FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: GYK61

Calculation Name: 4P4H-I-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P4H

Chain ID: I

ChEMBL ID:

UniProt ID: O95786

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -777327.536016
FMO2-HF: Nuclear repulsion 737024.622292
FMO2-HF: Total energy -40302.913723
FMO2-MP2: Total energy -40417.77784


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(I:1:MET)


Summations of interaction energy for fragment #1(I:1:MET)
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.
-4.619-2.210.036-1.107-1.3370
Interaction energy analysis for fragmet #1(I:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.152 / q_NPA : 0.023
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].
4I3PHE00.1660.0333.856-2.116-0.756-0.004-0.755-0.6010.002
5I3PHE0-0.0920.0854.9400.1810.1810.0000.0000.0000.000
6I4ALA00.106-0.1254.2571.3351.460-0.002-0.036-0.0860.000
7I4ALA0-0.0510.1323.941-0.372-0.344-0.0010.001-0.0280.000
8I5GLU00.042-0.1065.1700.3330.385-0.002-0.008-0.0410.000
9I5GLU-1-0.879-0.7964.1480.6530.907-0.001-0.035-0.2180.000
10I6ASP00.135-0.1076.9710.2270.2270.0000.0000.0000.000
11I6ASP-1-0.975-0.8259.1330.1410.1410.0000.0000.0000.000
12I7LYS0-0.032-0.1448.9930.2510.2510.0000.0000.0000.000
13I7LYS10.8881.0779.0480.9560.9560.0000.0000.0000.000
14I8THR00.043-0.0929.5370.2080.2080.0000.0000.0000.000
15I8THR0-0.0390.0778.468-0.033-0.0330.0000.0000.0000.000
16I9TYR00.076-0.07910.9990.1190.1190.0000.0000.0000.000
17I9TYR0-0.0030.13212.2830.0510.0510.0000.0000.0000.000
18I10LYS00.102-0.08013.1920.0990.0990.0000.0000.0000.000
19I10LYS10.8821.06514.0500.3130.3130.0000.0000.0000.000
20I11TYR00.002-0.09414.0200.0950.0950.0000.0000.0000.000
21I11TYR0-0.1050.04214.047-0.037-0.0370.0000.0000.0000.000
22I12ILE00.052-0.08915.1830.0500.0500.0000.0000.0000.000
23I12ILE0-0.0660.08613.8310.0080.0080.0000.0000.0000.000
24I13CYS00.103-0.11817.1050.0460.0460.0000.0000.0000.000
25I13CYS0-0.1760.06517.1110.0270.0270.0000.0000.0000.000
26I14ARG00.027-0.09718.7740.0530.0530.0000.0000.0000.000
27I14ARG10.8031.01015.0540.5980.5980.0000.0000.0000.000
28I15ASN00.081-0.04619.6880.0470.0470.0000.0000.0000.000
29I15ASN0-0.0870.07419.133-0.020-0.0200.0000.0000.0000.000
30I16PHE00.127-0.07321.116-0.018-0.0180.0000.0000.0000.000
31I16PHE0-0.0720.09820.9570.0080.0080.0000.0000.0000.000
32I17SER0-0.009-0.10622.1210.0100.0100.0000.0000.0000.000
33I17SER00.0030.08325.5830.0050.0050.0000.0000.0000.000
34I18ASN00.077-0.07422.0910.0360.0360.0000.0000.0000.000
35I18ASN0-0.0810.06421.2430.0230.0230.0000.0000.0000.000
36I19PHE00.085-0.08920.8550.0010.0010.0000.0000.0000.000
37I19PHE0-0.0790.09616.8310.0070.0070.0000.0000.0000.000
38I20CYS00.063-0.15021.9840.0230.0230.0000.0000.0000.000
39I20CYS0-0.0900.11926.3660.0060.0060.0000.0000.0000.000
40I21ASN00.128-0.05325.1360.0270.0270.0000.0000.0000.000
41I21ASN0-0.0650.09226.0400.0120.0120.0000.0000.0000.000
42I22VAL00.121-0.07422.0140.0140.0140.0000.0000.0000.000
43I22VAL0-0.0260.12220.183-0.001-0.0010.0000.0000.0000.000
44I23LYS00.052-0.08623.3530.0160.0160.0000.0000.0000.000
45I23LYS10.7540.99425.6550.1470.1470.0000.0000.0000.000
46I24VAL00.131-0.09722.670-0.008-0.0080.0000.0000.0000.000
47I24VAL0-0.0370.11622.7990.0010.0010.0000.0000.0000.000
48I25VAL00.082-0.10723.3250.0080.0080.0000.0000.0000.000
49I25VAL0-0.0390.11627.598-0.001-0.0010.0000.0000.0000.000
50I26LYS00.061-0.10624.8490.0170.0170.0000.0000.0000.000
51I26LYS10.8311.00824.6550.1370.1370.0000.0000.0000.000
52I27ILE00.067-0.04220.5020.0070.0070.0000.0000.0000.000
53I27ILE0-0.0840.08717.888-0.002-0.0020.0000.0000.0000.000
54I28LEU00.053-0.11119.397-0.007-0.0070.0000.0000.0000.000
55I28LEU0-0.1000.08319.7070.0030.0030.0000.0000.0000.000
56I29PRO0-0.010-0.11919.8190.0290.0290.0000.0000.0000.000
57I30TYR00.0190.02218.5840.0310.0310.0000.0000.0000.000
58I30TYR0-0.0560.08818.143-0.002-0.0020.0000.0000.0000.000
59I31LEU00.117-0.07815.095-0.038-0.0380.0000.0000.0000.000
60I31LEU0-0.1100.09714.139-0.001-0.0010.0000.0000.0000.000
61I32PRO00.040-0.10714.1740.0350.0350.0000.0000.0000.000
62I33CYS00.0920.02711.9890.0540.0540.0000.0000.0000.000
63I33CYS0-0.1210.09811.248-0.039-0.0390.0000.0000.0000.000
64I34LEU00.073-0.11413.3380.0930.0930.0000.0000.0000.000
65I34LEU0-0.1220.08515.475-0.008-0.0080.0000.0000.0000.000
66I35THR00.060-0.06916.358-0.022-0.0220.0000.0000.0000.000
67I35THR0-0.0570.04016.872-0.011-0.0110.0000.0000.0000.000
68I36ALA00.155-0.07918.583-0.040-0.0400.0000.0000.0000.000
69I36ALA0-0.0360.12922.8330.0010.0010.0000.0000.0000.000
70I37ARG00.111-0.09121.871-0.034-0.0340.0000.0000.0000.000
71I37ARG10.8611.07922.099-0.174-0.1740.0000.0000.0000.000
72I38ASP00.034-0.10919.398-0.025-0.0250.0000.0000.0000.000
73I38ASP-1-0.814-0.75117.9410.3050.3050.0000.0000.0000.000
74I39GLN00.076-0.09320.925-0.034-0.0340.0000.0000.0000.000
75I39GLN0-0.0510.11618.837-0.027-0.0270.0000.0000.0000.000
76I40ASP00.126-0.06222.479-0.030-0.0300.0000.0000.0000.000
77I40ASP-1-0.995-0.86425.3150.1270.1270.0000.0000.0000.000
78I41ARG00.158-0.06324.590-0.023-0.0230.0000.0000.0000.000
79I41ARG10.7891.01019.808-0.142-0.1420.0000.0000.0000.000
80I42LEU00.038-0.09922.702-0.013-0.0130.0000.0000.0000.000
81I42LEU0-0.0740.09819.485-0.003-0.0030.0000.0000.0000.000
82I43ARG00.113-0.07924.115-0.023-0.0230.0000.0000.0000.000
83I43ARG10.8001.01423.304-0.049-0.0490.0000.0000.0000.000
84I44ALA00.140-0.07427.007-0.016-0.0160.0000.0000.0000.000
85I44ALA0-0.0850.11828.5450.0030.0030.0000.0000.0000.000
86I45THR0-0.019-0.10426.929-0.007-0.0070.0000.0000.0000.000
87I45THR0-0.0770.02926.1540.0020.0020.0000.0000.0000.000
88I46CYS00.189-0.05327.317-0.009-0.0090.0000.0000.0000.000
89I46CYS0-0.1730.06526.558-0.006-0.0060.0000.0000.0000.000
90I47THR0-0.078-0.09228.469-0.012-0.0120.0000.0000.0000.000
91I47THR0-0.0700.04030.7380.0010.0010.0000.0000.0000.000
92I48LEU00.107-0.08631.931-0.007-0.0070.0000.0000.0000.000
93I48LEU0-0.0940.10832.2970.0020.0020.0000.0000.0000.000
94I49SER0-0.010-0.11330.600-0.003-0.0030.0000.0000.0000.000
95I49SER0-0.0520.06529.6880.0020.0020.0000.0000.0000.000
96I50GLY00.053-0.04731.318-0.010-0.0100.0000.0000.0000.000
97I51ASN00.1770.05627.6990.0040.0040.0000.0000.0000.000
98I51ASN0-0.1460.02626.1920.0060.0060.0000.0000.0000.000
99I52ARG00.084-0.10626.423-0.002-0.0020.0000.0000.0000.000
100I52ARG10.8321.05327.2130.1360.1360.0000.0000.0000.000
101I53ASP00.045-0.12126.221-0.020-0.0200.0000.0000.0000.000
102I53ASP-1-0.904-0.79529.319-0.066-0.0660.0000.0000.0000.000
103I54THR00.046-0.10925.5140.0020.0020.0000.0000.0000.000
104I54THR0-0.0670.07524.0650.0070.0070.0000.0000.0000.000
105I55LEU00.045-0.11522.2140.0190.0190.0000.0000.0000.000
106I55LEU0-0.1250.09821.974-0.004-0.0040.0000.0000.0000.000
107I56TRP00.135-0.08620.661-0.018-0.0180.0000.0000.0000.000
108I56TRP0-0.0490.12121.3250.0100.0100.0000.0000.0000.000
109I57HIS00.057-0.10420.218-0.003-0.0030.0000.0000.0000.000
110I57HIS0-0.0610.11722.8990.0130.0130.0000.0000.0000.000
111I58LEU00.139-0.06019.5220.0470.0470.0000.0000.0000.000
112I58LEU0-0.1060.09218.1650.0010.0010.0000.0000.0000.000
113I59PHE00.043-0.09916.1240.0430.0430.0000.0000.0000.000
114I59PHE0-0.0330.09116.495-0.017-0.0170.0000.0000.0000.000
115I60ASN00.117-0.07815.374-0.007-0.0070.0000.0000.0000.000
116I60ASN0-0.0790.09118.5300.0460.0460.0000.0000.0000.000
117I61THR00.030-0.09716.6780.0550.0550.0000.0000.0000.000
118I61THR0-0.0910.05316.6650.0110.0110.0000.0000.0000.000
119I62LEU00.062-0.07113.5780.1250.1250.0000.0000.0000.000
120I62LEU0-0.0800.08712.612-0.010-0.0100.0000.0000.0000.000
121I63GLN00.078-0.07610.9660.1240.1240.0000.0000.0000.000
122I63GLN0-0.1030.07312.210-0.037-0.0370.0000.0000.0000.000
123I64ARG00.015-0.08711.5900.0840.0840.0000.0000.0000.000
124I64ARG10.7911.00614.591-0.215-0.2150.0000.0000.0000.000
125I65ARG00.040-0.11911.1150.1160.1160.0000.0000.0000.000
126I65ARG10.7750.98911.572-0.493-0.4930.0000.0000.0000.000
127I66PRO00.011-0.0906.943-0.163-0.1630.0000.0000.0000.000
128I67GLY00.0600.0144.860-0.043-0.0430.0000.0000.0000.000
129I68TRP00.088-0.0225.793-0.449-0.4490.0000.0000.0000.000
130I68TRP0-0.0930.1038.333-0.171-0.1710.0000.0000.0000.000
131I69VAL00.044-0.1117.3480.1900.1900.0000.0000.0000.000
132I69VAL0-0.0620.1186.755-0.021-0.0210.0000.0000.0000.000
133I70GLU00.056-0.1107.116-0.053-0.0530.0000.0000.0000.000
134I70GLU-1-0.886-0.7865.400-3.014-3.0140.0000.0000.0000.000
135I71TYR00.075-0.0948.4960.0430.0430.0000.0000.0000.000
136I71TYR0-0.0520.0949.244-0.056-0.0560.0000.0000.0000.000
137I72PHE00.090-0.07011.0560.0660.0660.0000.0000.0000.000
138I72PHE0-0.0930.07611.7780.0270.0270.0000.0000.0000.000
139I73ILE00.080-0.09411.8080.1090.1090.0000.0000.0000.000
140I73ILE0-0.0860.09710.3200.0080.0080.0000.0000.0000.000
141I74ALA00.136-0.10113.1500.0520.0520.0000.0000.0000.000
142I74ALA0-0.0480.13413.8230.0100.0100.0000.0000.0000.000
143I75ALA00.127-0.09314.9910.0470.0470.0000.0000.0000.000
144I75ALA0-0.0900.09515.8830.0080.0080.0000.0000.0000.000
145I76LEU00.012-0.14216.5010.0660.0660.0000.0000.0000.000
146I76LEU0-0.0810.11215.8800.0050.0050.0000.0000.0000.000
147I77ARG00.047-0.10017.7030.0370.0370.0000.0000.0000.000
148I77ARG10.7690.97115.4930.6200.6200.0000.0000.0000.000
149I78GLY00.014-0.08019.1250.0280.0280.0000.0000.0000.000
150I79CYS00.074-0.04120.8420.0330.0330.0000.0000.0000.000
151I79CYS0-0.1900.11221.3430.0100.0100.0000.0000.0000.000
152I80LYS00.047-0.05622.4990.0160.0160.0000.0000.0000.000
153I80LYS10.8561.04124.9010.1790.1790.0000.0000.0000.000
154I81LEU00.024-0.10321.9310.0130.0130.0000.0000.0000.000
155I81LEU0-0.0780.07921.1570.0020.0020.0000.0000.0000.000
156I82VAL00.129-0.08520.762-0.043-0.0430.0000.0000.0000.000
157I82VAL0-0.0650.09521.0680.0040.0040.0000.0000.0000.000
158I83ASP00.126-0.10120.240-0.063-0.0630.0000.0000.0000.000
159I83ASP-1-0.933-0.82923.417-0.321-0.3210.0000.0000.0000.000
160I84LEU00.135-0.07020.111-0.056-0.0560.0000.0000.0000.000
161I84LEU0-0.1450.08418.9180.0120.0120.0000.0000.0000.000
162I85ALA00.109-0.10716.545-0.070-0.0700.0000.0000.0000.000
163I85ALA0-0.0830.09316.6410.0110.0110.0000.0000.0000.000
164I86ASP00.035-0.09515.524-0.141-0.1410.0000.0000.0000.000
165I86ASP-1-0.856-0.75717.631-0.610-0.6100.0000.0000.0000.000
166I87GLU00.094-0.08316.012-0.115-0.1150.0000.0000.0000.000
167I87GLU-1-0.876-0.76817.614-0.482-0.4820.0000.0000.0000.000
168I88VAL00.040-0.12313.969-0.088-0.0880.0000.0000.0000.000
169I88VAL0-0.1050.07611.9060.0090.0090.0000.0000.0000.000
170I89ALA00.121-0.08211.549-0.271-0.2710.0000.0000.0000.000
171I89ALA0-0.0780.09912.8840.0280.0280.0000.0000.0000.000
172I90SER00.030-0.09011.267-0.312-0.3120.0000.0000.0000.000
173I90SER0-0.0270.08514.9460.0700.0700.0000.0000.0000.000
174I91VAL00.048-0.08912.427-0.122-0.1220.0000.0000.0000.000
175I91VAL0-0.1190.08512.2150.0230.0230.0000.0000.0000.000
176I92TYR00.062-0.0958.649-0.029-0.0290.0000.0000.0000.000
177I92TYR0-0.0960.0514.062-1.258-1.1050.000-0.049-0.1050.000
178I93GLN00.069-0.1007.271-0.922-0.9220.0000.0000.0000.000
179I93GLN0-0.0540.1226.2150.2220.2220.0000.0000.0000.000
180I94SER00.032-0.1008.637-0.120-0.1200.0000.0000.0000.000
181I94SER0-0.0660.05011.2490.1260.1260.0000.0000.0000.000
182I95TYR0-0.069-0.0958.3630.3380.3380.0000.0000.0000.000
183I95TYR0-0.0520.0897.5000.2190.2190.0000.0000.0000.000
184I96GLN00.116-0.1165.821-0.009-0.001-0.0020.000-0.0060.000
185I96GLN0-0.0820.1043.850-2.374-1.9450.048-0.225-0.252-0.002
186I97PRO0-0.046-0.1076.7120.6080.6080.0000.0000.0000.000