FMO DATABASE

FMODB ID: 5J44Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1218425.963467
FMO2-HF: Nuclear repulsion	1164775.479821
FMO2-HF: Total energy	-53650.483646
FMO2-MP2: Total energy	-53804.501448

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.
-1.489	-0.312	-0.016	-0.496	-0.664	0.002

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 : 0.000 / 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	0.044	0.026	3.793	-0.442	0.703	-0.015	-0.493	-0.637	0.002
4	A	7	PRO	0	0.038	0.006	6.525	0.370	0.370	0.000	0.000	0.000	0.000
5	A	8	GLY	0	0.041	0.028	9.287	-0.033	-0.033	0.000	0.000	0.000	0.000
6	A	9	TRP	0	-0.105	-0.054	7.851	0.078	0.078	0.000	0.000	0.000	0.000
7	A	10	VAL	0	0.049	0.028	7.635	0.056	0.056	0.000	0.000	0.000	0.000
8	A	11	PRO	0	0.029	0.010	5.263	-0.068	-0.036	-0.001	-0.003	-0.027	0.000
9	A	12	THR	0	0.011	0.011	7.104	-0.574	-0.574	0.000	0.000	0.000	0.000
10	A	13	PRO	0	-0.007	-0.010	8.515	0.219	0.219	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.000	-0.009	8.856	-0.197	-0.197	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.008	0.015	6.612	-0.322	-0.322	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.017	-0.016	7.797	-0.241	-0.241	0.000	0.000	0.000	0.000
14	A	18	GLY	0	0.108	0.054	10.904	-0.037	-0.037	0.000	0.000	0.000	0.000
15	A	19	PHE	0	0.003	0.006	13.213	0.006	0.006	0.000	0.000	0.000	0.000
16	A	20	PHE	0	0.032	-0.004	14.837	-0.033	-0.033	0.000	0.000	0.000	0.000
17	A	21	SER	0	0.122	0.053	19.348	0.008	0.008	0.000	0.000	0.000	0.000
18	A	22	ARG	1	0.862	0.960	19.374	0.118	0.118	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.858	-0.930	24.406	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.060	-0.030	23.962	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	25	SER	0	0.020	0.019	27.452	0.006	0.006	0.000	0.000	0.000	0.000
22	A	26	TRP	0	0.038	0.009	24.014	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	27	SER	0	0.012	-0.004	25.381	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.957	0.979	25.662	0.043	0.043	0.000	0.000	0.000	0.000
25	A	29	ALA	0	0.036	0.037	22.629	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.649	-0.792	20.954	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.062	-0.052	20.859	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	32	PHE	0	-0.053	-0.035	17.833	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	33	CYS	0	-0.064	0.004	14.622	-0.022	-0.022	0.000	0.000	0.000	0.000
30	A	34	ARG	1	0.885	0.934	16.525	0.026	0.026	0.000	0.000	0.000	0.000
31	A	35	ARG	1	0.870	0.948	17.990	0.119	0.119	0.000	0.000	0.000	0.000
32	A	36	TRP	0	-0.019	0.004	12.817	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.020	0.022	13.798	-0.079	-0.079	0.000	0.000	0.000	0.000
34	A	38	PRO	0	-0.025	-0.038	15.010	0.039	0.039	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.046	0.035	13.573	-0.038	-0.038	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.040	-0.012	13.186	0.045	0.045	0.000	0.000	0.000	0.000
37	A	41	HIS	0	-0.062	-0.053	14.415	-0.010	-0.010	0.000	0.000	0.000	0.000
38	A	42	LEU	0	0.009	0.002	16.218	0.010	0.010	0.000	0.000	0.000	0.000
39	A	43	ALA	0	-0.015	-0.015	15.848	0.008	0.008	0.000	0.000	0.000	0.000
40	A	44	ALA	0	0.016	0.021	16.690	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	45	VAL	0	0.015	0.001	17.052	0.041	0.041	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.832	0.879	12.741	-0.375	-0.375	0.000	0.000	0.000	0.000
43	A	47	SER	0	-0.010	-0.014	17.905	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.046	0.019	20.069	0.007	0.007	0.000	0.000	0.000	0.000
45	A	49	ALA	0	0.004	0.001	17.393	0.001	0.001	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.731	-0.850	14.602	0.398	0.398	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.045	-0.025	16.605	0.004	0.004	0.000	0.000	0.000	0.000
48	A	52	ARG	1	0.943	0.974	18.884	-0.274	-0.274	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.062	0.049	12.221	0.010	0.010	0.000	0.000	0.000	0.000
50	A	54	LEU	0	-0.058	-0.032	15.652	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	55	ALA	0	-0.012	-0.008	17.032	-0.028	-0.028	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.856	-0.927	15.801	0.427	0.427	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.060	-0.024	13.128	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.085	-0.055	16.103	-0.044	-0.044	0.000	0.000	0.000	0.000
55	A	59	ASN	0	-0.071	-0.053	19.401	-0.042	-0.042	0.000	0.000	0.000	0.000
56	A	60	ALA	0	-0.014	0.015	18.648	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	61	SEP	-2	-1.754	-1.847	19.685	0.376	0.376	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.911	0.940	17.016	-0.220	-0.220	0.000	0.000	0.000	0.000
59	A	63	GLY	0	-0.055	-0.040	16.452	0.037	0.037	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.023	0.024	15.563	-0.022	-0.022	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.915	-0.957	10.900	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	66	GLY	0	-0.020	-0.024	12.998	-0.029	-0.029	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.076	-0.044	14.893	0.003	0.003	0.000	0.000	0.000	0.000
64	A	68	GLY	0	-0.013	-0.001	15.955	-0.027	-0.027	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.913	-0.941	16.949	0.046	0.046	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.031	0.015	18.801	0.008	0.008	0.000	0.000	0.000	0.000
67	A	71	ALA	0	-0.115	-0.072	20.848	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.879	-0.937	22.914	0.037	0.037	0.000	0.000	0.000	0.000
69	A	73	GLY	0	-0.021	-0.014	26.123	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.853	0.927	26.185	-0.022	-0.022	0.000	0.000	0.000	0.000
71	A	75	VAL	0	0.025	0.027	20.915	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	76	TRP	0	-0.127	-0.063	23.477	0.014	0.014	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.066	0.032	20.398	0.005	0.005	0.000	0.000	0.000	0.000
74	A	78	GLY	0	0.059	0.013	20.565	-0.017	-0.017	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.060	0.000	21.790	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	80	HIS	0	-0.013	-0.031	24.971	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	81	ARG	1	0.909	0.961	28.187	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.013	0.003	29.819	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	83	ALA	0	0.004	-0.004	32.415	0.003	0.003	0.000	0.000	0.000	0.000
80	A	84	GLY	0	0.054	0.029	36.106	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	85	SER	0	-0.027	0.000	33.851	0.001	0.001	0.000	0.000	0.000	0.000
82	A	86	ARG	1	0.982	0.976	35.778	-0.018	-0.018	0.000	0.000	0.000	0.000
83	A	87	SER	0	0.015	0.008	32.281	0.002	0.002	0.000	0.000	0.000	0.000
84	A	88	TRP	0	-0.036	-0.011	28.924	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.937	0.968	26.651	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	90	TRP	0	0.060	0.040	21.160	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.095	-0.064	21.006	0.000	0.000	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.778	-0.878	17.039	0.086	0.086	0.000	0.000	0.000	0.000
89	A	93	GLY	0	-0.020	0.002	18.803	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	94	THR	0	-0.089	-0.054	17.785	0.011	0.011	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.007	0.000	20.964	-0.008	-0.008	0.000	0.000	0.000	0.000
92	A	96	PRO	0	-0.028	-0.018	23.320	0.014	0.014	0.000	0.000	0.000	0.000
93	A	97	ARG	1	0.957	0.968	22.771	-0.141	-0.141	0.000	0.000	0.000	0.000
94	A	98	PHE	0	0.000	0.004	22.329	0.002	0.002	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.015	-0.020	24.568	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	100	SER	0	-0.026	-0.002	25.883	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	101	TRP	0	0.010	0.005	27.535	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	102	HIS	0	0.131	0.071	30.302	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.921	0.944	32.338	-0.086	-0.086	0.000	0.000	0.000	0.000
100	A	104	THR	0	0.025	0.014	35.368	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	105	ALA	0	0.032	0.003	37.328	0.000	0.000	0.000	0.000	0.000	0.000
102	A	106	LYS	1	0.954	0.966	38.774	-0.034	-0.034	0.000	0.000	0.000	0.000
103	A	107	ALA	0	0.063	0.051	33.818	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.876	0.941	33.388	-0.066	-0.066	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.910	0.962	35.549	-0.033	-0.033	0.000	0.000	0.000	0.000
106	A	110	GLY	0	0.047	0.024	36.890	0.001	0.001	0.000	0.000	0.000	0.000
107	A	111	GLY	0	-0.013	-0.007	34.668	-0.003	-0.003	0.000	0.000	0.000	0.000
108	A	112	ARG	1	0.892	0.951	33.009	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	113	CYS	0	-0.036	-0.011	28.367	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.047	0.025	26.362	0.000	0.000	0.000	0.000	0.000	0.000
111	A	115	ALA	0	-0.012	0.005	25.632	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	116	LEU	0	0.004	-0.012	21.087	0.000	0.000	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.659	0.788	25.472	-0.079	-0.079	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.799	-0.899	27.135	0.070	0.070	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.837	-0.913	28.139	0.063	0.063	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.798	-0.878	29.149	0.083	0.083	0.000	0.000	0.000	0.000
117	A	121	ALA	0	0.063	0.045	25.342	0.011	0.011	0.000	0.000	0.000	0.000
118	A	122	PHE	0	0.019	0.013	22.637	0.018	0.018	0.000	0.000	0.000	0.000
119	A	123	THR	0	-0.002	-0.007	23.199	0.016	0.016	0.000	0.000	0.000	0.000
120	A	124	SER	0	-0.053	-0.039	25.433	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	125	TRP	0	0.068	0.043	23.178	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	126	ALA	0	-0.020	-0.016	27.968	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	127	ALA	0	-0.065	-0.022	30.129	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.820	0.881	30.747	-0.030	-0.030	0.000	0.000	0.000	0.000
125	A	129	PRO	0	0.037	0.004	32.673	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	131	THR	0	0.003	-0.005	30.930	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.759	-0.838	31.819	0.017	0.017	0.000	0.000	0.000	0.000
128	A	133	ARG	1	0.857	0.912	29.574	0.025	0.025	0.000	0.000	0.000	0.000
129	A	134	ASN	0	0.042	0.020	27.215	0.005	0.005	0.000	0.000	0.000	0.000
130	A	135	ALA	0	0.104	0.081	23.090	-0.010	-0.010	0.000	0.000	0.000	0.000
131	A	136	PHE	0	-0.054	-0.060	19.320	0.003	0.003	0.000	0.000	0.000	0.000
132	A	137	VAL	0	0.076	0.044	15.778	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	139	LYS	1	0.888	0.935	11.621	-0.283	-0.283	0.000	0.000	0.000	0.000
134	A	140	ALA	0	0.001	0.005	9.389	-0.036	-0.036	0.000	0.000	0.000	0.000
135	A	141	ALA	0	-0.037	-0.027	8.702	0.073	0.073	0.000	0.000	0.000	0.000
136	A	142	ALA	0	0.003	0.000	6.544	-0.167	-0.167	0.000	0.000	0.000	0.000

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