FMO DATABASE

FMODB ID: 396ML

Calculation Name: 4RUV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4RUV

Chain ID: A

ChEMBL ID:

UniProt ID: Q2G000

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:

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	106
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-861898.920071
FMO2-HF: Nuclear repulsion	818759.530491
FMO2-HF: Total energy	-43139.38958
FMO2-MP2: Total energy	-43263.5676

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-16.443	-6.729	12.723	-6.873	-15.562	-0.03

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : 0.001

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	3	SER	0	0.010	0.021	3.784	-0.985	0.760	-0.020	-0.809	-0.916	0.005
4	A	4	ILE	0	0.031	0.021	5.937	0.125	0.125	0.000	0.000	0.000	0.000
5	A	5	LYS	1	0.988	0.990	8.572	-0.128	-0.128	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.063	-0.052	11.793	-0.021	-0.021	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.132	0.057	13.686	0.067	0.067	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.866	-0.930	15.905	0.273	0.273	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.042	-0.022	11.697	0.041	0.041	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.054	0.020	10.720	0.038	0.038	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.888	0.936	12.660	-0.226	-0.226	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.059	-0.027	14.389	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.009	0.006	9.176	-0.001	-0.001	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.011	0.008	11.684	0.044	0.044	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.061	-0.017	13.340	-0.037	-0.037	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.041	-0.042	13.095	-0.049	-0.049	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.832	-0.929	15.057	0.292	0.292	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.057	-0.014	12.736	-0.051	-0.051	0.000	0.000	0.000	0.000
19	A	19	PRO	0	-0.013	0.019	12.498	0.041	0.041	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.013	0.018	8.178	0.059	0.059	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.001	0.006	5.737	-0.213	-0.145	-0.001	-0.007	-0.059	0.000
22	A	22	VAL	0	-0.011	-0.009	5.641	0.843	0.989	-0.001	-0.011	-0.135	0.000
23	A	23	LYS	1	0.790	0.886	2.381	-1.497	-0.321	0.995	-0.437	-1.735	0.002
24	A	24	PHE	0	-0.008	-0.008	5.294	-0.189	-0.104	-0.001	-0.010	-0.074	0.000
25	A	25	GLU	-1	-0.813	-0.935	6.121	0.002	0.002	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.034	0.004	8.858	-0.030	-0.030	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.039	0.021	11.312	-0.080	-0.080	0.000	0.000	0.000	0.000
28	A	28	TRP	0	0.028	0.010	12.525	-0.080	-0.080	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.029	0.030	11.643	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	30	PRO	0	-0.013	-0.010	11.809	-0.076	-0.076	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.829	-0.931	11.480	-0.281	-0.281	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.060	-0.025	7.818	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.934	0.950	7.268	0.178	0.178	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.007	0.002	8.762	-0.192	-0.192	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.015	0.017	4.144	-0.098	0.078	0.000	-0.027	-0.149	0.000
36	A	36	ASP	-1	-0.808	-0.910	3.438	-4.042	-3.465	0.026	-0.247	-0.356	-0.002
37	A	37	LEU	0	-0.100	-0.037	5.537	-0.111	-0.111	0.000	0.000	0.000	0.000
38	A	38	TRP	0	-0.013	-0.012	7.193	0.120	0.120	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.009	0.000	2.475	-0.136	-0.108	2.173	-0.428	-1.772	-0.003
40	A	40	ASP	-1	-0.870	-0.933	4.982	-4.356	-4.234	-0.001	-0.005	-0.115	0.000
41	A	41	PRO	0	-0.001	-0.012	5.905	0.389	0.389	0.000	0.000	0.000	0.000
42	A	42	ILE	0	-0.017	0.006	6.093	0.297	0.297	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.009	-0.023	2.716	-0.752	0.130	0.270	-0.232	-0.920	-0.002
44	A	44	GLU	-1	-0.948	-0.963	5.684	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	GLN	0	-0.034	-0.012	9.147	0.177	0.177	0.000	0.000	0.000	0.000
46	A	46	TYR	0	-0.108	-0.069	8.085	0.197	0.197	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.088	0.034	8.543	0.167	0.167	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.975	-0.965	9.559	0.429	0.429	0.000	0.000	0.000	0.000
49	A	49	TYR	0	-0.084	-0.042	8.710	0.043	0.043	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.010	0.003	6.518	0.044	0.044	0.000	0.000	0.000	0.000
51	A	51	TRP	0	0.032	0.013	2.238	-3.447	-1.875	3.175	-1.170	-3.577	-0.002
52	A	52	TYR	0	-0.030	-0.030	2.539	-3.920	-1.210	1.593	-2.116	-2.186	-0.024
53	A	53	THR	0	0.036	0.012	2.083	1.685	1.894	4.514	-1.313	-3.410	-0.004
54	A	54	VAL	0	0.010	-0.004	4.189	-1.133	-1.065	0.002	-0.047	-0.023	0.000
55	A	55	ASN	0	0.027	0.014	7.950	0.066	0.066	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.856	0.877	10.352	-0.179	-0.179	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.854	-0.916	13.141	0.072	0.072	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.987	-0.963	11.763	0.059	0.059	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.049	-0.030	11.298	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.879	-0.945	14.957	0.192	0.192	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.870	-0.933	17.581	0.209	0.209	0.000	0.000	0.000	0.000
62	A	62	VAL	0	-0.021	-0.012	12.714	0.010	0.010	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.026	0.005	13.710	0.044	0.044	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.022	-0.024	15.768	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.921	-0.945	19.073	0.216	0.216	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.110	-0.059	15.079	0.023	0.023	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.935	-0.974	16.601	0.254	0.254	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.013	-0.002	12.571	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.036	-0.020	15.218	-0.039	-0.039	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.042	-0.021	14.546	-0.057	-0.057	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.074	0.008	10.434	0.085	0.085	0.000	0.000	0.000	0.000
72	A	72	PRO	0	0.043	-0.004	6.753	-0.061	-0.061	0.000	0.000	0.000	0.000
73	A	73	SER	0	-0.030	-0.043	8.722	-0.155	-0.155	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.013	0.002	4.372	0.181	0.331	-0.001	-0.014	-0.135	0.000
75	A	75	LEU	0	-0.044	-0.006	7.878	-0.295	-0.295	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.017	0.017	9.274	0.336	0.336	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.014	-0.006	10.916	-0.119	-0.119	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.917	0.961	13.490	-0.300	-0.300	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.058	-0.045	16.162	-0.036	-0.036	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.015	0.020	16.848	-0.035	-0.035	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.912	-0.933	18.100	0.293	0.293	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.824	0.896	14.531	-0.345	-0.345	0.000	0.000	0.000	0.000
83	A	83	ILE	0	-0.026	-0.021	15.147	-0.056	-0.056	0.000	0.000	0.000	0.000
84	A	84	ALA	0	0.007	0.009	13.571	-0.059	-0.059	0.000	0.000	0.000	0.000
85	A	85	HIS	0	0.026	0.008	12.848	0.132	0.132	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.009	0.018	9.200	-0.086	-0.086	0.000	0.000	0.000	0.000
87	A	87	HIS	0	0.041	-0.004	11.261	0.088	0.088	0.000	0.000	0.000	0.000
88	A	88	SER	0	0.067	0.032	11.400	-0.060	-0.060	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.089	-0.045	12.413	-0.072	-0.072	0.000	0.000	0.000	0.000
90	A	90	ASN	0	-0.061	-0.029	14.256	-0.052	-0.052	0.000	0.000	0.000	0.000
91	A	91	ALA	0	0.026	0.018	8.933	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.912	0.950	9.870	0.057	0.057	0.000	0.000	0.000	0.000
93	A	93	SER	0	0.000	0.008	11.694	-0.049	-0.049	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.089	0.026	9.877	0.048	0.048	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.909	-0.938	10.922	-0.158	-0.158	0.000	0.000	0.000	0.000
96	A	96	GLN	0	0.011	-0.006	12.639	0.020	0.020	0.000	0.000	0.000	0.000
97	A	97	VAL	0	-0.015	-0.007	6.721	0.087	0.087	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.935	-0.966	10.045	-0.341	-0.341	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.039	-0.018	11.787	0.072	0.072	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.001	0.003	10.129	0.041	0.041	0.000	0.000	0.000	0.000
101	A	101	LEU	0	0.000	-0.004	7.623	0.076	0.076	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.043	0.024	12.220	0.031	0.031	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.995	-1.014	15.372	0.066	0.066	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.070	-0.024	13.525	0.033	0.033	0.000	0.000	0.000	0.000
105	A	105	PHE	0	-0.015	-0.005	11.090	0.026	0.026	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.875	0.962	16.386	-0.088	-0.088	0.000	0.000	0.000	0.000

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