FMO DATABASE

FMODB ID: YZ212

Calculation Name: 4WJ7-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WJ7

Chain ID: D

ChEMBL ID:

UniProt ID: Q9BSQ5

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1011383.774806
FMO2-HF: Nuclear repulsion	963929.505603
FMO2-HF: Total energy	-47454.269203
FMO2-MP2: Total energy	-47592.890436

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(D:63:ILE)

Summations of interaction energy for fragment #1(D:63: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.
-9.249	-2.244	5.712	-5.197	-7.522	-0.022

Interaction energy analysis for fragmet #1(D:63: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 : 0.011

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

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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	D	65	LYS	1	0.806	0.905	3.443	-1.325	2.140	0.002	-1.796	-1.671	0.001
4	D	66	GLU	-1	-0.840	-0.918	5.254	-0.636	-0.583	-0.001	-0.003	-0.050	0.000
5	D	67	VAL	0	-0.061	-0.030	8.994	0.079	0.079	0.000	0.000	0.000	0.000
6	D	68	LYS	1	0.876	0.938	11.347	0.497	0.497	0.000	0.000	0.000	0.000
7	D	69	TYR	0	-0.008	-0.009	14.478	-0.018	-0.018	0.000	0.000	0.000	0.000
8	D	70	LEU	0	-0.013	-0.011	15.879	0.051	0.051	0.000	0.000	0.000	0.000
9	D	71	GLY	0	0.048	0.008	18.364	0.036	0.036	0.000	0.000	0.000	0.000
10	D	72	GLN	0	-0.019	0.000	18.691	-0.044	-0.044	0.000	0.000	0.000	0.000
11	D	73	LEU	0	-0.026	-0.010	20.233	0.032	0.032	0.000	0.000	0.000	0.000
12	D	74	THR	0	0.077	0.022	22.700	-0.010	-0.010	0.000	0.000	0.000	0.000
13	D	75	SER	0	-0.054	-0.036	25.035	0.009	0.009	0.000	0.000	0.000	0.000
14	D	76	ILE	0	0.022	0.027	24.183	0.014	0.014	0.000	0.000	0.000	0.000
15	D	77	PRO	0	0.042	0.014	26.981	0.001	0.001	0.000	0.000	0.000	0.000
16	D	78	GLY	0	0.036	0.003	26.311	-0.009	-0.009	0.000	0.000	0.000	0.000
17	D	79	TYR	0	-0.037	-0.017	26.473	-0.003	-0.003	0.000	0.000	0.000	0.000
18	D	80	LEU	0	-0.024	0.009	22.716	0.003	0.003	0.000	0.000	0.000	0.000
19	D	81	ASN	0	0.087	0.030	24.676	-0.014	-0.014	0.000	0.000	0.000	0.000
20	D	82	PRO	0	0.034	0.025	19.565	-0.003	-0.003	0.000	0.000	0.000	0.000
21	D	83	SER	0	0.018	0.009	20.980	-0.011	-0.011	0.000	0.000	0.000	0.000
22	D	84	SER	0	-0.108	-0.065	23.264	0.013	0.013	0.000	0.000	0.000	0.000
23	D	85	ARG	1	0.960	0.960	24.042	0.156	0.156	0.000	0.000	0.000	0.000
24	D	86	THR	0	0.029	0.002	25.091	-0.008	-0.008	0.000	0.000	0.000	0.000
25	D	87	GLU	-1	-0.800	-0.879	26.590	-0.145	-0.145	0.000	0.000	0.000	0.000
26	D	88	ILE	0	0.006	0.011	20.485	-0.004	-0.004	0.000	0.000	0.000	0.000
27	D	89	LEU	0	0.036	0.003	23.616	-0.008	-0.008	0.000	0.000	0.000	0.000
28	D	90	HIS	0	-0.021	0.014	25.727	0.010	0.010	0.000	0.000	0.000	0.000
29	D	91	PHE	0	-0.010	-0.024	25.530	0.005	0.005	0.000	0.000	0.000	0.000
30	D	92	ILE	0	0.045	0.027	21.051	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	93	ASP	-1	-0.800	-0.885	25.207	-0.158	-0.158	0.000	0.000	0.000	0.000
32	D	94	ASN	0	0.012	0.002	28.449	0.010	0.010	0.000	0.000	0.000	0.000
33	D	95	ALA	0	0.041	0.035	25.917	0.006	0.006	0.000	0.000	0.000	0.000
34	D	96	LYS	1	0.886	0.949	25.489	0.190	0.190	0.000	0.000	0.000	0.000
35	D	97	ARG	1	0.810	0.887	28.628	0.147	0.147	0.000	0.000	0.000	0.000
36	D	98	ALA	0	-0.073	-0.025	30.682	0.008	0.008	0.000	0.000	0.000	0.000
37	D	99	HIS	0	-0.053	-0.039	29.652	0.005	0.005	0.000	0.000	0.000	0.000
38	D	100	GLN	0	-0.035	-0.019	26.507	-0.011	-0.011	0.000	0.000	0.000	0.000
39	D	101	LEU	0	-0.022	-0.003	21.680	-0.022	-0.022	0.000	0.000	0.000	0.000
40	D	102	PRO	0	0.001	0.022	22.374	0.023	0.023	0.000	0.000	0.000	0.000
41	D	103	GLY	0	-0.012	-0.018	24.650	-0.005	-0.005	0.000	0.000	0.000	0.000
42	D	104	HIS	0	-0.031	-0.022	25.780	-0.004	-0.004	0.000	0.000	0.000	0.000
43	D	105	LEU	0	-0.005	-0.005	19.773	-0.015	-0.015	0.000	0.000	0.000	0.000
44	D	106	THR	0	-0.027	-0.010	22.531	0.010	0.010	0.000	0.000	0.000	0.000
45	D	107	GLN	0	-0.019	-0.026	19.201	-0.020	-0.020	0.000	0.000	0.000	0.000
46	D	108	GLU	-1	-0.865	-0.916	19.302	-0.247	-0.247	0.000	0.000	0.000	0.000
47	D	109	HIS	0	-0.056	-0.021	19.018	-0.016	-0.016	0.000	0.000	0.000	0.000
48	D	110	ASP	-1	-0.773	-0.880	15.118	-0.462	-0.462	0.000	0.000	0.000	0.000
49	D	111	ALA	0	-0.033	-0.032	12.873	0.024	0.024	0.000	0.000	0.000	0.000
50	D	112	VAL	0	0.034	0.026	7.598	-0.066	-0.066	0.000	0.000	0.000	0.000
51	D	113	LEU	0	-0.018	-0.010	5.203	0.124	0.124	0.000	0.000	0.000	0.000
52	D	114	SER	0	-0.007	-0.005	3.334	-0.987	-0.609	0.004	-0.174	-0.208	0.000
53	D	115	LEU	0	-0.010	-0.007	2.415	0.417	1.954	1.104	-0.768	-1.874	0.003
54	D	116	SER	0	0.003	-0.010	2.180	-5.812	-4.446	3.108	-2.189	-2.285	-0.027
55	D	117	ALA	0	0.044	0.018	4.842	-0.030	0.011	-0.001	-0.006	-0.034	0.000
56	D	118	TYR	0	-0.036	-0.015	8.278	-0.016	-0.016	0.000	0.000	0.000	0.000
57	D	119	ASN	0	-0.059	-0.039	8.209	-0.026	-0.026	0.000	0.000	0.000	0.000
58	D	120	VAL	0	0.056	0.048	7.137	-0.385	-0.385	0.000	0.000	0.000	0.000
59	D	121	LYS	1	0.901	0.954	7.502	1.227	1.227	0.000	0.000	0.000	0.000
60	D	122	LEU	0	0.013	0.006	8.733	-0.307	-0.307	0.000	0.000	0.000	0.000
61	D	123	ALA	0	-0.006	-0.008	11.274	0.164	0.164	0.000	0.000	0.000	0.000
62	D	124	TRP	0	0.047	0.024	12.768	-0.075	-0.075	0.000	0.000	0.000	0.000
63	D	125	ARG	1	0.920	0.950	13.691	0.429	0.429	0.000	0.000	0.000	0.000
64	D	126	ASP	-1	-0.990	-0.980	15.576	-0.236	-0.236	0.000	0.000	0.000	0.000
65	D	127	GLY	0	0.058	0.023	18.820	0.026	0.026	0.000	0.000	0.000	0.000
66	D	128	GLU	-1	-1.010	-0.990	13.382	-0.399	-0.399	0.000	0.000	0.000	0.000
67	D	129	ASP	-1	-0.924	-0.950	15.072	-0.348	-0.348	0.000	0.000	0.000	0.000
68	D	130	ILE	0	-0.046	-0.043	14.028	-0.087	-0.087	0.000	0.000	0.000	0.000
69	D	131	ILE	0	-0.047	-0.009	14.486	0.053	0.053	0.000	0.000	0.000	0.000
70	D	132	LEU	0	0.003	-0.005	14.472	0.071	0.071	0.000	0.000	0.000	0.000
71	D	133	ARG	1	0.896	0.944	11.661	0.378	0.378	0.000	0.000	0.000	0.000
72	D	134	VAL	0	0.035	0.022	12.234	0.110	0.110	0.000	0.000	0.000	0.000
73	D	135	PRO	0	0.014	0.005	11.849	-0.125	-0.125	0.000	0.000	0.000	0.000
74	D	136	ILE	0	0.069	0.022	8.386	-0.003	-0.003	0.000	0.000	0.000	0.000
75	D	137	HIS	0	-0.028	-0.017	12.489	0.021	0.021	0.000	0.000	0.000	0.000
76	D	138	ASP	-1	-0.911	-0.948	15.486	-0.262	-0.262	0.000	0.000	0.000	0.000
77	D	139	ILE	0	-0.018	-0.023	12.349	-0.018	-0.018	0.000	0.000	0.000	0.000
78	D	140	ALA	0	-0.028	-0.013	15.649	0.036	0.036	0.000	0.000	0.000	0.000
79	D	141	ALA	0	-0.036	-0.031	16.265	0.030	0.030	0.000	0.000	0.000	0.000
80	D	142	VAL	0	0.011	0.004	11.324	-0.045	-0.045	0.000	0.000	0.000	0.000
81	D	143	SER	0	-0.024	-0.021	14.564	0.037	0.037	0.000	0.000	0.000	0.000
82	D	144	TYR	0	-0.024	-0.017	14.989	-0.022	-0.022	0.000	0.000	0.000	0.000
83	D	145	VAL	0	-0.039	-0.018	16.598	0.041	0.041	0.000	0.000	0.000	0.000
84	D	146	ARG	1	0.831	0.905	19.604	0.168	0.168	0.000	0.000	0.000	0.000
85	D	147	ASP	-1	-0.896	-0.939	21.203	-0.173	-0.173	0.000	0.000	0.000	0.000
86	D	148	ASP	-1	-0.883	-0.929	23.332	-0.148	-0.148	0.000	0.000	0.000	0.000
87	D	149	ALA	0	-0.015	-0.010	23.642	0.004	0.004	0.000	0.000	0.000	0.000
88	D	150	ALA	0	0.014	0.018	20.254	-0.017	-0.017	0.000	0.000	0.000	0.000
89	D	151	HIS	0	0.051	0.011	16.570	0.018	0.018	0.000	0.000	0.000	0.000
90	D	152	LEU	0	0.010	0.006	16.000	-0.048	-0.048	0.000	0.000	0.000	0.000
91	D	153	VAL	0	-0.013	-0.009	11.071	0.025	0.025	0.000	0.000	0.000	0.000
92	D	154	VAL	0	-0.002	-0.002	14.470	-0.031	-0.031	0.000	0.000	0.000	0.000
93	D	155	LEU	0	0.033	0.013	10.393	0.013	0.013	0.000	0.000	0.000	0.000
94	D	156	LYS	1	0.853	0.939	14.879	0.244	0.244	0.000	0.000	0.000	0.000
95	D	157	THR	0	0.000	-0.001	15.034	-0.014	-0.014	0.000	0.000	0.000	0.000
96	D	158	ALA	0	-0.008	0.025	17.816	0.037	0.037	0.000	0.000	0.000	0.000
97	D	159	GLN	0	0.023	0.000	19.830	-0.039	-0.039	0.000	0.000	0.000	0.000
98	D	192	ALA	0	-0.010	-0.003	27.678	0.006	0.006	0.000	0.000	0.000	0.000
99	D	193	CYS	0	-0.117	-0.049	22.559	-0.005	-0.005	0.000	0.000	0.000	0.000
100	D	194	CYS	0	-0.002	0.002	20.311	0.022	0.022	0.000	0.000	0.000	0.000
101	D	195	LEU	0	-0.013	-0.002	19.093	-0.008	-0.008	0.000	0.000	0.000	0.000
102	D	196	VAL	0	0.022	0.021	13.897	0.011	0.011	0.000	0.000	0.000	0.000
103	D	197	ILE	0	-0.017	-0.016	15.875	-0.017	-0.017	0.000	0.000	0.000	0.000
104	D	198	LEU	0	0.037	0.022	10.764	-0.027	-0.027	0.000	0.000	0.000	0.000
105	D	199	ALA	0	-0.006	-0.010	14.485	0.065	0.065	0.000	0.000	0.000	0.000
106	D	200	ALA	0	0.029	0.025	12.410	-0.048	-0.048	0.000	0.000	0.000	0.000
107	D	201	GLU	-1	-0.845	-0.925	10.892	-0.449	-0.449	0.000	0.000	0.000	0.000
108	D	202	SER	0	-0.009	-0.021	13.743	0.063	0.063	0.000	0.000	0.000	0.000
109	D	203	LYS	1	0.845	0.898	14.756	0.135	0.135	0.000	0.000	0.000	0.000
110	D	204	VAL	0	0.018	0.003	13.169	-0.019	-0.019	0.000	0.000	0.000	0.000
111	D	205	ALA	0	0.016	0.029	10.401	-0.021	-0.021	0.000	0.000	0.000	0.000
112	D	206	ALA	0	0.023	0.013	10.071	-0.099	-0.099	0.000	0.000	0.000	0.000
113	D	207	GLU	-1	-0.814	-0.899	11.448	-0.217	-0.217	0.000	0.000	0.000	0.000
114	D	208	GLU	-1	-0.849	-0.902	6.433	-0.582	-0.582	0.000	0.000	0.000	0.000
115	D	209	LEU	0	0.008	-0.004	5.776	-0.031	-0.031	0.000	0.000	0.000	0.000
116	D	210	CYS	0	-0.063	-0.041	7.854	-0.029	-0.029	0.000	0.000	0.000	0.000
117	D	211	CYS	0	-0.034	-0.009	8.381	0.067	0.067	0.000	0.000	0.000	0.000
118	D	212	LEU	0	0.005	0.000	2.422	-0.437	-0.272	1.496	-0.261	-1.400	0.001
119	D	213	LEU	0	-0.013	-0.020	5.659	0.071	0.071	0.000	0.000	0.000	0.000
120	D	214	GLY	0	0.000	-0.002	7.814	0.075	0.075	0.000	0.000	0.000	0.000
121	D	215	GLN	0	-0.048	-0.036	6.925	-0.026	-0.026	0.000	0.000	0.000	0.000
122	D	216	VAL	0	-0.055	-0.010	5.795	0.091	0.091	0.000	0.000	0.000	0.000
123	D	217	PHE	0	-0.031	0.007	8.670	0.077	0.077	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:63:ILE)