FMO DATABASE

FMODB ID: 1NMLZ

Calculation Name: 1KMZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KMZ

Chain ID: A

ChEMBL ID:

UniProt ID: O05205

Base Structure: X-ray

Registration Date: 2023-09-23

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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1058995.170733
FMO2-HF: Nuclear repulsion	1010232.531437
FMO2-HF: Total energy	-48762.639296
FMO2-MP2: Total energy	-48908.398713

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(A:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

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.
-6.418	-0.88	5.015	-4.426	-6.128	-0.034

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / 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

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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	5	ILE	0	0.027	0.022	3.846	-0.467	1.023	-0.019	-0.739	-0.732	0.001
4	A	6	SER	0	-0.058	-0.027	6.363	0.350	0.350	0.000	0.000	0.000	0.000
5	A	7	LEU	0	0.045	0.006	8.493	0.177	0.177	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.011	0.024	10.537	-0.125	-0.125	0.000	0.000	0.000	0.000
7	A	9	ALA	0	0.010	0.006	13.290	0.056	0.056	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.017	-0.015	15.726	-0.007	-0.007	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.028	0.024	19.234	0.014	0.014	0.000	0.000	0.000	0.000
10	A	12	VAL	0	-0.080	-0.045	21.449	0.005	0.005	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.900	-0.976	24.885	-0.096	-0.096	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.878	-0.934	28.307	-0.066	-0.066	0.000	0.000	0.000	0.000
13	A	15	MET	0	0.027	0.021	23.038	-0.009	-0.009	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.056	0.034	27.607	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.916	0.947	30.505	0.081	0.081	0.000	0.000	0.000	0.000
16	A	18	SER	0	-0.037	-0.009	24.649	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.036	0.007	24.330	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.898	-0.934	27.424	-0.069	-0.069	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.047	-0.029	26.759	0.003	0.003	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.038	0.010	23.668	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.926	0.969	26.870	0.073	0.073	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.801	0.906	29.058	0.079	0.079	0.000	0.000	0.000	0.000
23	A	25	LEU	0	-0.071	-0.029	26.770	0.002	0.002	0.000	0.000	0.000	0.000
24	A	26	GLY	0	-0.015	-0.004	27.376	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.035	-0.007	22.497	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.928	-0.964	24.262	-0.057	-0.057	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.056	-0.037	23.830	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	30	PRO	0	0.002	0.003	23.500	0.009	0.009	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.030	0.007	26.502	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.945	-0.978	29.152	-0.025	-0.025	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.012	0.011	25.610	0.001	0.001	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.874	-0.949	27.263	-0.069	-0.069	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.069	-0.038	29.756	0.001	0.001	0.000	0.000	0.000	0.000
34	A	36	ALA	0	-0.036	-0.002	24.575	0.005	0.005	0.000	0.000	0.000	0.000
35	A	37	PRO	0	-0.017	0.003	23.366	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	38	HIS	1	0.813	0.821	16.034	0.141	0.141	0.000	0.000	0.000	0.000
37	A	39	THR	0	0.013	0.015	20.889	0.019	0.019	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.822	-0.892	15.955	-0.169	-0.169	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.022	0.018	18.830	0.024	0.024	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.058	-0.033	17.038	-0.030	-0.030	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.023	0.013	16.190	0.014	0.014	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.884	-0.938	17.073	-0.137	-0.137	0.000	0.000	0.000	0.000
43	A	45	GLY	0	-0.043	-0.023	14.762	-0.045	-0.045	0.000	0.000	0.000	0.000
44	A	46	GLY	0	-0.049	-0.029	13.258	0.010	0.010	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.060	-0.023	10.527	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.884	0.946	12.737	0.191	0.191	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.007	0.015	14.110	-0.065	-0.065	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.010	-0.017	15.741	0.039	0.039	0.000	0.000	0.000	0.000
49	A	51	TRP	0	-0.007	-0.006	17.448	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.781	-0.863	17.596	-0.163	-0.163	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.012	0.010	20.930	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.064	0.032	23.297	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.937	-0.972	24.843	-0.076	-0.076	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.020	-0.015	20.561	0.010	0.010	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.037	0.042	19.423	0.002	0.002	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.880	0.932	21.315	0.092	0.092	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.130	-0.073	22.568	0.010	0.010	0.000	0.000	0.000	0.000
58	A	60	TYR	0	-0.020	-0.024	16.460	0.015	0.015	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.857	-0.907	18.875	-0.155	-0.155	0.000	0.000	0.000	0.000
60	A	62	PRO	0	-0.005	-0.006	20.911	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.945	-0.972	22.315	-0.110	-0.110	0.000	0.000	0.000	0.000
62	A	64	TRP	0	-0.034	0.000	20.852	0.008	0.008	0.000	0.000	0.000	0.000
63	A	65	GLN	0	-0.014	-0.026	23.790	0.015	0.015	0.000	0.000	0.000	0.000
64	A	66	ALA	0	0.052	0.038	25.327	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	67	PRO	0	-0.083	-0.058	24.963	0.000	0.000	0.000	0.000	0.000	0.000
66	A	68	THR	0	0.009	0.007	24.866	0.007	0.007	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.005	0.007	25.748	0.000	0.000	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.064	0.022	22.358	0.003	0.003	0.000	0.000	0.000	0.000
69	A	71	HIS	0	0.017	0.034	17.371	0.006	0.006	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.977	0.968	20.108	0.169	0.169	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.076	-0.039	14.884	0.009	0.009	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.062	0.046	12.975	0.009	0.009	0.000	0.000	0.000	0.000
73	A	75	ILE	0	-0.030	-0.011	8.284	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.064	0.043	8.221	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	77	PHE	0	-0.020	-0.026	2.681	-0.837	-0.142	0.228	-0.220	-0.703	0.000
76	A	78	GLU	-1	-0.910	-0.953	4.290	0.330	0.568	0.000	-0.069	-0.170	0.000
77	A	79	PHE	0	-0.040	-0.043	2.399	-4.415	-1.674	4.796	-3.305	-4.232	-0.035
78	A	80	PRO	0	-0.007	-0.002	3.465	-0.627	-0.358	0.011	-0.080	-0.200	0.000
79	A	81	ASP	-1	-0.821	-0.888	6.125	0.673	0.673	0.000	0.000	0.000	0.000
80	A	82	THR	0	0.034	-0.007	8.238	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	83	ALA	0	0.017	0.013	10.315	-0.080	-0.080	0.000	0.000	0.000	0.000
82	A	84	SER	0	-0.010	-0.042	5.574	-0.055	-0.055	0.000	0.000	0.000	0.000
83	A	85	VAL	0	-0.033	0.000	6.738	-0.176	-0.176	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.819	-0.902	7.831	0.011	0.011	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.862	0.957	8.643	-0.106	-0.106	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.968	0.988	4.145	0.457	0.562	-0.001	-0.013	-0.091	0.000
87	A	89	TYR	0	0.041	0.015	7.498	-0.057	-0.057	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.029	-0.019	10.286	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	91	GLU	-1	-0.906	-0.957	8.542	-0.068	-0.068	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.030	-0.014	7.726	-0.030	-0.030	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.017	0.004	11.627	0.012	0.012	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.966	-0.989	14.761	-0.065	-0.065	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.071	-0.022	13.963	0.009	0.009	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.048	-0.030	15.905	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.076	-0.033	12.706	-0.018	-0.018	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.891	-0.949	15.878	-0.159	-0.159	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.009	-0.008	14.943	-0.030	-0.030	0.000	0.000	0.000	0.000
98	A	100	HIS	0	-0.087	-0.062	15.291	0.011	0.011	0.000	0.000	0.000	0.000
99	A	101	LEU	0	0.021	0.003	15.577	0.026	0.026	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.909	0.962	14.771	0.021	0.021	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.022	-0.006	12.127	0.002	0.002	0.000	0.000	0.000	0.000
102	A	104	TRP	0	-0.056	-0.012	14.342	0.022	0.022	0.000	0.000	0.000	0.000
103	A	105	ASN	0	-0.003	-0.011	15.219	0.013	0.013	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.022	0.025	15.946	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	107	VAL	0	0.006	-0.013	17.643	0.017	0.017	0.000	0.000	0.000	0.000
106	A	108	TRP	0	-0.007	0.004	13.925	0.022	0.022	0.000	0.000	0.000	0.000
107	A	109	GLY	0	-0.005	0.003	17.201	0.005	0.005	0.000	0.000	0.000	0.000
108	A	110	GLN	0	0.026	-0.005	12.000	0.006	0.006	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.792	0.898	11.360	-0.119	-0.119	0.000	0.000	0.000	0.000
110	A	112	TYR	0	-0.004	-0.004	10.865	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.016	0.007	10.374	0.044	0.044	0.000	0.000	0.000	0.000
112	A	114	ILE	0	0.002	0.018	10.690	-0.057	-0.057	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.008	0.010	10.086	0.044	0.044	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.925	0.969	12.762	0.168	0.168	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.832	-0.892	12.904	-0.392	-0.392	0.000	0.000	0.000	0.000
116	A	118	PRO	0	-0.016	-0.037	14.151	0.035	0.035	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.974	-0.982	17.152	-0.241	-0.241	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.024	0.001	18.107	0.018	0.018	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.105	-0.066	14.801	0.039	0.039	0.000	0.000	0.000	0.000
120	A	122	VAL	0	0.008	0.007	13.557	-0.011	-0.011	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.009	-0.009	7.911	-0.066	-0.066	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.840	-0.927	9.486	-0.307	-0.307	0.000	0.000	0.000	0.000
123	A	125	LEU	0	-0.060	-0.040	5.293	-0.222	-0.222	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.006	0.001	6.161	0.164	0.164	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.055	0.020	6.656	0.054	0.054	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.001	0.013	8.831	-0.097	-0.097	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.031	-0.018	11.981	0.066	0.066	0.000	0.000	0.000	0.000
128	A	130	PRO	0	-0.024	0.000	14.961	-0.014	-0.014	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)