FMO DATABASE

FMODB ID: 764GK

Calculation Name: 3V7D-A-Xray372

Preferred Name:

Target Type:

Ligand Name: phosphoserine

ligand 3-letter code: SEP

PDB ID: 3V7D

Chain ID: A

ChEMBL ID:

UniProt ID: P07834

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	139
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1197800.362496
FMO2-HF: Nuclear repulsion	1141692.917868
FMO2-HF: Total energy	-56107.444628
FMO2-MP2: Total energy	-56271.481888

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:3:THR)

Summations of interaction energy for fragment #1(A:3:THR)

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.
-12.643	-7.563	1.331	-2.707	-3.705	-0.02

Interaction energy analysis for fragmet #1(A:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.009

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	5	ASN	0	0.039	0.007	2.869	-5.081	-2.155	0.245	-1.418	-1.754	-0.005
4	A	6	VAL	0	-0.047	-0.019	5.630	0.773	0.773	0.000	0.000	0.000	0.000
5	A	7	VAL	0	-0.021	-0.017	8.817	-0.133	-0.133	0.000	0.000	0.000	0.000
6	A	8	LEU	0	0.017	0.017	12.185	0.132	0.132	0.000	0.000	0.000	0.000
7	A	9	VAL	0	-0.024	-0.019	14.719	-0.006	-0.006	0.000	0.000	0.000	0.000
8	A	10	SER	0	0.042	0.016	18.269	0.031	0.031	0.000	0.000	0.000	0.000
9	A	11	GLY	0	-0.001	-0.008	20.965	0.029	0.029	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.878	-0.935	24.001	-0.307	-0.307	0.000	0.000	0.000	0.000
11	A	13	GLY	0	-0.041	-0.015	22.933	0.015	0.015	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.884	-0.895	20.580	-0.434	-0.434	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.909	0.945	15.749	0.441	0.441	0.000	0.000	0.000	0.000
14	A	16	PHE	0	0.058	0.032	14.399	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.043	-0.028	8.984	0.035	0.035	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.025	0.024	8.606	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.770	-0.894	2.719	-11.873	-10.146	1.083	-1.230	-1.579	-0.015
18	A	20	LYS	1	0.906	0.948	3.669	2.049	2.258	0.001	-0.029	-0.181	0.000
19	A	21	LYS	1	0.828	0.890	3.925	1.499	1.717	0.002	-0.030	-0.191	0.000
20	A	22	ILE	0	0.003	0.006	5.906	0.619	0.619	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.028	0.012	7.672	0.475	0.475	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.841	-0.891	8.415	-0.350	-0.350	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.844	0.926	10.749	1.059	1.059	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.054	-0.037	13.206	0.132	0.132	0.000	0.000	0.000	0.000
25	A	27	LEU	0	0.025	-0.003	14.392	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.013	0.013	16.736	0.043	0.043	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.014	-0.005	10.087	0.032	0.032	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.878	0.916	11.774	0.512	0.512	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.011	-0.020	13.471	0.064	0.064	0.000	0.000	0.000	0.000
30	A	32	TYR	0	-0.019	-0.005	14.280	0.061	0.061	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.074	-0.047	9.393	0.019	0.019	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.122	-0.053	13.519	0.109	0.109	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.925	-0.933	15.653	-0.020	-0.020	0.000	0.000	0.000	0.000
34	A	75	ILE	0	-0.002	-0.012	10.561	0.013	0.013	0.000	0.000	0.000	0.000
35	A	76	VAL	0	-0.005	-0.005	11.728	-0.176	-0.176	0.000	0.000	0.000	0.000
36	A	77	MET	0	0.001	0.022	14.418	0.085	0.085	0.000	0.000	0.000	0.000
37	A	78	PRO	0	-0.003	0.004	15.967	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	79	VAL	0	-0.009	-0.015	17.493	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	80	PRO	0	0.011	0.005	20.314	0.005	0.005	0.000	0.000	0.000	0.000
40	A	81	ASN	0	-0.025	-0.029	24.042	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	82	VAL	0	0.031	0.037	21.672	0.003	0.003	0.000	0.000	0.000	0.000
42	A	83	ARG	1	0.935	0.949	23.477	0.290	0.290	0.000	0.000	0.000	0.000
43	A	84	SER	0	0.002	-0.045	21.684	-0.044	-0.044	0.000	0.000	0.000	0.000
44	A	85	SER	0	0.000	0.005	21.285	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	86	VAL	0	0.031	0.019	22.612	-0.033	-0.033	0.000	0.000	0.000	0.000
46	A	87	LEU	0	0.001	-0.004	16.598	-0.033	-0.033	0.000	0.000	0.000	0.000
47	A	88	GLN	0	-0.022	-0.009	17.761	-0.056	-0.056	0.000	0.000	0.000	0.000
48	A	89	LYS	1	0.852	0.922	17.914	0.473	0.473	0.000	0.000	0.000	0.000
49	A	90	VAL	0	-0.003	-0.004	16.657	-0.045	-0.045	0.000	0.000	0.000	0.000
50	A	91	ILE	0	0.006	0.001	12.407	-0.064	-0.064	0.000	0.000	0.000	0.000
51	A	92	GLU	-1	-0.803	-0.874	14.061	-0.780	-0.780	0.000	0.000	0.000	0.000
52	A	93	TRP	0	-0.055	-0.041	15.765	-0.078	-0.078	0.000	0.000	0.000	0.000
53	A	94	ALA	0	-0.022	-0.026	12.750	0.001	0.001	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.911	-0.968	9.999	-2.067	-2.067	0.000	0.000	0.000	0.000
55	A	96	HIS	1	0.838	0.938	11.929	0.699	0.699	0.000	0.000	0.000	0.000
56	A	97	HIS	1	0.737	0.840	14.592	0.721	0.721	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.908	0.964	8.664	1.613	1.613	0.000	0.000	0.000	0.000
58	A	99	ASP	-1	-0.845	-0.917	10.754	-1.360	-1.360	0.000	0.000	0.000	0.000
59	A	100	SER	0	-0.072	-0.021	12.794	0.141	0.141	0.000	0.000	0.000	0.000
60	A	101	ASN	0	0.002	0.007	15.397	-0.052	-0.052	0.000	0.000	0.000	0.000
61	A	102	PHE	0	-0.008	-0.016	16.657	0.020	0.020	0.000	0.000	0.000	0.000
62	A	103	PRO	0	-0.026	-0.004	20.513	0.008	0.008	0.000	0.000	0.000	0.000
63	A	104	ASP	-1	-0.919	-0.956	22.560	-0.232	-0.232	0.000	0.000	0.000	0.000
64	A	113	SER	0	0.021	-0.003	32.416	0.001	0.001	0.000	0.000	0.000	0.000
65	A	114	ALA	0	0.007	0.009	28.551	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	115	PRO	0	0.055	0.037	29.752	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	116	VAL	0	0.008	0.004	26.398	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	117	ASP	-1	-0.800	-0.888	21.959	-0.465	-0.465	0.000	0.000	0.000	0.000
69	A	118	SER	0	0.010	-0.020	25.643	-0.011	-0.011	0.000	0.000	0.000	0.000
70	A	119	TRP	0	0.019	0.008	18.812	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	120	ASP	-1	-0.753	-0.862	21.335	-0.555	-0.555	0.000	0.000	0.000	0.000
72	A	121	ARG	1	0.872	0.927	23.931	0.299	0.299	0.000	0.000	0.000	0.000
73	A	122	GLU	-1	-0.896	-0.952	26.185	-0.306	-0.306	0.000	0.000	0.000	0.000
74	A	123	PHE	0	-0.061	-0.020	20.218	0.004	0.004	0.000	0.000	0.000	0.000
75	A	124	LEU	0	-0.030	-0.022	24.376	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	125	LYS	1	0.891	0.970	26.703	0.297	0.297	0.000	0.000	0.000	0.000
77	A	126	VAL	0	-0.048	-0.017	26.924	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	127	ASP	-1	-0.863	-0.931	30.226	-0.267	-0.267	0.000	0.000	0.000	0.000
79	A	128	GLN	0	0.019	-0.039	31.603	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	129	GLU	-1	-0.870	-0.927	32.521	-0.226	-0.226	0.000	0.000	0.000	0.000
81	A	130	MET	0	-0.009	0.005	26.452	-0.024	-0.024	0.000	0.000	0.000	0.000
82	A	131	LEU	0	-0.030	-0.017	27.644	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	132	TYR	0	0.002	0.000	28.430	-0.011	-0.011	0.000	0.000	0.000	0.000
84	A	133	GLU	-1	-0.786	-0.889	26.794	-0.317	-0.317	0.000	0.000	0.000	0.000
85	A	134	ILE	0	-0.013	-0.014	22.915	-0.027	-0.027	0.000	0.000	0.000	0.000
86	A	135	ILE	0	-0.038	-0.011	23.975	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	136	LEU	0	0.004	0.003	25.768	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	137	ALA	0	0.022	0.015	21.601	0.000	0.000	0.000	0.000	0.000	0.000
89	A	138	ALA	0	-0.004	0.000	20.850	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	139	ASN	0	-0.025	-0.010	21.813	0.002	0.002	0.000	0.000	0.000	0.000
91	A	140	TYR	0	-0.021	-0.001	20.689	0.021	0.021	0.000	0.000	0.000	0.000
92	A	141	LEU	0	-0.017	-0.014	16.934	0.001	0.001	0.000	0.000	0.000	0.000
93	A	142	ASN	0	0.009	0.015	18.323	-0.045	-0.045	0.000	0.000	0.000	0.000
94	A	143	ILE	0	0.008	0.008	16.660	-0.035	-0.035	0.000	0.000	0.000	0.000
95	A	144	LYS	1	0.942	0.941	19.435	0.293	0.293	0.000	0.000	0.000	0.000
96	A	145	PRO	0	0.009	0.007	18.835	0.013	0.013	0.000	0.000	0.000	0.000
97	A	146	LEU	0	0.018	0.019	19.344	0.016	0.016	0.000	0.000	0.000	0.000
98	A	147	LEU	0	0.041	0.013	21.633	0.025	0.025	0.000	0.000	0.000	0.000
99	A	148	ASP	-1	-0.846	-0.904	24.553	-0.282	-0.282	0.000	0.000	0.000	0.000
100	A	149	ALA	0	-0.048	-0.024	23.934	0.025	0.025	0.000	0.000	0.000	0.000
101	A	150	GLY	0	0.072	0.024	25.677	0.017	0.017	0.000	0.000	0.000	0.000
102	A	151	CYS	0	-0.011	-0.013	27.428	0.025	0.025	0.000	0.000	0.000	0.000
103	A	152	LYS	1	0.835	0.907	27.361	0.300	0.300	0.000	0.000	0.000	0.000
104	A	153	VAL	0	-0.015	-0.003	28.590	0.016	0.016	0.000	0.000	0.000	0.000
105	A	154	VAL	0	0.046	0.016	31.269	0.013	0.013	0.000	0.000	0.000	0.000
106	A	155	ALA	0	-0.009	-0.006	33.702	0.014	0.014	0.000	0.000	0.000	0.000
107	A	156	GLU	-1	-0.879	-0.932	34.103	-0.186	-0.186	0.000	0.000	0.000	0.000
108	A	157	MET	0	-0.074	-0.020	35.165	0.004	0.004	0.000	0.000	0.000	0.000
109	A	158	ILE	0	0.008	0.009	37.648	0.010	0.010	0.000	0.000	0.000	0.000
110	A	159	ARG	1	0.846	0.911	38.258	0.186	0.186	0.000	0.000	0.000	0.000
111	A	160	GLY	0	-0.039	-0.022	40.752	0.000	0.000	0.000	0.000	0.000	0.000
112	A	161	ARG	1	0.816	0.921	42.322	0.149	0.149	0.000	0.000	0.000	0.000
113	A	162	SER	0	-0.004	-0.033	45.314	0.003	0.003	0.000	0.000	0.000	0.000
114	A	163	PRO	0	0.073	0.011	47.228	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	164	GLU	-1	-0.832	-0.902	48.004	-0.114	-0.114	0.000	0.000	0.000	0.000
116	A	165	GLU	-1	-0.808	-0.869	46.014	-0.130	-0.130	0.000	0.000	0.000	0.000
117	A	166	ILE	0	-0.002	0.009	42.527	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	167	ARG	1	0.820	0.903	43.681	0.102	0.102	0.000	0.000	0.000	0.000
119	A	168	ARG	1	0.930	0.971	45.342	0.123	0.123	0.000	0.000	0.000	0.000
120	A	169	THR	0	-0.071	-0.031	39.663	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	170	PHE	0	-0.001	-0.001	36.613	-0.008	-0.008	0.000	0.000	0.000	0.000
122	A	171	ASN	0	-0.066	-0.014	41.342	0.004	0.004	0.000	0.000	0.000	0.000
123	A	172	ILE	0	-0.002	0.001	42.063	0.001	0.001	0.000	0.000	0.000	0.000
124	A	173	VAL	0	-0.013	-0.016	45.763	0.004	0.004	0.000	0.000	0.000	0.000
125	A	174	ASN	0	-0.038	-0.049	49.286	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	175	ASP	-1	-0.931	-0.958	50.751	-0.100	-0.100	0.000	0.000	0.000	0.000
127	A	176	PHE	0	-0.012	0.011	50.730	0.003	0.003	0.000	0.000	0.000	0.000
128	A	177	THR	0	0.028	0.010	55.255	0.001	0.001	0.000	0.000	0.000	0.000
129	A	178	PRO	0	0.026	-0.015	58.814	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	179	GLU	-1	-1.002	-0.989	60.959	-0.063	-0.063	0.000	0.000	0.000	0.000
131	A	180	GLU	-1	-0.898	-0.960	56.191	-0.077	-0.077	0.000	0.000	0.000	0.000
132	A	181	GLU	-1	-0.808	-0.893	54.268	-0.096	-0.096	0.000	0.000	0.000	0.000
133	A	182	ALA	0	-0.048	-0.031	57.034	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	183	ALA	0	-0.051	-0.038	59.224	0.001	0.001	0.000	0.000	0.000	0.000
135	A	184	ILE	0	0.056	0.040	52.719	0.000	0.000	0.000	0.000	0.000	0.000
136	A	185	ARG	1	0.925	0.971	55.121	0.085	0.085	0.000	0.000	0.000	0.000
137	A	186	ARG	1	0.859	0.926	56.282	0.068	0.068	0.000	0.000	0.000	0.000
138	A	187	GLU	-1	-0.929	-0.951	53.723	-0.086	-0.086	0.000	0.000	0.000	0.000
139	A	188	ASN	0	-0.053	-0.007	54.516	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:THR)