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: 8NZ5Y

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 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 186
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -770643.12057
FMO2-HF: Nuclear repulsion 730342.770798
FMO2-HF: Total energy -40300.349772
FMO2-MP2: Total energy -40415.137445


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.
-1.70.9580.012-1.348-1.322-0.001
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 : 0.124 / q_NPA : -0.007
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].
4I3PHE00.1710.0423.751-1.4750.509-0.001-1.132-0.8510.000
5I3PHE0-0.1020.0725.2790.1190.1190.0000.0000.0000.000
6I4ALA00.087-0.1274.8260.9230.985-0.002-0.005-0.0550.000
7I4ALA0-0.0470.1454.705-0.131-0.111-0.001-0.006-0.0120.000
8I5GLU00.046-0.1555.7800.4070.4070.0000.0000.0000.000
9I5GLU-1-0.928-0.7884.8720.9891.183-0.001-0.023-0.1700.000
10I6ASP00.152-0.1097.4820.2720.2720.0000.0000.0000.000
11I6ASP-1-0.969-0.8079.418-0.404-0.4040.0000.0000.0000.000
12I7LYS0-0.051-0.1759.6200.2230.2230.0000.0000.0000.000
13I7LYS10.8791.09110.1160.6770.6770.0000.0000.0000.000
14I8THR0-0.003-0.10810.3530.0950.0950.0000.0000.0000.000
15I8THR0-0.0090.0909.129-0.005-0.0050.0000.0000.0000.000
16I9TYR00.115-0.07711.6930.0950.0950.0000.0000.0000.000
17I9TYR0-0.0060.14213.0320.0250.0250.0000.0000.0000.000
18I10LYS00.097-0.08713.8230.0700.0700.0000.0000.0000.000
19I10LYS10.8521.06014.5800.3250.3250.0000.0000.0000.000
20I11TYR0-0.006-0.13514.7170.0550.0550.0000.0000.0000.000
21I11TYR0-0.0800.08214.706-0.030-0.0300.0000.0000.0000.000
22I12ILE00.050-0.08415.8390.0210.0210.0000.0000.0000.000
23I12ILE0-0.0700.09514.4390.0060.0060.0000.0000.0000.000
24I13CYS00.087-0.12217.6710.0330.0330.0000.0000.0000.000
25I13CYS0-0.1690.09317.8990.0120.0120.0000.0000.0000.000
26I14ARG00.081-0.06019.4710.0280.0280.0000.0000.0000.000
27I14ARG10.8351.01416.4270.3480.3480.0000.0000.0000.000
28I15ASN00.070-0.07220.2910.0230.0230.0000.0000.0000.000
29I15ASN0-0.0840.08320.009-0.024-0.0240.0000.0000.0000.000
30I16PHE00.169-0.05021.7460.0030.0030.0000.0000.0000.000
31I16PHE0-0.0820.09521.6430.0070.0070.0000.0000.0000.000
32I17SER0-0.041-0.12322.6190.0140.0140.0000.0000.0000.000
33I17SER00.0050.08726.4160.0010.0010.0000.0000.0000.000
34I18ASN00.075-0.10222.8930.0170.0170.0000.0000.0000.000
35I18ASN0-0.0880.08921.8950.0110.0110.0000.0000.0000.000
36I19PHE00.072-0.10621.8040.0030.0030.0000.0000.0000.000
37I19PHE0-0.0860.10817.5070.0060.0060.0000.0000.0000.000
38I20CYS00.065-0.14622.9250.0180.0180.0000.0000.0000.000
39I20CYS0-0.0720.11627.359-0.001-0.0010.0000.0000.0000.000
40I21ASN00.067-0.10725.9400.0100.0100.0000.0000.0000.000
41I21ASN0-0.0730.09926.3950.0080.0080.0000.0000.0000.000
42I22VAL00.085-0.14123.2910.0080.0080.0000.0000.0000.000
43I22VAL0-0.0200.15821.4250.0010.0010.0000.0000.0000.000
44I23LYS00.027-0.08024.688-0.002-0.0020.0000.0000.0000.000
45I23LYS10.8501.04827.1290.0060.0060.0000.0000.0000.000
46I24VAL00.125-0.12523.6600.0060.0060.0000.0000.0000.000
47I24VAL0-0.0110.13123.1380.0000.0000.0000.0000.0000.000
48I25VAL00.072-0.11724.2110.0140.0140.0000.0000.0000.000
49I25VAL0-0.0310.12128.418-0.001-0.0010.0000.0000.0000.000
50I26LYS00.040-0.08926.0630.0100.0100.0000.0000.0000.000
51I26LYS10.8521.04726.185-0.022-0.0220.0000.0000.0000.000
52I27ILE00.111-0.08921.6390.0080.0080.0000.0000.0000.000
53I27ILE0-0.0520.11418.864-0.003-0.0030.0000.0000.0000.000
54I28LEU00.027-0.10120.5130.0200.0200.0000.0000.0000.000
55I28LEU0-0.1180.07420.5250.0000.0000.0000.0000.0000.000
56I29PRO0-0.014-0.10720.4640.0230.0230.0000.0000.0000.000
57I30TYR00.0270.00619.7680.0200.0200.0000.0000.0000.000
58I30TYR0-0.0690.09919.360-0.003-0.0030.0000.0000.0000.000
59I31LEU00.080-0.09816.1310.0260.0260.0000.0000.0000.000
60I31LEU0-0.1270.09215.139-0.003-0.0030.0000.0000.0000.000
61I32PRO00.071-0.08414.683-0.008-0.0080.0000.0000.0000.000
62I33CYS00.117-0.00312.423-0.010-0.0100.0000.0000.0000.000
63I33CYS0-0.0930.13111.848-0.002-0.0020.0000.0000.0000.000
64I34LEU00.029-0.14913.7330.0140.0140.0000.0000.0000.000
65I34LEU0-0.1020.10915.501-0.009-0.0090.0000.0000.0000.000
66I35THR00.033-0.07716.528-0.003-0.0030.0000.0000.0000.000
67I35THR0-0.0350.07916.539-0.014-0.0140.0000.0000.0000.000
68I36ALA00.159-0.06118.580-0.017-0.0170.0000.0000.0000.000
69I36ALA0-0.0450.12322.810-0.001-0.0010.0000.0000.0000.000
70I37ARG00.119-0.08421.900-0.016-0.0160.0000.0000.0000.000
71I37ARG10.8751.07921.542-0.115-0.1150.0000.0000.0000.000
72I38ASP00.071-0.12119.531-0.023-0.0230.0000.0000.0000.000
73I38ASP-1-0.847-0.79617.4880.2080.2080.0000.0000.0000.000
74I39GLN00.089-0.11121.026-0.018-0.0180.0000.0000.0000.000
75I39GLN0-0.0390.12919.926-0.022-0.0220.0000.0000.0000.000
76I40ASP00.060-0.11322.865-0.014-0.0140.0000.0000.0000.000
77I40ASP-1-0.988-0.84125.7940.0940.0940.0000.0000.0000.000
78I41ARG00.156-0.05224.579-0.012-0.0120.0000.0000.0000.000
79I41ARG10.7480.99620.074-0.099-0.0990.0000.0000.0000.000
80I42LEU00.043-0.12923.369-0.014-0.0140.0000.0000.0000.000
81I42LEU0-0.0930.10320.1830.0000.0000.0000.0000.0000.000
82I43ARG00.082-0.07924.696-0.012-0.0120.0000.0000.0000.000
83I43ARG10.8601.04824.221-0.102-0.1020.0000.0000.0000.000
84I44ALA00.149-0.11327.337-0.008-0.0080.0000.0000.0000.000
85I44ALA0-0.0770.15129.0060.0000.0000.0000.0000.0000.000
86I45THR00.008-0.10527.685-0.006-0.0060.0000.0000.0000.000
87I45THR0-0.0770.06326.835-0.001-0.0010.0000.0000.0000.000
88I46CYS00.145-0.08928.117-0.008-0.0080.0000.0000.0000.000
89I46CYS0-0.2110.06927.3880.0000.0000.0000.0000.0000.000
90I47THR0-0.057-0.05929.278-0.005-0.0050.0000.0000.0000.000
91I47THR0-0.0840.02131.5860.0010.0010.0000.0000.0000.000
92I48LEU00.213-0.15732.739-0.004-0.0040.0000.0000.0000.000
93I48LEU0-0.1350.14432.9260.0010.0010.0000.0000.0000.000
94I49SER0-0.010-0.08031.536-0.003-0.0030.0000.0000.0000.000
95I49SER0-0.0200.10030.619-0.001-0.0010.0000.0000.0000.000
96I50GLY00.029-0.04132.344-0.006-0.0060.0000.0000.0000.000
97I51ASN00.1740.05628.7830.0030.0030.0000.0000.0000.000
98I51ASN0-0.1230.04727.0400.0080.0080.0000.0000.0000.000
99I52ARG00.106-0.07627.6490.0030.0030.0000.0000.0000.000
100I52ARG10.8391.06327.8810.0380.0380.0000.0000.0000.000
101I53ASP00.037-0.13127.749-0.009-0.0090.0000.0000.0000.000
102I53ASP-1-0.926-0.81130.054-0.012-0.0120.0000.0000.0000.000
103I54THR00.027-0.09726.437-0.003-0.0030.0000.0000.0000.000
104I54THR0-0.0260.07224.6650.0040.0040.0000.0000.0000.000
105I55LEU00.030-0.12023.3030.0130.0130.0000.0000.0000.000
106I55LEU0-0.1180.11022.999-0.001-0.0010.0000.0000.0000.000
107I56TRP00.138-0.11021.7100.0030.0030.0000.0000.0000.000
108I56TRP0-0.0360.13222.3090.0050.0050.0000.0000.0000.000
109I57HIS00.027-0.12121.217-0.007-0.0070.0000.0000.0000.000
110I57HIS0-0.0730.11922.9750.0050.0050.0000.0000.0000.000
111I58LEU00.146-0.10420.0990.0180.0180.0000.0000.0000.000
112I58LEU0-0.1060.11418.8600.0010.0010.0000.0000.0000.000
113I59PHE00.059-0.10516.9390.0360.0360.0000.0000.0000.000
114I59PHE0-0.0390.09617.216-0.006-0.0060.0000.0000.0000.000
115I60ASN00.080-0.09415.9970.0030.0030.0000.0000.0000.000
116I60ASN0-0.0700.11818.8950.0210.0210.0000.0000.0000.000
117I61THR00.025-0.11616.7520.0020.0020.0000.0000.0000.000
118I61THR0-0.0420.08417.0840.0000.0000.0000.0000.0000.000
119I62LEU00.073-0.09214.1790.0420.0420.0000.0000.0000.000
120I62LEU0-0.0850.11213.4700.0020.0020.0000.0000.0000.000
121I63GLN00.061-0.07911.3920.1020.1020.0000.0000.0000.000
122I63GLN0-0.0430.10912.302-0.045-0.0450.0000.0000.0000.000
123I64ARG00.057-0.08311.025-0.027-0.0270.0000.0000.0000.000
124I64ARG10.7690.98314.083-0.071-0.0710.0000.0000.0000.000
125I65ARG0-0.013-0.12211.1150.0220.0220.0000.0000.0000.000
126I65ARG10.7971.01111.704-0.280-0.2800.0000.0000.0000.000
127I66PRO00.005-0.0966.709-0.060-0.0600.0000.0000.0000.000
128I67GLY00.0900.0335.4180.0600.0600.0000.0000.0000.000
129I68TRP00.097-0.0046.298-0.146-0.1460.0000.0000.0000.000
130I68TRP0-0.0950.1058.729-0.068-0.0680.0000.0000.0000.000
131I69VAL00.080-0.1018.321-0.001-0.0010.0000.0000.0000.000
132I69VAL0-0.0430.1367.747-0.023-0.0230.0000.0000.0000.000
133I70GLU00.058-0.1218.141-0.326-0.3260.0000.0000.0000.000
134I70GLU-1-0.927-0.8206.5290.3570.3570.0000.0000.0000.000
135I71TYR00.043-0.1089.496-0.141-0.1410.0000.0000.0000.000
136I71TYR0-0.0550.0849.3380.0080.0080.0000.0000.0000.000
137I72PHE00.080-0.09011.943-0.056-0.0560.0000.0000.0000.000
138I72PHE0-0.0970.07412.870-0.009-0.0090.0000.0000.0000.000
139I73ILE00.105-0.07612.878-0.042-0.0420.0000.0000.0000.000
140I73ILE0-0.0980.10811.144-0.005-0.0050.0000.0000.0000.000
141I74ALA00.071-0.14414.488-0.039-0.0390.0000.0000.0000.000
142I74ALA0-0.0710.15015.6280.0010.0010.0000.0000.0000.000
143I75ALA00.228-0.09116.2500.0240.0240.0000.0000.0000.000
144I75ALA0-0.1520.10916.747-0.001-0.0010.0000.0000.0000.000
145I76LEU0-0.031-0.16217.685-0.002-0.0020.0000.0000.0000.000
146I76LEU0-0.0510.12417.069-0.004-0.0040.0000.0000.0000.000
147I77ARG00.049-0.14718.649-0.015-0.0150.0000.0000.0000.000
148I77ARG10.8301.06315.5390.1010.1010.0000.0000.0000.000
149I78GLY00.017-0.06420.382-0.005-0.0050.0000.0000.0000.000
150I79CYS00.035-0.04222.3070.0020.0020.0000.0000.0000.000
151I79CYS0-0.1390.08722.6480.0000.0000.0000.0000.0000.000
152I80LYS00.070-0.08723.785-0.007-0.0070.0000.0000.0000.000
153I80LYS10.8491.05725.947-0.005-0.0050.0000.0000.0000.000
154I81LEU00.077-0.11722.861-0.004-0.0040.0000.0000.0000.000
155I81LEU0-0.1110.10822.1830.0010.0010.0000.0000.0000.000
156I82VAL00.056-0.10721.207-0.015-0.0150.0000.0000.0000.000
157I82VAL0-0.0070.09021.2410.0040.0040.0000.0000.0000.000
158I83ASP00.169-0.06420.985-0.016-0.0160.0000.0000.0000.000
159I83ASP-1-1.028-0.83924.154-0.105-0.1050.0000.0000.0000.000
160I84LEU00.184-0.06620.834-0.027-0.0270.0000.0000.0000.000
161I84LEU0-0.1510.07619.6740.0070.0070.0000.0000.0000.000
162I85ALA00.098-0.12117.457-0.034-0.0340.0000.0000.0000.000
163I85ALA0-0.1010.10517.5410.0080.0080.0000.0000.0000.000
164I86ASP00.035-0.15916.184-0.032-0.0320.0000.0000.0000.000
165I86ASP-1-0.897-0.77019.042-0.149-0.1490.0000.0000.0000.000
166I87GLU00.074-0.07916.595-0.059-0.0590.0000.0000.0000.000
167I87GLU-1-0.893-0.80518.397-0.191-0.1910.0000.0000.0000.000
168I88VAL00.068-0.17714.716-0.072-0.0720.0000.0000.0000.000
169I88VAL0-0.1240.11012.6790.0080.0080.0000.0000.0000.000
170I89ALA00.130-0.09312.017-0.111-0.1110.0000.0000.0000.000
171I89ALA0-0.0990.11313.0800.0170.0170.0000.0000.0000.000
172I90SER00.015-0.07211.679-0.146-0.1460.0000.0000.0000.000
173I90SER0-0.0420.07215.428-0.010-0.0100.0000.0000.0000.000
174I91VAL00.064-0.08312.612-0.111-0.1110.0000.0000.0000.000
175I91VAL0-0.0970.08512.6900.0080.0080.0000.0000.0000.000
176I92TYR00.045-0.0829.195-0.120-0.1200.0000.0000.0000.000
177I92TYR0-0.0540.1034.280-0.863-0.802-0.001-0.016-0.0440.000
178I93GLN00.045-0.1267.884-0.554-0.5540.0000.0000.0000.000
179I93GLN0-0.0510.1196.9560.0910.0910.0000.0000.0000.000
180I94SER00.048-0.1019.101-0.099-0.0990.0000.0000.0000.000
181I94SER0-0.0910.04711.6630.0480.0480.0000.0000.0000.000
182I95TYR0-0.059-0.1179.0020.1480.1480.0000.0000.0000.000
183I95TYR0-0.0950.0818.2570.1120.1120.0000.0000.0000.000
184I96GLN00.130-0.1185.911-0.0020.004-0.0020.001-0.0060.000
185I96GLN0-0.0700.1243.994-1.864-1.5330.020-0.167-0.184-0.001
186I97PRO0-0.001-0.0827.0670.3170.3170.0000.0000.0000.000