FMO DATABASE

FMODB ID: 2J54R

Calculation Name: 4PU3-D-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 4PU3

Chain ID: D

ChEMBL ID:

UniProt ID: Q8EIX3

Base Structure: X-ray

Registration Date: 2023-06-26

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	71
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-391716.880441
FMO2-HF: Nuclear repulsion	364453.09503
FMO2-HF: Total energy	-27263.785411
FMO2-MP2: Total energy	-27342.601778

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(D:19:ILE)

Summations of interaction energy for fragment #1(D:19:ILE)

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.
-0.729	2.15	0.033	-1.298	-1.613	0.003

Interaction energy analysis for fragmet #1(D:19:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.038 / q_NPA : 0.014

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

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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	D	21	ALA	0	-0.005	0.003	3.431	-1.517	1.319	0.034	-1.295	-1.575	0.003
4	D	22	SER	0	0.009	-0.004	4.878	0.109	0.152	-0.001	-0.003	-0.038	0.000
5	D	23	PRO	0	-0.007	0.008	8.038	0.057	0.057	0.000	0.000	0.000	0.000
6	D	24	LEU	0	0.045	0.027	10.051	-0.111	-0.111	0.000	0.000	0.000	0.000
7	D	25	ASN	0	0.026	0.019	12.067	0.041	0.041	0.000	0.000	0.000	0.000
8	D	26	GLN	0	0.023	0.003	14.212	-0.048	-0.048	0.000	0.000	0.000	0.000
9	D	27	GLN	0	0.025	0.003	13.297	-0.047	-0.047	0.000	0.000	0.000	0.000
10	D	28	SER	0	0.017	-0.009	9.260	-0.026	-0.026	0.000	0.000	0.000	0.000
11	D	29	LEU	0	0.043	0.041	10.166	-0.191	-0.191	0.000	0.000	0.000	0.000
12	D	30	GLY	0	0.061	0.039	12.437	-0.002	-0.002	0.000	0.000	0.000	0.000
13	D	31	LEU	0	-0.035	-0.032	8.355	0.027	0.027	0.000	0.000	0.000	0.000
14	D	32	LEU	0	0.031	0.023	7.687	-0.072	-0.072	0.000	0.000	0.000	0.000
15	D	33	ILE	0	0.012	0.001	9.091	0.110	0.110	0.000	0.000	0.000	0.000
16	D	34	LYS	1	0.861	0.919	10.841	0.566	0.566	0.000	0.000	0.000	0.000
17	D	35	GLU	-1	-0.790	-0.882	5.961	-0.502	-0.502	0.000	0.000	0.000	0.000
18	D	36	ARG	1	0.899	0.973	8.680	0.622	0.622	0.000	0.000	0.000	0.000
19	D	37	ARG	1	0.810	0.869	10.533	0.431	0.431	0.000	0.000	0.000	0.000
20	D	38	LYS	1	0.751	0.838	9.138	0.496	0.496	0.000	0.000	0.000	0.000
21	D	39	SER	0	-0.032	-0.027	8.965	0.107	0.107	0.000	0.000	0.000	0.000
22	D	40	ALA	0	-0.037	-0.002	11.231	0.075	0.075	0.000	0.000	0.000	0.000
23	D	41	ALA	0	-0.024	-0.008	14.236	0.024	0.024	0.000	0.000	0.000	0.000
24	D	42	LEU	0	0.023	0.028	16.117	0.012	0.012	0.000	0.000	0.000	0.000
25	D	43	THR	0	0.024	0.000	17.424	-0.031	-0.031	0.000	0.000	0.000	0.000
26	D	44	GLN	0	-0.019	-0.038	17.293	0.020	0.020	0.000	0.000	0.000	0.000
27	D	45	ASP	-1	-0.777	-0.888	20.057	-0.124	-0.124	0.000	0.000	0.000	0.000
28	D	46	VAL	0	0.020	0.025	22.386	0.000	0.000	0.000	0.000	0.000	0.000
29	D	47	ALA	0	0.045	0.030	18.826	-0.001	-0.001	0.000	0.000	0.000	0.000
30	D	48	ALA	0	-0.018	-0.004	20.843	-0.008	-0.008	0.000	0.000	0.000	0.000
31	D	49	MET	0	0.008	-0.006	22.544	0.006	0.006	0.000	0.000	0.000	0.000
32	D	50	LEU	0	-0.022	-0.002	22.791	0.005	0.005	0.000	0.000	0.000	0.000
33	D	51	CYS	0	-0.048	-0.014	20.728	-0.007	-0.007	0.000	0.000	0.000	0.000
34	D	52	GLY	0	0.012	0.022	23.470	-0.003	-0.003	0.000	0.000	0.000	0.000
35	D	53	VAL	0	-0.073	-0.050	22.640	-0.002	-0.002	0.000	0.000	0.000	0.000
36	D	54	THR	0	0.068	0.035	25.615	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	55	LYS	1	0.947	0.931	22.881	0.101	0.101	0.000	0.000	0.000	0.000
38	D	56	LYS	1	0.942	0.978	22.435	0.140	0.140	0.000	0.000	0.000	0.000
39	D	57	THR	0	-0.003	-0.004	23.227	-0.013	-0.013	0.000	0.000	0.000	0.000
40	D	58	LEU	0	0.057	0.039	17.229	-0.020	-0.020	0.000	0.000	0.000	0.000
41	D	59	ILE	0	-0.042	-0.017	18.585	-0.041	-0.041	0.000	0.000	0.000	0.000
42	D	60	ARG	1	0.815	0.889	18.793	0.203	0.203	0.000	0.000	0.000	0.000
43	D	61	VAL	0	0.020	0.008	16.648	-0.023	-0.023	0.000	0.000	0.000	0.000
44	D	62	GLU	-1	-0.770	-0.848	14.539	-0.423	-0.423	0.000	0.000	0.000	0.000
45	D	63	LYS	1	0.859	0.939	14.082	0.198	0.198	0.000	0.000	0.000	0.000
46	D	64	GLY	0	0.013	0.011	16.140	-0.007	-0.007	0.000	0.000	0.000	0.000
47	D	65	GLU	-1	-0.934	-0.955	16.714	-0.225	-0.225	0.000	0.000	0.000	0.000
48	D	66	ASP	-1	-0.862	-0.937	20.440	-0.259	-0.259	0.000	0.000	0.000	0.000
49	D	67	VAL	0	-0.050	-0.025	20.960	0.019	0.019	0.000	0.000	0.000	0.000
50	D	68	TYR	0	0.033	0.023	24.013	-0.001	-0.001	0.000	0.000	0.000	0.000
51	D	69	ILE	0	0.086	0.031	22.008	-0.012	-0.012	0.000	0.000	0.000	0.000
52	D	70	SER	0	0.062	0.028	23.375	-0.015	-0.015	0.000	0.000	0.000	0.000
53	D	71	THR	0	-0.020	-0.022	22.056	0.007	0.007	0.000	0.000	0.000	0.000
54	D	72	VAL	0	0.018	0.020	18.088	-0.006	-0.006	0.000	0.000	0.000	0.000
55	D	73	PHE	0	0.049	0.007	19.468	-0.029	-0.029	0.000	0.000	0.000	0.000
56	D	74	LYS	1	0.892	0.986	21.643	0.196	0.196	0.000	0.000	0.000	0.000
57	D	75	ILE	0	-0.031	-0.031	16.986	0.006	0.006	0.000	0.000	0.000	0.000
58	D	76	LEU	0	-0.037	-0.015	15.013	-0.019	-0.019	0.000	0.000	0.000	0.000
59	D	77	ASP	-1	-0.843	-0.927	17.738	-0.245	-0.245	0.000	0.000	0.000	0.000
60	D	78	GLY	0	-0.042	-0.015	20.496	0.019	0.019	0.000	0.000	0.000	0.000
61	D	79	LEU	0	-0.079	-0.048	14.487	0.016	0.016	0.000	0.000	0.000	0.000
62	D	80	GLY	0	0.039	0.030	15.798	-0.013	-0.013	0.000	0.000	0.000	0.000
63	D	81	ILE	0	-0.092	-0.047	12.684	-0.030	-0.030	0.000	0.000	0.000	0.000
64	D	82	ASP	-1	-0.869	-0.916	14.902	-0.244	-0.244	0.000	0.000	0.000	0.000
65	D	83	ILE	0	-0.075	-0.043	14.541	-0.068	-0.068	0.000	0.000	0.000	0.000
66	D	84	VAL	0	0.011	-0.005	16.044	0.051	0.051	0.000	0.000	0.000	0.000
67	D	85	SER	0	-0.018	0.000	16.768	-0.035	-0.035	0.000	0.000	0.000	0.000
68	D	86	ALA	0	0.007	0.006	15.582	0.029	0.029	0.000	0.000	0.000	0.000
69	D	95	GLY	0	0.019	0.025	30.846	0.000	0.000	0.000	0.000	0.000	0.000
70	D	96	TRP	0	-0.006	-0.038	31.468	-0.003	-0.003	0.000	0.000	0.000	0.000
71	D	97	TYR	0	-0.013	0.013	30.039	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:19:ILE)