FMO DATABASE

FMODB ID: N1KGQ

Calculation Name: 3JYB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JYB

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-19

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1371580.259999
FMO2-HF: Nuclear repulsion	1315519.382982
FMO2-HF: Total energy	-56060.877017
FMO2-MP2: Total energy	-56227.229436

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:48:GLN)

Summations of interaction energy for fragment #1(A:48:GLN)

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.
-18.226	-12.728	4.207	-3.271	-6.435	0.01

Interaction energy analysis for fragmet #1(A:48:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : -0.010

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	50	TRP	0	0.040	0.035	3.512	-2.435	-0.310	-0.008	-0.988	-1.130	0.000
4	A	51	ARG	1	0.875	0.941	2.381	-11.576	-10.064	1.800	-1.132	-2.180	0.005
5	A	52	LEU	0	0.015	0.002	6.299	-0.193	-0.193	0.000	0.000	0.000	0.000
6	A	53	LEU	0	0.020	0.017	9.740	0.240	0.240	0.000	0.000	0.000	0.000
7	A	54	ARG	1	0.861	0.918	12.731	-0.488	-0.488	0.000	0.000	0.000	0.000
8	A	55	ASP	-1	-0.732	-0.835	16.309	0.452	0.452	0.000	0.000	0.000	0.000
9	A	56	GLU	-1	-0.788	-0.903	19.304	0.315	0.315	0.000	0.000	0.000	0.000
10	A	57	SER	0	-0.043	-0.037	22.181	-0.039	-0.039	0.000	0.000	0.000	0.000
11	A	58	ALA	0	-0.015	-0.007	22.711	-0.027	-0.027	0.000	0.000	0.000	0.000
12	A	59	GLN	0	-0.026	-0.013	23.723	-0.018	-0.018	0.000	0.000	0.000	0.000
13	A	60	LEU	0	-0.035	-0.002	18.069	0.003	0.003	0.000	0.000	0.000	0.000
14	A	61	ARG	1	0.946	0.965	21.803	-0.334	-0.334	0.000	0.000	0.000	0.000
15	A	62	ILE	0	0.019	0.004	17.667	0.036	0.036	0.000	0.000	0.000	0.000
16	A	63	ALA	0	0.024	0.012	19.210	0.041	0.041	0.000	0.000	0.000	0.000
17	A	64	ASP	-1	-0.790	-0.882	20.591	0.459	0.459	0.000	0.000	0.000	0.000
18	A	65	VAL	0	0.006	0.009	14.633	0.053	0.053	0.000	0.000	0.000	0.000
19	A	66	LEU	0	-0.022	-0.008	15.458	0.105	0.105	0.000	0.000	0.000	0.000
20	A	67	GLN	0	-0.081	-0.042	16.879	0.043	0.043	0.000	0.000	0.000	0.000
21	A	68	ARG	1	0.839	0.916	15.440	-0.575	-0.575	0.000	0.000	0.000	0.000
22	A	69	LYS	1	0.923	0.965	11.315	-0.771	-0.771	0.000	0.000	0.000	0.000
23	A	70	GLU	-1	-0.806	-0.900	9.964	1.511	1.511	0.000	0.000	0.000	0.000
24	A	71	GLN	0	-0.031	-0.023	10.245	0.217	0.217	0.000	0.000	0.000	0.000
25	A	72	PHE	0	0.002	0.011	8.175	-0.052	-0.052	0.000	0.000	0.000	0.000
26	A	73	ARG	1	0.805	0.885	6.325	-1.447	-1.447	0.000	0.000	0.000	0.000
27	A	74	PRO	0	-0.001	-0.009	2.295	-2.794	-1.128	2.415	-1.119	-2.962	0.005
28	A	75	LEU	0	-0.012	0.002	4.208	-0.547	-0.352	0.000	-0.032	-0.163	0.000
29	A	76	ALA	0	-0.003	-0.001	5.328	-0.103	-0.103	0.000	0.000	0.000	0.000
30	A	77	LYS	1	0.917	0.956	7.621	-0.221	-0.221	0.000	0.000	0.000	0.000
31	A	78	ARG	1	0.850	0.922	6.535	-1.201	-1.201	0.000	0.000	0.000	0.000
32	A	79	SER	0	0.054	0.017	10.187	-0.071	-0.071	0.000	0.000	0.000	0.000
33	A	80	PHE	0	-0.077	-0.030	12.637	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	81	ILE	0	0.046	0.007	14.712	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	82	PHE	0	-0.013	0.003	14.191	0.003	0.003	0.000	0.000	0.000	0.000
36	A	83	PRO	0	0.038	0.002	20.097	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	84	ALA	0	-0.012	0.008	23.292	0.021	0.021	0.000	0.000	0.000	0.000
38	A	85	SER	0	-0.007	-0.001	23.137	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	86	PRO	0	0.026	0.007	24.897	0.004	0.004	0.000	0.000	0.000	0.000
40	A	87	GLN	0	-0.036	-0.008	18.881	0.046	0.046	0.000	0.000	0.000	0.000
41	A	88	ALA	0	-0.001	-0.003	20.448	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	89	VAL	0	-0.028	-0.004	14.714	0.054	0.054	0.000	0.000	0.000	0.000
43	A	90	TRP	0	-0.010	-0.014	14.498	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	91	LEU	0	-0.001	0.008	9.811	0.103	0.103	0.000	0.000	0.000	0.000
45	A	92	GLN	0	0.001	-0.017	8.261	0.183	0.183	0.000	0.000	0.000	0.000
46	A	93	VAL	0	-0.008	-0.004	8.093	0.059	0.059	0.000	0.000	0.000	0.000
47	A	94	GLN	0	0.005	0.013	5.910	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	95	LEU	0	0.009	0.004	7.981	0.158	0.158	0.000	0.000	0.000	0.000
49	A	96	PRO	0	0.026	0.019	9.200	-0.049	-0.049	0.000	0.000	0.000	0.000
50	A	97	ALA	0	0.013	0.013	11.938	0.023	0.023	0.000	0.000	0.000	0.000
51	A	98	GLN	0	0.004	0.010	12.701	-0.045	-0.045	0.000	0.000	0.000	0.000
52	A	99	LYS	1	0.951	0.958	16.785	-0.075	-0.075	0.000	0.000	0.000	0.000
53	A	100	VAL	0	0.027	0.021	18.520	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	101	PRO	0	0.022	0.007	19.922	0.028	0.028	0.000	0.000	0.000	0.000
55	A	102	SER	0	0.023	0.025	17.264	0.014	0.014	0.000	0.000	0.000	0.000
56	A	103	TRP	0	0.012	0.000	18.279	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	104	LEU	0	-0.020	0.011	13.207	0.031	0.031	0.000	0.000	0.000	0.000
58	A	105	TRP	0	0.050	0.017	16.199	-0.027	-0.027	0.000	0.000	0.000	0.000
59	A	106	ILE	0	-0.017	-0.030	15.993	0.050	0.050	0.000	0.000	0.000	0.000
60	A	107	PHE	0	0.031	0.035	18.011	-0.029	-0.029	0.000	0.000	0.000	0.000
61	A	108	ALA	0	0.035	-0.010	19.105	0.012	0.012	0.000	0.000	0.000	0.000
62	A	109	PRO	0	0.002	0.017	20.795	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	110	ARG	1	0.921	0.952	24.136	-0.127	-0.127	0.000	0.000	0.000	0.000
64	A	111	VAL	0	-0.030	0.015	20.631	0.006	0.006	0.000	0.000	0.000	0.000
65	A	112	GLN	0	0.016	0.012	24.060	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	113	TYR	0	-0.024	-0.016	25.253	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	114	LEU	0	0.041	0.022	19.491	0.021	0.021	0.000	0.000	0.000	0.000
68	A	115	ASP	-1	-0.819	-0.890	20.859	0.286	0.286	0.000	0.000	0.000	0.000
69	A	116	TYR	0	0.038	0.031	16.865	0.033	0.033	0.000	0.000	0.000	0.000
70	A	117	TYR	0	-0.008	-0.018	17.924	-0.040	-0.040	0.000	0.000	0.000	0.000
71	A	118	LEU	0	0.001	0.012	16.645	0.045	0.045	0.000	0.000	0.000	0.000
72	A	119	VAL	0	-0.021	-0.012	16.189	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	120	GLN	0	0.045	-0.010	16.413	0.044	0.044	0.000	0.000	0.000	0.000
74	A	121	ASP	-1	-0.824	-0.891	18.681	0.266	0.266	0.000	0.000	0.000	0.000
75	A	122	GLY	0	-0.005	0.005	18.792	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	123	GLN	0	-0.046	-0.025	19.899	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	124	LEU	0	-0.021	-0.023	20.577	0.020	0.020	0.000	0.000	0.000	0.000
78	A	125	VAL	0	0.014	0.019	21.057	-0.027	-0.027	0.000	0.000	0.000	0.000
79	A	126	ARG	1	0.932	0.953	21.852	-0.302	-0.302	0.000	0.000	0.000	0.000
80	A	127	ASP	-1	-0.790	-0.887	21.714	0.350	0.350	0.000	0.000	0.000	0.000
81	A	128	GLN	0	0.011	0.007	22.983	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	129	HIS	1	0.772	0.855	23.578	-0.268	-0.268	0.000	0.000	0.000	0.000
83	A	130	THR	0	0.062	0.020	23.634	-0.019	-0.019	0.000	0.000	0.000	0.000
84	A	131	GLY	0	0.048	0.034	25.188	0.014	0.014	0.000	0.000	0.000	0.000
85	A	132	GLU	-1	-0.826	-0.914	26.076	0.148	0.148	0.000	0.000	0.000	0.000
86	A	133	SER	0	-0.047	-0.029	28.734	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	134	ARG	1	0.754	0.863	25.237	-0.241	-0.241	0.000	0.000	0.000	0.000
88	A	135	PRO	0	0.029	0.014	30.735	0.000	0.000	0.000	0.000	0.000	0.000
89	A	136	PHE	0	-0.016	-0.020	33.560	0.004	0.004	0.000	0.000	0.000	0.000
90	A	137	GLN	0	0.012	0.030	28.680	0.004	0.004	0.000	0.000	0.000	0.000
91	A	138	GLU	-1	-0.892	-0.936	32.066	0.130	0.130	0.000	0.000	0.000	0.000
92	A	139	ARG	1	0.809	0.866	25.616	-0.175	-0.175	0.000	0.000	0.000	0.000
93	A	140	PRO	0	0.003	0.012	27.885	-0.006	-0.006	0.000	0.000	0.000	0.000
94	A	141	LEU	0	0.030	0.034	24.612	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	142	PRO	0	0.057	0.027	28.684	0.007	0.007	0.000	0.000	0.000	0.000
96	A	143	SER	0	-0.042	-0.032	25.873	0.007	0.007	0.000	0.000	0.000	0.000
97	A	144	ARG	1	0.858	0.927	26.661	-0.126	-0.126	0.000	0.000	0.000	0.000
98	A	145	SER	0	0.011	0.006	22.331	0.019	0.019	0.000	0.000	0.000	0.000
99	A	146	TYR	0	-0.050	-0.028	20.653	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	147	LEU	0	0.024	0.009	20.556	0.014	0.014	0.000	0.000	0.000	0.000
101	A	148	PHE	0	-0.036	-0.020	18.700	-0.012	-0.012	0.000	0.000	0.000	0.000
102	A	149	SER	0	-0.014	0.007	19.224	0.021	0.021	0.000	0.000	0.000	0.000
103	A	150	LEU	0	-0.029	-0.028	14.897	0.018	0.018	0.000	0.000	0.000	0.000
104	A	151	PRO	0	-0.025	0.001	18.687	-0.025	-0.025	0.000	0.000	0.000	0.000
105	A	152	VAL	0	-0.002	-0.007	19.446	0.014	0.014	0.000	0.000	0.000	0.000
106	A	153	ASP	-1	-0.798	-0.905	20.516	0.234	0.234	0.000	0.000	0.000	0.000
107	A	154	GLY	0	-0.007	0.004	20.280	-0.008	-0.008	0.000	0.000	0.000	0.000
108	A	155	LYS	1	0.824	0.903	18.540	-0.241	-0.241	0.000	0.000	0.000	0.000
109	A	156	PRO	0	-0.024	-0.002	13.432	0.010	0.010	0.000	0.000	0.000	0.000
110	A	157	MET	0	0.004	0.005	13.254	0.004	0.004	0.000	0.000	0.000	0.000
111	A	158	THR	0	-0.096	-0.059	10.653	0.121	0.121	0.000	0.000	0.000	0.000
112	A	159	LEU	0	0.015	0.026	12.241	-0.060	-0.060	0.000	0.000	0.000	0.000
113	A	160	TYR	0	0.011	-0.009	12.467	0.143	0.143	0.000	0.000	0.000	0.000
114	A	161	VAL	0	-0.017	-0.015	14.438	-0.068	-0.068	0.000	0.000	0.000	0.000
115	A	162	ARG	1	0.865	0.959	15.761	-0.318	-0.318	0.000	0.000	0.000	0.000
116	A	163	MET	0	-0.017	-0.013	14.800	-0.048	-0.048	0.000	0.000	0.000	0.000
117	A	164	THR	0	0.003	0.004	19.815	0.007	0.007	0.000	0.000	0.000	0.000
118	A	165	SER	0	-0.012	-0.039	22.870	-0.018	-0.018	0.000	0.000	0.000	0.000
119	A	166	ASN	0	0.012	0.023	25.504	0.004	0.004	0.000	0.000	0.000	0.000
120	A	167	HIS	0	0.041	0.021	26.654	-0.020	-0.020	0.000	0.000	0.000	0.000
121	A	168	PRO	0	-0.024	-0.033	24.265	0.016	0.016	0.000	0.000	0.000	0.000
122	A	169	LEU	0	0.003	0.032	19.051	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	170	MET	0	-0.028	-0.024	18.465	0.003	0.003	0.000	0.000	0.000	0.000
124	A	171	ALA	0	-0.010	-0.003	15.927	0.006	0.006	0.000	0.000	0.000	0.000
125	A	172	TRP	0	0.007	-0.001	15.038	0.008	0.008	0.000	0.000	0.000	0.000
126	A	173	PHE	0	-0.010	-0.004	9.706	-0.001	-0.001	0.000	0.000	0.000	0.000
127	A	174	ASP	-1	-0.754	-0.863	11.394	0.698	0.698	0.000	0.000	0.000	0.000
128	A	175	GLN	0	-0.095	-0.054	12.321	0.041	0.041	0.000	0.000	0.000	0.000
129	A	176	ILE	0	-0.025	-0.005	13.929	-0.014	-0.014	0.000	0.000	0.000	0.000
130	A	177	ASP	-1	-0.785	-0.916	17.110	0.152	0.152	0.000	0.000	0.000	0.000
131	A	178	GLU	-1	-0.948	-0.979	19.562	0.080	0.080	0.000	0.000	0.000	0.000
132	A	179	ALA	0	0.063	0.032	22.127	-0.004	-0.004	0.000	0.000	0.000	0.000
133	A	180	GLY	0	-0.025	-0.017	20.291	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	181	LEU	0	-0.065	-0.033	21.337	0.000	0.000	0.000	0.000	0.000	0.000
135	A	182	VAL	0	-0.013	-0.015	23.411	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	183	GLY	0	0.002	0.017	24.941	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	184	LEU	0	-0.089	-0.038	21.086	0.003	0.003	0.000	0.000	0.000	0.000
138	A	185	GLU	-1	-0.858	-0.908	25.177	0.091	0.091	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:48:GLN)