FMO DATABASE

FMODB ID: Z66NN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1317797.351143
FMO2-HF: Nuclear repulsion	1259869.166725
FMO2-HF: Total energy	-57928.184418
FMO2-MP2: Total energy	-58101.044112

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.
-11.683	-4.704	1.715	-3.08	-5.611	-0.024

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 : -0.040 / q_NPA : -0.020

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	0.854	0.925	3.809	0.548	1.874	-0.018	-0.501	-0.807	0.001
4	B	5	VAL	0	-0.010	-0.013	6.091	0.047	0.047	0.000	0.000	0.000	0.000
5	B	6	GLY	0	-0.050	-0.023	9.516	-0.087	-0.087	0.000	0.000	0.000	0.000
6	B	7	ASP	-1	-0.861	-0.911	6.675	-1.186	-1.186	0.000	0.000	0.000	0.000
7	B	8	THR	0	-0.056	-0.042	9.984	0.218	0.218	0.000	0.000	0.000	0.000
8	B	9	VAL	0	0.027	0.024	6.731	-0.124	-0.124	0.000	0.000	0.000	0.000
9	B	10	VAL	0	-0.011	-0.009	10.086	0.135	0.135	0.000	0.000	0.000	0.000
10	B	11	TYR	0	0.042	0.011	11.513	0.046	0.046	0.000	0.000	0.000	0.000
11	B	12	PRO	0	0.026	0.022	13.011	-0.007	-0.007	0.000	0.000	0.000	0.000
12	B	13	HIS	0	-0.024	-0.032	16.011	0.027	0.027	0.000	0.000	0.000	0.000
13	B	14	HIS	0	-0.054	-0.016	16.731	0.022	0.022	0.000	0.000	0.000	0.000
14	B	15	GLY	0	-0.002	0.003	16.992	-0.004	-0.004	0.000	0.000	0.000	0.000
15	B	16	ALA	0	-0.020	-0.004	14.877	-0.003	-0.003	0.000	0.000	0.000	0.000
16	B	17	ALA	0	0.004	-0.012	12.079	0.050	0.050	0.000	0.000	0.000	0.000
17	B	18	LEU	0	0.004	0.013	12.213	-0.069	-0.069	0.000	0.000	0.000	0.000
18	B	19	VAL	0	0.009	0.003	7.681	0.177	0.177	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.892	-0.952	10.933	0.151	0.151	0.000	0.000	0.000	0.000
20	B	21	ALA	0	-0.026	-0.031	11.325	-0.032	-0.032	0.000	0.000	0.000	0.000
21	B	22	ILE	0	0.017	0.013	5.370	0.047	0.047	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.832	-0.886	9.493	0.353	0.353	0.000	0.000	0.000	0.000
23	B	24	THR	0	-0.012	-0.019	11.275	0.167	0.167	0.000	0.000	0.000	0.000
24	B	25	ARG	1	0.849	0.934	13.733	-0.545	-0.545	0.000	0.000	0.000	0.000
25	B	26	THR	0	0.049	0.012	16.632	0.041	0.041	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.040	-0.026	15.751	-0.024	-0.024	0.000	0.000	0.000	0.000
27	B	28	LYS	1	0.815	0.893	19.767	-0.281	-0.281	0.000	0.000	0.000	0.000
28	B	29	GLY	0	0.052	0.057	20.189	-0.028	-0.028	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.885	-0.944	18.863	0.323	0.323	0.000	0.000	0.000	0.000
30	B	31	GLN	0	0.004	-0.009	16.005	0.009	0.009	0.000	0.000	0.000	0.000
31	B	32	LYS	1	0.817	0.892	11.998	-0.859	-0.859	0.000	0.000	0.000	0.000
32	B	33	GLU	-1	-0.882	-0.941	5.850	2.998	2.998	0.000	0.000	0.000	0.000
33	B	34	TYR	0	-0.029	-0.026	9.892	0.076	0.076	0.000	0.000	0.000	0.000
34	B	35	LEU	0	0.048	0.034	5.795	-0.027	-0.027	0.000	0.000	0.000	0.000
35	B	36	VAL	0	-0.064	-0.030	9.880	-0.192	-0.192	0.000	0.000	0.000	0.000
36	B	37	LEU	0	0.024	0.008	8.920	-0.056	-0.056	0.000	0.000	0.000	0.000
37	B	38	LYS	1	0.890	0.950	13.053	-0.161	-0.161	0.000	0.000	0.000	0.000
38	B	39	VAL	0	0.015	0.018	15.805	-0.046	-0.046	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.031	0.010	17.768	0.010	0.010	0.000	0.000	0.000	0.000
40	B	41	GLN	0	-0.038	-0.013	20.561	0.010	0.010	0.000	0.000	0.000	0.000
41	B	42	GLY	0	0.022	0.000	22.051	0.011	0.011	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-1.001	-0.992	22.241	0.089	0.089	0.000	0.000	0.000	0.000
43	B	44	LEU	0	0.023	0.034	18.896	0.019	0.019	0.000	0.000	0.000	0.000
44	B	45	THR	0	-0.021	-0.019	17.516	0.001	0.001	0.000	0.000	0.000	0.000
45	B	46	VAL	0	-0.001	-0.002	14.220	0.003	0.003	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.842	0.913	13.775	-0.339	-0.339	0.000	0.000	0.000	0.000
47	B	48	VAL	0	0.010	0.009	9.751	-0.090	-0.090	0.000	0.000	0.000	0.000
48	B	49	PRO	0	0.003	0.009	10.374	0.179	0.179	0.000	0.000	0.000	0.000
49	B	50	ALA	0	0.077	0.022	5.191	-0.172	-0.172	0.000	0.000	0.000	0.000
50	B	51	GLU	-1	-0.837	-0.892	6.053	1.087	1.087	0.000	0.000	0.000	0.000
51	B	52	ASN	0	-0.004	-0.022	7.803	-0.256	-0.256	0.000	0.000	0.000	0.000
52	B	53	ALA	0	0.020	0.021	5.967	-0.250	-0.250	0.000	0.000	0.000	0.000
53	B	54	GLU	-1	-0.902	-0.955	6.846	0.051	0.051	0.000	0.000	0.000	0.000
54	B	55	TYR	0	-0.033	-0.011	8.473	-0.181	-0.181	0.000	0.000	0.000	0.000
55	B	56	VAL	0	-0.075	-0.024	10.780	-0.077	-0.077	0.000	0.000	0.000	0.000
56	B	57	GLY	0	-0.044	-0.022	11.282	-0.055	-0.055	0.000	0.000	0.000	0.000
57	B	58	VAL	0	-0.042	-0.025	7.140	-0.105	-0.105	0.000	0.000	0.000	0.000
58	B	59	ARG	1	0.951	0.962	5.344	0.666	0.666	0.000	0.000	0.000	0.000
59	B	60	ASP	-1	-0.813	-0.925	3.088	-1.885	-1.231	0.036	-0.171	-0.519	0.000
60	B	61	VAL	0	-0.016	0.004	3.522	-2.019	-1.398	0.015	-0.257	-0.379	-0.002
61	B	62	VAL	0	-0.018	-0.009	4.382	0.306	0.396	-0.001	-0.007	-0.082	0.000
62	B	63	GLY	0	0.081	0.053	6.753	0.191	0.191	0.000	0.000	0.000	0.000
63	B	64	GLN	0	-0.018	-0.028	10.498	-0.019	-0.019	0.000	0.000	0.000	0.000
64	B	65	GLU	-1	-0.871	-0.944	12.051	-0.490	-0.490	0.000	0.000	0.000	0.000
65	B	66	GLY	0	-0.021	-0.018	8.926	0.042	0.042	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.027	0.008	9.874	0.019	0.019	0.000	0.000	0.000	0.000
67	B	68	ASP	-1	-0.848	-0.898	11.148	-0.328	-0.328	0.000	0.000	0.000	0.000
68	B	69	LYS	1	0.895	0.968	11.113	0.350	0.350	0.000	0.000	0.000	0.000
69	B	70	VAL	0	0.021	-0.002	7.900	0.077	0.077	0.000	0.000	0.000	0.000
70	B	71	PHE	0	0.061	0.016	11.236	0.058	0.058	0.000	0.000	0.000	0.000
71	B	72	GLN	0	-0.065	-0.036	14.514	0.052	0.052	0.000	0.000	0.000	0.000
72	B	73	VAL	0	-0.086	-0.054	11.936	0.044	0.044	0.000	0.000	0.000	0.000
73	B	74	LEU	0	0.020	0.006	12.370	0.039	0.039	0.000	0.000	0.000	0.000
74	B	75	ARG	1	0.981	0.997	15.868	0.284	0.284	0.000	0.000	0.000	0.000
75	B	76	ALA	0	-0.042	0.008	18.496	0.023	0.023	0.000	0.000	0.000	0.000
76	B	77	PRO	0	0.020	0.019	20.177	0.004	0.004	0.000	0.000	0.000	0.000
77	B	85	TRP	0	0.085	0.011	25.138	0.001	0.001	0.000	0.000	0.000	0.000
78	B	86	SER	0	0.069	0.020	24.178	-0.005	-0.005	0.000	0.000	0.000	0.000
79	B	87	ARG	1	0.946	0.993	22.705	-0.018	-0.018	0.000	0.000	0.000	0.000
80	B	88	ARG	1	0.958	0.986	20.354	0.039	0.039	0.000	0.000	0.000	0.000
81	B	89	TYR	0	0.002	0.009	19.219	0.000	0.000	0.000	0.000	0.000	0.000
82	B	90	LYS	1	0.987	0.975	18.322	-0.094	-0.094	0.000	0.000	0.000	0.000
83	B	91	ALA	0	0.016	0.024	16.717	0.015	0.015	0.000	0.000	0.000	0.000
84	B	92	ASN	0	0.042	0.002	14.618	0.003	0.003	0.000	0.000	0.000	0.000
85	B	93	LEU	0	-0.031	-0.022	13.441	-0.012	-0.012	0.000	0.000	0.000	0.000
86	B	94	GLU	-1	-0.920	-0.963	12.564	0.227	0.227	0.000	0.000	0.000	0.000
87	B	95	LYS	1	0.793	0.902	10.613	0.113	0.113	0.000	0.000	0.000	0.000
88	B	96	LEU	0	-0.022	-0.014	8.799	-0.011	-0.011	0.000	0.000	0.000	0.000
89	B	97	ALA	0	-0.028	0.001	8.181	-0.015	-0.015	0.000	0.000	0.000	0.000
90	B	98	SER	0	-0.029	-0.027	6.484	0.061	0.061	0.000	0.000	0.000	0.000
91	B	99	GLY	0	0.045	0.032	3.525	-0.458	-0.147	0.003	-0.076	-0.237	0.000
92	B	100	ASP	-1	-0.750	-0.858	2.680	-1.019	0.326	0.726	-0.591	-1.479	-0.007
93	B	101	VAL	0	0.112	0.050	3.746	-0.441	-0.061	0.004	-0.084	-0.299	0.001
94	B	102	ASN	0	-0.045	-0.034	5.338	-0.014	-0.010	-0.001	-0.002	-0.001	0.000
95	B	103	LYS	1	0.855	0.923	8.000	0.140	0.140	0.000	0.000	0.000	0.000
96	B	104	VAL	0	0.044	0.016	5.989	0.040	0.040	0.000	0.000	0.000	0.000
97	B	105	ALA	0	0.055	0.040	8.855	0.021	0.021	0.000	0.000	0.000	0.000
98	B	106	GLU	-1	-0.887	-0.926	10.922	-0.104	-0.104	0.000	0.000	0.000	0.000
99	B	107	VAL	0	-0.065	-0.024	12.061	0.030	0.030	0.000	0.000	0.000	0.000
100	B	108	VAL	0	0.003	-0.009	11.697	0.027	0.027	0.000	0.000	0.000	0.000
101	B	109	ARG	1	0.826	0.897	14.256	0.190	0.190	0.000	0.000	0.000	0.000
102	B	110	ASP	-1	-0.879	-0.919	16.669	-0.105	-0.105	0.000	0.000	0.000	0.000
103	B	111	LEU	0	-0.108	-0.062	16.160	0.022	0.022	0.000	0.000	0.000	0.000
104	B	112	TRP	0	0.090	0.036	18.154	0.012	0.012	0.000	0.000	0.000	0.000
105	B	113	ARG	1	0.903	0.938	19.877	0.168	0.168	0.000	0.000	0.000	0.000
106	B	114	ARG	1	0.801	0.875	20.970	0.076	0.076	0.000	0.000	0.000	0.000
107	B	115	ASP	-1	-0.863	-0.923	22.193	-0.086	-0.086	0.000	0.000	0.000	0.000
108	B	116	GLN	0	-0.001	0.013	23.926	0.005	0.005	0.000	0.000	0.000	0.000
109	B	117	GLU	-1	-0.890	-0.935	26.271	-0.070	-0.070	0.000	0.000	0.000	0.000
110	B	118	ARG	1	0.798	0.888	28.070	0.059	0.059	0.000	0.000	0.000	0.000
111	B	119	GLY	0	0.053	0.063	26.600	0.005	0.005	0.000	0.000	0.000	0.000
112	B	120	LEU	0	-0.079	-0.040	20.495	0.007	0.007	0.000	0.000	0.000	0.000
113	B	121	SER	0	0.024	0.013	24.300	0.004	0.004	0.000	0.000	0.000	0.000
114	B	122	ALA	0	0.063	0.015	23.664	-0.007	-0.007	0.000	0.000	0.000	0.000
115	B	123	GLY	0	-0.009	-0.011	22.068	-0.004	-0.004	0.000	0.000	0.000	0.000
116	B	124	GLU	-1	-0.797	-0.894	19.803	-0.045	-0.045	0.000	0.000	0.000	0.000
117	B	125	LYS	1	0.910	0.948	19.057	0.070	0.070	0.000	0.000	0.000	0.000
118	B	126	ARG	1	0.958	0.984	18.825	0.006	0.006	0.000	0.000	0.000	0.000
119	B	127	MET	0	-0.062	-0.011	15.089	-0.015	-0.015	0.000	0.000	0.000	0.000
120	B	128	LEU	0	0.029	0.004	14.395	-0.021	-0.021	0.000	0.000	0.000	0.000
121	B	129	ALA	0	0.011	0.003	14.754	-0.033	-0.033	0.000	0.000	0.000	0.000
122	B	130	LYS	1	0.952	0.981	11.371	-0.009	-0.009	0.000	0.000	0.000	0.000
123	B	131	ALA	0	-0.002	0.001	10.265	-0.052	-0.052	0.000	0.000	0.000	0.000
124	B	132	ARG	1	0.852	0.879	9.972	0.189	0.189	0.000	0.000	0.000	0.000
125	B	133	GLN	0	-0.011	0.010	10.811	-0.054	-0.054	0.000	0.000	0.000	0.000
126	B	134	ILE	0	0.003	-0.005	5.254	-0.044	-0.044	0.000	0.000	0.000	0.000
127	B	135	LEU	0	0.000	-0.001	6.710	-0.250	-0.250	0.000	0.000	0.000	0.000
128	B	136	VAL	0	0.006	-0.004	8.144	-0.114	-0.114	0.000	0.000	0.000	0.000
129	B	137	GLY	0	0.021	0.027	8.066	0.017	0.017	0.000	0.000	0.000	0.000
130	B	138	GLU	-1	-0.916	-0.979	2.780	-8.212	-5.964	0.951	-1.391	-1.808	-0.017
131	B	139	LEU	0	-0.063	-0.028	5.646	0.074	0.074	0.000	0.000	0.000	0.000
132	B	140	ALA	0	-0.030	-0.020	8.930	0.074	0.074	0.000	0.000	0.000	0.000
133	B	141	LEU	0	0.027	0.021	6.021	0.116	0.116	0.000	0.000	0.000	0.000
134	B	142	ALA	0	-0.035	-0.006	7.775	0.100	0.100	0.000	0.000	0.000	0.000
135	B	143	GLU	-1	-0.963	-0.986	9.471	-0.382	-0.382	0.000	0.000	0.000	0.000
136	B	144	SER	0	-0.085	-0.040	12.079	0.097	0.097	0.000	0.000	0.000	0.000
137	B	145	THR	0	-0.055	-0.026	13.243	0.102	0.102	0.000	0.000	0.000	0.000
138	B	146	ASP	-1	-0.892	-0.958	13.403	-0.515	-0.515	0.000	0.000	0.000	0.000
139	B	147	ASP	-1	-0.996	-1.000	13.041	-0.395	-0.395	0.000	0.000	0.000	0.000
140	B	148	ALA	0	0.025	0.013	14.682	0.050	0.050	0.000	0.000	0.000	0.000
141	B	149	LYS	1	0.957	0.965	17.312	0.272	0.272	0.000	0.000	0.000	0.000
142	B	150	ALA	0	0.061	0.044	12.286	0.007	0.007	0.000	0.000	0.000	0.000
143	B	151	GLU	-1	-0.911	-0.973	14.398	-0.284	-0.284	0.000	0.000	0.000	0.000
144	B	152	THR	0	-0.012	0.002	15.746	0.022	0.022	0.000	0.000	0.000	0.000
145	B	153	ILE	0	0.041	0.027	15.249	0.025	0.025	0.000	0.000	0.000	0.000
146	B	154	LEU	0	-0.022	-0.010	12.870	0.016	0.016	0.000	0.000	0.000	0.000
147	B	155	ASP	-1	-0.770	-0.862	15.758	-0.221	-0.221	0.000	0.000	0.000	0.000
148	B	156	GLU	-1	-0.923	-0.950	19.294	-0.200	-0.200	0.000	0.000	0.000	0.000
149	B	157	VAL	0	-0.098	-0.052	15.819	0.018	0.018	0.000	0.000	0.000	0.000
150	B	158	LEU	0	-0.101	-0.053	16.542	0.016	0.016	0.000	0.000	0.000	0.000
151	B	159	ALA	0	-0.072	-0.028	19.709	0.020	0.020	0.000	0.000	0.000	0.000
152	B	160	ALA	0	-0.053	-0.016	22.595	0.017	0.017	0.000	0.000	0.000	0.000

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