FMO DATABASE

FMODB ID: M9N7Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1765635.347987
FMO2-HF: Nuclear repulsion	1699512.655007
FMO2-HF: Total energy	-66122.692979
FMO2-MP2: Total energy	-66316.293974

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.
-1.313	1.467	2.149	-1.402	-3.526	-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 : -0.016 / 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	7	HIS	0	0.028	0.023	2.483	-2.177	0.175	2.152	-1.334	-3.170	-0.002
4	A	8	PRO	0	0.005	0.004	5.321	0.329	0.374	-0.001	-0.001	-0.042	0.000
5	A	9	LEU	0	0.019	0.011	9.118	-0.057	-0.057	0.000	0.000	0.000	0.000
6	A	10	SER	0	-0.030	-0.030	11.577	0.079	0.079	0.000	0.000	0.000	0.000
7	A	11	LYS	1	1.035	0.991	14.542	0.166	0.166	0.000	0.000	0.000	0.000
8	A	12	LYS	1	0.947	0.976	18.021	0.192	0.192	0.000	0.000	0.000	0.000
9	A	13	ASP	-1	-0.804	-0.886	14.384	-0.290	-0.290	0.000	0.000	0.000	0.000
10	A	14	VAL	0	0.030	0.015	15.620	0.028	0.028	0.000	0.000	0.000	0.000
11	A	15	LYS	1	0.900	0.935	17.793	0.119	0.119	0.000	0.000	0.000	0.000
12	A	16	GLU	-1	-0.878	-0.918	19.442	-0.075	-0.075	0.000	0.000	0.000	0.000
13	A	17	ILE	0	0.045	0.026	15.376	0.014	0.014	0.000	0.000	0.000	0.000
14	A	18	ILE	0	0.000	0.001	19.992	0.017	0.017	0.000	0.000	0.000	0.000
15	A	19	ALA	0	-0.014	0.007	22.888	0.012	0.012	0.000	0.000	0.000	0.000
16	A	20	GLN	0	-0.012	-0.025	20.545	0.022	0.022	0.000	0.000	0.000	0.000
17	A	21	LEU	0	0.002	-0.003	20.599	0.010	0.010	0.000	0.000	0.000	0.000
18	A	22	SER	0	-0.019	-0.029	24.468	0.008	0.008	0.000	0.000	0.000	0.000
19	A	23	GLN	0	-0.082	-0.025	27.565	0.005	0.005	0.000	0.000	0.000	0.000
20	A	24	MET	0	-0.091	-0.031	22.594	0.005	0.005	0.000	0.000	0.000	0.000
21	A	25	PHE	0	0.005	-0.017	23.757	0.006	0.006	0.000	0.000	0.000	0.000
22	A	26	GLY	0	0.061	0.046	29.061	0.003	0.003	0.000	0.000	0.000	0.000
23	A	27	GLU	-1	-0.874	-0.955	29.472	0.013	0.013	0.000	0.000	0.000	0.000
24	A	28	GLU	-1	-0.853	-0.906	29.287	0.031	0.031	0.000	0.000	0.000	0.000
25	A	29	ILE	0	0.011	0.008	26.908	0.004	0.004	0.000	0.000	0.000	0.000
26	A	30	ALA	0	-0.017	-0.006	25.258	0.008	0.008	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.790	0.872	24.435	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	32	LYS	1	0.794	0.879	24.952	-0.093	-0.093	0.000	0.000	0.000	0.000
29	A	33	MET	0	-0.074	-0.007	21.310	0.011	0.011	0.000	0.000	0.000	0.000
30	A	34	LEU	0	-0.026	-0.018	17.771	0.008	0.008	0.000	0.000	0.000	0.000
31	A	35	ASN	0	0.022	0.016	21.103	-0.023	-0.023	0.000	0.000	0.000	0.000
32	A	36	LYS	1	0.942	0.946	20.934	0.032	0.032	0.000	0.000	0.000	0.000
33	A	37	LYS	1	0.872	0.926	21.157	0.002	0.002	0.000	0.000	0.000	0.000
34	A	38	ASP	-1	-0.778	-0.853	17.461	0.037	0.037	0.000	0.000	0.000	0.000
35	A	39	GLU	-1	-0.857	-0.920	12.209	-0.076	-0.076	0.000	0.000	0.000	0.000
36	A	40	VAL	0	-0.030	-0.011	12.794	0.051	0.051	0.000	0.000	0.000	0.000
37	A	41	LYS	1	0.770	0.870	7.692	-0.159	-0.159	0.000	0.000	0.000	0.000
38	A	42	VAL	0	-0.004	0.006	6.781	0.242	0.242	0.000	0.000	0.000	0.000
39	A	43	ALA	0	0.012	0.007	4.275	-0.948	-0.881	-0.001	-0.039	-0.027	0.000
40	A	44	GLU	-1	-0.808	-0.877	3.726	-0.929	-0.613	-0.001	-0.028	-0.287	0.000
41	A	45	PHE	0	-0.030	-0.006	5.525	0.847	0.847	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.732	-0.855	8.269	0.096	0.096	0.000	0.000	0.000	0.000
43	A	47	LYS	1	0.800	0.867	7.262	0.411	0.411	0.000	0.000	0.000	0.000
44	A	48	THR	0	-0.099	-0.044	11.267	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	49	THR	0	-0.055	-0.040	11.671	-0.016	-0.016	0.000	0.000	0.000	0.000
46	A	50	GLU	-1	-0.776	-0.850	8.805	-0.404	-0.404	0.000	0.000	0.000	0.000
47	A	51	ILE	0	0.009	0.003	8.420	0.046	0.046	0.000	0.000	0.000	0.000
48	A	52	ILE	0	0.008	-0.003	9.002	-0.081	-0.081	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.016	-0.013	7.671	0.106	0.106	0.000	0.000	0.000	0.000
50	A	54	VAL	0	0.012	0.007	11.555	-0.114	-0.114	0.000	0.000	0.000	0.000
51	A	55	ASN	0	-0.009	-0.035	14.226	0.023	0.023	0.000	0.000	0.000	0.000
52	A	56	ASP	-1	-0.812	-0.887	9.373	0.428	0.428	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.926	0.974	11.730	-0.057	-0.057	0.000	0.000	0.000	0.000
54	A	58	PRO	0	0.005	0.006	11.676	-0.063	-0.063	0.000	0.000	0.000	0.000
55	A	59	MET	0	-0.012	0.003	13.054	-0.035	-0.035	0.000	0.000	0.000	0.000
56	A	60	PHE	0	0.011	-0.012	14.409	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.021	0.031	13.406	0.047	0.047	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.787	0.852	11.231	0.292	0.292	0.000	0.000	0.000	0.000
59	A	63	ARG	1	0.914	0.952	13.576	-0.073	-0.073	0.000	0.000	0.000	0.000
60	A	64	LYS	1	0.863	0.899	15.336	0.113	0.113	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.838	-0.897	15.422	-0.153	-0.153	0.000	0.000	0.000	0.000
62	A	66	LEU	0	-0.011	0.010	17.921	0.010	0.010	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.004	-0.006	16.033	0.006	0.006	0.000	0.000	0.000	0.000
64	A	68	PHE	0	0.013	-0.015	17.903	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	69	PRO	0	0.004	0.006	18.093	0.021	0.021	0.000	0.000	0.000	0.000
66	A	70	LEU	0	0.026	0.014	13.482	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.032	0.007	18.014	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	72	ILE	0	0.011	0.009	16.087	-0.025	-0.025	0.000	0.000	0.000	0.000
69	A	73	ALA	0	0.015	0.006	18.298	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	74	LEU	0	0.005	-0.001	20.031	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	75	TYR	0	0.008	-0.003	22.531	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	76	ASN	0	0.011	0.009	19.731	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	77	LEU	0	0.012	0.012	23.448	-0.014	-0.014	0.000	0.000	0.000	0.000
74	A	78	SER	0	-0.055	-0.032	25.840	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.856	-0.899	27.331	0.138	0.138	0.000	0.000	0.000	0.000
76	A	80	GLU	-1	-0.908	-0.926	26.098	0.105	0.105	0.000	0.000	0.000	0.000
77	A	81	GLU	-1	-0.958	-0.976	29.763	0.059	0.059	0.000	0.000	0.000	0.000
78	A	82	ASP	-1	-0.776	-0.861	31.415	0.075	0.075	0.000	0.000	0.000	0.000
79	A	83	LEU	0	0.021	0.003	27.062	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	84	ARG	1	0.796	0.869	31.488	-0.071	-0.071	0.000	0.000	0.000	0.000
81	A	85	LYS	1	0.846	0.912	34.458	-0.053	-0.053	0.000	0.000	0.000	0.000
82	A	86	TRP	0	0.043	0.026	26.182	-0.003	-0.003	0.000	0.000	0.000	0.000
83	A	87	PRO	0	0.005	0.007	30.682	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	88	ARG	1	0.816	0.884	27.892	-0.013	-0.013	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.822	0.933	29.365	-0.041	-0.041	0.000	0.000	0.000	0.000
86	A	90	VAL	0	0.007	-0.013	30.784	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	91	VAL	0	-0.025	-0.012	31.809	0.008	0.008	0.000	0.000	0.000	0.000
88	A	92	VAL	0	-0.023	-0.016	32.521	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	93	ASP	-1	-0.786	-0.893	35.240	0.063	0.063	0.000	0.000	0.000	0.000
90	A	94	GLU	-1	-0.941	-0.994	36.166	0.072	0.072	0.000	0.000	0.000	0.000
91	A	95	GLY	0	-0.013	0.000	36.454	0.004	0.004	0.000	0.000	0.000	0.000
92	A	96	ALA	0	-0.004	-0.014	34.362	0.001	0.001	0.000	0.000	0.000	0.000
93	A	97	VAL	0	-0.013	-0.004	30.962	0.005	0.005	0.000	0.000	0.000	0.000
94	A	98	PRO	0	-0.024	-0.013	30.862	0.009	0.009	0.000	0.000	0.000	0.000
95	A	99	HIS	0	0.004	-0.001	30.863	0.008	0.008	0.000	0.000	0.000	0.000
96	A	100	ILE	0	0.009	0.007	27.403	0.004	0.004	0.000	0.000	0.000	0.000
97	A	101	LEU	0	-0.047	-0.018	25.959	0.010	0.010	0.000	0.000	0.000	0.000
98	A	102	ASN	0	-0.063	-0.027	26.020	0.020	0.020	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.028	0.025	25.398	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	104	ALA	0	-0.072	-0.020	26.265	-0.010	-0.010	0.000	0.000	0.000	0.000
101	A	105	ASP	-1	-0.774	-0.875	27.948	0.064	0.064	0.000	0.000	0.000	0.000
102	A	106	VAL	0	0.042	0.023	29.460	0.000	0.000	0.000	0.000	0.000	0.000
103	A	107	MET	0	-0.036	-0.017	31.926	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	108	ALA	0	0.053	0.007	35.572	0.002	0.002	0.000	0.000	0.000	0.000
105	A	109	PRO	0	-0.067	-0.036	38.155	0.000	0.000	0.000	0.000	0.000	0.000
106	A	110	GLY	0	0.018	0.039	37.328	0.000	0.000	0.000	0.000	0.000	0.000
107	A	111	ILE	0	-0.054	-0.023	34.493	0.004	0.004	0.000	0.000	0.000	0.000
108	A	112	VAL	0	0.029	0.018	37.565	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	113	ASP	-1	-0.866	-0.932	37.711	0.039	0.039	0.000	0.000	0.000	0.000
110	A	114	ALA	0	0.007	0.006	35.266	0.004	0.004	0.000	0.000	0.000	0.000
111	A	115	ASP	-1	-0.816	-0.895	33.581	0.027	0.027	0.000	0.000	0.000	0.000
112	A	116	GLU	-1	-0.811	-0.890	35.688	0.020	0.020	0.000	0.000	0.000	0.000
113	A	117	GLY	0	-0.013	0.007	35.727	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	118	ILE	0	-0.068	-0.021	31.627	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	119	LYS	1	0.849	0.906	32.883	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	120	GLU	-1	-0.908	-0.955	32.250	0.010	0.010	0.000	0.000	0.000	0.000
117	A	121	GLY	0	-0.010	-0.015	29.326	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.801	-0.878	27.707	0.005	0.005	0.000	0.000	0.000	0.000
119	A	123	PHE	0	-0.016	-0.006	20.409	0.007	0.007	0.000	0.000	0.000	0.000
120	A	124	VAL	0	-0.017	-0.016	25.641	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	125	PHE	0	0.016	0.001	25.128	0.011	0.011	0.000	0.000	0.000	0.000
122	A	126	VAL	0	-0.014	-0.006	26.528	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	127	VAL	0	0.002	0.005	27.886	0.013	0.013	0.000	0.000	0.000	0.000
124	A	128	GLU	-1	-0.773	-0.874	30.398	0.089	0.089	0.000	0.000	0.000	0.000
125	A	129	GLU	-1	-0.862	-0.952	33.174	0.060	0.060	0.000	0.000	0.000	0.000
126	A	130	LYS	1	0.903	0.966	35.923	-0.079	-0.079	0.000	0.000	0.000	0.000
127	A	131	TYR	0	-0.057	-0.043	32.920	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	132	GLY	0	0.041	0.030	32.586	0.002	0.002	0.000	0.000	0.000	0.000
129	A	133	ARG	1	0.770	0.861	27.881	-0.133	-0.133	0.000	0.000	0.000	0.000
130	A	134	PRO	0	-0.006	-0.007	24.688	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	135	LEU	0	-0.035	-0.022	25.901	0.013	0.013	0.000	0.000	0.000	0.000
132	A	136	ALA	0	0.001	-0.016	23.368	0.015	0.015	0.000	0.000	0.000	0.000
133	A	137	ILE	0	-0.021	0.014	18.833	-0.010	-0.010	0.000	0.000	0.000	0.000
134	A	138	GLY	0	0.015	-0.008	23.242	0.006	0.006	0.000	0.000	0.000	0.000
135	A	139	ILE	0	-0.016	0.012	23.389	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	140	ALA	0	0.003	0.009	26.726	0.003	0.003	0.000	0.000	0.000	0.000
137	A	141	LEU	0	-0.038	-0.029	29.823	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	142	MET	0	-0.028	0.002	32.806	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	143	SER	0	0.049	0.021	34.542	0.002	0.002	0.000	0.000	0.000	0.000
140	A	144	GLY	0	0.044	0.017	36.228	0.003	0.003	0.000	0.000	0.000	0.000
141	A	145	LYS	1	0.880	0.912	36.877	-0.014	-0.014	0.000	0.000	0.000	0.000
142	A	146	VAL	0	-0.009	-0.008	39.222	0.001	0.001	0.000	0.000	0.000	0.000
143	A	147	MET	0	-0.063	-0.031	32.252	0.003	0.003	0.000	0.000	0.000	0.000
144	A	148	LYS	1	0.850	0.929	38.437	-0.029	-0.029	0.000	0.000	0.000	0.000
145	A	149	GLU	-1	-0.917	-0.939	41.130	0.020	0.020	0.000	0.000	0.000	0.000
146	A	150	LYS	1	0.845	0.934	41.056	-0.021	-0.021	0.000	0.000	0.000	0.000
147	A	151	ASN	0	0.088	0.042	41.796	0.001	0.001	0.000	0.000	0.000	0.000
148	A	152	ARG	1	0.925	0.947	41.630	-0.025	-0.025	0.000	0.000	0.000	0.000
149	A	153	GLY	0	0.057	0.026	39.111	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	154	LYS	1	0.840	0.897	31.132	-0.043	-0.043	0.000	0.000	0.000	0.000
151	A	155	ALA	0	0.062	0.029	34.092	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	156	VAL	0	0.021	0.007	27.640	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	157	LYS	1	0.860	0.928	25.921	-0.054	-0.054	0.000	0.000	0.000	0.000
154	A	158	VAL	0	0.006	0.002	23.515	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	159	ILE	0	-0.086	-0.049	19.641	-0.006	-0.006	0.000	0.000	0.000	0.000
156	A	160	HIS	0	-0.033	-0.035	17.666	0.020	0.020	0.000	0.000	0.000	0.000
157	A	161	HIS	0	-0.013	-0.015	19.946	-0.023	-0.023	0.000	0.000	0.000	0.000
158	A	162	ALA	0	0.056	0.023	20.654	0.029	0.029	0.000	0.000	0.000	0.000
159	A	163	ARG	1	0.902	0.948	21.126	-0.181	-0.181	0.000	0.000	0.000	0.000
160	A	164	ASP	-1	-0.728	-0.818	17.673	0.290	0.290	0.000	0.000	0.000	0.000
161	A	165	LYS	1	0.837	0.870	14.779	-0.318	-0.318	0.000	0.000	0.000	0.000
162	A	166	ILE	0	0.023	0.021	13.146	0.092	0.092	0.000	0.000	0.000	0.000
163	A	167	TRP	0	0.023	0.016	14.146	0.078	0.078	0.000	0.000	0.000	0.000
164	A	168	GLU	-1	-0.835	-0.897	15.602	0.416	0.416	0.000	0.000	0.000	0.000
165	A	169	VAL	0	-0.047	-0.015	10.342	0.037	0.037	0.000	0.000	0.000	0.000
166	A	170	THR	0	-0.095	-0.059	11.424	0.125	0.125	0.000	0.000	0.000	0.000
167	A	171	ALA	0	-0.009	0.009	13.488	-0.030	-0.030	0.000	0.000	0.000	0.000

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