FMO DATABASE

FMODB ID: LZQ19

Calculation Name: 1KAG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KAG

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6D7

Base Structure: X-ray

Registration Date: 2023-06-22

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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1813121.051139
FMO2-HF: Nuclear repulsion	1746414.317076
FMO2-HF: Total energy	-66706.734063
FMO2-MP2: Total energy	-66903.454233

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:GLU)

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

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.
62.021	67.379	2.461	-3.469	-4.352	0.025

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.921 / q_NPA : -0.976

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	A	5	ARG	1	0.896	0.965	2.041	-60.455	-55.243	2.461	-3.432	-4.242	0.025
4	A	6	ASN	0	-0.006	-0.014	3.854	-3.665	-3.609	0.001	-0.028	-0.030	0.000
5	A	7	ILE	0	0.022	0.025	5.552	1.818	1.818	0.000	0.000	0.000	0.000
6	A	8	PHE	0	-0.043	-0.018	8.764	-2.170	-2.170	0.000	0.000	0.000	0.000
7	A	9	LEU	0	0.000	0.018	12.429	-0.338	-0.338	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.045	0.030	15.031	-1.124	-1.124	0.000	0.000	0.000	0.000
9	A	11	GLY	0	0.069	0.022	17.998	0.080	0.080	0.000	0.000	0.000	0.000
10	A	12	PRO	0	-0.003	0.031	21.289	-0.090	-0.090	0.000	0.000	0.000	0.000
11	A	13	MET	0	0.003	0.004	23.633	0.513	0.513	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.055	0.006	25.939	-0.133	-0.133	0.000	0.000	0.000	0.000
13	A	15	ALA	0	0.039	0.031	21.631	-0.042	-0.042	0.000	0.000	0.000	0.000
14	A	16	GLY	0	-0.007	-0.022	20.488	0.604	0.604	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.834	0.933	17.782	-13.986	-13.986	0.000	0.000	0.000	0.000
16	A	18	SER	0	0.023	-0.008	17.253	0.651	0.651	0.000	0.000	0.000	0.000
17	A	19	THR	0	-0.080	-0.033	18.966	-0.111	-0.111	0.000	0.000	0.000	0.000
18	A	20	ILE	0	0.027	0.012	14.068	0.119	0.119	0.000	0.000	0.000	0.000
19	A	21	GLY	0	0.072	0.029	13.215	0.839	0.839	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.838	0.896	13.035	-12.690	-12.690	0.000	0.000	0.000	0.000
21	A	23	GLN	0	-0.056	-0.031	14.179	-0.062	-0.062	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.050	0.029	8.575	0.175	0.175	0.000	0.000	0.000	0.000
23	A	25	ALA	0	-0.003	0.007	9.301	1.175	1.175	0.000	0.000	0.000	0.000
24	A	26	GLN	0	-0.031	-0.023	10.740	0.557	0.557	0.000	0.000	0.000	0.000
25	A	27	GLN	0	-0.055	-0.041	9.749	-0.852	-0.852	0.000	0.000	0.000	0.000
26	A	28	LEU	0	0.016	0.017	4.223	0.557	0.647	-0.001	-0.009	-0.080	0.000
27	A	29	ASN	0	-0.068	-0.015	7.054	0.380	0.380	0.000	0.000	0.000	0.000
28	A	30	MET	0	-0.037	-0.018	5.423	1.674	1.674	0.000	0.000	0.000	0.000
29	A	31	GLU	-1	-0.779	-0.861	9.950	17.694	17.694	0.000	0.000	0.000	0.000
30	A	32	PHE	0	0.008	-0.003	12.939	0.605	0.605	0.000	0.000	0.000	0.000
31	A	33	TYR	0	-0.045	-0.046	14.574	-1.182	-1.182	0.000	0.000	0.000	0.000
32	A	34	ASP	-1	-0.790	-0.888	16.938	13.983	13.983	0.000	0.000	0.000	0.000
33	A	35	SER	0	0.068	0.013	19.580	-0.181	-0.181	0.000	0.000	0.000	0.000
34	A	36	ASP	-1	-0.874	-0.921	21.210	11.998	11.998	0.000	0.000	0.000	0.000
35	A	37	GLN	0	-0.028	-0.030	21.347	-0.743	-0.743	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.787	-0.853	21.621	12.659	12.659	0.000	0.000	0.000	0.000
37	A	39	ILE	0	0.017	0.008	23.788	-0.295	-0.295	0.000	0.000	0.000	0.000
38	A	40	GLU	-1	-0.699	-0.807	26.807	10.150	10.150	0.000	0.000	0.000	0.000
39	A	41	LYS	1	0.778	0.864	24.245	-12.608	-12.608	0.000	0.000	0.000	0.000
40	A	42	ARG	1	0.702	0.804	22.938	-12.642	-12.642	0.000	0.000	0.000	0.000
41	A	43	THR	0	-0.050	-0.039	29.064	-0.284	-0.284	0.000	0.000	0.000	0.000
42	A	44	GLY	0	-0.031	0.002	31.713	-0.302	-0.302	0.000	0.000	0.000	0.000
43	A	45	ALA	0	-0.024	-0.006	32.853	-0.281	-0.281	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.843	-0.915	32.129	9.621	9.621	0.000	0.000	0.000	0.000
45	A	47	VAL	0	0.034	0.002	27.788	-0.116	-0.116	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.037	0.026	30.865	0.005	0.005	0.000	0.000	0.000	0.000
47	A	49	TRP	0	0.011	0.006	33.615	-0.125	-0.125	0.000	0.000	0.000	0.000
48	A	50	VAL	0	0.000	-0.011	31.512	-0.138	-0.138	0.000	0.000	0.000	0.000
49	A	51	PHE	0	-0.046	-0.024	32.187	-0.031	-0.031	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.913	-0.961	34.005	8.213	8.213	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.100	-0.046	37.423	-0.237	-0.237	0.000	0.000	0.000	0.000
52	A	54	GLU	-1	-0.834	-0.867	33.163	9.330	9.330	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.029	0.026	36.770	-0.035	-0.035	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.794	-0.891	31.749	10.312	10.312	0.000	0.000	0.000	0.000
55	A	57	GLU	-1	-0.965	-0.982	32.659	8.865	8.865	0.000	0.000	0.000	0.000
56	A	58	GLY	0	0.059	0.034	32.825	0.267	0.267	0.000	0.000	0.000	0.000
57	A	59	PHE	0	0.009	0.003	27.569	0.400	0.400	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.732	0.813	27.573	-10.259	-10.259	0.000	0.000	0.000	0.000
59	A	61	ASP	-1	-0.851	-0.913	27.543	11.234	11.234	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.854	0.881	27.540	-9.427	-9.427	0.000	0.000	0.000	0.000
61	A	63	GLU	-1	-0.782	-0.898	23.891	12.759	12.759	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.848	-0.886	23.324	12.998	12.998	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.744	0.861	22.792	-10.947	-10.947	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.013	0.008	21.613	0.567	0.567	0.000	0.000	0.000	0.000
65	A	67	ILE	0	0.012	-0.007	17.864	0.789	0.789	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.054	-0.014	18.014	1.376	1.376	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.790	-0.866	18.040	14.094	14.094	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.046	-0.029	16.552	0.796	0.796	0.000	0.000	0.000	0.000
69	A	71	THR	0	-0.055	-0.047	13.688	1.232	1.232	0.000	0.000	0.000	0.000
70	A	72	GLU	-1	-0.819	-0.891	13.163	18.282	18.282	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.771	0.905	13.463	-18.378	-18.378	0.000	0.000	0.000	0.000
72	A	74	GLN	0	0.005	0.001	9.453	2.680	2.680	0.000	0.000	0.000	0.000
73	A	75	GLY	0	0.013	0.006	7.096	-1.170	-1.170	0.000	0.000	0.000	0.000
74	A	76	ILE	0	-0.023	-0.015	8.148	-2.316	-2.316	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.002	-0.001	8.945	2.028	2.028	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.015	-0.001	11.373	-1.693	-1.693	0.000	0.000	0.000	0.000
77	A	79	ALA	0	-0.019	-0.008	14.382	0.343	0.343	0.000	0.000	0.000	0.000
78	A	80	THR	0	0.034	0.008	16.812	-0.226	-0.226	0.000	0.000	0.000	0.000
79	A	81	GLY	0	0.099	0.057	19.313	-0.383	-0.383	0.000	0.000	0.000	0.000
80	A	82	GLY	0	-0.051	-0.020	22.783	0.310	0.310	0.000	0.000	0.000	0.000
81	A	83	GLY	0	0.007	0.006	24.838	-0.239	-0.239	0.000	0.000	0.000	0.000
82	A	84	SER	0	0.001	-0.007	21.584	0.176	0.176	0.000	0.000	0.000	0.000
83	A	85	VAL	0	0.024	0.008	20.536	0.025	0.025	0.000	0.000	0.000	0.000
84	A	86	LYS	1	0.855	0.930	23.028	-10.439	-10.439	0.000	0.000	0.000	0.000
85	A	87	SER	0	-0.076	-0.048	24.324	-0.226	-0.226	0.000	0.000	0.000	0.000
86	A	88	ARG	1	0.933	0.934	23.486	-11.139	-11.139	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.818	-0.880	22.174	13.058	13.058	0.000	0.000	0.000	0.000
88	A	90	THR	0	0.002	-0.011	20.173	0.863	0.863	0.000	0.000	0.000	0.000
89	A	91	ARG	1	0.853	0.913	18.607	-12.531	-12.531	0.000	0.000	0.000	0.000
90	A	92	ASN	0	0.040	0.028	17.290	1.196	1.196	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.829	0.914	15.901	-13.328	-13.328	0.000	0.000	0.000	0.000
92	A	94	LEU	0	-0.025	-0.017	14.400	1.439	1.439	0.000	0.000	0.000	0.000
93	A	95	SER	0	0.062	0.013	12.591	1.787	1.787	0.000	0.000	0.000	0.000
94	A	96	ALA	0	-0.015	0.000	11.383	2.447	2.447	0.000	0.000	0.000	0.000
95	A	97	ARG	1	0.782	0.882	10.248	-16.396	-16.396	0.000	0.000	0.000	0.000
96	A	98	GLY	0	-0.005	-0.014	8.056	2.137	2.137	0.000	0.000	0.000	0.000
97	A	99	VAL	0	-0.009	-0.004	5.693	-0.543	-0.543	0.000	0.000	0.000	0.000
98	A	100	VAL	0	-0.022	-0.003	8.852	-1.859	-1.859	0.000	0.000	0.000	0.000
99	A	101	VAL	0	-0.005	-0.011	10.459	-0.265	-0.265	0.000	0.000	0.000	0.000
100	A	102	TYR	0	-0.009	-0.016	13.203	-1.120	-1.120	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.061	-0.033	15.441	-0.125	-0.125	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.863	-0.937	18.801	12.464	12.464	0.000	0.000	0.000	0.000
103	A	105	THR	0	-0.046	-0.057	21.999	-0.091	-0.091	0.000	0.000	0.000	0.000
104	A	106	THR	0	0.002	-0.021	25.048	-0.114	-0.114	0.000	0.000	0.000	0.000
105	A	107	ILE	0	0.037	0.014	28.713	0.029	0.029	0.000	0.000	0.000	0.000
106	A	108	GLU	-1	-0.796	-0.891	30.341	9.879	9.879	0.000	0.000	0.000	0.000
107	A	109	LYS	1	0.779	0.878	26.098	-10.614	-10.614	0.000	0.000	0.000	0.000
108	A	110	GLN	0	-0.018	-0.012	27.821	-0.092	-0.092	0.000	0.000	0.000	0.000
109	A	111	LEU	0	-0.014	0.005	29.749	-0.129	-0.129	0.000	0.000	0.000	0.000
110	A	112	ALA	0	-0.033	-0.013	29.594	-0.259	-0.259	0.000	0.000	0.000	0.000
111	A	113	ARG	1	0.943	0.961	29.664	-9.122	-9.122	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.040	-0.050	29.247	-0.136	-0.136	0.000	0.000	0.000	0.000
113	A	115	GLN	0	0.096	0.060	28.256	0.493	0.493	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.719	0.846	23.491	-11.532	-11.532	0.000	0.000	0.000	0.000
115	A	117	ASP	-1	-0.711	-0.825	25.419	10.427	10.427	0.000	0.000	0.000	0.000
116	A	118	LYS	1	0.795	0.879	24.872	-10.340	-10.340	0.000	0.000	0.000	0.000
117	A	119	LYS	1	0.827	0.943	23.250	-10.907	-10.907	0.000	0.000	0.000	0.000
118	A	120	ARG	1	0.745	0.836	24.553	-10.204	-10.204	0.000	0.000	0.000	0.000
119	A	121	PRO	0	0.027	0.018	24.932	-0.306	-0.306	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.049	-0.026	27.423	0.285	0.285	0.000	0.000	0.000	0.000
121	A	123	LEU	0	-0.018	0.000	28.256	-0.186	-0.186	0.000	0.000	0.000	0.000
122	A	124	HIS	0	0.027	0.014	30.645	-0.090	-0.090	0.000	0.000	0.000	0.000
123	A	125	VAL	0	0.000	0.003	33.061	0.218	0.218	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.905	-0.952	35.314	8.034	8.034	0.000	0.000	0.000	0.000
125	A	127	THR	0	-0.045	-0.025	33.363	0.213	0.213	0.000	0.000	0.000	0.000
126	A	128	PRO	0	0.010	0.008	34.594	-0.258	-0.258	0.000	0.000	0.000	0.000
127	A	129	PRO	0	0.035	0.004	37.434	0.071	0.071	0.000	0.000	0.000	0.000
128	A	130	ARG	1	0.864	0.911	35.897	-8.280	-8.280	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.837	-0.922	36.615	7.804	7.804	0.000	0.000	0.000	0.000
130	A	132	VAL	0	-0.012	0.000	35.546	0.127	0.127	0.000	0.000	0.000	0.000
131	A	133	LEU	0	0.001	0.003	31.697	0.267	0.267	0.000	0.000	0.000	0.000
132	A	134	GLU	-1	-0.804	-0.898	32.294	8.786	8.786	0.000	0.000	0.000	0.000
133	A	135	ALA	0	-0.013	0.006	33.749	0.173	0.173	0.000	0.000	0.000	0.000
134	A	136	LEU	0	-0.026	-0.017	30.556	0.209	0.209	0.000	0.000	0.000	0.000
135	A	137	ALA	0	0.008	0.004	28.928	0.342	0.342	0.000	0.000	0.000	0.000
136	A	138	ASN	0	-0.048	-0.040	29.287	0.356	0.356	0.000	0.000	0.000	0.000
137	A	139	GLU	-1	-0.816	-0.873	29.844	10.308	10.308	0.000	0.000	0.000	0.000
138	A	140	ARG	1	0.812	0.878	25.905	-10.644	-10.644	0.000	0.000	0.000	0.000
139	A	141	ASN	0	-0.048	-0.018	25.038	0.309	0.309	0.000	0.000	0.000	0.000
140	A	142	PRO	0	0.071	0.035	24.071	0.591	0.591	0.000	0.000	0.000	0.000
141	A	143	LEU	0	-0.047	-0.022	24.055	0.455	0.455	0.000	0.000	0.000	0.000
142	A	144	TYR	0	-0.043	-0.037	20.409	0.484	0.484	0.000	0.000	0.000	0.000
143	A	145	GLU	-1	-0.852	-0.938	19.307	13.703	13.703	0.000	0.000	0.000	0.000
144	A	146	GLU	-1	-0.902	-0.925	19.932	14.349	14.349	0.000	0.000	0.000	0.000
145	A	147	ILE	0	-0.055	-0.023	16.661	0.408	0.408	0.000	0.000	0.000	0.000
146	A	148	ALA	0	-0.033	-0.014	15.525	1.347	1.347	0.000	0.000	0.000	0.000
147	A	149	ASP	-1	-0.841	-0.900	10.844	28.522	28.522	0.000	0.000	0.000	0.000
148	A	150	VAL	0	-0.037	-0.024	10.337	0.006	0.006	0.000	0.000	0.000	0.000
149	A	151	THR	0	0.030	0.012	13.517	-0.261	-0.261	0.000	0.000	0.000	0.000
150	A	152	ILE	0	-0.016	0.000	13.760	-0.187	-0.187	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.875	0.935	17.937	-12.262	-12.262	0.000	0.000	0.000	0.000
152	A	154	THR	0	0.014	0.000	18.330	-0.137	-0.137	0.000	0.000	0.000	0.000
153	A	155	ASP	-1	-0.776	-0.859	20.371	12.539	12.539	0.000	0.000	0.000	0.000
154	A	156	ASP	-1	-0.832	-0.882	22.898	10.600	10.600	0.000	0.000	0.000	0.000
155	A	157	GLN	0	0.018	0.008	18.947	-0.323	-0.323	0.000	0.000	0.000	0.000
156	A	158	SER	0	-0.033	-0.013	20.366	0.112	0.112	0.000	0.000	0.000	0.000
157	A	159	ALA	0	0.064	0.015	17.633	0.370	0.370	0.000	0.000	0.000	0.000
158	A	160	LYS	1	0.994	1.005	15.639	-12.364	-12.364	0.000	0.000	0.000	0.000
159	A	161	VAL	0	-0.022	0.011	15.160	0.664	0.664	0.000	0.000	0.000	0.000
160	A	162	VAL	0	0.027	0.020	14.939	0.533	0.533	0.000	0.000	0.000	0.000
161	A	163	ALA	0	0.006	0.001	11.777	0.850	0.850	0.000	0.000	0.000	0.000
162	A	164	ASN	0	-0.006	-0.014	10.696	1.850	1.850	0.000	0.000	0.000	0.000
163	A	165	GLN	0	0.010	0.006	11.395	0.842	0.842	0.000	0.000	0.000	0.000
164	A	166	ILE	0	0.012	0.001	9.023	0.532	0.532	0.000	0.000	0.000	0.000
165	A	167	ILE	0	-0.009	-0.004	6.229	1.640	1.640	0.000	0.000	0.000	0.000
166	A	168	HIS	0	-0.046	-0.035	7.499	0.424	0.424	0.000	0.000	0.000	0.000
167	A	169	MET	0	-0.069	-0.032	10.101	0.140	0.140	0.000	0.000	0.000	0.000
168	A	170	LEU	0	-0.049	-0.006	5.046	0.760	0.760	0.000	0.000	0.000	0.000
169	A	171	GLU	-1	-0.952	-0.967	5.903	30.411	30.411	0.000	0.000	0.000	0.000

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