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: 4J38N

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2008812.949785
FMO2-HF: Nuclear repulsion 1926116.086763
FMO2-HF: Total energy -82696.863022
FMO2-MP2: Total energy -82939.746892


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.
-16.413-13.22710.733-6.187-7.7350.016
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 : 0.034 / 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].
3B152TYR0-0.005-0.0043.845-1.4550.027-0.018-0.719-0.7460.002
4B153TRP00.0430.0116.5410.2900.2900.0000.0000.0000.000
5B154THR0-0.016-0.00210.334-0.005-0.0050.0000.0000.0000.000
6B155ARG10.8920.94312.1350.1790.1790.0000.0000.0000.000
7B156PRO00.0540.04412.6880.0620.0620.0000.0000.0000.000
8B157GLU-1-0.707-0.86314.559-0.244-0.2440.0000.0000.0000.000
9B158ARG10.7510.86617.8630.2440.2440.0000.0000.0000.000
10B159MET0-0.073-0.03513.4470.0400.0400.0000.0000.0000.000
11B160ASP-1-0.747-0.84618.010-0.087-0.0870.0000.0000.0000.000
12B161LYS10.9010.96120.4700.0390.0390.0000.0000.0000.000
13B162LYS10.8830.93919.8060.0550.0550.0000.0000.0000.000
14B163LEU00.0000.00823.1930.0130.0130.0000.0000.0000.000
15B164LEU0-0.057-0.03125.952-0.009-0.0090.0000.0000.0000.000
16B165ALA00.0380.02028.2920.0070.0070.0000.0000.0000.000
17B166VAL0-0.033-0.01231.586-0.006-0.0060.0000.0000.0000.000
18B167PRO00.008-0.01233.5890.0030.0030.0000.0000.0000.000
19B168ALA00.0470.01435.5690.0030.0030.0000.0000.0000.000
20B169ALA0-0.009-0.00236.751-0.002-0.0020.0000.0000.0000.000
21B170ASN00.0090.01734.1910.0000.0000.0000.0000.0000.000
22B171THR0-0.025-0.01729.5620.0020.0020.0000.0000.0000.000
23B172VAL00.0370.03926.237-0.007-0.0070.0000.0000.0000.000
24B173ARG10.8840.94723.170-0.003-0.0030.0000.0000.0000.000
25B174PHE00.0450.03420.751-0.016-0.0160.0000.0000.0000.000
26B175ARG10.8600.91217.7920.0060.0060.0000.0000.0000.000
27B176CYS00.0230.02513.912-0.009-0.0090.0000.0000.0000.000
28B177PRO0-0.072-0.03013.3320.0540.0540.0000.0000.0000.000
29B178ALA00.0420.0268.312-0.088-0.0880.0000.0000.0000.000
30B179ALA00.0090.0027.6120.1070.1070.0000.0000.0000.000
31B180GLY00.0600.0213.762-0.477-0.4370.001-0.0500.0090.000
32B181ASN0-0.0420.0202.514-3.246-1.7710.418-0.731-1.162-0.004
33B182PRO00.027-0.0053.7260.7801.1700.013-0.119-0.2840.000
34B183THR00.041-0.0075.4311.1201.1200.0000.0000.0000.000
35B184PRO0-0.0360.0185.7290.0820.0820.0000.0000.0000.000
36B185SER00.0540.0197.586-0.662-0.6620.0000.0000.0000.000
37B186ILE0-0.040-0.00510.2340.0190.0190.0000.0000.0000.000
38B187SER0-0.0240.00112.877-0.086-0.0860.0000.0000.0000.000
39B188TRP00.0530.00914.894-0.049-0.0490.0000.0000.0000.000
40B189LEU00.015-0.01317.8270.0110.0110.0000.0000.0000.000
41B190LYS10.9421.00520.874-0.128-0.1280.0000.0000.0000.000
42B191ASN0-0.0190.00224.207-0.003-0.0030.0000.0000.0000.000
43B192GLY0-0.013-0.01721.576-0.007-0.0070.0000.0000.0000.000
44B193ARG10.8690.90821.910-0.177-0.1770.0000.0000.0000.000
45B194GLU-1-0.879-0.93320.4830.3140.3140.0000.0000.0000.000
46B195PHE00.0580.02121.641-0.030-0.0300.0000.0000.0000.000
47B196ARG10.9340.93323.012-0.155-0.1550.0000.0000.0000.000
48B197GLY00.1100.01025.146-0.013-0.0130.0000.0000.0000.000
49B198GLU-1-0.911-0.93725.7980.1400.1400.0000.0000.0000.000
50B199HIS0-0.104-0.02026.295-0.002-0.0020.0000.0000.0000.000
51B200ARG10.8250.92328.818-0.107-0.1070.0000.0000.0000.000
52B201ILE00.1850.08231.8260.0030.0030.0000.0000.0000.000
53B202GLY0-0.0180.01333.0890.0020.0020.0000.0000.0000.000
54B203GLY0-0.052-0.01830.7880.0020.0020.0000.0000.0000.000
55B204ILE0-0.0490.00324.019-0.006-0.0060.0000.0000.0000.000
56B205LYS10.9330.94926.145-0.086-0.0860.0000.0000.0000.000
57B206LEU0-0.049-0.00119.238-0.015-0.0150.0000.0000.0000.000
58B207ARG10.9110.94821.072-0.088-0.0880.0000.0000.0000.000
59B208HIS00.0880.03117.031-0.032-0.0320.0000.0000.0000.000
60B209GLN00.0460.02215.8610.0670.0670.0000.0000.0000.000
61B210GLN0-0.052-0.02215.888-0.032-0.0320.0000.0000.0000.000
62B211TRP00.0820.0369.720-0.117-0.1170.0000.0000.0000.000
63B212SER0-0.025-0.02416.080-0.044-0.0440.0000.0000.0000.000
64B213LEU00.0500.02219.5060.0290.0290.0000.0000.0000.000
65B214VAL0-0.069-0.04921.901-0.017-0.0170.0000.0000.0000.000
66B215MET00.0040.01724.8140.0110.0110.0000.0000.0000.000
67B216GLU-1-0.823-0.92628.2470.0580.0580.0000.0000.0000.000
68B217SER0-0.025-0.01331.8830.0010.0010.0000.0000.0000.000
69B218VAL0-0.0360.00930.7360.0030.0030.0000.0000.0000.000
70B219VAL00.1040.03633.397-0.006-0.0060.0000.0000.0000.000
71B220PRO00.1170.05733.7880.0060.0060.0000.0000.0000.000
72B221SER0-0.011-0.01633.9860.0020.0020.0000.0000.0000.000
73B222ASP-1-0.938-0.99029.9500.0940.0940.0000.0000.0000.000
74B223ARG10.8270.92729.017-0.049-0.0490.0000.0000.0000.000
75B224GLY00.0380.00127.5430.0020.0020.0000.0000.0000.000
76B225ASN0-0.059-0.03423.1880.0010.0010.0000.0000.0000.000
77B226TYR00.0520.03621.3700.0180.0180.0000.0000.0000.000
78B227THR0-0.059-0.09515.829-0.028-0.0280.0000.0000.0000.000
79B228CYS0-0.068-0.00714.2400.0130.0130.0000.0000.0000.000
80B229VAL00.016-0.02511.197-0.048-0.0480.0000.0000.0000.000
81B230VAL00.0250.0166.6720.0390.0390.0000.0000.0000.000
82B231GLU-1-0.923-0.9347.1471.0901.0900.0000.0000.0000.000
83B232ASN0-0.003-0.0462.569-7.494-6.1541.330-1.155-1.5160.016
84B233LYS10.9270.9705.469-2.020-2.0200.0000.0000.0000.000
85B234PHE0-0.015-0.0041.730-2.370-4.8518.860-3.072-3.3070.005
86B235GLY00.0210.0133.170-2.133-1.2270.131-0.376-0.661-0.003
87B236SER0-0.012-0.0243.7420.8270.861-0.0020.035-0.0680.000
88B237ILE0-0.0020.0246.004-0.355-0.3550.0000.0000.0000.000
89B238ARG10.9380.9608.248-0.303-0.3030.0000.0000.0000.000
90B239GLN00.0190.01311.858-0.052-0.0520.0000.0000.0000.000
91B240THR00.0730.06215.0110.0470.0470.0000.0000.0000.000
92B241TYR0-0.062-0.03517.995-0.035-0.0350.0000.0000.0000.000
93B242THR00.012-0.00421.6430.0170.0170.0000.0000.0000.000
94B243LEU0-0.0640.01225.152-0.010-0.0100.0000.0000.0000.000
95B244ASP-1-0.847-0.97227.5800.0390.0390.0000.0000.0000.000
96B245VAL0-0.0070.02031.3570.0000.0000.0000.0000.0000.000
97B246LEU00.0170.02734.2220.0000.0000.0000.0000.0000.000
98B247GLU-1-0.902-0.97537.7830.0370.0370.0000.0000.0000.000
99B248ARG10.8040.88840.722-0.011-0.0110.0000.0000.0000.000
100B249SER00.0570.03743.2950.0010.0010.0000.0000.0000.000
101B250PRO0-0.0030.00846.156-0.002-0.0020.0000.0000.0000.000
102B251HIS0-0.075-0.05048.6580.0010.0010.0000.0000.0000.000
103B252ARG10.9641.00252.115-0.013-0.0130.0000.0000.0000.000
104B253PRO0-0.034-0.00854.0650.0010.0010.0000.0000.0000.000
105B254ILE00.0100.01152.0600.0000.0000.0000.0000.0000.000
106B255LEU00.025-0.00555.7160.0000.0000.0000.0000.0000.000
107B256GLN00.0090.01957.6610.0010.0010.0000.0000.0000.000
108B257ALA00.0120.00458.832-0.001-0.0010.0000.0000.0000.000
109B258GLY0-0.012-0.01662.2030.0000.0000.0000.0000.0000.000
110B259LEU0-0.0100.02161.1240.0000.0000.0000.0000.0000.000
111B260PRO00.025-0.02163.6080.0000.0000.0000.0000.0000.000
112B261ALA00.0240.01066.4180.0000.0000.0000.0000.0000.000
113B262ASN0-0.018-0.00869.015-0.001-0.0010.0000.0000.0000.000
114B263GLN0-0.024-0.00371.6740.0010.0010.0000.0000.0000.000
115B264THR0-0.022-0.01974.3350.0000.0000.0000.0000.0000.000
116B265ALA0-0.023-0.01276.7980.0000.0000.0000.0000.0000.000
117B266VAL00.0850.06778.8500.0000.0000.0000.0000.0000.000
118B267LEU0-0.0280.05380.9910.0000.0000.0000.0000.0000.000
119B268GLY00.011-0.00881.1510.0000.0000.0000.0000.0000.000
120B269SER0-0.131-0.12978.0990.0000.0000.0000.0000.0000.000
121B270ASP-1-0.963-0.96972.8830.0060.0060.0000.0000.0000.000
122B271VAL0-0.029-0.01172.8210.0010.0010.0000.0000.0000.000
123B272GLU-1-0.847-0.94766.7310.0080.0080.0000.0000.0000.000
124B273PHE0-0.0130.01167.6590.0000.0000.0000.0000.0000.000
125B274HIS0-0.029-0.01362.4060.0010.0010.0000.0000.0000.000
126B275CYS0-0.002-0.03060.4950.0000.0000.0000.0000.0000.000
127B276LYS10.9711.02056.128-0.016-0.0160.0000.0000.0000.000
128B277VAL00.016-0.01854.4890.0000.0000.0000.0000.0000.000
129B278TYR00.0340.04545.506-0.001-0.0010.0000.0000.0000.000
130B279SER0-0.019-0.06750.337-0.001-0.0010.0000.0000.0000.000
131B280ASP-1-0.814-0.85545.2200.0100.0100.0000.0000.0000.000
132B281ALA0-0.025-0.01047.851-0.001-0.0010.0000.0000.0000.000
133B282GLN00.041-0.00248.6410.0000.0000.0000.0000.0000.000
134B283PRO0-0.0120.01851.336-0.001-0.0010.0000.0000.0000.000
135B284HIS0-0.044-0.02254.674-0.001-0.0010.0000.0000.0000.000
136B285ILE00.0070.00256.9220.0000.0000.0000.0000.0000.000
137B286GLN0-0.0050.00860.149-0.001-0.0010.0000.0000.0000.000
138B287TRP00.0480.01463.3810.0010.0010.0000.0000.0000.000
139B288LEU0-0.034-0.02067.050-0.001-0.0010.0000.0000.0000.000
140B289LYS10.9050.97170.059-0.004-0.0040.0000.0000.0000.000
141B290HIS00.0440.01271.712-0.001-0.0010.0000.0000.0000.000
142B291VAL0-0.077-0.02875.7320.0000.0000.0000.0000.0000.000
143B292GLU-1-0.918-0.97178.6830.0040.0040.0000.0000.0000.000
144B293VAL0-0.0200.00680.2430.0000.0000.0000.0000.0000.000
145B294ASN0-0.018-0.02082.8830.0000.0000.0000.0000.0000.000
146B295GLY00.0180.01486.7210.0000.0000.0000.0000.0000.000
147B296SER00.0440.03683.5460.0000.0000.0000.0000.0000.000
148B297LYS10.9680.99876.051-0.006-0.0060.0000.0000.0000.000
149B298VAL0-0.042-0.03077.5780.0000.0000.0000.0000.0000.000
150B299GLY00.0710.04178.4250.0000.0000.0000.0000.0000.000
151B300PRO0-0.042-0.04779.0090.0000.0000.0000.0000.0000.000
152B301ASP-1-0.873-0.91374.3780.0010.0010.0000.0000.0000.000
153B302GLY0-0.112-0.05374.9060.0000.0000.0000.0000.0000.000
154B303THR0-0.041-0.03671.3670.0000.0000.0000.0000.0000.000
155B304PRO0-0.058-0.04073.0860.0000.0000.0000.0000.0000.000
156B305TYR00.0310.05574.5490.0000.0000.0000.0000.0000.000
157B306VAL0-0.018-0.03271.4600.0000.0000.0000.0000.0000.000
158B307THR0-0.003-0.02073.367-0.001-0.0010.0000.0000.0000.000
159B308VAL00.0140.00967.5700.0000.0000.0000.0000.0000.000
160B309LEU0-0.009-0.00769.2170.0000.0000.0000.0000.0000.000
161B310LYS10.9150.95468.529-0.003-0.0030.0000.0000.0000.000
162B311THR00.0390.02164.5040.0000.0000.0000.0000.0000.000
163B312ALA0-0.118-0.04267.0160.0010.0010.0000.0000.0000.000
164B313GLY00.1020.05667.2600.0000.0000.0000.0000.0000.000
165B314ALA0-0.024-0.01262.273-0.001-0.0010.0000.0000.0000.000
166B315ASN0-0.041-0.00956.6080.0000.0000.0000.0000.0000.000
167B316THR0-0.023-0.03560.3070.0000.0000.0000.0000.0000.000
168B317THR00.0580.02659.2930.0000.0000.0000.0000.0000.000
169B318ASP-1-0.827-0.89455.9450.0150.0150.0000.0000.0000.000
170B319LYS10.8420.94050.970-0.008-0.0080.0000.0000.0000.000
171B320GLU-1-0.938-0.97751.0380.0160.0160.0000.0000.0000.000
172B321LEU0-0.122-0.06054.5710.0010.0010.0000.0000.0000.000
173B322GLU-1-0.890-0.95057.8650.0060.0060.0000.0000.0000.000
174B323VAL0-0.008-0.02660.4890.0000.0000.0000.0000.0000.000
175B324LEU0-0.0600.00263.950-0.001-0.0010.0000.0000.0000.000
176B325SER00.038-0.00667.1470.0000.0000.0000.0000.0000.000
177B326LEU0-0.060-0.03169.726-0.001-0.0010.0000.0000.0000.000
178B327HIS00.0770.02773.3960.0000.0000.0000.0000.0000.000
179B328ASN0-0.001-0.01075.7430.0000.0000.0000.0000.0000.000
180B329VAL0-0.0130.00976.6600.0000.0000.0000.0000.0000.000
181B330THR00.1210.07279.3970.0000.0000.0000.0000.0000.000
182B331PHE00.0210.00782.0090.0000.0000.0000.0000.0000.000
183B332GLU-1-1.069-1.02482.3690.0030.0030.0000.0000.0000.000
184B333ASP-1-0.876-0.95577.3730.0040.0040.0000.0000.0000.000
185B334ALA0-0.006-0.01177.8040.0000.0000.0000.0000.0000.000
186B335GLY0-0.0230.00178.3550.0000.0000.0000.0000.0000.000
187B336GLU-1-0.869-0.95072.7880.0080.0080.0000.0000.0000.000
188B337TYR0-0.053-0.04970.574-0.001-0.0010.0000.0000.0000.000
189B338THR0-0.011-0.03567.0080.0010.0010.0000.0000.0000.000
190B339CYS0-0.0270.01162.138-0.001-0.0010.0000.0000.0000.000
191B340LEU0-0.001-0.03463.0280.0010.0010.0000.0000.0000.000
192B341ALA00.0490.03058.087-0.001-0.0010.0000.0000.0000.000
193B342GLY00.025-0.00259.0570.0000.0000.0000.0000.0000.000
194B343ASN00.0700.01352.021-0.001-0.0010.0000.0000.0000.000
195B344SER00.0220.00351.975-0.001-0.0010.0000.0000.0000.000
196B345ILE0-0.149-0.04549.842-0.001-0.0010.0000.0000.0000.000
197B346GLY00.0310.00254.3620.0010.0010.0000.0000.0000.000
198B347PHE00.0570.03357.5270.0000.0000.0000.0000.0000.000
199B348SER0-0.079-0.03858.6350.0010.0010.0000.0000.0000.000
200B349HIS00.008-0.00760.5940.0000.0000.0000.0000.0000.000
201B350HIS10.8060.92661.444-0.012-0.0120.0000.0000.0000.000
202B351SER00.0460.03665.487-0.001-0.0010.0000.0000.0000.000
203B352ALA0-0.0300.00668.8930.0010.0010.0000.0000.0000.000
204B353TRP00.0320.01371.325-0.001-0.0010.0000.0000.0000.000
205B354LEU00.0310.02974.4150.0010.0010.0000.0000.0000.000
206B355VAL00.0030.00776.4330.0000.0000.0000.0000.0000.000
207B356VAL00.0150.01779.7890.0000.0000.0000.0000.0000.000
208B357LEU00.030-0.00682.0290.0000.0000.0000.0000.0000.000
209B358PRO0-0.039-0.04385.0900.0000.0000.0000.0000.0000.000
210B359ALA00.0270.00286.3620.0000.0000.0000.0000.0000.000
211B360GLU-1-0.938-0.93888.2840.0060.0060.0000.0000.0000.000
212B361GLU-1-0.934-0.96386.1100.0080.0080.0000.0000.0000.000
213B362GLU-1-1.050-1.02489.9880.0080.0080.0000.0000.0000.000