FMO DATABASE

FMODB ID: 6NRZZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-391805.156751
FMO2-HF: Nuclear repulsion	364541.142895
FMO2-HF: Total energy	-27264.013856
FMO2-MP2: Total energy	-27342.788621

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.
0.039	2.416	0.002	-1.064	-1.316	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 : 0.045 / q_NPA : 0.018

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	0.004	0.002	3.619	-0.878	1.443	0.003	-1.059	-1.266	0.003
4	D	22	SER	0	0.021	0.006	4.740	0.140	0.196	-0.001	-0.005	-0.050	0.000
5	D	23	PRO	0	-0.025	-0.007	7.654	0.097	0.097	0.000	0.000	0.000	0.000
6	D	24	LEU	0	0.036	0.024	9.959	-0.069	-0.069	0.000	0.000	0.000	0.000
7	D	25	ASN	0	0.037	0.029	11.508	0.044	0.044	0.000	0.000	0.000	0.000
8	D	26	GLN	0	-0.001	-0.010	13.738	-0.066	-0.066	0.000	0.000	0.000	0.000
9	D	27	GLN	0	0.016	0.007	13.119	-0.034	-0.034	0.000	0.000	0.000	0.000
10	D	28	SER	0	0.020	-0.008	8.924	-0.035	-0.035	0.000	0.000	0.000	0.000
11	D	29	LEU	0	0.034	0.024	9.981	-0.180	-0.180	0.000	0.000	0.000	0.000
12	D	30	GLY	0	0.066	0.033	12.458	0.027	0.027	0.000	0.000	0.000	0.000
13	D	31	LEU	0	-0.046	-0.037	7.940	0.057	0.057	0.000	0.000	0.000	0.000
14	D	32	LEU	0	0.023	0.016	7.657	-0.062	-0.062	0.000	0.000	0.000	0.000
15	D	33	ILE	0	0.019	0.006	9.041	0.142	0.142	0.000	0.000	0.000	0.000
16	D	34	LYS	1	0.809	0.903	10.567	0.557	0.557	0.000	0.000	0.000	0.000
17	D	35	GLU	-1	-0.779	-0.880	5.962	-0.395	-0.395	0.000	0.000	0.000	0.000
18	D	36	ARG	1	0.881	0.963	8.654	0.591	0.591	0.000	0.000	0.000	0.000
19	D	37	ARG	1	0.816	0.870	10.572	0.381	0.381	0.000	0.000	0.000	0.000
20	D	38	LYS	1	0.744	0.842	8.915	0.400	0.400	0.000	0.000	0.000	0.000
21	D	39	SER	0	-0.027	-0.025	8.961	0.120	0.120	0.000	0.000	0.000	0.000
22	D	40	ALA	0	-0.020	0.004	11.314	0.060	0.060	0.000	0.000	0.000	0.000
23	D	41	ALA	0	-0.018	-0.008	14.407	0.014	0.014	0.000	0.000	0.000	0.000
24	D	42	LEU	0	0.021	0.032	16.275	0.005	0.005	0.000	0.000	0.000	0.000
25	D	43	THR	0	0.035	0.005	17.513	-0.027	-0.027	0.000	0.000	0.000	0.000
26	D	44	GLN	0	-0.019	-0.033	17.251	0.017	0.017	0.000	0.000	0.000	0.000
27	D	45	ASP	-1	-0.790	-0.883	20.133	-0.115	-0.115	0.000	0.000	0.000	0.000
28	D	46	VAL	0	0.022	0.020	22.204	-0.002	-0.002	0.000	0.000	0.000	0.000
29	D	47	ALA	0	0.049	0.022	18.628	-0.002	-0.002	0.000	0.000	0.000	0.000
30	D	48	ALA	0	-0.017	-0.007	20.630	-0.009	-0.009	0.000	0.000	0.000	0.000
31	D	49	MET	0	-0.001	-0.009	22.537	0.003	0.003	0.000	0.000	0.000	0.000
32	D	50	LEU	0	-0.007	0.006	22.533	0.005	0.005	0.000	0.000	0.000	0.000
33	D	51	CYS	0	-0.038	0.004	20.598	-0.009	-0.009	0.000	0.000	0.000	0.000
34	D	52	GLY	0	0.018	0.014	23.325	-0.006	-0.006	0.000	0.000	0.000	0.000
35	D	53	VAL	0	-0.068	-0.042	22.598	-0.003	-0.003	0.000	0.000	0.000	0.000
36	D	54	THR	0	0.062	0.035	25.894	0.003	0.003	0.000	0.000	0.000	0.000
37	D	55	LYS	1	0.917	0.917	22.708	0.089	0.089	0.000	0.000	0.000	0.000
38	D	56	LYS	1	0.943	0.974	22.388	0.134	0.134	0.000	0.000	0.000	0.000
39	D	57	THR	0	-0.005	-0.008	23.203	-0.010	-0.010	0.000	0.000	0.000	0.000
40	D	58	LEU	0	0.048	0.029	16.999	-0.021	-0.021	0.000	0.000	0.000	0.000
41	D	59	ILE	0	-0.038	-0.020	18.445	-0.040	-0.040	0.000	0.000	0.000	0.000
42	D	60	ARG	1	0.792	0.887	18.732	0.208	0.208	0.000	0.000	0.000	0.000
43	D	61	VAL	0	0.073	0.034	16.270	-0.033	-0.033	0.000	0.000	0.000	0.000
44	D	62	GLU	-1	-0.778	-0.851	14.249	-0.401	-0.401	0.000	0.000	0.000	0.000
45	D	63	LYS	1	0.834	0.909	13.933	0.219	0.219	0.000	0.000	0.000	0.000
46	D	64	GLY	0	0.026	0.020	15.696	-0.022	-0.022	0.000	0.000	0.000	0.000
47	D	65	GLU	-1	-0.889	-0.922	16.757	-0.209	-0.209	0.000	0.000	0.000	0.000
48	D	66	ASP	-1	-0.840	-0.922	20.337	-0.262	-0.262	0.000	0.000	0.000	0.000
49	D	67	VAL	0	-0.037	-0.018	20.848	0.023	0.023	0.000	0.000	0.000	0.000
50	D	68	TYR	0	0.043	0.029	23.885	-0.008	-0.008	0.000	0.000	0.000	0.000
51	D	69	ILE	0	0.099	0.046	21.692	-0.010	-0.010	0.000	0.000	0.000	0.000
52	D	70	SER	0	0.047	0.024	23.241	-0.014	-0.014	0.000	0.000	0.000	0.000
53	D	71	THR	0	-0.030	-0.026	22.463	0.018	0.018	0.000	0.000	0.000	0.000
54	D	72	VAL	0	0.015	0.014	17.888	-0.006	-0.006	0.000	0.000	0.000	0.000
55	D	73	PHE	0	0.030	0.010	19.397	-0.023	-0.023	0.000	0.000	0.000	0.000
56	D	74	LYS	1	0.872	0.948	20.914	0.184	0.184	0.000	0.000	0.000	0.000
57	D	75	ILE	0	-0.021	-0.018	16.764	0.012	0.012	0.000	0.000	0.000	0.000
58	D	76	LEU	0	-0.020	-0.006	14.979	-0.020	-0.020	0.000	0.000	0.000	0.000
59	D	77	ASP	-1	-0.856	-0.930	17.409	-0.231	-0.231	0.000	0.000	0.000	0.000
60	D	78	GLY	0	-0.026	-0.009	20.171	0.017	0.017	0.000	0.000	0.000	0.000
61	D	79	LEU	0	-0.072	-0.040	14.292	0.019	0.019	0.000	0.000	0.000	0.000
62	D	80	GLY	0	0.032	0.025	15.491	-0.009	-0.009	0.000	0.000	0.000	0.000
63	D	81	ILE	0	-0.101	-0.047	12.128	-0.024	-0.024	0.000	0.000	0.000	0.000
64	D	82	ASP	-1	-0.865	-0.926	14.708	-0.267	-0.267	0.000	0.000	0.000	0.000
65	D	83	ILE	0	-0.065	-0.036	14.286	-0.083	-0.083	0.000	0.000	0.000	0.000
66	D	84	VAL	0	0.002	-0.005	16.076	0.053	0.053	0.000	0.000	0.000	0.000
67	D	85	SER	0	-0.022	-0.008	16.551	-0.041	-0.041	0.000	0.000	0.000	0.000
68	D	86	ALA	0	0.015	0.017	15.539	0.027	0.027	0.000	0.000	0.000	0.000
69	D	95	GLY	0	0.029	0.024	31.192	0.000	0.000	0.000	0.000	0.000	0.000
70	D	96	TRP	0	-0.030	-0.044	31.894	-0.002	-0.002	0.000	0.000	0.000	0.000
71	D	97	TYR	0	0.001	0.020	29.915	0.001	0.001	0.000	0.000	0.000	0.000

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