FMO DATABASE

FMODB ID: 5JQYZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1355225.48347
FMO2-HF: Nuclear repulsion	1298651.474345
FMO2-HF: Total energy	-56574.009125
FMO2-MP2: Total energy	-56739.164636

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.
-39.536	-50.614	41.398	-18.561	-11.757	0.148

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 : -0.767 / q_NPA : -0.858

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	-0.844	-0.931	2.493	39.046	44.959	1.629	-3.728	-3.814	0.033
4	C	5	THR	0	-0.082	-0.095	1.585	-51.323	-68.996	39.739	-14.758	-7.308	0.110
5	C	6	GLU	-1	-0.836	-0.897	3.545	16.567	17.155	0.031	-0.071	-0.547	0.005
6	C	7	VAL	0	-0.027	-0.006	5.661	-7.981	-7.887	-0.001	-0.004	-0.088	0.000
7	C	8	ILE	0	0.029	0.018	5.471	-5.460	-5.460	0.000	0.000	0.000	0.000
8	C	9	VAL	0	0.008	-0.005	7.364	-5.301	-5.301	0.000	0.000	0.000	0.000
9	C	10	LYS	1	0.818	0.912	8.963	-33.250	-33.250	0.000	0.000	0.000	0.000
10	C	11	ASP	-1	-0.864	-0.917	11.110	22.646	22.646	0.000	0.000	0.000	0.000
11	C	12	PHE	0	-0.025	-0.017	11.971	-2.456	-2.456	0.000	0.000	0.000	0.000
12	C	13	ASN	0	-0.054	-0.051	12.732	-3.050	-3.050	0.000	0.000	0.000	0.000
13	C	14	SER	0	0.024	0.007	15.234	-1.563	-1.563	0.000	0.000	0.000	0.000
14	C	15	ILE	0	-0.015	-0.013	15.564	-1.422	-1.422	0.000	0.000	0.000	0.000
15	C	16	LEU	0	-0.041	-0.022	17.807	-1.248	-1.248	0.000	0.000	0.000	0.000
16	C	17	GLU	-1	-0.973	-0.993	19.383	14.441	14.441	0.000	0.000	0.000	0.000
17	C	18	GLU	-1	-0.859	-0.918	21.485	11.973	11.973	0.000	0.000	0.000	0.000
18	C	19	LEU	0	-0.077	-0.010	22.698	-0.706	-0.706	0.000	0.000	0.000	0.000
19	C	20	THR	0	-0.016	-0.022	24.663	-0.395	-0.395	0.000	0.000	0.000	0.000
20	C	21	PHE	0	0.007	-0.010	28.206	-0.506	-0.506	0.000	0.000	0.000	0.000
21	C	22	ASN	0	0.006	0.001	28.280	0.725	0.725	0.000	0.000	0.000	0.000
22	C	23	SER	0	0.018	0.015	26.010	-0.211	-0.211	0.000	0.000	0.000	0.000
23	C	24	ARG	1	0.990	0.989	25.772	-11.015	-11.015	0.000	0.000	0.000	0.000
24	C	25	PRO	0	0.049	0.037	24.934	0.377	0.377	0.000	0.000	0.000	0.000
25	C	26	ILE	0	0.053	0.053	21.022	0.509	0.509	0.000	0.000	0.000	0.000
26	C	27	ILE	0	0.011	0.003	20.949	0.664	0.664	0.000	0.000	0.000	0.000
27	C	28	THR	0	-0.058	-0.039	21.563	0.498	0.498	0.000	0.000	0.000	0.000
28	C	29	THR	0	-0.009	-0.004	17.338	0.450	0.450	0.000	0.000	0.000	0.000
29	C	30	LEU	0	0.014	0.003	16.558	0.901	0.901	0.000	0.000	0.000	0.000
30	C	31	THR	0	-0.028	-0.029	16.895	0.533	0.533	0.000	0.000	0.000	0.000
31	C	32	LYS	1	0.962	0.979	17.269	-14.878	-14.878	0.000	0.000	0.000	0.000
32	C	33	LEU	0	0.003	0.011	11.831	0.634	0.634	0.000	0.000	0.000	0.000
33	C	34	ALA	0	0.009	0.007	12.884	1.693	1.693	0.000	0.000	0.000	0.000
34	C	35	GLU	-1	-0.888	-0.934	14.733	17.364	17.364	0.000	0.000	0.000	0.000
35	C	36	GLU	-1	-0.929	-0.973	12.938	20.874	20.874	0.000	0.000	0.000	0.000
36	C	37	ASN	0	-0.048	-0.027	8.784	4.700	4.700	0.000	0.000	0.000	0.000
37	C	38	ILE	0	0.032	0.027	10.308	1.086	1.086	0.000	0.000	0.000	0.000
38	C	39	SER	0	-0.035	-0.017	6.807	-1.847	-1.847	0.000	0.000	0.000	0.000
39	C	40	CYS	0	-0.021	-0.011	6.781	3.808	3.808	0.000	0.000	0.000	0.000
40	C	41	ALA	0	0.022	0.011	8.985	-2.002	-2.002	0.000	0.000	0.000	0.000
41	C	42	GLN	0	-0.034	-0.031	12.067	-2.127	-2.127	0.000	0.000	0.000	0.000
42	C	43	TYR	0	0.062	0.034	6.442	-3.069	-3.069	0.000	0.000	0.000	0.000
43	C	44	PHE	0	0.002	0.005	10.187	-1.157	-1.157	0.000	0.000	0.000	0.000
44	C	45	VAL	0	-0.002	-0.006	14.120	-1.542	-1.542	0.000	0.000	0.000	0.000
45	C	46	ASP	-1	-0.835	-0.910	13.703	18.965	18.965	0.000	0.000	0.000	0.000
46	C	47	ALA	0	-0.007	0.005	14.978	-1.132	-1.132	0.000	0.000	0.000	0.000
47	C	48	ILE	0	0.011	-0.002	16.875	-1.246	-1.246	0.000	0.000	0.000	0.000
48	C	49	GLU	-1	-0.827	-0.925	19.813	13.196	13.196	0.000	0.000	0.000	0.000
49	C	50	SER	0	-0.027	-0.005	19.477	-1.151	-1.151	0.000	0.000	0.000	0.000
50	C	51	ARG	1	0.836	0.909	20.969	-13.946	-13.946	0.000	0.000	0.000	0.000
51	C	52	ILE	0	0.010	0.008	22.724	-0.749	-0.749	0.000	0.000	0.000	0.000
52	C	53	GLU	-1	-0.843	-0.895	24.838	10.934	10.934	0.000	0.000	0.000	0.000
53	C	54	LYS	1	0.864	0.912	23.115	-13.288	-13.288	0.000	0.000	0.000	0.000
54	C	55	CYS	0	-0.064	-0.001	26.143	-0.372	-0.372	0.000	0.000	0.000	0.000
55	C	56	MET	0	0.047	0.022	27.778	-0.420	-0.420	0.000	0.000	0.000	0.000
56	C	57	PRO	0	0.058	0.003	31.104	0.185	0.185	0.000	0.000	0.000	0.000
57	C	58	LYS	1	0.946	0.962	32.724	-8.278	-8.278	0.000	0.000	0.000	0.000
58	C	59	GLN	0	-0.002	0.002	27.577	-0.307	-0.307	0.000	0.000	0.000	0.000
59	C	60	LYS	1	0.813	0.907	28.043	-10.365	-10.365	0.000	0.000	0.000	0.000
60	C	61	LEU	0	-0.003	0.002	28.102	0.250	0.250	0.000	0.000	0.000	0.000
61	C	62	TYR	0	0.007	0.009	27.483	-0.024	-0.024	0.000	0.000	0.000	0.000
62	C	63	ALA	0	0.046	0.036	23.705	0.364	0.364	0.000	0.000	0.000	0.000
63	C	64	PHE	0	0.036	0.002	24.065	0.386	0.386	0.000	0.000	0.000	0.000
64	C	65	TYR	0	-0.013	-0.025	26.370	-0.116	-0.116	0.000	0.000	0.000	0.000
65	C	66	ALA	0	0.021	0.018	21.251	0.057	0.057	0.000	0.000	0.000	0.000
66	C	67	LEU	0	-0.012	0.012	22.060	0.287	0.287	0.000	0.000	0.000	0.000
67	C	68	ASP	-1	-0.789	-0.877	23.090	11.052	11.052	0.000	0.000	0.000	0.000
68	C	69	SER	0	-0.024	-0.019	23.342	-0.285	-0.285	0.000	0.000	0.000	0.000
69	C	70	ILE	0	0.031	0.028	17.919	0.005	0.005	0.000	0.000	0.000	0.000
70	C	71	CYS	0	-0.052	-0.023	21.329	0.160	0.160	0.000	0.000	0.000	0.000
71	C	72	LYS	1	0.824	0.887	23.545	-10.759	-10.759	0.000	0.000	0.000	0.000
72	C	73	ASN	0	-0.107	-0.054	22.974	-0.651	-0.651	0.000	0.000	0.000	0.000
73	C	74	VAL	0	0.041	0.047	17.535	-0.037	-0.037	0.000	0.000	0.000	0.000
74	C	75	GLY	0	0.006	0.012	21.018	-0.130	-0.130	0.000	0.000	0.000	0.000
75	C	76	SER	0	-0.044	-0.004	20.663	0.421	0.421	0.000	0.000	0.000	0.000
76	C	77	PRO	0	0.059	0.018	15.733	0.403	0.403	0.000	0.000	0.000	0.000
77	C	78	TYR	0	0.007	-0.030	14.115	-0.233	-0.233	0.000	0.000	0.000	0.000
78	C	79	THR	0	0.042	0.018	19.456	-0.140	-0.140	0.000	0.000	0.000	0.000
79	C	80	ILE	0	0.027	0.029	21.318	-0.472	-0.472	0.000	0.000	0.000	0.000
80	C	81	TYR	0	-0.034	-0.024	14.508	-0.766	-0.766	0.000	0.000	0.000	0.000
81	C	82	PHE	0	0.066	0.022	19.367	-0.277	-0.277	0.000	0.000	0.000	0.000
82	C	83	SER	0	-0.047	-0.046	22.638	-0.723	-0.723	0.000	0.000	0.000	0.000
83	C	84	ARG	1	0.823	0.928	17.821	-16.346	-16.346	0.000	0.000	0.000	0.000
84	C	85	ASN	0	-0.034	-0.034	22.123	-0.911	-0.911	0.000	0.000	0.000	0.000
85	C	86	LEU	0	-0.009	0.013	25.785	-0.443	-0.443	0.000	0.000	0.000	0.000
86	C	87	PHE	0	0.011	-0.003	27.581	-0.338	-0.338	0.000	0.000	0.000	0.000
87	C	88	ASN	0	0.004	-0.003	28.664	-0.590	-0.590	0.000	0.000	0.000	0.000
88	C	89	LEU	0	0.054	0.032	24.239	-0.326	-0.326	0.000	0.000	0.000	0.000
89	C	90	TYR	0	0.005	0.003	28.710	-0.296	-0.296	0.000	0.000	0.000	0.000
90	C	91	LYS	1	0.935	0.976	31.434	-8.735	-8.735	0.000	0.000	0.000	0.000
91	C	92	ARG	1	0.891	0.927	28.323	-10.733	-10.733	0.000	0.000	0.000	0.000
92	C	93	THR	0	0.016	-0.002	30.198	-0.099	-0.099	0.000	0.000	0.000	0.000
93	C	94	TYR	0	0.040	0.009	32.713	-0.263	-0.263	0.000	0.000	0.000	0.000
94	C	95	LEU	0	-0.040	-0.024	36.096	-0.292	-0.292	0.000	0.000	0.000	0.000
95	C	96	LEU	0	-0.032	-0.002	33.380	-0.197	-0.197	0.000	0.000	0.000	0.000
96	C	97	VAL	0	-0.041	-0.001	34.188	0.045	0.045	0.000	0.000	0.000	0.000
97	C	98	ASP	-1	-0.779	-0.846	37.330	7.977	7.977	0.000	0.000	0.000	0.000
98	C	99	ASN	0	0.091	0.025	39.794	0.258	0.258	0.000	0.000	0.000	0.000
99	C	100	THR	0	0.011	0.002	40.365	-0.060	-0.060	0.000	0.000	0.000	0.000
100	C	101	THR	0	-0.062	-0.064	34.897	0.164	0.164	0.000	0.000	0.000	0.000
101	C	102	ARG	1	0.852	0.922	36.838	-7.702	-7.702	0.000	0.000	0.000	0.000
102	C	103	THR	0	-0.002	-0.006	38.597	0.022	0.022	0.000	0.000	0.000	0.000
103	C	104	LYS	1	0.909	0.960	35.468	-8.543	-8.543	0.000	0.000	0.000	0.000
104	C	105	LEU	0	0.038	0.019	32.215	0.170	0.170	0.000	0.000	0.000	0.000
105	C	106	ILE	0	0.015	0.026	35.136	0.128	0.128	0.000	0.000	0.000	0.000
106	C	107	ASN	0	-0.003	-0.014	37.668	-0.110	-0.110	0.000	0.000	0.000	0.000
107	C	108	MET	0	-0.042	-0.001	30.419	0.122	0.122	0.000	0.000	0.000	0.000
108	C	109	PHE	0	0.016	0.009	33.475	0.154	0.154	0.000	0.000	0.000	0.000
109	C	110	LYS	1	0.918	0.953	34.678	-7.719	-7.719	0.000	0.000	0.000	0.000
110	C	111	LEU	0	-0.008	-0.007	33.384	-0.019	-0.019	0.000	0.000	0.000	0.000
111	C	112	TRP	0	-0.040	-0.036	29.063	0.227	0.227	0.000	0.000	0.000	0.000
112	C	113	LEU	0	0.008	0.007	32.654	0.146	0.146	0.000	0.000	0.000	0.000
113	C	114	ASN	0	-0.023	-0.022	35.497	0.095	0.095	0.000	0.000	0.000	0.000
114	C	115	PRO	0	0.005	0.023	30.364	-0.062	-0.062	0.000	0.000	0.000	0.000
115	C	116	ASN	0	-0.060	-0.050	28.429	-0.174	-0.174	0.000	0.000	0.000	0.000
116	C	117	ASP	-1	-0.886	-0.924	32.953	8.186	8.186	0.000	0.000	0.000	0.000
117	C	118	THR	0	-0.025	-0.018	31.294	-0.110	-0.110	0.000	0.000	0.000	0.000
118	C	119	GLY	0	0.001	0.009	34.743	-0.074	-0.074	0.000	0.000	0.000	0.000
119	C	120	LEU	0	-0.035	-0.020	32.313	-0.118	-0.118	0.000	0.000	0.000	0.000
120	C	121	PRO	0	-0.035	-0.022	32.379	0.237	0.237	0.000	0.000	0.000	0.000
121	C	122	LEU	0	-0.044	-0.008	26.817	0.184	0.184	0.000	0.000	0.000	0.000
122	C	123	PHE	0	-0.028	-0.040	24.707	0.490	0.490	0.000	0.000	0.000	0.000
123	C	124	GLU	-1	-0.890	-0.934	27.971	10.725	10.725	0.000	0.000	0.000	0.000
124	C	125	GLY	0	0.015	0.008	29.543	0.159	0.159	0.000	0.000	0.000	0.000
125	C	126	SER	0	-0.041	-0.028	31.717	-0.120	-0.120	0.000	0.000	0.000	0.000
126	C	127	ALA	0	0.016	0.012	29.560	-0.170	-0.170	0.000	0.000	0.000	0.000
127	C	128	LEU	0	0.042	0.017	31.668	-0.189	-0.189	0.000	0.000	0.000	0.000
128	C	129	GLU	-1	-0.803	-0.912	34.121	8.378	8.378	0.000	0.000	0.000	0.000
129	C	130	LYS	1	0.870	0.940	33.911	-9.402	-9.402	0.000	0.000	0.000	0.000
130	C	131	ILE	0	-0.003	0.001	31.451	-0.152	-0.152	0.000	0.000	0.000	0.000
131	C	132	GLU	-1	-0.905	-0.944	36.063	7.781	7.781	0.000	0.000	0.000	0.000
132	C	133	GLN	0	0.030	0.005	39.243	-0.373	-0.373	0.000	0.000	0.000	0.000
133	C	134	PHE	0	-0.056	-0.027	37.267	-0.173	-0.173	0.000	0.000	0.000	0.000
134	C	135	LEU	0	0.014	0.000	37.555	-0.186	-0.186	0.000	0.000	0.000	0.000
135	C	136	ILE	0	-0.015	-0.013	41.188	-0.183	-0.183	0.000	0.000	0.000	0.000
136	C	137	LYS	1	0.855	0.931	42.863	-7.499	-7.499	0.000	0.000	0.000	0.000
137	C	138	ALA	0	-0.032	-0.004	42.149	-0.103	-0.103	0.000	0.000	0.000	0.000
138	C	139	SER	0	-0.046	-0.016	44.125	-0.034	-0.034	0.000	0.000	0.000	0.000
139	C	140	ALA	0	0.004	0.007	45.889	-0.140	-0.140	0.000	0.000	0.000	0.000
140	C	141	ALA	0	-0.020	-0.003	48.992	0.022	0.022	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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