FMO DATABASE

FMODB ID: KGRZ3

Calculation Name: 3PH0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PH0

Chain ID: A

ChEMBL ID:

UniProt ID: Q1EHA4

Base Structure: X-ray

Registration Date: 2023-09-20

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	65
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-346577.998158
FMO2-HF: Nuclear repulsion	320700.711941
FMO2-HF: Total energy	-25877.286217
FMO2-MP2: Total energy	-25952.762532

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A: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.
-2.044	-0.705	-0.007	-0.693	-0.639	0.001

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / 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 ES EX CT+mix DI(MP2)

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].
3	A	3	THR	0	-0.016	-0.009	3.765	-0.488	0.851	-0.007	-0.693	-0.639	0.001
4	A	4	ASN	0	0.027	-0.005	6.391	0.357	0.357	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.024	0.021	9.458	0.100	0.100	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.772	-0.897	5.654	-2.596	-2.596	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.030	-0.013	8.819	0.206	0.206	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.812	0.893	11.503	0.360	0.360	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.008	-0.003	12.591	0.061	0.061	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.042	-0.022	11.574	0.032	0.032	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.010	0.000	14.093	0.053	0.053	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.034	-0.014	15.600	0.034	0.034	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.751	-0.868	17.582	-0.175	-0.175	0.000	0.000	0.000	0.000
14	A	14	PRO	0	0.010	0.002	19.241	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.055	-0.019	22.051	0.009	0.009	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.041	0.017	15.482	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.020	-0.001	18.193	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	18	ARG	1	0.887	0.941	19.284	0.145	0.145	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.906	-0.949	22.112	-0.193	-0.193	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.019	0.014	15.861	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	HIS	0	0.012	0.002	19.843	0.010	0.010	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.025	0.011	21.254	0.008	0.008	0.000	0.000	0.000	0.000
23	A	23	GLN	0	-0.003	-0.012	21.631	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.004	0.010	17.399	0.005	0.005	0.000	0.000	0.000	0.000
25	A	25	VAL	0	0.008	-0.005	22.001	0.010	0.010	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.082	-0.039	24.827	0.017	0.017	0.000	0.000	0.000	0.000
27	A	27	ALA	0	0.030	0.014	23.691	0.011	0.011	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.005	-0.002	23.013	0.010	0.010	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.018	0.010	25.534	0.011	0.011	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.828	-0.894	28.499	-0.138	-0.138	0.000	0.000	0.000	0.000
31	A	31	VAL	0	-0.030	0.003	25.406	0.010	0.010	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.810	0.878	25.494	0.224	0.224	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.812	0.891	29.981	0.142	0.142	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.798	0.880	27.666	0.165	0.165	0.000	0.000	0.000	0.000
35	A	35	LEU	0	-0.001	0.006	28.508	0.008	0.008	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.003	0.004	33.031	0.006	0.006	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.845	0.901	35.621	0.111	0.111	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.026	0.024	32.845	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	GLY	0	-0.001	0.023	33.907	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	THR	0	0.027	-0.016	31.268	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	41	GLN	0	0.009	-0.022	30.668	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.074	0.055	33.382	0.007	0.007	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.000	-0.001	32.152	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	TYR	0	-0.030	0.001	31.101	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	45	GLN	0	0.015	0.004	26.044	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	GLN	0	0.021	0.022	26.674	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.032	0.003	25.933	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.049	-0.031	25.147	0.004	0.004	0.000	0.000	0.000	0.000
49	A	49	GLN	0	0.029	0.021	20.698	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.847	-0.893	21.558	-0.204	-0.204	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.004	-0.011	21.991	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.837	-0.912	20.668	-0.254	-0.254	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.027	-0.011	17.627	-0.038	-0.038	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.004	0.004	17.271	-0.049	-0.049	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.786	-0.882	18.873	-0.267	-0.267	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.011	-0.007	15.132	-0.021	-0.021	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.016	0.002	14.358	-0.067	-0.067	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.004	-0.018	15.126	-0.044	-0.044	0.000	0.000	0.000	0.000
59	A	59	ASN	0	-0.031	-0.018	15.563	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.018	0.000	10.029	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	61	ILE	0	0.016	0.015	12.637	-0.045	-0.045	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.861	-0.925	14.504	-0.329	-0.329	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.844	0.925	12.717	0.575	0.575	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.020	0.003	8.724	-0.080	-0.080	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.784	0.898	11.827	0.414	0.414	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)