FMO DATABASE

FMODB ID: YV4J2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1220932.317779
FMO2-HF: Nuclear repulsion	1167281.541949
FMO2-HF: Total energy	-53650.775829
FMO2-MP2: Total energy	-53804.773459

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.
-1.007	-0.097	-0.002	-0.406	-0.502	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 : 0.008 / q_NPA : -0.011

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	0.040	0.029	3.846	-0.560	0.350	-0.002	-0.406	-0.502	0.001
4	A	7	PRO	0	0.034	0.007	6.501	0.408	0.408	0.000	0.000	0.000	0.000
5	A	8	GLY	0	0.032	0.013	9.440	-0.097	-0.097	0.000	0.000	0.000	0.000
6	A	9	TRP	0	-0.136	-0.066	8.076	-0.041	-0.041	0.000	0.000	0.000	0.000
7	A	10	VAL	0	0.038	0.029	8.130	0.173	0.173	0.000	0.000	0.000	0.000
8	A	11	PRO	0	0.043	0.004	5.263	-0.236	-0.236	0.000	0.000	0.000	0.000
9	A	12	THR	0	0.003	0.006	6.907	-0.456	-0.456	0.000	0.000	0.000	0.000
10	A	13	PRO	0	-0.018	-0.017	8.221	0.023	0.023	0.000	0.000	0.000	0.000
11	A	14	GLY	0	0.013	0.008	8.752	-0.106	-0.106	0.000	0.000	0.000	0.000
12	A	15	GLY	0	0.006	0.007	6.899	-0.232	-0.232	0.000	0.000	0.000	0.000
13	A	17	LEU	0	-0.015	-0.016	7.529	-0.187	-0.187	0.000	0.000	0.000	0.000
14	A	18	GLY	0	0.107	0.052	10.720	0.027	0.027	0.000	0.000	0.000	0.000
15	A	19	PHE	0	0.008	0.006	13.146	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	20	PHE	0	0.031	-0.006	14.867	-0.024	-0.024	0.000	0.000	0.000	0.000
17	A	21	SER	0	0.117	0.058	19.616	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	22	ARG	1	0.862	0.956	19.162	0.119	0.119	0.000	0.000	0.000	0.000
19	A	23	GLU	-1	-0.766	-0.873	24.601	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	24	LEU	0	-0.075	-0.040	23.833	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	25	SER	0	0.018	0.017	27.414	0.005	0.005	0.000	0.000	0.000	0.000
22	A	26	TRP	0	0.013	0.000	24.046	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	27	SER	0	0.026	0.003	25.180	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.943	0.980	25.964	0.054	0.054	0.000	0.000	0.000	0.000
25	A	29	ALA	0	0.036	0.032	22.486	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	30	GLU	-1	-0.671	-0.791	20.912	-0.115	-0.115	0.000	0.000	0.000	0.000
27	A	31	SER	0	-0.047	-0.050	20.875	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	32	PHE	0	-0.067	-0.036	17.668	-0.014	-0.014	0.000	0.000	0.000	0.000
29	A	33	CYS	0	-0.059	0.006	14.506	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	34	ARG	1	0.892	0.935	16.621	0.080	0.080	0.000	0.000	0.000	0.000
31	A	35	ARG	1	0.874	0.949	18.354	0.143	0.143	0.000	0.000	0.000	0.000
32	A	36	TRP	0	-0.005	0.007	12.352	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	37	GLY	0	0.024	0.023	14.090	-0.081	-0.081	0.000	0.000	0.000	0.000
34	A	38	PRO	0	-0.011	-0.027	15.578	0.040	0.040	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.035	0.029	14.018	-0.050	-0.050	0.000	0.000	0.000	0.000
36	A	40	SER	0	-0.049	-0.015	13.373	0.001	0.001	0.000	0.000	0.000	0.000
37	A	41	HIS	0	-0.048	-0.044	14.613	0.008	0.008	0.000	0.000	0.000	0.000
38	A	42	LEU	0	0.007	-0.013	16.298	0.002	0.002	0.000	0.000	0.000	0.000
39	A	43	ALA	0	-0.002	-0.003	15.946	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	44	ALA	0	0.007	0.007	16.944	0.010	0.010	0.000	0.000	0.000	0.000
41	A	45	VAL	0	0.009	0.002	16.953	0.024	0.024	0.000	0.000	0.000	0.000
42	A	46	ARG	1	0.829	0.879	12.693	-0.111	-0.111	0.000	0.000	0.000	0.000
43	A	47	SER	0	-0.006	-0.018	17.548	0.001	0.001	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.034	0.012	19.640	0.008	0.008	0.000	0.000	0.000	0.000
45	A	49	ALA	0	0.006	0.007	16.898	0.006	0.006	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.742	-0.848	14.307	0.196	0.196	0.000	0.000	0.000	0.000
47	A	51	LEU	0	-0.045	-0.026	16.259	0.003	0.003	0.000	0.000	0.000	0.000
48	A	52	ARG	1	0.913	0.981	18.497	-0.228	-0.228	0.000	0.000	0.000	0.000
49	A	53	LEU	0	0.081	0.046	11.923	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	54	LEU	0	-0.059	-0.031	15.278	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	55	ALA	0	-0.001	-0.004	16.885	-0.019	-0.019	0.000	0.000	0.000	0.000
52	A	56	GLU	-1	-0.858	-0.942	15.829	0.421	0.421	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.068	-0.029	13.406	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	58	LEU	0	-0.054	-0.032	16.312	-0.040	-0.040	0.000	0.000	0.000	0.000
55	A	59	ASN	0	-0.097	-0.065	19.785	-0.041	-0.041	0.000	0.000	0.000	0.000
56	A	60	ALA	0	-0.002	0.012	19.209	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	61	SEP	-2	-1.775	-1.856	20.289	0.408	0.408	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.917	0.945	17.501	-0.283	-0.283	0.000	0.000	0.000	0.000
59	A	63	GLY	0	-0.034	-0.021	17.006	0.050	0.050	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.028	0.014	15.300	-0.046	-0.046	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.886	-0.946	11.064	0.143	0.143	0.000	0.000	0.000	0.000
62	A	66	GLY	0	-0.013	-0.016	13.098	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	67	SER	0	-0.093	-0.054	15.334	-0.026	-0.026	0.000	0.000	0.000	0.000
64	A	68	GLY	0	-0.032	-0.004	15.740	-0.034	-0.034	0.000	0.000	0.000	0.000
65	A	69	GLU	-1	-0.905	-0.939	16.735	0.102	0.102	0.000	0.000	0.000	0.000
66	A	70	GLY	0	0.040	0.021	19.316	0.003	0.003	0.000	0.000	0.000	0.000
67	A	71	ALA	0	-0.074	-0.046	21.258	-0.023	-0.023	0.000	0.000	0.000	0.000
68	A	72	ASP	-1	-0.907	-0.956	23.482	0.041	0.041	0.000	0.000	0.000	0.000
69	A	73	GLY	0	-0.011	-0.014	26.415	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	74	ARG	1	0.810	0.906	25.943	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	75	VAL	0	0.019	0.027	20.593	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	76	TRP	0	-0.137	-0.076	23.236	0.008	0.008	0.000	0.000	0.000	0.000
73	A	77	ILE	0	0.078	0.038	19.923	0.001	0.001	0.000	0.000	0.000	0.000
74	A	78	GLY	0	0.051	0.024	20.527	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	79	LEU	0	-0.059	-0.001	21.756	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	80	HIS	0	-0.010	-0.035	24.961	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	81	ARG	1	0.907	0.946	28.055	0.005	0.005	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.003	0.009	29.788	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	83	ALA	0	0.039	0.015	32.492	0.004	0.004	0.000	0.000	0.000	0.000
80	A	84	GLY	0	0.041	0.024	36.072	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	85	SER	0	-0.023	0.003	33.458	0.001	0.001	0.000	0.000	0.000	0.000
82	A	86	ARG	1	0.987	0.994	35.450	0.008	0.008	0.000	0.000	0.000	0.000
83	A	87	SER	0	0.024	0.008	32.200	0.003	0.003	0.000	0.000	0.000	0.000
84	A	88	TRP	0	-0.006	-0.003	28.846	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.911	0.959	26.524	0.034	0.034	0.000	0.000	0.000	0.000
86	A	90	TRP	0	0.054	0.042	21.066	0.001	0.001	0.000	0.000	0.000	0.000
87	A	91	SER	0	-0.074	-0.057	20.945	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	92	ASP	-1	-0.772	-0.872	16.953	-0.043	-0.043	0.000	0.000	0.000	0.000
89	A	93	GLY	0	-0.032	-0.006	19.107	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	94	THR	0	-0.090	-0.064	17.619	0.015	0.015	0.000	0.000	0.000	0.000
91	A	95	ALA	0	0.027	0.004	20.925	0.003	0.003	0.000	0.000	0.000	0.000
92	A	96	PRO	0	-0.043	-0.022	23.018	0.009	0.009	0.000	0.000	0.000	0.000
93	A	97	ARG	1	0.968	0.975	22.453	-0.074	-0.074	0.000	0.000	0.000	0.000
94	A	98	PHE	0	-0.007	-0.002	22.127	0.008	0.008	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.033	-0.026	24.620	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	100	SER	0	-0.010	-0.002	25.353	0.002	0.002	0.000	0.000	0.000	0.000
97	A	101	TRP	0	0.011	0.005	26.995	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	102	HIS	0	0.109	0.078	29.854	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	103	ARG	1	0.932	0.967	32.001	-0.062	-0.062	0.000	0.000	0.000	0.000
100	A	104	THR	0	0.030	0.006	35.173	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	105	ALA	0	0.032	0.007	36.913	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	106	LYS	1	0.948	0.982	38.385	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	107	ALA	0	0.056	0.034	33.308	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	108	ARG	1	0.878	0.925	32.989	-0.039	-0.039	0.000	0.000	0.000	0.000
105	A	109	ARG	1	0.901	0.945	35.193	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	110	GLY	0	0.030	0.018	36.506	0.001	0.001	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.004	-0.001	34.215	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	112	ARG	1	0.844	0.919	32.788	0.021	0.021	0.000	0.000	0.000	0.000
109	A	113	CYS	0	-0.054	-0.010	27.919	-0.006	-0.006	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.046	0.023	26.041	0.003	0.003	0.000	0.000	0.000	0.000
111	A	115	ALA	0	-0.001	0.004	25.275	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	116	LEU	0	0.012	0.001	20.434	0.000	0.000	0.000	0.000	0.000	0.000
113	A	117	ARG	1	0.678	0.786	24.974	-0.058	-0.058	0.000	0.000	0.000	0.000
114	A	118	ASP	-1	-0.769	-0.886	27.118	0.058	0.058	0.000	0.000	0.000	0.000
115	A	119	GLU	-1	-0.848	-0.914	28.053	0.047	0.047	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.774	-0.842	28.879	0.063	0.063	0.000	0.000	0.000	0.000
117	A	121	ALA	0	0.081	0.056	25.542	0.010	0.010	0.000	0.000	0.000	0.000
118	A	122	PHE	0	-0.006	-0.009	22.466	0.013	0.013	0.000	0.000	0.000	0.000
119	A	123	THR	0	-0.022	-0.020	23.153	0.006	0.006	0.000	0.000	0.000	0.000
120	A	124	SER	0	-0.047	-0.044	25.053	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	125	TRP	0	0.071	0.043	22.794	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	126	ALA	0	-0.005	-0.007	27.636	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	127	ALA	0	-0.065	-0.020	29.708	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	128	ARG	1	0.837	0.890	30.509	-0.009	-0.009	0.000	0.000	0.000	0.000
125	A	129	PRO	0	0.045	0.001	32.408	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	131	THR	0	0.018	-0.003	30.544	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	132	GLU	-1	-0.758	-0.829	31.694	0.002	0.002	0.000	0.000	0.000	0.000
128	A	133	ARG	1	0.804	0.882	29.401	0.028	0.028	0.000	0.000	0.000	0.000
129	A	134	ASN	0	0.043	0.018	27.116	0.010	0.010	0.000	0.000	0.000	0.000
130	A	135	ALA	0	0.096	0.069	23.413	-0.012	-0.012	0.000	0.000	0.000	0.000
131	A	136	PHE	0	-0.066	-0.058	19.350	0.000	0.000	0.000	0.000	0.000	0.000
132	A	137	VAL	0	0.081	0.047	15.692	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	139	LYS	1	0.862	0.917	11.668	-0.051	-0.051	0.000	0.000	0.000	0.000
134	A	140	ALA	0	0.005	0.013	9.530	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	141	ALA	0	-0.031	-0.019	8.898	-0.015	-0.015	0.000	0.000	0.000	0.000
136	A	142	ALA	0	-0.001	-0.002	7.009	-0.095	-0.095	0.000	0.000	0.000	0.000

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