FMO DATABASE

FMODB ID: Q12LY

Calculation Name: 3SUM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SUM

Chain ID: A

ChEMBL ID:

UniProt ID: B2C3I4

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1185712.584163
FMO2-HF: Nuclear repulsion	1133012.645183
FMO2-HF: Total energy	-52699.93898
FMO2-MP2: Total energy	-52852.047379

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:22:ASN)

Summations of interaction energy for fragment #1(A:22:ASN)

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.
1.999	4.811	0.014	-0.774	-2.053	0.002

Interaction energy analysis for fragmet #1(A:22:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.032

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	24	LEU	0	0.013	0.011	3.678	1.076	2.745	0.001	-0.574	-1.097	0.002
4	A	25	ILE	0	-0.011	-0.003	6.128	-0.753	-0.753	0.000	0.000	0.000	0.000
5	A	26	LYS	1	0.925	0.948	9.838	-0.622	-0.622	0.000	0.000	0.000	0.000
6	A	27	TRP	0	-0.030	-0.016	12.553	-0.048	-0.048	0.000	0.000	0.000	0.000
7	A	28	ASP	-1	-0.843	-0.929	16.176	0.226	0.226	0.000	0.000	0.000	0.000
8	A	29	ASP	-1	-0.897	-0.955	19.242	0.280	0.280	0.000	0.000	0.000	0.000
9	A	30	LYS	1	0.856	0.919	21.781	-0.133	-0.133	0.000	0.000	0.000	0.000
10	A	31	PHE	0	-0.046	-0.041	18.293	-0.023	-0.023	0.000	0.000	0.000	0.000
11	A	32	GLN	0	-0.001	-0.010	21.899	0.057	0.057	0.000	0.000	0.000	0.000
12	A	33	ASN	0	0.001	0.010	24.403	-0.026	-0.026	0.000	0.000	0.000	0.000
13	A	34	ASP	-1	-0.849	-0.928	27.306	0.171	0.171	0.000	0.000	0.000	0.000
14	A	35	THR	0	-0.044	-0.028	29.524	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	36	LEU	0	-0.020	-0.003	26.409	-0.020	-0.020	0.000	0.000	0.000	0.000
16	A	37	SER	0	0.032	0.007	29.883	0.007	0.007	0.000	0.000	0.000	0.000
17	A	38	ILE	0	0.031	0.000	27.792	0.003	0.003	0.000	0.000	0.000	0.000
18	A	39	SER	0	-0.067	-0.041	27.415	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	40	GLU	-1	-0.927	-0.939	27.394	0.041	0.041	0.000	0.000	0.000	0.000
20	A	41	PHE	0	-0.027	0.004	22.330	0.006	0.006	0.000	0.000	0.000	0.000
21	A	42	LYS	1	0.825	0.883	19.224	0.067	0.067	0.000	0.000	0.000	0.000
22	A	43	CYS	0	-0.042	0.005	17.084	0.037	0.037	0.000	0.000	0.000	0.000
23	A	44	SER	0	0.053	0.039	22.764	0.010	0.010	0.000	0.000	0.000	0.000
24	A	45	ALA	0	0.014	-0.004	26.482	0.007	0.007	0.000	0.000	0.000	0.000
25	A	46	ALA	0	-0.033	-0.025	23.400	0.004	0.004	0.000	0.000	0.000	0.000
26	A	47	LEU	0	0.024	0.006	22.975	0.013	0.013	0.000	0.000	0.000	0.000
27	A	48	ALA	0	0.030	0.018	26.323	0.010	0.010	0.000	0.000	0.000	0.000
28	A	49	LYS	1	0.908	0.946	27.701	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	50	LEU	0	-0.016	0.007	23.452	0.006	0.006	0.000	0.000	0.000	0.000
30	A	51	GLY	0	0.086	0.057	27.728	0.018	0.018	0.000	0.000	0.000	0.000
31	A	52	PRO	0	-0.012	-0.016	30.720	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	53	ASP	-1	-0.830	-0.905	32.419	0.080	0.080	0.000	0.000	0.000	0.000
33	A	54	PRO	0	-0.034	-0.024	31.608	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	55	LYS	1	0.883	0.946	32.932	-0.073	-0.073	0.000	0.000	0.000	0.000
35	A	56	HIS	0	-0.097	-0.056	36.043	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	57	PRO	0	-0.010	0.008	32.808	0.007	0.007	0.000	0.000	0.000	0.000
37	A	58	PRO	0	-0.004	0.024	29.607	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	59	THR	0	-0.086	-0.056	32.508	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	60	LYS	1	0.872	0.924	31.135	-0.115	-0.115	0.000	0.000	0.000	0.000
40	A	61	LEU	0	-0.018	-0.002	23.723	0.006	0.006	0.000	0.000	0.000	0.000
41	A	62	GLY	0	0.037	0.000	27.469	0.016	0.016	0.000	0.000	0.000	0.000
42	A	63	GLU	-1	-0.881	-0.920	29.580	0.122	0.122	0.000	0.000	0.000	0.000
43	A	64	VAL	0	-0.067	-0.020	24.941	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	65	LEU	0	-0.015	-0.025	26.297	0.021	0.021	0.000	0.000	0.000	0.000
45	A	66	ASN	0	-0.032	-0.030	20.435	0.004	0.004	0.000	0.000	0.000	0.000
46	A	67	PHE	0	0.014	0.079	23.158	0.041	0.041	0.000	0.000	0.000	0.000
47	A	68	PRO	0	0.004	-0.009	23.429	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	69	HIS	0	-0.008	-0.034	19.378	0.050	0.050	0.000	0.000	0.000	0.000
49	A	70	PHE	0	-0.033	-0.016	19.016	0.007	0.007	0.000	0.000	0.000	0.000
50	A	71	VAL	0	0.015	-0.011	13.782	0.060	0.060	0.000	0.000	0.000	0.000
51	A	72	ALA	0	-0.008	0.022	15.895	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	73	ALA	0	0.019	-0.012	11.637	0.107	0.107	0.000	0.000	0.000	0.000
53	A	74	PRO	0	0.017	0.025	9.647	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	75	GLU	-1	-0.819	-0.909	12.857	-0.130	-0.130	0.000	0.000	0.000	0.000
55	A	76	ALA	0	-0.035	0.010	13.722	-0.115	-0.115	0.000	0.000	0.000	0.000
56	A	77	GLN	0	-0.022	-0.038	6.238	0.054	0.054	0.000	0.000	0.000	0.000
57	A	78	THR	0	-0.009	-0.015	11.001	0.173	0.173	0.000	0.000	0.000	0.000
58	A	79	GLU	-1	-0.868	-0.921	13.318	-0.155	-0.155	0.000	0.000	0.000	0.000
59	A	81	GLY	0	0.029	0.013	19.501	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	82	SER	0	-0.068	-0.034	15.813	0.042	0.042	0.000	0.000	0.000	0.000
61	A	83	CYS	0	-0.038	0.011	17.183	0.092	0.092	0.000	0.000	0.000	0.000
62	A	84	TRP	0	0.005	-0.013	8.620	0.038	0.038	0.000	0.000	0.000	0.000
63	A	85	LYS	1	0.894	0.953	13.147	-0.918	-0.918	0.000	0.000	0.000	0.000
64	A	86	LEU	0	-0.011	-0.003	9.818	0.245	0.245	0.000	0.000	0.000	0.000
65	A	87	ARG	1	0.920	0.957	9.835	-1.406	-1.406	0.000	0.000	0.000	0.000
66	A	88	TYR	0	-0.012	-0.030	9.212	0.602	0.602	0.000	0.000	0.000	0.000
67	A	89	LYS	1	0.827	0.906	10.826	-1.518	-1.518	0.000	0.000	0.000	0.000
68	A	90	GLY	0	-0.021	-0.007	12.859	0.013	0.013	0.000	0.000	0.000	0.000
69	A	91	ASN	0	-0.072	-0.031	14.736	-0.201	-0.201	0.000	0.000	0.000	0.000
70	A	92	HIS	0	0.028	-0.016	14.013	0.242	0.242	0.000	0.000	0.000	0.000
71	A	93	ALA	0	-0.012	0.004	14.826	-0.119	-0.119	0.000	0.000	0.000	0.000
72	A	94	PHE	0	0.022	0.005	15.154	0.103	0.103	0.000	0.000	0.000	0.000
73	A	95	VAL	0	0.021	0.006	13.879	-0.040	-0.040	0.000	0.000	0.000	0.000
74	A	96	THR	0	0.031	0.008	16.627	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	97	VAL	0	-0.045	-0.007	14.298	0.022	0.022	0.000	0.000	0.000	0.000
76	A	98	VAL	0	0.020	-0.003	17.094	-0.051	-0.051	0.000	0.000	0.000	0.000
77	A	99	ASP	-1	-0.729	-0.863	18.258	0.054	0.054	0.000	0.000	0.000	0.000
78	A	100	ARG	1	0.778	0.878	15.666	0.088	0.088	0.000	0.000	0.000	0.000
79	A	101	VAL	0	-0.018	0.002	12.641	0.040	0.040	0.000	0.000	0.000	0.000
80	A	102	GLU	-1	-0.832	-0.916	14.145	-0.202	-0.202	0.000	0.000	0.000	0.000
81	A	103	GLU	-1	-0.910	-0.942	9.928	-0.530	-0.530	0.000	0.000	0.000	0.000
82	A	104	ALA	0	-0.014	-0.021	7.344	0.091	0.091	0.000	0.000	0.000	0.000
83	A	105	ASN	0	-0.059	-0.036	4.034	-0.301	0.193	0.001	-0.104	-0.392	0.000
84	A	106	LEU	0	0.033	0.025	6.013	0.747	0.747	0.000	0.000	0.000	0.000
85	A	107	PHE	0	0.033	0.001	7.912	-0.139	-0.139	0.000	0.000	0.000	0.000
86	A	108	VAL	0	-0.017	-0.012	10.993	0.164	0.164	0.000	0.000	0.000	0.000
87	A	109	GLY	0	0.054	0.018	14.155	-0.064	-0.064	0.000	0.000	0.000	0.000
88	A	110	GLY	0	0.034	0.032	16.173	-0.019	-0.019	0.000	0.000	0.000	0.000
89	A	111	THR	0	0.052	0.008	18.620	0.080	0.080	0.000	0.000	0.000	0.000
90	A	112	ASP	-1	-0.800	-0.894	19.714	0.478	0.478	0.000	0.000	0.000	0.000
91	A	113	LEU	0	-0.017	0.022	16.007	0.048	0.048	0.000	0.000	0.000	0.000
92	A	114	VAL	0	0.006	-0.001	14.014	0.091	0.091	0.000	0.000	0.000	0.000
93	A	115	LYS	1	0.877	0.963	16.054	-0.360	-0.360	0.000	0.000	0.000	0.000
94	A	116	ASN	0	-0.065	-0.033	18.581	0.007	0.007	0.000	0.000	0.000	0.000
95	A	117	LEU	0	-0.034	0.004	11.853	0.037	0.037	0.000	0.000	0.000	0.000
96	A	118	THR	0	-0.053	-0.063	12.040	0.115	0.115	0.000	0.000	0.000	0.000
97	A	119	THR	0	0.033	0.008	14.608	-0.024	-0.024	0.000	0.000	0.000	0.000
98	A	120	PHE	0	-0.017	-0.015	16.157	0.037	0.037	0.000	0.000	0.000	0.000
99	A	121	ASN	0	-0.034	-0.020	18.208	-0.030	-0.030	0.000	0.000	0.000	0.000
100	A	122	GLY	0	0.041	0.018	21.863	-0.035	-0.035	0.000	0.000	0.000	0.000
101	A	123	ALA	0	-0.002	0.008	19.682	-0.032	-0.032	0.000	0.000	0.000	0.000
102	A	124	PRO	0	0.024	0.030	18.904	0.099	0.099	0.000	0.000	0.000	0.000
103	A	125	GLU	-1	-0.777	-0.857	14.549	1.159	1.159	0.000	0.000	0.000	0.000
104	A	126	GLY	0	0.031	-0.002	13.183	0.031	0.031	0.000	0.000	0.000	0.000
105	A	127	TYR	0	-0.057	-0.020	13.973	-0.054	-0.054	0.000	0.000	0.000	0.000
106	A	128	ASP	-1	-0.831	-0.926	17.113	0.520	0.520	0.000	0.000	0.000	0.000
107	A	129	TRP	0	-0.078	-0.030	11.771	-0.127	-0.127	0.000	0.000	0.000	0.000
108	A	130	GLY	0	0.029	0.024	14.922	-0.071	-0.071	0.000	0.000	0.000	0.000
109	A	131	THR	0	-0.082	-0.042	8.381	-0.094	-0.094	0.000	0.000	0.000	0.000
110	A	132	ALA	0	0.021	0.014	9.329	-0.063	-0.063	0.000	0.000	0.000	0.000
111	A	133	GLN	0	-0.012	-0.004	3.742	2.393	2.931	0.013	-0.093	-0.457	0.000
112	A	134	LEU	0	-0.033	-0.016	5.125	-1.087	-1.087	0.000	0.000	0.000	0.000
113	A	135	PHE	0	-0.036	-0.020	4.751	0.984	1.095	-0.001	-0.003	-0.107	0.000
114	A	136	SER	0	-0.002	-0.013	5.793	0.346	0.346	0.000	0.000	0.000	0.000
115	A	137	ALA	0	0.002	-0.002	6.666	-0.470	-0.470	0.000	0.000	0.000	0.000
116	A	138	TYR	0	-0.054	-0.035	7.596	0.028	0.028	0.000	0.000	0.000	0.000
117	A	139	GLN	0	-0.005	0.012	10.309	-0.040	-0.040	0.000	0.000	0.000	0.000
118	A	140	VAL	0	-0.017	-0.021	13.492	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	141	ASP	-1	-0.741	-0.828	16.727	0.169	0.169	0.000	0.000	0.000	0.000
120	A	142	GLY	0	0.107	0.031	20.331	0.033	0.033	0.000	0.000	0.000	0.000
121	A	143	SER	0	-0.031	-0.017	21.689	0.019	0.019	0.000	0.000	0.000	0.000
122	A	144	CYS	0	-0.074	-0.028	19.774	0.019	0.019	0.000	0.000	0.000	0.000
123	A	146	GLN	0	-0.018	-0.019	21.854	-0.045	-0.045	0.000	0.000	0.000	0.000
124	A	147	GLN	0	-0.011	-0.001	21.153	-0.041	-0.041	0.000	0.000	0.000	0.000
125	A	148	ASN	0	0.004	-0.007	25.910	0.009	0.009	0.000	0.000	0.000	0.000
126	A	149	THR	0	-0.043	-0.051	23.777	-0.019	-0.019	0.000	0.000	0.000	0.000
127	A	150	GLY	0	-0.006	0.006	27.246	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	151	LYS	1	0.847	0.919	23.493	-0.165	-0.165	0.000	0.000	0.000	0.000
129	A	152	GLN	0	-0.011	-0.002	27.165	0.000	0.000	0.000	0.000	0.000	0.000
130	A	154	GLY	0	-0.003	-0.005	22.821	0.007	0.007	0.000	0.000	0.000	0.000
131	A	155	ASP	-1	-0.889	-0.961	20.331	0.529	0.529	0.000	0.000	0.000	0.000
132	A	156	PRO	0	-0.018	0.026	16.506	0.097	0.097	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:22:ASN)