FMO DATABASE

FMODB ID: 72ZYK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-391596.289321
FMO2-HF: Nuclear repulsion	364332.982086
FMO2-HF: Total energy	-27263.307235
FMO2-MP2: Total energy	-27342.141766

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.
-0.078	2.264	0.061	-0.986	-1.416	-0.001

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 : 0.043 / q_NPA : 0.000

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	-0.010	-0.003	3.300	-1.098	1.201	0.062	-0.983	-1.377	-0.001
4	D	22	SER	0	-0.004	-0.010	4.905	0.308	0.351	-0.001	-0.003	-0.039	0.000
5	D	23	PRO	0	-0.001	0.011	7.968	0.099	0.099	0.000	0.000	0.000	0.000
6	D	24	LEU	0	0.056	0.034	10.109	-0.133	-0.133	0.000	0.000	0.000	0.000
7	D	25	ASN	0	0.029	0.030	12.109	0.047	0.047	0.000	0.000	0.000	0.000
8	D	26	GLN	0	0.040	-0.001	14.319	-0.009	-0.009	0.000	0.000	0.000	0.000
9	D	27	GLN	0	0.030	0.003	13.415	-0.042	-0.042	0.000	0.000	0.000	0.000
10	D	28	SER	0	-0.009	-0.021	9.282	-0.005	-0.005	0.000	0.000	0.000	0.000
11	D	29	LEU	0	0.062	0.049	9.749	-0.131	-0.131	0.000	0.000	0.000	0.000
12	D	30	GLY	0	0.066	0.038	12.041	0.046	0.046	0.000	0.000	0.000	0.000
13	D	31	LEU	0	-0.040	-0.034	8.113	0.066	0.066	0.000	0.000	0.000	0.000
14	D	32	LEU	0	0.035	0.028	7.567	0.029	0.029	0.000	0.000	0.000	0.000
15	D	33	ILE	0	0.011	0.003	8.779	0.217	0.217	0.000	0.000	0.000	0.000
16	D	34	LYS	1	0.904	0.956	10.546	0.490	0.490	0.000	0.000	0.000	0.000
17	D	35	GLU	-1	-0.920	-0.964	5.550	-0.231	-0.231	0.000	0.000	0.000	0.000
18	D	36	ARG	1	0.932	1.018	8.596	0.187	0.187	0.000	0.000	0.000	0.000
19	D	37	ARG	1	0.812	0.888	10.652	0.212	0.212	0.000	0.000	0.000	0.000
20	D	38	LYS	1	0.899	0.928	10.811	0.092	0.092	0.000	0.000	0.000	0.000
21	D	39	SER	0	-0.027	-0.040	9.268	0.151	0.151	0.000	0.000	0.000	0.000
22	D	40	ALA	0	-0.028	0.003	11.549	0.048	0.048	0.000	0.000	0.000	0.000
23	D	41	ALA	0	-0.026	-0.008	14.498	-0.024	-0.024	0.000	0.000	0.000	0.000
24	D	42	LEU	0	0.017	0.023	16.279	-0.029	-0.029	0.000	0.000	0.000	0.000
25	D	43	THR	0	0.015	-0.009	17.451	-0.028	-0.028	0.000	0.000	0.000	0.000
26	D	44	GLN	0	-0.054	-0.061	16.790	0.013	0.013	0.000	0.000	0.000	0.000
27	D	45	ASP	-1	-0.891	-0.969	19.919	-0.050	-0.050	0.000	0.000	0.000	0.000
28	D	46	VAL	0	0.053	0.042	22.333	-0.003	-0.003	0.000	0.000	0.000	0.000
29	D	47	ALA	0	0.035	0.025	18.845	-0.001	-0.001	0.000	0.000	0.000	0.000
30	D	48	ALA	0	-0.034	-0.013	20.835	-0.010	-0.010	0.000	0.000	0.000	0.000
31	D	49	MET	0	-0.006	-0.005	22.412	-0.001	-0.001	0.000	0.000	0.000	0.000
32	D	50	LEU	0	-0.019	-0.005	23.231	0.000	0.000	0.000	0.000	0.000	0.000
33	D	51	CYS	0	-0.050	-0.008	20.656	-0.004	-0.004	0.000	0.000	0.000	0.000
34	D	52	GLY	0	0.013	0.023	23.420	-0.009	-0.009	0.000	0.000	0.000	0.000
35	D	53	VAL	0	-0.076	-0.049	22.426	-0.011	-0.011	0.000	0.000	0.000	0.000
36	D	54	THR	0	0.075	0.034	25.424	0.002	0.002	0.000	0.000	0.000	0.000
37	D	55	LYS	1	1.066	1.011	22.652	0.059	0.059	0.000	0.000	0.000	0.000
38	D	56	LYS	1	0.939	0.977	22.102	0.118	0.118	0.000	0.000	0.000	0.000
39	D	57	THR	0	0.007	0.004	22.803	-0.020	-0.020	0.000	0.000	0.000	0.000
40	D	58	LEU	0	0.061	0.040	17.210	-0.022	-0.022	0.000	0.000	0.000	0.000
41	D	59	ILE	0	-0.043	-0.017	18.200	-0.036	-0.036	0.000	0.000	0.000	0.000
42	D	60	ARG	1	0.851	0.901	18.521	0.178	0.178	0.000	0.000	0.000	0.000
43	D	61	VAL	0	0.030	0.016	16.263	-0.029	-0.029	0.000	0.000	0.000	0.000
44	D	62	GLU	-1	-0.781	-0.882	14.215	-0.289	-0.289	0.000	0.000	0.000	0.000
45	D	63	LYS	1	0.855	0.929	13.847	0.208	0.208	0.000	0.000	0.000	0.000
46	D	64	GLY	0	0.013	0.012	16.017	-0.027	-0.027	0.000	0.000	0.000	0.000
47	D	65	GLU	-1	-1.002	-0.989	16.538	-0.238	-0.238	0.000	0.000	0.000	0.000
48	D	66	ASP	-1	-0.852	-0.922	20.284	-0.238	-0.238	0.000	0.000	0.000	0.000
49	D	67	VAL	0	-0.070	-0.029	20.574	0.025	0.025	0.000	0.000	0.000	0.000
50	D	68	TYR	0	0.024	0.018	23.622	-0.001	-0.001	0.000	0.000	0.000	0.000
51	D	69	ILE	0	0.082	0.031	21.688	-0.005	-0.005	0.000	0.000	0.000	0.000
52	D	70	SER	0	0.050	0.023	23.063	-0.005	-0.005	0.000	0.000	0.000	0.000
53	D	71	THR	0	-0.031	-0.021	21.941	0.015	0.015	0.000	0.000	0.000	0.000
54	D	72	VAL	0	0.021	0.020	17.752	0.003	0.003	0.000	0.000	0.000	0.000
55	D	73	PHE	0	0.060	0.008	19.242	-0.014	-0.014	0.000	0.000	0.000	0.000
56	D	74	LYS	1	0.917	0.992	21.450	0.130	0.130	0.000	0.000	0.000	0.000
57	D	75	ILE	0	-0.025	-0.029	16.806	0.015	0.015	0.000	0.000	0.000	0.000
58	D	76	LEU	0	-0.050	-0.023	14.769	0.004	0.004	0.000	0.000	0.000	0.000
59	D	77	ASP	-1	-0.836	-0.921	17.681	-0.101	-0.101	0.000	0.000	0.000	0.000
60	D	78	GLY	0	-0.046	-0.017	20.515	0.025	0.025	0.000	0.000	0.000	0.000
61	D	79	LEU	0	-0.094	-0.057	14.602	0.026	0.026	0.000	0.000	0.000	0.000
62	D	80	GLY	0	0.013	0.011	16.001	0.033	0.033	0.000	0.000	0.000	0.000
63	D	81	ILE	0	-0.104	-0.053	12.476	0.009	0.009	0.000	0.000	0.000	0.000
64	D	82	ASP	-1	-0.859	-0.914	15.045	-0.063	-0.063	0.000	0.000	0.000	0.000
65	D	83	ILE	0	-0.082	-0.045	14.569	-0.051	-0.051	0.000	0.000	0.000	0.000
66	D	84	VAL	0	0.014	-0.004	15.936	0.039	0.039	0.000	0.000	0.000	0.000
67	D	85	SER	0	-0.025	-0.005	16.665	-0.045	-0.045	0.000	0.000	0.000	0.000
68	D	86	ALA	0	0.007	0.006	15.465	0.032	0.032	0.000	0.000	0.000	0.000
69	D	95	GLY	0	0.016	0.024	30.757	-0.001	-0.001	0.000	0.000	0.000	0.000
70	D	96	TRP	0	0.004	-0.034	31.344	-0.002	-0.002	0.000	0.000	0.000	0.000
71	D	97	TYR	0	-0.020	0.010	29.905	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)