FMO DATABASE

FMODB ID: R88Q8

Calculation Name: 4KK4-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 4KK4

Chain ID: A

ChEMBL ID:

UniProt ID: P39155

Base Structure: X-ray

Registration Date: 2023-09-21

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	152
LigandCharge	SEP=-2
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1513598.33243
FMO2-HF: Nuclear repulsion	1453291.653365
FMO2-HF: Total energy	-60306.679066
FMO2-MP2: Total energy	-60481.730186

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:1:MET)

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

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.
-38.446	-30.655	22.658	-12.599	-17.851	-0.073

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : 0.008

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	3	ILE	0	-0.022	-0.012	3.135	-2.883	-1.003	0.046	-0.676	-1.250	0.003
4	A	4	ILE	0	0.016	0.011	5.908	0.399	0.399	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.010	0.002	9.554	-0.083	-0.083	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.019	-0.003	12.416	0.002	0.002	0.000	0.000	0.000	0.000
7	A	7	SEP	-2	-1.556	-1.702	15.464	0.314	0.314	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.020	0.004	19.140	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.026	-0.007	22.731	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.019	0.010	17.239	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.008	0.008	20.721	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.032	-0.007	22.002	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.796	0.850	19.238	-0.132	-0.132	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.006	-0.008	15.922	0.022	0.022	0.000	0.000	0.000	0.000
15	A	15	PRO	0	0.025	0.021	15.726	0.034	0.034	0.000	0.000	0.000	0.000
16	A	16	MET	0	-0.023	-0.003	16.879	0.015	0.015	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.027	0.005	14.019	0.012	0.012	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.777	-0.859	12.139	0.500	0.500	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.001	-0.005	12.676	0.043	0.043	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.019	-0.017	14.993	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.021	-0.005	6.132	-0.018	-0.018	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.896	0.957	10.453	-0.516	-0.516	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.007	0.005	11.569	-0.037	-0.037	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.024	-0.024	11.978	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.028	0.011	8.382	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.887	-0.931	10.188	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.779	0.881	12.830	-0.193	-0.193	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.822	-0.893	11.275	0.390	0.390	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.029	0.024	11.254	0.028	0.028	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.078	-0.030	5.573	-0.046	-0.046	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.037	-0.031	2.723	-0.525	0.441	0.214	-0.344	-0.836	-0.003
32	A	32	VAL	0	-0.016	-0.012	2.468	-2.827	-0.083	1.334	-1.520	-2.558	-0.010
33	A	33	ASN	0	-0.030	-0.012	3.409	-3.344	-1.895	0.842	-0.632	-1.660	0.006
34	A	34	VAL	0	-0.041	-0.024	4.775	-0.860	-0.907	-0.001	0.026	0.022	0.000
35	A	35	ARG	1	0.838	0.893	7.455	-1.082	-1.082	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.051	-0.048	10.635	-0.091	-0.091	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.022	0.018	13.876	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.019	-0.016	16.491	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.005	-0.011	19.263	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	PHE	0	-0.041	-0.023	21.092	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	41	ALA	0	-0.006	0.019	21.567	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.009	0.001	23.508	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.030	0.008	22.250	0.006	0.006	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.089	-0.045	23.423	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.028	0.028	25.224	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.976	0.991	23.743	-0.078	-0.078	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.047	0.023	22.073	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.006	-0.012	24.040	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.018	-0.004	26.828	0.005	0.005	0.000	0.000	0.000	0.000
50	A	50	HIS	0	-0.015	-0.014	28.608	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.055	0.037	23.328	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.027	-0.023	24.061	0.009	0.009	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.820	-0.901	25.155	0.091	0.091	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.014	-0.003	24.951	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.002	0.002	19.137	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	PHE	0	-0.002	0.009	23.186	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.843	-0.906	25.867	0.088	0.088	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.720	0.845	22.021	-0.168	-0.168	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.030	-0.012	22.617	0.004	0.004	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.025	0.001	17.963	0.003	0.003	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.023	0.001	21.200	-0.002	-0.002	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.018	0.006	19.010	0.011	0.011	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.058	-0.036	20.487	-0.014	-0.014	0.000	0.000	0.000	0.000
64	A	64	HIS	0	-0.002	-0.016	16.256	0.019	0.019	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.041	-0.025	19.096	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.021	-0.019	19.121	0.017	0.017	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.012	-0.014	17.227	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	68	PRO	0	-0.018	-0.006	19.122	0.006	0.006	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.002	-0.003	14.175	0.021	0.021	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.020	-0.042	16.294	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.820	-0.931	15.667	0.009	0.009	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.844	-0.904	13.810	0.082	0.082	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.065	0.002	11.600	0.055	0.055	0.000	0.000	0.000	0.000
74	A	74	MET	0	0.002	0.003	10.716	-0.008	-0.008	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.988	-0.988	11.047	-0.172	-0.172	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.038	-0.004	7.956	-0.041	-0.041	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.038	0.003	6.170	0.196	0.196	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.814	-0.878	1.859	-10.417	-15.309	15.637	-5.809	-4.936	-0.051
79	A	79	LEU	0	-0.068	-0.033	4.553	0.606	0.784	-0.001	-0.028	-0.149	0.000
80	A	80	VAL	0	0.017	0.006	6.308	0.075	0.075	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.012	-0.006	8.824	0.031	0.031	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.021	0.008	11.540	0.016	0.016	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.014	-0.001	15.018	0.012	0.012	0.000	0.000	0.000	0.000
84	A	84	THR	0	0.012	-0.003	17.882	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	HIS	0	0.058	0.012	19.438	0.005	0.005	0.000	0.000	0.000	0.000
86	A	86	GLN	0	-0.002	-0.003	21.080	-0.011	-0.011	0.000	0.000	0.000	0.000
87	A	87	HIS	0	0.011	0.016	18.743	0.001	0.001	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.884	0.934	16.483	-0.141	-0.141	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.023	-0.017	18.291	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	90	ILE	0	-0.010	0.007	21.505	-0.008	-0.008	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.054	0.027	15.154	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.035	-0.021	18.572	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.103	-0.061	19.371	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.021	-0.010	20.595	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	95	PHE	0	0.031	0.012	16.942	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.030	0.015	17.533	-0.010	-0.010	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.853	0.923	16.573	0.072	0.072	0.000	0.000	0.000	0.000
98	A	98	TYR	0	0.046	0.022	12.865	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.869	0.936	13.520	-0.028	-0.028	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.876	-0.936	13.766	0.032	0.032	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.811	0.916	8.418	0.375	0.375	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.032	-0.009	9.768	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.002	-0.005	10.228	0.027	0.027	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.011	-0.013	13.600	0.005	0.005	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.022	0.006	12.486	0.021	0.021	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.825	0.894	14.372	-0.141	-0.141	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.750	-0.827	15.812	0.173	0.173	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.014	-0.008	7.565	-0.028	-0.028	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.014	-0.003	12.515	0.043	0.043	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.051	-0.031	14.261	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.006	0.018	17.008	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.091	-0.050	18.664	-0.028	-0.028	0.000	0.000	0.000	0.000
113	A	113	HIS	0	-0.008	-0.014	20.128	0.004	0.004	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.027	0.011	21.418	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.865	-0.935	20.714	0.137	0.137	0.000	0.000	0.000	0.000
116	A	116	VAL	0	0.005	0.016	18.410	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.007	-0.014	21.587	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.775	-0.905	24.647	0.123	0.123	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.013	0.023	24.522	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.012	-0.007	26.947	-0.006	-0.006	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.039	-0.015	28.652	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.011	0.006	30.946	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.016	-0.046	32.203	0.001	0.001	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.007	-0.009	29.305	0.006	0.006	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.840	-0.893	30.051	0.091	0.091	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.059	0.037	28.631	0.007	0.007	0.000	0.000	0.000	0.000
127	A	127	TYR	0	-0.009	-0.010	25.482	0.009	0.009	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.752	0.858	25.375	-0.083	-0.083	0.000	0.000	0.000	0.000
129	A	129	GLN	0	0.018	0.010	25.760	0.008	0.008	0.000	0.000	0.000	0.000
130	A	130	THR	0	-0.018	-0.025	22.290	0.010	0.010	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.782	0.851	21.248	-0.125	-0.125	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.774	-0.848	20.671	0.169	0.169	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.807	-0.892	21.103	0.182	0.182	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.011	-0.012	16.759	0.020	0.020	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.793	-0.882	16.720	0.228	0.228	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.967	-0.976	17.219	0.223	0.223	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.014	0.000	15.759	0.030	0.030	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.019	-0.003	11.660	0.056	0.056	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.844	0.905	12.483	-0.167	-0.167	0.000	0.000	0.000	0.000
140	A	140	GLN	0	-0.062	-0.020	14.368	0.006	0.006	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.035	0.018	8.420	0.055	0.055	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.004	0.006	8.981	0.194	0.194	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.870	0.912	9.682	-0.245	-0.245	0.000	0.000	0.000	0.000
144	A	144	GLN	0	-0.039	-0.021	10.848	-0.007	-0.007	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.071	0.021	4.780	-0.077	-0.002	-0.001	-0.002	-0.071	0.000
146	A	146	LYS	1	0.787	0.891	6.854	0.014	0.014	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.820	0.909	8.928	-0.854	-0.854	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.833	-0.884	5.397	2.953	2.953	0.000	0.000	0.000	0.000
149	A	149	ARG	1	0.960	0.955	6.303	0.169	0.169	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.816	0.886	3.394	-3.092	-2.412	0.022	-0.198	-0.504	0.001
151	A	151	LEU	0	-0.011	0.015	2.277	-6.671	-3.142	3.641	-2.936	-4.234	-0.007
152	A	152	GLU	-1	-0.978	-0.963	2.741	-11.454	-10.225	0.925	-0.480	-1.675	-0.012

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