Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: YVYM2

Calculation Name: 1RY7-B-Xray372

Preferred Name: Acidic fibroblast growth factor

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1RY7

Chain ID: B

ChEMBL ID: CHEMBL2120

UniProt ID: P05230

Base Structure: X-ray

Registration Date: 2023-09-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2001193.362045
FMO2-HF: Nuclear repulsion 1918492.081257
FMO2-HF: Total energy -82701.280788
FMO2-MP2: Total energy -82943.454666


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:150:ALA)


Summations of interaction energy for fragment #1(B:150:ALA)
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.
-19.543-19.67217.868-8.012-9.7280.003
Interaction energy analysis for fragmet #1(B:150:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : -0.001
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].
3B152TYR00.0100.0013.872-1.348-0.056-0.014-0.559-0.7190.002
4B153TRP00.0540.0086.6250.3350.3350.0000.0000.0000.000
5B154THR0-0.005-0.01810.408-0.067-0.0670.0000.0000.0000.000
6B155ARG10.8720.93712.3490.1300.1300.0000.0000.0000.000
7B156PRO00.0700.04212.9720.0510.0510.0000.0000.0000.000
8B157GLU-1-0.723-0.83514.939-0.181-0.1810.0000.0000.0000.000
9B158ARG10.7550.84118.2040.1950.1950.0000.0000.0000.000
10B159MET0-0.049-0.01313.5270.0350.0350.0000.0000.0000.000
11B160ASP-1-0.774-0.85818.709-0.051-0.0510.0000.0000.0000.000
12B161LYS10.8590.94620.7200.0140.0140.0000.0000.0000.000
13B162LYS10.8490.88720.9770.0470.0470.0000.0000.0000.000
14B163LEU00.0290.03523.4350.0130.0130.0000.0000.0000.000
15B164LEU0-0.039-0.02726.465-0.008-0.0080.0000.0000.0000.000
16B165ALA00.0740.04928.6080.0080.0080.0000.0000.0000.000
17B166VAL0-0.073-0.03231.673-0.005-0.0050.0000.0000.0000.000
18B167PRO00.0440.01333.8630.0020.0020.0000.0000.0000.000
19B168ALA00.0400.01735.8280.0040.0040.0000.0000.0000.000
20B169ALA0-0.004-0.00537.142-0.003-0.0030.0000.0000.0000.000
21B170ASN00.0260.02633.2790.0020.0020.0000.0000.0000.000
22B171THR0-0.006-0.01129.8780.0070.0070.0000.0000.0000.000
23B172VAL00.0000.01126.476-0.008-0.0080.0000.0000.0000.000
24B173ARG10.9350.95823.621-0.031-0.0310.0000.0000.0000.000
25B174PHE00.0520.03920.951-0.016-0.0160.0000.0000.0000.000
26B175ARG10.8550.90718.056-0.055-0.0550.0000.0000.0000.000
27B176CYS00.0060.03213.575-0.016-0.0160.0000.0000.0000.000
28B177PRO0-0.042-0.02813.2080.0460.0460.0000.0000.0000.000
29B178ALA00.0620.0428.628-0.098-0.0980.0000.0000.0000.000
30B179ALA0-0.0120.0037.7640.1200.1200.0000.0000.0000.000
31B180GLY00.0650.0153.738-0.545-0.4210.006-0.095-0.0360.000
32B181ASN0-0.0230.0212.009-6.240-7.1837.066-3.022-3.101-0.017
33B182PRO00.018-0.0053.582-0.3440.1680.025-0.175-0.363-0.001
34B183THR00.036-0.0034.9541.6311.645-0.001-0.001-0.0110.000
35B184PRO0-0.0590.0115.3820.0680.162-0.001-0.007-0.0860.000
36B185SER00.0620.0227.014-0.826-0.8260.0000.0000.0000.000
37B186ILE0-0.061-0.0359.9970.0290.0290.0000.0000.0000.000
38B187SER0-0.0090.01312.755-0.077-0.0770.0000.0000.0000.000
39B188TRP00.040-0.00815.016-0.055-0.0550.0000.0000.0000.000
40B189LEU0-0.0350.00618.0080.0070.0070.0000.0000.0000.000
41B190LYS10.8550.92220.920-0.129-0.1290.0000.0000.0000.000
42B191ASN00.0300.00224.323-0.004-0.0040.0000.0000.0000.000
43B192GLY00.0040.00622.179-0.009-0.0090.0000.0000.0000.000
44B193ARG10.8700.92922.106-0.166-0.1660.0000.0000.0000.000
45B194GLU-1-0.842-0.91620.7600.3170.3170.0000.0000.0000.000
46B195PHE0-0.033-0.02122.079-0.032-0.0320.0000.0000.0000.000
47B196ARG10.8970.91323.378-0.159-0.1590.0000.0000.0000.000
48B197GLY00.004-0.01025.207-0.012-0.0120.0000.0000.0000.000
49B198GLU-1-0.786-0.87926.2810.1460.1460.0000.0000.0000.000
50B199HIS0-0.050-0.00726.6770.0020.0020.0000.0000.0000.000
51B200ARG10.7620.87129.399-0.106-0.1060.0000.0000.0000.000
52B201ILE00.0790.03332.0610.0040.0040.0000.0000.0000.000
53B202GLY00.0040.00233.7490.0000.0000.0000.0000.0000.000
54B203GLY0-0.0030.01730.9250.0020.0020.0000.0000.0000.000
55B204ILE0-0.067-0.02124.203-0.006-0.0060.0000.0000.0000.000
56B205LYS10.8570.90426.780-0.092-0.0920.0000.0000.0000.000
57B206LEU0-0.0260.00019.827-0.010-0.0100.0000.0000.0000.000
58B207ARG10.8670.92520.741-0.139-0.1390.0000.0000.0000.000
59B208HIS00.1350.06816.134-0.038-0.0380.0000.0000.0000.000
60B209GLN00.0430.01515.6020.0610.0610.0000.0000.0000.000
61B210GLN0-0.032-0.00616.402-0.042-0.0420.0000.0000.0000.000
62B211TRP00.0410.0259.478-0.124-0.1240.0000.0000.0000.000
63B212SER0-0.039-0.02915.733-0.050-0.0500.0000.0000.0000.000
64B213LEU00.0510.02519.2640.0250.0250.0000.0000.0000.000
65B214VAL0-0.030-0.02721.911-0.022-0.0220.0000.0000.0000.000
66B215MET00.0210.01525.5810.0130.0130.0000.0000.0000.000
67B216GLU-1-0.785-0.87528.5400.0780.0780.0000.0000.0000.000
68B217SER00.0260.01332.0410.0020.0020.0000.0000.0000.000
69B218VAL0-0.038-0.00530.4980.0040.0040.0000.0000.0000.000
70B219VAL00.0870.03633.584-0.007-0.0070.0000.0000.0000.000
71B220PRO00.0760.03734.2150.0060.0060.0000.0000.0000.000
72B221SER00.0280.02234.4110.0000.0000.0000.0000.0000.000
73B222ASP-1-0.844-0.91230.1040.1080.1080.0000.0000.0000.000
74B223ARG10.8760.96628.987-0.057-0.0570.0000.0000.0000.000
75B224GLY0-0.003-0.02227.7790.0040.0040.0000.0000.0000.000
76B225ASN0-0.013-0.00823.782-0.007-0.0070.0000.0000.0000.000
77B226TYR00.001-0.02521.7200.0180.0180.0000.0000.0000.000
78B227THR0-0.045-0.03916.014-0.014-0.0140.0000.0000.0000.000
79B228CYS0-0.051-0.01314.9410.0190.0190.0000.0000.0000.000
80B229VAL00.014-0.02011.455-0.052-0.0520.0000.0000.0000.000
81B230VAL00.0120.0077.1320.0450.0450.0000.0000.0000.000
82B231GLU-1-0.929-0.9646.8520.9260.9260.0000.0000.0000.000
83B232ASN00.010-0.0152.243-7.446-9.1285.623-1.716-2.2250.020
84B233LYS10.9490.9735.139-2.106-2.1060.0000.0000.0000.000
85B234PHE0-0.0060.0021.864-1.878-2.3685.063-2.019-2.5550.003
86B235GLY00.0370.0263.373-1.643-0.7290.102-0.417-0.599-0.004
87B236SER0-0.053-0.0404.2540.7850.821-0.001-0.001-0.0330.000
88B237ILE0-0.0140.0146.348-0.302-0.3020.0000.0000.0000.000
89B238ARG10.9740.9768.723-0.315-0.3150.0000.0000.0000.000
90B239GLN00.005-0.00212.396-0.063-0.0630.0000.0000.0000.000
91B240THR00.0230.03015.5170.0510.0510.0000.0000.0000.000
92B241TYR0-0.028-0.01318.242-0.029-0.0290.0000.0000.0000.000
93B242THR0-0.021-0.01622.1460.0180.0180.0000.0000.0000.000
94B243LEU0-0.057-0.00925.735-0.010-0.0100.0000.0000.0000.000
95B244ASP-1-0.829-0.92227.9340.0480.0480.0000.0000.0000.000
96B245VAL00.003-0.00531.702-0.001-0.0010.0000.0000.0000.000
97B246LEU00.0230.01734.650-0.001-0.0010.0000.0000.0000.000
98B247GLU-1-0.904-0.96638.2480.0430.0430.0000.0000.0000.000
99B248ARG10.8020.87440.905-0.018-0.0180.0000.0000.0000.000
100B249SER00.0210.01643.3400.0010.0010.0000.0000.0000.000
101B250PRO0-0.028-0.00746.215-0.002-0.0020.0000.0000.0000.000
102B251HIS0-0.025-0.03348.7570.0000.0000.0000.0000.0000.000
103B252ARG10.9380.96952.274-0.016-0.0160.0000.0000.0000.000
104B253PRO0-0.0100.00154.5120.0010.0010.0000.0000.0000.000
105B254ILE0-0.023-0.00352.0030.0000.0000.0000.0000.0000.000
106B255LEU00.0540.02155.7340.0000.0000.0000.0000.0000.000
107B256GLN00.0120.02058.2390.0010.0010.0000.0000.0000.000
108B257ALA00.009-0.00559.308-0.001-0.0010.0000.0000.0000.000
109B258GLY00.0100.00362.4250.0000.0000.0000.0000.0000.000
110B259LEU0-0.0270.01861.1640.0000.0000.0000.0000.0000.000
111B260PRO00.0400.01763.5870.0000.0000.0000.0000.0000.000
112B261ALA0-0.013-0.00966.7410.0000.0000.0000.0000.0000.000
113B262ASN00.003-0.01369.463-0.001-0.0010.0000.0000.0000.000
114B263GLN0-0.035-0.00472.4800.0010.0010.0000.0000.0000.000
115B264THR00.0150.00274.9290.0000.0000.0000.0000.0000.000
116B265ALA0-0.0100.00377.2430.0000.0000.0000.0000.0000.000
117B266VAL00.0380.02979.3030.0000.0000.0000.0000.0000.000
118B267LEU00.0200.01381.2610.0000.0000.0000.0000.0000.000
119B268GLY0-0.020-0.01181.6410.0000.0000.0000.0000.0000.000
120B269SER0-0.059-0.05278.7250.0000.0000.0000.0000.0000.000
121B270ASP-1-0.923-0.95673.5460.0070.0070.0000.0000.0000.000
122B271VAL0-0.029-0.00672.8340.0010.0010.0000.0000.0000.000
123B272GLU-1-0.798-0.89266.2450.0100.0100.0000.0000.0000.000
124B273PHE0-0.0270.00368.2110.0010.0010.0000.0000.0000.000
125B274HIS0-0.032-0.04463.1280.0000.0000.0000.0000.0000.000
126B275CYS0-0.035-0.04061.3960.0000.0000.0000.0000.0000.000
127B276LYS10.9721.01056.052-0.019-0.0190.0000.0000.0000.000
128B277VAL00.008-0.02055.4880.0000.0000.0000.0000.0000.000
129B278TYR00.0450.04146.3520.0000.0000.0000.0000.0000.000
130B279SER0-0.003-0.04751.1520.0000.0000.0000.0000.0000.000
131B280ASP-1-0.817-0.84945.2580.0180.0180.0000.0000.0000.000
132B281ALA00.0120.00747.872-0.001-0.0010.0000.0000.0000.000
133B282GLN00.0100.00148.9600.0000.0000.0000.0000.0000.000
134B283PRO00.0150.01151.4370.0000.0000.0000.0000.0000.000
135B284HIS0-0.028-0.01554.967-0.001-0.0010.0000.0000.0000.000
136B285ILE00.0190.00557.1300.0000.0000.0000.0000.0000.000
137B286GLN0-0.036-0.00960.303-0.001-0.0010.0000.0000.0000.000
138B287TRP00.0550.02963.7640.0010.0010.0000.0000.0000.000
139B288LEU0-0.024-0.01367.065-0.001-0.0010.0000.0000.0000.000
140B289LYS10.9330.98770.274-0.006-0.0060.0000.0000.0000.000
141B290HIS00.006-0.01172.023-0.001-0.0010.0000.0000.0000.000
142B291VAL0-0.025-0.01976.0740.0000.0000.0000.0000.0000.000
143B292GLU-1-0.858-0.95079.2660.0060.0060.0000.0000.0000.000
144B293VAL0-0.022-0.00580.6620.0000.0000.0000.0000.0000.000
145B294ASN0-0.048-0.03683.4730.0000.0000.0000.0000.0000.000
146B295GLY00.0360.02186.5780.0000.0000.0000.0000.0000.000
147B296SER0-0.006-0.00282.9370.0000.0000.0000.0000.0000.000
148B297LYS10.8950.96076.358-0.008-0.0080.0000.0000.0000.000
149B298VAL0-0.072-0.03277.9800.0000.0000.0000.0000.0000.000
150B299GLY00.0750.05178.4670.0000.0000.0000.0000.0000.000
151B300PRO0-0.028-0.03279.6080.0000.0000.0000.0000.0000.000
152B301ASP-1-0.920-0.94974.8130.0040.0040.0000.0000.0000.000
153B302GLY0-0.026-0.00275.0770.0000.0000.0000.0000.0000.000
154B303THR0-0.058-0.04171.8910.0010.0010.0000.0000.0000.000
155B304PRO0-0.022-0.02473.2540.0000.0000.0000.0000.0000.000
156B305TYR00.0280.04174.6910.0000.0000.0000.0000.0000.000
157B306VAL0-0.024-0.02071.3190.0000.0000.0000.0000.0000.000
158B307THR0-0.0120.00074.075-0.001-0.0010.0000.0000.0000.000
159B308VAL00.018-0.00467.8640.0010.0010.0000.0000.0000.000
160B309LEU0-0.020-0.00469.4630.0000.0000.0000.0000.0000.000
161B310LYS10.9200.97168.557-0.005-0.0050.0000.0000.0000.000
162B311THR0-0.048-0.02864.7080.0000.0000.0000.0000.0000.000
163B312ALA0-0.033-0.02067.5920.0000.0000.0000.0000.0000.000
164B313GLY00.0430.02967.1060.0000.0000.0000.0000.0000.000
165B314ALA0-0.0130.00062.289-0.001-0.0010.0000.0000.0000.000
166B315ASN00.001-0.00756.9170.0000.0000.0000.0000.0000.000
167B316THR0-0.027-0.02460.5170.0010.0010.0000.0000.0000.000
168B317THR00.0020.01860.2630.0000.0000.0000.0000.0000.000
169B318ASP-1-0.810-0.91656.2820.0160.0160.0000.0000.0000.000
170B319LYS10.7980.89752.026-0.011-0.0110.0000.0000.0000.000
171B320GLU-1-0.948-0.96351.4680.0180.0180.0000.0000.0000.000
172B321LEU0-0.092-0.05354.7270.0010.0010.0000.0000.0000.000
173B322GLU-1-0.937-0.95857.5520.0080.0080.0000.0000.0000.000
174B323VAL0-0.023-0.03160.4730.0010.0010.0000.0000.0000.000
175B324LEU0-0.035-0.00864.038-0.001-0.0010.0000.0000.0000.000
176B325SER00.0490.03367.5350.0000.0000.0000.0000.0000.000
177B326LEU0-0.041-0.04470.120-0.001-0.0010.0000.0000.0000.000
178B327HIS00.0290.03073.8880.0000.0000.0000.0000.0000.000
179B328ASN00.001-0.02176.0700.0000.0000.0000.0000.0000.000
180B329VAL0-0.0320.00676.9120.0000.0000.0000.0000.0000.000
181B330THR00.1080.04379.6980.0000.0000.0000.0000.0000.000
182B331PHE0-0.026-0.01782.3610.0000.0000.0000.0000.0000.000
183B332GLU-1-0.991-0.99183.0510.0040.0040.0000.0000.0000.000
184B333ASP-1-0.889-0.93778.0220.0060.0060.0000.0000.0000.000
185B334ALA00.0070.02178.2990.0000.0000.0000.0000.0000.000
186B335GLY00.012-0.01078.4770.0000.0000.0000.0000.0000.000
187B336GLU-1-0.850-0.88773.4550.0090.0090.0000.0000.0000.000
188B337TYR0-0.008-0.03171.026-0.001-0.0010.0000.0000.0000.000
189B338THR0-0.049-0.03167.2200.0010.0010.0000.0000.0000.000
190B339CYS0-0.0210.00862.203-0.001-0.0010.0000.0000.0000.000
191B340LEU0-0.009-0.02062.9840.0010.0010.0000.0000.0000.000
192B341ALA00.0580.02258.412-0.001-0.0010.0000.0000.0000.000
193B342GLY00.027-0.00459.3720.0010.0010.0000.0000.0000.000
194B343ASN00.029-0.00252.4800.0000.0000.0000.0000.0000.000
195B344SER0-0.0100.00452.042-0.001-0.0010.0000.0000.0000.000
196B345ILE0-0.081-0.02749.7780.0000.0000.0000.0000.0000.000
197B346GLY00.0260.02154.4980.0010.0010.0000.0000.0000.000
198B347PHE00.0260.01158.0000.0000.0000.0000.0000.0000.000
199B348SER0-0.066-0.03958.8760.0010.0010.0000.0000.0000.000
200B349HIS00.0470.03361.016-0.001-0.0010.0000.0000.0000.000
201B350HIS10.7760.88761.413-0.014-0.0140.0000.0000.0000.000
202B351SER00.013-0.02165.704-0.001-0.0010.0000.0000.0000.000
203B352ALA0-0.0130.01569.3650.0010.0010.0000.0000.0000.000
204B353TRP00.0240.00071.701-0.001-0.0010.0000.0000.0000.000
205B354LEU00.0020.01475.0020.0010.0010.0000.0000.0000.000
206B355VAL0-0.017-0.01076.8690.0000.0000.0000.0000.0000.000
207B356VAL0-0.002-0.00480.1240.0000.0000.0000.0000.0000.000
208B357LEU0-0.0060.00282.5740.0000.0000.0000.0000.0000.000
209B358PRO0-0.017-0.01485.5940.0000.0000.0000.0000.0000.000
210B359ALA00.004-0.01186.6850.0000.0000.0000.0000.0000.000
211B360GLU-1-0.928-0.96688.4150.0070.0070.0000.0000.0000.000
212B361GLU-1-0.943-0.96586.4330.0090.0090.0000.0000.0000.000
213B362GLU-1-1.015-1.00090.0920.0090.0090.0000.0000.0000.000