FMO DATABASE

FMODB ID: 1NVNZ

Calculation Name: 4G3K-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G3K

Chain ID: A

ChEMBL ID:

UniProt ID: O66591

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	155
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1480831.422202
FMO2-HF: Nuclear repulsion	1421370.813927
FMO2-HF: Total energy	-59460.608275
FMO2-MP2: Total energy	-59637.59149

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:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
-196.524	-193.403	22.947	-12.663	-13.405	0.144

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.758 / q_NPA : -0.884

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	4	LYS	1	0.855	0.902	1.798	-90.567	-90.010	16.181	-8.873	-7.864	0.088
4	A	5	VAL	0	0.044	0.030	1.969	-33.388	-31.388	6.755	-3.529	-5.227	0.055
5	A	6	GLH	0	-0.047	-0.054	3.978	-13.224	-12.660	0.011	-0.261	-0.314	0.001
6	A	7	ILE	0	-0.007	-0.003	5.917	-6.943	-6.943	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.855	-0.914	6.422	43.675	43.675	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.026	-0.033	7.564	-5.438	-5.438	0.000	0.000	0.000	0.000
9	A	10	LEU	0	-0.007	-0.010	9.864	-3.252	-3.252	0.000	0.000	0.000	0.000
10	A	11	TYR	0	0.016	0.029	11.327	-2.896	-2.896	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.821	-0.897	12.500	18.684	18.684	0.000	0.000	0.000	0.000
12	A	13	VAL	0	-0.031	-0.021	13.764	-1.774	-1.774	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.034	-0.030	15.432	-1.508	-1.508	0.000	0.000	0.000	0.000
14	A	15	LYS	1	0.853	0.930	15.971	-20.241	-20.241	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.016	-0.005	17.761	-0.888	-0.888	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.033	-0.016	18.736	-0.810	-0.810	0.000	0.000	0.000	0.000
17	A	18	SER	0	-0.033	-0.024	21.099	-0.569	-0.569	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.080	-0.037	23.279	-0.546	-0.546	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.036	-0.025	24.946	-0.697	-0.697	0.000	0.000	0.000	0.000
20	A	21	LEU	0	0.041	0.010	26.618	0.247	0.247	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.038	-0.017	28.284	0.170	0.170	0.000	0.000	0.000	0.000
22	A	23	LEU	0	0.040	0.019	23.815	0.497	0.497	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.849	-0.915	25.316	11.005	11.005	0.000	0.000	0.000	0.000
24	A	25	THR	0	-0.007	-0.005	26.768	0.058	0.058	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.042	-0.028	21.841	0.453	0.453	0.000	0.000	0.000	0.000
26	A	27	VAL	0	0.013	-0.013	20.871	0.760	0.760	0.000	0.000	0.000	0.000
27	A	28	PRO	0	0.020	0.013	20.187	0.744	0.744	0.000	0.000	0.000	0.000
28	A	29	TYR	0	-0.020	-0.007	19.732	0.742	0.742	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.045	0.027	15.949	1.086	1.086	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.000	-0.021	15.393	1.177	1.177	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.939	0.974	15.777	-15.308	-15.308	0.000	0.000	0.000	0.000
32	A	33	LEU	0	-0.001	0.003	13.057	0.625	0.625	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.014	0.000	10.870	1.684	1.684	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.838	0.908	10.996	-14.917	-14.917	0.000	0.000	0.000	0.000
35	A	36	LYS	1	0.874	0.931	12.273	-17.341	-17.341	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.003	0.024	8.007	0.312	0.312	0.000	0.000	0.000	0.000
37	A	38	MET	0	0.006	0.012	5.375	4.223	4.223	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.013	0.017	7.424	-0.403	-0.403	0.000	0.000	0.000	0.000
39	A	40	PHE	0	-0.020	-0.008	9.572	-1.229	-1.229	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-0.837	-0.921	12.173	14.770	14.770	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.759	0.856	15.900	-14.238	-14.238	0.000	0.000	0.000	0.000
42	A	43	LEU	0	-0.002	0.017	14.194	-0.401	-0.401	0.000	0.000	0.000	0.000
43	A	44	THR	0	-0.002	-0.032	18.545	-0.316	-0.316	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.021	0.013	21.416	0.343	0.343	0.000	0.000	0.000	0.000
45	A	46	THR	0	-0.009	-0.013	23.170	-0.452	-0.452	0.000	0.000	0.000	0.000
46	A	47	ILE	0	0.006	0.005	25.246	0.168	0.168	0.000	0.000	0.000	0.000
47	A	48	TYR	0	0.010	-0.001	28.606	-0.226	-0.226	0.000	0.000	0.000	0.000
48	A	49	ASP	-1	-0.724	-0.814	32.275	8.063	8.063	0.000	0.000	0.000	0.000
49	A	50	PRO	0	-0.079	-0.047	34.483	-0.088	-0.088	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.062	-0.049	36.430	-0.159	-0.159	0.000	0.000	0.000	0.000
51	A	52	THR	0	-0.050	-0.055	39.129	-0.156	-0.156	0.000	0.000	0.000	0.000
52	A	53	ASP	-1	-0.802	-0.865	34.825	8.595	8.595	0.000	0.000	0.000	0.000
53	A	54	GLN	0	0.000	0.016	35.937	0.165	0.165	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.038	-0.027	30.874	0.177	0.177	0.000	0.000	0.000	0.000
55	A	56	VAL	0	-0.020	-0.009	32.257	-0.186	-0.186	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.009	0.007	27.055	0.039	0.039	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.803	0.860	25.685	-10.737	-10.737	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.007	0.018	24.204	-0.127	-0.127	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.028	0.004	23.079	0.142	0.142	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.031	-0.007	17.651	-0.101	-0.101	0.000	0.000	0.000	0.000
61	A	62	SER	0	0.013	0.006	20.105	-0.378	-0.378	0.000	0.000	0.000	0.000
62	A	63	GLY	0	0.014	-0.008	20.095	0.759	0.759	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.953	0.985	22.374	-11.080	-11.080	0.000	0.000	0.000	0.000
64	A	65	PHE	0	0.035	0.013	22.259	0.493	0.493	0.000	0.000	0.000	0.000
65	A	66	PRO	0	-0.008	-0.005	26.167	-0.254	-0.254	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.962	0.967	29.319	-8.281	-8.281	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.884	-0.922	32.096	8.546	8.546	0.000	0.000	0.000	0.000
68	A	69	GLY	0	-0.025	0.001	29.438	-0.057	-0.057	0.000	0.000	0.000	0.000
69	A	70	PHE	0	0.007	0.008	28.157	0.392	0.392	0.000	0.000	0.000	0.000
70	A	71	LYS	1	0.809	0.894	19.239	-13.628	-13.628	0.000	0.000	0.000	0.000
71	A	72	LYS	1	0.920	0.945	24.660	-10.967	-10.967	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.064	0.031	23.231	-0.246	-0.246	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.767	-0.825	24.154	11.333	11.333	0.000	0.000	0.000	0.000
74	A	75	GLY	0	0.020	0.019	26.130	-0.232	-0.232	0.000	0.000	0.000	0.000
75	A	76	ILE	0	-0.028	-0.013	25.837	-0.189	-0.189	0.000	0.000	0.000	0.000
76	A	77	THR	0	-0.041	-0.029	23.917	-0.036	-0.036	0.000	0.000	0.000	0.000
77	A	78	GLY	0	0.055	0.024	27.251	0.069	0.069	0.000	0.000	0.000	0.000
78	A	79	LYS	1	0.839	0.899	29.589	-8.772	-8.772	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.049	0.031	27.497	-0.055	-0.055	0.000	0.000	0.000	0.000
80	A	81	TRP	0	0.047	0.016	24.945	0.029	0.029	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.818	0.892	26.494	-8.765	-8.765	0.000	0.000	0.000	0.000
82	A	83	HIS	0	0.023	0.020	28.422	-0.144	-0.144	0.000	0.000	0.000	0.000
83	A	84	GLY	0	-0.003	0.007	26.471	0.040	0.040	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.021	-0.010	23.314	0.424	0.424	0.000	0.000	0.000	0.000
85	A	86	PRO	0	-0.012	-0.019	18.845	-0.209	-0.209	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.010	0.009	20.901	-0.336	-0.336	0.000	0.000	0.000	0.000
87	A	88	VAL	0	0.000	-0.009	16.479	0.427	0.427	0.000	0.000	0.000	0.000
88	A	89	ILE	0	0.005	0.012	19.422	-0.515	-0.515	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.023	-0.014	17.284	0.389	0.389	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.826	-0.884	18.192	12.866	12.866	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.014	0.011	20.650	-0.351	-0.351	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.037	-0.039	22.842	-0.491	-0.491	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.005	0.002	25.163	-0.362	-0.362	0.000	0.000	0.000	0.000
94	A	110	LYS	1	0.832	0.897	14.419	-17.671	-17.671	0.000	0.000	0.000	0.000
95	A	111	LYS	1	0.893	0.942	16.236	-14.320	-14.320	0.000	0.000	0.000	0.000
96	A	112	ILE	0	-0.008	-0.012	15.951	0.842	0.842	0.000	0.000	0.000	0.000
97	A	113	ALA	0	0.009	0.024	14.849	-0.743	-0.743	0.000	0.000	0.000	0.000
98	A	114	PHE	0	-0.003	-0.011	16.528	0.329	0.329	0.000	0.000	0.000	0.000
99	A	115	ILE	0	0.006	0.003	12.909	-0.096	-0.096	0.000	0.000	0.000	0.000
100	A	116	ALA	0	0.029	0.017	17.341	-0.064	-0.064	0.000	0.000	0.000	0.000
101	A	117	VAL	0	0.006	-0.004	16.541	-0.096	-0.096	0.000	0.000	0.000	0.000
102	A	118	PRO	0	-0.011	0.006	19.854	-0.187	-0.187	0.000	0.000	0.000	0.000
103	A	119	ILE	0	-0.007	-0.004	22.026	0.328	0.328	0.000	0.000	0.000	0.000
104	A	120	LYS	1	0.896	0.929	23.411	-12.677	-12.677	0.000	0.000	0.000	0.000
105	A	121	SER	0	0.037	0.020	26.051	0.410	0.410	0.000	0.000	0.000	0.000
106	A	122	GLY	0	0.014	0.010	28.790	-0.298	-0.298	0.000	0.000	0.000	0.000
107	A	123	GLY	0	-0.013	0.004	30.283	-0.295	-0.295	0.000	0.000	0.000	0.000
108	A	124	LYS	1	0.963	0.971	30.014	-8.138	-8.138	0.000	0.000	0.000	0.000
109	A	125	VAL	0	0.013	0.008	26.872	0.301	0.301	0.000	0.000	0.000	0.000
110	A	126	ILE	0	-0.013	-0.007	27.986	-0.358	-0.358	0.000	0.000	0.000	0.000
111	A	127	GLY	0	0.028	0.004	27.012	-0.206	-0.206	0.000	0.000	0.000	0.000
112	A	128	VAL	0	-0.060	-0.002	22.352	0.167	0.167	0.000	0.000	0.000	0.000
113	A	129	LEU	0	0.028	0.023	16.787	-0.168	-0.168	0.000	0.000	0.000	0.000
114	A	130	SER	0	-0.005	-0.007	18.829	0.100	0.100	0.000	0.000	0.000	0.000
115	A	131	ALA	0	-0.027	-0.017	14.785	0.111	0.111	0.000	0.000	0.000	0.000
116	A	132	ASP	-1	-0.790	-0.864	16.234	13.483	13.483	0.000	0.000	0.000	0.000
117	A	133	LYS	1	0.856	0.931	8.025	-24.918	-24.918	0.000	0.000	0.000	0.000
118	A	134	GLU	-1	-0.781	-0.857	12.955	17.608	17.608	0.000	0.000	0.000	0.000
119	A	135	ILE	0	-0.026	-0.018	10.690	1.864	1.864	0.000	0.000	0.000	0.000
120	A	136	ASN	0	-0.017	-0.037	9.827	-1.446	-1.446	0.000	0.000	0.000	0.000
121	A	137	GLU	-1	-0.845	-0.932	11.775	18.145	18.145	0.000	0.000	0.000	0.000
122	A	138	LYS	1	0.921	0.980	8.449	-23.702	-23.702	0.000	0.000	0.000	0.000
123	A	139	ASP	-1	-0.847	-0.893	7.323	32.673	32.673	0.000	0.000	0.000	0.000
124	A	140	SER	0	0.043	0.017	7.596	-1.776	-1.776	0.000	0.000	0.000	0.000
125	A	141	LEU	0	0.025	0.002	8.942	0.833	0.833	0.000	0.000	0.000	0.000
126	A	142	ASP	-1	-0.820	-0.889	11.364	20.182	20.182	0.000	0.000	0.000	0.000
127	A	143	GLU	-1	-0.760	-0.817	5.749	28.956	28.956	0.000	0.000	0.000	0.000
128	A	144	TYR	0	-0.037	-0.041	5.706	0.194	0.194	0.000	0.000	0.000	0.000
129	A	145	THR	0	-0.005	-0.016	9.280	-1.272	-1.272	0.000	0.000	0.000	0.000
130	A	146	ARG	1	0.790	0.861	9.199	-24.791	-24.791	0.000	0.000	0.000	0.000
131	A	147	PHE	0	0.039	0.014	8.600	-0.836	-0.836	0.000	0.000	0.000	0.000
132	A	148	LEU	0	0.013	-0.002	10.709	-0.856	-0.856	0.000	0.000	0.000	0.000
133	A	149	SER	0	-0.004	-0.022	13.322	-1.448	-1.448	0.000	0.000	0.000	0.000
134	A	150	MET	0	-0.028	0.010	11.448	-0.705	-0.705	0.000	0.000	0.000	0.000
135	A	151	ILE	0	0.011	0.007	12.498	-0.902	-0.902	0.000	0.000	0.000	0.000
136	A	152	ALA	0	0.010	0.005	15.991	-0.887	-0.887	0.000	0.000	0.000	0.000
137	A	153	THR	0	-0.020	-0.018	18.594	-1.003	-1.003	0.000	0.000	0.000	0.000
138	A	154	LEU	0	-0.035	-0.018	16.181	-0.660	-0.660	0.000	0.000	0.000	0.000
139	A	155	ILE	0	0.038	0.013	19.164	-0.643	-0.643	0.000	0.000	0.000	0.000
140	A	156	ALA	0	0.010	0.009	21.896	-0.667	-0.667	0.000	0.000	0.000	0.000
141	A	157	ASN	0	-0.014	0.010	22.481	-1.069	-1.069	0.000	0.000	0.000	0.000
142	A	158	SER	0	0.057	0.028	24.008	-0.299	-0.299	0.000	0.000	0.000	0.000
143	A	159	PHE	0	0.031	0.020	25.813	-0.528	-0.528	0.000	0.000	0.000	0.000
144	A	160	SER	0	-0.051	-0.051	27.848	-0.561	-0.561	0.000	0.000	0.000	0.000
145	A	161	LEU	0	-0.019	-0.006	28.591	-0.401	-0.401	0.000	0.000	0.000	0.000
146	A	162	GLU	-1	-0.762	-0.863	29.914	9.643	9.643	0.000	0.000	0.000	0.000
147	A	163	ARG	1	0.783	0.855	30.875	-10.007	-10.007	0.000	0.000	0.000	0.000
148	A	164	LYS	1	0.908	0.975	32.394	-9.725	-9.725	0.000	0.000	0.000	0.000
149	A	165	VAL	0	0.093	0.050	33.950	-0.271	-0.271	0.000	0.000	0.000	0.000
150	A	166	GLN	0	-0.030	-0.008	35.833	-0.108	-0.108	0.000	0.000	0.000	0.000
151	A	167	ALA	0	-0.043	-0.023	37.640	-0.257	-0.257	0.000	0.000	0.000	0.000
152	A	168	GLU	-1	-0.900	-0.961	37.916	8.338	8.338	0.000	0.000	0.000	0.000
153	A	169	ARG	1	0.927	0.965	38.737	-8.139	-8.139	0.000	0.000	0.000	0.000
154	A	170	LYS	1	0.896	0.951	41.742	-7.544	-7.544	0.000	0.000	0.000	0.000
155	A	171	SER	0	-0.019	0.012	44.329	-0.190	-0.190	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)