FMO DATABASE

FMODB ID: 3J9VL

Calculation Name: 3D7Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7Q

Chain ID: A

ChEMBL ID:

UniProt ID: B2JAN5

Base Structure: X-ray

Registration Date: 2023-09-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-947718.270765
FMO2-HF: Nuclear repulsion	900986.874889
FMO2-HF: Total energy	-46731.395875
FMO2-MP2: Total energy	-46866.744349

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-21.559	-19.639	13.823	-8	-7.744	-0.046

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.016 / q_NPA : -0.017

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	2	ASP	-1	-0.858	-0.929	1.934	-12.740	-11.429	9.256	-5.728	-4.839	-0.059
4	A	3	LYS	1	0.825	0.899	2.246	-7.720	-7.869	4.509	-1.887	-2.473	0.011
5	A	4	LEU	0	0.027	0.028	4.125	-2.242	-1.869	0.020	-0.163	-0.230	0.002
6	A	5	ASN	0	0.032	0.002	6.143	-0.060	-0.060	0.000	0.000	0.000	0.000
7	A	6	GLU	-1	-0.845	-0.905	6.928	1.088	1.088	0.000	0.000	0.000	0.000
8	A	7	TYR	0	-0.017	-0.053	8.151	-0.223	-0.223	0.000	0.000	0.000	0.000
9	A	8	ARG	1	0.810	0.877	9.954	-0.021	-0.021	0.000	0.000	0.000	0.000
10	A	9	THR	0	-0.053	-0.024	11.248	-0.114	-0.114	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.794	0.896	10.925	-0.995	-0.995	0.000	0.000	0.000	0.000
12	A	11	VAL	0	0.022	0.009	14.032	-0.065	-0.065	0.000	0.000	0.000	0.000
13	A	12	ARG	1	0.907	0.942	15.768	-0.089	-0.089	0.000	0.000	0.000	0.000
14	A	13	GLN	0	-0.009	0.005	16.685	0.000	0.000	0.000	0.000	0.000	0.000
15	A	14	LEU	0	-0.019	-0.001	18.433	-0.030	-0.030	0.000	0.000	0.000	0.000
16	A	15	LEU	0	0.031	0.004	19.317	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	16	THR	0	-0.010	-0.023	21.355	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	17	LYS	1	0.819	0.914	21.533	-0.213	-0.213	0.000	0.000	0.000	0.000
19	A	18	HIS	1	0.824	0.884	23.923	-0.153	-0.153	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.007	0.007	26.177	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	20	GLN	0	-0.028	-0.032	26.326	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	21	TYR	0	-0.046	-0.017	27.176	0.000	0.000	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.843	0.926	31.191	-0.050	-0.050	0.000	0.000	0.000	0.000
24	A	23	PRO	0	0.018	0.020	33.283	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	24	SER	0	-0.016	-0.011	36.060	0.001	0.001	0.000	0.000	0.000	0.000
26	A	25	TYR	0	-0.026	-0.017	37.917	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	26	GLY	0	0.015	-0.002	40.554	0.000	0.000	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.924	-0.948	42.133	0.024	0.024	0.000	0.000	0.000	0.000
29	A	28	VAL	0	-0.057	-0.033	36.235	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.805	-0.892	34.748	0.039	0.039	0.000	0.000	0.000	0.000
31	A	30	VAL	0	-0.041	-0.028	29.508	0.002	0.002	0.000	0.000	0.000	0.000
32	A	31	GLU	-1	-0.901	-0.946	29.843	0.023	0.023	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.001	-0.020	23.252	0.002	0.002	0.000	0.000	0.000	0.000
34	A	33	ILE	0	-0.017	-0.002	23.974	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	34	PHE	0	-0.041	-0.030	19.457	0.016	0.016	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.809	-0.878	18.950	-0.078	-0.078	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.826	-0.919	13.233	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.964	-0.966	14.433	-0.272	-0.272	0.000	0.000	0.000	0.000
39	A	38	HIS	0	-0.077	-0.069	15.425	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.800	-0.856	11.765	-0.052	-0.052	0.000	0.000	0.000	0.000
41	A	40	HIS	0	-0.099	-0.062	14.937	0.021	0.021	0.000	0.000	0.000	0.000
42	A	41	TYR	0	-0.028	-0.034	13.647	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	42	GLN	0	-0.010	-0.030	19.596	0.012	0.012	0.000	0.000	0.000	0.000
44	A	43	ILE	0	-0.011	0.002	23.181	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	44	ILE	0	-0.023	-0.012	26.171	0.003	0.003	0.000	0.000	0.000	0.000
46	A	45	SER	0	0.039	0.033	29.623	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	46	VAL	0	-0.030	-0.014	32.763	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.009	0.001	35.528	-0.001	-0.001	0.000	0.000	0.000	0.000
49	A	48	TRP	0	-0.016	-0.003	39.265	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	49	ASN	0	0.059	0.022	42.489	0.002	0.002	0.000	0.000	0.000	0.000
51	A	50	ASN	0	0.028	0.019	44.529	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	51	GLN	0	-0.010	-0.022	46.815	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	52	HIS	0	-0.013	0.013	41.512	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.894	0.952	37.424	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	54	ILE	0	-0.029	-0.012	36.933	0.002	0.002	0.000	0.000	0.000	0.000
56	A	55	TYR	0	0.006	-0.016	32.028	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	56	GLY	0	0.022	0.011	32.885	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	57	PRO	0	-0.025	-0.013	27.230	0.002	0.002	0.000	0.000	0.000	0.000
59	A	58	ILE	0	0.008	0.020	28.375	0.003	0.003	0.000	0.000	0.000	0.000
60	A	59	MET	0	-0.043	-0.019	22.941	0.014	0.014	0.000	0.000	0.000	0.000
61	A	60	HIS	0	-0.011	-0.006	20.365	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.038	-0.011	17.051	0.015	0.015	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.713	-0.831	16.206	0.050	0.050	0.000	0.000	0.000	0.000
64	A	63	ILE	0	-0.033	-0.016	9.730	0.061	0.061	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.880	0.946	11.764	-0.110	-0.110	0.000	0.000	0.000	0.000
66	A	65	ASN	0	-0.029	-0.031	9.651	0.020	0.020	0.000	0.000	0.000	0.000
67	A	66	ASN	0	-0.048	-0.031	3.185	0.626	1.011	0.038	-0.222	-0.202	0.000
68	A	67	LYS	1	0.881	0.958	7.287	-0.201	-0.201	0.000	0.000	0.000	0.000
69	A	68	ILE	0	0.023	0.011	10.435	-0.102	-0.102	0.000	0.000	0.000	0.000
70	A	69	TRP	0	0.017	0.014	13.416	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	70	ILE	0	0.021	-0.005	16.607	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	71	GLN	0	-0.043	-0.032	19.458	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	72	GLN	0	0.011	0.001	22.059	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	73	ASN	0	0.005	-0.001	24.360	0.007	0.007	0.000	0.000	0.000	0.000
75	A	74	THR	0	-0.032	-0.002	26.813	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	75	THR	0	-0.069	-0.041	28.047	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	76	GLU	-1	-0.887	-0.953	30.191	0.098	0.098	0.000	0.000	0.000	0.000
78	A	77	ALA	0	-0.020	0.002	26.604	0.005	0.005	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.836	-0.915	23.766	0.189	0.189	0.000	0.000	0.000	0.000
80	A	79	ILE	0	0.042	-0.003	19.941	0.014	0.014	0.000	0.000	0.000	0.000
81	A	80	ALA	0	0.009	0.008	19.367	0.032	0.032	0.000	0.000	0.000	0.000
82	A	81	LEU	0	0.002	-0.003	19.550	0.036	0.036	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.772	-0.856	21.298	0.197	0.197	0.000	0.000	0.000	0.000
84	A	83	LEU	0	-0.026	-0.020	15.303	0.023	0.023	0.000	0.000	0.000	0.000
85	A	84	MET	0	-0.049	-0.023	16.383	0.044	0.044	0.000	0.000	0.000	0.000
86	A	85	GLU	-1	-0.935	-0.951	17.855	0.256	0.256	0.000	0.000	0.000	0.000
87	A	86	MET	0	-0.101	-0.042	16.281	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	87	GLY	0	0.023	0.016	14.671	0.068	0.068	0.000	0.000	0.000	0.000
89	A	88	ILE	0	-0.047	-0.022	11.641	0.164	0.164	0.000	0.000	0.000	0.000
90	A	89	ASP	-1	-0.802	-0.908	12.227	0.395	0.395	0.000	0.000	0.000	0.000
91	A	90	LYS	1	0.939	0.959	13.939	-0.281	-0.281	0.000	0.000	0.000	0.000
92	A	91	GLN	0	-0.060	-0.032	14.324	-0.058	-0.058	0.000	0.000	0.000	0.000
93	A	92	ASP	-1	-0.761	-0.857	8.927	1.168	1.168	0.000	0.000	0.000	0.000
94	A	93	ILE	0	0.003	0.028	12.046	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	94	VAL	0	-0.013	-0.005	14.610	-0.027	-0.027	0.000	0.000	0.000	0.000
96	A	95	ILE	0	0.014	0.009	17.129	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.049	0.023	20.417	-0.016	-0.016	0.000	0.000	0.000	0.000
98	A	97	PHE	0	-0.003	0.002	21.320	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	98	HIS	0	-0.001	0.015	23.887	0.000	0.000	0.000	0.000	0.000	0.000
100	A	99	THR	0	0.050	-0.006	24.134	0.002	0.002	0.000	0.000	0.000	0.000
101	A	100	PRO	0	0.073	0.019	23.039	0.008	0.008	0.000	0.000	0.000	0.000
102	A	101	LYS	1	0.867	0.925	24.175	-0.083	-0.083	0.000	0.000	0.000	0.000
103	A	102	MET	0	0.031	0.043	26.841	0.001	0.001	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.850	0.938	19.376	-0.130	-0.130	0.000	0.000	0.000	0.000
105	A	104	GLN	0	-0.025	-0.006	22.916	0.005	0.005	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.072	-0.034	24.379	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	106	SER	0	-0.029	-0.023	24.334	0.003	0.003	0.000	0.000	0.000	0.000
108	A	107	GLY	0	0.021	0.027	23.215	0.005	0.005	0.000	0.000	0.000	0.000
109	A	108	PHE	0	-0.007	-0.007	18.376	0.018	0.018	0.000	0.000	0.000	0.000
110	A	109	ALA	0	0.000	0.016	15.163	-0.016	-0.016	0.000	0.000	0.000	0.000
111	A	110	VAL	0	-0.027	-0.033	17.140	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	111	GLU	-1	-0.839	-0.909	13.740	0.170	0.170	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)