FMO DATABASE

FMODB ID: G5J21

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1059020.615926
FMO2-HF: Nuclear repulsion	1010257.458398
FMO2-HF: Total energy	-48763.157528
FMO2-MP2: Total energy	-48908.922102

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.
-8.475	-2.11	5.214	-5.003	-6.576	-0.03

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 : 0.005 / q_NPA : 0.010

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	0.022	0.016	3.846	-0.961	1.333	-0.020	-1.251	-1.023	0.005
4	A	6	SER	0	-0.041	-0.019	6.438	0.166	0.166	0.000	0.000	0.000	0.000
5	A	7	LEU	0	0.037	0.007	8.566	0.168	0.168	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.003	0.016	10.596	-0.075	-0.075	0.000	0.000	0.000	0.000
7	A	9	ALA	0	0.008	0.001	13.350	0.034	0.034	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.009	-0.007	15.776	0.011	0.011	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.017	0.018	19.281	0.006	0.006	0.000	0.000	0.000	0.000
10	A	12	VAL	0	-0.070	-0.039	21.486	0.002	0.002	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.892	-0.969	24.926	-0.070	-0.070	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.873	-0.936	28.344	-0.077	-0.077	0.000	0.000	0.000	0.000
13	A	15	MET	0	0.031	0.034	23.030	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.047	0.030	27.657	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.911	0.949	30.560	0.083	0.083	0.000	0.000	0.000	0.000
16	A	18	SER	0	-0.027	-0.005	25.543	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.035	0.005	24.213	-0.010	-0.010	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.900	-0.926	27.486	-0.101	-0.101	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.042	-0.029	26.556	0.001	0.001	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.045	0.014	23.409	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.871	0.925	26.938	0.120	0.120	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.799	0.897	29.129	0.108	0.108	0.000	0.000	0.000	0.000
23	A	25	LEU	0	-0.078	-0.031	26.896	0.003	0.003	0.000	0.000	0.000	0.000
24	A	26	GLY	0	-0.014	-0.003	27.450	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.041	-0.009	22.507	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.928	-0.965	24.345	-0.153	-0.153	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.050	-0.031	23.954	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	30	PRO	0	0.009	0.005	23.444	0.014	0.014	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.033	0.007	26.520	0.005	0.005	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.955	-0.984	29.183	-0.077	-0.077	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.019	0.013	25.661	0.004	0.004	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.839	-0.914	27.318	-0.107	-0.107	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.058	-0.026	29.782	0.007	0.007	0.000	0.000	0.000	0.000
34	A	36	ALA	0	-0.039	-0.008	24.651	0.008	0.008	0.000	0.000	0.000	0.000
35	A	37	PRO	0	0.000	0.007	23.544	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	38	HIS	1	0.820	0.843	16.073	0.188	0.188	0.000	0.000	0.000	0.000
37	A	39	THR	0	0.003	0.000	20.942	0.012	0.012	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.822	-0.895	16.030	-0.310	-0.310	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.006	0.011	18.908	0.025	0.025	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.049	-0.030	16.942	-0.043	-0.043	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.021	0.016	16.375	0.035	0.035	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.886	-0.941	17.090	-0.384	-0.384	0.000	0.000	0.000	0.000
43	A	45	GLY	0	-0.047	-0.025	14.762	-0.054	-0.054	0.000	0.000	0.000	0.000
44	A	46	GLY	0	-0.045	-0.026	13.271	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.061	-0.026	10.707	-0.021	-0.021	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.888	0.937	12.811	0.454	0.454	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.004	0.020	14.180	-0.050	-0.050	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.003	-0.017	15.780	0.030	0.030	0.000	0.000	0.000	0.000
49	A	51	TRP	0	0.005	-0.004	17.507	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.798	-0.877	17.777	-0.157	-0.157	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.016	-0.012	20.970	0.000	0.000	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.066	0.028	23.326	0.004	0.004	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.898	-0.935	24.863	-0.052	-0.052	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.026	-0.022	20.808	0.014	0.014	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.038	0.039	19.448	0.010	0.010	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.862	0.914	21.332	0.052	0.052	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.125	-0.064	22.531	0.014	0.014	0.000	0.000	0.000	0.000
58	A	60	TYR	0	-0.018	-0.024	16.350	0.014	0.014	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.852	-0.917	18.814	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	62	PRO	0	0.003	-0.003	20.907	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.954	-0.978	22.597	0.025	0.025	0.000	0.000	0.000	0.000
62	A	64	TRP	0	-0.029	-0.003	20.875	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	65	GLN	0	-0.020	-0.017	23.794	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	66	ALA	0	0.055	0.042	25.339	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	67	PRO	0	-0.087	-0.060	24.759	0.003	0.003	0.000	0.000	0.000	0.000
66	A	68	THR	0	0.008	0.007	25.177	0.002	0.002	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.010	0.007	25.721	0.006	0.006	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.070	0.025	22.361	0.010	0.010	0.000	0.000	0.000	0.000
69	A	71	HIS	0	0.019	0.031	17.180	0.002	0.002	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.979	0.986	20.126	0.126	0.126	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.061	-0.045	14.747	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.055	0.043	12.967	0.029	0.029	0.000	0.000	0.000	0.000
73	A	75	ILE	0	-0.028	-0.007	8.399	-0.049	-0.049	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.051	0.035	8.265	0.075	0.075	0.000	0.000	0.000	0.000
75	A	77	PHE	0	-0.014	-0.021	2.696	-0.958	-0.267	0.231	-0.220	-0.701	0.000
76	A	78	GLU	-1	-0.867	-0.915	4.368	-0.448	-0.218	-0.001	-0.063	-0.166	0.000
77	A	79	PHE	0	-0.030	-0.038	2.412	-4.343	-1.536	4.995	-3.393	-4.409	-0.035
78	A	80	PRO	0	-0.012	-0.007	3.479	-1.010	-0.759	0.010	-0.066	-0.196	0.000
79	A	81	ASP	-1	-0.795	-0.869	6.113	1.304	1.304	0.000	0.000	0.000	0.000
80	A	82	THR	0	0.054	0.002	8.259	0.179	0.179	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.029	-0.006	10.337	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	84	SER	0	-0.029	-0.059	5.533	0.180	0.180	0.000	0.000	0.000	0.000
83	A	85	VAL	0	-0.026	0.004	6.739	0.140	0.140	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.787	-0.859	7.858	0.433	0.433	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.838	0.914	8.601	-1.062	-1.062	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.904	0.942	4.339	-2.042	-1.950	-0.001	-0.010	-0.081	0.000
87	A	89	TYR	0	0.047	0.016	7.489	-0.214	-0.214	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.034	-0.019	10.300	-0.095	-0.095	0.000	0.000	0.000	0.000
89	A	91	GLU	-1	-0.800	-0.867	8.386	1.379	1.379	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.021	-0.010	7.707	-0.096	-0.096	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.014	0.006	11.620	-0.077	-0.077	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.995	-0.992	14.733	0.383	0.383	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.048	-0.020	13.904	-0.030	-0.030	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.049	-0.031	15.887	-0.040	-0.040	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.073	-0.030	12.800	-0.053	-0.053	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.866	-0.942	15.869	0.043	0.043	0.000	0.000	0.000	0.000
97	A	99	GLY	0	-0.002	-0.007	14.902	0.001	0.001	0.000	0.000	0.000	0.000
98	A	100	HIS	0	-0.063	-0.035	15.256	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	101	LEU	0	0.021	0.003	15.544	0.002	0.002	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.918	0.965	14.735	-0.152	-0.152	0.000	0.000	0.000	0.000
101	A	103	PRO	0	0.014	-0.008	12.136	-0.032	-0.032	0.000	0.000	0.000	0.000
102	A	104	TRP	0	-0.067	-0.017	14.362	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	105	ASN	0	0.003	-0.003	15.193	0.048	0.048	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.029	0.030	15.927	-0.019	-0.019	0.000	0.000	0.000	0.000
105	A	107	VAL	0	0.004	-0.016	17.636	0.002	0.002	0.000	0.000	0.000	0.000
106	A	108	TRP	0	-0.006	0.006	13.972	0.009	0.009	0.000	0.000	0.000	0.000
107	A	109	GLY	0	-0.009	0.003	17.206	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	110	GLN	0	0.025	0.000	11.795	0.020	0.020	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.758	0.844	11.420	-0.429	-0.429	0.000	0.000	0.000	0.000
110	A	112	TYR	0	-0.054	-0.061	10.850	0.024	0.024	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.018	0.009	10.302	0.045	0.045	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.008	0.015	10.671	-0.043	-0.043	0.000	0.000	0.000	0.000
113	A	115	VAL	0	0.010	0.012	9.974	0.051	0.051	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.872	0.943	12.734	-0.040	-0.040	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.851	-0.900	12.797	-0.170	-0.170	0.000	0.000	0.000	0.000
116	A	118	PRO	0	-0.011	-0.035	14.189	0.018	0.018	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.972	-0.980	17.153	-0.122	-0.122	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.018	0.004	18.113	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.119	-0.075	14.883	0.008	0.008	0.000	0.000	0.000	0.000
120	A	122	VAL	0	0.015	0.013	13.659	0.020	0.020	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.003	-0.007	7.876	-0.083	-0.083	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.805	-0.883	9.490	-0.058	-0.058	0.000	0.000	0.000	0.000
123	A	125	LEU	0	-0.053	-0.031	5.420	-0.138	-0.138	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.014	0.001	6.152	0.080	0.080	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.047	0.015	6.656	0.058	0.058	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.010	0.007	8.833	-0.042	-0.042	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.009	-0.008	11.983	0.091	0.091	0.000	0.000	0.000	0.000
128	A	130	PRO	0	-0.030	-0.004	14.960	-0.049	-0.049	0.000	0.000	0.000	0.000

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