FMO DATABASE

FMODB ID: 14RYZ

Calculation Name: 4YKB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4YKB

Chain ID: A

ChEMBL ID:

UniProt ID: A8I5N5

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:

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1697743.630335
FMO2-HF: Nuclear repulsion	1633519.784504
FMO2-HF: Total energy	-64223.845831
FMO2-MP2: Total energy	-64413.182531

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:81:SER)

Summations of interaction energy for fragment #1(A:81: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.
-15.153	-9.745	2.437	-3.488	-4.357	-0.001

Interaction energy analysis for fragmet #1(A:81:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.001

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	83	LYS	1	0.871	0.932	3.890	-0.783	1.152	-0.009	-0.959	-0.966	0.002
4	A	84	GLU	-1	-0.870	-0.963	2.099	-4.449	-4.027	1.689	-0.829	-1.282	-0.004
5	A	85	ALA	0	0.031	0.033	2.503	-1.832	-0.056	0.744	-0.995	-1.525	0.006
6	A	86	VAL	0	-0.074	-0.040	3.904	0.447	0.653	0.004	-0.068	-0.143	0.000
7	A	87	MET	0	-0.077	-0.041	6.368	0.358	0.358	0.000	0.000	0.000	0.000
8	A	88	GLU	-1	-0.938	-0.964	3.336	-9.466	-8.343	0.010	-0.627	-0.506	-0.005
9	A	89	VAL	0	-0.075	-0.023	7.678	0.375	0.375	0.000	0.000	0.000	0.000
10	A	90	GLN	0	0.016	0.012	10.039	0.041	0.041	0.000	0.000	0.000	0.000
11	A	91	LEU	0	-0.018	-0.014	13.400	0.080	0.080	0.000	0.000	0.000	0.000
12	A	92	SER	0	-0.007	0.005	16.297	0.023	0.023	0.000	0.000	0.000	0.000
13	A	93	SER	0	-0.018	-0.031	19.243	0.024	0.024	0.000	0.000	0.000	0.000
14	A	94	THR	0	-0.074	-0.054	22.574	0.001	0.001	0.000	0.000	0.000	0.000
15	A	95	ALA	0	-0.016	-0.009	25.780	0.008	0.008	0.000	0.000	0.000	0.000
16	A	96	GLY	0	-0.008	0.002	26.049	0.007	0.007	0.000	0.000	0.000	0.000
17	A	97	ILE	0	-0.040	-0.020	21.920	0.001	0.001	0.000	0.000	0.000	0.000
18	A	98	ASP	-1	-0.806	-0.873	20.217	-0.327	-0.327	0.000	0.000	0.000	0.000
19	A	99	TYR	0	-0.017	-0.057	17.055	0.030	0.030	0.000	0.000	0.000	0.000
20	A	100	THR	0	-0.046	-0.045	16.003	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	101	VAL	0	0.043	0.029	15.977	-0.022	-0.022	0.000	0.000	0.000	0.000
22	A	102	LEU	0	-0.023	-0.011	15.800	0.014	0.014	0.000	0.000	0.000	0.000
23	A	103	ARG	1	0.849	0.890	11.473	0.724	0.724	0.000	0.000	0.000	0.000
24	A	104	ASP	-1	-0.769	-0.865	11.911	-0.655	-0.655	0.000	0.000	0.000	0.000
25	A	105	HIS	1	0.839	0.903	13.085	0.150	0.150	0.000	0.000	0.000	0.000
26	A	106	LEU	0	-0.008	-0.008	11.433	0.043	0.043	0.000	0.000	0.000	0.000
27	A	107	ALA	0	-0.005	0.002	8.516	0.086	0.086	0.000	0.000	0.000	0.000
28	A	108	ASN	0	-0.036	-0.020	9.044	-0.283	-0.283	0.000	0.000	0.000	0.000
29	A	109	GLY	0	0.006	0.016	11.502	0.101	0.101	0.000	0.000	0.000	0.000
30	A	110	GLU	-1	-0.830	-0.868	12.545	-0.112	-0.112	0.000	0.000	0.000	0.000
31	A	111	PHE	0	0.014	-0.025	11.050	-0.040	-0.040	0.000	0.000	0.000	0.000
32	A	112	ARG	1	0.815	0.882	16.656	-0.068	-0.068	0.000	0.000	0.000	0.000
33	A	113	GLU	-1	-0.863	-0.945	18.864	0.030	0.030	0.000	0.000	0.000	0.000
34	A	114	ALA	0	0.019	0.010	16.119	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	115	GLU	-1	-0.795	-0.838	18.212	0.072	0.072	0.000	0.000	0.000	0.000
36	A	116	ASP	-1	-0.771	-0.850	20.890	0.016	0.016	0.000	0.000	0.000	0.000
37	A	117	GLU	-1	-0.849	-0.925	20.093	-0.123	-0.123	0.000	0.000	0.000	0.000
38	A	118	THR	0	-0.013	-0.013	19.306	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	119	ARG	1	0.823	0.889	21.527	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	120	ALA	0	0.019	0.014	24.890	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	121	LEU	0	-0.009	-0.010	20.378	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	122	LEU	0	-0.008	0.002	24.523	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	123	ILE	0	-0.053	-0.028	26.024	0.000	0.000	0.000	0.000	0.000	0.000
44	A	124	LYS	1	0.855	0.916	24.548	0.116	0.116	0.000	0.000	0.000	0.000
45	A	125	LEU	0	-0.022	0.002	23.294	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	126	ALA	0	-0.034	-0.007	27.987	0.002	0.002	0.000	0.000	0.000	0.000
47	A	127	GLY	0	0.058	0.034	30.842	0.003	0.003	0.000	0.000	0.000	0.000
48	A	128	PRO	0	0.017	-0.006	33.396	0.004	0.004	0.000	0.000	0.000	0.000
49	A	129	GLU	-1	-0.779	-0.871	36.100	-0.028	-0.028	0.000	0.000	0.000	0.000
50	A	130	ALA	0	0.012	0.013	33.002	0.005	0.005	0.000	0.000	0.000	0.000
51	A	131	VAL	0	0.026	0.007	31.765	0.004	0.004	0.000	0.000	0.000	0.000
52	A	132	LYS	1	0.782	0.881	34.234	0.032	0.032	0.000	0.000	0.000	0.000
53	A	133	ARG	1	0.745	0.831	36.660	0.016	0.016	0.000	0.000	0.000	0.000
54	A	134	ASN	0	-0.015	-0.004	31.947	0.000	0.000	0.000	0.000	0.000	0.000
55	A	135	TRP	0	0.047	0.013	29.330	0.007	0.007	0.000	0.000	0.000	0.000
56	A	136	VAL	0	0.048	0.050	29.777	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	137	TYR	0	-0.028	-0.012	33.057	0.010	0.010	0.000	0.000	0.000	0.000
58	A	138	PHE	0	0.052	0.013	33.108	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	139	THR	0	-0.004	-0.002	34.070	0.000	0.000	0.000	0.000	0.000	0.000
60	A	140	GLU	-1	-0.706	-0.833	33.505	-0.019	-0.019	0.000	0.000	0.000	0.000
61	A	141	VAL	0	0.022	0.011	28.208	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	142	LYS	1	0.859	0.921	29.584	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	143	ASN	0	-0.030	-0.011	31.863	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	144	ILE	0	-0.021	0.019	25.387	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	145	SER	0	0.009	-0.012	24.796	0.005	0.005	0.000	0.000	0.000	0.000
66	A	146	VAL	0	0.041	-0.002	23.027	0.002	0.002	0.000	0.000	0.000	0.000
67	A	147	THR	0	-0.020	-0.012	21.067	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	148	ASP	-1	-0.651	-0.742	19.968	-0.179	-0.179	0.000	0.000	0.000	0.000
69	A	149	PHE	0	0.044	0.011	20.162	0.001	0.001	0.000	0.000	0.000	0.000
70	A	150	GLN	0	0.008	0.003	17.743	0.041	0.041	0.000	0.000	0.000	0.000
71	A	151	THR	0	-0.014	-0.003	15.839	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	152	LEU	0	0.012	0.009	15.233	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	153	ASP	-1	-0.805	-0.864	15.653	0.123	0.123	0.000	0.000	0.000	0.000
74	A	154	ASN	0	-0.020	-0.027	11.891	0.096	0.096	0.000	0.000	0.000	0.000
75	A	155	LEU	0	0.039	0.037	10.782	0.019	0.019	0.000	0.000	0.000	0.000
76	A	156	TRP	0	0.019	-0.008	10.928	0.081	0.081	0.000	0.000	0.000	0.000
77	A	157	LYS	1	0.850	0.950	10.498	0.012	0.012	0.000	0.000	0.000	0.000
78	A	158	ALA	0	0.019	0.009	6.634	0.310	0.310	0.000	0.000	0.000	0.000
79	A	159	SER	0	-0.039	-0.029	6.649	0.576	0.576	0.000	0.000	0.000	0.000
80	A	160	SER	0	0.032	-0.010	8.948	0.144	0.144	0.000	0.000	0.000	0.000
81	A	161	ASN	0	-0.015	-0.003	5.046	0.503	0.449	-0.001	-0.010	0.065	0.000
82	A	162	ASN	0	-0.008	-0.010	7.633	-0.397	-0.397	0.000	0.000	0.000	0.000
83	A	163	LYS	1	0.812	0.901	11.180	-1.038	-1.038	0.000	0.000	0.000	0.000
84	A	164	PHE	0	-0.005	-0.011	13.084	-0.091	-0.091	0.000	0.000	0.000	0.000
85	A	165	GLY	0	0.049	0.024	14.120	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	166	TYR	0	0.010	0.002	16.610	0.015	0.015	0.000	0.000	0.000	0.000
87	A	167	SER	0	-0.058	-0.061	16.862	0.021	0.021	0.000	0.000	0.000	0.000
88	A	168	VAL	0	0.005	0.011	14.935	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	169	GLN	0	-0.032	-0.042	18.309	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	170	LYS	1	0.777	0.865	21.436	-0.067	-0.067	0.000	0.000	0.000	0.000
91	A	171	GLU	-1	-0.820	-0.860	18.709	0.338	0.338	0.000	0.000	0.000	0.000
92	A	172	ILE	0	0.011	0.010	20.063	-0.010	-0.010	0.000	0.000	0.000	0.000
93	A	173	TRP	0	0.029	0.009	23.527	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	174	VAL	0	-0.008	-0.015	26.109	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	175	GLN	0	0.024	0.032	22.472	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	176	ASN	0	-0.073	-0.048	26.426	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	177	GLN	0	0.018	0.015	29.325	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	178	LYS	1	0.903	0.957	30.404	-0.085	-0.085	0.000	0.000	0.000	0.000
99	A	179	ARG	1	0.856	0.916	31.817	-0.103	-0.103	0.000	0.000	0.000	0.000
100	A	180	TRP	0	0.027	0.007	28.327	0.013	0.013	0.000	0.000	0.000	0.000
101	A	181	PRO	0	0.029	0.016	31.085	0.010	0.010	0.000	0.000	0.000	0.000
102	A	182	LYS	1	0.881	0.957	28.231	-0.191	-0.191	0.000	0.000	0.000	0.000
103	A	183	PHE	0	0.028	0.016	24.336	0.014	0.014	0.000	0.000	0.000	0.000
104	A	184	PHE	0	0.038	-0.009	26.780	0.015	0.015	0.000	0.000	0.000	0.000
105	A	185	LYS	1	0.853	0.947	27.948	-0.141	-0.141	0.000	0.000	0.000	0.000
106	A	186	GLN	0	-0.009	-0.010	23.102	-0.011	-0.011	0.000	0.000	0.000	0.000
107	A	187	ILE	0	-0.010	0.006	21.717	0.032	0.032	0.000	0.000	0.000	0.000
108	A	188	ASP	-1	-0.844	-0.915	23.207	0.294	0.294	0.000	0.000	0.000	0.000
109	A	189	TRP	0	-0.053	-0.037	22.957	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	190	THR	0	-0.048	-0.049	26.951	-0.015	-0.015	0.000	0.000	0.000	0.000
111	A	191	GLN	0	-0.044	-0.011	24.832	-0.026	-0.026	0.000	0.000	0.000	0.000
112	A	192	GLY	0	0.049	0.026	28.954	-0.011	-0.011	0.000	0.000	0.000	0.000
113	A	193	GLU	-1	-0.855	-0.916	31.901	0.142	0.142	0.000	0.000	0.000	0.000
114	A	194	ASN	0	0.014	0.002	33.553	0.000	0.000	0.000	0.000	0.000	0.000
115	A	195	ASN	0	-0.063	-0.036	34.457	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	196	ASN	0	0.030	0.031	32.691	-0.004	-0.004	0.000	0.000	0.000	0.000
117	A	197	TYR	0	-0.029	-0.031	31.933	0.005	0.005	0.000	0.000	0.000	0.000
118	A	198	ARG	1	0.804	0.915	26.930	-0.183	-0.183	0.000	0.000	0.000	0.000
119	A	199	LYS	1	0.953	0.981	29.984	-0.090	-0.090	0.000	0.000	0.000	0.000
120	A	200	TRP	0	-0.017	0.003	25.912	0.001	0.001	0.000	0.000	0.000	0.000
121	A	201	PRO	0	-0.049	-0.044	26.750	-0.010	-0.010	0.000	0.000	0.000	0.000
122	A	202	MET	0	-0.025	-0.036	26.529	0.008	0.008	0.000	0.000	0.000	0.000
123	A	203	GLU	-1	-0.852	-0.906	27.571	0.154	0.154	0.000	0.000	0.000	0.000
124	A	204	PHE	0	-0.012	-0.012	23.241	0.008	0.008	0.000	0.000	0.000	0.000
125	A	205	ILE	0	0.006	0.000	18.755	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	206	TYR	0	-0.069	-0.063	18.663	0.029	0.029	0.000	0.000	0.000	0.000
127	A	207	SER	0	0.002	-0.036	15.257	-0.039	-0.039	0.000	0.000	0.000	0.000
128	A	208	MET	0	0.038	0.022	7.929	-0.099	-0.099	0.000	0.000	0.000	0.000
129	A	209	ASP	-1	-0.836	-0.875	12.800	0.760	0.760	0.000	0.000	0.000	0.000
130	A	210	ALA	0	-0.028	0.007	15.573	-0.018	-0.018	0.000	0.000	0.000	0.000
131	A	211	PRO	0	0.019	-0.001	16.355	0.080	0.080	0.000	0.000	0.000	0.000
132	A	212	ARG	1	0.775	0.853	14.669	-0.505	-0.505	0.000	0.000	0.000	0.000
133	A	213	GLY	0	0.044	0.009	17.125	-0.051	-0.051	0.000	0.000	0.000	0.000
134	A	214	HIS	0	-0.042	-0.010	18.851	-0.060	-0.060	0.000	0.000	0.000	0.000
135	A	215	LEU	0	0.038	0.039	16.944	-0.045	-0.045	0.000	0.000	0.000	0.000
136	A	216	PRO	0	0.042	0.031	17.751	0.032	0.032	0.000	0.000	0.000	0.000
137	A	217	LEU	0	0.042	0.035	20.040	0.009	0.009	0.000	0.000	0.000	0.000
138	A	218	THR	0	-0.034	-0.046	23.870	-0.022	-0.022	0.000	0.000	0.000	0.000
139	A	219	ASN	0	0.028	0.030	26.969	-0.007	-0.007	0.000	0.000	0.000	0.000
140	A	220	ALA	0	0.009	0.018	29.892	-0.003	-0.003	0.000	0.000	0.000	0.000
141	A	221	LEU	0	0.021	0.000	31.942	-0.007	-0.007	0.000	0.000	0.000	0.000
142	A	222	ARG	1	0.823	0.895	34.365	-0.023	-0.023	0.000	0.000	0.000	0.000
143	A	223	GLY	0	-0.004	0.003	35.874	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	224	THR	0	0.059	0.023	31.952	0.005	0.005	0.000	0.000	0.000	0.000
145	A	225	GLN	0	-0.036	-0.023	32.181	0.000	0.000	0.000	0.000	0.000	0.000
146	A	226	LEU	0	-0.002	0.002	29.818	-0.003	-0.003	0.000	0.000	0.000	0.000
147	A	227	PHE	0	0.054	0.020	23.899	-0.007	-0.007	0.000	0.000	0.000	0.000
148	A	228	GLN	0	-0.025	-0.015	27.910	0.006	0.006	0.000	0.000	0.000	0.000
149	A	229	ALA	0	-0.021	-0.010	29.577	-0.002	-0.002	0.000	0.000	0.000	0.000
150	A	230	ILE	0	-0.008	0.009	24.003	-0.009	-0.009	0.000	0.000	0.000	0.000
151	A	231	MET	0	-0.021	-0.001	24.608	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-0.815	-0.906	26.140	0.053	0.053	0.000	0.000	0.000	0.000
153	A	233	HIS	0	0.016	0.032	25.678	-0.005	-0.005	0.000	0.000	0.000	0.000
154	A	234	PRO	0	0.046	0.015	25.941	0.006	0.006	0.000	0.000	0.000	0.000
155	A	235	ALA	0	0.006	0.015	21.763	-0.010	-0.010	0.000	0.000	0.000	0.000
156	A	236	PHE	0	-0.043	-0.038	19.208	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	237	GLU	-1	-0.844	-0.895	22.803	0.072	0.072	0.000	0.000	0.000	0.000
158	A	238	LYS	1	0.811	0.909	21.475	0.037	0.037	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:81:SER)