FMO DATABASE

FMODB ID: 7M6RK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1766870.842634
FMO2-HF: Nuclear repulsion	1700747.891825
FMO2-HF: Total energy	-66122.950809
FMO2-MP2: Total energy	-66316.510524

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.
-1.054	1.926	1.551	-1.246	-3.285	-0.002

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 : -0.012 / q_NPA : -0.020

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	0.033	0.028	2.544	-1.965	0.566	1.554	-1.183	-2.902	-0.002
4	A	8	PRO	0	0.018	0.007	5.078	0.331	0.374	-0.001	-0.002	-0.040	0.000
5	A	9	LEU	0	0.017	0.010	8.931	-0.071	-0.071	0.000	0.000	0.000	0.000
6	A	10	SER	0	-0.009	-0.036	11.225	0.090	0.090	0.000	0.000	0.000	0.000
7	A	11	LYS	1	0.996	0.972	14.205	0.190	0.190	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.885	0.951	17.568	0.220	0.220	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.790	-0.858	14.080	-0.350	-0.350	0.000	0.000	0.000	0.000
10	A	14	VAL	0	0.032	0.018	15.693	0.028	0.028	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.915	0.950	17.722	0.147	0.147	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.866	-0.923	18.786	-0.131	-0.131	0.000	0.000	0.000	0.000
13	A	17	ILE	0	0.057	0.027	15.077	0.015	0.015	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.008	0.009	19.658	0.020	0.020	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.010	0.008	22.620	0.015	0.015	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.006	-0.018	20.110	0.018	0.018	0.000	0.000	0.000	0.000
17	A	21	LEU	0	-0.002	-0.004	20.709	0.012	0.012	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.013	-0.029	24.380	0.012	0.012	0.000	0.000	0.000	0.000
19	A	23	GLN	0	-0.079	-0.029	27.253	0.006	0.006	0.000	0.000	0.000	0.000
20	A	24	MET	0	-0.089	-0.028	22.557	0.006	0.006	0.000	0.000	0.000	0.000
21	A	25	PHE	0	0.016	-0.011	23.882	0.007	0.007	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.064	0.045	29.207	0.005	0.005	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.877	-0.950	28.912	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	28	GLU	-1	-0.822	-0.891	28.943	0.010	0.010	0.000	0.000	0.000	0.000
25	A	29	ILE	0	-0.001	0.012	26.677	0.004	0.004	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.017	-0.007	25.054	0.005	0.005	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.772	0.853	24.233	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.777	0.883	25.083	-0.065	-0.065	0.000	0.000	0.000	0.000
29	A	33	MET	0	-0.065	-0.007	21.181	0.011	0.011	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.044	-0.032	17.721	0.004	0.004	0.000	0.000	0.000	0.000
31	A	35	ASN	0	0.025	0.007	21.057	-0.012	-0.012	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.947	0.956	20.688	0.046	0.046	0.000	0.000	0.000	0.000
33	A	37	LYS	1	0.861	0.918	20.909	0.022	0.022	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.758	-0.836	17.258	0.004	0.004	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.836	-0.915	11.976	-0.098	-0.098	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.050	-0.024	12.680	0.034	0.034	0.000	0.000	0.000	0.000
37	A	41	LYS	1	0.764	0.869	7.952	-0.094	-0.094	0.000	0.000	0.000	0.000
38	A	42	VAL	0	-0.006	0.000	6.593	0.241	0.241	0.000	0.000	0.000	0.000
39	A	43	ALA	0	0.011	0.019	4.116	-1.115	-0.986	-0.001	-0.046	-0.082	0.000
40	A	44	GLU	-1	-0.820	-0.889	4.149	-0.519	-0.242	-0.001	-0.015	-0.261	0.000
41	A	45	PHE	0	-0.037	-0.012	5.840	0.539	0.539	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.712	-0.825	8.530	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.795	0.866	7.224	0.499	0.499	0.000	0.000	0.000	0.000
44	A	48	THR	0	-0.099	-0.055	11.442	-0.013	-0.013	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.068	-0.052	11.687	0.015	0.015	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.774	-0.850	8.799	-0.590	-0.590	0.000	0.000	0.000	0.000
47	A	51	ILE	0	0.006	-0.003	8.405	0.112	0.112	0.000	0.000	0.000	0.000
48	A	52	ILE	0	0.011	0.001	8.978	-0.106	-0.106	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.007	-0.006	7.914	0.133	0.133	0.000	0.000	0.000	0.000
50	A	54	VAL	0	-0.021	-0.008	11.850	-0.111	-0.111	0.000	0.000	0.000	0.000
51	A	55	ASN	0	0.012	-0.020	14.042	0.014	0.014	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.776	-0.867	8.789	0.445	0.445	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.902	0.971	11.298	0.014	0.014	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.013	0.001	11.730	-0.076	-0.076	0.000	0.000	0.000	0.000
55	A	59	MET	0	-0.014	0.000	13.203	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	60	PHE	0	0.024	-0.012	14.474	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.019	0.033	13.585	0.001	0.001	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.762	0.831	11.190	0.417	0.417	0.000	0.000	0.000	0.000
59	A	63	ARG	1	0.906	0.944	13.664	0.012	0.012	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.848	0.898	15.052	0.177	0.177	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.845	-0.907	15.479	-0.215	-0.215	0.000	0.000	0.000	0.000
62	A	66	LEU	0	0.002	0.024	17.560	0.011	0.011	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.003	-0.008	16.366	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	68	PHE	0	0.015	-0.012	18.040	0.010	0.010	0.000	0.000	0.000	0.000
65	A	69	PRO	0	0.003	0.005	18.154	0.009	0.009	0.000	0.000	0.000	0.000
66	A	70	LEU	0	0.025	0.018	13.486	0.000	0.000	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.022	0.004	18.014	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	72	ILE	0	0.023	0.010	16.166	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	73	ALA	0	0.007	0.011	18.032	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	74	LEU	0	0.003	-0.005	19.849	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	75	TYR	0	0.024	0.010	22.473	-0.012	-0.012	0.000	0.000	0.000	0.000
72	A	76	ASN	0	-0.023	-0.003	20.173	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	77	LEU	0	0.017	0.016	23.422	-0.011	-0.011	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.045	-0.044	25.871	-0.010	-0.010	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.861	-0.899	27.383	0.120	0.120	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.880	-0.920	26.320	0.081	0.081	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.885	-0.936	29.111	0.037	0.037	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.785	-0.862	31.400	0.053	0.053	0.000	0.000	0.000	0.000
79	A	83	LEU	0	0.022	0.002	27.025	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.764	0.850	31.370	-0.054	-0.054	0.000	0.000	0.000	0.000
81	A	85	LYS	1	0.829	0.885	34.468	-0.034	-0.034	0.000	0.000	0.000	0.000
82	A	86	TRP	0	0.011	0.015	26.228	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	87	PRO	0	0.010	0.011	30.581	0.000	0.000	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.770	0.859	27.680	0.019	0.019	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.827	0.931	29.331	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	90	VAL	0	0.004	-0.014	30.802	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.027	-0.005	31.943	0.006	0.006	0.000	0.000	0.000	0.000
88	A	92	VAL	0	-0.012	-0.013	32.352	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	93	ASP	-1	-0.762	-0.877	35.236	0.047	0.047	0.000	0.000	0.000	0.000
90	A	94	GLU	-1	-0.955	-0.997	35.980	0.059	0.059	0.000	0.000	0.000	0.000
91	A	95	GLY	0	-0.011	-0.001	36.530	0.004	0.004	0.000	0.000	0.000	0.000
92	A	96	ALA	0	-0.013	-0.019	34.663	0.001	0.001	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.021	-0.012	31.107	0.004	0.004	0.000	0.000	0.000	0.000
94	A	98	PRO	0	-0.029	-0.017	30.845	0.007	0.007	0.000	0.000	0.000	0.000
95	A	99	HIS	0	0.007	0.007	30.743	0.006	0.006	0.000	0.000	0.000	0.000
96	A	100	ILE	0	0.020	0.022	27.333	0.002	0.002	0.000	0.000	0.000	0.000
97	A	101	LEU	0	-0.057	-0.012	26.050	0.008	0.008	0.000	0.000	0.000	0.000
98	A	102	ASN	0	-0.057	-0.034	26.703	0.017	0.017	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.027	0.024	25.201	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	104	ALA	0	-0.052	-0.016	26.042	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	105	ASP	-1	-0.745	-0.851	28.187	0.027	0.027	0.000	0.000	0.000	0.000
102	A	106	VAL	0	0.046	0.025	29.726	0.002	0.002	0.000	0.000	0.000	0.000
103	A	107	MET	0	-0.022	-0.014	32.075	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.015	-0.004	35.583	0.002	0.002	0.000	0.000	0.000	0.000
105	A	109	PRO	0	-0.057	-0.036	38.093	0.000	0.000	0.000	0.000	0.000	0.000
106	A	110	GLY	0	-0.001	0.035	37.283	0.001	0.001	0.000	0.000	0.000	0.000
107	A	111	ILE	0	-0.036	-0.024	35.345	0.004	0.004	0.000	0.000	0.000	0.000
108	A	112	VAL	0	0.017	0.012	37.834	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.840	-0.908	37.881	0.021	0.021	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.013	0.008	35.226	0.003	0.003	0.000	0.000	0.000	0.000
111	A	115	ASP	-1	-0.803	-0.887	33.278	0.003	0.003	0.000	0.000	0.000	0.000
112	A	116	GLU	-1	-0.842	-0.904	35.450	0.004	0.004	0.000	0.000	0.000	0.000
113	A	117	GLY	0	0.011	0.021	35.776	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	118	ILE	0	-0.066	-0.023	31.596	-0.005	-0.005	0.000	0.000	0.000	0.000
115	A	119	LYS	1	0.836	0.895	33.101	0.021	0.021	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.826	-0.906	32.616	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	121	GLY	0	-0.003	-0.005	29.463	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.799	-0.871	27.941	-0.028	-0.028	0.000	0.000	0.000	0.000
119	A	123	PHE	0	-0.015	-0.006	20.608	0.006	0.006	0.000	0.000	0.000	0.000
120	A	124	VAL	0	-0.008	-0.007	25.845	0.000	0.000	0.000	0.000	0.000	0.000
121	A	125	PHE	0	0.020	0.004	25.105	0.006	0.006	0.000	0.000	0.000	0.000
122	A	126	VAL	0	-0.021	-0.005	26.539	-0.006	-0.006	0.000	0.000	0.000	0.000
123	A	127	VAL	0	0.007	0.003	27.811	0.010	0.010	0.000	0.000	0.000	0.000
124	A	128	GLU	-1	-0.749	-0.856	30.329	0.069	0.069	0.000	0.000	0.000	0.000
125	A	129	GLU	-1	-0.854	-0.949	33.159	0.044	0.044	0.000	0.000	0.000	0.000
126	A	130	LYS	1	0.889	0.965	35.880	-0.066	-0.066	0.000	0.000	0.000	0.000
127	A	131	TYR	0	-0.052	-0.057	33.043	-0.003	-0.003	0.000	0.000	0.000	0.000
128	A	132	GLY	0	0.037	0.028	32.360	0.002	0.002	0.000	0.000	0.000	0.000
129	A	133	ARG	1	0.789	0.873	27.962	-0.113	-0.113	0.000	0.000	0.000	0.000
130	A	134	PRO	0	-0.017	-0.013	24.471	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.033	-0.015	26.031	0.012	0.012	0.000	0.000	0.000	0.000
132	A	136	ALA	0	0.002	-0.018	23.447	0.012	0.012	0.000	0.000	0.000	0.000
133	A	137	ILE	0	-0.007	0.016	19.017	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	138	GLY	0	0.016	-0.010	23.430	0.004	0.004	0.000	0.000	0.000	0.000
135	A	139	ILE	0	-0.011	0.011	23.569	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	140	ALA	0	0.009	0.008	26.912	0.005	0.005	0.000	0.000	0.000	0.000
137	A	141	LEU	0	-0.058	-0.041	30.101	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	142	MET	0	-0.040	-0.011	33.101	0.000	0.000	0.000	0.000	0.000	0.000
139	A	143	SER	0	0.021	-0.002	34.836	0.002	0.002	0.000	0.000	0.000	0.000
140	A	144	GLY	0	-0.009	-0.006	36.263	0.003	0.003	0.000	0.000	0.000	0.000
141	A	145	LYS	1	0.878	0.915	36.925	0.001	0.001	0.000	0.000	0.000	0.000
142	A	146	VAL	0	0.029	0.014	39.330	0.002	0.002	0.000	0.000	0.000	0.000
143	A	147	MET	0	-0.069	-0.036	32.278	0.003	0.003	0.000	0.000	0.000	0.000
144	A	148	LYS	1	0.818	0.916	38.467	-0.012	-0.012	0.000	0.000	0.000	0.000
145	A	149	GLU	-1	-0.853	-0.906	41.354	0.006	0.006	0.000	0.000	0.000	0.000
146	A	150	LYS	1	0.769	0.883	41.344	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	151	ASN	0	0.077	0.038	41.683	0.000	0.000	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.946	0.954	41.954	-0.011	-0.011	0.000	0.000	0.000	0.000
149	A	153	GLY	0	0.056	0.029	39.284	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	154	LYS	1	0.823	0.892	31.375	-0.015	-0.015	0.000	0.000	0.000	0.000
151	A	155	ALA	0	0.079	0.036	34.288	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	156	VAL	0	0.020	0.008	27.788	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	157	LYS	1	0.808	0.898	25.578	-0.017	-0.017	0.000	0.000	0.000	0.000
154	A	158	VAL	0	0.021	0.009	23.726	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	159	ILE	0	-0.065	-0.036	20.202	-0.008	-0.008	0.000	0.000	0.000	0.000
156	A	160	HIS	0	0.006	-0.016	17.486	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	161	HIS	0	-0.024	-0.027	19.896	-0.018	-0.018	0.000	0.000	0.000	0.000
158	A	162	ALA	0	0.050	0.031	20.525	0.026	0.026	0.000	0.000	0.000	0.000
159	A	163	ARG	1	0.881	0.935	20.860	-0.149	-0.149	0.000	0.000	0.000	0.000
160	A	164	ASP	-1	-0.740	-0.825	17.496	0.209	0.209	0.000	0.000	0.000	0.000
161	A	165	LYS	1	0.833	0.869	14.621	-0.259	-0.259	0.000	0.000	0.000	0.000
162	A	166	ILE	0	0.018	0.024	13.006	0.078	0.078	0.000	0.000	0.000	0.000
163	A	167	TRP	0	0.031	0.021	13.943	0.070	0.070	0.000	0.000	0.000	0.000
164	A	168	GLU	-1	-0.825	-0.901	15.588	0.364	0.364	0.000	0.000	0.000	0.000
165	A	169	VAL	0	-0.054	-0.010	10.198	0.054	0.054	0.000	0.000	0.000	0.000
166	A	170	THR	0	-0.087	-0.062	11.117	0.117	0.117	0.000	0.000	0.000	0.000
167	A	171	ALA	0	-0.020	0.004	13.538	-0.025	-0.025	0.000	0.000	0.000	0.000

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