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: 5J38Z

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2006312.800653
FMO2-HF: Nuclear repulsion 1923613.872731
FMO2-HF: Total energy -82698.927921
FMO2-MP2: Total energy -82941.440824


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.
-10.886-7.5069.046-5.464-6.9620.001
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 : 0.023 / q_NPA : -0.005
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].
3B152TYR0-0.001-0.0083.845-1.1910.260-0.018-0.688-0.7450.002
4B153TRP00.0460.0106.6070.2620.2620.0000.0000.0000.000
5B154THR0-0.005-0.01010.4020.0010.0010.0000.0000.0000.000
6B155ARG10.8840.94612.1890.1800.1800.0000.0000.0000.000
7B156PRO00.0430.04012.7430.0530.0530.0000.0000.0000.000
8B157GLU-1-0.705-0.84214.625-0.211-0.2110.0000.0000.0000.000
9B158ARG10.7590.85118.0090.2290.2290.0000.0000.0000.000
10B159MET0-0.071-0.02613.5370.0370.0370.0000.0000.0000.000
11B160ASP-1-0.754-0.84818.084-0.073-0.0730.0000.0000.0000.000
12B161LYS10.8990.96620.5440.0330.0330.0000.0000.0000.000
13B162LYS10.8670.91820.1080.0460.0460.0000.0000.0000.000
14B163LEU00.0080.01323.1990.0120.0120.0000.0000.0000.000
15B164LEU0-0.055-0.03625.903-0.009-0.0090.0000.0000.0000.000
16B165ALA00.0350.02228.2960.0060.0060.0000.0000.0000.000
17B166VAL0-0.043-0.01731.351-0.005-0.0050.0000.0000.0000.000
18B167PRO00.0370.00533.5910.0030.0030.0000.0000.0000.000
19B168ALA00.0370.00735.5680.0020.0020.0000.0000.0000.000
20B169ALA0-0.012-0.00536.756-0.002-0.0020.0000.0000.0000.000
21B170ASN00.0170.02433.626-0.001-0.0010.0000.0000.0000.000
22B171THR0-0.025-0.02129.6630.0030.0030.0000.0000.0000.000
23B172VAL00.0140.03026.270-0.007-0.0070.0000.0000.0000.000
24B173ARG10.9080.95623.1390.0020.0020.0000.0000.0000.000
25B174PHE00.0430.03320.760-0.015-0.0150.0000.0000.0000.000
26B175ARG10.8640.91317.8490.0120.0120.0000.0000.0000.000
27B176CYS00.0070.02413.836-0.007-0.0070.0000.0000.0000.000
28B177PRO0-0.060-0.03013.3310.0490.0490.0000.0000.0000.000
29B178ALA00.0350.0308.325-0.079-0.0790.0000.0000.0000.000
30B179ALA0-0.006-0.0017.6100.1150.1150.0000.0000.0000.000
31B180GLY00.0670.0253.790-0.477-0.4400.001-0.0500.0120.000
32B181ASN0-0.0480.0242.530-3.975-2.3660.679-0.906-1.382-0.007
33B182PRO00.032-0.0073.7250.5350.9320.013-0.121-0.2880.000
34B183THR00.039-0.0095.4551.0821.0820.0000.0000.0000.000
35B184PRO0-0.0440.0155.7320.1490.1490.0000.0000.0000.000
36B185SER00.0590.0197.586-0.614-0.6140.0000.0000.0000.000
37B186ILE0-0.039-0.01910.2200.0140.0140.0000.0000.0000.000
38B187SER0-0.031-0.00512.865-0.078-0.0780.0000.0000.0000.000
39B188TRP00.0660.00914.883-0.048-0.0480.0000.0000.0000.000
40B189LEU00.0070.00418.0080.0120.0120.0000.0000.0000.000
41B190LYS10.8780.95020.867-0.115-0.1150.0000.0000.0000.000
42B191ASN0-0.0010.01524.201-0.001-0.0010.0000.0000.0000.000
43B192GLY0-0.010-0.01921.578-0.006-0.0060.0000.0000.0000.000
44B193ARG10.8670.90621.905-0.163-0.1630.0000.0000.0000.000
45B194GLU-1-0.883-0.93820.6550.2850.2850.0000.0000.0000.000
46B195PHE00.0350.02921.620-0.026-0.0260.0000.0000.0000.000
47B196ARG10.9210.93723.001-0.143-0.1430.0000.0000.0000.000
48B197GLY00.1090.03325.149-0.012-0.0120.0000.0000.0000.000
49B198GLU-1-0.913-0.94125.7850.1290.1290.0000.0000.0000.000
50B199HIS0-0.075-0.03226.515-0.004-0.0040.0000.0000.0000.000
51B200ARG10.7800.89328.892-0.091-0.0910.0000.0000.0000.000
52B201ILE00.1780.07831.8160.0030.0030.0000.0000.0000.000
53B202GLY0-0.0240.00533.0800.0020.0020.0000.0000.0000.000
54B203GLY0-0.056-0.02130.7740.0010.0010.0000.0000.0000.000
55B204ILE0-0.057-0.02123.962-0.004-0.0040.0000.0000.0000.000
56B205LYS10.8780.91926.124-0.077-0.0770.0000.0000.0000.000
57B206LEU0-0.034-0.00219.458-0.014-0.0140.0000.0000.0000.000
58B207ARG10.9220.95621.190-0.076-0.0760.0000.0000.0000.000
59B208HIS00.0710.02617.033-0.030-0.0300.0000.0000.0000.000
60B209GLN00.0380.02015.8770.0640.0640.0000.0000.0000.000
61B210GLN0-0.046-0.02115.919-0.029-0.0290.0000.0000.0000.000
62B211TRP00.0860.0449.801-0.108-0.1080.0000.0000.0000.000
63B212SER0-0.039-0.03016.080-0.039-0.0390.0000.0000.0000.000
64B213LEU00.0520.02319.4990.0260.0260.0000.0000.0000.000
65B214VAL0-0.059-0.04221.894-0.015-0.0150.0000.0000.0000.000
66B215MET00.0170.02325.3870.0120.0120.0000.0000.0000.000
67B216GLU-1-0.783-0.89628.2400.0540.0540.0000.0000.0000.000
68B217SER0-0.015-0.01331.8770.0020.0020.0000.0000.0000.000
69B218VAL0-0.0420.00030.4890.0030.0030.0000.0000.0000.000
70B219VAL00.1300.05033.393-0.005-0.0050.0000.0000.0000.000
71B220PRO00.1160.06633.7850.0060.0060.0000.0000.0000.000
72B221SER00.0180.00833.9840.0010.0010.0000.0000.0000.000
73B222ASP-1-0.887-0.94229.8530.0910.0910.0000.0000.0000.000
74B223ARG10.8580.94328.942-0.046-0.0460.0000.0000.0000.000
75B224GLY00.0480.00427.5420.0020.0020.0000.0000.0000.000
76B225ASN0-0.057-0.04523.3350.0010.0010.0000.0000.0000.000
77B226TYR00.0070.01421.4020.0160.0160.0000.0000.0000.000
78B227THR0-0.025-0.03115.817-0.020-0.0200.0000.0000.0000.000
79B228CYS0-0.074-0.00714.3100.0140.0140.0000.0000.0000.000
80B229VAL0-0.010-0.03311.337-0.034-0.0340.0000.0000.0000.000
81B230VAL00.0230.0116.7330.0430.0430.0000.0000.0000.000
82B231GLU-1-0.938-0.9427.1321.0211.0210.0000.0000.0000.000
83B232ASN0-0.001-0.0383.009-2.058-1.0860.543-0.582-0.9330.004
84B233LYS10.9520.9765.449-1.971-1.9710.0000.0000.0000.000
85B234PHE0-0.017-0.0061.689-1.775-3.8057.700-2.779-2.8920.005
86B235GLY00.0270.0193.176-1.992-1.0810.130-0.371-0.669-0.003
87B236SER0-0.019-0.0233.7420.7160.749-0.0020.033-0.0650.000
88B237ILE0-0.0160.0205.907-0.311-0.3110.0000.0000.0000.000
89B238ARG11.0000.9908.253-0.326-0.3260.0000.0000.0000.000
90B239GLN0-0.006-0.01411.861-0.044-0.0440.0000.0000.0000.000
91B240THR00.0410.02315.0170.0430.0430.0000.0000.0000.000
92B241TYR0-0.045-0.04217.886-0.032-0.0320.0000.0000.0000.000
93B242THR00.0110.00721.6460.0180.0180.0000.0000.0000.000
94B243LEU0-0.083-0.01425.155-0.010-0.0100.0000.0000.0000.000
95B244ASP-1-0.834-0.93227.5810.0390.0390.0000.0000.0000.000
96B245VAL0-0.015-0.00331.358-0.001-0.0010.0000.0000.0000.000
97B246LEU00.0290.03334.2220.0000.0000.0000.0000.0000.000
98B247GLU-1-0.893-0.97037.7840.0350.0350.0000.0000.0000.000
99B248ARG10.7800.85740.809-0.010-0.0100.0000.0000.0000.000
100B249SER00.0290.01843.2960.0010.0010.0000.0000.0000.000
101B250PRO0-0.037-0.00346.052-0.002-0.0020.0000.0000.0000.000
102B251HIS0-0.021-0.03648.6590.0000.0000.0000.0000.0000.000
103B252ARG10.9530.99852.115-0.012-0.0120.0000.0000.0000.000
104B253PRO0-0.029-0.00854.0660.0010.0010.0000.0000.0000.000
105B254ILE0-0.011-0.00151.9410.0000.0000.0000.0000.0000.000
106B255LEU00.0600.02255.7170.0000.0000.0000.0000.0000.000
107B256GLN00.0140.02557.6200.0010.0010.0000.0000.0000.000
108B257ALA00.0340.01258.832-0.001-0.0010.0000.0000.0000.000
109B258GLY0-0.009-0.00762.2030.0000.0000.0000.0000.0000.000
110B259LEU0-0.0160.02561.1930.0000.0000.0000.0000.0000.000
111B260PRO00.015-0.02363.6100.0000.0000.0000.0000.0000.000
112B261ALA00.0230.01466.4200.0000.0000.0000.0000.0000.000
113B262ASN0-0.026-0.01769.016-0.001-0.0010.0000.0000.0000.000
114B263GLN0-0.041-0.01171.9250.0010.0010.0000.0000.0000.000
115B264THR00.002-0.00974.3370.0000.0000.0000.0000.0000.000
116B265ALA0-0.008-0.00376.8010.0000.0000.0000.0000.0000.000
117B266VAL00.0500.04678.8540.0000.0000.0000.0000.0000.000
118B267LEU0-0.0010.01180.9960.0000.0000.0000.0000.0000.000
119B268GLY0-0.012-0.01781.1570.0000.0000.0000.0000.0000.000
120B269SER0-0.070-0.05377.9930.0000.0000.0000.0000.0000.000
121B270ASP-1-0.967-0.96772.8990.0060.0060.0000.0000.0000.000
122B271VAL0-0.005-0.00372.7910.0000.0000.0000.0000.0000.000
123B272GLU-1-0.830-0.92166.5180.0080.0080.0000.0000.0000.000
124B273PHE0-0.0170.00267.6580.0000.0000.0000.0000.0000.000
125B274HIS0-0.042-0.03462.4630.0010.0010.0000.0000.0000.000
126B275CYS00.031-0.00460.5600.0000.0000.0000.0000.0000.000
127B276LYS10.9561.01455.619-0.016-0.0160.0000.0000.0000.000
128B277VAL0-0.007-0.03054.8520.0000.0000.0000.0000.0000.000
129B278TYR00.0350.04345.8250.0000.0000.0000.0000.0000.000
130B279SER00.000-0.05650.344-0.001-0.0010.0000.0000.0000.000
131B280ASP-1-0.794-0.82345.1580.0100.0100.0000.0000.0000.000
132B281ALA0-0.016-0.00547.855-0.001-0.0010.0000.0000.0000.000
133B282GLN00.0400.00348.6970.0000.0000.0000.0000.0000.000
134B283PRO0-0.0050.02051.342-0.001-0.0010.0000.0000.0000.000
135B284HIS0-0.026-0.02154.6790.0000.0000.0000.0000.0000.000
136B285ILE00.0220.00356.9050.0000.0000.0000.0000.0000.000
137B286GLN0-0.0170.00860.154-0.001-0.0010.0000.0000.0000.000
138B287TRP00.0540.01863.6520.0010.0010.0000.0000.0000.000
139B288LEU0-0.042-0.02567.055-0.001-0.0010.0000.0000.0000.000
140B289LYS10.9470.98970.064-0.004-0.0040.0000.0000.0000.000
141B290HIS00.007-0.00671.485-0.001-0.0010.0000.0000.0000.000
142B291VAL0-0.079-0.03375.7350.0000.0000.0000.0000.0000.000
143B292GLU-1-0.902-0.96478.6870.0040.0040.0000.0000.0000.000
144B293VAL0-0.018-0.00180.1920.0000.0000.0000.0000.0000.000
145B294ASN0-0.031-0.02482.8880.0000.0000.0000.0000.0000.000
146B295GLY00.0240.01786.7250.0000.0000.0000.0000.0000.000
147B296SER00.0170.02883.0060.0000.0000.0000.0000.0000.000
148B297LYS10.9510.98376.154-0.006-0.0060.0000.0000.0000.000
149B298VAL0-0.050-0.03377.5830.0000.0000.0000.0000.0000.000
150B299GLY00.0770.04478.4290.0000.0000.0000.0000.0000.000
151B300PRO0-0.030-0.03779.0120.0000.0000.0000.0000.0000.000
152B301ASP-1-0.881-0.92174.4380.0010.0010.0000.0000.0000.000
153B302GLY0-0.104-0.04674.9080.0000.0000.0000.0000.0000.000
154B303THR0-0.037-0.03671.2040.0000.0000.0000.0000.0000.000
155B304PRO0-0.057-0.04073.1390.0000.0000.0000.0000.0000.000
156B305TYR00.0210.04774.5530.0000.0000.0000.0000.0000.000
157B306VAL0-0.023-0.03471.2290.0000.0000.0000.0000.0000.000
158B307THR0-0.003-0.00873.3900.0000.0000.0000.0000.0000.000
159B308VAL00.0100.00367.5530.0000.0000.0000.0000.0000.000
160B309LEU0-0.022-0.00769.2060.0000.0000.0000.0000.0000.000
161B310LYS10.9380.95968.555-0.003-0.0030.0000.0000.0000.000
162B311THR00.0440.01864.5040.0000.0000.0000.0000.0000.000
163B312ALA0-0.108-0.05467.0240.0000.0000.0000.0000.0000.000
164B313GLY00.0840.06267.2710.0000.0000.0000.0000.0000.000
165B314ALA0-0.018-0.00962.428-0.001-0.0010.0000.0000.0000.000
166B315ASN0-0.0120.00256.6820.0000.0000.0000.0000.0000.000
167B316THR0-0.046-0.04460.3150.0000.0000.0000.0000.0000.000
168B317THR00.0550.03159.3000.0000.0000.0000.0000.0000.000
169B318ASP-1-0.788-0.88955.9830.0140.0140.0000.0000.0000.000
170B319LYS10.7820.90151.727-0.009-0.0090.0000.0000.0000.000
171B320GLU-1-0.926-0.96151.1610.0150.0150.0000.0000.0000.000
172B321LEU0-0.123-0.05554.5760.0010.0010.0000.0000.0000.000
173B322GLU-1-0.904-0.96357.5350.0060.0060.0000.0000.0000.000
174B323VAL0-0.041-0.03060.4940.0000.0000.0000.0000.0000.000
175B324LEU0-0.0360.00563.955-0.001-0.0010.0000.0000.0000.000
176B325SER00.020-0.00567.1530.0000.0000.0000.0000.0000.000
177B326LEU0-0.068-0.03469.732-0.001-0.0010.0000.0000.0000.000
178B327HIS00.0280.01273.4020.0000.0000.0000.0000.0000.000
179B328ASN00.020-0.00175.7500.0000.0000.0000.0000.0000.000
180B329VAL0-0.032-0.00176.4740.0000.0000.0000.0000.0000.000
181B330THR00.1430.08579.4020.0000.0000.0000.0000.0000.000
182B331PHE00.0340.01482.0150.0000.0000.0000.0000.0000.000
183B332GLU-1-1.060-1.02382.3860.0030.0030.0000.0000.0000.000
184B333ASP-1-0.898-0.96177.3740.0040.0040.0000.0000.0000.000
185B334ALA00.003-0.00577.8080.0000.0000.0000.0000.0000.000
186B335GLY0-0.027-0.00578.3620.0000.0000.0000.0000.0000.000
187B336GLU-1-0.798-0.87973.1430.0070.0070.0000.0000.0000.000
188B337TYR0-0.029-0.04670.543-0.001-0.0010.0000.0000.0000.000
189B338THR0-0.028-0.02767.3840.0000.0000.0000.0000.0000.000
190B339CYS0-0.022-0.00462.314-0.001-0.0010.0000.0000.0000.000
191B340LEU0-0.019-0.02963.0240.0010.0010.0000.0000.0000.000
192B341ALA00.0520.02658.142-0.001-0.0010.0000.0000.0000.000
193B342GLY00.022-0.00159.0610.0000.0000.0000.0000.0000.000
194B343ASN00.049-0.00351.9940.0000.0000.0000.0000.0000.000
195B344SER0-0.0170.00651.893-0.001-0.0010.0000.0000.0000.000
196B345ILE0-0.109-0.03749.730-0.001-0.0010.0000.0000.0000.000
197B346GLY00.0400.00454.3650.0010.0010.0000.0000.0000.000
198B347PHE00.0550.03557.5300.0000.0000.0000.0000.0000.000
199B348SER0-0.076-0.04358.5460.0010.0010.0000.0000.0000.000
200B349HIS00.0170.00060.596-0.001-0.0010.0000.0000.0000.000
201B350HIS10.7810.90261.289-0.011-0.0110.0000.0000.0000.000
202B351SER00.024-0.01165.488-0.001-0.0010.0000.0000.0000.000
203B352ALA0-0.0060.01768.8950.0010.0010.0000.0000.0000.000
204B353TRP00.017-0.00171.327-0.001-0.0010.0000.0000.0000.000
205B354LEU00.0210.02574.4180.0010.0010.0000.0000.0000.000
206B355VAL00.0030.00176.4360.0000.0000.0000.0000.0000.000
207B356VAL0-0.004-0.00379.6050.0000.0000.0000.0000.0000.000
208B357LEU00.0170.00482.0330.0000.0000.0000.0000.0000.000
209B358PRO0-0.039-0.03285.0940.0000.0000.0000.0000.0000.000
210B359ALA00.0140.00486.3660.0000.0000.0000.0000.0000.000
211B360GLU-1-0.932-0.96088.2880.0060.0060.0000.0000.0000.000
212B361GLU-1-0.949-0.96086.2490.0080.0080.0000.0000.0000.000
213B362GLU-1-1.028-1.01389.9880.0080.0080.0000.0000.0000.000