FMO DATABASE

FMODB ID: 2NQ7R

Calculation Name: 3DWV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DWV

Chain ID: A

ChEMBL ID:

UniProt ID: Q869A5

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	162
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1657289.430888
FMO2-HF: Nuclear repulsion	1593678.657809
FMO2-HF: Total energy	-63610.773078
FMO2-MP2: Total energy	-63797.158019

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:9:MET)

Summations of interaction energy for fragment #1(A:9: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.
-27.265	-26.003	23.17	-9.501	-14.93	0.044

Interaction energy analysis for fragmet #1(A:9:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.083 / q_NPA : 0.043

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	11	ALA	0	0.025	0.014	3.167	-1.518	0.677	-0.005	-0.976	-1.214	0.000
4	A	12	ALA	0	-0.052	-0.007	2.588	-0.558	0.463	1.002	-0.638	-1.384	-0.003
5	A	13	SER	0	-0.050	-0.039	4.365	0.915	1.041	0.000	-0.020	-0.105	0.000
6	A	14	SER	0	-0.032	-0.040	8.044	0.078	0.078	0.000	0.000	0.000	0.000
7	A	15	ILE	0	-0.004	-0.031	7.865	-0.032	-0.032	0.000	0.000	0.000	0.000
8	A	16	PHE	0	-0.013	-0.008	8.917	-0.252	-0.252	0.000	0.000	0.000	0.000
9	A	17	ASP	-1	-0.783	-0.828	6.812	0.333	0.333	0.000	0.000	0.000	0.000
10	A	18	PHE	0	-0.037	-0.034	3.014	-2.197	-0.983	0.354	-0.346	-1.223	-0.003
11	A	19	GLU	-1	-0.921	-0.946	8.098	-0.630	-0.630	0.000	0.000	0.000	0.000
12	A	20	VAL	0	-0.025	-0.026	10.114	-0.117	-0.117	0.000	0.000	0.000	0.000
13	A	21	LEU	0	0.020	0.030	12.601	0.067	0.067	0.000	0.000	0.000	0.000
14	A	22	ASP	-1	-0.757	-0.899	16.057	-0.235	-0.235	0.000	0.000	0.000	0.000
15	A	23	ALA	0	-0.026	-0.017	18.850	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	24	ASP	-1	-0.905	-0.924	21.157	-0.180	-0.180	0.000	0.000	0.000	0.000
17	A	25	HIS	0	-0.049	-0.040	19.131	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	26	LYS	1	0.821	0.907	19.892	0.179	0.179	0.000	0.000	0.000	0.000
19	A	27	PRO	0	0.019	-0.007	17.199	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	28	TYR	0	-0.026	-0.025	15.665	0.048	0.048	0.000	0.000	0.000	0.000
21	A	29	ASN	0	0.018	0.007	16.114	-0.030	-0.030	0.000	0.000	0.000	0.000
22	A	30	LEU	0	0.026	0.002	11.329	0.041	0.041	0.000	0.000	0.000	0.000
23	A	31	VAL	0	0.025	0.000	15.373	0.048	0.048	0.000	0.000	0.000	0.000
24	A	32	GLN	0	-0.066	-0.025	16.447	0.047	0.047	0.000	0.000	0.000	0.000
25	A	33	HIS	0	0.035	0.024	16.740	-0.013	-0.013	0.000	0.000	0.000	0.000
26	A	34	LYS	1	0.821	0.904	14.621	-0.185	-0.185	0.000	0.000	0.000	0.000
27	A	35	GLY	0	0.007	0.008	18.150	-0.020	-0.020	0.000	0.000	0.000	0.000
28	A	36	SER	0	-0.053	-0.025	20.196	0.003	0.003	0.000	0.000	0.000	0.000
29	A	37	PRO	0	-0.029	0.008	18.391	0.009	0.009	0.000	0.000	0.000	0.000
30	A	38	LEU	0	-0.003	-0.017	14.751	-0.041	-0.041	0.000	0.000	0.000	0.000
31	A	39	LEU	0	-0.028	-0.003	16.703	0.045	0.045	0.000	0.000	0.000	0.000
32	A	40	ILE	0	0.011	0.003	11.470	-0.044	-0.044	0.000	0.000	0.000	0.000
33	A	41	TYR	0	0.042	0.015	14.433	0.036	0.036	0.000	0.000	0.000	0.000
34	A	42	ASN	0	-0.009	0.006	14.009	-0.021	-0.021	0.000	0.000	0.000	0.000
35	A	43	VAL	0	-0.033	-0.019	15.769	0.044	0.044	0.000	0.000	0.000	0.000
36	A	44	ALA	0	0.066	0.031	18.944	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	45	SER	0	-0.042	-0.025	21.743	0.007	0.007	0.000	0.000	0.000	0.000
38	A	46	LYS	1	0.958	0.982	25.377	0.074	0.074	0.000	0.000	0.000	0.000
39	A	47	CYS	0	-0.035	0.015	27.770	0.004	0.004	0.000	0.000	0.000	0.000
40	A	48	GLY	0	0.023	0.012	29.505	0.005	0.005	0.000	0.000	0.000	0.000
41	A	49	TYR	0	0.000	0.009	29.500	0.005	0.005	0.000	0.000	0.000	0.000
42	A	50	THR	0	0.022	0.002	24.945	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	51	LYS	1	0.900	0.947	24.442	0.018	0.018	0.000	0.000	0.000	0.000
44	A	52	GLY	0	0.132	0.089	27.453	0.010	0.010	0.000	0.000	0.000	0.000
45	A	53	GLY	0	0.012	0.011	23.498	0.003	0.003	0.000	0.000	0.000	0.000
46	A	54	TYR	0	-0.006	-0.015	23.964	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	55	GLU	-1	-0.895	-0.937	25.582	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	56	THR	0	-0.021	-0.006	23.989	0.001	0.001	0.000	0.000	0.000	0.000
49	A	57	ALA	0	0.001	0.011	22.432	0.006	0.006	0.000	0.000	0.000	0.000
50	A	58	THR	0	-0.002	-0.021	23.894	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	59	THR	0	-0.050	-0.034	26.955	0.001	0.001	0.000	0.000	0.000	0.000
52	A	60	LEU	0	-0.022	-0.011	23.492	0.004	0.004	0.000	0.000	0.000	0.000
53	A	61	TYR	0	-0.002	-0.004	23.677	0.000	0.000	0.000	0.000	0.000	0.000
54	A	62	ASN	0	-0.032	-0.046	25.622	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	63	LYS	1	0.786	0.906	29.180	-0.053	-0.053	0.000	0.000	0.000	0.000
56	A	64	TYR	0	-0.002	-0.033	26.229	0.004	0.004	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.849	0.937	26.054	0.028	0.028	0.000	0.000	0.000	0.000
58	A	66	SER	0	-0.034	-0.012	27.013	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	67	GLN	0	-0.047	-0.034	27.942	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	68	GLY	0	0.023	0.022	25.298	0.011	0.011	0.000	0.000	0.000	0.000
61	A	69	PHE	0	-0.012	-0.001	20.589	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	70	THR	0	0.010	-0.007	18.821	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	71	VAL	0	-0.015	-0.006	19.175	0.023	0.023	0.000	0.000	0.000	0.000
64	A	72	LEU	0	0.008	0.012	14.949	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	73	ALA	0	-0.005	-0.003	16.917	0.015	0.015	0.000	0.000	0.000	0.000
66	A	74	PHE	0	0.082	0.026	11.845	-0.029	-0.029	0.000	0.000	0.000	0.000
67	A	75	PRO	0	-0.046	-0.028	15.509	0.016	0.016	0.000	0.000	0.000	0.000
68	A	76	SER	0	0.062	0.021	15.902	-0.045	-0.045	0.000	0.000	0.000	0.000
69	A	77	ASN	0	-0.044	-0.048	15.698	0.072	0.072	0.000	0.000	0.000	0.000
70	A	78	GLN	0	-0.049	-0.032	18.211	0.029	0.029	0.000	0.000	0.000	0.000
71	A	79	PHE	0	0.006	0.013	16.673	0.033	0.033	0.000	0.000	0.000	0.000
72	A	80	GLY	0	0.068	0.028	17.169	-0.047	-0.047	0.000	0.000	0.000	0.000
73	A	81	GLY	0	0.062	0.047	19.130	0.014	0.014	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.087	-0.046	14.601	0.048	0.048	0.000	0.000	0.000	0.000
75	A	83	GLU	-1	-0.732	-0.834	14.168	-0.500	-0.500	0.000	0.000	0.000	0.000
76	A	84	PRO	0	-0.041	-0.022	15.403	0.038	0.038	0.000	0.000	0.000	0.000
77	A	85	GLY	0	-0.052	-0.022	18.051	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	86	ASN	0	0.050	0.014	21.785	0.001	0.001	0.000	0.000	0.000	0.000
79	A	87	GLU	-1	-0.881	-0.939	22.948	-0.157	-0.157	0.000	0.000	0.000	0.000
80	A	88	GLU	-1	-0.863	-0.927	24.553	-0.081	-0.081	0.000	0.000	0.000	0.000
81	A	89	GLU	-1	-0.948	-0.985	26.551	-0.076	-0.076	0.000	0.000	0.000	0.000
82	A	90	ILE	0	-0.024	-0.047	24.655	0.002	0.002	0.000	0.000	0.000	0.000
83	A	91	LYS	1	0.749	0.868	28.100	0.083	0.083	0.000	0.000	0.000	0.000
84	A	92	GLU	-1	-0.897	-0.917	30.549	-0.062	-0.062	0.000	0.000	0.000	0.000
85	A	93	PHE	0	0.000	0.001	31.130	0.006	0.006	0.000	0.000	0.000	0.000
86	A	94	VAL	0	0.022	0.009	31.895	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	96	THR	0	-0.004	-0.006	29.556	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	97	LYS	1	0.975	0.979	25.587	0.154	0.154	0.000	0.000	0.000	0.000
89	A	98	PHE	0	0.027	0.012	22.219	0.012	0.012	0.000	0.000	0.000	0.000
90	A	99	LYS	1	0.878	0.922	25.911	0.086	0.086	0.000	0.000	0.000	0.000
91	A	100	ALA	0	0.022	0.018	24.456	0.007	0.007	0.000	0.000	0.000	0.000
92	A	101	GLU	-1	-0.805	-0.884	26.605	-0.037	-0.037	0.000	0.000	0.000	0.000
93	A	102	PHE	0	-0.010	0.006	21.526	0.000	0.000	0.000	0.000	0.000	0.000
94	A	103	PRO	0	0.013	0.002	19.830	-0.013	-0.013	0.000	0.000	0.000	0.000
95	A	104	ILE	0	-0.053	-0.023	19.557	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	105	MET	0	-0.033	-0.008	14.797	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	106	ALA	0	0.025	0.013	15.946	0.023	0.023	0.000	0.000	0.000	0.000
98	A	107	LYS	1	0.823	0.896	15.875	0.242	0.242	0.000	0.000	0.000	0.000
99	A	108	ILE	0	-0.018	0.005	10.584	-0.050	-0.050	0.000	0.000	0.000	0.000
100	A	109	ASN	0	-0.016	0.016	12.135	0.081	0.081	0.000	0.000	0.000	0.000
101	A	110	VAL	0	-0.030	-0.024	10.177	-0.149	-0.149	0.000	0.000	0.000	0.000
102	A	111	ASN	0	-0.073	-0.053	10.279	0.020	0.020	0.000	0.000	0.000	0.000
103	A	112	GLY	0	0.078	0.027	11.542	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	113	GLU	-1	-0.953	-0.973	10.053	-0.645	-0.645	0.000	0.000	0.000	0.000
105	A	114	ASN	0	-0.006	-0.005	10.240	-0.072	-0.072	0.000	0.000	0.000	0.000
106	A	115	ALA	0	-0.051	-0.009	7.510	0.021	0.021	0.000	0.000	0.000	0.000
107	A	116	HIS	0	0.048	0.034	7.282	-0.706	-0.706	0.000	0.000	0.000	0.000
108	A	117	PRO	0	0.050	0.007	3.042	-0.618	-0.115	0.070	-0.099	-0.475	0.000
109	A	118	LEU	0	0.037	0.037	2.417	-4.758	-3.646	1.530	-1.091	-1.551	-0.018
110	A	119	TYR	0	0.059	0.006	4.929	0.758	0.838	-0.001	-0.001	-0.078	0.000
111	A	120	GLU	-1	-0.772	-0.860	3.100	-0.601	-0.140	0.100	-0.104	-0.457	0.000
112	A	121	TYR	0	-0.051	-0.033	2.256	0.776	2.689	2.574	-1.373	-3.114	-0.003
113	A	122	MET	0	-0.001	0.016	3.306	1.376	0.857	0.080	0.727	-0.287	-0.001
114	A	123	LYS	1	0.749	0.859	6.705	0.651	0.651	0.000	0.000	0.000	0.000
115	A	124	LYS	1	0.851	0.905	2.184	-18.164	-25.008	17.466	-5.580	-5.042	0.072
116	A	125	THR	0	-0.030	-0.005	6.500	-0.064	-0.064	0.000	0.000	0.000	0.000
117	A	126	LYS	1	0.808	0.905	8.554	-0.988	-0.988	0.000	0.000	0.000	0.000
118	A	127	PRO	0	0.028	0.021	11.208	-0.164	-0.164	0.000	0.000	0.000	0.000
119	A	128	GLY	0	0.002	-0.002	12.413	-0.131	-0.131	0.000	0.000	0.000	0.000
120	A	129	ILE	0	0.019	-0.002	16.055	0.027	0.027	0.000	0.000	0.000	0.000
121	A	130	LEU	0	0.015	0.011	18.381	-0.029	-0.029	0.000	0.000	0.000	0.000
122	A	131	ALA	0	0.013	-0.006	18.050	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	132	THR	0	0.044	0.026	13.798	0.039	0.039	0.000	0.000	0.000	0.000
124	A	133	LYS	1	0.863	0.914	6.323	0.027	0.027	0.000	0.000	0.000	0.000
125	A	134	ALA	0	0.021	0.027	11.284	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	135	ILE	0	0.002	0.009	10.930	0.092	0.092	0.000	0.000	0.000	0.000
127	A	136	LYS	1	0.875	0.946	14.050	-0.124	-0.124	0.000	0.000	0.000	0.000
128	A	137	TRP	0	0.056	0.030	17.771	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	138	ASN	0	0.058	0.034	18.241	-0.024	-0.024	0.000	0.000	0.000	0.000
130	A	139	PHE	0	0.015	-0.013	19.311	0.020	0.020	0.000	0.000	0.000	0.000
131	A	140	THR	0	-0.045	-0.025	15.451	0.037	0.037	0.000	0.000	0.000	0.000
132	A	141	SER	0	-0.017	-0.007	15.230	-0.028	-0.028	0.000	0.000	0.000	0.000
133	A	142	PHE	0	-0.014	-0.010	10.390	0.048	0.048	0.000	0.000	0.000	0.000
134	A	143	LEU	0	-0.006	0.007	14.000	-0.063	-0.063	0.000	0.000	0.000	0.000
135	A	144	ILE	0	-0.035	-0.015	11.390	0.101	0.101	0.000	0.000	0.000	0.000
136	A	145	ASP	-1	-0.766	-0.890	14.742	0.398	0.398	0.000	0.000	0.000	0.000
137	A	146	ARG	1	0.900	0.935	16.745	-0.177	-0.177	0.000	0.000	0.000	0.000
138	A	147	ASP	-1	-0.840	-0.898	15.586	0.236	0.236	0.000	0.000	0.000	0.000
139	A	148	GLY	0	0.037	0.009	12.889	-0.038	-0.038	0.000	0.000	0.000	0.000
140	A	149	VAL	0	0.031	0.014	10.880	0.151	0.151	0.000	0.000	0.000	0.000
141	A	150	PRO	0	-0.018	-0.020	8.337	-0.187	-0.187	0.000	0.000	0.000	0.000
142	A	151	VAL	0	0.037	0.032	11.674	0.118	0.118	0.000	0.000	0.000	0.000
143	A	152	GLU	-1	-0.835	-0.904	15.021	0.363	0.363	0.000	0.000	0.000	0.000
144	A	153	ARG	1	0.781	0.888	11.292	-0.336	-0.336	0.000	0.000	0.000	0.000
145	A	154	PHE	0	0.001	0.014	15.546	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	155	SER	0	0.012	-0.004	18.109	-0.022	-0.022	0.000	0.000	0.000	0.000
147	A	156	PRO	0	-0.009	-0.010	20.150	0.005	0.005	0.000	0.000	0.000	0.000
148	A	157	GLY	0	0.007	-0.001	22.362	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	158	ALA	0	-0.046	-0.003	22.733	0.005	0.005	0.000	0.000	0.000	0.000
150	A	159	SER	0	-0.002	-0.032	24.688	-0.014	-0.014	0.000	0.000	0.000	0.000
151	A	160	VAL	0	0.025	-0.014	26.208	0.009	0.009	0.000	0.000	0.000	0.000
152	A	161	LYS	1	0.864	0.913	27.073	-0.084	-0.084	0.000	0.000	0.000	0.000
153	A	162	ASP	-1	-0.821	-0.880	25.199	0.105	0.105	0.000	0.000	0.000	0.000
154	A	163	ILE	0	-0.019	-0.009	21.089	0.019	0.019	0.000	0.000	0.000	0.000
155	A	164	GLU	-1	-0.747	-0.852	23.657	0.082	0.082	0.000	0.000	0.000	0.000
156	A	165	GLU	-1	-0.814	-0.876	26.079	0.114	0.114	0.000	0.000	0.000	0.000
157	A	166	LYS	1	0.816	0.902	21.144	-0.249	-0.249	0.000	0.000	0.000	0.000
158	A	167	LEU	0	0.019	0.007	21.513	0.015	0.015	0.000	0.000	0.000	0.000
159	A	168	ILE	0	0.041	0.025	23.178	0.000	0.000	0.000	0.000	0.000	0.000
160	A	169	PRO	0	-0.012	-0.005	24.513	-0.005	-0.005	0.000	0.000	0.000	0.000
161	A	170	LEU	0	-0.033	-0.006	19.065	0.007	0.007	0.000	0.000	0.000	0.000
162	A	171	LEU	0	-0.056	-0.022	23.005	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:9:MET)