FMO DATABASE

FMODB ID: 85JYY

Calculation Name: 1US8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1US8

Chain ID: A

ChEMBL ID:

UniProt ID: P58301

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1193572.555557
FMO2-HF: Nuclear repulsion	1140777.10928
FMO2-HF: Total energy	-52795.446276
FMO2-MP2: Total energy	-52951.58096

3D Structure Molmil

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:MET)

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

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.
-18.531	-10.7	13.633	-6.386	-15.077	-0.02

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / 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	3	LEU	0	-0.005	-0.009	2.503	-1.307	1.479	0.715	-1.288	-2.213	0.005
4	A	4	GLU	-1	-0.768	-0.864	4.613	-1.513	-1.438	-0.001	-0.013	-0.062	0.000
5	A	5	ARG	1	0.933	0.956	8.250	0.951	0.951	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.013	0.012	8.924	-0.042	-0.042	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.005	0.002	10.723	0.036	0.036	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.029	-0.019	13.235	0.041	0.041	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.862	0.908	15.761	0.197	0.197	0.000	0.000	0.000	0.000
10	A	10	ASN	0	-0.001	-0.002	19.341	0.020	0.020	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.014	0.002	15.268	0.028	0.028	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.818	0.880	17.081	-0.118	-0.118	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.066	0.036	20.710	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	HIS	0	-0.028	0.010	17.046	-0.027	-0.027	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.069	0.030	20.530	0.013	0.013	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.844	-0.923	20.612	-0.195	-0.195	0.000	0.000	0.000	0.000
17	A	17	THR	0	0.002	0.008	16.344	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	18	VAL	0	-0.018	-0.019	15.142	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.003	0.003	12.365	0.024	0.024	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.862	-0.917	11.712	-0.972	-0.972	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.046	-0.017	7.951	0.116	0.116	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.864	0.910	10.419	0.825	0.825	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.828	-0.918	9.072	-2.934	-2.934	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.008	0.014	10.600	0.289	0.289	0.000	0.000	0.000	0.000
25	A	25	ILE	0	-0.004	-0.012	11.128	-0.138	-0.138	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.015	-0.018	10.437	0.176	0.176	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.004	-0.001	12.960	0.067	0.067	0.000	0.000	0.000	0.000
28	A	28	ILE	0	0.004	0.002	11.557	0.038	0.038	0.000	0.000	0.000	0.000
29	A	29	ILE	0	0.000	0.006	16.002	0.062	0.062	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.050	0.022	19.768	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	GLN	0	0.048	0.033	21.474	0.022	0.022	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.024	0.017	22.790	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.022	0.011	23.669	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.059	-0.054	21.662	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.069	0.040	19.811	-0.018	-0.018	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.897	0.938	16.699	0.128	0.128	0.000	0.000	0.000	0.000
37	A	37	SER	0	0.029	0.015	15.286	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	SER	0	0.014	0.003	14.813	0.025	0.025	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.017	0.017	12.060	0.016	0.016	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.047	0.014	10.313	-0.028	-0.028	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.824	-0.899	10.219	0.231	0.231	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.008	-0.005	11.621	0.064	0.064	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.017	0.012	5.720	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.016	0.012	7.056	0.059	0.059	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.035	-0.013	8.516	0.105	0.105	0.000	0.000	0.000	0.000
46	A	46	GLY	0	-0.004	-0.005	8.628	0.042	0.042	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.007	0.004	2.803	-0.722	-0.092	0.238	-0.141	-0.728	-0.001
48	A	48	TYR	0	-0.023	-0.049	5.426	0.307	0.307	0.000	0.000	0.000	0.000
49	A	49	TRP	0	-0.053	-0.009	9.433	-0.034	-0.034	0.000	0.000	0.000	0.000
50	A	50	PRO	0	-0.039	-0.024	12.801	0.017	0.017	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.069	0.031	11.284	0.032	0.032	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.861	0.922	15.241	-0.359	-0.359	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.063	0.059	12.599	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	68	ASP	-1	-0.728	-0.869	24.151	0.005	0.005	0.000	0.000	0.000	0.000
55	A	69	THR	0	-0.030	0.002	17.868	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	70	TYR	0	-0.020	-0.016	16.953	0.009	0.009	0.000	0.000	0.000	0.000
57	A	71	ILE	0	0.018	0.010	11.555	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	72	ASP	-1	-0.830	-0.858	12.346	-0.313	-0.313	0.000	0.000	0.000	0.000
59	A	73	LEU	0	0.024	0.018	4.773	-0.077	-0.032	-0.001	-0.001	-0.043	0.000
60	A	74	ILE	0	-0.019	-0.012	8.457	0.145	0.145	0.000	0.000	0.000	0.000
61	A	75	PHE	0	0.016	-0.001	2.944	-1.247	-0.189	0.186	-0.272	-0.973	-0.002
62	A	76	GLU	-1	-0.829	-0.887	4.107	-3.021	-2.629	0.000	-0.106	-0.286	0.000
63	A	77	LYS	1	0.841	0.888	2.339	-9.805	-7.364	4.229	-2.906	-3.764	-0.025
64	A	78	ASP	-1	-0.782	-0.879	3.588	2.652	2.787	0.008	0.021	-0.164	0.000
65	A	79	GLY	0	0.023	0.020	5.479	-0.275	-0.275	0.000	0.000	0.000	0.000
66	A	80	THR	0	-0.050	-0.010	7.212	-0.177	-0.177	0.000	0.000	0.000	0.000
67	A	81	LYS	1	0.822	0.895	6.788	1.168	1.168	0.000	0.000	0.000	0.000
68	A	82	TYR	0	0.009	-0.010	6.331	0.307	0.307	0.000	0.000	0.000	0.000
69	A	83	ARG	1	0.821	0.873	8.139	0.062	0.062	0.000	0.000	0.000	0.000
70	A	84	ILE	0	-0.028	-0.007	6.974	0.176	0.176	0.000	0.000	0.000	0.000
71	A	85	THR	0	-0.036	-0.032	10.308	-0.078	-0.078	0.000	0.000	0.000	0.000
72	A	86	ARG	1	0.775	0.880	9.759	-0.289	-0.289	0.000	0.000	0.000	0.000
73	A	87	ARG	1	0.891	0.930	15.205	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	88	PHE	0	-0.024	-0.015	15.207	0.023	0.023	0.000	0.000	0.000	0.000
75	A	89	LEU	0	-0.040	-0.011	20.843	-0.016	-0.016	0.000	0.000	0.000	0.000
76	A	90	LYS	1	0.871	0.905	21.167	-0.045	-0.045	0.000	0.000	0.000	0.000
77	A	91	GLY	0	-0.033	-0.018	26.664	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	92	TYR	0	0.006	0.014	26.602	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	93	SER	0	0.013	0.008	28.777	0.005	0.005	0.000	0.000	0.000	0.000
80	A	94	SER	0	-0.015	-0.011	27.100	0.003	0.003	0.000	0.000	0.000	0.000
81	A	95	GLY	0	0.044	0.030	24.963	0.001	0.001	0.000	0.000	0.000	0.000
82	A	96	GLU	-1	-0.825	-0.888	18.761	0.217	0.217	0.000	0.000	0.000	0.000
83	A	97	ILE	0	-0.008	0.005	19.563	0.008	0.008	0.000	0.000	0.000	0.000
84	A	98	HIS	0	0.002	-0.014	14.841	-0.011	-0.011	0.000	0.000	0.000	0.000
85	A	99	ALA	0	0.012	0.000	14.976	0.016	0.016	0.000	0.000	0.000	0.000
86	A	100	MET	0	0.017	0.029	8.054	-0.030	-0.030	0.000	0.000	0.000	0.000
87	A	101	LYS	1	0.855	0.913	11.656	0.065	0.065	0.000	0.000	0.000	0.000
88	A	102	ARG	1	0.991	0.995	10.963	-0.182	-0.182	0.000	0.000	0.000	0.000
89	A	103	LEU	0	-0.030	-0.002	12.328	0.010	0.010	0.000	0.000	0.000	0.000
90	A	104	VAL	0	-0.043	-0.031	14.246	0.040	0.040	0.000	0.000	0.000	0.000
91	A	105	GLY	0	0.043	0.023	16.700	0.013	0.013	0.000	0.000	0.000	0.000
92	A	106	ASN	0	-0.013	-0.012	18.110	-0.072	-0.072	0.000	0.000	0.000	0.000
93	A	107	GLU	-1	-0.819	-0.878	19.108	-0.052	-0.052	0.000	0.000	0.000	0.000
94	A	108	TRP	0	0.044	0.013	11.139	0.006	0.006	0.000	0.000	0.000	0.000
95	A	109	LYS	1	0.865	0.919	16.921	0.048	0.048	0.000	0.000	0.000	0.000
96	A	110	HIS	0	0.007	-0.011	15.673	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	111	VAL	0	-0.025	-0.004	11.569	-0.017	-0.017	0.000	0.000	0.000	0.000
98	A	112	THR	0	-0.002	0.004	14.273	0.036	0.036	0.000	0.000	0.000	0.000
99	A	113	GLU	-1	-0.818	-0.877	16.717	0.218	0.218	0.000	0.000	0.000	0.000
100	A	114	PRO	0	-0.018	-0.005	17.569	0.030	0.030	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.028	-0.055	17.819	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	116	SER	0	0.021	-0.012	16.029	0.056	0.056	0.000	0.000	0.000	0.000
103	A	117	LYS	1	0.984	0.994	15.579	-0.326	-0.326	0.000	0.000	0.000	0.000
104	A	118	ALA	0	-0.007	0.006	16.541	0.072	0.072	0.000	0.000	0.000	0.000
105	A	119	ILE	0	0.005	0.001	11.428	0.069	0.069	0.000	0.000	0.000	0.000
106	A	120	SER	0	0.002	0.018	11.816	0.121	0.121	0.000	0.000	0.000	0.000
107	A	121	ALA	0	-0.002	-0.009	12.306	0.151	0.151	0.000	0.000	0.000	0.000
108	A	122	PHE	0	0.002	-0.003	9.992	0.059	0.059	0.000	0.000	0.000	0.000
109	A	123	MET	0	0.039	0.011	4.557	0.010	0.098	-0.001	-0.003	-0.083	0.000
110	A	124	GLU	-1	-0.856	-0.922	8.822	1.994	1.994	0.000	0.000	0.000	0.000
111	A	125	LYS	1	0.852	0.924	11.295	-0.986	-0.986	0.000	0.000	0.000	0.000
112	A	126	LEU	0	-0.054	-0.002	5.857	0.032	0.032	0.000	0.000	0.000	0.000
113	A	127	ILE	0	-0.004	-0.030	2.578	0.199	-1.105	5.455	-0.909	-3.241	0.003
114	A	128	PRO	0	0.047	0.053	6.325	-0.205	-0.205	0.000	0.000	0.000	0.000
115	A	129	TYR	0	0.056	0.020	8.173	0.287	0.287	0.000	0.000	0.000	0.000
116	A	130	ASN	0	0.025	0.003	9.364	0.148	0.148	0.000	0.000	0.000	0.000
117	A	131	ILE	0	0.039	0.030	6.861	-0.198	-0.198	0.000	0.000	0.000	0.000
118	A	132	PHE	0	0.024	0.003	2.832	-1.953	-1.379	1.689	-0.430	-1.832	0.002
119	A	133	LEU	0	-0.037	-0.036	6.655	-0.461	-0.461	0.000	0.000	0.000	0.000
120	A	134	ASN	0	-0.080	-0.046	10.052	-0.393	-0.393	0.000	0.000	0.000	0.000
121	A	135	ALA	0	-0.022	0.002	7.865	-0.220	-0.220	0.000	0.000	0.000	0.000
122	A	136	ILE	0	-0.052	-0.010	2.559	-1.171	-0.260	1.116	-0.338	-1.688	-0.002
123	A	137	TYR	0	-0.036	-0.018	6.632	-0.487	-0.487	0.000	0.000	0.000	0.000
124	A	138	ILE	0	0.047	0.023	9.041	-0.057	-0.057	0.000	0.000	0.000	0.000
125	A	139	ARG	1	0.891	0.940	12.715	-0.227	-0.227	0.000	0.000	0.000	0.000
126	A	140	GLN	0	-0.042	-0.037	15.610	0.003	0.003	0.000	0.000	0.000	0.000
127	A	141	GLY	0	0.049	0.035	19.300	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	142	GLN	0	0.025	0.014	12.772	-0.045	-0.045	0.000	0.000	0.000	0.000
129	A	143	ILE	0	0.001	0.005	17.198	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	144	ASP	-1	-0.813	-0.912	20.433	0.092	0.092	0.000	0.000	0.000	0.000
131	A	145	ALA	0	-0.046	-0.016	21.337	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	146	ILE	0	-0.049	-0.007	19.936	0.005	0.005	0.000	0.000	0.000	0.000
133	A	147	LEU	0	-0.081	-0.044	23.212	-0.025	-0.025	0.000	0.000	0.000	0.000

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