FMO DATABASE

FMODB ID: 2NG2R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1200372.98371
FMO2-HF: Nuclear repulsion	1144265.27034
FMO2-HF: Total energy	-56107.71337
FMO2-MP2: Total energy	-56271.744872

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.
-13.504	-8.298	2.177	-2.947	-4.437	-0.026

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 : 0.022 / q_NPA : 0.003

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	0.034	0.003	2.957	-3.574	-1.099	0.189	-1.114	-1.551	-0.004
4	A	6	VAL	0	-0.034	-0.012	5.516	0.834	0.834	0.000	0.000	0.000	0.000
5	A	7	VAL	0	-0.019	-0.013	8.776	-0.125	-0.125	0.000	0.000	0.000	0.000
6	A	8	LEU	0	0.027	0.021	12.243	0.139	0.139	0.000	0.000	0.000	0.000
7	A	9	VAL	0	-0.029	-0.018	14.805	0.006	0.006	0.000	0.000	0.000	0.000
8	A	10	SER	0	0.025	0.004	18.427	0.027	0.027	0.000	0.000	0.000	0.000
9	A	11	GLY	0	-0.007	-0.012	21.197	0.032	0.032	0.000	0.000	0.000	0.000
10	A	12	GLU	-1	-0.841	-0.918	24.246	-0.320	-0.320	0.000	0.000	0.000	0.000
11	A	13	GLY	0	-0.025	-0.005	23.332	0.018	0.018	0.000	0.000	0.000	0.000
12	A	14	GLU	-1	-0.881	-0.902	20.555	-0.439	-0.439	0.000	0.000	0.000	0.000
13	A	15	ARG	1	0.908	0.945	15.627	0.452	0.452	0.000	0.000	0.000	0.000
14	A	16	PHE	0	0.060	0.026	14.692	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.042	-0.028	8.887	0.015	0.015	0.000	0.000	0.000	0.000
16	A	18	VAL	0	0.021	0.029	8.485	0.010	0.010	0.000	0.000	0.000	0.000
17	A	19	ASP	-1	-0.777	-0.901	2.634	-15.009	-12.893	1.961	-1.733	-2.344	-0.022
18	A	20	LYS	1	0.877	0.933	3.678	2.345	2.581	0.002	-0.035	-0.203	0.000
19	A	21	LYS	1	0.805	0.879	3.392	1.902	2.281	0.025	-0.065	-0.339	0.000
20	A	22	ILE	0	0.003	0.010	5.739	0.721	0.721	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.026	0.010	7.624	0.531	0.531	0.000	0.000	0.000	0.000
22	A	24	GLU	-1	-0.797	-0.879	7.951	-0.607	-0.607	0.000	0.000	0.000	0.000
23	A	25	ARG	1	0.810	0.918	10.435	1.213	1.213	0.000	0.000	0.000	0.000
24	A	26	SER	0	-0.060	-0.035	12.836	0.143	0.143	0.000	0.000	0.000	0.000
25	A	27	LEU	0	0.022	-0.008	14.122	-0.023	-0.023	0.000	0.000	0.000	0.000
26	A	28	LEU	0	-0.014	0.015	16.483	0.040	0.040	0.000	0.000	0.000	0.000
27	A	29	LEU	0	0.007	-0.009	9.876	0.026	0.026	0.000	0.000	0.000	0.000
28	A	30	LYS	1	0.862	0.910	11.310	0.717	0.717	0.000	0.000	0.000	0.000
29	A	31	ASN	0	0.001	-0.003	13.264	0.042	0.042	0.000	0.000	0.000	0.000
30	A	32	TYR	0	-0.023	-0.030	14.075	0.070	0.070	0.000	0.000	0.000	0.000
31	A	33	LEU	0	-0.074	-0.045	9.093	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	34	ASN	0	-0.121	-0.051	13.141	0.096	0.096	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.930	-0.941	15.533	-0.093	-0.093	0.000	0.000	0.000	0.000
34	A	75	ILE	0	0.002	-0.009	10.043	0.020	0.020	0.000	0.000	0.000	0.000
35	A	76	VAL	0	-0.004	-0.004	11.482	-0.191	-0.191	0.000	0.000	0.000	0.000
36	A	77	MET	0	0.020	0.040	14.277	0.078	0.078	0.000	0.000	0.000	0.000
37	A	78	PRO	0	-0.012	0.004	16.009	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	79	VAL	0	0.000	-0.016	17.408	-0.010	-0.010	0.000	0.000	0.000	0.000
39	A	80	PRO	0	0.038	0.019	20.326	0.008	0.008	0.000	0.000	0.000	0.000
40	A	81	ASN	0	-0.029	-0.036	24.066	0.003	0.003	0.000	0.000	0.000	0.000
41	A	82	VAL	0	0.010	0.034	21.538	0.006	0.006	0.000	0.000	0.000	0.000
42	A	83	ARG	1	0.895	0.939	23.329	0.301	0.301	0.000	0.000	0.000	0.000
43	A	84	SER	0	-0.006	-0.048	21.590	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	85	SER	0	0.023	0.015	21.199	-0.047	-0.047	0.000	0.000	0.000	0.000
45	A	86	VAL	0	0.009	0.013	22.385	-0.038	-0.038	0.000	0.000	0.000	0.000
46	A	87	LEU	0	-0.007	-0.003	16.330	-0.040	-0.040	0.000	0.000	0.000	0.000
47	A	88	GLN	0	-0.001	0.004	17.658	-0.067	-0.067	0.000	0.000	0.000	0.000
48	A	89	LYS	1	0.848	0.918	17.948	0.486	0.486	0.000	0.000	0.000	0.000
49	A	90	VAL	0	0.006	-0.005	16.387	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	91	ILE	0	0.001	0.001	12.406	-0.077	-0.077	0.000	0.000	0.000	0.000
51	A	92	GLU	-1	-0.815	-0.887	14.011	-0.785	-0.785	0.000	0.000	0.000	0.000
52	A	93	TRP	0	-0.045	-0.032	15.991	-0.063	-0.063	0.000	0.000	0.000	0.000
53	A	94	ALA	0	-0.007	-0.014	12.303	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	95	GLU	-1	-0.922	-0.981	9.909	-2.226	-2.226	0.000	0.000	0.000	0.000
55	A	96	HIS	1	0.805	0.927	11.997	0.725	0.725	0.000	0.000	0.000	0.000
56	A	97	HIS	1	0.772	0.850	14.149	0.800	0.800	0.000	0.000	0.000	0.000
57	A	98	ARG	1	0.869	0.941	8.523	1.710	1.710	0.000	0.000	0.000	0.000
58	A	99	ASP	-1	-0.804	-0.892	10.490	-1.401	-1.401	0.000	0.000	0.000	0.000
59	A	100	SER	0	-0.052	-0.009	12.345	0.154	0.154	0.000	0.000	0.000	0.000
60	A	101	ASN	0	0.014	0.011	15.454	-0.057	-0.057	0.000	0.000	0.000	0.000
61	A	102	PHE	0	0.002	-0.017	16.480	0.009	0.009	0.000	0.000	0.000	0.000
62	A	103	PRO	0	-0.016	0.008	20.365	0.010	0.010	0.000	0.000	0.000	0.000
63	A	104	ASP	-1	-0.938	-0.971	22.713	-0.274	-0.274	0.000	0.000	0.000	0.000
64	A	113	SER	0	0.020	-0.003	32.369	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	114	ALA	0	0.022	0.015	28.558	0.000	0.000	0.000	0.000	0.000	0.000
66	A	115	PRO	0	0.051	0.032	29.372	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	116	VAL	0	0.011	0.006	25.977	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	117	ASP	-1	-0.785	-0.890	21.423	-0.501	-0.501	0.000	0.000	0.000	0.000
69	A	118	SER	0	-0.002	-0.020	24.985	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	119	TRP	0	0.019	0.016	18.763	0.012	0.012	0.000	0.000	0.000	0.000
71	A	120	ASP	-1	-0.788	-0.884	20.862	-0.598	-0.598	0.000	0.000	0.000	0.000
72	A	121	ARG	1	0.909	0.938	23.543	0.316	0.316	0.000	0.000	0.000	0.000
73	A	122	GLU	-1	-0.798	-0.872	26.354	-0.296	-0.296	0.000	0.000	0.000	0.000
74	A	123	PHE	0	-0.071	-0.030	20.256	0.003	0.003	0.000	0.000	0.000	0.000
75	A	124	LEU	0	-0.003	-0.008	24.356	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	125	LYS	1	0.774	0.894	26.571	0.318	0.318	0.000	0.000	0.000	0.000
77	A	126	VAL	0	-0.059	-0.029	26.855	0.002	0.002	0.000	0.000	0.000	0.000
78	A	127	ASP	-1	-0.836	-0.919	30.097	-0.280	-0.280	0.000	0.000	0.000	0.000
79	A	128	GLN	0	0.011	-0.031	31.487	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	129	GLU	-1	-0.873	-0.926	32.441	-0.239	-0.239	0.000	0.000	0.000	0.000
81	A	130	MET	0	-0.024	-0.008	26.592	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	131	LEU	0	-0.013	-0.010	27.420	-0.029	-0.029	0.000	0.000	0.000	0.000
83	A	132	TYR	0	-0.002	0.008	28.266	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	133	GLU	-1	-0.782	-0.896	26.566	-0.344	-0.344	0.000	0.000	0.000	0.000
85	A	134	ILE	0	-0.020	-0.017	22.921	-0.031	-0.031	0.000	0.000	0.000	0.000
86	A	135	ILE	0	-0.022	-0.004	23.919	-0.027	-0.027	0.000	0.000	0.000	0.000
87	A	136	LEU	0	-0.014	-0.005	25.685	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	137	ALA	0	0.016	0.004	21.417	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	138	ALA	0	-0.012	-0.009	20.744	-0.034	-0.034	0.000	0.000	0.000	0.000
90	A	139	ASN	0	-0.021	-0.008	21.648	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	140	TYR	0	-0.018	-0.002	20.326	0.014	0.014	0.000	0.000	0.000	0.000
92	A	141	LEU	0	-0.001	-0.007	16.558	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	142	ASN	0	0.000	0.017	17.983	-0.059	-0.059	0.000	0.000	0.000	0.000
94	A	143	ILE	0	0.022	0.014	16.630	-0.049	-0.049	0.000	0.000	0.000	0.000
95	A	144	LYS	1	0.927	0.943	19.255	0.337	0.337	0.000	0.000	0.000	0.000
96	A	145	PRO	0	0.014	0.005	18.910	0.016	0.016	0.000	0.000	0.000	0.000
97	A	146	LEU	0	0.007	0.017	19.205	0.019	0.019	0.000	0.000	0.000	0.000
98	A	147	LEU	0	0.050	0.025	21.654	0.029	0.029	0.000	0.000	0.000	0.000
99	A	148	ASP	-1	-0.837	-0.899	24.523	-0.318	-0.318	0.000	0.000	0.000	0.000
100	A	149	ALA	0	-0.057	-0.030	23.957	0.027	0.027	0.000	0.000	0.000	0.000
101	A	150	GLY	0	0.058	0.021	25.617	0.019	0.019	0.000	0.000	0.000	0.000
102	A	151	CYS	0	-0.012	-0.017	27.377	0.027	0.027	0.000	0.000	0.000	0.000
103	A	152	LYS	1	0.838	0.916	26.893	0.332	0.332	0.000	0.000	0.000	0.000
104	A	153	VAL	0	-0.012	0.001	28.565	0.017	0.017	0.000	0.000	0.000	0.000
105	A	154	VAL	0	0.037	0.011	31.234	0.015	0.015	0.000	0.000	0.000	0.000
106	A	155	ALA	0	-0.003	-0.001	33.541	0.015	0.015	0.000	0.000	0.000	0.000
107	A	156	GLU	-1	-0.859	-0.929	34.007	-0.199	-0.199	0.000	0.000	0.000	0.000
108	A	157	MET	0	-0.074	-0.029	35.025	0.006	0.006	0.000	0.000	0.000	0.000
109	A	158	ILE	0	0.023	0.013	37.483	0.011	0.011	0.000	0.000	0.000	0.000
110	A	159	ARG	1	0.805	0.902	37.500	0.199	0.199	0.000	0.000	0.000	0.000
111	A	160	GLY	0	-0.031	-0.010	40.394	0.001	0.001	0.000	0.000	0.000	0.000
112	A	161	ARG	1	0.791	0.890	41.854	0.154	0.154	0.000	0.000	0.000	0.000
113	A	162	SER	0	0.008	-0.030	45.065	0.002	0.002	0.000	0.000	0.000	0.000
114	A	163	PRO	0	0.066	0.008	47.295	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	164	GLU	-1	-0.782	-0.865	47.919	-0.122	-0.122	0.000	0.000	0.000	0.000
116	A	165	GLU	-1	-0.783	-0.845	45.918	-0.135	-0.135	0.000	0.000	0.000	0.000
117	A	166	ILE	0	0.005	0.023	42.395	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	167	ARG	1	0.804	0.881	43.728	0.108	0.108	0.000	0.000	0.000	0.000
119	A	168	ARG	1	0.853	0.923	45.631	0.128	0.128	0.000	0.000	0.000	0.000
120	A	169	THR	0	-0.059	-0.036	39.611	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	170	PHE	0	-0.011	-0.009	36.529	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	171	ASN	0	-0.052	-0.019	41.360	0.004	0.004	0.000	0.000	0.000	0.000
123	A	172	ILE	0	-0.008	0.011	42.093	0.003	0.003	0.000	0.000	0.000	0.000
124	A	173	VAL	0	-0.013	-0.020	45.698	0.004	0.004	0.000	0.000	0.000	0.000
125	A	174	ASN	0	-0.043	-0.045	49.271	-0.003	-0.003	0.000	0.000	0.000	0.000
126	A	175	ASP	-1	-0.908	-0.952	50.848	-0.108	-0.108	0.000	0.000	0.000	0.000
127	A	176	PHE	0	-0.008	0.008	50.382	0.004	0.004	0.000	0.000	0.000	0.000
128	A	177	THR	0	0.050	0.025	55.193	0.001	0.001	0.000	0.000	0.000	0.000
129	A	178	PRO	0	0.009	-0.021	58.593	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	179	GLU	-1	-0.979	-0.979	60.685	-0.069	-0.069	0.000	0.000	0.000	0.000
131	A	180	GLU	-1	-0.879	-0.944	55.970	-0.085	-0.085	0.000	0.000	0.000	0.000
132	A	181	GLU	-1	-0.816	-0.884	53.918	-0.103	-0.103	0.000	0.000	0.000	0.000
133	A	182	ALA	0	-0.018	-0.013	56.617	-0.001	-0.001	0.000	0.000	0.000	0.000
134	A	183	ALA	0	-0.052	-0.008	58.686	0.001	0.001	0.000	0.000	0.000	0.000
135	A	184	ILE	0	0.067	0.033	52.250	0.000	0.000	0.000	0.000	0.000	0.000
136	A	185	ARG	1	0.894	0.950	54.954	0.090	0.090	0.000	0.000	0.000	0.000
137	A	186	ARG	1	0.802	0.880	56.034	0.076	0.076	0.000	0.000	0.000	0.000
138	A	187	GLU	-1	-0.908	-0.943	53.678	-0.093	-0.093	0.000	0.000	0.000	0.000
139	A	188	ASN	0	-0.068	-0.018	54.362	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)