FMO DATABASE

FMODB ID: 9M862

Calculation Name: 3D79-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D79

Chain ID: A

ChEMBL ID:

UniProt ID: O58465

Base Structure: X-ray

Registration Date: 2023-09-27

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1763479.934313
FMO2-HF: Nuclear repulsion	1697358.09643
FMO2-HF: Total energy	-66121.837883
FMO2-MP2: Total energy	-66315.363172

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:5:ILE)

Summations of interaction energy for fragment #1(A:5:ILE)

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.
-0.572	2.071	1.785	-1.316	-3.112	-0.003

Interaction energy analysis for fragmet #1(A:5:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.014

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	7	HIS	0	0.038	0.027	2.319	-1.372	0.873	1.786	-1.246	-2.785	-0.003
4	A	8	PRO	0	0.007	0.008	5.747	0.332	0.332	0.000	0.000	0.000	0.000
5	A	9	LEU	0	0.030	0.016	9.384	-0.079	-0.079	0.000	0.000	0.000	0.000
6	A	10	SER	0	0.018	0.015	11.852	0.110	0.110	0.000	0.000	0.000	0.000
7	A	11	LYS	1	1.023	0.990	14.872	0.206	0.206	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.923	0.959	18.355	0.267	0.267	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.830	-0.920	14.292	-0.408	-0.408	0.000	0.000	0.000	0.000
10	A	14	VAL	0	0.005	0.006	15.933	0.029	0.029	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.883	0.923	17.963	0.166	0.166	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.872	-0.925	19.590	-0.129	-0.129	0.000	0.000	0.000	0.000
13	A	17	ILE	0	0.035	0.022	15.316	0.015	0.015	0.000	0.000	0.000	0.000
14	A	18	ILE	0	-0.005	-0.005	19.978	0.023	0.023	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.009	0.002	22.937	0.017	0.017	0.000	0.000	0.000	0.000
16	A	20	GLN	0	0.026	0.003	20.061	0.025	0.025	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.002	-0.008	20.303	0.014	0.014	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.011	-0.017	24.241	0.014	0.014	0.000	0.000	0.000	0.000
19	A	23	GLN	0	-0.077	-0.022	27.356	0.005	0.005	0.000	0.000	0.000	0.000
20	A	24	MET	0	-0.098	-0.036	22.345	0.007	0.007	0.000	0.000	0.000	0.000
21	A	25	PHE	0	0.001	-0.014	23.643	0.007	0.007	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.063	0.044	28.820	0.006	0.006	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.883	-0.966	29.232	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	28	GLU	-1	-0.942	-0.963	29.236	0.017	0.017	0.000	0.000	0.000	0.000
25	A	29	ILE	0	0.022	0.011	26.596	0.004	0.004	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.007	-0.002	25.031	0.006	0.006	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.871	0.937	24.401	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.920	0.955	24.964	-0.064	-0.064	0.000	0.000	0.000	0.000
29	A	33	MET	0	-0.046	0.006	21.158	0.009	0.009	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.022	-0.011	17.731	0.002	0.002	0.000	0.000	0.000	0.000
31	A	35	ASN	0	0.023	0.021	21.112	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.930	0.936	20.934	0.060	0.060	0.000	0.000	0.000	0.000
33	A	37	LYS	1	0.853	0.912	21.221	0.019	0.019	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.770	-0.855	17.504	0.009	0.009	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.940	-0.964	12.536	-0.084	-0.084	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.031	-0.012	12.880	0.049	0.049	0.000	0.000	0.000	0.000
37	A	41	LYS	1	0.847	0.913	7.524	-0.213	-0.213	0.000	0.000	0.000	0.000
38	A	42	VAL	0	-0.004	0.008	6.659	0.270	0.270	0.000	0.000	0.000	0.000
39	A	43	ALA	0	0.001	-0.002	4.057	-1.109	-1.018	-0.001	-0.041	-0.049	0.000
40	A	44	GLU	-1	-0.825	-0.881	3.546	-1.080	-0.773	0.000	-0.029	-0.278	0.000
41	A	45	PHE	0	-0.034	-0.005	5.370	0.853	0.853	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.787	-0.917	8.121	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.823	0.875	7.379	0.660	0.660	0.000	0.000	0.000	0.000
44	A	48	THR	0	-0.085	-0.028	11.443	-0.021	-0.021	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.021	-0.001	11.613	0.026	0.026	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.788	-0.874	8.272	-0.855	-0.855	0.000	0.000	0.000	0.000
47	A	51	ILE	0	0.007	0.001	8.202	0.142	0.142	0.000	0.000	0.000	0.000
48	A	52	ILE	0	0.005	-0.004	8.758	-0.159	-0.159	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.027	-0.022	7.735	0.143	0.143	0.000	0.000	0.000	0.000
50	A	54	VAL	0	0.019	0.012	11.576	-0.115	-0.115	0.000	0.000	0.000	0.000
51	A	55	ASN	0	-0.009	-0.024	14.233	0.034	0.034	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.856	-0.921	10.212	0.414	0.414	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.939	0.981	11.742	-0.029	-0.029	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.000	0.000	11.748	-0.088	-0.088	0.000	0.000	0.000	0.000
55	A	59	MET	0	-0.016	-0.004	13.089	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	60	PHE	0	0.016	-0.005	14.158	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.016	0.026	13.159	0.015	0.015	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.829	0.894	10.629	0.560	0.560	0.000	0.000	0.000	0.000
59	A	63	ARG	1	0.919	0.961	13.413	0.036	0.036	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.909	0.945	15.281	0.228	0.228	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.888	-0.948	15.384	-0.260	-0.260	0.000	0.000	0.000	0.000
62	A	66	LEU	0	-0.009	0.012	17.756	0.018	0.018	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.020	-0.015	15.707	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	68	PHE	0	0.015	-0.009	17.680	0.011	0.011	0.000	0.000	0.000	0.000
65	A	69	PRO	0	0.012	0.011	17.853	0.009	0.009	0.000	0.000	0.000	0.000
66	A	70	LEU	0	0.015	0.007	13.231	0.001	0.001	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.035	0.012	17.760	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	72	ILE	0	0.017	0.008	16.024	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	73	ALA	0	0.010	0.005	18.086	-0.008	-0.008	0.000	0.000	0.000	0.000
70	A	74	LEU	0	0.003	-0.002	19.827	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	75	TYR	0	-0.007	-0.009	22.403	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.021	0.016	19.915	-0.012	-0.012	0.000	0.000	0.000	0.000
73	A	77	LEU	0	0.029	0.018	23.162	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.073	-0.040	25.875	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.865	-0.911	27.371	0.140	0.140	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-1.065	-1.019	25.854	0.105	0.105	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.955	-0.980	29.733	0.048	0.048	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.795	-0.885	31.329	0.064	0.064	0.000	0.000	0.000	0.000
79	A	83	LEU	0	0.012	-0.002	26.795	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.843	0.908	31.224	-0.060	-0.060	0.000	0.000	0.000	0.000
81	A	85	LYS	1	0.884	0.931	34.197	-0.037	-0.037	0.000	0.000	0.000	0.000
82	A	86	TRP	0	0.050	0.029	25.916	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	87	PRO	0	-0.002	0.015	30.414	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.892	0.921	27.050	0.027	0.027	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.821	0.933	29.128	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	90	VAL	0	0.014	-0.009	30.546	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.025	-0.012	31.572	0.008	0.008	0.000	0.000	0.000	0.000
88	A	92	VAL	0	-0.027	-0.015	32.351	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	93	ASP	-1	-0.805	-0.911	35.009	0.050	0.050	0.000	0.000	0.000	0.000
90	A	94	GLU	-1	-0.945	-0.992	35.941	0.065	0.065	0.000	0.000	0.000	0.000
91	A	95	GLY	0	-0.013	-0.003	36.237	0.005	0.005	0.000	0.000	0.000	0.000
92	A	96	ALA	0	0.021	0.001	34.118	0.001	0.001	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.013	-0.002	30.721	0.004	0.004	0.000	0.000	0.000	0.000
94	A	98	PRO	0	-0.023	-0.013	30.656	0.008	0.008	0.000	0.000	0.000	0.000
95	A	99	HIS	0	-0.012	-0.009	30.676	0.006	0.006	0.000	0.000	0.000	0.000
96	A	100	ILE	0	0.014	0.011	27.175	0.002	0.002	0.000	0.000	0.000	0.000
97	A	101	LEU	0	-0.052	-0.022	25.696	0.008	0.008	0.000	0.000	0.000	0.000
98	A	102	ASN	0	-0.062	-0.029	25.837	0.024	0.024	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.029	0.029	25.226	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	104	ALA	0	-0.073	-0.020	26.101	-0.012	-0.012	0.000	0.000	0.000	0.000
101	A	105	ASP	-1	-0.812	-0.901	27.531	0.028	0.028	0.000	0.000	0.000	0.000
102	A	106	VAL	0	0.041	0.022	29.244	0.003	0.003	0.000	0.000	0.000	0.000
103	A	107	MET	0	-0.023	-0.004	31.731	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.054	0.006	35.382	0.003	0.003	0.000	0.000	0.000	0.000
105	A	109	PRO	0	-0.075	-0.040	37.956	0.001	0.001	0.000	0.000	0.000	0.000
106	A	110	GLY	0	0.031	0.041	37.116	0.001	0.001	0.000	0.000	0.000	0.000
107	A	111	ILE	0	-0.056	-0.022	34.367	0.004	0.004	0.000	0.000	0.000	0.000
108	A	112	VAL	0	0.023	0.015	37.342	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.863	-0.939	37.426	0.023	0.023	0.000	0.000	0.000	0.000
110	A	114	ALA	0	-0.010	-0.004	35.029	0.003	0.003	0.000	0.000	0.000	0.000
111	A	115	ASP	-1	-0.818	-0.891	33.375	0.002	0.002	0.000	0.000	0.000	0.000
112	A	116	GLU	-1	-0.871	-0.939	35.452	0.002	0.002	0.000	0.000	0.000	0.000
113	A	117	GLY	0	-0.041	-0.012	35.499	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	118	ILE	0	-0.074	-0.018	31.383	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	119	LYS	1	0.930	0.953	32.714	0.035	0.035	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.941	-0.967	32.057	-0.021	-0.021	0.000	0.000	0.000	0.000
117	A	121	GLY	0	-0.021	-0.019	29.160	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.870	-0.924	27.531	-0.038	-0.038	0.000	0.000	0.000	0.000
119	A	123	PHE	0	-0.025	-0.014	20.331	0.007	0.007	0.000	0.000	0.000	0.000
120	A	124	VAL	0	-0.008	-0.010	25.435	0.000	0.000	0.000	0.000	0.000	0.000
121	A	125	PHE	0	-0.001	-0.008	24.907	0.006	0.006	0.000	0.000	0.000	0.000
122	A	126	VAL	0	-0.013	-0.003	26.291	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	127	VAL	0	-0.001	0.005	27.644	0.012	0.012	0.000	0.000	0.000	0.000
124	A	128	GLU	-1	-0.782	-0.891	30.152	0.081	0.081	0.000	0.000	0.000	0.000
125	A	129	GLU	-1	-0.887	-0.966	32.930	0.049	0.049	0.000	0.000	0.000	0.000
126	A	130	LYS	1	0.908	0.969	35.683	-0.075	-0.075	0.000	0.000	0.000	0.000
127	A	131	TYR	0	-0.071	-0.049	32.790	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	132	GLY	0	0.044	0.033	32.328	0.002	0.002	0.000	0.000	0.000	0.000
129	A	133	ARG	1	0.786	0.881	28.136	-0.127	-0.127	0.000	0.000	0.000	0.000
130	A	134	PRO	0	0.002	-0.003	24.481	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.038	-0.027	25.656	0.015	0.015	0.000	0.000	0.000	0.000
132	A	136	ALA	0	0.001	-0.013	23.141	0.014	0.014	0.000	0.000	0.000	0.000
133	A	137	ILE	0	-0.022	0.014	18.628	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	138	GLY	0	0.018	-0.008	23.035	0.004	0.004	0.000	0.000	0.000	0.000
135	A	139	ILE	0	-0.018	0.012	23.368	-0.007	-0.007	0.000	0.000	0.000	0.000
136	A	140	ALA	0	0.007	0.010	26.540	0.006	0.006	0.000	0.000	0.000	0.000
137	A	141	LEU	0	-0.040	-0.031	29.698	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	142	MET	0	-0.028	0.001	32.632	0.000	0.000	0.000	0.000	0.000	0.000
139	A	143	SER	0	0.045	0.021	34.346	0.001	0.001	0.000	0.000	0.000	0.000
140	A	144	GLY	0	0.060	0.026	36.010	0.003	0.003	0.000	0.000	0.000	0.000
141	A	145	LYS	1	0.950	0.961	36.660	0.005	0.005	0.000	0.000	0.000	0.000
142	A	146	VAL	0	-0.024	-0.015	39.074	0.002	0.002	0.000	0.000	0.000	0.000
143	A	147	MET	0	-0.067	-0.036	32.036	0.004	0.004	0.000	0.000	0.000	0.000
144	A	148	LYS	1	0.859	0.933	38.227	-0.011	-0.011	0.000	0.000	0.000	0.000
145	A	149	GLU	-1	-0.959	-0.952	40.908	0.007	0.007	0.000	0.000	0.000	0.000
146	A	150	LYS	1	0.898	0.955	40.944	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	151	ASN	0	0.099	0.050	41.591	0.000	0.000	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.915	0.940	41.450	-0.011	-0.011	0.000	0.000	0.000	0.000
149	A	153	GLY	0	0.044	0.019	38.939	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	154	LYS	1	0.870	0.910	30.896	-0.017	-0.017	0.000	0.000	0.000	0.000
151	A	155	ALA	0	0.066	0.028	33.902	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	156	VAL	0	0.025	0.013	27.472	-0.005	-0.005	0.000	0.000	0.000	0.000
153	A	157	LYS	1	0.856	0.928	25.579	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	158	VAL	0	0.009	0.001	23.237	-0.006	-0.006	0.000	0.000	0.000	0.000
155	A	159	ILE	0	-0.091	-0.049	19.227	-0.009	-0.009	0.000	0.000	0.000	0.000
156	A	160	HIS	0	-0.036	-0.034	17.396	0.006	0.006	0.000	0.000	0.000	0.000
157	A	161	HIS	0	-0.008	-0.014	19.746	-0.021	-0.021	0.000	0.000	0.000	0.000
158	A	162	ALA	0	0.057	0.025	20.445	0.028	0.028	0.000	0.000	0.000	0.000
159	A	163	ARG	1	0.905	0.949	20.934	-0.178	-0.178	0.000	0.000	0.000	0.000
160	A	164	ASP	-1	-0.722	-0.823	17.680	0.235	0.235	0.000	0.000	0.000	0.000
161	A	165	LYS	1	0.900	0.908	14.574	-0.335	-0.335	0.000	0.000	0.000	0.000
162	A	166	ILE	0	0.017	0.019	12.956	0.094	0.094	0.000	0.000	0.000	0.000
163	A	167	TRP	0	0.031	0.029	13.931	0.083	0.083	0.000	0.000	0.000	0.000
164	A	168	GLU	-1	-0.898	-0.936	15.449	0.447	0.447	0.000	0.000	0.000	0.000
165	A	169	VAL	0	-0.048	-0.014	10.239	0.055	0.055	0.000	0.000	0.000	0.000
166	A	170	THR	0	-0.102	-0.068	11.424	0.129	0.129	0.000	0.000	0.000	0.000
167	A	171	ALA	0	-0.013	0.006	13.452	-0.020	-0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ILE)