FMO DATABASE

FMODB ID: LJKN9

Calculation Name: 3PU6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PU6

Chain ID: A

ChEMBL ID:

UniProt ID: Q7MR08

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	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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1365163.001163
FMO2-HF: Nuclear repulsion	1308407.519591
FMO2-HF: Total energy	-56755.481572
FMO2-MP2: Total energy	-56921.043331

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:1:LEU)

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

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.
-13.668	-5.296	6.808	-5.509	-9.672	-0.038

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.002 / q_NPA : 0.005

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	3	LYS	1	0.893	0.973	2.726	0.324	3.618	0.342	-1.384	-2.252	0.004
4	A	4	VAL	0	0.023	0.006	5.645	0.248	0.248	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.009	0.005	9.223	0.091	0.091	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.051	-0.026	12.240	0.028	0.028	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.046	-0.007	15.209	0.036	0.036	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.005	-0.002	18.410	0.004	0.004	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.059	0.030	21.441	0.006	0.006	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.018	-0.011	25.041	-0.004	-0.004	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.769	-0.889	26.478	-0.196	-0.196	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.023	-0.005	29.243	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.848	0.935	31.289	0.130	0.130	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.067	0.042	32.119	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.774	-0.882	29.137	-0.128	-0.128	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.871	-0.961	27.664	-0.176	-0.176	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.029	0.024	26.009	-0.014	-0.014	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.006	0.002	23.041	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.028	0.010	20.030	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	ILE	0	-0.021	-0.002	19.984	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	21	ALA	0	-0.010	-0.016	21.541	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.007	-0.003	16.065	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.039	0.003	16.968	-0.027	-0.027	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.854	0.901	17.273	0.195	0.195	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.015	0.013	18.378	0.002	0.002	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.013	-0.012	12.211	0.003	0.003	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.932	-0.970	14.082	-0.435	-0.435	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-1.008	-0.983	15.440	-0.228	-0.228	0.000	0.000	0.000	0.000
29	A	29	GLN	0	-0.016	-0.016	15.796	0.018	0.018	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.114	-0.043	9.992	0.058	0.058	0.000	0.000	0.000	0.000
31	A	31	PRO	0	0.073	0.028	10.918	-0.142	-0.142	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.977	-0.995	5.487	-0.777	-0.777	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.056	-0.016	6.419	-0.780	-0.780	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.029	-0.007	8.930	0.158	0.158	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.019	0.004	10.932	-0.056	-0.056	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.074	-0.039	13.223	0.015	0.015	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.021	0.004	16.237	0.010	0.010	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.038	0.017	19.688	0.009	0.009	0.000	0.000	0.000	0.000
39	A	39	TYR	0	-0.025	-0.004	21.031	0.021	0.021	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.869	-0.937	23.774	-0.190	-0.190	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.081	-0.031	24.814	0.012	0.012	0.000	0.000	0.000	0.000
42	A	42	PRO	0	0.085	0.038	20.042	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.861	-0.951	20.110	-0.258	-0.258	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.107	-0.062	21.955	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.885	-0.942	17.432	-0.410	-0.410	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.038	-0.017	17.271	-0.046	-0.046	0.000	0.000	0.000	0.000
47	A	47	GLY	0	-0.057	-0.018	17.382	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	48	LYS	1	1.011	0.987	15.832	0.412	0.412	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.018	0.026	12.211	-0.077	-0.077	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.872	0.925	12.904	0.239	0.239	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.973	-0.979	13.693	-0.382	-0.382	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.023	0.007	8.174	0.004	0.004	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.011	-0.019	8.910	-0.200	-0.200	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.003	0.007	6.816	-0.154	-0.154	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.838	-0.903	2.417	-8.631	-5.665	5.484	-3.403	-5.046	-0.040
56	A	56	VAL	0	-0.031	-0.038	3.344	0.061	0.592	0.017	-0.082	-0.467	0.000
57	A	57	ILE	0	0.004	0.015	5.752	-0.146	-0.146	0.000	0.000	0.000	0.000
58	A	58	VAL	0	0.003	0.008	9.324	0.129	0.129	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.024	-0.003	11.624	-0.027	-0.027	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.002	-0.008	15.163	0.034	0.034	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.836	-0.936	17.623	-0.224	-0.224	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.003	0.022	21.436	0.010	0.010	0.000	0.000	0.000	0.000
63	A	63	MET	0	-0.069	-0.018	23.539	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	64	SER	0	0.025	0.011	26.331	0.009	0.009	0.000	0.000	0.000	0.000
65	A	65	GLY	0	-0.020	-0.019	30.051	0.002	0.002	0.000	0.000	0.000	0.000
66	A	66	PHE	0	-0.045	-0.021	32.813	0.001	0.001	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.824	0.898	27.629	0.119	0.119	0.000	0.000	0.000	0.000
68	A	68	GLU	-1	-0.810	-0.908	29.106	-0.109	-0.109	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.051	-0.020	27.406	0.006	0.006	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.858	-0.908	24.639	-0.096	-0.096	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.070	-0.055	18.833	-0.013	-0.013	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.880	-0.936	19.932	-0.120	-0.120	0.000	0.000	0.000	0.000
73	A	73	PHE	0	-0.054	-0.032	11.565	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.008	0.002	15.765	0.021	0.021	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.794	-0.910	11.426	-0.285	-0.285	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.028	-0.019	13.140	0.038	0.038	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.024	0.009	11.064	0.017	0.017	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.882	-0.863	13.297	-0.048	-0.048	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.860	-0.939	15.699	-0.140	-0.140	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.942	0.966	18.932	0.044	0.044	0.000	0.000	0.000	0.000
81	A	81	THR	0	-0.035	-0.088	17.362	0.004	0.004	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.011	-0.008	18.208	-0.011	-0.011	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.065	-0.028	19.813	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.082	-0.039	23.056	0.008	0.008	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.063	-0.034	21.085	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	86	THR	0	0.030	0.020	22.362	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	87	HIS	0	-0.011	0.002	23.611	0.005	0.005	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.040	-0.029	25.432	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.043	0.016	21.530	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	90	PRO	0	0.023	0.007	22.925	0.002	0.002	0.000	0.000	0.000	0.000
91	A	91	THR	0	0.062	0.037	20.457	0.004	0.004	0.000	0.000	0.000	0.000
92	A	92	PRO	0	0.004	0.017	22.025	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.024	-0.012	22.283	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.034	0.029	18.802	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.010	-0.003	17.502	-0.028	-0.028	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.050	-0.028	17.473	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	97	TYR	0	0.008	0.015	17.510	0.013	0.013	0.000	0.000	0.000	0.000
98	A	98	LEU	0	0.007	-0.005	13.929	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	99	ARG	1	0.855	0.944	13.688	0.170	0.170	0.000	0.000	0.000	0.000
100	A	100	GLY	0	-0.045	-0.009	14.257	0.013	0.013	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.087	-0.034	11.769	0.016	0.016	0.000	0.000	0.000	0.000
102	A	102	CYS	0	-0.064	-0.024	7.948	-0.046	-0.046	0.000	0.000	0.000	0.000
103	A	103	SER	0	0.042	0.022	8.384	0.016	0.016	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.913	0.963	5.661	0.357	0.357	0.000	0.000	0.000	0.000
105	A	105	THR	0	0.015	0.008	8.670	-0.131	-0.131	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.014	-0.019	8.437	0.081	0.081	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.016	0.004	12.321	-0.035	-0.035	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.011	-0.004	14.363	0.016	0.016	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.015	0.000	16.912	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.045	0.013	19.494	0.013	0.013	0.000	0.000	0.000	0.000
111	A	111	SER	0	-0.061	-0.022	22.714	0.004	0.004	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.018	0.011	26.272	0.002	0.002	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.061	0.021	29.028	0.004	0.004	0.000	0.000	0.000	0.000
114	A	114	LEU	0	0.018	-0.008	32.812	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.968	-0.983	34.406	-0.078	-0.078	0.000	0.000	0.000	0.000
116	A	116	ASN	0	-0.003	-0.010	33.075	0.005	0.005	0.000	0.000	0.000	0.000
117	A	117	VAL	0	-0.036	-0.004	30.624	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.081	-0.034	33.622	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	119	HIS	0	-0.007	0.004	36.775	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.060	-0.032	36.161	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.008	-0.022	35.002	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.918	-0.940	33.239	-0.127	-0.127	0.000	0.000	0.000	0.000
123	A	123	GLY	0	-0.018	-0.007	31.056	0.005	0.005	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.055	-0.019	25.916	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.009	-0.024	30.537	0.008	0.008	0.000	0.000	0.000	0.000
126	A	126	GLN	0	-0.066	-0.051	30.342	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	127	GLY	0	0.051	0.035	29.803	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	128	ALA	0	0.067	0.037	27.357	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	129	SER	0	-0.005	-0.018	25.845	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.891	-0.943	25.217	-0.106	-0.106	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.021	-0.022	24.156	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	132	ALA	0	0.021	0.017	21.403	-0.012	-0.012	0.000	0.000	0.000	0.000
133	A	133	PHE	0	0.001	-0.002	20.068	-0.021	-0.021	0.000	0.000	0.000	0.000
134	A	134	VAL	0	-0.019	-0.006	19.911	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	135	ALA	0	0.009	0.001	18.006	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.013	-0.012	15.170	-0.027	-0.027	0.000	0.000	0.000	0.000
137	A	137	GLY	0	-0.036	-0.013	14.955	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.949	0.968	14.744	0.137	0.137	0.000	0.000	0.000	0.000
139	A	139	ILE	0	0.030	0.031	10.285	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.906	0.939	10.072	0.150	0.150	0.000	0.000	0.000	0.000
141	A	141	GLU	-1	-0.952	-0.976	10.843	-0.063	-0.063	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.032	-0.016	7.115	0.057	0.057	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.856	-0.956	6.209	-0.532	-0.532	0.000	0.000	0.000	0.000
144	A	144	GLY	0	-0.047	-0.016	6.188	0.155	0.155	0.000	0.000	0.000	0.000
145	A	145	MET	0	-0.074	-0.029	6.937	0.110	0.110	0.000	0.000	0.000	0.000
146	A	146	LEU	0	-0.025	-0.011	2.495	-0.901	-0.175	0.888	-0.304	-1.311	0.000
147	A	147	LYS	1	0.883	0.963	3.284	-0.624	0.231	0.077	-0.336	-0.596	-0.002

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