FMO DATABASE

FMODB ID: VQN81

Calculation Name: 3EJF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EJF

Chain ID: A

ChEMBL ID:

UniProt ID: P0C6Y1

Base Structure: X-ray

Registration Date: 2023-09-22

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1685378.569187
FMO2-HF: Nuclear repulsion	1619599.93113
FMO2-HF: Total energy	-65778.638058
FMO2-MP2: Total energy	-65966.55841

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:6:LYS)

Summations of interaction energy for fragment #1(A:6:LYS)

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.
-124.909	-118.696	7.607	-5.886	-7.936	-0.034

Interaction energy analysis for fragmet #1(A:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.946 / q_NPA : 0.962

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	8	LYS	1	0.936	0.952	3.090	17.723	19.729	0.110	-1.006	-1.110	-0.002
4	A	9	PHE	0	0.009	-0.002	5.762	0.083	0.083	0.000	0.000	0.000	0.000
5	A	10	LEU	0	0.018	0.026	6.722	-0.955	-0.955	0.000	0.000	0.000	0.000
6	A	11	GLU	-1	-0.895	-0.932	7.318	-24.939	-24.939	0.000	0.000	0.000	0.000
7	A	12	TYR	0	0.063	0.014	9.519	-0.665	-0.665	0.000	0.000	0.000	0.000
8	A	13	LYS	1	0.807	0.896	10.580	19.170	19.170	0.000	0.000	0.000	0.000
9	A	14	THR	0	0.047	0.022	14.243	-0.249	-0.249	0.000	0.000	0.000	0.000
10	A	15	CYS	0	-0.021	-0.023	17.634	0.348	0.348	0.000	0.000	0.000	0.000
11	A	16	VAL	0	0.027	0.029	20.103	-0.144	-0.144	0.000	0.000	0.000	0.000
12	A	17	GLY	0	-0.010	-0.013	23.731	0.344	0.344	0.000	0.000	0.000	0.000
13	A	18	ASP	-1	-0.797	-0.886	24.423	-10.958	-10.958	0.000	0.000	0.000	0.000
14	A	19	LEU	0	0.007	0.015	20.774	-0.365	-0.365	0.000	0.000	0.000	0.000
15	A	20	THR	0	-0.049	-0.055	21.924	-0.462	-0.462	0.000	0.000	0.000	0.000
16	A	21	VAL	0	-0.016	-0.004	22.235	-0.215	-0.215	0.000	0.000	0.000	0.000
17	A	22	VAL	0	0.009	0.002	17.802	-0.442	-0.442	0.000	0.000	0.000	0.000
18	A	23	ILE	0	0.016	0.012	17.739	-0.792	-0.792	0.000	0.000	0.000	0.000
19	A	24	ALA	0	-0.008	0.004	17.806	-0.418	-0.418	0.000	0.000	0.000	0.000
20	A	25	LYS	1	0.852	0.917	16.130	14.156	14.156	0.000	0.000	0.000	0.000
21	A	26	ALA	0	0.007	0.006	13.655	-0.547	-0.547	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.014	-0.010	13.260	-0.839	-0.839	0.000	0.000	0.000	0.000
23	A	28	ASP	-1	-0.910	-0.952	14.714	-14.343	-14.343	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.802	-0.873	12.626	-16.024	-16.024	0.000	0.000	0.000	0.000
25	A	30	PHE	0	-0.045	-0.039	8.886	-1.200	-1.200	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.764	0.906	9.359	14.446	14.446	0.000	0.000	0.000	0.000
27	A	32	GLU	-1	-0.923	-0.963	8.473	-23.270	-23.270	0.000	0.000	0.000	0.000
28	A	33	PHE	0	-0.004	-0.012	9.268	-1.506	-1.506	0.000	0.000	0.000	0.000
29	A	34	CYS	0	-0.005	0.027	10.802	1.322	1.322	0.000	0.000	0.000	0.000
30	A	35	ILE	0	-0.011	-0.005	12.643	-0.160	-0.160	0.000	0.000	0.000	0.000
31	A	36	VAL	0	0.034	0.014	14.434	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	37	ASN	0	-0.024	-0.035	16.888	0.939	0.939	0.000	0.000	0.000	0.000
33	A	38	ALA	0	0.003	0.011	20.506	-0.347	-0.347	0.000	0.000	0.000	0.000
34	A	39	ALA	0	-0.010	0.000	22.616	0.640	0.640	0.000	0.000	0.000	0.000
35	A	40	ASN	0	0.001	-0.019	24.351	0.085	0.085	0.000	0.000	0.000	0.000
36	A	41	GLU	-1	-0.758	-0.861	26.331	-10.840	-10.840	0.000	0.000	0.000	0.000
37	A	42	HIS	0	-0.035	-0.018	27.534	-0.067	-0.067	0.000	0.000	0.000	0.000
38	A	43	MET	0	-0.050	-0.011	22.682	-0.059	-0.059	0.000	0.000	0.000	0.000
39	A	44	THR	0	0.028	0.010	27.133	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	45	HIS	0	-0.012	-0.023	24.559	0.291	0.291	0.000	0.000	0.000	0.000
41	A	46	GLY	0	0.059	0.031	28.942	0.134	0.134	0.000	0.000	0.000	0.000
42	A	47	SER	0	-0.040	-0.028	30.759	0.208	0.208	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.026	0.015	29.177	-0.313	-0.313	0.000	0.000	0.000	0.000
44	A	49	VAL	0	0.044	0.006	22.749	0.111	0.111	0.000	0.000	0.000	0.000
45	A	50	ALA	0	0.055	0.044	25.156	-0.162	-0.162	0.000	0.000	0.000	0.000
46	A	51	LYS	1	0.787	0.891	26.162	9.417	9.417	0.000	0.000	0.000	0.000
47	A	52	ALA	0	0.020	0.014	25.835	0.077	0.077	0.000	0.000	0.000	0.000
48	A	53	ILE	0	0.001	-0.008	20.791	-0.085	-0.085	0.000	0.000	0.000	0.000
49	A	54	ALA	0	0.017	0.005	24.280	-0.106	-0.106	0.000	0.000	0.000	0.000
50	A	55	ASP	-1	-0.832	-0.890	26.903	-9.559	-9.559	0.000	0.000	0.000	0.000
51	A	56	PHE	0	-0.071	-0.037	21.911	0.088	0.088	0.000	0.000	0.000	0.000
52	A	57	CYS	0	-0.084	-0.049	22.375	-0.270	-0.270	0.000	0.000	0.000	0.000
53	A	58	GLY	0	0.036	0.029	24.637	0.055	0.055	0.000	0.000	0.000	0.000
54	A	59	LEU	0	-0.004	-0.014	28.035	-0.239	-0.239	0.000	0.000	0.000	0.000
55	A	60	ASP	-1	-0.852	-0.917	27.072	-10.604	-10.604	0.000	0.000	0.000	0.000
56	A	61	PHE	0	-0.014	-0.013	21.755	-0.298	-0.298	0.000	0.000	0.000	0.000
57	A	62	VAL	0	0.005	0.004	25.608	-0.173	-0.173	0.000	0.000	0.000	0.000
58	A	63	GLU	-1	-0.867	-0.941	28.346	-9.508	-9.508	0.000	0.000	0.000	0.000
59	A	64	TYR	0	-0.023	-0.011	21.487	-0.048	-0.048	0.000	0.000	0.000	0.000
60	A	65	CYS	0	-0.059	-0.015	24.580	-0.317	-0.317	0.000	0.000	0.000	0.000
61	A	66	GLU	-1	-0.853	-0.919	26.295	-9.242	-9.242	0.000	0.000	0.000	0.000
62	A	67	ASP	-1	-0.804	-0.904	29.334	-9.668	-9.668	0.000	0.000	0.000	0.000
63	A	68	TYR	0	-0.015	-0.002	22.662	-0.024	-0.024	0.000	0.000	0.000	0.000
64	A	69	VAL	0	-0.003	-0.006	27.123	0.039	0.039	0.000	0.000	0.000	0.000
65	A	70	LYS	1	0.748	0.873	29.059	9.694	9.694	0.000	0.000	0.000	0.000
66	A	71	LYS	1	0.800	0.895	29.400	10.478	10.478	0.000	0.000	0.000	0.000
67	A	72	HIS	0	-0.059	-0.024	25.886	0.149	0.149	0.000	0.000	0.000	0.000
68	A	73	GLY	0	0.024	0.030	28.792	-0.054	-0.054	0.000	0.000	0.000	0.000
69	A	74	PRO	0	-0.014	-0.019	28.277	-0.398	-0.398	0.000	0.000	0.000	0.000
70	A	75	GLN	0	-0.067	-0.038	23.297	-0.719	-0.719	0.000	0.000	0.000	0.000
71	A	76	GLN	0	-0.004	-0.033	22.556	0.118	0.118	0.000	0.000	0.000	0.000
72	A	77	ARG	1	0.869	0.920	12.508	21.358	21.358	0.000	0.000	0.000	0.000
73	A	78	LEU	0	0.001	0.009	19.339	0.201	0.201	0.000	0.000	0.000	0.000
74	A	79	VAL	0	0.014	0.016	14.089	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	80	THR	0	-0.009	-0.009	17.255	0.369	0.369	0.000	0.000	0.000	0.000
76	A	81	PRO	0	0.001	0.006	18.023	-0.832	-0.832	0.000	0.000	0.000	0.000
77	A	82	SER	0	0.010	-0.033	18.156	0.676	0.676	0.000	0.000	0.000	0.000
78	A	83	PHE	0	0.020	0.008	20.343	0.442	0.442	0.000	0.000	0.000	0.000
79	A	84	VAL	0	0.032	0.027	19.796	0.571	0.571	0.000	0.000	0.000	0.000
80	A	85	LYS	1	0.950	0.970	18.190	13.077	13.077	0.000	0.000	0.000	0.000
81	A	86	GLY	0	0.032	0.009	14.990	0.271	0.271	0.000	0.000	0.000	0.000
82	A	87	ILE	0	-0.008	0.011	13.953	-1.062	-1.062	0.000	0.000	0.000	0.000
83	A	88	GLN	0	-0.046	-0.010	8.705	-0.116	-0.116	0.000	0.000	0.000	0.000
84	A	89	CYS	0	-0.023	-0.017	13.219	-0.378	-0.378	0.000	0.000	0.000	0.000
85	A	90	VAL	0	0.021	0.019	15.585	-0.339	-0.339	0.000	0.000	0.000	0.000
86	A	91	ASN	0	-0.066	-0.036	13.351	1.059	1.059	0.000	0.000	0.000	0.000
87	A	92	ASN	0	-0.023	-0.016	16.410	0.787	0.787	0.000	0.000	0.000	0.000
88	A	93	VAL	0	0.026	0.007	16.486	-0.021	-0.021	0.000	0.000	0.000	0.000
89	A	94	VAL	0	-0.028	0.010	19.764	0.535	0.535	0.000	0.000	0.000	0.000
90	A	95	GLY	0	0.000	0.000	22.389	-0.436	-0.436	0.000	0.000	0.000	0.000
91	A	96	PRO	0	-0.031	-0.024	23.531	0.284	0.284	0.000	0.000	0.000	0.000
92	A	97	ARG	1	0.882	0.918	26.529	10.790	10.790	0.000	0.000	0.000	0.000
93	A	98	HIS	0	0.043	0.009	29.943	-0.105	-0.105	0.000	0.000	0.000	0.000
94	A	99	GLY	0	-0.019	-0.010	33.237	0.100	0.100	0.000	0.000	0.000	0.000
95	A	100	ASP	-1	-0.848	-0.916	28.989	-10.868	-10.868	0.000	0.000	0.000	0.000
96	A	101	ASN	0	-0.002	0.000	31.818	0.205	0.205	0.000	0.000	0.000	0.000
97	A	102	ASN	0	-0.056	-0.044	27.941	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	103	LEU	0	0.058	0.030	27.212	-0.514	-0.514	0.000	0.000	0.000	0.000
99	A	104	HIS	0	-0.005	-0.002	22.348	0.022	0.022	0.000	0.000	0.000	0.000
100	A	105	GLU	-1	-0.792	-0.894	23.125	-12.637	-12.637	0.000	0.000	0.000	0.000
101	A	106	LYS	1	0.822	0.907	22.175	10.845	10.845	0.000	0.000	0.000	0.000
102	A	107	LEU	0	-0.004	-0.005	22.014	-0.524	-0.524	0.000	0.000	0.000	0.000
103	A	108	VAL	0	-0.005	0.013	17.733	-0.892	-0.892	0.000	0.000	0.000	0.000
104	A	109	ALA	0	-0.010	-0.008	17.552	-1.246	-1.246	0.000	0.000	0.000	0.000
105	A	110	ALA	0	-0.011	-0.003	17.567	-0.856	-0.856	0.000	0.000	0.000	0.000
106	A	111	TYR	0	0.017	-0.007	15.533	-0.857	-0.857	0.000	0.000	0.000	0.000
107	A	112	LYS	1	0.873	0.937	13.214	21.003	21.003	0.000	0.000	0.000	0.000
108	A	113	ASN	0	-0.011	-0.003	12.846	-2.194	-2.194	0.000	0.000	0.000	0.000
109	A	114	VAL	0	-0.004	0.011	11.614	0.144	0.144	0.000	0.000	0.000	0.000
110	A	115	LEU	0	-0.025	0.007	6.848	-0.824	-0.824	0.000	0.000	0.000	0.000
111	A	116	VAL	0	0.027	0.004	8.603	2.785	2.785	0.000	0.000	0.000	0.000
112	A	117	ASP	-1	-0.902	-0.942	7.222	-34.143	-34.143	0.000	0.000	0.000	0.000
113	A	118	GLY	0	-0.027	-0.020	5.121	2.647	2.647	0.000	0.000	0.000	0.000
114	A	119	VAL	0	-0.021	0.002	5.642	-0.738	-0.738	0.000	0.000	0.000	0.000
115	A	120	VAL	0	-0.028	-0.002	2.050	-6.735	-7.490	6.728	-2.580	-3.394	-0.012
116	A	121	ASN	0	-0.002	-0.016	4.494	-1.016	-0.909	-0.001	-0.014	-0.092	0.000
117	A	122	TYR	0	0.032	0.013	6.411	2.643	2.643	0.000	0.000	0.000	0.000
118	A	123	VAL	0	0.011	0.015	10.766	0.533	0.533	0.000	0.000	0.000	0.000
119	A	124	VAL	0	-0.007	-0.014	13.490	0.113	0.113	0.000	0.000	0.000	0.000
120	A	125	PRO	0	0.033	0.035	16.288	0.447	0.447	0.000	0.000	0.000	0.000
121	A	126	VAL	0	0.033	0.001	19.607	-0.486	-0.486	0.000	0.000	0.000	0.000
122	A	127	LEU	0	-0.012	0.000	18.553	0.702	0.702	0.000	0.000	0.000	0.000
123	A	128	SER	0	0.042	0.004	22.746	0.061	0.061	0.000	0.000	0.000	0.000
124	A	129	LEU	0	0.016	0.013	26.061	0.366	0.366	0.000	0.000	0.000	0.000
125	A	130	GLY	0	-0.013	0.008	28.609	0.344	0.344	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.055	-0.013	28.113	0.349	0.349	0.000	0.000	0.000	0.000
127	A	132	PHE	0	0.008	-0.007	31.123	0.012	0.012	0.000	0.000	0.000	0.000
128	A	133	GLY	0	0.016	0.005	32.839	-0.118	-0.118	0.000	0.000	0.000	0.000
129	A	134	VAL	0	-0.028	-0.010	26.788	-0.212	-0.212	0.000	0.000	0.000	0.000
130	A	135	ASP	-1	-0.813	-0.900	29.171	-10.366	-10.366	0.000	0.000	0.000	0.000
131	A	136	PHE	0	-0.015	-0.040	25.897	-0.425	-0.425	0.000	0.000	0.000	0.000
132	A	137	LYS	1	0.845	0.943	25.258	9.764	9.764	0.000	0.000	0.000	0.000
133	A	138	MET	0	0.018	0.024	25.307	-0.401	-0.401	0.000	0.000	0.000	0.000
134	A	139	SER	0	-0.022	-0.016	23.127	-0.849	-0.849	0.000	0.000	0.000	0.000
135	A	140	ILE	0	0.010	0.001	20.411	-0.773	-0.773	0.000	0.000	0.000	0.000
136	A	141	ASP	-1	-0.821	-0.890	20.313	-13.765	-13.765	0.000	0.000	0.000	0.000
137	A	142	ALA	0	-0.018	-0.015	20.480	-0.706	-0.706	0.000	0.000	0.000	0.000
138	A	143	MET	0	-0.046	-0.011	15.890	-0.998	-0.998	0.000	0.000	0.000	0.000
139	A	144	ARG	1	0.837	0.895	15.801	14.363	14.363	0.000	0.000	0.000	0.000
140	A	145	GLU	-1	-0.854	-0.918	15.840	-16.674	-16.674	0.000	0.000	0.000	0.000
141	A	146	ALA	0	-0.061	-0.033	14.724	-1.080	-1.080	0.000	0.000	0.000	0.000
142	A	147	PHE	0	0.026	-0.011	11.458	-1.787	-1.787	0.000	0.000	0.000	0.000
143	A	148	GLU	-1	-0.886	-0.936	10.782	-26.119	-26.119	0.000	0.000	0.000	0.000
144	A	149	GLY	0	-0.001	0.013	9.940	-0.518	-0.518	0.000	0.000	0.000	0.000
145	A	150	CYS	0	-0.098	-0.033	6.521	-5.148	-5.148	0.000	0.000	0.000	0.000
146	A	151	THR	0	-0.038	-0.036	2.564	-5.778	-2.908	0.695	-1.488	-2.076	-0.016
147	A	152	ILE	0	-0.016	-0.001	3.315	-14.115	-12.637	0.062	-0.623	-0.918	-0.004
148	A	153	ARG	1	0.845	0.916	3.521	31.045	31.552	0.013	-0.175	-0.346	0.000
149	A	154	VAL	0	0.018	0.012	7.145	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	155	LEU	0	-0.037	-0.011	10.747	0.962	0.962	0.000	0.000	0.000	0.000
151	A	156	LEU	0	0.020	0.018	13.598	0.141	0.141	0.000	0.000	0.000	0.000
152	A	157	PHE	0	0.003	-0.017	16.736	0.720	0.720	0.000	0.000	0.000	0.000
153	A	158	SER	0	0.004	-0.026	19.775	0.164	0.164	0.000	0.000	0.000	0.000
154	A	159	LEU	0	0.001	0.009	23.482	0.085	0.085	0.000	0.000	0.000	0.000
155	A	160	SER	0	-0.033	-0.013	26.475	0.426	0.426	0.000	0.000	0.000	0.000
156	A	161	GLN	0	0.009	-0.026	25.284	-0.362	-0.362	0.000	0.000	0.000	0.000
157	A	162	GLU	-1	-0.816	-0.907	26.679	-10.030	-10.030	0.000	0.000	0.000	0.000
158	A	163	HIS	0	-0.011	-0.006	24.292	-0.513	-0.513	0.000	0.000	0.000	0.000
159	A	164	ILE	0	0.029	0.010	20.209	-0.445	-0.445	0.000	0.000	0.000	0.000
160	A	165	ASP	-1	-0.794	-0.880	23.007	-10.851	-10.851	0.000	0.000	0.000	0.000
161	A	166	TYR	0	-0.084	-0.064	24.481	0.193	0.193	0.000	0.000	0.000	0.000
162	A	167	PHE	0	0.014	0.002	15.956	-0.431	-0.431	0.000	0.000	0.000	0.000
163	A	168	ASP	-1	-0.862	-0.947	20.754	-13.678	-13.678	0.000	0.000	0.000	0.000
164	A	169	VAL	0	-0.074	-0.036	22.277	-0.050	-0.050	0.000	0.000	0.000	0.000
165	A	170	THR	0	-0.049	-0.020	22.332	-0.167	-0.167	0.000	0.000	0.000	0.000
166	A	171	CYS	0	-0.092	-0.002	18.950	-0.792	-0.792	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LYS)