0000.0000.0000.000
70B124THR00.0220.00218.021-0.024-0.0240.0000.0000.0000.000
71B125CYS0-0.014-0.00620.0800.0260.0260.0000.0000.0000.000
72B126HIS00.1120.08023.328-0.002-0.0020.0000.0000.0000.000
73B127ALA00.003-0.01924.7230.0140.0140.0000.0000.0000.000
74B128SER0-0.046-0.00327.8070.0100.0100.0000.0000.0000.000
75B129ALA00.0060.01027.2370.0080.0080.0000.0000.0000.000
76B130LYS10.9150.95229.2000.1060.1060.0000.0000.0000.000
77B131VAL0-0.025-0.01528.0400.0050.0050.0000.0000.0000.000
78B132GLY00.0650.03024.526-0.007-0.0070.0000.0000.0000.000
79B133THR0-0.035-0.00721.4210.0180.0180.0000.0000.0000.000
80B134ARG10.8630.90819.0970.1200.1200.0000.0000.0000.000
81B135LEU00.0020.00516.7050.0230.0230.0000.0000.0000.000
82B136MET0-0.0090.02915.812-0.009-0.0090.0000.0000.0000.000
83B137PHE00.0580.02012.3850.0050.0050.0000.0000.0000.000
84B138ASP-1-0.796-0.87713.762-0.127-0.1270.0000.0000.0000.000
85B139HIS10.8310.88310.274-0.008-0.0080.0000.0000.0000.000
86B140ASN0-0.085-0.04110.7050.0010.0010.0000.0000.0000.000
87B141GLY00.0400.01411.986-0.050-0.0500.0000.0000.0000.000
88B142LYS10.9761.00212.5450.1150.1150.0000.0000.0000.000
89B143ILE00.0060.00416.2530.0130.0130.0000.0000.0000.000
90B144ILE0-0.052-0.01916.4700.0260.0260.0000.0000.0000.000
91B145GLN0-0.015-0.02419.4590.0140.0140.0000.0000.0000.000
92B146LYS10.9020.94320.1720.1420.1420.0000.0000.0000.000
93B147THR0-0.032-0.00822.5050.0140.0140.0000.0000.0000.000
94B148PRO00.0330.01924.175-0.014-0.0140.0000.0000.0000.000
95B149TYR0-0.029-0.04223.1850.0070.0070.0000.0000.0000.000
96B150PRO00.0150.02425.612-0.007-0.0070.0000.0000.0000.000
97B151ARG10.8480.90719.1750.2260.2260.0000.0000.0000.000
98B152PRO00.0180.01923.9670.0010.0010.0000.0000.0000.000
99B153ARG10.8930.94523.7010.1830.1830.0000.0000.0000.000
100B154GLY00.0060.01820.5070.0050.0050.0000.0000.0000.000
101B155THR00.005-0.01115.1440.0150.0150.0000.0000.0000.000
102B156THR0-0.0240.00415.5050.0140.0140.0000.0000.0000.000
103B157VAL00.0320.0269.4920.0120.0120.0000.0000.0000.000
104B158SER0-0.039-0.04511.8670.0070.0070.0000.0000.0000.000
105B159VAL00.0270.0126.2710.0010.0010.0000.0000.0000.000
106B160GLN0-0.009-0.0149.3720.0560.0560.0000.0000.0000.000
107B161GLN00.0070.00410.7560.0480.0480.0000.0000.0000.000
108B162LEU00.0410.0313.559-0.419-0.0100.009-0.074-0.3450.000
109B163PHE00.006-0.0222.900-1.0330.0470.154-0.281-0.9530.001
110B164SER0-0.0010.0067.5470.0270.0270.0000.0000.0000.000
111B165THR0-0.031-0.0208.6480.0520.0520.0000.0000.0000.000
112B166LEU0-0.013-0.0046.8010.0520.0520.0000.0000.0000.000
113B167PRO00.0640.02310.3990.1450.1450.0000.0000.0000.000
114B168VAL00.0190.01511.883-0.011-0.0110.0000.0000.0000.000
115B169ARG10.9250.9655.183-2.388-2.258-0.001-0.026-0.1030.000
116B170HIS00.0060.0159.168-0.006-0.0060.0000.0000.0000.000
117B171LYS10.9250.94510.677-0.463-0.4630.0000.0000.0000.000
118B172GLU-1-0.770-0.85710.8220.5930.5930.0000.0000.0000.000
119B173PHE0-0.035-0.0058.601-0.024-0.0240.0000.0000.0000.000
120B174GLN00.0510.02210.510-0.099-0.0990.0000.0000.0000.000
121B175ARG10.8200.87913.863-0.558-0.5580.0000.0000.0000.000
122B176ASN0-0.120-0.05312.079-0.119-0.1190.0000.0000.0000.000
123B177ILE00.0770.04711.945-0.007-0.0070.0000.0000.0000.000
124B178LYS10.9760.99213.903-0.191-0.1910.0000.0000.0000.000
125B179LYS10.9600.97112.117-0.428-0.4280.0000.0000.0000.000
126B180GLU-1-0.821-0.8997.7210.6130.6130.0000.0000.0000.000
127B181TYR00.0550.01810.446-0.064-0.0640.0000.0000.0000.000
128B182ALA0-0.019-0.00812.627-0.048-0.0480.0000.0000.0000.000
129B183LYS10.8660.9187.086-0.529-0.5290.0000.0000.0000.000
130B184MET00.0050.0068.724-0.053-0.0530.0000.0000.0000.000
131B185VAL0-0.033-0.01310.418-0.053-0.0530.0000.0000.0000.000
132B186GLN0-0.013-0.00513.607-0.020-0.0200.0000.0000.0000.000
133B187VAL00.006-0.0038.936-0.020-0.0200.0000.0000.0000.000
134B188LEU00.0040.00212.108-0.032-0.0320.0000.0000.0000.000
135B189HIS00.0580.01613.816-0.022-0.0220.0000.0000.0000.000
136B190ALA00.0000.01314.730-0.001-0.0010.0000.0000.0000.000
137B191TYR00.0450.00411.027-0.003-0.0030.0000.0000.0000.000
138B192CYS0-0.066-0.01216.3010.0050.0050.0000.0000.0000.000
139B193ILE0-0.028-0.02219.0620.0090.0090.0000.0000.0000.000
140B194ILE0-0.043-0.01417.9960.0090.0090.0000.0000.0000.000
141B195SER0-0.004-0.01818.164-0.012-0.0120.0000.0000.0000.000
142B196ALA0-0.047-0.01320.7660.0090.0090.0000.0000.0000.000
143B197GLY0-0.017-0.01124.182-0.010-0.0100.0000.0000.0000.000
144B198ILE0-0.023-0.00919.180-0.004-0.0040.0000.0000.0000.000
145B199ARG10.7350.83821.5940.1510.1510.0000.0000.0000.000
146B200VAL00.000-0.00516.504-0.015-0.0150.0000.0000.0000.000
147B201SER0-0.047-0.04718.2810.0300.0300.0000.0000.0000.000
148B202CYS00.0080.01715.172-0.015-0.0150.0000.0000.0000.000
149B203THR00.0210.02417.2980.0250.0250.0000.0000.0000.000
150B204ASN00.0550.01517.059-0.007-0.0070.0000.0000.0000.000
151B205GLN0-0.069-0.05018.639-0.006-0.0060.0000.0000.0000.000
152B206LEU00.0070.03319.2230.0090.0090.0000.0000.0000.000
153B207GLY00.0490.01820.453-0.005-0.0050.0000.0000.0000.000
154B208GLN0-0.024-0.00822.385-0.012-0.0120.0000.0000.0000.000
155B209GLY0-0.0030.01724.759-0.006-0.0060.0000.0000.0000.000
156B210LYS10.9770.98825.393-0.008-0.0080.0000.0000.0000.000
157B211ARG10.8330.89318.0760.0540.0540.0000.0000.0000.000
158B212GLN0-0.045-0.02322.573-0.001-0.0010.0000.0000.0000.000
159B213PRO00.0400.00921.845-0.005-0.0050.0000.0000.0000.000
160B214VAL0-0.059-0.02017.6110.0120.0120.0000.0000.0000.000
161B215VAL00.008-0.00518.3210.0070.0070.0000.0000.0000.000
162B216CYS0-0.019-0.02520.858-0.013-0.0130.0000.0000.0000.000
163B217THR00.0150.04021.3090.0100.0100.0000.0000.0000.000
164B218GLY00.025-0.00523.877-0.002-0.0020.0000.0000.0000.000
165B219GLY00.0050.01324.9590.0020.0020.0000.0000.0000.000
166B220SER0-0.026-0.04125.909-0.001-0.0010.0000.0000.0000.000
167B221PRO00.0450.02026.908-0.010-0.0100.0000.0000.0000.000
168B222SER00.0130.00628.847-0.001-0.0010.0000.0000.0000.000
169B223ILE00.0640.01924.5670.0000.0000.0000.0000.0000.000
170B224LYS10.9440.97926.4810.0520.0520.0000.0000.0000.000
171B225GLU-1-0.836-0.88428.959-0.071-0.0710.0000.0000.0000.000
172B226ASN00.0010.01123.5360.0110.0110.0000.0000.0000.000
173B227ILE0-0.007-0.00124.6520.0030.0030.0000.0000.0000.000
174B228GLY0-0.0090.00525.7190.0070.0070.0000.0000.0000.000
175B229SER0-0.090-0.04325.0690.0050.0050.0000.0000.0000.000
176B230VAL0-0.038-0.00821.0090.0040.0040.0000.0000.0000.000
177B231PHE0-0.035-0.03021.0450.0100.0100.0000.0000.0000.000
178B232GLY00.0350.02625.9890.0080.0080.0000.0000.0000.000
179B233GLN00.046-0.01329.432-0.003-0.0030.0000.0000.0000.000
180B234LYS10.8840.95032.1400.0140.0140.0000.0000.0000.000
181B235GLN0-0.005-0.00327.3640.0060.0060.0000.0000.0000.000
182B236LEU00.0240.00029.3630.0000.0000.0000.0000.0000.000
183B237GLN00.0050.01832.3160.0010.0010.0000.0000.0000.000
184B238SER00.0120.01533.1610.0000.0000.0000.0000.0000.000
185B239LEU0-0.064-0.02128.9900.0010.0010.0000.0000.0000.000
186B240ILE00.0140.00133.1740.0000.0000.0000.0000.0000.000
187B241PRO0-0.017-0.01432.349-0.002-0.0020.0000.0000.0000.000
188B242PHE00.022-0.01228.1540.0040.0040.0000.0000.0000.000
189B243VAL0-0.024-0.03232.724-0.003-0.0030.0000.0000.0000.000
190B244GLN0-0.001-0.00432.908-0.001-0.0010.0000.0000.0000.000
191B245LEU0-0.0170.00335.5630.0010.0010.0000.0000.0000.000
192B246PRO00.0050.00037.194-0.002-0.0020.0000.0000.0000.000
193B247PRO0-0.018-0.00936.4050.0020.0020.0000.0000.0000.000
194B248SER00.0390.00638.3640.0020.0020.0000.0000.0000.000
195B249ASP-1-0.838-0.92440.638-0.025-0.0250.0000.0000.0000.000
196B250SER00.0600.02941.7860.0000.0000.0000.0000.0000.000
197B251VAL0-0.036-0.00436.1540.0010.0010.0000.0000.0000.000
198B252CYS0-0.050-0.03237.481-0.001-0.0010.0000.0000.0000.000
199B253GLU-1-0.906-0.95138.405-0.014-0.0140.0000.0000.0000.000
200B254GLU-1-0.866-0.90836.897-0.009-0.0090.0000.0000.0000.000
201B255TYR0-0.079-0.03830.4130.0020.0020.0000.0000.0000.000
202B256GLY0-0.024-0.00435.294-0.002-0.0020.0000.0000.0000.000
203B257LEU0-0.068-0.02834.007-0.002-0.0020.0000.0000.0000.000
204B258SER00.015-0.01638.2790.0020.0020.0000.0000.0000.000
205B259CYS00.0390.00440.706-0.002-0.0020.0000.0000.0000.000
206B260SER00.0240.01242.941-0.001-0.0010.0000.0000.0000.000
207B261ASP-1-0.796-0.86837.318-0.043-0.0430.0000.0000.0000.000
208B262ALA0-0.026-0.01437.769-0.004-0.0040.0000.0000.0000.000
209B263LEU0-0.029-0.02038.771-0.003-0.0030.0000.0000.0000.000
210B264HIS10.8030.90934.6500.0560.0560.0000.0000.0000.000
211B265ASN00.001-0.00633.606-0.007-0.0070.0000.0000.0000.000
212B266LEU00.0440.02731.072-0.001-0.0010.0000.0000.0000.000
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