FMO DATABASE

FMODB ID: MNZ3Z

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	OptH
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	-1197540.818671
FMO2-HF: Nuclear repulsion	1141433.875116
FMO2-HF: Total energy	-56106.943555
FMO2-MP2: Total energy	-56270.95728

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.
-9.23	-2.805	0.937	-3.375	-3.986	-0.01

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 : 0.033 / q_NPA : 0.016

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	0.043	0.012	2.885	-5.141	-0.748	0.219	-2.294	-2.317	0.001
4	A	6	VAL	0	-0.035	-0.010	5.658	0.416	0.416	0.000	0.000	0.000	0.000
5	A	7	VAL	0	-0.028	-0.022	8.833	-0.058	-0.058	0.000	0.000	0.000	0.000
6	A	8	LEU	0	0.015	0.014	12.219	0.122	0.122	0.000	0.000	0.000	0.000
7	A	9	VAL	0	-0.024	-0.016	14.761	-0.013	-0.013	0.000	0.000	0.000	0.000
8	A	10	SER	0	0.040	0.010	18.311	0.042	0.042	0.000	0.000	0.000	0.000
9	A	11	GLY	0	0.000	-0.008	21.020	0.000	0.000	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.877	-0.933	24.045	-0.268	-0.268	0.000	0.000	0.000	0.000
11	A	13	GLY	0	-0.044	-0.016	22.977	0.001	0.001	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.896	-0.915	20.663	-0.450	-0.450	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.920	0.951	15.539	0.808	0.808	0.000	0.000	0.000	0.000
14	A	16	PHE	0	0.049	0.031	14.418	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.040	-0.026	9.131	-0.092	-0.092	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.030	0.020	8.596	0.079	0.079	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.777	-0.901	2.849	-6.713	-5.026	0.719	-1.042	-1.364	-0.011
18	A	20	LYS	1	0.936	0.970	3.724	2.182	2.371	0.000	-0.024	-0.165	0.000
19	A	21	LYS	1	0.927	0.959	4.279	-0.277	-0.121	-0.001	-0.015	-0.140	0.000
20	A	22	ILE	0	0.006	0.012	5.967	0.324	0.324	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.010	0.002	7.725	0.196	0.196	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.965	-0.986	8.636	0.146	0.146	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.859	0.942	10.756	0.059	0.059	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.064	-0.037	13.224	0.036	0.036	0.000	0.000	0.000	0.000
25	A	27	LEU	0	0.025	-0.003	14.397	-0.018	-0.018	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.023	0.005	16.734	0.007	0.007	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.022	0.000	10.051	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.954	0.967	12.417	-0.167	-0.167	0.000	0.000	0.000	0.000
29	A	31	ASN	0	-0.025	-0.028	13.443	0.047	0.047	0.000	0.000	0.000	0.000
30	A	32	TYR	0	0.008	0.019	14.480	0.013	0.013	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.096	-0.057	9.351	-0.065	-0.065	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.078	-0.026	13.461	0.041	0.041	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.961	-0.958	15.580	-0.100	-0.100	0.000	0.000	0.000	0.000
34	A	75	ILE	0	0.011	-0.009	10.491	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	76	VAL	0	-0.024	-0.012	11.723	-0.130	-0.130	0.000	0.000	0.000	0.000
36	A	77	MET	0	-0.003	0.015	14.436	0.093	0.093	0.000	0.000	0.000	0.000
37	A	78	PRO	0	-0.009	-0.002	15.970	-0.028	-0.028	0.000	0.000	0.000	0.000
38	A	79	VAL	0	0.000	-0.006	17.593	0.022	0.022	0.000	0.000	0.000	0.000
39	A	80	PRO	0	0.012	0.003	20.346	0.007	0.007	0.000	0.000	0.000	0.000
40	A	81	ASN	0	-0.028	-0.032	24.073	0.012	0.012	0.000	0.000	0.000	0.000
41	A	82	VAL	0	0.038	0.042	21.588	0.019	0.019	0.000	0.000	0.000	0.000
42	A	83	ARG	1	0.958	0.976	23.537	0.176	0.176	0.000	0.000	0.000	0.000
43	A	84	SER	0	0.013	-0.024	21.760	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	85	SER	0	-0.010	0.000	21.370	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	86	VAL	0	0.033	0.017	22.705	0.001	0.001	0.000	0.000	0.000	0.000
46	A	87	LEU	0	0.001	-0.002	16.650	0.008	0.008	0.000	0.000	0.000	0.000
47	A	88	GLN	0	0.004	-0.001	17.848	-0.046	-0.046	0.000	0.000	0.000	0.000
48	A	89	LYS	1	0.871	0.938	18.013	0.174	0.174	0.000	0.000	0.000	0.000
49	A	90	VAL	0	-0.006	-0.002	16.676	0.019	0.019	0.000	0.000	0.000	0.000
50	A	91	ILE	0	-0.007	-0.004	12.484	0.015	0.015	0.000	0.000	0.000	0.000
51	A	92	GLU	-1	-0.880	-0.927	14.161	-0.229	-0.229	0.000	0.000	0.000	0.000
52	A	93	TRP	0	-0.052	-0.028	15.936	0.049	0.049	0.000	0.000	0.000	0.000
53	A	94	ALA	0	-0.018	-0.028	12.844	0.066	0.066	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.897	-0.957	10.319	-0.762	-0.762	0.000	0.000	0.000	0.000
55	A	96	HIS	1	0.860	0.954	12.096	0.141	0.141	0.000	0.000	0.000	0.000
56	A	97	HIS	1	0.731	0.831	14.736	0.063	0.063	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.939	0.973	8.974	-0.217	-0.217	0.000	0.000	0.000	0.000
58	A	99	ASP	-1	-0.876	-0.932	10.731	0.801	0.801	0.000	0.000	0.000	0.000
59	A	100	SER	0	-0.103	-0.039	12.882	-0.019	-0.019	0.000	0.000	0.000	0.000
60	A	101	ASN	0	0.019	0.009	15.456	0.003	0.003	0.000	0.000	0.000	0.000
61	A	102	PHE	0	-0.030	-0.032	16.922	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	103	PRO	0	-0.017	-0.001	20.555	0.014	0.014	0.000	0.000	0.000	0.000
63	A	104	ASP	-1	-0.922	-0.953	22.920	0.077	0.077	0.000	0.000	0.000	0.000
64	A	113	SER	0	0.017	-0.007	32.516	0.002	0.002	0.000	0.000	0.000	0.000
65	A	114	ALA	0	0.005	0.010	28.655	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	115	PRO	0	0.052	0.026	29.477	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	116	VAL	0	0.001	0.002	26.684	0.008	0.008	0.000	0.000	0.000	0.000
68	A	117	ASP	-1	-0.820	-0.903	22.705	0.041	0.041	0.000	0.000	0.000	0.000
69	A	118	SER	0	-0.009	-0.028	25.773	-0.014	-0.014	0.000	0.000	0.000	0.000
70	A	119	TRP	0	0.037	0.018	19.111	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	120	ASP	-1	-0.771	-0.879	21.635	-0.048	-0.048	0.000	0.000	0.000	0.000
72	A	121	ARG	1	0.876	0.937	24.079	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	122	GLU	-1	-0.930	-0.961	26.301	-0.068	-0.068	0.000	0.000	0.000	0.000
74	A	123	PHE	0	-0.011	0.005	20.834	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	124	LEU	0	-0.019	-0.012	24.411	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	125	LYS	1	0.924	0.983	26.856	0.067	0.067	0.000	0.000	0.000	0.000
77	A	126	VAL	0	-0.060	-0.023	27.061	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	127	ASP	-1	-0.872	-0.937	30.357	-0.125	-0.125	0.000	0.000	0.000	0.000
79	A	128	GLN	0	0.022	-0.045	31.693	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	129	GLU	-1	-0.872	-0.922	32.602	-0.121	-0.121	0.000	0.000	0.000	0.000
81	A	130	MET	0	-0.003	0.007	26.274	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	131	LEU	0	-0.036	-0.019	27.726	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	132	TYR	0	0.011	0.001	28.505	0.003	0.003	0.000	0.000	0.000	0.000
84	A	133	GLU	-1	-0.818	-0.925	27.014	-0.192	-0.192	0.000	0.000	0.000	0.000
85	A	134	ILE	0	-0.014	-0.013	23.022	-0.016	-0.016	0.000	0.000	0.000	0.000
86	A	135	ILE	0	-0.037	-0.011	24.040	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	136	LEU	0	-0.001	0.001	25.820	0.002	0.002	0.000	0.000	0.000	0.000
88	A	137	ALA	0	0.022	0.015	21.622	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	138	ALA	0	-0.004	0.001	20.901	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	139	ASN	0	-0.026	-0.012	21.852	0.019	0.019	0.000	0.000	0.000	0.000
91	A	140	TYR	0	-0.020	0.001	20.882	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	141	LEU	0	-0.019	-0.015	16.999	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	142	ASN	0	0.004	0.015	18.344	0.010	0.010	0.000	0.000	0.000	0.000
94	A	143	ILE	0	0.013	0.002	16.527	0.012	0.012	0.000	0.000	0.000	0.000
95	A	144	LYS	1	0.994	0.993	19.472	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	145	PRO	0	0.001	0.009	18.805	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	146	LEU	0	0.023	0.020	19.540	0.003	0.003	0.000	0.000	0.000	0.000
98	A	147	LEU	0	0.033	0.009	21.727	0.000	0.000	0.000	0.000	0.000	0.000
99	A	148	ASP	-1	-0.876	-0.953	24.661	0.002	0.002	0.000	0.000	0.000	0.000
100	A	149	ALA	0	-0.055	-0.027	24.056	0.004	0.004	0.000	0.000	0.000	0.000
101	A	150	GLY	0	0.071	0.021	25.788	0.001	0.001	0.000	0.000	0.000	0.000
102	A	151	CYS	0	-0.005	-0.009	27.539	0.001	0.001	0.000	0.000	0.000	0.000
103	A	152	LYS	1	0.851	0.926	27.072	-0.019	-0.019	0.000	0.000	0.000	0.000
104	A	153	VAL	0	-0.014	-0.001	28.674	0.005	0.005	0.000	0.000	0.000	0.000
105	A	154	VAL	0	0.046	0.014	31.394	0.001	0.001	0.000	0.000	0.000	0.000
106	A	155	ALA	0	-0.008	-0.006	33.811	0.002	0.002	0.000	0.000	0.000	0.000
107	A	156	GLU	-1	-0.932	-0.972	34.229	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	157	MET	0	-0.072	-0.021	35.221	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	158	ILE	0	0.001	0.006	37.779	0.000	0.000	0.000	0.000	0.000	0.000
110	A	159	ARG	1	0.900	0.948	38.544	0.005	0.005	0.000	0.000	0.000	0.000
111	A	160	GLY	0	-0.046	-0.024	40.869	0.000	0.000	0.000	0.000	0.000	0.000
112	A	161	ARG	1	0.921	0.989	42.537	0.027	0.027	0.000	0.000	0.000	0.000
113	A	162	SER	0	0.008	0.006	45.440	0.000	0.000	0.000	0.000	0.000	0.000
114	A	163	PRO	0	0.073	0.010	47.350	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	164	GLU	-1	-0.839	-0.916	48.124	-0.035	-0.035	0.000	0.000	0.000	0.000
116	A	165	GLU	-1	-0.930	-0.974	46.153	-0.024	-0.024	0.000	0.000	0.000	0.000
117	A	166	ILE	0	-0.007	-0.002	42.629	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	167	ARG	1	0.917	0.959	43.793	0.027	0.027	0.000	0.000	0.000	0.000
119	A	168	ARG	1	0.932	0.972	45.423	0.040	0.040	0.000	0.000	0.000	0.000
120	A	169	THR	0	-0.068	-0.022	39.848	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	170	PHE	0	-0.007	0.003	36.917	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	171	ASN	0	-0.055	-0.008	41.422	0.000	0.000	0.000	0.000	0.000	0.000
123	A	172	ILE	0	0.001	0.003	42.309	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	173	VAL	0	-0.005	-0.014	45.837	0.002	0.002	0.000	0.000	0.000	0.000
125	A	174	ASN	0	-0.048	-0.034	49.358	0.001	0.001	0.000	0.000	0.000	0.000
126	A	175	ASP	-1	-0.918	-0.953	50.653	-0.039	-0.039	0.000	0.000	0.000	0.000
127	A	176	PHE	0	-0.008	0.010	50.935	0.001	0.001	0.000	0.000	0.000	0.000
128	A	177	THR	0	0.022	0.009	55.316	0.000	0.000	0.000	0.000	0.000	0.000
129	A	178	PRO	0	0.036	-0.009	58.876	0.001	0.001	0.000	0.000	0.000	0.000
130	A	179	GLU	-1	-1.004	-0.991	61.024	-0.017	-0.017	0.000	0.000	0.000	0.000
131	A	180	GLU	-1	-0.895	-0.957	56.270	-0.019	-0.019	0.000	0.000	0.000	0.000
132	A	181	GLU	-1	-0.927	-0.960	55.464	-0.024	-0.024	0.000	0.000	0.000	0.000
133	A	182	ALA	0	-0.049	-0.036	57.130	0.002	0.002	0.000	0.000	0.000	0.000
134	A	183	ALA	0	-0.031	-0.023	59.322	0.002	0.002	0.000	0.000	0.000	0.000
135	A	184	ILE	0	0.058	0.037	52.821	0.002	0.002	0.000	0.000	0.000	0.000
136	A	185	ARG	1	0.922	0.972	55.205	0.013	0.013	0.000	0.000	0.000	0.000
137	A	186	ARG	1	0.848	0.915	56.374	0.012	0.012	0.000	0.000	0.000	0.000
138	A	187	GLU	-1	-0.923	-0.949	53.791	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	188	ASN	0	-0.059	-0.008	54.587	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)