FMO DATABASE

FMODB ID: 66KVZ

Calculation Name: 3JRZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3JRZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q84B82

Base Structure: X-ray

Registration Date: 2023-06-19

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	OptHSide
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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-805872.86906
FMO2-HF: Nuclear repulsion	764943.973378
FMO2-HF: Total energy	-40928.895682
FMO2-MP2: Total energy	-41048.904909

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:SER)

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

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.
-14.188	-7.762	4.555	-4.963	-6.018	-0.036

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.008

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

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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	PHE	0	-0.032	-0.042	3.680	-1.841	-0.342	0.009	-0.591	-0.918	0.002
4	A	5	THR	0	-0.015	-0.012	2.104	-0.707	1.404	1.652	-1.616	-2.147	-0.016
5	A	6	LEU	0	-0.037	-0.021	4.602	0.654	0.728	-0.001	-0.020	-0.053	0.000
6	A	7	TYR	0	0.022	-0.006	3.243	-1.694	-1.101	0.019	-0.276	-0.335	0.002
7	A	8	LYS	1	0.875	0.937	9.090	-0.212	-0.212	0.000	0.000	0.000	0.000
8	A	9	ASN	0	-0.041	-0.020	12.757	0.108	0.108	0.000	0.000	0.000	0.000
9	A	10	LYS	1	0.844	0.896	13.923	-0.347	-0.347	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.824	-0.867	17.197	0.098	0.098	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.933	0.953	19.289	-0.159	-0.159	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.055	-0.033	22.696	-0.011	-0.011	0.000	0.000	0.000	0.000
13	A	14	SER	0	-0.020	-0.044	19.689	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.009	0.022	19.017	-0.018	-0.018	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.943	0.958	20.024	-0.026	-0.026	0.000	0.000	0.000	0.000
16	A	17	THR	0	-0.004	0.005	22.281	-0.007	-0.007	0.000	0.000	0.000	0.000
17	A	18	TYR	0	-0.044	-0.026	17.419	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.043	0.033	17.236	0.025	0.025	0.000	0.000	0.000	0.000
19	A	20	TYR	0	0.039	0.015	12.344	0.053	0.053	0.000	0.000	0.000	0.000
20	A	21	PHE	0	-0.028	-0.005	10.734	-0.019	-0.019	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.026	0.020	7.956	0.035	0.035	0.000	0.000	0.000	0.000
22	A	23	ASP	-1	-0.822	-0.919	4.997	1.460	1.460	0.000	0.000	0.000	0.000
23	A	24	VAL	0	0.015	0.001	6.811	-0.828	-0.828	0.000	0.000	0.000	0.000
24	A	25	GLN	0	-0.010	0.015	7.263	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	26	SER	0	0.010	0.006	5.898	-0.421	-0.421	0.000	0.000	0.000	0.000
26	A	27	ASP	-1	-0.733	-0.884	2.393	-10.357	-8.407	2.878	-2.449	-2.379	-0.024
27	A	28	LEU	0	-0.040	-0.018	5.200	0.474	0.507	-0.001	0.000	-0.032	0.000
28	A	29	LEU	0	-0.063	-0.035	8.095	0.236	0.236	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.790	-0.896	4.568	0.707	0.873	-0.001	-0.011	-0.154	0.000
30	A	31	ASN	0	-0.093	-0.039	7.531	0.294	0.294	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.017	0.031	10.655	0.058	0.058	0.000	0.000	0.000	0.000
32	A	33	ASN	0	-0.006	-0.020	10.939	0.208	0.208	0.000	0.000	0.000	0.000
33	A	34	THR	0	-0.040	-0.014	12.375	0.063	0.063	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.795	0.898	5.537	-1.301	-1.301	0.000	0.000	0.000	0.000
35	A	36	LEU	0	0.005	0.005	9.967	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.020	0.006	9.081	-0.071	-0.071	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.014	0.003	11.428	0.018	0.018	0.000	0.000	0.000	0.000
38	A	39	PRO	0	-0.009	0.012	12.991	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	40	LEU	0	0.006	0.003	12.919	-0.040	-0.040	0.000	0.000	0.000	0.000
40	A	41	THR	0	-0.042	-0.045	16.445	0.043	0.043	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.048	0.024	20.018	-0.018	-0.018	0.000	0.000	0.000	0.000
42	A	43	ILE	0	0.038	0.018	21.965	0.002	0.002	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.910	-0.968	24.031	-0.064	-0.064	0.000	0.000	0.000	0.000
44	A	45	LEU	0	-0.084	-0.035	23.910	0.010	0.010	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.060	-0.024	23.159	0.003	0.003	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.763	-0.853	27.126	-0.056	-0.056	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.783	0.868	30.544	0.054	0.054	0.000	0.000	0.000	0.000
48	A	49	LYS	1	0.851	0.909	24.994	0.102	0.102	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.042	0.036	28.133	0.003	0.003	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.020	0.005	24.434	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	52	SER	0	-0.068	-0.067	21.268	0.013	0.013	0.000	0.000	0.000	0.000
52	A	53	HIS	0	-0.024	0.009	23.108	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	54	LEU	0	0.055	0.032	21.608	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	55	CYS	0	-0.050	-0.008	20.429	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.073	0.044	17.160	0.027	0.027	0.000	0.000	0.000	0.000
56	A	57	THR	0	-0.027	-0.008	19.437	0.023	0.023	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.037	-0.013	14.306	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	59	HIS	1	0.837	0.888	17.346	0.230	0.230	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.012	0.004	13.273	-0.036	-0.036	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.863	-0.925	15.933	-0.069	-0.069	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.886	-0.945	13.713	-0.110	-0.110	0.000	0.000	0.000	0.000
62	A	63	GLY	0	-0.014	-0.014	17.448	0.021	0.021	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.850	-0.892	18.960	-0.163	-0.163	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.027	-0.026	17.093	0.021	0.021	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.012	-0.004	19.582	-0.019	-0.019	0.000	0.000	0.000	0.000
66	A	67	MET	0	0.007	0.009	12.916	0.002	0.002	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.003	-0.005	17.580	0.005	0.005	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.037	-0.013	17.098	0.003	0.003	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.011	-0.009	18.478	-0.004	-0.004	0.000	0.000	0.000	0.000
70	A	71	GLN	0	-0.070	-0.022	19.339	0.034	0.034	0.000	0.000	0.000	0.000
71	A	72	MET	0	-0.020	0.010	14.593	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.013	-0.006	15.278	0.028	0.028	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.030	0.024	13.989	0.009	0.009	0.000	0.000	0.000	0.000
74	A	75	VAL	0	-0.025	-0.007	11.694	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	76	PRO	0	0.030	0.003	12.703	0.057	0.057	0.000	0.000	0.000	0.000
76	A	77	VAL	0	0.055	0.016	7.704	-0.040	-0.040	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.881	0.938	10.128	-0.461	-0.461	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.030	-0.017	11.910	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.018	0.027	6.959	-0.120	-0.120	0.000	0.000	0.000	0.000
80	A	81	SER	0	0.008	-0.002	9.486	0.099	0.099	0.000	0.000	0.000	0.000
81	A	82	GLU	-1	-0.828	-0.912	10.254	0.148	0.148	0.000	0.000	0.000	0.000
82	A	83	PRO	0	0.020	0.017	5.911	-0.069	-0.069	0.000	0.000	0.000	0.000
83	A	84	VAL	0	-0.037	-0.023	7.789	-0.010	-0.010	0.000	0.000	0.000	0.000
84	A	85	ASN	0	0.036	0.011	8.821	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	86	GLU	-1	-0.852	-0.894	5.321	-1.460	-1.460	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.005	-0.002	7.276	0.300	0.300	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.018	-0.023	6.443	0.166	0.166	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.031	-0.028	8.430	0.129	0.129	0.000	0.000	0.000	0.000
89	A	90	PHE	0	-0.016	-0.009	11.560	0.098	0.098	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.964	0.988	9.367	0.894	0.894	0.000	0.000	0.000	0.000
91	A	92	ASN	0	-0.025	-0.018	11.673	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	93	GLU	-1	-0.808	-0.887	15.112	-0.299	-0.299	0.000	0.000	0.000	0.000
93	A	94	ILE	0	0.003	-0.001	11.329	0.037	0.037	0.000	0.000	0.000	0.000
94	A	95	ILE	0	-0.010	-0.014	11.177	0.041	0.041	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.015	0.012	14.800	0.059	0.059	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.001	0.015	17.553	0.046	0.046	0.000	0.000	0.000	0.000
97	A	98	ILE	0	-0.024	-0.028	13.342	0.040	0.040	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.882	-0.929	17.855	-0.258	-0.258	0.000	0.000	0.000	0.000
99	A	100	PHE	0	-0.021	0.005	20.101	0.042	0.042	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.070	-0.036	19.649	0.029	0.029	0.000	0.000	0.000	0.000
101	A	102	ILE	0	-0.086	-0.041	18.641	0.025	0.025	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.060	-0.054	22.779	0.026	0.026	0.000	0.000	0.000	0.000
103	A	104	GLY	0	-0.020	0.022	25.187	0.015	0.015	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.015	-0.022	26.251	-0.010	-0.010	0.000	0.000	0.000	0.000

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