FMO DATABASE

FMODB ID: 6NNGZ

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	OptH
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	-1317306.979582
FMO2-HF: Nuclear repulsion	1259379.687498
FMO2-HF: Total energy	-57927.292084
FMO2-MP2: Total energy	-58100.228288

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.
-10.634	-4.306	2.199	-2.89	-5.639	-0.02

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 : -0.042 / q_NPA : -0.018

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	0.863	0.941	3.809	1.152	2.462	-0.017	-0.450	-0.843	0.002
4	B	5	VAL	0	-0.010	-0.018	6.346	-0.510	-0.510	0.000	0.000	0.000	0.000
5	B	6	GLY	0	-0.058	-0.030	10.070	-0.071	-0.071	0.000	0.000	0.000	0.000
6	B	7	ASP	-1	-0.822	-0.894	6.236	-0.735	-0.735	0.000	0.000	0.000	0.000
7	B	8	THR	0	-0.061	-0.047	9.809	0.178	0.178	0.000	0.000	0.000	0.000
8	B	9	VAL	0	0.016	0.019	6.385	-0.179	-0.179	0.000	0.000	0.000	0.000
9	B	10	VAL	0	-0.008	-0.008	9.735	0.190	0.190	0.000	0.000	0.000	0.000
10	B	11	TYR	0	0.024	0.006	11.293	-0.070	-0.070	0.000	0.000	0.000	0.000
11	B	12	PRO	0	0.029	0.019	12.759	0.053	0.053	0.000	0.000	0.000	0.000
12	B	13	HIS	0	-0.026	-0.028	15.869	0.037	0.037	0.000	0.000	0.000	0.000
13	B	14	HIS	0	-0.050	-0.014	16.251	0.043	0.043	0.000	0.000	0.000	0.000
14	B	15	GLY	0	0.000	0.004	16.764	0.022	0.022	0.000	0.000	0.000	0.000
15	B	16	ALA	0	-0.020	-0.003	14.546	-0.034	-0.034	0.000	0.000	0.000	0.000
16	B	17	ALA	0	0.005	-0.012	11.793	0.071	0.071	0.000	0.000	0.000	0.000
17	B	18	LEU	0	0.007	0.012	11.872	-0.080	-0.080	0.000	0.000	0.000	0.000
18	B	19	VAL	0	0.014	0.005	7.337	0.094	0.094	0.000	0.000	0.000	0.000
19	B	20	GLU	-1	-0.975	-0.987	10.643	0.489	0.489	0.000	0.000	0.000	0.000
20	B	21	ALA	0	0.015	-0.003	11.979	0.045	0.045	0.000	0.000	0.000	0.000
21	B	22	ILE	0	0.008	0.007	5.846	-0.067	-0.067	0.000	0.000	0.000	0.000
22	B	23	GLU	-1	-0.881	-0.924	10.008	0.445	0.445	0.000	0.000	0.000	0.000
23	B	24	THR	0	0.000	-0.013	11.402	0.146	0.146	0.000	0.000	0.000	0.000
24	B	25	ARG	1	0.901	0.967	13.835	-0.465	-0.465	0.000	0.000	0.000	0.000
25	B	26	THR	0	0.043	0.012	16.440	0.015	0.015	0.000	0.000	0.000	0.000
26	B	27	ILE	0	-0.056	-0.042	16.000	-0.021	-0.021	0.000	0.000	0.000	0.000
27	B	28	LYS	1	0.817	0.906	19.958	-0.202	-0.202	0.000	0.000	0.000	0.000
28	B	29	GLY	0	0.074	0.063	19.891	-0.026	-0.026	0.000	0.000	0.000	0.000
29	B	30	GLU	-1	-0.911	-0.961	18.690	0.217	0.217	0.000	0.000	0.000	0.000
30	B	31	GLN	0	0.029	0.002	15.726	0.051	0.051	0.000	0.000	0.000	0.000
31	B	32	LYS	1	0.883	0.958	11.808	-0.448	-0.448	0.000	0.000	0.000	0.000
32	B	33	GLU	-1	-0.882	-0.941	6.008	2.942	2.942	0.000	0.000	0.000	0.000
33	B	34	TYR	0	-0.037	-0.029	9.661	-0.159	-0.159	0.000	0.000	0.000	0.000
34	B	35	LEU	0	0.050	0.030	5.544	0.201	0.201	0.000	0.000	0.000	0.000
35	B	36	VAL	0	-0.054	-0.023	9.600	-0.250	-0.250	0.000	0.000	0.000	0.000
36	B	37	LEU	0	0.024	0.009	8.780	0.007	0.007	0.000	0.000	0.000	0.000
37	B	38	LYS	1	0.921	0.955	12.864	-0.237	-0.237	0.000	0.000	0.000	0.000
38	B	39	VAL	0	0.027	0.030	15.666	-0.042	-0.042	0.000	0.000	0.000	0.000
39	B	40	ALA	0	0.033	0.008	17.504	0.016	0.016	0.000	0.000	0.000	0.000
40	B	41	GLN	0	-0.043	-0.018	20.267	0.019	0.019	0.000	0.000	0.000	0.000
41	B	42	GLY	0	0.019	0.002	21.811	-0.001	-0.001	0.000	0.000	0.000	0.000
42	B	43	ASP	-1	-0.994	-0.988	22.069	0.094	0.094	0.000	0.000	0.000	0.000
43	B	44	LEU	0	0.023	0.034	18.393	0.019	0.019	0.000	0.000	0.000	0.000
44	B	45	THR	0	-0.022	-0.023	17.195	0.018	0.018	0.000	0.000	0.000	0.000
45	B	46	VAL	0	-0.003	-0.003	13.740	-0.007	-0.007	0.000	0.000	0.000	0.000
46	B	47	ARG	1	0.839	0.916	13.500	-0.342	-0.342	0.000	0.000	0.000	0.000
47	B	48	VAL	0	-0.010	-0.002	9.504	-0.075	-0.075	0.000	0.000	0.000	0.000
48	B	49	PRO	0	0.004	0.010	10.177	0.148	0.148	0.000	0.000	0.000	0.000
49	B	50	ALA	0	0.078	0.021	5.098	-0.158	-0.158	0.000	0.000	0.000	0.000
50	B	51	GLU	-1	-0.893	-0.952	6.025	0.119	0.119	0.000	0.000	0.000	0.000
51	B	52	ASN	0	-0.002	-0.029	7.924	-0.170	-0.170	0.000	0.000	0.000	0.000
52	B	53	ALA	0	0.030	0.016	5.896	-0.072	-0.072	0.000	0.000	0.000	0.000
53	B	54	GLU	-1	-0.889	-0.949	6.732	-0.764	-0.764	0.000	0.000	0.000	0.000
54	B	55	TYR	0	-0.076	-0.009	8.355	0.003	0.003	0.000	0.000	0.000	0.000
55	B	56	VAL	0	-0.070	-0.023	10.762	0.011	0.011	0.000	0.000	0.000	0.000
56	B	57	GLY	0	-0.031	-0.015	11.216	0.012	0.012	0.000	0.000	0.000	0.000
57	B	58	VAL	0	-0.045	-0.027	6.891	-0.034	-0.034	0.000	0.000	0.000	0.000
58	B	59	ARG	1	0.968	0.965	5.236	1.208	1.208	0.000	0.000	0.000	0.000
59	B	60	ASP	-1	-0.835	-0.927	2.946	-2.250	-1.377	0.110	-0.244	-0.739	-0.001
60	B	61	VAL	0	-0.012	0.003	3.491	-2.075	-1.430	0.017	-0.278	-0.384	-0.002
61	B	62	VAL	0	0.003	0.002	4.392	0.399	0.483	-0.001	-0.005	-0.079	0.000
62	B	63	GLY	0	0.072	0.044	6.897	0.180	0.180	0.000	0.000	0.000	0.000
63	B	64	GLN	0	-0.007	-0.015	10.616	-0.007	-0.007	0.000	0.000	0.000	0.000
64	B	65	GLU	-1	-0.853	-0.928	11.893	-0.344	-0.344	0.000	0.000	0.000	0.000
65	B	66	GLY	0	-0.031	-0.025	8.838	0.082	0.082	0.000	0.000	0.000	0.000
66	B	67	LEU	0	0.042	0.012	9.615	0.045	0.045	0.000	0.000	0.000	0.000
67	B	68	ASP	-1	-0.868	-0.914	11.155	-0.211	-0.211	0.000	0.000	0.000	0.000
68	B	69	LYS	1	0.868	0.953	10.903	-0.031	-0.031	0.000	0.000	0.000	0.000
69	B	70	VAL	0	0.048	0.009	7.876	0.092	0.092	0.000	0.000	0.000	0.000
70	B	71	PHE	0	0.059	0.014	11.085	0.053	0.053	0.000	0.000	0.000	0.000
71	B	72	GLN	0	-0.051	-0.034	14.420	0.080	0.080	0.000	0.000	0.000	0.000
72	B	73	VAL	0	-0.086	-0.044	11.799	0.038	0.038	0.000	0.000	0.000	0.000
73	B	74	LEU	0	0.004	0.005	12.330	0.035	0.035	0.000	0.000	0.000	0.000
74	B	75	ARG	1	0.989	1.001	15.693	0.191	0.191	0.000	0.000	0.000	0.000
75	B	76	ALA	0	-0.038	0.006	18.314	0.015	0.015	0.000	0.000	0.000	0.000
76	B	77	PRO	0	0.012	0.014	20.069	0.004	0.004	0.000	0.000	0.000	0.000
77	B	85	TRP	0	0.090	0.015	24.839	0.003	0.003	0.000	0.000	0.000	0.000
78	B	86	SER	0	0.069	0.021	24.063	0.001	0.001	0.000	0.000	0.000	0.000
79	B	87	ARG	1	0.935	0.985	22.445	-0.159	-0.159	0.000	0.000	0.000	0.000
80	B	88	ARG	1	0.977	0.987	20.291	-0.051	-0.051	0.000	0.000	0.000	0.000
81	B	89	TYR	0	0.017	0.019	19.086	0.002	0.002	0.000	0.000	0.000	0.000
82	B	90	LYS	1	0.974	0.967	18.134	-0.214	-0.214	0.000	0.000	0.000	0.000
83	B	91	ALA	0	0.023	0.029	16.446	0.035	0.035	0.000	0.000	0.000	0.000
84	B	92	ASN	0	0.047	0.006	14.483	0.065	0.065	0.000	0.000	0.000	0.000
85	B	93	LEU	0	-0.045	-0.027	13.328	-0.006	-0.006	0.000	0.000	0.000	0.000
86	B	94	GLU	-1	-0.911	-0.962	12.331	0.593	0.593	0.000	0.000	0.000	0.000
87	B	95	LYS	1	0.809	0.919	10.316	-0.130	-0.130	0.000	0.000	0.000	0.000
88	B	96	LEU	0	-0.025	-0.015	8.594	0.072	0.072	0.000	0.000	0.000	0.000
89	B	97	ALA	0	-0.022	0.002	8.073	-0.070	-0.070	0.000	0.000	0.000	0.000
90	B	98	SER	0	-0.034	-0.029	6.174	-0.003	-0.003	0.000	0.000	0.000	0.000
91	B	99	GLY	0	0.044	0.032	3.398	0.416	0.824	0.005	-0.122	-0.292	0.000
92	B	100	ASP	-1	-0.810	-0.895	2.395	-0.053	0.618	1.858	-0.685	-1.844	-0.011
93	B	101	VAL	0	0.114	0.045	3.512	-0.730	-0.319	0.008	-0.103	-0.317	0.001
94	B	102	ASN	0	0.003	-0.015	5.282	-0.221	-0.215	-0.001	-0.002	-0.002	0.000
95	B	103	LYS	1	0.883	0.959	7.790	-0.883	-0.883	0.000	0.000	0.000	0.000
96	B	104	VAL	0	0.048	0.016	5.746	-0.043	-0.043	0.000	0.000	0.000	0.000
97	B	105	ALA	0	0.047	0.035	8.874	-0.032	-0.032	0.000	0.000	0.000	0.000
98	B	106	GLU	-1	-0.897	-0.948	10.956	0.257	0.257	0.000	0.000	0.000	0.000
99	B	107	VAL	0	-0.068	-0.024	12.022	-0.004	-0.004	0.000	0.000	0.000	0.000
100	B	108	VAL	0	-0.001	-0.012	11.837	-0.001	-0.001	0.000	0.000	0.000	0.000
101	B	109	ARG	1	0.838	0.909	14.397	-0.022	-0.022	0.000	0.000	0.000	0.000
102	B	110	ASP	-1	-0.894	-0.939	16.740	0.061	0.061	0.000	0.000	0.000	0.000
103	B	111	LEU	0	-0.125	-0.072	16.466	0.007	0.007	0.000	0.000	0.000	0.000
104	B	112	TRP	0	0.097	0.040	18.314	0.003	0.003	0.000	0.000	0.000	0.000
105	B	113	ARG	1	0.915	0.944	20.050	0.043	0.043	0.000	0.000	0.000	0.000
106	B	114	ARG	1	0.811	0.886	21.134	-0.016	-0.016	0.000	0.000	0.000	0.000
107	B	115	ASP	-1	-0.958	-0.992	22.401	-0.067	-0.067	0.000	0.000	0.000	0.000
108	B	116	GLN	0	-0.002	0.020	23.881	-0.002	-0.002	0.000	0.000	0.000	0.000
109	B	117	GLU	-1	-0.952	-0.966	26.461	-0.014	-0.014	0.000	0.000	0.000	0.000
110	B	118	ARG	1	0.858	0.917	28.098	-0.011	-0.011	0.000	0.000	0.000	0.000
111	B	119	GLY	0	0.071	0.072	26.768	0.002	0.002	0.000	0.000	0.000	0.000
112	B	120	LEU	0	-0.097	-0.047	20.710	0.011	0.011	0.000	0.000	0.000	0.000
113	B	121	SER	0	0.024	0.016	24.022	-0.002	-0.002	0.000	0.000	0.000	0.000
114	B	122	ALA	0	0.058	0.009	23.798	-0.007	-0.007	0.000	0.000	0.000	0.000
115	B	123	GLY	0	-0.020	-0.024	22.148	-0.010	-0.010	0.000	0.000	0.000	0.000
116	B	124	GLU	-1	-0.781	-0.888	19.896	0.036	0.036	0.000	0.000	0.000	0.000
117	B	125	LYS	1	0.973	0.994	19.198	0.039	0.039	0.000	0.000	0.000	0.000
118	B	126	ARG	1	0.959	0.989	19.090	0.004	0.004	0.000	0.000	0.000	0.000
119	B	127	MET	0	-0.057	-0.012	15.036	-0.015	-0.015	0.000	0.000	0.000	0.000
120	B	128	LEU	0	0.035	0.009	14.557	-0.017	-0.017	0.000	0.000	0.000	0.000
121	B	129	ALA	0	0.014	0.003	15.004	-0.035	-0.035	0.000	0.000	0.000	0.000
122	B	130	LYS	1	0.950	0.983	11.517	0.010	0.010	0.000	0.000	0.000	0.000
123	B	131	ALA	0	-0.001	0.000	10.473	-0.069	-0.069	0.000	0.000	0.000	0.000
124	B	132	ARG	1	0.906	0.931	10.261	0.175	0.175	0.000	0.000	0.000	0.000
125	B	133	GLN	0	0.002	0.015	10.679	-0.080	-0.080	0.000	0.000	0.000	0.000
126	B	134	ILE	0	-0.005	-0.006	5.621	-0.053	-0.053	0.000	0.000	0.000	0.000
127	B	135	LEU	0	-0.006	-0.003	6.810	-0.246	-0.246	0.000	0.000	0.000	0.000
128	B	136	VAL	0	0.014	-0.003	8.250	-0.108	-0.108	0.000	0.000	0.000	0.000
129	B	137	GLY	0	0.016	0.024	8.323	0.008	0.008	0.000	0.000	0.000	0.000
130	B	138	GLU	-1	-0.925	-0.979	3.154	-7.112	-5.192	0.220	-1.001	-1.139	-0.009
131	B	139	LEU	0	-0.060	-0.023	5.906	0.064	0.064	0.000	0.000	0.000	0.000
132	B	140	ALA	0	-0.033	-0.023	9.139	0.070	0.070	0.000	0.000	0.000	0.000
133	B	141	LEU	0	0.032	0.022	6.305	0.099	0.099	0.000	0.000	0.000	0.000
134	B	142	ALA	0	-0.030	-0.002	8.043	0.093	0.093	0.000	0.000	0.000	0.000
135	B	143	GLU	-1	-0.974	-0.994	9.754	-0.354	-0.354	0.000	0.000	0.000	0.000
136	B	144	SER	0	-0.085	-0.054	12.414	0.097	0.097	0.000	0.000	0.000	0.000
137	B	145	THR	0	-0.062	-0.012	13.582	0.105	0.105	0.000	0.000	0.000	0.000
138	B	146	ASP	-1	-0.874	-0.954	13.775	-0.704	-0.704	0.000	0.000	0.000	0.000
139	B	147	ASP	-1	-1.015	-1.008	13.514	-0.501	-0.501	0.000	0.000	0.000	0.000
140	B	148	ALA	0	0.040	0.021	14.987	0.053	0.053	0.000	0.000	0.000	0.000
141	B	149	LYS	1	0.950	0.962	17.603	0.324	0.324	0.000	0.000	0.000	0.000
142	B	150	ALA	0	0.070	0.044	12.511	0.017	0.017	0.000	0.000	0.000	0.000
143	B	151	GLU	-1	-0.940	-0.983	14.615	-0.302	-0.302	0.000	0.000	0.000	0.000
144	B	152	THR	0	0.016	0.017	15.893	0.030	0.030	0.000	0.000	0.000	0.000
145	B	153	ILE	0	0.032	0.024	15.298	0.033	0.033	0.000	0.000	0.000	0.000
146	B	154	LEU	0	-0.032	-0.019	12.859	0.030	0.030	0.000	0.000	0.000	0.000
147	B	155	ASP	-1	-0.823	-0.909	15.808	-0.207	-0.207	0.000	0.000	0.000	0.000
148	B	156	GLU	-1	-0.935	-0.959	19.329	-0.175	-0.175	0.000	0.000	0.000	0.000
149	B	157	VAL	0	-0.094	-0.046	15.815	0.025	0.025	0.000	0.000	0.000	0.000
150	B	158	LEU	0	-0.111	-0.060	16.590	0.027	0.027	0.000	0.000	0.000	0.000
151	B	159	ALA	0	-0.070	-0.024	19.648	0.022	0.022	0.000	0.000	0.000	0.000
152	B	160	ALA	0	-0.062	-0.020	22.563	0.021	0.021	0.000	0.000	0.000	0.000

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