FMO DATABASE

FMODB ID: 4JK6N

Calculation Name: 1SZA-C-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 1SZA

Chain ID: C

ChEMBL ID:

UniProt ID: P39081

Base Structure: X-ray

Registration Date: 2023-09-23

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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1343486.609482
FMO2-HF: Nuclear repulsion	1286912.729736
FMO2-HF: Total energy	-56573.879746
FMO2-MP2: Total energy	-56738.978569

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(C:2:ASP)

Summations of interaction energy for fragment #1(C:2:ASP)

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.
-33.594	-36.87	31.176	-15.491	-12.408	0.127

Interaction energy analysis for fragmet #1(C:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.797 / q_NPA : -0.892

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	C	4	ASP	-1	-0.841	-0.938	2.858	43.358	48.985	1.233	-3.242	-3.618	0.026
4	C	5	THR	0	-0.058	-0.071	1.717	-51.826	-61.360	29.897	-12.036	-8.327	0.096
5	C	6	GLU	-1	-0.849	-0.902	3.592	16.550	17.181	0.046	-0.213	-0.463	0.005
6	C	7	VAL	0	-0.014	-0.012	6.007	-6.814	-6.814	0.000	0.000	0.000	0.000
7	C	8	ILE	0	0.020	0.026	5.262	-5.259	-5.259	0.000	0.000	0.000	0.000
8	C	9	VAL	0	0.001	-0.011	7.570	-5.078	-5.078	0.000	0.000	0.000	0.000
9	C	10	LYS	1	0.818	0.915	9.001	-31.892	-31.892	0.000	0.000	0.000	0.000
10	C	11	ASP	-1	-0.873	-0.940	11.196	21.578	21.578	0.000	0.000	0.000	0.000
11	C	12	PHE	0	-0.035	-0.014	12.214	-2.281	-2.281	0.000	0.000	0.000	0.000
12	C	13	ASN	0	-0.067	-0.062	12.907	-2.921	-2.921	0.000	0.000	0.000	0.000
13	C	14	SER	0	0.031	0.021	15.430	-1.441	-1.441	0.000	0.000	0.000	0.000
14	C	15	ILE	0	-0.004	0.003	15.973	-1.331	-1.331	0.000	0.000	0.000	0.000
15	C	16	LEU	0	-0.028	-0.015	18.120	-1.235	-1.235	0.000	0.000	0.000	0.000
16	C	17	GLU	-1	-1.006	-1.008	19.116	14.261	14.261	0.000	0.000	0.000	0.000
17	C	18	GLU	-1	-0.876	-0.932	21.856	12.032	12.032	0.000	0.000	0.000	0.000
18	C	19	LEU	0	-0.114	-0.039	23.193	-0.705	-0.705	0.000	0.000	0.000	0.000
19	C	20	THR	0	-0.011	-0.016	25.110	-0.318	-0.318	0.000	0.000	0.000	0.000
20	C	21	PHE	0	-0.013	-0.016	28.598	-0.519	-0.519	0.000	0.000	0.000	0.000
21	C	22	ASN	0	-0.011	-0.013	28.702	0.690	0.690	0.000	0.000	0.000	0.000
22	C	23	SER	0	0.030	0.027	26.361	-0.232	-0.232	0.000	0.000	0.000	0.000
23	C	24	ARG	1	1.011	0.994	26.331	-10.883	-10.883	0.000	0.000	0.000	0.000
24	C	25	PRO	0	0.049	0.033	25.134	0.383	0.383	0.000	0.000	0.000	0.000
25	C	26	ILE	0	0.064	0.048	21.452	0.510	0.510	0.000	0.000	0.000	0.000
26	C	27	ILE	0	0.013	0.005	21.276	0.638	0.638	0.000	0.000	0.000	0.000
27	C	28	THR	0	-0.053	-0.042	21.820	0.475	0.475	0.000	0.000	0.000	0.000
28	C	29	THR	0	-0.012	-0.009	17.599	0.439	0.439	0.000	0.000	0.000	0.000
29	C	30	LEU	0	0.016	0.009	16.698	0.896	0.896	0.000	0.000	0.000	0.000
30	C	31	THR	0	-0.022	-0.021	16.927	0.589	0.589	0.000	0.000	0.000	0.000
31	C	32	LYS	1	0.973	0.989	17.287	-14.872	-14.872	0.000	0.000	0.000	0.000
32	C	33	LEU	0	0.006	0.015	12.045	0.596	0.596	0.000	0.000	0.000	0.000
33	C	34	ALA	0	0.011	0.013	12.822	1.787	1.787	0.000	0.000	0.000	0.000
34	C	35	GLU	-1	-0.893	-0.951	14.578	17.083	17.083	0.000	0.000	0.000	0.000
35	C	36	GLU	-1	-0.928	-0.968	13.007	20.238	20.238	0.000	0.000	0.000	0.000
36	C	37	ASN	0	-0.064	-0.033	8.751	4.722	4.722	0.000	0.000	0.000	0.000
37	C	38	ILE	0	0.040	0.026	10.322	1.151	1.151	0.000	0.000	0.000	0.000
38	C	39	SER	0	-0.029	-0.007	6.849	-1.767	-1.767	0.000	0.000	0.000	0.000
39	C	40	CYS	0	-0.030	-0.018	6.797	3.234	3.234	0.000	0.000	0.000	0.000
40	C	41	ALA	0	0.023	0.010	9.001	-1.914	-1.914	0.000	0.000	0.000	0.000
41	C	42	GLN	0	-0.038	-0.047	11.981	-1.882	-1.882	0.000	0.000	0.000	0.000
42	C	43	TYR	0	0.054	0.033	5.956	-2.909	-2.909	0.000	0.000	0.000	0.000
43	C	44	PHE	0	0.001	0.001	10.162	-1.373	-1.373	0.000	0.000	0.000	0.000
44	C	45	VAL	0	-0.017	-0.011	14.182	-1.477	-1.477	0.000	0.000	0.000	0.000
45	C	46	ASP	-1	-0.845	-0.913	13.900	17.980	17.980	0.000	0.000	0.000	0.000
46	C	47	ALA	0	-0.009	0.004	15.030	-1.099	-1.099	0.000	0.000	0.000	0.000
47	C	48	ILE	0	0.016	-0.004	16.890	-1.173	-1.173	0.000	0.000	0.000	0.000
48	C	49	GLU	-1	-0.836	-0.921	19.893	12.893	12.893	0.000	0.000	0.000	0.000
49	C	50	SER	0	-0.017	-0.004	19.274	-1.106	-1.106	0.000	0.000	0.000	0.000
50	C	51	ARG	1	0.896	0.958	21.045	-13.635	-13.635	0.000	0.000	0.000	0.000
51	C	52	ILE	0	0.016	0.007	22.689	-0.736	-0.736	0.000	0.000	0.000	0.000
52	C	53	GLU	-1	-0.881	-0.924	24.632	10.884	10.884	0.000	0.000	0.000	0.000
53	C	54	LYS	1	0.857	0.917	22.680	-13.035	-13.035	0.000	0.000	0.000	0.000
54	C	55	CYS	0	-0.079	-0.008	26.055	-0.436	-0.436	0.000	0.000	0.000	0.000
55	C	56	MET	0	0.057	0.025	27.679	-0.356	-0.356	0.000	0.000	0.000	0.000
56	C	57	PRO	0	0.060	0.007	31.356	0.170	0.170	0.000	0.000	0.000	0.000
57	C	58	LYS	1	0.956	0.965	33.143	-8.135	-8.135	0.000	0.000	0.000	0.000
58	C	59	GLN	0	-0.003	-0.005	28.725	-0.164	-0.164	0.000	0.000	0.000	0.000
59	C	60	LYS	1	0.835	0.915	28.513	-10.196	-10.196	0.000	0.000	0.000	0.000
60	C	61	LEU	0	-0.008	-0.001	28.753	0.221	0.221	0.000	0.000	0.000	0.000
61	C	62	TYR	0	0.014	0.001	27.946	-0.008	-0.008	0.000	0.000	0.000	0.000
62	C	63	ALA	0	0.030	0.031	24.378	0.357	0.357	0.000	0.000	0.000	0.000
63	C	64	PHE	0	0.046	0.006	24.565	0.391	0.391	0.000	0.000	0.000	0.000
64	C	65	TYR	0	-0.024	-0.022	26.873	-0.141	-0.141	0.000	0.000	0.000	0.000
65	C	66	ALA	0	0.023	0.023	21.696	0.061	0.061	0.000	0.000	0.000	0.000
66	C	67	LEU	0	-0.004	0.015	22.330	0.319	0.319	0.000	0.000	0.000	0.000
67	C	68	ASP	-1	-0.792	-0.882	23.382	10.980	10.980	0.000	0.000	0.000	0.000
68	C	69	SER	0	-0.031	-0.027	23.353	-0.237	-0.237	0.000	0.000	0.000	0.000
69	C	70	ILE	0	0.027	0.027	18.252	0.022	0.022	0.000	0.000	0.000	0.000
70	C	71	CYS	0	-0.043	-0.019	21.586	0.230	0.230	0.000	0.000	0.000	0.000
71	C	72	LYS	1	0.821	0.884	23.611	-10.686	-10.686	0.000	0.000	0.000	0.000
72	C	73	ASN	0	-0.100	-0.060	23.315	-0.608	-0.608	0.000	0.000	0.000	0.000
73	C	74	VAL	0	0.025	0.050	17.758	0.049	0.049	0.000	0.000	0.000	0.000
74	C	75	GLY	0	0.011	0.024	21.192	-0.163	-0.163	0.000	0.000	0.000	0.000
75	C	76	SER	0	-0.050	-0.024	21.031	0.652	0.652	0.000	0.000	0.000	0.000
76	C	77	PRO	0	0.074	0.026	15.720	0.270	0.270	0.000	0.000	0.000	0.000
77	C	78	TYR	0	0.006	-0.023	14.146	-0.076	-0.076	0.000	0.000	0.000	0.000
78	C	79	THR	0	0.037	0.014	19.451	-0.179	-0.179	0.000	0.000	0.000	0.000
79	C	80	ILE	0	0.006	0.015	20.714	-0.496	-0.496	0.000	0.000	0.000	0.000
80	C	81	TYR	0	-0.029	-0.033	14.367	-0.896	-0.896	0.000	0.000	0.000	0.000
81	C	82	PHE	0	0.052	0.023	19.405	-0.224	-0.224	0.000	0.000	0.000	0.000
82	C	83	SER	0	-0.026	-0.022	22.428	-0.728	-0.728	0.000	0.000	0.000	0.000
83	C	84	ARG	1	0.843	0.941	17.806	-15.963	-15.963	0.000	0.000	0.000	0.000
84	C	85	ASN	0	-0.037	-0.031	22.137	-0.902	-0.902	0.000	0.000	0.000	0.000
85	C	86	LEU	0	0.028	0.028	25.826	-0.376	-0.376	0.000	0.000	0.000	0.000
86	C	87	PHE	0	-0.003	-0.009	27.577	-0.344	-0.344	0.000	0.000	0.000	0.000
87	C	88	ASN	0	0.003	-0.009	28.814	-0.529	-0.529	0.000	0.000	0.000	0.000
88	C	89	LEU	0	0.055	0.033	24.316	-0.350	-0.350	0.000	0.000	0.000	0.000
89	C	90	TYR	0	0.010	0.002	28.841	-0.284	-0.284	0.000	0.000	0.000	0.000
90	C	91	LYS	1	0.941	0.974	31.538	-8.601	-8.601	0.000	0.000	0.000	0.000
91	C	92	ARG	1	0.918	0.955	28.369	-10.454	-10.454	0.000	0.000	0.000	0.000
92	C	93	THR	0	0.014	0.000	30.288	-0.096	-0.096	0.000	0.000	0.000	0.000
93	C	94	TYR	0	0.029	0.009	32.825	-0.244	-0.244	0.000	0.000	0.000	0.000
94	C	95	LEU	0	-0.059	-0.039	36.185	-0.262	-0.262	0.000	0.000	0.000	0.000
95	C	96	LEU	0	-0.024	0.003	33.044	-0.166	-0.166	0.000	0.000	0.000	0.000
96	C	97	VAL	0	-0.051	0.000	34.447	0.015	0.015	0.000	0.000	0.000	0.000
97	C	98	ASP	-1	-0.800	-0.878	37.404	7.850	7.850	0.000	0.000	0.000	0.000
98	C	99	ASN	0	0.091	0.013	40.186	0.223	0.223	0.000	0.000	0.000	0.000
99	C	100	THR	0	0.005	0.013	40.732	-0.039	-0.039	0.000	0.000	0.000	0.000
100	C	101	THR	0	-0.062	-0.068	35.341	0.149	0.149	0.000	0.000	0.000	0.000
101	C	102	ARG	1	0.883	0.945	37.168	-7.588	-7.588	0.000	0.000	0.000	0.000
102	C	103	THR	0	-0.011	-0.005	39.056	0.010	0.010	0.000	0.000	0.000	0.000
103	C	104	LYS	1	0.920	0.959	35.942	-8.433	-8.433	0.000	0.000	0.000	0.000
104	C	105	LEU	0	0.028	0.022	32.612	0.179	0.179	0.000	0.000	0.000	0.000
105	C	106	ILE	0	0.023	0.031	35.550	0.129	0.129	0.000	0.000	0.000	0.000
106	C	107	ASN	0	0.001	-0.007	37.907	-0.116	-0.116	0.000	0.000	0.000	0.000
107	C	108	MET	0	-0.027	0.007	30.788	0.105	0.105	0.000	0.000	0.000	0.000
108	C	109	PHE	0	0.025	0.008	33.684	0.167	0.167	0.000	0.000	0.000	0.000
109	C	110	LYS	1	0.929	0.959	35.020	-7.658	-7.658	0.000	0.000	0.000	0.000
110	C	111	LEU	0	-0.001	-0.004	33.921	-0.032	-0.032	0.000	0.000	0.000	0.000
111	C	112	TRP	0	-0.058	-0.034	29.244	0.118	0.118	0.000	0.000	0.000	0.000
112	C	113	LEU	0	-0.007	-0.008	32.964	0.150	0.150	0.000	0.000	0.000	0.000
113	C	114	ASN	0	-0.028	-0.012	35.610	0.081	0.081	0.000	0.000	0.000	0.000
114	C	115	PRO	0	0.007	0.020	30.709	-0.080	-0.080	0.000	0.000	0.000	0.000
115	C	116	ASN	0	-0.060	-0.048	28.686	-0.123	-0.123	0.000	0.000	0.000	0.000
116	C	117	ASP	-1	-0.898	-0.929	33.227	8.126	8.126	0.000	0.000	0.000	0.000
117	C	118	THR	0	-0.016	-0.006	31.675	-0.092	-0.092	0.000	0.000	0.000	0.000
118	C	119	GLY	0	0.002	0.007	35.092	-0.108	-0.108	0.000	0.000	0.000	0.000
119	C	120	LEU	0	-0.040	-0.024	32.842	-0.127	-0.127	0.000	0.000	0.000	0.000
120	C	121	PRO	0	-0.029	-0.018	32.847	0.211	0.211	0.000	0.000	0.000	0.000
121	C	122	LEU	0	-0.009	0.009	26.995	0.194	0.194	0.000	0.000	0.000	0.000
122	C	123	PHE	0	-0.046	-0.040	24.762	0.428	0.428	0.000	0.000	0.000	0.000
123	C	124	GLU	-1	-0.894	-0.933	27.959	10.519	10.519	0.000	0.000	0.000	0.000
124	C	125	GLY	0	0.003	0.000	28.830	0.275	0.275	0.000	0.000	0.000	0.000
125	C	126	SER	0	0.032	-0.002	31.048	-0.159	-0.159	0.000	0.000	0.000	0.000
126	C	127	ALA	0	-0.037	-0.013	29.560	-0.228	-0.228	0.000	0.000	0.000	0.000
127	C	128	LEU	0	0.066	0.020	31.696	-0.180	-0.180	0.000	0.000	0.000	0.000
128	C	129	GLU	-1	-0.849	-0.918	33.943	8.229	8.229	0.000	0.000	0.000	0.000
129	C	130	LYS	1	0.882	0.931	33.203	-9.449	-9.449	0.000	0.000	0.000	0.000
130	C	131	ILE	0	-0.020	-0.011	31.622	-0.180	-0.180	0.000	0.000	0.000	0.000
131	C	132	GLU	-1	-0.904	-0.940	36.219	7.643	7.643	0.000	0.000	0.000	0.000
132	C	133	GLN	0	0.000	-0.007	39.311	-0.320	-0.320	0.000	0.000	0.000	0.000
133	C	134	PHE	0	-0.065	-0.035	37.424	-0.176	-0.176	0.000	0.000	0.000	0.000
134	C	135	LEU	0	0.023	0.006	37.856	-0.160	-0.160	0.000	0.000	0.000	0.000
135	C	136	ILE	0	-0.007	0.003	41.426	-0.181	-0.181	0.000	0.000	0.000	0.000
136	C	137	LYS	1	0.896	0.956	42.969	-7.392	-7.392	0.000	0.000	0.000	0.000
137	C	138	ALA	0	-0.039	-0.015	42.192	-0.110	-0.110	0.000	0.000	0.000	0.000
138	C	139	SER	0	-0.063	-0.015	44.180	-0.041	-0.041	0.000	0.000	0.000	0.000
139	C	140	ALA	0	0.029	0.008	45.911	-0.129	-0.129	0.000	0.000	0.000	0.000
140	C	141	ALA	0	-0.026	-0.002	49.151	0.030	0.030	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:2:ASP)