FMO DATABASE

FMODB ID: 2NVKR

Calculation Name: 4MQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4MQ3

Chain ID: A

ChEMBL ID:

UniProt ID: P16088

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	129
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1118104.287239
FMO2-HF: Nuclear repulsion	1067283.371697
FMO2-HF: Total energy	-50820.915542
FMO2-MP2: Total energy	-50967.699809

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:60:MET)

Summations of interaction energy for fragment #1(A:60:MET)

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.
-17.297	-17.12	18.542	-8.641	-10.076	-0.075

Interaction energy analysis for fragmet #1(A:60:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.050 / q_NPA : -0.038

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	62	ILE	0	-0.003	0.016	2.306	-1.629	1.131	3.026	-1.766	-4.019	-0.001
4	A	63	TRP	0	0.019	-0.001	4.874	0.052	0.221	-0.001	-0.015	-0.153	0.000
5	A	64	GLN	0	0.010	0.004	8.110	0.049	0.049	0.000	0.000	0.000	0.000
6	A	65	MET	0	-0.020	-0.020	10.988	-0.036	-0.036	0.000	0.000	0.000	0.000
7	A	66	ASP	-1	-0.773	-0.878	14.529	-0.003	-0.003	0.000	0.000	0.000	0.000
8	A	67	CYS	0	-0.095	-0.037	18.233	-0.013	-0.013	0.000	0.000	0.000	0.000
9	A	68	THR	0	0.053	0.042	21.711	0.008	0.008	0.000	0.000	0.000	0.000
10	A	69	HIS	0	-0.043	-0.040	24.018	0.000	0.000	0.000	0.000	0.000	0.000
11	A	70	PHE	0	0.016	-0.008	27.681	0.003	0.003	0.000	0.000	0.000	0.000
12	A	71	ASP	-1	-0.857	-0.919	29.629	-0.013	-0.013	0.000	0.000	0.000	0.000
13	A	72	GLY	0	-0.009	0.000	32.897	0.000	0.000	0.000	0.000	0.000	0.000
14	A	73	LYS	1	0.804	0.900	30.116	0.017	0.017	0.000	0.000	0.000	0.000
15	A	74	ILE	0	0.016	0.010	25.275	0.002	0.002	0.000	0.000	0.000	0.000
16	A	75	ILE	0	0.003	0.003	22.076	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	76	LEU	0	0.013	0.026	18.094	0.003	0.003	0.000	0.000	0.000	0.000
18	A	77	VAL	0	-0.007	-0.019	16.830	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	78	GLY	0	0.017	-0.006	13.742	0.001	0.001	0.000	0.000	0.000	0.000
20	A	79	ILE	0	-0.010	0.005	9.731	0.005	0.005	0.000	0.000	0.000	0.000
21	A	80	HIS	0	0.000	0.020	3.651	0.749	1.038	-0.001	-0.125	-0.163	0.000
22	A	81	VAL	0	0.001	-0.016	5.143	-0.067	-0.067	0.000	0.000	0.000	0.000
23	A	82	GLU	-1	-0.822	-0.890	1.970	-16.886	-20.573	15.519	-6.434	-5.398	-0.075
24	A	83	SER	0	-0.057	-0.049	4.863	0.020	0.093	-0.001	-0.005	-0.066	0.000
25	A	84	GLY	0	-0.004	0.003	7.997	0.141	0.141	0.000	0.000	0.000	0.000
26	A	85	TYR	0	-0.049	-0.009	10.044	0.064	0.064	0.000	0.000	0.000	0.000
27	A	86	ILE	0	0.003	0.001	11.582	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	87	TRP	0	0.014	0.007	14.407	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	88	ALA	0	0.002	-0.016	16.030	0.011	0.011	0.000	0.000	0.000	0.000
30	A	89	GLN	0	-0.017	-0.003	19.233	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	90	ILE	0	0.028	0.021	22.217	0.002	0.002	0.000	0.000	0.000	0.000
32	A	91	ILE	0	-0.049	-0.025	23.418	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	92	SER	0	-0.004	-0.020	26.405	0.002	0.002	0.000	0.000	0.000	0.000
34	A	93	GLN	0	0.019	0.002	28.863	0.004	0.004	0.000	0.000	0.000	0.000
35	A	94	GLU	-1	-0.812	-0.893	25.801	-0.032	-0.032	0.000	0.000	0.000	0.000
36	A	95	THR	0	-0.001	0.006	27.132	0.001	0.001	0.000	0.000	0.000	0.000
37	A	96	ALA	0	0.066	0.043	24.858	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	97	ASP	-1	-0.811	-0.885	24.541	-0.048	-0.048	0.000	0.000	0.000	0.000
39	A	98	CYS	0	-0.064	-0.026	25.815	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	99	THR	0	0.018	0.004	20.708	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	100	VAL	0	0.007	-0.010	20.354	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	101	LYS	1	0.941	0.987	20.988	0.036	0.036	0.000	0.000	0.000	0.000
43	A	102	ALA	0	0.026	0.016	21.135	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	103	VAL	0	0.029	0.010	15.773	-0.008	-0.008	0.000	0.000	0.000	0.000
45	A	104	LEU	0	0.014	0.011	16.825	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	105	GLN	0	-0.026	-0.019	17.991	0.005	0.005	0.000	0.000	0.000	0.000
47	A	106	LEU	0	-0.014	0.009	12.222	0.007	0.007	0.000	0.000	0.000	0.000
48	A	107	LEU	0	0.012	-0.020	12.637	-0.010	-0.010	0.000	0.000	0.000	0.000
49	A	108	SER	0	-0.068	-0.038	14.133	0.021	0.021	0.000	0.000	0.000	0.000
50	A	109	ALA	0	-0.062	-0.023	14.936	0.026	0.026	0.000	0.000	0.000	0.000
51	A	110	HIS	0	-0.005	0.000	9.702	-0.020	-0.020	0.000	0.000	0.000	0.000
52	A	111	ASN	0	-0.015	0.000	6.164	-0.065	-0.065	0.000	0.000	0.000	0.000
53	A	112	VAL	0	-0.036	-0.018	6.766	-0.076	-0.076	0.000	0.000	0.000	0.000
54	A	113	THR	0	-0.037	-0.029	3.868	0.068	0.641	0.000	-0.296	-0.277	0.001
55	A	114	GLU	-1	-0.865	-0.945	5.915	-0.120	-0.120	0.000	0.000	0.000	0.000
56	A	115	LEU	0	0.006	0.010	7.484	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	116	GLN	0	-0.041	-0.026	6.947	0.121	0.121	0.000	0.000	0.000	0.000
58	A	117	THR	0	0.037	0.005	11.526	0.005	0.005	0.000	0.000	0.000	0.000
59	A	118	ASP	-1	-0.733	-0.856	15.340	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	119	ASN	0	-0.095	-0.042	18.107	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	120	GLY	0	0.069	0.040	20.191	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	121	PRO	0	0.023	-0.005	22.839	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	122	ASN	0	-0.015	-0.019	23.931	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	123	PHE	0	0.027	0.013	18.219	-0.006	-0.006	0.000	0.000	0.000	0.000
65	A	124	LYS	1	0.861	0.954	19.022	0.061	0.061	0.000	0.000	0.000	0.000
66	A	125	ASN	0	-0.019	-0.017	21.186	0.007	0.007	0.000	0.000	0.000	0.000
67	A	126	GLN	0	0.033	-0.009	22.454	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	127	LYS	1	0.802	0.901	23.739	0.043	0.043	0.000	0.000	0.000	0.000
69	A	128	MET	0	0.004	0.007	18.220	-0.007	-0.007	0.000	0.000	0.000	0.000
70	A	129	GLU	-1	-0.872	-0.922	18.864	-0.095	-0.095	0.000	0.000	0.000	0.000
71	A	130	GLY	0	0.018	0.015	19.110	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	131	VAL	0	-0.018	-0.013	18.200	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	132	LEU	0	0.006	-0.001	13.515	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	133	ASN	0	-0.051	-0.038	15.223	-0.024	-0.024	0.000	0.000	0.000	0.000
75	A	134	TYR	0	-0.050	-0.015	17.176	0.005	0.005	0.000	0.000	0.000	0.000
76	A	135	MET	0	-0.040	-0.021	14.773	0.021	0.021	0.000	0.000	0.000	0.000
77	A	136	GLY	0	-0.004	0.013	13.777	0.002	0.002	0.000	0.000	0.000	0.000
78	A	137	VAL	0	-0.063	-0.016	9.891	-0.056	-0.056	0.000	0.000	0.000	0.000
79	A	138	LYS	1	0.867	0.923	8.647	0.382	0.382	0.000	0.000	0.000	0.000
80	A	139	HIS	0	-0.021	-0.020	10.594	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	140	LYN	0	0.012	0.030	8.903	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	141	PHE	0	0.052	0.007	12.044	0.019	0.019	0.000	0.000	0.000	0.000
83	A	142	GLY	0	0.014	0.007	15.412	0.000	0.000	0.000	0.000	0.000	0.000
84	A	143	ILE	0	0.018	0.008	17.705	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	144	PRO	0	0.046	0.010	19.328	0.009	0.009	0.000	0.000	0.000	0.000
86	A	145	GLY	0	0.085	0.049	19.410	0.000	0.000	0.000	0.000	0.000	0.000
87	A	146	ASN	0	-0.092	-0.032	15.261	0.024	0.024	0.000	0.000	0.000	0.000
88	A	147	PRO	0	0.033	-0.014	14.585	0.012	0.012	0.000	0.000	0.000	0.000
89	A	148	GLN	0	-0.064	-0.016	10.796	0.017	0.017	0.000	0.000	0.000	0.000
90	A	149	SER	0	-0.016	-0.028	10.523	0.053	0.053	0.000	0.000	0.000	0.000
91	A	150	GLN	0	-0.047	-0.039	12.657	-0.030	-0.030	0.000	0.000	0.000	0.000
92	A	151	ALA	0	0.057	0.041	14.192	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	152	LEU	0	-0.015	0.010	9.225	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	153	VAL	0	-0.006	-0.004	13.802	-0.034	-0.034	0.000	0.000	0.000	0.000
95	A	154	GLU	-1	-0.890	-0.943	15.347	0.031	0.031	0.000	0.000	0.000	0.000
96	A	155	ASN	0	-0.025	-0.029	17.552	-0.021	-0.021	0.000	0.000	0.000	0.000
97	A	156	VAL	0	-0.002	0.019	14.587	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	157	ASN	0	0.002	-0.022	17.927	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	158	HIS	0	-0.024	-0.005	20.707	-0.010	-0.010	0.000	0.000	0.000	0.000
100	A	159	THR	0	-0.016	-0.025	20.543	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	160	LEU	0	-0.018	-0.007	20.194	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	161	LYS	1	0.876	0.927	22.409	0.008	0.008	0.000	0.000	0.000	0.000
103	A	162	VAL	0	0.048	0.033	25.707	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	163	TRP	0	-0.005	-0.007	22.517	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	164	ILE	0	-0.009	-0.003	24.696	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	165	GLN	0	-0.015	-0.018	27.968	0.001	0.001	0.000	0.000	0.000	0.000
107	A	166	LYS	1	0.777	0.894	29.410	0.010	0.010	0.000	0.000	0.000	0.000
108	A	167	PHE	0	0.002	-0.013	26.271	0.000	0.000	0.000	0.000	0.000	0.000
109	A	168	LEU	0	0.017	0.025	31.291	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	169	PRO	0	-0.048	-0.012	33.508	0.000	0.000	0.000	0.000	0.000	0.000
111	A	170	GLU	-1	-0.853	-0.912	33.144	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	171	THR	0	-0.059	-0.045	30.831	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	172	THR	0	0.021	0.005	34.286	0.000	0.000	0.000	0.000	0.000	0.000
114	A	173	SER	0	0.005	-0.004	32.083	0.000	0.000	0.000	0.000	0.000	0.000
115	A	174	LEU	0	0.059	0.031	29.132	0.000	0.000	0.000	0.000	0.000	0.000
116	A	175	ASP	-1	-0.859	-0.933	26.899	-0.037	-0.037	0.000	0.000	0.000	0.000
117	A	176	ASN	0	-0.004	0.009	27.259	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	177	ALA	0	0.013	0.011	28.257	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	178	LEU	0	0.003	0.001	22.430	0.000	0.000	0.000	0.000	0.000	0.000
120	A	179	SER	0	-0.007	-0.006	23.755	-0.005	-0.005	0.000	0.000	0.000	0.000
121	A	180	LEU	0	-0.016	-0.007	23.671	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	181	ALA	0	-0.015	0.013	23.830	0.000	0.000	0.000	0.000	0.000	0.000
123	A	182	VAL	0	0.031	0.006	18.302	0.000	0.000	0.000	0.000	0.000	0.000
124	A	183	HIS	0	0.007	0.009	19.461	-0.012	-0.012	0.000	0.000	0.000	0.000
125	A	184	SER	0	-0.052	-0.057	20.753	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	185	LEU	0	-0.022	0.005	17.728	0.006	0.006	0.000	0.000	0.000	0.000
127	A	186	ASN	0	-0.048	-0.029	15.012	-0.031	-0.031	0.000	0.000	0.000	0.000
128	A	187	LYS	1	0.853	0.933	17.460	0.019	0.019	0.000	0.000	0.000	0.000
129	A	188	LYS	1	0.968	1.002	13.838	0.162	0.162	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:60:MET)