FMO DATABASE

FMODB ID: 2JVYR

Calculation Name: 3MSO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MSO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I1Z5

Base Structure: X-ray

Registration Date: 2023-09-20

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	134
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1163534.491267
FMO2-HF: Nuclear repulsion	1111352.614784
FMO2-HF: Total energy	-52181.876484
FMO2-MP2: Total energy	-52332.586008

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:2:THR)

Summations of interaction energy for fragment #1(A:2: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.
-3.213	-0.612	0.089	-0.911	-1.776	0.002

Interaction energy analysis for fragmet #1(A:2: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 : -0.008

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	4	LEU	0	-0.006	-0.008	2.765	-1.245	0.928	0.087	-0.804	-1.456	0.002
4	A	5	PRO	0	-0.023	-0.005	4.573	-0.229	-0.142	-0.001	-0.013	-0.072	0.000
5	A	6	LEU	0	-0.029	-0.017	6.430	-0.060	-0.060	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.874	-0.941	9.160	0.037	0.037	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.008	-0.015	11.270	-0.095	-0.095	0.000	0.000	0.000	0.000
8	A	9	ASN	0	-0.008	0.000	12.090	-0.048	-0.048	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.057	0.034	11.340	-0.039	-0.039	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.019	-0.013	7.873	-0.150	-0.150	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.005	0.002	8.591	-0.150	-0.150	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.026	-0.017	11.115	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	14	LEU	0	-0.019	0.002	5.379	-0.039	-0.039	0.000	0.000	0.000	0.000
14	A	15	ALA	0	-0.017	-0.009	7.436	-0.121	-0.121	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.893	-0.953	8.332	-0.224	-0.224	0.000	0.000	0.000	0.000
16	A	17	TRP	0	-0.003	-0.016	10.025	0.103	0.103	0.000	0.000	0.000	0.000
17	A	18	HIS	0	-0.015	-0.022	5.373	0.312	0.312	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.004	0.011	9.867	0.067	0.067	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.070	-0.041	11.895	0.076	0.076	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.016	0.015	12.211	0.057	0.057	0.000	0.000	0.000	0.000
21	A	22	ALA	0	-0.023	-0.005	11.637	0.049	0.049	0.000	0.000	0.000	0.000
22	A	23	ARG	1	0.797	0.894	13.605	0.336	0.336	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.820	0.899	16.503	0.314	0.314	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.812	-0.874	18.226	-0.181	-0.181	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.004	-0.003	16.689	-0.015	-0.015	0.000	0.000	0.000	0.000
26	A	27	SER	0	-0.015	-0.025	19.963	0.016	0.016	0.000	0.000	0.000	0.000
27	A	28	GLY	0	-0.030	-0.018	20.168	0.016	0.016	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.024	0.008	17.124	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	PRO	0	-0.012	-0.022	19.672	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	31	ARG	1	0.883	0.956	17.652	0.208	0.208	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.005	0.004	14.570	0.009	0.009	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.047	-0.004	17.817	-0.013	-0.013	0.000	0.000	0.000	0.000
33	A	34	HIS	0	0.060	0.047	20.253	0.013	0.013	0.000	0.000	0.000	0.000
34	A	35	PRO	0	0.005	-0.012	22.473	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.904	-0.958	25.826	-0.090	-0.090	0.000	0.000	0.000	0.000
36	A	37	ALA	0	-0.054	-0.014	21.412	0.001	0.001	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.027	-0.017	22.470	0.011	0.011	0.000	0.000	0.000	0.000
38	A	39	PHE	0	0.008	0.010	19.715	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.858	0.911	21.688	0.148	0.148	0.000	0.000	0.000	0.000
40	A	41	SER	0	0.054	0.022	22.046	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.027	0.026	22.162	0.010	0.010	0.000	0.000	0.000	0.000
42	A	43	MET	0	-0.019	-0.018	24.073	0.013	0.013	0.000	0.000	0.000	0.000
43	A	44	ALA	0	-0.051	-0.025	27.383	0.010	0.010	0.000	0.000	0.000	0.000
44	A	45	HIS	0	0.045	0.031	27.569	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.912	0.955	28.606	0.079	0.079	0.000	0.000	0.000	0.000
46	A	47	PRO	0	0.020	0.020	26.256	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	48	TYR	0	-0.055	-0.037	25.960	0.009	0.009	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.007	-0.007	25.997	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.044	0.030	26.617	0.007	0.007	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.007	0.000	24.190	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	52	PRO	0	-0.022	-0.020	24.976	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.021	0.012	27.038	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.038	0.016	21.284	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	55	SER	0	0.024	0.011	22.184	-0.024	-0.024	0.000	0.000	0.000	0.000
55	A	56	MET	0	0.011	0.018	23.267	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	57	ILE	0	-0.015	0.002	23.740	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.030	0.021	18.030	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	59	ASN	0	-0.033	-0.025	20.879	-0.017	-0.017	0.000	0.000	0.000	0.000
59	A	60	THR	0	-0.058	-0.034	22.755	0.004	0.004	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.001	-0.013	19.672	0.004	0.004	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.013	-0.005	17.343	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	63	THR	0	-0.071	-0.040	20.171	0.002	0.002	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.042	-0.007	23.420	0.011	0.011	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.011	-0.009	18.378	0.013	0.013	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.849	-0.894	20.985	-0.219	-0.219	0.000	0.000	0.000	0.000
66	A	67	ASP	-1	-0.867	-0.960	19.119	-0.219	-0.219	0.000	0.000	0.000	0.000
67	A	68	PHE	0	-0.047	-0.012	12.348	0.002	0.002	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.001	0.002	12.714	-0.030	-0.030	0.000	0.000	0.000	0.000
69	A	70	TYR	0	-0.004	-0.020	7.886	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	71	HIS	0	-0.047	-0.051	9.021	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.796	0.891	6.973	-0.114	-0.114	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.032	0.011	3.935	-1.481	-1.140	0.003	-0.094	-0.248	0.000
73	A	74	LEU	0	-0.047	-0.021	6.092	0.616	0.616	0.000	0.000	0.000	0.000
74	A	75	ALA	0	0.056	0.028	7.442	-0.211	-0.211	0.000	0.000	0.000	0.000
75	A	76	SER	0	-0.047	-0.033	9.034	0.107	0.107	0.000	0.000	0.000	0.000
76	A	77	ALA	0	-0.002	-0.023	12.109	0.005	0.005	0.000	0.000	0.000	0.000
77	A	78	ASP	-1	-0.860	-0.921	14.420	-0.056	-0.056	0.000	0.000	0.000	0.000
78	A	79	GLY	0	0.034	0.034	11.161	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.920	0.977	12.001	-0.011	-0.011	0.000	0.000	0.000	0.000
80	A	81	SER	0	-0.030	-0.020	12.696	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	82	VAL	0	-0.021	0.005	6.849	0.005	0.005	0.000	0.000	0.000	0.000
82	A	83	VAL	0	0.007	0.000	9.340	0.055	0.055	0.000	0.000	0.000	0.000
83	A	84	LEU	0	-0.012	-0.004	6.845	-0.083	-0.083	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.738	-0.844	9.590	-0.079	-0.079	0.000	0.000	0.000	0.000
85	A	86	PHE	0	0.021	0.014	10.563	-0.094	-0.094	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.022	0.000	13.141	0.067	0.067	0.000	0.000	0.000	0.000
87	A	88	ALA	0	0.016	0.014	15.956	-0.040	-0.040	0.000	0.000	0.000	0.000
88	A	89	ARG	1	0.877	0.936	18.772	0.197	0.197	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.031	0.022	22.562	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	91	GLY	0	-0.004	-0.004	25.414	0.013	0.013	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.911	-0.957	27.314	-0.099	-0.099	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.895	0.942	26.444	0.100	0.100	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.882	-0.918	22.773	-0.159	-0.159	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.090	-0.046	19.284	0.016	0.016	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.791	0.867	15.164	0.182	0.182	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.044	0.010	16.450	0.030	0.030	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.056	-0.017	13.693	-0.022	-0.022	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.739	-0.859	12.309	-0.457	-0.457	0.000	0.000	0.000	0.000
99	A	100	MET	0	-0.054	-0.033	12.402	-0.049	-0.049	0.000	0.000	0.000	0.000
100	A	101	ILE	0	-0.002	0.007	11.107	0.027	0.027	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.974	0.999	13.034	0.119	0.119	0.000	0.000	0.000	0.000
102	A	103	PHE	0	-0.007	-0.025	10.572	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.779	-0.895	15.704	-0.112	-0.112	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.868	-0.944	17.165	-0.069	-0.069	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.889	-0.938	18.384	-0.067	-0.067	0.000	0.000	0.000	0.000
106	A	107	GLY	0	-0.001	-0.002	15.329	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.750	0.893	15.563	0.060	0.060	0.000	0.000	0.000	0.000
108	A	109	ILE	0	0.000	0.001	14.391	0.001	0.001	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.014	-0.011	17.266	0.028	0.028	0.000	0.000	0.000	0.000
110	A	111	ASP	-1	-0.909	-0.944	18.407	-0.140	-0.140	0.000	0.000	0.000	0.000
111	A	112	PHE	0	0.029	0.019	14.756	-0.027	-0.027	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.909	-0.961	17.433	-0.123	-0.123	0.000	0.000	0.000	0.000
113	A	114	VAL	0	0.018	0.014	17.241	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	115	MET	0	-0.047	-0.013	18.438	0.035	0.035	0.000	0.000	0.000	0.000
115	A	116	VAL	0	0.021	0.007	18.952	-0.023	-0.023	0.000	0.000	0.000	0.000
116	A	117	ARG	1	0.905	0.972	20.329	0.133	0.133	0.000	0.000	0.000	0.000
117	A	118	PRO	0	0.022	0.004	22.130	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	119	MET	0	0.074	0.022	25.472	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	120	SER	0	0.019	0.005	28.466	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	121	GLY	0	0.044	0.022	24.976	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	122	LEU	0	0.012	0.008	24.784	-0.007	-0.007	0.000	0.000	0.000	0.000
122	A	123	GLN	0	-0.005	-0.023	26.358	0.002	0.002	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.028	0.030	27.418	0.001	0.001	0.000	0.000	0.000	0.000
124	A	125	LEU	0	0.007	0.003	22.557	0.000	0.000	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.023	-0.006	26.373	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	127	GLU	-1	-0.977	-0.988	29.006	-0.089	-0.089	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.898	-0.952	27.817	-0.119	-0.119	0.000	0.000	0.000	0.000
128	A	129	MET	0	-0.021	-0.013	25.315	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	130	GLY	0	0.005	0.008	28.723	0.002	0.002	0.000	0.000	0.000	0.000
130	A	131	ARG	1	0.857	0.940	32.447	0.108	0.108	0.000	0.000	0.000	0.000
131	A	132	ARG	1	0.949	0.963	27.890	0.154	0.154	0.000	0.000	0.000	0.000
132	A	133	LEU	0	-0.061	0.003	30.534	0.000	0.000	0.000	0.000	0.000	0.000
133	A	134	ALA	0	-0.017	-0.001	32.599	0.007	0.007	0.000	0.000	0.000	0.000
134	A	135	SER	0	-0.040	-0.023	32.300	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)