FMO DATABASE

FMODB ID: ZVV7N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1507556.525223
FMO2-HF: Nuclear repulsion	1447250.07236
FMO2-HF: Total energy	-60306.452863
FMO2-MP2: Total energy	-60481.456429

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.
-34.385	-25.921	19.071	-10.764	-16.769	-0.082

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 : 0.003 / q_NPA : 0.005

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	-0.033	-0.020	3.069	-2.827	-1.385	0.123	-0.209	-1.356	0.004
4	A	4	ILE	0	0.017	0.009	5.561	0.288	0.288	0.000	0.000	0.000	0.000
5	A	5	PHE	0	-0.021	-0.004	9.164	-0.017	-0.017	0.000	0.000	0.000	0.000
6	A	6	VAL	0	0.024	-0.002	12.170	-0.040	-0.040	0.000	0.000	0.000	0.000
7	A	7	SEP	-2	-1.568	-1.710	15.105	0.372	0.372	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.034	0.015	18.806	-0.015	-0.015	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.040	0.011	22.132	-0.015	-0.015	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.004	-0.008	17.049	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.008	0.002	20.297	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.056	-0.014	21.969	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.856	0.880	19.391	-0.164	-0.164	0.000	0.000	0.000	0.000
14	A	14	SER	0	-0.008	-0.008	15.692	0.030	0.030	0.000	0.000	0.000	0.000
15	A	15	PRO	0	0.027	0.028	15.649	0.047	0.047	0.000	0.000	0.000	0.000
16	A	16	MET	0	-0.016	-0.003	17.081	0.022	0.022	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.014	0.004	13.971	0.029	0.029	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.770	-0.854	12.100	0.491	0.491	0.000	0.000	0.000	0.000
19	A	19	ALA	0	-0.014	-0.007	12.854	0.073	0.073	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.020	-0.015	15.282	0.013	0.013	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.022	-0.010	6.317	0.001	0.001	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.894	0.947	10.490	-0.468	-0.468	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.006	0.008	11.727	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.033	-0.029	12.260	-0.031	-0.031	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.011	-0.005	8.319	-0.027	-0.027	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.897	-0.934	10.388	0.449	0.449	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.836	0.924	12.046	-0.396	-0.396	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.871	-0.942	11.797	0.627	0.627	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.006	0.024	10.909	-0.013	-0.013	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.083	-0.043	5.991	-0.042	-0.042	0.000	0.000	0.000	0.000
31	A	31	ASN	0	-0.057	-0.034	3.594	0.673	1.319	0.014	-0.186	-0.475	-0.001
32	A	32	VAL	0	0.008	-0.003	2.360	-3.012	-0.864	2.648	-1.733	-3.063	-0.019
33	A	33	ASN	0	-0.038	-0.020	3.351	-2.692	-1.371	0.794	-0.489	-1.626	0.003
34	A	34	VAL	0	-0.041	-0.020	4.697	-0.689	-0.712	0.000	0.037	-0.014	0.000
35	A	35	ARG	1	0.865	0.905	7.775	-0.311	-0.311	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.029	-0.040	10.719	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.018	0.013	13.719	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	38	GLY	0	-0.039	-0.011	16.058	0.026	0.026	0.000	0.000	0.000	0.000
39	A	39	VAL	0	-0.007	-0.020	18.729	-0.021	-0.021	0.000	0.000	0.000	0.000
40	A	40	PHE	0	-0.066	-0.035	20.493	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.020	0.025	21.309	0.005	0.005	0.000	0.000	0.000	0.000
42	A	42	SER	0	-0.021	-0.005	23.253	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	43	PRO	0	0.035	0.008	21.801	0.010	0.010	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.095	-0.043	23.180	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.038	0.027	24.428	0.002	0.002	0.000	0.000	0.000	0.000
46	A	46	LYS	1	0.995	1.012	23.296	-0.056	-0.056	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.053	0.027	22.123	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	THR	0	-0.016	-0.020	24.046	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.038	0.001	26.635	0.010	0.010	0.000	0.000	0.000	0.000
50	A	50	HIS	0	-0.013	-0.002	28.685	0.000	0.000	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.049	0.035	23.109	0.009	0.009	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.032	-0.024	24.174	0.015	0.015	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.824	-0.910	25.370	0.128	0.128	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.028	0.003	24.887	0.003	0.003	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.008	-0.003	19.207	0.011	0.011	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.008	0.018	23.266	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.839	-0.903	25.924	0.133	0.133	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.729	0.861	22.604	-0.255	-0.255	0.000	0.000	0.000	0.000
59	A	59	HIS	0	-0.036	-0.017	23.126	0.012	0.012	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.015	0.001	18.116	0.015	0.015	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.002	-0.002	21.200	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.016	-0.002	19.139	0.017	0.017	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.058	-0.036	19.932	-0.027	-0.027	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.010	-0.006	16.584	0.030	0.030	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.030	-0.015	18.747	-0.024	-0.024	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.029	-0.027	18.879	0.006	0.006	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.016	-0.015	17.394	-0.031	-0.031	0.000	0.000	0.000	0.000
68	A	68	PRO	0	-0.019	-0.002	18.909	0.021	0.021	0.000	0.000	0.000	0.000
69	A	69	LEU	0	0.024	0.008	13.538	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	70	THR	0	0.005	-0.002	15.935	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.838	-0.946	15.349	-0.161	-0.161	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.917	-0.963	13.605	-0.259	-0.259	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.047	-0.015	11.549	-0.076	-0.076	0.000	0.000	0.000	0.000
74	A	74	MET	0	-0.013	0.003	10.448	-0.028	-0.028	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.991	-0.980	10.540	-0.811	-0.811	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.042	0.018	7.035	-0.039	-0.039	0.000	0.000	0.000	0.000
77	A	77	ALA	0	-0.040	0.009	6.041	-0.392	-0.392	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.812	-0.894	1.953	-7.314	-11.012	12.933	-4.794	-4.441	-0.042
79	A	79	LEU	0	-0.085	-0.048	4.201	0.736	0.917	-0.001	-0.019	-0.160	0.000
80	A	80	VAL	0	0.013	0.002	5.879	-0.074	-0.074	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.009	-0.003	8.925	0.045	0.045	0.000	0.000	0.000	0.000
82	A	82	ALA	0	-0.001	-0.004	11.406	-0.022	-0.022	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.012	-0.001	15.049	0.030	0.030	0.000	0.000	0.000	0.000
84	A	84	THR	0	0.013	-0.007	17.870	-0.003	-0.003	0.000	0.000	0.000	0.000
85	A	85	HIS	0	0.048	-0.007	19.342	0.008	0.008	0.000	0.000	0.000	0.000
86	A	86	GLN	0	0.005	-0.002	21.072	-0.018	-0.018	0.000	0.000	0.000	0.000
87	A	87	HIS	0	0.015	0.013	18.331	0.002	0.002	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.877	0.935	16.228	-0.256	-0.256	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.025	-0.022	18.040	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	90	ILE	0	0.002	0.009	21.085	-0.017	-0.017	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.042	0.023	14.682	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.025	-0.012	18.030	-0.025	-0.025	0.000	0.000	0.000	0.000
93	A	93	SER	0	-0.106	-0.057	18.858	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	94	GLN	0	-0.026	-0.009	20.126	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	95	PHE	0	0.028	0.010	16.272	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.043	0.021	16.744	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.880	0.938	16.168	0.242	0.242	0.000	0.000	0.000	0.000
98	A	98	TYR	0	0.032	0.001	12.264	-0.032	-0.032	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.913	0.960	12.808	-0.031	-0.031	0.000	0.000	0.000	0.000
100	A	100	ASP	-1	-0.913	-0.952	13.192	0.115	0.115	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.815	0.911	7.893	0.632	0.632	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.038	-0.012	9.549	0.044	0.044	0.000	0.000	0.000	0.000
103	A	103	PHE	0	0.009	0.004	10.268	0.017	0.017	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.019	-0.015	13.382	0.009	0.009	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.038	0.015	12.603	0.048	0.048	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.827	0.889	14.459	-0.219	-0.219	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-0.754	-0.817	15.818	0.308	0.308	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.008	-0.004	8.007	0.015	0.015	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.024	-0.002	12.442	0.057	0.057	0.000	0.000	0.000	0.000
110	A	110	THR	0	-0.039	-0.039	14.576	-0.023	-0.023	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.000	0.017	17.468	-0.026	-0.026	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.095	-0.052	19.019	-0.044	-0.044	0.000	0.000	0.000	0.000
113	A	113	HIS	0	0.002	-0.009	20.254	0.008	0.008	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.022	0.009	21.253	-0.013	-0.013	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.862	-0.925	20.710	0.208	0.208	0.000	0.000	0.000	0.000
116	A	116	VAL	0	-0.002	0.014	18.543	0.001	0.001	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.002	-0.021	21.585	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	118	ASP	-1	-0.818	-0.924	24.569	0.151	0.151	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.007	0.020	24.442	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	120	PHE	0	0.000	-0.006	26.907	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	121	GLY	0	-0.041	-0.016	28.604	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.007	0.009	30.869	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	123	SER	0	-0.021	-0.049	32.171	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.013	-0.003	29.274	0.010	0.010	0.000	0.000	0.000	0.000
125	A	125	ASP	-1	-0.858	-0.909	29.982	0.129	0.129	0.000	0.000	0.000	0.000
126	A	126	ILE	0	0.054	0.038	28.694	0.011	0.011	0.000	0.000	0.000	0.000
127	A	127	TYR	0	0.004	-0.031	25.197	0.013	0.013	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.736	0.857	25.331	-0.120	-0.120	0.000	0.000	0.000	0.000
129	A	129	GLN	0	0.039	0.024	25.703	0.012	0.012	0.000	0.000	0.000	0.000
130	A	130	THR	0	-0.012	-0.008	21.959	0.014	0.014	0.000	0.000	0.000	0.000
131	A	131	ARG	1	0.781	0.861	21.251	-0.188	-0.188	0.000	0.000	0.000	0.000
132	A	132	ASP	-1	-0.798	-0.875	20.808	0.258	0.258	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.785	-0.882	20.898	0.275	0.275	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.011	-0.020	16.601	0.032	0.032	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.817	-0.898	16.764	0.371	0.371	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.956	-0.968	17.113	0.351	0.351	0.000	0.000	0.000	0.000
137	A	137	LEU	0	0.004	-0.001	15.758	0.039	0.039	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.010	-0.001	11.704	0.084	0.084	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.846	0.906	12.406	-0.287	-0.287	0.000	0.000	0.000	0.000
140	A	140	GLN	0	-0.050	-0.012	13.913	0.015	0.015	0.000	0.000	0.000	0.000
141	A	141	LEU	0	0.025	0.016	8.485	0.057	0.057	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.000	0.009	9.036	0.236	0.236	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.882	0.911	9.748	-0.444	-0.444	0.000	0.000	0.000	0.000
144	A	144	GLN	0	-0.037	-0.027	10.750	0.030	0.030	0.000	0.000	0.000	0.000
145	A	145	LEU	0	0.072	0.031	4.205	-0.117	-0.026	-0.001	-0.009	-0.081	0.000
146	A	146	LYS	1	0.861	0.949	6.936	-0.436	-0.436	0.000	0.000	0.000	0.000
147	A	147	LYS	1	0.797	0.902	9.167	-0.996	-0.996	0.000	0.000	0.000	0.000
148	A	148	ASP	-1	-0.820	-0.885	5.954	3.615	3.615	0.000	0.000	0.000	0.000
149	A	149	ARG	1	0.962	0.959	6.239	-0.238	-0.238	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.845	0.907	3.710	-5.101	-4.444	0.022	-0.207	-0.471	0.001
151	A	151	LEU	0	-0.066	-0.015	2.351	-5.236	-2.272	2.151	-1.941	-3.174	-0.010
152	A	152	GLU	-1	-0.950	-0.953	2.863	-11.689	-8.954	0.388	-1.214	-1.908	-0.018

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