FMO DATABASE

FMODB ID: R99Y8

Calculation Name: 4KBM-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4KBM

Chain ID: B

ChEMBL ID:

UniProt ID: P9WJG3

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:

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1320927.548084
FMO2-HF: Nuclear repulsion	1262998.685479
FMO2-HF: Total energy	-57928.862605
FMO2-MP2: Total energy	-58101.66206

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:2:ILE)

Summations of interaction energy for fragment #1(B:2: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.
-14.254	-5.103	2.097	-4.27	-6.977	-0.031

Interaction energy analysis for fragmet #1(B:2:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.012

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	B	4	LYS	1	0.821	0.905	3.799	0.003	1.332	-0.002	-0.554	-0.773	0.002
4	B	5	VAL	0	-0.014	-0.009	6.388	0.142	0.142	0.000	0.000	0.000	0.000
5	B	6	GLY	0	-0.037	-0.010	9.906	-0.085	-0.085	0.000	0.000	0.000	0.000
6	B	7	ASP	-1	-0.783	-0.868	6.814	-1.087	-1.087	0.000	0.000	0.000	0.000
7	B	8	THR	0	-0.056	-0.047	9.346	0.199	0.199	0.000	0.000	0.000	0.000
8	B	9	VAL	0	0.027	0.031	6.396	-0.085	-0.085	0.000	0.000	0.000	0.000
9	B	10	VAL	0	-0.001	-0.008	9.678	0.051	0.051	0.000	0.000	0.000	0.000
10	B	11	TYR	0	0.046	0.011	11.083	0.098	0.098	0.000	0.000	0.000	0.000
11	B	12	PRO	0	0.015	0.015	13.372	-0.043	-0.043	0.000	0.000	0.000	0.000
12	B	13	HIS	0	-0.014	-0.029	16.221	0.016	0.016	0.000	0.000	0.000	0.000
13	B	14	HIS	0	-0.062	-0.013	16.929	0.000	0.000	0.000	0.000	0.000	0.000
14	B	15	GLY	0	0.014	0.004	16.972	-0.015	-0.015	0.000	0.000	0.000	0.000
15	B	16	ALA	0	0.000	0.005	14.450	0.012	0.012	0.000	0.000	0.000	0.000
16	B	17	ALA	0	-0.008	-0.021	11.936	0.033	0.033	0.000	0.000	0.000	0.000
17	B	18	LEU	0	0.012	0.031	11.729	-0.034	-0.034	0.000	0.000	0.000	0.000
18	B	19	VAL	0	-0.005	-0.005	7.463	0.140	0.140	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.894	-0.957	10.836	0.088	0.088	0.000	0.000	0.000	0.000
20	B	21	ALA	0	-0.018	-0.028	11.906	-0.049	-0.049	0.000	0.000	0.000	0.000
21	B	22	ILE	0	0.019	0.007	5.565	0.084	0.084	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.799	-0.856	9.813	0.259	0.259	0.000	0.000	0.000	0.000
23	B	24	THR	0	-0.002	-0.009	11.139	0.150	0.150	0.000	0.000	0.000	0.000
24	B	25	ARG	1	0.858	0.927	13.404	-0.464	-0.464	0.000	0.000	0.000	0.000
25	B	26	THR	0	-0.005	-0.015	16.215	0.035	0.035	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.018	-0.017	16.229	-0.012	-0.012	0.000	0.000	0.000	0.000
27	B	28	LYS	1	0.800	0.892	20.090	-0.252	-0.252	0.000	0.000	0.000	0.000
28	B	29	GLY	0	0.045	0.048	20.866	-0.024	-0.024	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.857	-0.924	19.050	0.290	0.290	0.000	0.000	0.000	0.000
30	B	31	GLN	0	0.000	-0.017	15.998	-0.006	-0.006	0.000	0.000	0.000	0.000
31	B	32	LYS	1	0.813	0.888	12.618	-0.775	-0.775	0.000	0.000	0.000	0.000
32	B	33	GLU	-1	-0.872	-0.930	5.713	2.318	2.318	0.000	0.000	0.000	0.000
33	B	34	TYR	0	-0.019	-0.031	10.325	0.119	0.119	0.000	0.000	0.000	0.000
34	B	35	LEU	0	0.038	0.041	6.038	-0.164	-0.164	0.000	0.000	0.000	0.000
35	B	36	VAL	0	-0.065	-0.035	10.064	-0.122	-0.122	0.000	0.000	0.000	0.000
36	B	37	LEU	0	0.011	0.004	8.842	-0.041	-0.041	0.000	0.000	0.000	0.000
37	B	38	LYS	1	0.822	0.902	12.973	-0.133	-0.133	0.000	0.000	0.000	0.000
38	B	39	VAL	0	0.001	0.009	15.477	-0.038	-0.038	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.008	-0.004	17.333	0.001	0.001	0.000	0.000	0.000	0.000
40	B	41	GLN	0	-0.031	-0.012	20.317	-0.002	-0.002	0.000	0.000	0.000	0.000
41	B	42	GLY	0	0.025	0.003	22.161	0.014	0.014	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.893	-0.931	21.701	0.098	0.098	0.000	0.000	0.000	0.000
43	B	44	LEU	0	0.026	0.033	18.824	0.018	0.018	0.000	0.000	0.000	0.000
44	B	45	THR	0	-0.009	-0.007	17.722	0.002	0.002	0.000	0.000	0.000	0.000
45	B	46	VAL	0	-0.001	0.010	14.385	0.017	0.017	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.829	0.885	13.961	-0.316	-0.316	0.000	0.000	0.000	0.000
47	B	48	VAL	0	0.007	0.009	9.943	-0.078	-0.078	0.000	0.000	0.000	0.000
48	B	49	PRO	0	0.001	0.007	10.895	0.129	0.129	0.000	0.000	0.000	0.000
49	B	50	ALA	0	0.050	0.012	5.752	-0.104	-0.104	0.000	0.000	0.000	0.000
50	B	51	GLU	-1	-0.845	-0.899	6.373	1.238	1.238	0.000	0.000	0.000	0.000
51	B	52	ASN	0	0.004	-0.012	8.298	-0.243	-0.243	0.000	0.000	0.000	0.000
52	B	53	ALA	0	0.011	0.011	6.363	-0.249	-0.249	0.000	0.000	0.000	0.000
53	B	54	GLU	-1	-0.901	-0.953	6.644	0.404	0.404	0.000	0.000	0.000	0.000
54	B	55	TYR	0	-0.035	-0.008	8.493	-0.240	-0.240	0.000	0.000	0.000	0.000
55	B	56	VAL	0	-0.078	-0.027	11.307	-0.102	-0.102	0.000	0.000	0.000	0.000
56	B	57	GLY	0	-0.008	-0.012	11.771	-0.059	-0.059	0.000	0.000	0.000	0.000
57	B	58	VAL	0	-0.034	-0.008	7.119	-0.123	-0.123	0.000	0.000	0.000	0.000
58	B	59	ARG	1	0.909	0.940	5.080	0.253	0.253	0.000	0.000	0.000	0.000
59	B	60	ASP	-1	-0.835	-0.931	2.581	-2.313	-1.327	0.324	-0.332	-0.977	-0.001
60	B	61	VAL	0	-0.004	-0.003	4.163	-0.908	-0.546	0.001	-0.044	-0.318	0.000
61	B	62	VAL	0	-0.052	-0.015	3.840	0.178	0.334	0.001	-0.022	-0.135	0.000
62	B	63	GLY	0	0.096	0.064	6.210	0.184	0.184	0.000	0.000	0.000	0.000
63	B	64	GLN	0	-0.009	-0.016	9.968	-0.033	-0.033	0.000	0.000	0.000	0.000
64	B	65	GLU	-1	-0.863	-0.944	11.928	-0.446	-0.446	0.000	0.000	0.000	0.000
65	B	66	GLY	0	-0.039	-0.025	8.417	0.024	0.024	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.010	0.003	9.379	0.003	0.003	0.000	0.000	0.000	0.000
67	B	68	ASP	-1	-0.842	-0.902	10.624	-0.316	-0.316	0.000	0.000	0.000	0.000
68	B	69	LYS	1	0.840	0.920	11.007	0.442	0.442	0.000	0.000	0.000	0.000
69	B	70	VAL	0	0.010	-0.006	7.490	0.055	0.055	0.000	0.000	0.000	0.000
70	B	71	PHE	0	0.062	0.011	10.867	0.055	0.055	0.000	0.000	0.000	0.000
71	B	72	GLN	0	-0.031	-0.013	14.139	0.035	0.035	0.000	0.000	0.000	0.000
72	B	73	VAL	0	-0.081	-0.037	11.564	0.038	0.038	0.000	0.000	0.000	0.000
73	B	74	LEU	0	0.020	0.014	11.954	0.034	0.034	0.000	0.000	0.000	0.000
74	B	75	ARG	1	0.961	0.986	15.440	0.278	0.278	0.000	0.000	0.000	0.000
75	B	76	ALA	0	-0.023	0.014	18.133	0.023	0.023	0.000	0.000	0.000	0.000
76	B	77	PRO	0	0.002	0.010	19.850	0.003	0.003	0.000	0.000	0.000	0.000
77	B	85	TRP	0	0.092	0.030	25.434	0.000	0.000	0.000	0.000	0.000	0.000
78	B	86	SER	0	0.064	0.014	24.146	-0.007	-0.007	0.000	0.000	0.000	0.000
79	B	87	ARG	1	0.955	0.999	22.640	0.038	0.038	0.000	0.000	0.000	0.000
80	B	88	ARG	1	0.923	0.953	20.104	0.076	0.076	0.000	0.000	0.000	0.000
81	B	89	TYR	0	-0.023	-0.010	19.151	-0.005	-0.005	0.000	0.000	0.000	0.000
82	B	90	LYS	1	0.989	0.980	18.339	-0.025	-0.025	0.000	0.000	0.000	0.000
83	B	91	ALA	0	0.008	0.017	16.691	0.002	0.002	0.000	0.000	0.000	0.000
84	B	92	ASN	0	0.043	-0.001	14.634	-0.015	-0.015	0.000	0.000	0.000	0.000
85	B	93	LEU	0	-0.011	-0.006	13.516	-0.018	-0.018	0.000	0.000	0.000	0.000
86	B	94	GLU	-1	-0.921	-0.968	12.467	0.032	0.032	0.000	0.000	0.000	0.000
87	B	95	LYS	1	0.789	0.900	10.676	0.176	0.176	0.000	0.000	0.000	0.000
88	B	96	LEU	0	-0.021	-0.008	8.957	-0.041	-0.041	0.000	0.000	0.000	0.000
89	B	97	ALA	0	-0.052	-0.020	8.116	-0.019	-0.019	0.000	0.000	0.000	0.000
90	B	98	SER	0	-0.041	-0.034	6.954	0.039	0.039	0.000	0.000	0.000	0.000
91	B	99	GLY	0	0.037	0.029	3.440	-0.536	-0.263	0.005	-0.077	-0.201	0.000
92	B	100	ASP	-1	-0.750	-0.851	2.909	-1.760	0.026	0.499	-0.794	-1.491	-0.007
93	B	101	VAL	0	0.097	0.042	3.195	-0.803	-0.048	0.047	-0.216	-0.586	0.002
94	B	102	ASN	0	-0.035	-0.020	5.016	0.027	0.043	-0.001	-0.008	-0.007	0.000
95	B	103	LYS	1	0.862	0.928	7.649	0.420	0.420	0.000	0.000	0.000	0.000
96	B	104	VAL	0	0.041	0.014	5.629	0.063	0.063	0.000	0.000	0.000	0.000
97	B	105	ALA	0	0.048	0.027	8.524	0.038	0.038	0.000	0.000	0.000	0.000
98	B	106	GLU	-1	-0.888	-0.935	10.598	-0.205	-0.205	0.000	0.000	0.000	0.000
99	B	107	VAL	0	-0.060	-0.022	11.807	0.040	0.040	0.000	0.000	0.000	0.000
100	B	108	VAL	0	0.020	0.000	11.528	0.035	0.035	0.000	0.000	0.000	0.000
101	B	109	ARG	1	0.840	0.903	14.141	0.249	0.249	0.000	0.000	0.000	0.000
102	B	110	ASP	-1	-0.864	-0.918	16.486	-0.156	-0.156	0.000	0.000	0.000	0.000
103	B	111	LEU	0	-0.130	-0.062	15.946	0.029	0.029	0.000	0.000	0.000	0.000
104	B	112	TRP	0	0.090	0.026	18.048	0.014	0.014	0.000	0.000	0.000	0.000
105	B	113	ARG	1	0.871	0.922	19.634	0.197	0.197	0.000	0.000	0.000	0.000
106	B	114	ARG	1	0.822	0.887	20.634	0.114	0.114	0.000	0.000	0.000	0.000
107	B	115	ASP	-1	-0.829	-0.907	22.317	-0.096	-0.096	0.000	0.000	0.000	0.000
108	B	116	GLN	0	0.003	0.015	23.523	0.007	0.007	0.000	0.000	0.000	0.000
109	B	117	GLU	-1	-0.875	-0.909	26.448	-0.086	-0.086	0.000	0.000	0.000	0.000
110	B	118	ARG	1	0.765	0.852	27.829	0.085	0.085	0.000	0.000	0.000	0.000
111	B	119	GLY	0	0.028	0.043	26.632	0.006	0.006	0.000	0.000	0.000	0.000
112	B	120	LEU	0	-0.057	-0.018	20.475	0.002	0.002	0.000	0.000	0.000	0.000
113	B	121	SER	0	0.029	0.008	24.272	0.004	0.004	0.000	0.000	0.000	0.000
114	B	122	ALA	0	0.066	0.017	23.590	-0.007	-0.007	0.000	0.000	0.000	0.000
115	B	123	GLY	0	-0.006	-0.002	21.848	-0.002	-0.002	0.000	0.000	0.000	0.000
116	B	124	GLU	-1	-0.779	-0.870	19.591	-0.089	-0.089	0.000	0.000	0.000	0.000
117	B	125	LYS	1	0.873	0.923	18.862	0.081	0.081	0.000	0.000	0.000	0.000
118	B	126	ARG	1	0.951	0.980	18.739	0.024	0.024	0.000	0.000	0.000	0.000
119	B	127	MET	0	-0.051	-0.002	14.883	-0.014	-0.014	0.000	0.000	0.000	0.000
120	B	128	LEU	0	0.049	0.019	14.198	-0.025	-0.025	0.000	0.000	0.000	0.000
121	B	129	ALA	0	0.009	0.010	14.677	-0.030	-0.030	0.000	0.000	0.000	0.000
122	B	130	LYS	1	0.963	0.985	11.068	0.046	0.046	0.000	0.000	0.000	0.000
123	B	131	ALA	0	-0.010	-0.004	10.289	-0.053	-0.053	0.000	0.000	0.000	0.000
124	B	132	ARG	1	0.788	0.835	10.054	0.181	0.181	0.000	0.000	0.000	0.000
125	B	133	GLN	0	-0.007	0.001	10.981	-0.045	-0.045	0.000	0.000	0.000	0.000
126	B	134	ILE	0	0.002	-0.001	5.132	-0.023	-0.023	0.000	0.000	0.000	0.000
127	B	135	LEU	0	-0.003	0.001	6.764	-0.229	-0.229	0.000	0.000	0.000	0.000
128	B	136	VAL	0	0.007	-0.008	8.095	-0.094	-0.094	0.000	0.000	0.000	0.000
129	B	137	GLY	0	0.037	0.032	8.289	0.051	0.051	0.000	0.000	0.000	0.000
130	B	138	GLU	-1	-0.900	-0.973	2.769	-9.848	-6.360	1.223	-2.223	-2.489	-0.027
131	B	139	LEU	0	-0.055	-0.017	5.623	0.117	0.117	0.000	0.000	0.000	0.000
132	B	140	ALA	0	0.011	0.005	8.849	0.080	0.080	0.000	0.000	0.000	0.000
133	B	141	LEU	0	-0.027	-0.008	5.547	0.118	0.118	0.000	0.000	0.000	0.000
134	B	142	ALA	0	-0.037	-0.010	7.362	0.110	0.110	0.000	0.000	0.000	0.000
135	B	143	GLU	-1	-0.944	-0.981	9.192	-0.341	-0.341	0.000	0.000	0.000	0.000
136	B	144	SER	0	-0.074	-0.033	11.892	0.091	0.091	0.000	0.000	0.000	0.000
137	B	145	THR	0	-0.066	-0.030	13.286	0.091	0.091	0.000	0.000	0.000	0.000
138	B	146	ASP	-1	-0.876	-0.947	13.814	-0.369	-0.369	0.000	0.000	0.000	0.000
139	B	147	ASP	-1	-0.906	-0.956	13.186	-0.282	-0.282	0.000	0.000	0.000	0.000
140	B	148	ALA	0	-0.024	-0.016	14.693	0.006	0.006	0.000	0.000	0.000	0.000
141	B	149	LYS	1	0.911	0.942	16.991	0.236	0.236	0.000	0.000	0.000	0.000
142	B	150	ALA	0	0.038	0.036	12.122	0.003	0.003	0.000	0.000	0.000	0.000
143	B	151	GLU	-1	-0.858	-0.936	14.192	-0.261	-0.261	0.000	0.000	0.000	0.000
144	B	152	THR	0	-0.019	-0.005	15.673	0.016	0.016	0.000	0.000	0.000	0.000
145	B	153	ILE	0	0.043	0.032	14.864	0.018	0.018	0.000	0.000	0.000	0.000
146	B	154	LEU	0	-0.001	0.002	12.549	0.006	0.006	0.000	0.000	0.000	0.000
147	B	155	ASP	-1	-0.809	-0.884	15.283	-0.213	-0.213	0.000	0.000	0.000	0.000
148	B	156	GLU	-1	-0.938	-0.969	18.899	-0.187	-0.187	0.000	0.000	0.000	0.000
149	B	157	VAL	0	-0.090	-0.045	15.257	0.012	0.012	0.000	0.000	0.000	0.000
150	B	158	LEU	0	-0.078	-0.042	16.219	0.015	0.015	0.000	0.000	0.000	0.000
151	B	159	ALA	0	-0.039	-0.017	19.222	0.018	0.018	0.000	0.000	0.000	0.000
152	B	160	ALA	0	-0.047	-0.004	21.805	0.015	0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:2:ILE)