FMO DATABASE

FMODB ID: 89RVY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1058575.3962
FMO2-HF: Nuclear repulsion	1009811.908185
FMO2-HF: Total energy	-48763.488015
FMO2-MP2: Total energy	-48909.21143

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.
-9.666	-3.229	5.735	-5.276	-6.895	-0.036

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 : 0.003 / q_NPA : 0.007

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	0.028	0.023	3.894	-1.092	1.171	-0.012	-1.283	-0.968	0.004
4	A	6	SER	0	-0.089	-0.061	6.397	0.081	0.081	0.000	0.000	0.000	0.000
5	A	7	LEU	0	0.036	0.006	8.437	0.179	0.179	0.000	0.000	0.000	0.000
6	A	8	PHE	0	0.006	0.013	10.588	-0.075	-0.075	0.000	0.000	0.000	0.000
7	A	9	ALA	0	0.014	0.004	13.286	0.038	0.038	0.000	0.000	0.000	0.000
8	A	10	VAL	0	-0.020	-0.017	15.694	0.010	0.010	0.000	0.000	0.000	0.000
9	A	11	VAL	0	0.021	0.022	19.199	0.006	0.006	0.000	0.000	0.000	0.000
10	A	12	VAL	0	-0.082	-0.048	21.510	0.001	0.001	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.878	-0.962	24.998	-0.080	-0.080	0.000	0.000	0.000	0.000
12	A	14	ASP	-1	-0.880	-0.936	28.229	-0.085	-0.085	0.000	0.000	0.000	0.000
13	A	15	MET	0	0.018	0.031	22.826	-0.015	-0.015	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.040	0.024	27.399	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.878	0.920	30.302	0.089	0.089	0.000	0.000	0.000	0.000
16	A	18	SER	0	0.001	0.013	25.354	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	19	LEU	0	0.012	0.004	24.265	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.874	-0.916	27.411	-0.106	-0.106	0.000	0.000	0.000	0.000
19	A	21	PHE	0	-0.057	-0.030	26.390	0.003	0.003	0.000	0.000	0.000	0.000
20	A	22	TYR	0	0.048	0.007	23.005	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	23	ARG	1	0.813	0.879	26.730	0.132	0.132	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.796	0.897	28.810	0.116	0.116	0.000	0.000	0.000	0.000
23	A	25	LEU	0	-0.070	-0.023	26.556	0.004	0.004	0.000	0.000	0.000	0.000
24	A	26	GLY	0	-0.018	-0.003	27.482	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	27	VAL	0	-0.043	-0.016	22.274	-0.012	-0.012	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.933	-0.965	24.348	-0.167	-0.167	0.000	0.000	0.000	0.000
27	A	29	ILE	0	-0.015	-0.017	23.465	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	30	PRO	0	0.042	0.018	23.601	0.017	0.017	0.000	0.000	0.000	0.000
29	A	31	ALA	0	0.056	0.025	26.587	0.005	0.005	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.941	-0.973	28.857	-0.087	-0.087	0.000	0.000	0.000	0.000
31	A	33	ALA	0	0.013	0.005	25.155	0.006	0.006	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.829	-0.895	26.759	-0.122	-0.122	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.047	-0.023	29.276	0.007	0.007	0.000	0.000	0.000	0.000
34	A	36	ALA	0	-0.041	-0.007	24.548	0.009	0.009	0.000	0.000	0.000	0.000
35	A	37	PRO	0	-0.011	0.000	23.415	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	38	HIS	1	0.830	0.856	15.845	0.217	0.217	0.000	0.000	0.000	0.000
37	A	39	THR	0	-0.007	-0.013	20.602	0.011	0.011	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.827	-0.895	15.787	-0.352	-0.352	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.024	0.017	18.505	0.031	0.031	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.053	-0.024	16.958	-0.046	-0.046	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.018	0.014	16.165	0.039	0.039	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.893	-0.952	16.729	-0.429	-0.429	0.000	0.000	0.000	0.000
43	A	45	GLY	0	-0.042	-0.023	14.405	-0.061	-0.061	0.000	0.000	0.000	0.000
44	A	46	GLY	0	-0.042	-0.018	12.806	-0.105	-0.105	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.039	-0.016	10.254	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.873	0.927	12.520	0.516	0.516	0.000	0.000	0.000	0.000
47	A	49	LEU	0	0.007	0.027	14.027	-0.050	-0.050	0.000	0.000	0.000	0.000
48	A	50	ALA	0	0.003	-0.013	15.665	0.024	0.024	0.000	0.000	0.000	0.000
49	A	51	TRP	0	-0.006	-0.012	17.487	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.800	-0.879	17.679	-0.179	-0.179	0.000	0.000	0.000	0.000
51	A	53	THR	0	0.000	-0.007	20.898	0.001	0.001	0.000	0.000	0.000	0.000
52	A	54	VAL	0	0.035	0.021	23.327	0.003	0.003	0.000	0.000	0.000	0.000
53	A	55	GLU	-1	-0.890	-0.938	24.877	-0.059	-0.059	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.015	-0.016	20.652	0.013	0.013	0.000	0.000	0.000	0.000
55	A	57	VAL	0	0.022	0.030	19.318	0.009	0.009	0.000	0.000	0.000	0.000
56	A	58	ARG	1	0.861	0.917	21.093	0.058	0.058	0.000	0.000	0.000	0.000
57	A	59	SER	0	-0.106	-0.058	21.934	0.016	0.016	0.000	0.000	0.000	0.000
58	A	60	TYR	0	-0.041	-0.032	16.173	0.016	0.016	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.835	-0.909	18.802	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	62	PRO	0	-0.009	-0.014	20.866	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.942	-0.969	23.163	0.021	0.021	0.000	0.000	0.000	0.000
62	A	64	TRP	0	-0.020	0.007	20.975	0.002	0.002	0.000	0.000	0.000	0.000
63	A	65	GLN	0	-0.055	-0.030	24.099	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	66	ALA	0	0.054	0.030	25.688	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	67	PRO	0	-0.063	-0.047	25.320	0.003	0.003	0.000	0.000	0.000	0.000
66	A	68	THR	0	-0.026	-0.006	25.318	0.002	0.002	0.000	0.000	0.000	0.000
67	A	69	GLY	0	-0.005	0.003	26.049	0.006	0.006	0.000	0.000	0.000	0.000
68	A	70	GLY	0	0.061	0.031	22.650	0.010	0.010	0.000	0.000	0.000	0.000
69	A	71	HIS	0	0.029	0.029	17.343	0.006	0.006	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.982	0.974	20.554	0.129	0.129	0.000	0.000	0.000	0.000
71	A	73	PHE	0	-0.032	-0.008	15.079	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	74	ALA	0	0.052	0.036	13.247	0.032	0.032	0.000	0.000	0.000	0.000
73	A	75	ILE	0	-0.023	-0.010	8.629	-0.051	-0.051	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.035	0.028	8.357	0.059	0.059	0.000	0.000	0.000	0.000
75	A	77	PHE	0	0.000	-0.018	2.981	-0.758	-0.272	0.076	-0.127	-0.435	0.000
76	A	78	GLU	-1	-0.802	-0.861	3.478	-0.952	-0.473	0.015	-0.191	-0.303	-0.001
77	A	79	PHE	0	-0.016	-0.028	2.475	-4.757	-1.919	5.634	-3.593	-4.879	-0.039
78	A	80	PRO	0	-0.025	-0.012	3.268	-1.110	-0.816	0.023	-0.076	-0.241	0.000
79	A	81	ASP	-1	-0.798	-0.872	5.851	1.339	1.339	0.000	0.000	0.000	0.000
80	A	82	THR	0	0.040	-0.001	7.992	0.166	0.166	0.000	0.000	0.000	0.000
81	A	83	ALA	0	-0.017	-0.004	10.464	-0.077	-0.077	0.000	0.000	0.000	0.000
82	A	84	SER	0	-0.042	-0.062	5.183	0.278	0.278	0.000	0.000	0.000	0.000
83	A	85	VAL	0	-0.035	0.008	6.539	0.151	0.151	0.000	0.000	0.000	0.000
84	A	86	ASP	-1	-0.774	-0.864	7.519	0.470	0.470	0.000	0.000	0.000	0.000
85	A	87	LYS	1	0.839	0.903	8.864	-1.101	-1.101	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.888	0.931	4.655	-2.208	-2.131	-0.001	-0.006	-0.069	0.000
87	A	89	TYR	0	0.056	0.019	7.620	-0.221	-0.221	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.037	-0.022	10.329	-0.101	-0.101	0.000	0.000	0.000	0.000
89	A	91	GLU	-1	-0.792	-0.864	8.882	1.402	1.402	0.000	0.000	0.000	0.000
90	A	92	LEU	0	-0.036	-0.001	7.919	-0.088	-0.088	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.019	0.012	12.082	-0.082	-0.082	0.000	0.000	0.000	0.000
92	A	94	ASP	-1	-0.988	-0.999	15.137	0.434	0.434	0.000	0.000	0.000	0.000
93	A	95	ALA	0	-0.040	-0.017	14.054	-0.035	-0.035	0.000	0.000	0.000	0.000
94	A	96	GLY	0	-0.036	-0.014	16.096	-0.041	-0.041	0.000	0.000	0.000	0.000
95	A	97	TYR	0	-0.049	-0.024	13.456	-0.056	-0.056	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.863	-0.945	15.850	0.037	0.037	0.000	0.000	0.000	0.000
97	A	99	GLY	0	0.016	-0.009	15.223	-0.009	-0.009	0.000	0.000	0.000	0.000
98	A	100	HIS	0	-0.058	-0.025	16.060	0.008	0.008	0.000	0.000	0.000	0.000
99	A	101	LEU	0	0.014	0.007	15.722	0.002	0.002	0.000	0.000	0.000	0.000
100	A	102	LYS	1	0.949	0.977	14.806	-0.152	-0.152	0.000	0.000	0.000	0.000
101	A	103	PRO	0	-0.005	-0.010	12.149	-0.034	-0.034	0.000	0.000	0.000	0.000
102	A	104	TRP	0	-0.065	-0.021	14.395	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	105	ASN	0	0.000	0.003	14.850	0.058	0.058	0.000	0.000	0.000	0.000
104	A	106	ALA	0	0.023	0.029	15.322	-0.019	-0.019	0.000	0.000	0.000	0.000
105	A	107	VAL	0	0.025	-0.014	17.123	0.002	0.002	0.000	0.000	0.000	0.000
106	A	108	TRP	0	-0.030	-0.005	13.610	0.016	0.016	0.000	0.000	0.000	0.000
107	A	109	GLY	0	0.014	0.019	16.994	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	110	GLN	0	0.018	-0.001	11.532	0.015	0.015	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.754	0.848	11.131	-0.431	-0.431	0.000	0.000	0.000	0.000
110	A	112	TYR	0	-0.038	-0.060	10.614	0.001	0.001	0.000	0.000	0.000	0.000
111	A	113	ALA	0	-0.004	0.000	10.422	0.050	0.050	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.021	0.003	10.710	-0.052	-0.052	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.038	-0.009	10.544	0.056	0.056	0.000	0.000	0.000	0.000
114	A	116	LYS	1	0.866	0.947	13.271	-0.036	-0.036	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.830	-0.894	13.328	-0.161	-0.161	0.000	0.000	0.000	0.000
116	A	118	PRO	0	-0.034	-0.041	14.737	0.018	0.018	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.952	-0.960	17.720	-0.120	-0.120	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.013	0.004	18.343	0.001	0.001	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.119	-0.078	15.518	0.004	0.004	0.000	0.000	0.000	0.000
120	A	122	VAL	0	0.008	0.004	14.041	0.011	0.011	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.026	-0.020	8.411	-0.084	-0.084	0.000	0.000	0.000	0.000
122	A	124	ASP	-1	-0.781	-0.866	9.659	-0.070	-0.070	0.000	0.000	0.000	0.000
123	A	125	LEU	0	-0.044	-0.030	5.823	-0.159	-0.159	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.000	-0.007	6.044	0.150	0.150	0.000	0.000	0.000	0.000
125	A	127	ALA	0	0.049	0.015	6.194	0.046	0.046	0.000	0.000	0.000	0.000
126	A	128	PRO	0	0.006	0.011	8.648	-0.066	-0.066	0.000	0.000	0.000	0.000
127	A	129	LEU	0	0.015	0.007	11.773	0.105	0.105	0.000	0.000	0.000	0.000
128	A	130	PRO	0	-0.080	-0.036	14.488	-0.061	-0.061	0.000	0.000	0.000	0.000

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