FMO DATABASE

FMODB ID: JL8Y9

Calculation Name: 4WJ7-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4WJ7

Chain ID: B

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	132
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1139579.119402
FMO2-HF: Nuclear repulsion	1088265.429482
FMO2-HF: Total energy	-51313.68992
FMO2-MP2: Total energy	-51463.722177

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(B:60:SER)

Summations of interaction energy for fragment #1(B:60:SER)

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.
0.391	2.277	-0.026	-0.938	-0.922	0

Interaction energy analysis for fragmet #1(B:60:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.039

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].
3	B	62	TYR	0	-0.046	-0.019	3.796	2.019	3.781	-0.025	-0.934	-0.803
4	B	63	ILE	0	0.015	0.015	6.726	-0.301	-0.301	0.000	0.000	0.000
5	B	64	GLU	-1	-0.808	-0.897	9.770	-0.110	-0.110	0.000	0.000	0.000
6	B	65	LYS	1	0.792	0.881	13.369	0.457	0.457	0.000	0.000	0.000
7	B	66	GLU	-1	-0.819	-0.883	16.431	-0.199	-0.199	0.000	0.000	0.000
8	B	67	VAL	0	-0.045	-0.021	19.206	0.002	0.002	0.000	0.000	0.000
9	B	68	LYS	1	0.857	0.928	21.904	0.106	0.106	0.000	0.000	0.000
10	B	69	TYR	0	0.002	-0.001	23.077	0.009	0.009	0.000	0.000	0.000
11	B	70	LEU	0	-0.018	-0.020	25.097	0.003	0.003	0.000	0.000	0.000
12	B	71	GLY	0	0.068	0.021	27.099	0.004	0.004	0.000	0.000	0.000
13	B	72	GLN	0	-0.019	-0.002	24.520	0.006	0.006	0.000	0.000	0.000
14	B	73	LEU	0	-0.033	-0.010	27.570	0.000	0.000	0.000	0.000	0.000
15	B	74	THR	0	0.066	0.021	28.836	0.006	0.006	0.000	0.000	0.000
16	B	75	SER	0	-0.038	-0.027	30.806	-0.005	-0.005	0.000	0.000	0.000
17	B	76	ILE	0	0.000	0.015	30.409	-0.007	-0.007	0.000	0.000	0.000
18	B	77	PRO	0	0.044	0.014	31.647	0.008	0.008	0.000	0.000	0.000
19	B	78	GLY	0	0.114	0.051	29.861	-0.003	-0.003	0.000	0.000	0.000
20	B	79	TYR	0	-0.053	-0.019	29.718	0.003	0.003	0.000	0.000	0.000
21	B	80	LEU	0	-0.028	0.009	28.773	-0.006	-0.006	0.000	0.000	0.000
22	B	81	ASN	0	0.078	0.034	29.418	0.004	0.004	0.000	0.000	0.000
23	B	82	PRO	0	0.040	0.025	25.244	-0.006	-0.006	0.000	0.000	0.000
24	B	83	SER	0	0.010	0.009	27.221	-0.012	-0.012	0.000	0.000	0.000
25	B	84	SER	0	-0.112	-0.065	29.017	-0.008	-0.008	0.000	0.000	0.000
26	B	85	ARG	1	0.934	0.950	31.622	0.056	0.056	0.000	0.000	0.000
27	B	86	THR	0	0.018	-0.005	32.691	0.000	0.000	0.000	0.000	0.000
28	B	87	GLU	-1	-0.799	-0.879	33.215	0.005	0.005	0.000	0.000	0.000
29	B	88	ILE	0	0.016	0.014	27.815	0.003	0.003	0.000	0.000	0.000
30	B	89	LEU	0	0.032	-0.003	31.787	0.000	0.000	0.000	0.000	0.000
31	B	90	HIS	0	-0.019	0.019	34.191	0.000	0.000	0.000	0.000	0.000
32	B	91	PHE	0	-0.002	-0.021	33.042	0.002	0.002	0.000	0.000	0.000
33	B	92	ILE	0	0.037	0.023	29.510	0.001	0.001	0.000	0.000	0.000
34	B	93	ASP	-1	-0.857	-0.930	33.731	-0.028	-0.028	0.000	0.000	0.000
35	B	94	ASN	0	-0.046	-0.024	37.266	-0.002	-0.002	0.000	0.000	0.000
36	B	95	ALA	0	0.041	0.031	34.291	0.001	0.001	0.000	0.000	0.000
37	B	96	LYS	1	0.850	0.933	34.159	0.035	0.035	0.000	0.000	0.000
38	B	97	ARG	1	0.874	0.928	37.390	0.013	0.013	0.000	0.000	0.000
39	B	98	ALA	0	-0.042	-0.010	38.958	0.001	0.001	0.000	0.000	0.000
40	B	99	HIS	0	-0.041	-0.023	38.543	0.001	0.001	0.000	0.000	0.000
41	B	100	GLN	0	-0.021	-0.007	34.791	0.000	0.000	0.000	0.000	0.000
42	B	101	LEU	0	-0.024	-0.012	30.188	0.001	0.001	0.000	0.000	0.000
43	B	102	PRO	0	-0.002	0.025	31.274	0.000	0.000	0.000	0.000	0.000
44	B	103	GLY	0	0.021	0.009	33.948	-0.001	-0.001	0.000	0.000	0.000
45	B	104	HIS	0	0.016	-0.021	31.220	0.001	0.001	0.000	0.000	0.000
46	B	105	LEU	0	-0.036	-0.023	31.604	-0.007	-0.007	0.000	0.000	0.000
47	B	106	THR	0	-0.027	0.001	31.285	-0.004	-0.004	0.000	0.000	0.000
48	B	107	GLN	0	-0.066	-0.056	29.437	-0.008	-0.008	0.000	0.000	0.000
49	B	108	GLU	-1	-0.916	-0.945	30.774	-0.053	-0.053	0.000	0.000	0.000
50	B	109	HIS	0	-0.026	-0.011	28.590	0.000	0.000	0.000	0.000	0.000
51	B	110	ASP	-1	-0.788	-0.883	25.829	-0.113	-0.113	0.000	0.000	0.000
52	B	111	ALA	0	-0.032	-0.015	21.611	0.008	0.008	0.000	0.000	0.000
53	B	112	VAL	0	0.006	0.015	16.508	-0.019	-0.019	0.000	0.000	0.000
54	B	113	LEU	0	-0.015	-0.012	14.016	0.041	0.041	0.000	0.000	0.000
55	B	114	SER	0	-0.071	-0.062	11.810	-0.052	-0.052	0.000	0.000	0.000
56	B	115	LEU	0	-0.014	-0.002	9.548	0.136	0.136	0.000	0.000	0.000
57	B	116	SER	0	0.024	-0.001	6.242	-0.097	-0.097	0.000	0.000	0.000
58	B	117	ALA	0	0.051	0.011	5.313	-0.281	-0.281	0.000	0.000	0.000
59	B	118	TYR	0	-0.012	0.006	4.252	-0.558	-0.434	-0.001	-0.004	-0.119
60	B	119	ASN	0	-0.003	-0.010	9.064	-0.228	-0.228	0.000	0.000	0.000
61	B	120	VAL	0	0.028	0.020	11.057	-0.003	-0.003	0.000	0.000	0.000
62	B	121	LYS	1	0.853	0.936	13.119	0.114	0.114	0.000	0.000	0.000
63	B	122	LEU	0	0.000	0.003	15.414	-0.056	-0.056	0.000	0.000	0.000
64	B	123	ALA	0	0.048	0.023	18.699	0.029	0.029	0.000	0.000	0.000
65	B	124	TRP	0	0.057	0.041	20.540	-0.025	-0.025	0.000	0.000	0.000
66	B	125	ARG	1	0.839	0.889	22.624	0.164	0.164	0.000	0.000	0.000
67	B	126	ASP	-1	-0.910	-0.945	24.116	-0.066	-0.066	0.000	0.000	0.000
68	B	127	GLY	0	0.007	-0.005	26.179	-0.005	-0.005	0.000	0.000	0.000
69	B	128	GLU	-1	-1.000	-0.993	20.164	-0.135	-0.135	0.000	0.000	0.000
70	B	129	ASP	-1	-0.929	-0.947	21.022	0.007	0.007	0.000	0.000	0.000
71	B	130	ILE	0	-0.078	-0.063	16.995	-0.002	-0.002	0.000	0.000	0.000
72	B	131	ILE	0	-0.056	-0.025	20.835	0.013	0.013	0.000	0.000	0.000
73	B	132	LEU	0	-0.010	-0.013	20.228	0.013	0.013	0.000	0.000	0.000
74	B	133	ARG	1	0.913	0.943	12.648	-0.363	-0.363	0.000	0.000	0.000
75	B	134	VAL	0	0.018	0.015	16.483	0.006	0.006	0.000	0.000	0.000
76	B	135	PRO	0	0.045	0.022	14.026	0.042	0.042	0.000	0.000	0.000
77	B	136	ILE	0	0.027	0.017	10.629	-0.087	-0.087	0.000	0.000	0.000
78	B	137	HIS	0	-0.057	-0.032	13.939	-0.009	-0.009	0.000	0.000	0.000
79	B	138	ASP	-1	-0.863	-0.918	16.266	0.244	0.244	0.000	0.000	0.000
80	B	139	ILE	0	-0.051	-0.027	15.165	-0.050	-0.050	0.000	0.000	0.000
81	B	140	ALA	0	-0.041	-0.015	18.786	0.001	0.001	0.000	0.000	0.000
82	B	141	ALA	0	-0.034	-0.030	20.402	-0.012	-0.012	0.000	0.000	0.000
83	B	142	VAL	0	0.007	0.004	17.837	0.007	0.007	0.000	0.000	0.000
84	B	143	SER	0	-0.033	-0.025	20.821	-0.010	-0.010	0.000	0.000	0.000
85	B	144	TYR	0	-0.025	-0.020	23.487	-0.004	-0.004	0.000	0.000	0.000
86	B	145	VAL	0	-0.039	-0.020	25.008	0.003	0.003	0.000	0.000	0.000
87	B	146	ARG	1	0.836	0.933	28.603	0.088	0.088	0.000	0.000	0.000
88	B	147	ASP	-1	-0.839	-0.911	30.459	-0.043	-0.043	0.000	0.000	0.000
89	B	148	ASP	-1	-0.905	-0.959	32.984	-0.064	-0.064	0.000	0.000	0.000
90	B	149	ALA	0	-0.033	-0.030	33.781	-0.006	-0.006	0.000	0.000	0.000
91	B	150	ALA	0	0.005	0.014	30.495	-0.008	-0.008	0.000	0.000	0.000
92	B	151	HIS	0	0.074	0.029	26.436	0.005	0.005	0.000	0.000	0.000
93	B	152	LEU	0	0.006	0.002	25.911	-0.007	-0.007	0.000	0.000	0.000
94	B	153	VAL	0	-0.008	-0.007	20.167	-0.005	-0.005	0.000	0.000	0.000
95	B	154	VAL	0	-0.002	-0.005	23.404	0.008	0.008	0.000	0.000	0.000
96	B	155	LEU	0	0.033	0.013	17.494	-0.003	-0.003	0.000	0.000	0.000
97	B	156	LYS	1	0.829	0.906	21.861	-0.041	-0.041	0.000	0.000	0.000
98	B	157	THR	0	0.009	0.006	20.258	0.004	0.004	0.000	0.000	0.000
99	B	158	ALA	0	0.012	0.005	21.925	-0.016	-0.016	0.000	0.000	0.000
100	B	159	GLN	0	0.001	-0.023	23.857	-0.013	-0.013	0.000	0.000	0.000
101	B	160	ASP	-1	-0.939	-0.959	24.534	0.154	0.154	0.000	0.000	0.000
102	B	191	GLU	-1	-0.971	-0.995	30.638	0.065	0.065	0.000	0.000	0.000
103	B	192	ALA	0	-0.045	-0.021	30.762	-0.003	-0.003	0.000	0.000	0.000
104	B	193	CYS	0	-0.080	-0.026	26.593	0.006	0.006	0.000	0.000	0.000
105	B	194	CYS	0	-0.001	0.009	25.097	-0.008	-0.008	0.000	0.000	0.000
106	B	195	LEU	0	-0.021	-0.005	25.529	-0.001	-0.001	0.000	0.000	0.000
107	B	196	VAL	0	0.023	0.015	21.589	-0.005	-0.005	0.000	0.000	0.000
108	B	197	ILE	0	-0.021	-0.013	23.919	-0.011	-0.011	0.000	0.000	0.000
109	B	198	LEU	0	0.039	0.022	19.843	-0.002	-0.002	0.000	0.000	0.000
110	B	199	ALA	0	-0.025	-0.020	24.149	0.001	0.001	0.000	0.000	0.000
111	B	200	ALA	0	0.022	0.025	22.547	-0.009	-0.009	0.000	0.000	0.000
112	B	201	GLU	-1	-0.834	-0.904	23.247	-0.198	-0.198	0.000	0.000	0.000
113	B	202	SER	0	-0.040	-0.054	24.500	0.007	0.007	0.000	0.000	0.000
114	B	203	LYS	1	0.893	0.950	24.942	0.141	0.141	0.000	0.000	0.000
115	B	204	VAL	0	0.009	-0.003	22.852	0.001	0.001	0.000	0.000	0.000
116	B	205	ALA	0	0.046	0.046	20.515	-0.022	-0.022	0.000	0.000	0.000
117	B	206	ALA	0	0.019	0.009	19.806	-0.009	-0.009	0.000	0.000	0.000
118	B	207	GLU	-1	-0.855	-0.948	20.430	-0.162	-0.162	0.000	0.000	0.000
119	B	208	GLU	-1	-0.799	-0.870	15.781	-0.480	-0.480	0.000	0.000	0.000
120	B	209	LEU	0	0.004	-0.004	15.684	-0.028	-0.028	0.000	0.000	0.000
121	B	210	CYS	0	-0.049	-0.028	15.879	0.025	0.025	0.000	0.000	0.000
122	B	211	CYS	0	-0.055	-0.024	15.980	0.024	0.024	0.000	0.000	0.000
123	B	212	LEU	0	-0.002	0.005	10.818	-0.017	-0.017	0.000	0.000	0.000
124	B	213	LEU	0	0.012	-0.009	11.611	0.024	0.024	0.000	0.000	0.000
125	B	214	GLY	0	0.006	0.016	13.515	0.061	0.061	0.000	0.000	0.000
126	B	215	GLN	0	-0.061	-0.048	9.908	0.083	0.083	0.000	0.000	0.000
127	B	216	VAL	0	-0.013	-0.005	7.866	0.010	0.010	0.000	0.000	0.000
128	B	217	PHE	0	0.017	-0.005	10.040	0.125	0.125	0.000	0.000	0.000
129	B	218	GLN	0	-0.099	-0.022	11.807	0.057	0.057	0.000	0.000	0.000
130	B	219	VAL	0	-0.016	0.000	8.160	-0.014	-0.014	0.000	0.000	0.000
131	B	220	VAL	0	-0.016	0.003	9.599	0.011	0.011	0.000	0.000	0.000
132	B	221	TYR	0	-0.008	-0.010	7.897	0.026	0.026	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:60:SER)