FMO DATABASE

FMODB ID: 17GRZ

Calculation Name: 3SMD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SMD

Chain ID: A

ChEMBL ID:

UniProt ID: A0REX4

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	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	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1240167.325961
FMO2-HF: Nuclear repulsion	1186684.071761
FMO2-HF: Total energy	-53483.254201
FMO2-MP2: Total energy	-53642.665134

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:LEU)

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

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.
-0.221	2.976	0.04	-0.979	-2.257	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.022

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	LEU	0	0.028	-0.008	3.858	-1.690	-0.245	-0.010	-0.716	-0.718	0.004
4	A	6	TYR	0	0.013	0.021	6.491	0.044	0.044	0.000	0.000	0.000	0.000
5	A	7	TYR	0	0.037	-0.013	3.666	-0.506	-0.111	0.004	-0.052	-0.347	0.000
6	A	8	LYS	1	0.849	0.925	2.988	0.077	0.735	0.047	-0.139	-0.566	0.000
7	A	9	LYS	1	0.880	0.936	4.458	0.224	0.354	0.000	-0.019	-0.111	0.000
8	A	10	ILE	0	0.002	0.000	7.709	0.051	0.051	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.834	0.899	4.588	-0.089	0.041	-0.001	-0.002	-0.126	0.000
10	A	12	GLU	-1	-0.861	-0.931	7.310	-0.342	-0.342	0.000	0.000	0.000	0.000
11	A	13	GLN	0	-0.032	-0.006	9.382	0.001	0.001	0.000	0.000	0.000	0.000
12	A	14	LEU	0	0.006	0.016	10.243	0.017	0.017	0.000	0.000	0.000	0.000
13	A	15	GLY	0	0.041	0.031	10.974	0.010	0.010	0.000	0.000	0.000	0.000
14	A	16	HIS	1	0.831	0.905	9.519	0.130	0.130	0.000	0.000	0.000	0.000
15	A	17	GLU	-1	-0.827	-0.890	11.428	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.013	-0.006	10.333	0.003	0.003	0.000	0.000	0.000	0.000
17	A	19	ILE	0	0.014	0.021	5.711	0.002	0.002	0.000	0.000	0.000	0.000
18	A	20	PHE	0	-0.026	-0.011	9.254	0.043	0.043	0.000	0.000	0.000	0.000
19	A	21	MET	0	0.005	-0.004	4.059	-0.051	0.112	0.000	-0.021	-0.142	0.000
20	A	22	PRO	0	0.040	0.023	9.414	0.023	0.023	0.000	0.000	0.000	0.000
21	A	23	SER	0	-0.006	0.000	9.073	0.238	0.238	0.000	0.000	0.000	0.000
22	A	24	VAL	0	-0.017	-0.002	10.816	-0.164	-0.164	0.000	0.000	0.000	0.000
23	A	25	ALA	0	0.014	0.000	12.031	0.088	0.088	0.000	0.000	0.000	0.000
24	A	26	ALA	0	0.024	0.010	14.530	-0.055	-0.055	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.035	-0.015	17.064	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	28	ILE	0	0.014	0.007	17.660	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	29	LYS	1	0.830	0.898	21.340	-0.145	-0.145	0.000	0.000	0.000	0.000
28	A	30	ASN	0	-0.034	-0.031	24.816	0.003	0.003	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.938	-0.970	26.962	0.067	0.067	0.000	0.000	0.000	0.000
30	A	32	GLN	0	-0.057	-0.031	30.069	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	33	GLY	0	-0.028	-0.015	29.406	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	34	GLU	-1	-0.894	-0.911	26.279	0.079	0.079	0.000	0.000	0.000	0.000
33	A	35	LEU	0	-0.035	-0.026	22.514	0.010	0.010	0.000	0.000	0.000	0.000
34	A	36	LEU	0	-0.032	-0.014	18.066	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	37	PHE	0	-0.012	-0.019	17.433	0.022	0.022	0.000	0.000	0.000	0.000
36	A	38	GLN	0	-0.032	-0.038	10.232	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	39	TYR	0	-0.054	-0.038	15.370	0.005	0.005	0.000	0.000	0.000	0.000
38	A	40	PRO	0	0.056	0.019	10.429	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	41	GLY	0	-0.005	0.006	11.298	0.000	0.000	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.014	-0.017	11.397	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.935	-0.948	13.293	-0.066	-0.066	0.000	0.000	0.000	0.000
42	A	44	TYR	0	-0.035	-0.014	14.452	0.018	0.018	0.000	0.000	0.000	0.000
43	A	45	TRP	0	0.007	0.001	16.026	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	46	SER	0	0.004	-0.022	12.584	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.021	-0.001	14.646	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	48	PRO	0	0.006	0.004	12.560	0.044	0.044	0.000	0.000	0.000	0.000
47	A	49	ALA	0	-0.010	-0.010	10.872	-0.061	-0.061	0.000	0.000	0.000	0.000
48	A	50	GLY	0	0.038	0.037	7.283	0.124	0.124	0.000	0.000	0.000	0.000
49	A	51	ALA	0	-0.038	-0.016	5.373	-0.408	-0.408	0.000	0.000	0.000	0.000
50	A	52	ILE	0	-0.015	-0.004	7.409	0.031	0.031	0.000	0.000	0.000	0.000
51	A	53	GLU	-1	-0.753	-0.855	6.892	0.460	0.460	0.000	0.000	0.000	0.000
52	A	54	PRO	0	-0.077	-0.056	9.676	-0.071	-0.071	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.005	0.003	12.733	-0.047	-0.047	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.786	-0.843	11.088	0.750	0.750	0.000	0.000	0.000	0.000
55	A	57	THR	0	-0.033	-0.045	15.154	0.000	0.000	0.000	0.000	0.000	0.000
56	A	58	PRO	0	-0.007	-0.022	15.127	0.049	0.049	0.000	0.000	0.000	0.000
57	A	59	GLU	-1	-0.857	-0.947	16.016	0.306	0.306	0.000	0.000	0.000	0.000
58	A	60	GLU	-1	-0.839	-0.886	16.519	0.265	0.265	0.000	0.000	0.000	0.000
59	A	61	ALA	0	0.017	0.025	11.826	0.025	0.025	0.000	0.000	0.000	0.000
60	A	62	VAL	0	-0.031	-0.024	12.588	0.095	0.095	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.041	-0.016	14.572	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	64	ARG	1	0.715	0.818	7.732	-1.403	-1.403	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.793	-0.899	7.532	2.388	2.388	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.004	-0.004	10.812	-0.066	-0.066	0.000	0.000	0.000	0.000
65	A	67	TRP	0	-0.038	0.013	13.380	-0.072	-0.072	0.000	0.000	0.000	0.000
66	A	68	GLU	-1	-0.846	-0.926	8.877	0.885	0.885	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.822	-0.903	8.625	0.299	0.299	0.000	0.000	0.000	0.000
68	A	70	THR	0	-0.101	-0.082	11.335	-0.124	-0.124	0.000	0.000	0.000	0.000
69	A	71	GLY	0	-0.002	0.007	14.972	-0.055	-0.055	0.000	0.000	0.000	0.000
70	A	72	LEU	0	-0.040	-0.019	16.809	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.996	0.995	17.960	-0.112	-0.112	0.000	0.000	0.000	0.000
72	A	74	VAL	0	-0.003	0.001	18.050	-0.031	-0.031	0.000	0.000	0.000	0.000
73	A	75	GLN	0	-0.031	-0.024	20.794	0.006	0.006	0.000	0.000	0.000	0.000
74	A	76	VAL	0	0.040	0.010	20.092	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	77	LYS	1	0.809	0.891	22.446	-0.142	-0.142	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.880	0.920	24.475	-0.149	-0.149	0.000	0.000	0.000	0.000
77	A	79	GLN	0	0.045	0.033	21.266	0.006	0.006	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.787	0.883	21.986	-0.169	-0.169	0.000	0.000	0.000	0.000
79	A	81	GLY	0	-0.021	-0.019	22.227	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	82	VAL	0	0.016	0.014	17.666	0.025	0.025	0.000	0.000	0.000	0.000
81	A	83	PHE	0	-0.041	-0.017	17.481	-0.038	-0.038	0.000	0.000	0.000	0.000
82	A	84	GLY	0	0.089	0.038	16.005	0.042	0.042	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.002	0.018	16.587	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.955	0.959	16.514	-0.062	-0.062	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.888	-0.942	16.951	0.077	0.077	0.000	0.000	0.000	0.000
86	A	88	PHE	0	0.007	0.001	13.811	0.003	0.003	0.000	0.000	0.000	0.000
87	A	89	ARG	1	0.784	0.876	12.486	-0.053	-0.053	0.000	0.000	0.000	0.000
88	A	90	TYR	0	0.042	0.021	7.451	-0.022	-0.022	0.000	0.000	0.000	0.000
89	A	91	THR	0	-0.068	-0.052	9.708	0.015	0.015	0.000	0.000	0.000	0.000
90	A	92	TYR	0	0.032	0.032	4.267	-0.465	-0.189	0.000	-0.030	-0.247	0.000
91	A	93	ALA	0	0.032	0.009	8.597	0.038	0.038	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.026	-0.024	6.676	0.020	0.020	0.000	0.000	0.000	0.000
93	A	95	GLY	0	-0.002	-0.008	10.242	0.024	0.024	0.000	0.000	0.000	0.000
94	A	96	ASP	-1	-0.847	-0.898	6.399	-0.146	-0.146	0.000	0.000	0.000	0.000
95	A	97	LYS	1	0.826	0.898	8.208	0.016	0.016	0.000	0.000	0.000	0.000
96	A	98	VAL	0	-0.008	-0.003	5.577	0.014	0.014	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.813	-0.896	9.052	0.094	0.094	0.000	0.000	0.000	0.000
98	A	100	TYR	0	0.007	0.021	5.265	-0.086	-0.086	0.000	0.000	0.000	0.000
99	A	101	ILE	0	-0.026	-0.014	11.192	-0.069	-0.069	0.000	0.000	0.000	0.000
100	A	102	VAL	0	-0.003	0.003	11.914	0.056	0.056	0.000	0.000	0.000	0.000
101	A	103	VAL	0	0.003	0.004	14.187	-0.071	-0.071	0.000	0.000	0.000	0.000
102	A	104	VAL	0	-0.015	-0.002	16.151	0.043	0.043	0.000	0.000	0.000	0.000
103	A	105	PHE	0	0.045	0.005	17.264	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	106	GLU	-1	-0.790	-0.858	19.927	0.150	0.150	0.000	0.000	0.000	0.000
105	A	107	CYS	0	-0.052	-0.022	19.828	0.006	0.006	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.767	-0.852	22.162	0.119	0.119	0.000	0.000	0.000	0.000
107	A	109	ILE	0	0.027	0.004	22.121	0.013	0.013	0.000	0.000	0.000	0.000
108	A	110	THR	0	-0.063	-0.034	23.458	-0.016	-0.016	0.000	0.000	0.000	0.000
109	A	111	SER	0	0.003	-0.012	23.675	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	112	GLY	0	0.012	0.026	21.258	0.019	0.019	0.000	0.000	0.000	0.000
111	A	113	LYS	1	0.880	0.929	20.421	-0.085	-0.085	0.000	0.000	0.000	0.000
112	A	114	LEU	0	0.069	0.041	18.808	0.015	0.015	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.788	0.910	10.736	-0.315	-0.315	0.000	0.000	0.000	0.000
114	A	123	LYS	1	0.896	0.945	14.652	-0.048	-0.048	0.000	0.000	0.000	0.000
115	A	124	LEU	0	-0.015	-0.012	14.700	0.023	0.023	0.000	0.000	0.000	0.000
116	A	125	GLN	0	-0.006	0.003	17.895	-0.032	-0.032	0.000	0.000	0.000	0.000
117	A	126	TYR	0	0.040	0.026	20.846	0.023	0.023	0.000	0.000	0.000	0.000
118	A	127	PHE	0	0.059	0.027	21.171	-0.011	-0.011	0.000	0.000	0.000	0.000
119	A	128	SER	0	0.033	-0.012	25.642	0.010	0.010	0.000	0.000	0.000	0.000
120	A	129	PHE	0	0.007	-0.015	27.221	0.003	0.003	0.000	0.000	0.000	0.000
121	A	130	SER	0	-0.034	-0.038	28.280	0.001	0.001	0.000	0.000	0.000	0.000
122	A	131	GLU	-1	-0.875	-0.889	27.950	0.048	0.048	0.000	0.000	0.000	0.000
123	A	132	LYS	1	0.760	0.896	23.394	-0.091	-0.091	0.000	0.000	0.000	0.000
124	A	133	PRO	0	0.005	0.021	20.195	-0.006	-0.006	0.000	0.000	0.000	0.000
125	A	134	PRO	0	-0.010	-0.005	21.011	0.011	0.011	0.000	0.000	0.000	0.000
126	A	135	LEU	0	0.006	-0.008	16.938	0.002	0.002	0.000	0.000	0.000	0.000
127	A	136	ALA	0	0.021	0.016	13.285	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	137	LEU	0	-0.013	0.006	11.499	0.003	0.003	0.000	0.000	0.000	0.000
129	A	138	PRO	0	0.019	0.027	15.792	0.001	0.001	0.000	0.000	0.000	0.000
130	A	139	TYR	0	0.007	-0.019	13.175	0.010	0.010	0.000	0.000	0.000	0.000
131	A	140	PRO	0	-0.002	0.000	19.815	-0.015	-0.015	0.000	0.000	0.000	0.000
132	A	141	ASP	-1	-0.733	-0.879	23.634	0.106	0.106	0.000	0.000	0.000	0.000
133	A	142	LYS	1	0.888	0.952	24.665	-0.140	-0.140	0.000	0.000	0.000	0.000
134	A	143	ILE	0	-0.033	-0.008	19.743	0.001	0.001	0.000	0.000	0.000	0.000
135	A	144	PHE	0	0.051	0.020	20.693	0.008	0.008	0.000	0.000	0.000	0.000
136	A	145	LEU	0	0.008	0.032	25.128	0.001	0.001	0.000	0.000	0.000	0.000

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