FMO DATABASE

FMODB ID: MVVLZ

Calculation Name: 4R7V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4R7V

Chain ID: A

ChEMBL ID:

UniProt ID: Q96B67

Base Structure: X-ray

Registration Date: 2023-06-21

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	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	158
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1461883.894102
FMO2-HF: Nuclear repulsion	1398719.263528
FMO2-HF: Total energy	-63164.630575
FMO2-MP2: Total energy	-63353.21273

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:4:GLY)

Summations of interaction energy for fragment #1(A:4: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.
-5.011	-0.152	6.768	-6.164	-5.462	-0.043

Interaction energy analysis for fragmet #1(A:4:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.063 / q_NPA : 0.029

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	6	VAL	0	0.059	0.030	3.805	0.288	1.960	-0.018	-0.890	-0.764	0.002
4	A	7	LYS	1	0.855	0.919	6.427	0.487	0.487	0.000	0.000	0.000	0.000
5	A	8	SER	0	0.031	0.016	9.267	0.128	0.128	0.000	0.000	0.000	0.000
6	A	9	LEU	0	0.046	0.018	11.762	-0.078	-0.078	0.000	0.000	0.000	0.000
7	A	10	THR	0	-0.025	-0.009	13.885	0.055	0.055	0.000	0.000	0.000	0.000
8	A	11	ILE	0	0.043	0.021	17.556	-0.011	-0.011	0.000	0.000	0.000	0.000
9	A	12	SER	0	-0.023	-0.010	20.479	0.009	0.009	0.000	0.000	0.000	0.000
10	A	13	PHE	0	-0.011	-0.015	23.063	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	14	ASP	-1	-0.832	-0.927	25.481	-0.130	-0.130	0.000	0.000	0.000	0.000
12	A	15	CYS	0	-0.010	-0.027	27.890	-0.002	-0.002	0.000	0.000	0.000	0.000
13	A	16	LEU	0	0.002	0.012	31.215	0.004	0.004	0.000	0.000	0.000	0.000
14	A	17	ASN	0	-0.053	-0.030	33.805	0.005	0.005	0.000	0.000	0.000	0.000
15	A	18	ASP	-1	-0.874	-0.930	33.143	-0.049	-0.049	0.000	0.000	0.000	0.000
16	A	19	SER	0	-0.045	-0.019	33.779	0.003	0.003	0.000	0.000	0.000	0.000
17	A	20	ASN	0	-0.031	-0.011	34.863	0.000	0.000	0.000	0.000	0.000	0.000
18	A	21	VAL	0	-0.021	-0.016	31.034	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	22	PRO	0	-0.001	0.004	30.587	0.005	0.005	0.000	0.000	0.000	0.000
20	A	23	VAL	0	-0.056	-0.020	33.543	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	24	TYR	0	0.007	0.001	30.756	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	25	SER	0	0.006	-0.026	36.578	0.001	0.001	0.000	0.000	0.000	0.000
23	A	26	SER	0	-0.015	-0.025	38.618	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	27	GLY	0	-0.025	-0.012	39.660	0.004	0.004	0.000	0.000	0.000	0.000
25	A	28	ASP	-1	-0.843	-0.898	35.917	-0.085	-0.085	0.000	0.000	0.000	0.000
26	A	29	THR	0	-0.023	-0.020	31.534	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	30	VAL	0	-0.033	-0.007	28.554	0.001	0.001	0.000	0.000	0.000	0.000
28	A	31	SER	0	0.045	0.007	27.727	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	32	GLY	0	0.012	0.006	24.769	0.003	0.003	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.841	0.936	19.737	0.144	0.144	0.000	0.000	0.000	0.000
31	A	34	VAL	0	-0.019	-0.002	15.398	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	35	ASN	0	-0.041	-0.025	15.856	0.020	0.020	0.000	0.000	0.000	0.000
33	A	36	LEU	0	-0.009	-0.012	9.259	-0.073	-0.073	0.000	0.000	0.000	0.000
34	A	37	GLU	-1	-0.871	-0.919	10.319	-0.102	-0.102	0.000	0.000	0.000	0.000
35	A	38	VAL	0	0.001	-0.007	4.081	-0.440	-0.389	0.000	-0.018	-0.033	0.000
36	A	39	THR	0	-0.002	0.003	3.457	0.068	0.216	0.003	-0.085	-0.066	0.000
37	A	40	GLY	0	0.025	0.006	2.475	-0.540	0.075	3.249	-2.257	-1.606	-0.017
38	A	41	GLU	-1	-0.877	-0.950	2.724	-1.451	-1.293	0.551	-0.225	-0.484	-0.003
39	A	42	ILE	0	-0.066	-0.036	2.398	-6.108	-3.977	2.984	-2.665	-2.450	-0.025
40	A	43	ARG	1	0.987	1.007	4.423	1.838	1.922	-0.001	-0.024	-0.059	0.000
41	A	44	VAL	0	-0.055	-0.047	7.872	-0.275	-0.275	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.776	0.889	10.633	0.597	0.597	0.000	0.000	0.000	0.000
43	A	46	SER	0	0.048	0.014	14.303	0.082	0.082	0.000	0.000	0.000	0.000
44	A	47	LEU	0	-0.034	-0.006	14.274	-0.110	-0.110	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.954	0.991	16.012	0.425	0.425	0.000	0.000	0.000	0.000
46	A	49	ILE	0	0.006	0.000	19.541	-0.032	-0.032	0.000	0.000	0.000	0.000
47	A	50	HIS	0	-0.053	-0.045	22.116	0.002	0.002	0.000	0.000	0.000	0.000
48	A	51	ALA	0	0.006	0.011	25.394	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	52	ARG	1	0.781	0.893	28.120	0.169	0.169	0.000	0.000	0.000	0.000
50	A	53	GLY	0	0.076	0.041	31.235	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	54	HIS	0	-0.089	-0.036	33.223	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	ALA	0	0.039	0.030	36.812	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	56	LYS	1	0.948	0.973	35.747	0.137	0.137	0.000	0.000	0.000	0.000
54	A	57	VAL	0	-0.007	0.007	40.662	0.001	0.001	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.916	0.947	39.829	0.106	0.106	0.000	0.000	0.000	0.000
56	A	59	TRP	0	-0.052	-0.034	46.013	0.001	0.001	0.000	0.000	0.000	0.000
57	A	60	THR	0	0.013	0.010	49.753	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	61	GLU	-1	-0.835	-0.897	52.386	-0.064	-0.064	0.000	0.000	0.000	0.000
59	A	62	SER	0	-0.009	-0.006	55.477	0.000	0.000	0.000	0.000	0.000	0.000
60	A	72	THR	0	-0.059	-0.058	54.192	0.001	0.001	0.000	0.000	0.000	0.000
61	A	73	GLN	0	-0.010	0.017	52.361	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	74	ASN	0	-0.019	-0.017	48.229	0.003	0.003	0.000	0.000	0.000	0.000
63	A	75	TYR	0	0.038	0.035	47.774	-0.003	-0.003	0.000	0.000	0.000	0.000
64	A	76	THR	0	-0.054	-0.055	43.052	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	77	GLU	-1	-0.943	-0.956	44.357	-0.084	-0.084	0.000	0.000	0.000	0.000
66	A	78	GLU	-1	-0.910	-0.957	36.451	-0.144	-0.144	0.000	0.000	0.000	0.000
67	A	79	VAL	0	0.037	0.028	40.615	0.002	0.002	0.000	0.000	0.000	0.000
68	A	80	GLU	-1	-0.889	-0.968	35.051	-0.155	-0.155	0.000	0.000	0.000	0.000
69	A	81	TYR	0	0.004	-0.005	37.383	0.005	0.005	0.000	0.000	0.000	0.000
70	A	82	PHE	0	0.045	0.009	31.542	0.003	0.003	0.000	0.000	0.000	0.000
71	A	83	ASN	0	-0.035	-0.021	31.020	-0.019	-0.019	0.000	0.000	0.000	0.000
72	A	84	HIS	0	0.078	0.059	27.108	0.009	0.009	0.000	0.000	0.000	0.000
73	A	85	LYS	1	0.908	0.938	26.263	0.189	0.189	0.000	0.000	0.000	0.000
74	A	86	ASP	-1	-0.839	-0.913	24.157	-0.186	-0.186	0.000	0.000	0.000	0.000
75	A	87	ILE	0	-0.037	-0.016	19.643	-0.037	-0.037	0.000	0.000	0.000	0.000
76	A	88	LEU	0	-0.013	0.005	18.129	0.010	0.010	0.000	0.000	0.000	0.000
77	A	89	ILE	0	-0.034	-0.025	13.054	0.006	0.006	0.000	0.000	0.000	0.000
78	A	90	GLY	0	-0.018	-0.009	16.430	-0.033	-0.033	0.000	0.000	0.000	0.000
79	A	91	HIS	0	0.057	0.014	17.160	0.022	0.022	0.000	0.000	0.000	0.000
80	A	92	GLU	-1	-0.969	-0.988	19.180	-0.283	-0.283	0.000	0.000	0.000	0.000
81	A	93	ARG	1	0.783	0.886	21.097	0.186	0.186	0.000	0.000	0.000	0.000
82	A	94	ASP	-1	-0.889	-0.963	18.059	-0.516	-0.516	0.000	0.000	0.000	0.000
83	A	95	ASP	-1	-0.851	-0.919	20.207	-0.209	-0.209	0.000	0.000	0.000	0.000
84	A	96	ASP	-1	-0.881	-0.913	18.266	-0.374	-0.374	0.000	0.000	0.000	0.000
85	A	97	ASN	0	-0.140	-0.093	21.180	0.033	0.033	0.000	0.000	0.000	0.000
86	A	98	SER	0	0.013	-0.018	22.602	0.030	0.030	0.000	0.000	0.000	0.000
87	A	99	GLU	-1	-0.838	-0.876	21.489	-0.205	-0.205	0.000	0.000	0.000	0.000
88	A	100	GLU	-1	-0.863	-0.924	17.088	-0.290	-0.290	0.000	0.000	0.000	0.000
89	A	101	GLY	0	-0.031	-0.018	16.963	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	102	PHE	0	-0.036	-0.040	11.966	-0.025	-0.025	0.000	0.000	0.000	0.000
91	A	103	HIS	0	0.060	0.049	11.354	0.100	0.100	0.000	0.000	0.000	0.000
92	A	104	THR	0	-0.003	-0.008	7.210	-0.220	-0.220	0.000	0.000	0.000	0.000
93	A	105	ILE	0	-0.061	-0.025	7.238	0.144	0.144	0.000	0.000	0.000	0.000
94	A	106	HIS	0	0.079	0.024	6.025	-0.069	-0.069	0.000	0.000	0.000	0.000
95	A	107	SER	0	-0.001	0.008	6.416	-0.135	-0.135	0.000	0.000	0.000	0.000
96	A	108	GLY	0	-0.004	0.005	7.311	-0.020	-0.020	0.000	0.000	0.000	0.000
97	A	109	ARG	1	0.841	0.912	9.858	0.022	0.022	0.000	0.000	0.000	0.000
98	A	110	HIS	1	0.826	0.901	9.525	0.233	0.233	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.792	-0.898	13.766	-0.190	-0.190	0.000	0.000	0.000	0.000
100	A	112	TYR	0	-0.026	-0.015	11.365	0.040	0.040	0.000	0.000	0.000	0.000
101	A	113	ALA	0	0.034	0.013	18.054	-0.013	-0.013	0.000	0.000	0.000	0.000
102	A	114	PHE	0	-0.006	-0.001	21.522	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	115	SER	0	0.038	0.006	24.058	0.009	0.009	0.000	0.000	0.000	0.000
104	A	116	PHE	0	-0.059	-0.021	27.377	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	117	GLU	-1	-0.898	-0.941	30.546	-0.090	-0.090	0.000	0.000	0.000	0.000
106	A	118	LEU	0	-0.053	-0.023	33.549	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	119	PRO	0	-0.009	-0.011	36.057	0.005	0.005	0.000	0.000	0.000	0.000
108	A	120	GLN	0	0.093	0.037	39.335	0.003	0.003	0.000	0.000	0.000	0.000
109	A	121	THR	0	-0.044	-0.004	42.431	0.003	0.003	0.000	0.000	0.000	0.000
110	A	122	PRO	0	0.038	0.017	42.994	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	123	LEU	0	0.016	0.014	37.987	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	124	ALA	0	0.029	0.029	41.542	0.002	0.002	0.000	0.000	0.000	0.000
113	A	125	THR	0	0.054	0.036	40.258	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	126	SER	0	-0.013	-0.005	35.610	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	127	PHE	0	-0.014	-0.003	38.458	0.006	0.006	0.000	0.000	0.000	0.000
116	A	128	GLU	-1	-0.739	-0.840	35.833	-0.139	-0.139	0.000	0.000	0.000	0.000
117	A	129	GLY	0	0.009	0.005	39.855	0.006	0.006	0.000	0.000	0.000	0.000
118	A	130	ARG	1	0.916	0.945	42.600	0.071	0.071	0.000	0.000	0.000	0.000
119	A	131	HIS	0	0.050	0.020	44.818	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	132	GLY	0	0.011	0.004	42.233	0.000	0.000	0.000	0.000	0.000	0.000
121	A	133	SER	0	-0.057	-0.017	37.951	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	134	VAL	0	-0.015	0.004	38.170	0.000	0.000	0.000	0.000	0.000	0.000
123	A	135	ARG	1	0.786	0.859	33.019	0.144	0.144	0.000	0.000	0.000	0.000
124	A	136	TYR	0	0.024	0.003	32.657	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	137	TRP	0	-0.039	-0.025	26.594	-0.010	-0.010	0.000	0.000	0.000	0.000
126	A	138	VAL	0	0.047	0.032	23.214	0.004	0.004	0.000	0.000	0.000	0.000
127	A	139	LYS	1	0.853	0.931	21.809	0.296	0.296	0.000	0.000	0.000	0.000
128	A	140	ALA	0	0.038	0.022	17.898	0.009	0.009	0.000	0.000	0.000	0.000
129	A	141	GLU	-1	-0.898	-0.969	17.514	-0.412	-0.412	0.000	0.000	0.000	0.000
130	A	142	LEU	0	0.005	0.006	9.487	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	143	HIS	0	0.016	-0.002	13.814	-0.091	-0.091	0.000	0.000	0.000	0.000
132	A	144	ARG	1	0.960	0.979	6.959	2.148	2.148	0.000	0.000	0.000	0.000
133	A	145	PRO	0	0.030	0.018	9.594	0.080	0.080	0.000	0.000	0.000	0.000
134	A	146	TRP	0	0.017	0.015	10.955	-0.179	-0.179	0.000	0.000	0.000	0.000
135	A	147	LEU	0	-0.038	-0.016	7.954	-0.128	-0.128	0.000	0.000	0.000	0.000
136	A	148	LEU	0	0.015	0.012	12.646	0.077	0.077	0.000	0.000	0.000	0.000
137	A	149	PRO	0	-0.012	-0.005	13.868	-0.117	-0.117	0.000	0.000	0.000	0.000
138	A	150	VAL	0	-0.034	-0.004	11.837	0.010	0.010	0.000	0.000	0.000	0.000
139	A	151	LYS	1	0.915	0.962	15.060	0.444	0.444	0.000	0.000	0.000	0.000
140	A	152	LEU	0	0.009	0.019	17.672	0.005	0.005	0.000	0.000	0.000	0.000
141	A	153	LYS	1	0.930	0.974	19.745	0.235	0.235	0.000	0.000	0.000	0.000
142	A	154	LYS	1	0.881	0.958	23.327	0.195	0.195	0.000	0.000	0.000	0.000
143	A	155	GLU	-1	-0.910	-0.965	25.154	-0.164	-0.164	0.000	0.000	0.000	0.000
144	A	156	PHE	0	-0.020	-0.008	28.800	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	157	THR	0	-0.009	-0.008	30.906	0.001	0.001	0.000	0.000	0.000	0.000
146	A	158	VAL	0	0.033	0.018	34.603	0.001	0.001	0.000	0.000	0.000	0.000
147	A	159	PHE	0	-0.008	-0.007	37.344	0.000	0.000	0.000	0.000	0.000	0.000
148	A	160	GLU	-1	-0.934	-0.967	40.996	-0.074	-0.074	0.000	0.000	0.000	0.000
149	A	161	HIS	0	-0.025	-0.021	43.582	0.003	0.003	0.000	0.000	0.000	0.000
150	A	162	ILE	0	-0.039	-0.024	39.968	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	163	ASP	-1	-0.877	-0.933	44.294	-0.051	-0.051	0.000	0.000	0.000	0.000
152	A	164	ILE	0	-0.060	-0.021	45.031	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	165	ASN	0	0.007	0.006	43.201	0.005	0.005	0.000	0.000	0.000	0.000
154	A	166	LEU	0	-0.028	-0.014	46.964	-0.001	-0.001	0.000	0.000	0.000	0.000
155	A	167	GLU	-1	-0.912	-0.961	48.267	-0.038	-0.038	0.000	0.000	0.000	0.000
156	A	168	HIS	0	-0.059	-0.023	50.767	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	169	HIS	0	0.016	0.011	50.718	0.002	0.002	0.000	0.000	0.000	0.000
158	A	170	HIS	0	-0.036	-0.015	55.706	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY)