FMO DATABASE

FMODB ID: 4J55N

Calculation Name: 1GZ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 1GZ2

Chain ID: A

ChEMBL ID:

UniProt ID: Q9PRS8

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	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	136
LigandCharge	SEP=-2
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1218827.623229
FMO2-HF: Nuclear repulsion	1165177.443578
FMO2-HF: Total energy	-53650.179651
FMO2-MP2: Total energy	-53804.261285

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(A:4:GLY)

Summations of interaction energy for fragment #1(A:4:GLY)

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.
-0.211	1.004	-0.015	-0.497	-0.703	0.001

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.001 / q_NPA : -0.013

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	A	6	GLY	0	0.045	0.028	3.793	-0.218	0.951	-0.014	-0.490	-0.665	0.001
4	A	7	PRO	0	0.028	0.005	6.525	0.061	0.061	0.000	0.000	0.000	0.000
5	A	8	GLY	0	0.056	0.031	9.284	0.082	0.082	0.000	0.000	0.000	0.000
6	A	9	TRP	0	-0.098	-0.049	7.752	0.188	0.188	0.000	0.000	0.000	0.000
7	A	10	VAL	0	0.047	0.027	7.631	-0.230	-0.230	0.000	0.000	0.000	0.000
8	A	11	PRO	0	0.020	0.003	4.328	0.008	0.054	-0.001	-0.007	-0.038	0.000
9	A	12	THR	0	0.055	0.024	6.113	0.246	0.246	0.000	0.000	0.000	0.000
10	A	13	PRO	0	-0.066	-0.022	7.644	0.069	0.069	0.000	0.000	0.000	0.000
11	A	14	GLY	0	-0.015	-0.027	8.326	-0.025	-0.025	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.012	0.017	6.508	0.199	0.199	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.019	-0.015	7.194	0.227	0.227	0.000	0.000	0.000	0.000
14	A	18	GLY	0	0.111	0.056	10.332	-0.146	-0.146	0.000	0.000	0.000	0.000
15	A	19	PHE	0	0.021	0.011	12.770	0.085	0.085	0.000	0.000	0.000	0.000
16	A	20	PHE	0	0.022	-0.008	14.851	0.000	0.000	0.000	0.000	0.000	0.000
17	A	21	SER	0	0.119	0.051	19.157	0.018	0.018	0.000	0.000	0.000	0.000
18	A	22	ARG	1	0.866	0.967	19.617	0.189	0.189	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.857	-0.938	24.147	-0.092	-0.092	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.084	-0.047	23.579	0.010	0.010	0.000	0.000	0.000	0.000
21	A	25	SER	0	0.014	0.019	27.101	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	26	TRP	0	0.040	0.015	23.884	0.000	0.000	0.000	0.000	0.000	0.000
23	A	27	SER	0	0.000	-0.011	25.160	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.966	0.973	25.633	0.051	0.051	0.000	0.000	0.000	0.000
25	A	29	ALA	0	0.039	0.041	22.227	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.654	-0.805	20.987	-0.043	-0.043	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.054	-0.042	20.916	0.006	0.006	0.000	0.000	0.000	0.000
28	A	32	PHE	0	-0.065	-0.041	17.865	0.011	0.011	0.000	0.000	0.000	0.000
29	A	33	CYS	0	-0.064	-0.002	14.220	0.033	0.033	0.000	0.000	0.000	0.000
30	A	34	ARG	1	0.898	0.934	16.731	0.005	0.005	0.000	0.000	0.000	0.000
31	A	35	ARG	1	0.870	0.947	18.470	0.092	0.092	0.000	0.000	0.000	0.000
32	A	36	TRP	0	-0.023	0.012	13.137	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.015	0.018	14.432	0.012	0.012	0.000	0.000	0.000	0.000
34	A	38	PRO	0	-0.030	-0.039	15.887	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.049	0.034	14.109	0.035	0.035	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.034	-0.002	13.627	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	41	HIS	0	-0.055	-0.046	14.640	0.025	0.025	0.000	0.000	0.000	0.000
38	A	42	LEU	0	-0.001	0.001	16.001	-0.030	-0.030	0.000	0.000	0.000	0.000
39	A	43	ALA	0	-0.009	-0.011	15.185	0.021	0.021	0.000	0.000	0.000	0.000
40	A	44	ALA	0	0.014	0.014	16.207	0.006	0.006	0.000	0.000	0.000	0.000
41	A	45	VAL	0	-0.004	-0.012	16.376	-0.011	-0.011	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.858	0.908	12.542	-0.052	-0.052	0.000	0.000	0.000	0.000
43	A	47	SER	0	-0.022	-0.019	16.912	0.006	0.006	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.044	0.019	19.085	-0.011	-0.011	0.000	0.000	0.000	0.000
45	A	49	ALA	0	-0.002	0.000	16.398	-0.011	-0.011	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.749	-0.880	13.624	-0.048	-0.048	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.040	-0.022	15.608	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	52	ARG	1	0.954	0.974	17.867	0.069	0.069	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.079	0.054	11.151	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	54	LEU	0	-0.051	-0.030	14.757	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	55	ALA	0	-0.014	-0.009	16.044	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.880	-0.932	15.261	-0.223	-0.223	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.062	-0.026	12.781	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.092	-0.060	15.743	0.004	0.004	0.000	0.000	0.000	0.000
55	A	59	ASN	0	-0.054	-0.037	18.966	0.014	0.014	0.000	0.000	0.000	0.000
56	A	60	ALA	0	-0.022	0.013	18.766	0.006	0.006	0.000	0.000	0.000	0.000
57	A	61	SEP	-2	-1.772	-1.866	19.685	-0.311	-0.311	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.914	0.964	17.170	0.213	0.213	0.000	0.000	0.000	0.000
59	A	63	GLY	0	-0.045	-0.056	16.497	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.025	0.021	15.519	0.007	0.007	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.912	-0.949	10.963	-0.597	-0.597	0.000	0.000	0.000	0.000
62	A	66	GLY	0	-0.023	-0.032	12.996	0.019	0.019	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.071	-0.040	14.891	0.050	0.050	0.000	0.000	0.000	0.000
64	A	68	GLY	0	-0.023	-0.010	15.952	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.888	-0.924	16.948	-0.213	-0.213	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.009	0.002	18.800	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	71	ALA	0	-0.127	-0.076	20.847	0.009	0.009	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.866	-0.928	22.698	-0.126	-0.126	0.000	0.000	0.000	0.000
69	A	73	GLY	0	-0.011	-0.009	25.728	0.012	0.012	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.819	0.908	25.578	0.066	0.066	0.000	0.000	0.000	0.000
71	A	75	VAL	0	0.044	0.034	20.070	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	76	TRP	0	-0.127	-0.067	22.863	0.012	0.012	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.063	0.031	19.682	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	78	GLY	0	0.058	0.010	20.022	0.009	0.009	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.049	0.001	21.371	0.014	0.014	0.000	0.000	0.000	0.000
76	A	80	HIS	0	-0.008	-0.030	24.499	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	81	ARG	1	0.922	0.971	27.808	0.020	0.020	0.000	0.000	0.000	0.000
78	A	82	PRO	0	-0.004	-0.007	29.699	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	83	ALA	0	0.016	-0.002	32.267	0.000	0.000	0.000	0.000	0.000	0.000
80	A	84	GLY	0	0.057	0.031	35.966	0.002	0.002	0.000	0.000	0.000	0.000
81	A	85	SER	0	-0.043	-0.013	33.629	0.003	0.003	0.000	0.000	0.000	0.000
82	A	86	ARG	1	0.989	0.980	35.608	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	87	SER	0	-0.002	-0.001	31.837	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	88	TRP	0	-0.034	-0.008	28.340	0.000	0.000	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.947	0.972	26.086	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	90	TRP	0	0.051	0.039	20.855	-0.013	-0.013	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.100	-0.063	20.727	0.011	0.011	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.775	-0.878	16.842	0.029	0.029	0.000	0.000	0.000	0.000
89	A	93	GLY	0	-0.023	0.001	18.892	0.019	0.019	0.000	0.000	0.000	0.000
90	A	94	THR	0	-0.086	-0.053	17.609	0.004	0.004	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.008	-0.001	20.836	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	96	PRO	0	-0.038	-0.020	22.964	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	97	ARG	1	0.960	0.968	22.200	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	98	PHE	0	0.010	0.008	21.661	0.000	0.000	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.022	-0.025	23.829	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	100	SER	0	-0.028	-0.006	24.891	0.004	0.004	0.000	0.000	0.000	0.000
97	A	101	TRP	0	0.006	0.005	26.552	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	102	HIS	0	0.126	0.055	29.371	0.005	0.005	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.917	0.938	31.339	0.031	0.031	0.000	0.000	0.000	0.000
100	A	104	THR	0	0.034	0.030	34.365	0.002	0.002	0.000	0.000	0.000	0.000
101	A	105	ALA	0	0.054	0.014	36.403	0.000	0.000	0.000	0.000	0.000	0.000
102	A	106	LYS	1	0.945	0.956	37.898	0.037	0.037	0.000	0.000	0.000	0.000
103	A	107	ALA	0	0.048	0.044	32.853	0.000	0.000	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.929	0.966	33.106	0.025	0.025	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.914	0.968	34.766	0.028	0.028	0.000	0.000	0.000	0.000
106	A	110	GLY	0	0.041	0.020	36.158	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	111	GLY	0	-0.009	-0.007	34.098	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	112	ARG	1	0.888	0.950	32.559	0.024	0.024	0.000	0.000	0.000	0.000
109	A	113	CYS	0	-0.026	-0.003	27.889	0.002	0.002	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.047	0.023	25.718	0.001	0.001	0.000	0.000	0.000	0.000
111	A	115	ALA	0	-0.018	0.003	24.867	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	116	LEU	0	0.002	-0.012	20.090	0.011	0.011	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.755	0.846	24.521	0.059	0.059	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.793	-0.888	26.265	-0.090	-0.090	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.910	-0.959	27.425	-0.068	-0.068	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.853	-0.914	28.207	-0.060	-0.060	0.000	0.000	0.000	0.000
117	A	121	ALA	0	0.061	0.043	24.734	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	122	PHE	0	0.021	0.009	21.744	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	123	THR	0	-0.009	-0.005	22.203	0.000	0.000	0.000	0.000	0.000	0.000
120	A	124	SER	0	-0.043	-0.021	24.428	0.012	0.012	0.000	0.000	0.000	0.000
121	A	125	TRP	0	0.063	0.041	22.218	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	126	ALA	0	-0.031	-0.022	27.024	0.007	0.007	0.000	0.000	0.000	0.000
123	A	127	ALA	0	-0.057	-0.019	29.352	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.813	0.888	29.915	0.054	0.054	0.000	0.000	0.000	0.000
125	A	129	PRO	0	0.031	0.004	32.115	0.003	0.003	0.000	0.000	0.000	0.000
126	A	131	THR	0	-0.003	-0.005	30.579	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.756	-0.844	31.141	-0.060	-0.060	0.000	0.000	0.000	0.000
128	A	133	ARG	1	0.881	0.931	29.343	0.072	0.072	0.000	0.000	0.000	0.000
129	A	134	ASN	0	0.054	0.032	26.437	0.001	0.001	0.000	0.000	0.000	0.000
130	A	135	ALA	0	0.107	0.082	22.574	0.000	0.000	0.000	0.000	0.000	0.000
131	A	136	PHE	0	-0.069	-0.064	19.069	0.014	0.014	0.000	0.000	0.000	0.000
132	A	137	VAL	0	0.076	0.045	15.008	-0.018	-0.018	0.000	0.000	0.000	0.000
133	A	139	LYS	1	0.947	0.975	11.083	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	140	ALA	0	0.006	0.008	9.359	0.065	0.065	0.000	0.000	0.000	0.000
135	A	141	ALA	0	-0.041	-0.029	8.747	0.015	0.015	0.000	0.000	0.000	0.000
136	A	142	ALA	0	0.001	-0.002	7.112	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)