FMO DATABASE

FMODB ID: 3914L

Calculation Name: 3DRX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DRX

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NXV2

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1407600.78704
FMO2-HF: Nuclear repulsion	1340723.837224
FMO2-HF: Total energy	-66876.949816
FMO2-MP2: Total energy	-67071.581152

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:34:ALA)

Summations of interaction energy for fragment #1(A:34: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.
-4.451	-1.137	4.656	-2.602	-5.366	-0.012

Interaction energy analysis for fragmet #1(A:34:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.019

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	36	ALA	0	-0.029	-0.010	3.819	-1.023	0.233	-0.012	-0.503	-0.741	0.002
4	A	37	GLN	0	-0.021	-0.021	2.348	-0.210	-0.192	4.223	-1.433	-2.808	-0.011
5	A	38	ARG	0	0.068	0.041	4.249	-1.099	-1.097	-0.001	-0.021	0.020	0.000
6	A	39	PRO	0	0.000	-0.008	4.409	-1.001	-0.888	-0.001	-0.009	-0.103	0.000
7	A	40	GLY	0	-0.015	0.011	4.621	0.380	0.442	-0.001	-0.002	-0.058	0.000
8	A	41	SER	0	0.028	0.020	3.551	0.350	0.506	0.004	-0.033	-0.127	0.000
9	A	42	VAL	0	-0.017	-0.006	5.114	-0.053	0.038	-0.001	-0.003	-0.087	0.000
10	A	43	SER	0	0.010	-0.025	2.810	-1.163	-0.246	0.384	-0.456	-0.845	-0.003
11	A	44	LYS	1	0.927	0.978	4.704	0.328	0.461	-0.001	-0.008	-0.124	0.000
12	A	45	TRP	0	0.046	0.020	3.039	-1.143	-0.577	0.062	-0.134	-0.493	0.000
13	A	46	VAL	0	0.015	0.003	8.224	-0.016	-0.016	0.000	0.000	0.000	0.000
14	A	47	ARG	1	0.852	0.927	11.891	-0.349	-0.349	0.000	0.000	0.000	0.000
15	A	48	LEU	0	-0.003	0.001	14.610	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	49	ASN	0	0.043	0.036	17.681	0.001	0.001	0.000	0.000	0.000	0.000
17	A	50	VAL	0	-0.003	0.002	20.210	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	51	GLY	0	0.074	0.029	22.833	0.002	0.002	0.000	0.000	0.000	0.000
19	A	52	GLY	0	-0.025	-0.023	24.625	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	53	THR	0	-0.020	-0.009	20.618	0.005	0.005	0.000	0.000	0.000	0.000
21	A	54	TYR	0	-0.095	-0.081	17.129	0.004	0.004	0.000	0.000	0.000	0.000
22	A	55	PHE	0	-0.014	0.001	15.848	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	56	LEU	0	-0.027	-0.005	8.318	0.005	0.005	0.000	0.000	0.000	0.000
24	A	57	THR	0	0.009	-0.004	9.878	-0.071	-0.071	0.000	0.000	0.000	0.000
25	A	58	THR	0	0.001	0.002	5.545	0.056	0.056	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.879	0.924	8.877	-0.135	-0.135	0.000	0.000	0.000	0.000
27	A	60	GLN	0	-0.010	0.009	6.996	-0.054	-0.054	0.000	0.000	0.000	0.000
28	A	61	THR	0	-0.012	-0.017	9.809	0.004	0.004	0.000	0.000	0.000	0.000
29	A	62	LEU	0	-0.039	-0.010	11.738	0.015	0.015	0.000	0.000	0.000	0.000
30	A	63	CYS	0	-0.031	0.006	14.288	0.019	0.019	0.000	0.000	0.000	0.000
31	A	64	ARG	1	0.893	0.959	15.294	0.211	0.211	0.000	0.000	0.000	0.000
32	A	65	ASP	-1	-0.843	-0.944	16.602	-0.095	-0.095	0.000	0.000	0.000	0.000
33	A	66	PRO	0	-0.002	-0.032	20.170	0.014	0.014	0.000	0.000	0.000	0.000
34	A	67	LYS	1	0.884	0.955	21.840	0.096	0.096	0.000	0.000	0.000	0.000
35	A	68	SER	0	0.030	0.038	20.953	0.012	0.012	0.000	0.000	0.000	0.000
36	A	69	PHE	0	0.039	0.004	22.761	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	70	LEU	0	0.019	-0.008	17.916	0.010	0.010	0.000	0.000	0.000	0.000
38	A	71	TYR	0	-0.034	0.015	18.404	0.005	0.005	0.000	0.000	0.000	0.000
39	A	72	ARG	1	0.868	0.933	19.083	-0.027	-0.027	0.000	0.000	0.000	0.000
40	A	73	LEU	0	0.002	0.007	16.019	0.007	0.007	0.000	0.000	0.000	0.000
41	A	75	GLN	0	0.029	0.005	14.013	0.000	0.000	0.000	0.000	0.000	0.000
42	A	76	ALA	0	-0.070	-0.059	13.935	0.023	0.023	0.000	0.000	0.000	0.000
43	A	77	ASP	-1	-0.791	-0.910	15.794	0.007	0.007	0.000	0.000	0.000	0.000
44	A	78	PRO	0	-0.089	-0.024	19.566	0.008	0.008	0.000	0.000	0.000	0.000
45	A	79	ASP	-1	-0.858	-0.922	22.200	0.031	0.031	0.000	0.000	0.000	0.000
46	A	80	LEU	0	-0.108	-0.046	22.242	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	81	ASP	-1	-0.826	-0.913	23.226	0.028	0.028	0.000	0.000	0.000	0.000
48	A	82	SER	0	-0.086	-0.057	22.600	0.007	0.007	0.000	0.000	0.000	0.000
49	A	83	ASP	-1	-0.882	-0.925	23.627	0.084	0.084	0.000	0.000	0.000	0.000
50	A	84	LYS	1	0.838	0.907	17.666	-0.187	-0.187	0.000	0.000	0.000	0.000
51	A	85	ASP	-1	-0.663	-0.754	21.046	0.199	0.199	0.000	0.000	0.000	0.000
52	A	86	GLU	-1	-0.926	-0.959	22.036	0.217	0.217	0.000	0.000	0.000	0.000
53	A	87	THR	0	-0.032	-0.045	18.891	0.035	0.035	0.000	0.000	0.000	0.000
54	A	88	GLY	0	-0.071	-0.052	17.604	0.047	0.047	0.000	0.000	0.000	0.000
55	A	89	ALA	0	-0.069	-0.039	17.482	0.000	0.000	0.000	0.000	0.000	0.000
56	A	90	TYR	0	0.034	0.014	15.620	-0.008	-0.008	0.000	0.000	0.000	0.000
57	A	91	LEU	0	0.020	0.017	20.119	0.006	0.006	0.000	0.000	0.000	0.000
58	A	92	ILE	0	-0.029	-0.022	20.853	-0.013	-0.013	0.000	0.000	0.000	0.000
59	A	93	ASP	-1	-0.923	-0.945	24.544	0.053	0.053	0.000	0.000	0.000	0.000
60	A	94	ARG	1	0.833	0.893	25.449	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	95	ASP	-1	-0.769	-0.854	26.762	0.048	0.048	0.000	0.000	0.000	0.000
62	A	96	PRO	0	0.019	0.008	23.105	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	97	THR	0	-0.052	-0.073	23.062	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	98	TYR	0	0.001	0.012	24.748	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	99	PHE	0	0.011	0.012	17.662	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	100	GLY	0	0.008	0.017	19.245	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	101	PRO	0	-0.018	-0.024	19.031	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	102	VAL	0	0.023	0.021	20.134	-0.019	-0.019	0.000	0.000	0.000	0.000
69	A	103	LEU	0	-0.005	-0.006	14.071	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	104	ASN	0	0.005	-0.026	15.584	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	105	TYR	0	-0.024	-0.016	16.302	-0.037	-0.037	0.000	0.000	0.000	0.000
72	A	106	LEU	0	-0.012	-0.008	15.222	-0.030	-0.030	0.000	0.000	0.000	0.000
73	A	107	ARG	1	0.880	0.955	11.060	-0.036	-0.036	0.000	0.000	0.000	0.000
74	A	108	HIS	0	-0.016	-0.010	12.811	-0.066	-0.066	0.000	0.000	0.000	0.000
75	A	109	GLY	0	-0.057	-0.015	15.273	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	110	LYS	1	0.911	0.949	18.638	0.213	0.213	0.000	0.000	0.000	0.000
77	A	111	LEU	0	0.040	0.020	20.348	0.003	0.003	0.000	0.000	0.000	0.000
78	A	112	VAL	0	-0.048	-0.035	21.194	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	113	ILE	0	0.016	0.004	23.155	0.004	0.004	0.000	0.000	0.000	0.000
80	A	114	ASN	0	0.005	0.015	23.941	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	115	LYS	1	0.985	0.968	26.965	0.026	0.026	0.000	0.000	0.000	0.000
82	A	116	ASP	-1	-0.981	-0.969	29.573	0.007	0.007	0.000	0.000	0.000	0.000
83	A	117	LEU	0	0.015	0.002	26.190	0.003	0.003	0.000	0.000	0.000	0.000
84	A	118	ALA	0	0.040	0.029	30.335	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	119	GLU	-1	-0.891	-0.968	30.122	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	120	GLU	-1	-0.862	-0.934	30.851	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	121	GLY	0	0.021	0.011	30.559	0.001	0.001	0.000	0.000	0.000	0.000
88	A	122	VAL	0	-0.028	-0.030	25.360	0.000	0.000	0.000	0.000	0.000	0.000
89	A	123	LEU	0	-0.059	-0.027	27.387	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	124	GLU	-1	-0.864	-0.943	29.424	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	125	GLU	-1	-0.800	-0.876	25.315	0.015	0.015	0.000	0.000	0.000	0.000
92	A	126	ALA	0	-0.073	-0.036	25.228	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	127	GLU	-1	-0.955	-0.990	26.310	-0.030	-0.030	0.000	0.000	0.000	0.000
94	A	128	PHE	0	0.006	0.022	25.585	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	129	TYR	0	-0.032	-0.024	22.565	0.001	0.001	0.000	0.000	0.000	0.000
96	A	130	ASN	0	-0.002	0.005	24.356	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	131	ILE	0	0.016	0.015	20.721	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	132	THR	0	0.057	0.020	24.395	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	133	SER	0	-0.068	-0.002	23.247	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	134	LEU	0	0.040	0.011	22.298	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	135	ILE	0	0.038	0.021	25.283	0.003	0.003	0.000	0.000	0.000	0.000
102	A	136	LYS	1	0.885	0.945	28.496	0.077	0.077	0.000	0.000	0.000	0.000
103	A	137	LEU	0	0.024	0.007	24.332	0.003	0.003	0.000	0.000	0.000	0.000
104	A	138	VAL	0	0.023	0.015	27.193	0.002	0.002	0.000	0.000	0.000	0.000
105	A	139	LYS	1	1.028	1.011	29.604	0.039	0.039	0.000	0.000	0.000	0.000
106	A	140	ASP	-1	-0.905	-0.944	31.281	-0.061	-0.061	0.000	0.000	0.000	0.000
107	A	141	LYS	1	0.965	0.995	27.896	0.056	0.056	0.000	0.000	0.000	0.000
108	A	142	ILE	0	0.023	0.014	32.217	0.003	0.003	0.000	0.000	0.000	0.000
109	A	143	ARG	1	0.898	0.937	34.815	0.047	0.047	0.000	0.000	0.000	0.000
110	A	144	GLU	-1	-0.989	-0.993	33.352	-0.053	-0.053	0.000	0.000	0.000	0.000
111	A	145	ARG	1	0.818	0.897	35.107	0.023	0.023	0.000	0.000	0.000	0.000
112	A	146	ASP	-1	-0.824	-0.884	37.369	-0.021	-0.021	0.000	0.000	0.000	0.000
113	A	147	SER	0	-0.090	-0.037	39.979	0.001	0.001	0.000	0.000	0.000	0.000
114	A	148	LYS	1	0.918	0.956	37.028	0.039	0.039	0.000	0.000	0.000	0.000
115	A	149	THR	0	-0.047	-0.022	40.379	0.002	0.002	0.000	0.000	0.000	0.000
116	A	150	SER	0	-0.011	-0.013	42.965	0.002	0.002	0.000	0.000	0.000	0.000
117	A	151	GLN	0	-0.004	-0.011	46.001	-0.002	-0.002	0.000	0.000	0.000	0.000
118	A	152	VAL	0	-0.047	-0.031	48.687	0.001	0.001	0.000	0.000	0.000	0.000
119	A	153	PRO	0	0.005	-0.008	52.354	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	154	VAL	0	0.031	0.044	52.520	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	155	LYS	1	0.947	0.984	54.581	0.021	0.021	0.000	0.000	0.000	0.000
122	A	156	HIS	0	0.045	0.019	56.575	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	157	VAL	0	-0.050	-0.019	58.185	0.000	0.000	0.000	0.000	0.000	0.000
124	A	158	TYR	0	0.030	0.002	60.889	0.000	0.000	0.000	0.000	0.000	0.000
125	A	159	ARG	1	0.893	0.946	62.788	0.021	0.021	0.000	0.000	0.000	0.000
126	A	160	VAL	0	0.038	0.013	66.322	0.000	0.000	0.000	0.000	0.000	0.000
127	A	161	LEU	0	-0.021	0.009	65.395	0.000	0.000	0.000	0.000	0.000	0.000
128	A	162	GLN	0	0.024	0.010	69.782	0.001	0.001	0.000	0.000	0.000	0.000
129	A	163	CYS	0	-0.099	-0.058	71.963	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	164	GLN	0	0.045	0.014	74.268	0.001	0.001	0.000	0.000	0.000	0.000
131	A	165	GLU	-1	-0.899	-0.950	75.711	-0.013	-0.013	0.000	0.000	0.000	0.000
132	A	166	GLU	-1	-0.861	-0.941	75.976	-0.015	-0.015	0.000	0.000	0.000	0.000
133	A	167	GLU	-1	-0.959	-0.969	72.099	-0.018	-0.018	0.000	0.000	0.000	0.000
134	A	168	LEU	0	0.049	0.031	71.239	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	169	THR	0	0.050	-0.005	68.741	0.000	0.000	0.000	0.000	0.000	0.000
136	A	170	GLN	0	-0.019	-0.002	68.123	0.000	0.000	0.000	0.000	0.000	0.000
137	A	171	MET	0	-0.008	0.006	66.687	-0.001	-0.001	0.000	0.000	0.000	0.000
138	A	172	VAL	0	-0.017	-0.023	65.566	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	173	SER	0	-0.022	-0.015	63.999	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	174	THR	0	-0.129	-0.050	62.010	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	175	MET	0	-0.026	0.016	60.761	-0.001	-0.001	0.000	0.000	0.000	0.000
142	A	176	SER	0	-0.045	-0.036	58.705	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	177	ASP	-1	-0.934	-0.973	52.412	-0.031	-0.031	0.000	0.000	0.000	0.000
144	A	178	GLY	0	0.020	0.012	54.509	0.000	0.000	0.000	0.000	0.000	0.000
145	A	179	TRP	0	-0.109	-0.055	55.233	0.001	0.001	0.000	0.000	0.000	0.000
146	A	180	LYS	1	0.953	0.981	55.036	0.021	0.021	0.000	0.000	0.000	0.000
147	A	181	PHE	0	0.057	0.008	60.537	0.000	0.000	0.000	0.000	0.000	0.000
148	A	182	GLU	-1	-0.907	-0.930	63.088	-0.015	-0.015	0.000	0.000	0.000	0.000
149	A	183	GLN	0	0.009	-0.010	66.007	0.001	0.001	0.000	0.000	0.000	0.000
150	A	184	LEU	0	-0.013	0.001	69.692	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	185	VAL	0	-0.005	-0.008	72.230	0.001	0.001	0.000	0.000	0.000	0.000
152	A	186	SER	0	-0.004	0.012	75.632	0.000	0.000	0.000	0.000	0.000	0.000
153	A	187	ILE	0	-0.036	-0.021	78.818	0.001	0.001	0.000	0.000	0.000	0.000
154	A	200	GLU	-1	-0.933	-0.961	78.540	-0.013	-0.013	0.000	0.000	0.000	0.000
155	A	201	PHE	0	0.022	0.002	74.917	0.001	0.001	0.000	0.000	0.000	0.000
156	A	202	LEU	0	-0.034	-0.012	73.909	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	203	CYS	0	-0.013	-0.007	67.898	0.000	0.000	0.000	0.000	0.000	0.000
158	A	204	VAL	0	-0.032	-0.006	66.972	-0.001	-0.001	0.000	0.000	0.000	0.000
159	A	205	VAL	0	0.001	0.010	62.542	0.000	0.000	0.000	0.000	0.000	0.000
160	A	206	SER	0	-0.026	-0.039	61.270	0.000	0.000	0.000	0.000	0.000	0.000
161	A	207	LYS	1	0.981	0.986	53.945	0.026	0.026	0.000	0.000	0.000	0.000
162	A	208	GLU	-1	-0.890	-0.939	52.915	-0.020	-0.020	0.000	0.000	0.000	0.000
163	A	209	LEU	0	-0.078	-0.046	53.230	-0.001	-0.001	0.000	0.000	0.000	0.000
164	A	210	HIS	0	-0.012	0.015	47.832	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:ALA)