FMO DATABASE

FMODB ID: Q12GY

Calculation Name: 3VJZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VJZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K0P4

Base Structure: X-ray

Registration Date: 2023-06-20

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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1666577.197275
FMO2-HF: Nuclear repulsion	1602280.135542
FMO2-HF: Total energy	-64297.061734
FMO2-MP2: Total energy	-64487.046141

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:HIS)

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

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.
-46.159	-39.394	7.731	-6.531	-7.965	-0.068

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.047

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	THR	0	0.024	0.025	3.857	-2.081	-0.805	-0.011	-0.523	-0.742	0.003
4	A	3	ALA	0	-0.009	-0.009	6.084	1.185	1.185	0.000	0.000	0.000	0.000
5	A	4	LEU	0	0.012	0.030	8.843	-0.520	-0.520	0.000	0.000	0.000	0.000
6	A	5	THR	0	-0.044	-0.027	11.385	0.421	0.421	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.030	-0.012	14.141	-0.022	-0.022	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.060	0.031	16.154	0.147	0.147	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.873	-0.951	18.492	-0.494	-0.494	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.880	-0.949	21.747	-0.690	-0.690	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.065	0.040	18.787	0.033	0.033	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.767	0.883	23.153	0.529	0.529	0.000	0.000	0.000	0.000
13	A	12	GLN	0	-0.096	-0.056	26.076	0.073	0.073	0.000	0.000	0.000	0.000
14	A	13	GLN	0	0.055	0.059	22.526	0.032	0.032	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.899	-0.949	27.928	-0.384	-0.384	0.000	0.000	0.000	0.000
16	A	15	PRO	0	-0.013	-0.021	29.166	-0.035	-0.035	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.018	-0.017	29.055	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.059	0.040	26.410	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.037	0.034	24.143	-0.061	-0.061	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.058	-0.040	24.117	-0.056	-0.056	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.022	-0.002	22.424	-0.059	-0.059	0.000	0.000	0.000	0.000
22	A	21	THR	0	0.053	0.020	19.590	-0.106	-0.106	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.045	-0.021	19.480	-0.126	-0.126	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.043	-0.022	19.610	-0.086	-0.086	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.010	-0.001	18.117	-0.053	-0.053	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.015	0.013	15.299	-0.177	-0.177	0.000	0.000	0.000	0.000
27	A	26	TYR	0	-0.037	-0.028	14.799	-0.130	-0.130	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.004	0.009	15.657	-0.077	-0.077	0.000	0.000	0.000	0.000
29	A	28	GLU	-1	-0.815	-0.923	10.010	-3.196	-3.196	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.082	-0.039	9.639	0.076	0.076	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.044	-0.041	11.153	-0.043	-0.043	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.027	-0.016	13.204	0.088	0.088	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.006	-0.006	6.655	-0.193	-0.193	0.000	0.000	0.000	0.000
34	A	33	THR	0	-0.001	0.024	6.805	-0.378	-0.378	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.031	-0.007	8.753	0.408	0.408	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.785	-0.884	12.230	-0.514	-0.514	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.880	-0.928	7.918	-0.260	-0.260	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.120	-0.063	11.380	0.206	0.206	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.027	0.001	13.043	0.146	0.146	0.000	0.000	0.000	0.000
40	A	39	SER	0	-0.094	-0.043	15.942	0.116	0.116	0.000	0.000	0.000	0.000
41	A	40	CYS	0	-0.113	-0.055	18.157	0.060	0.060	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.012	-0.010	16.834	0.041	0.041	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.025	0.008	17.714	-0.032	-0.032	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.858	-0.941	14.419	-0.820	-0.820	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.868	-0.946	16.456	-0.622	-0.622	0.000	0.000	0.000	0.000
46	A	45	GLN	0	-0.028	-0.023	19.088	-0.070	-0.070	0.000	0.000	0.000	0.000
47	A	46	HIS	0	-0.047	-0.023	12.683	-0.243	-0.243	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.024	-0.013	14.810	-0.198	-0.198	0.000	0.000	0.000	0.000
49	A	48	LEU	0	-0.053	-0.029	15.949	-0.056	-0.056	0.000	0.000	0.000	0.000
50	A	49	THR	0	-0.006	-0.003	14.441	0.035	0.035	0.000	0.000	0.000	0.000
51	A	50	ALA	0	0.032	0.029	12.563	-0.067	-0.067	0.000	0.000	0.000	0.000
52	A	51	PHE	0	-0.032	-0.028	14.138	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	52	CYS	0	-0.003	-0.001	17.292	0.081	0.081	0.000	0.000	0.000	0.000
54	A	53	TYR	0	-0.012	0.001	11.625	0.189	0.189	0.000	0.000	0.000	0.000
55	A	54	LEU	0	-0.025	-0.024	15.423	0.010	0.010	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.807	-0.893	16.348	-0.736	-0.736	0.000	0.000	0.000	0.000
57	A	56	SER	0	-0.022	-0.020	18.763	0.043	0.043	0.000	0.000	0.000	0.000
58	A	57	GLN	0	0.012	0.020	15.395	0.064	0.064	0.000	0.000	0.000	0.000
59	A	58	VAL	0	-0.080	-0.044	17.734	0.076	0.076	0.000	0.000	0.000	0.000
60	A	59	GLU	-1	-0.882	-0.944	20.239	-0.588	-0.588	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.992	-0.991	22.682	-0.566	-0.566	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.036	0.019	21.300	0.058	0.058	0.000	0.000	0.000	0.000
63	A	62	GLY	0	-0.074	-0.030	20.698	0.014	0.014	0.000	0.000	0.000	0.000
64	A	63	PHE	0	-0.003	-0.046	15.911	-0.137	-0.137	0.000	0.000	0.000	0.000
65	A	64	VAL	0	-0.020	0.001	15.648	-0.175	-0.175	0.000	0.000	0.000	0.000
66	A	65	GLN	0	0.024	0.016	15.592	-0.042	-0.042	0.000	0.000	0.000	0.000
67	A	66	LEU	0	0.007	0.028	11.862	-0.144	-0.144	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.063	-0.056	10.556	-0.331	-0.331	0.000	0.000	0.000	0.000
69	A	68	ALA	0	-0.059	-0.026	10.937	-0.272	-0.272	0.000	0.000	0.000	0.000
70	A	69	SER	0	-0.030	-0.017	12.364	0.032	0.032	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.059	0.021	9.042	-0.117	-0.117	0.000	0.000	0.000	0.000
72	A	71	TYR	0	-0.026	-0.060	6.686	-0.025	-0.025	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.080	0.042	7.722	0.193	0.193	0.000	0.000	0.000	0.000
74	A	73	GLU	-1	-0.906	-0.953	2.169	-30.814	-27.182	7.581	-5.329	-5.883	-0.066
75	A	74	TYR	0	0.008	-0.009	2.922	-3.050	-1.193	0.161	-0.679	-1.340	-0.005
76	A	75	ILE	0	-0.008	0.011	6.853	1.071	1.071	0.000	0.000	0.000	0.000
77	A	76	PHE	0	-0.017	-0.016	9.543	0.617	0.617	0.000	0.000	0.000	0.000
78	A	77	ARG	1	0.827	0.901	5.253	1.418	1.418	0.000	0.000	0.000	0.000
79	A	78	ASN	0	0.077	0.065	5.508	0.240	0.240	0.000	0.000	0.000	0.000
80	A	79	PRO	0	0.014	0.004	8.103	0.167	0.167	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.074	0.054	11.769	0.179	0.179	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.045	0.014	13.528	0.166	0.166	0.000	0.000	0.000	0.000
83	A	82	ASP	-1	-0.921	-0.978	15.264	-0.327	-0.327	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.036	-0.029	14.546	0.125	0.125	0.000	0.000	0.000	0.000
85	A	84	LEU	0	0.075	0.048	17.205	0.078	0.078	0.000	0.000	0.000	0.000
86	A	85	ARG	1	0.819	0.884	18.139	0.556	0.556	0.000	0.000	0.000	0.000
87	A	86	ARG	1	0.874	0.918	19.251	0.344	0.344	0.000	0.000	0.000	0.000
88	A	87	TRP	0	0.033	0.026	20.022	0.036	0.036	0.000	0.000	0.000	0.000
89	A	88	LYS	1	0.791	0.884	23.971	0.309	0.309	0.000	0.000	0.000	0.000
90	A	89	ILE	0	0.100	0.095	22.531	0.023	0.023	0.000	0.000	0.000	0.000
91	A	90	LYS	1	0.852	0.909	22.917	0.342	0.342	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.013	0.005	23.668	0.001	0.001	0.000	0.000	0.000	0.000
93	A	92	VAL	0	0.123	0.059	19.443	-0.008	-0.008	0.000	0.000	0.000	0.000
94	A	93	PRO	0	-0.016	-0.010	18.711	-0.045	-0.045	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.881	0.949	19.152	0.378	0.378	0.000	0.000	0.000	0.000
96	A	95	VAL	0	0.022	0.019	20.185	0.025	0.025	0.000	0.000	0.000	0.000
97	A	96	LEU	0	0.020	0.018	15.113	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.839	-0.899	16.172	-0.598	-0.598	0.000	0.000	0.000	0.000
99	A	98	LYS	1	0.800	0.918	17.501	0.398	0.398	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.061	0.026	16.793	0.031	0.031	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.925	0.967	9.983	0.886	0.886	0.000	0.000	0.000	0.000
102	A	101	ALA	0	-0.043	-0.018	13.931	0.007	0.007	0.000	0.000	0.000	0.000
103	A	102	LEU	0	0.020	0.015	16.238	0.057	0.057	0.000	0.000	0.000	0.000
104	A	103	TYR	0	-0.072	-0.051	7.159	-0.015	-0.015	0.000	0.000	0.000	0.000
105	A	104	GLU	-1	-0.938	-0.988	9.951	-0.687	-0.687	0.000	0.000	0.000	0.000
106	A	105	GLN	0	-0.088	-0.035	12.849	0.133	0.133	0.000	0.000	0.000	0.000
107	A	106	HIS	0	-0.043	-0.029	14.244	0.103	0.103	0.000	0.000	0.000	0.000
108	A	107	GLY	0	0.049	0.029	10.513	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	108	LYS	1	0.980	0.992	5.825	-0.511	-0.511	0.000	0.000	0.000	0.000
110	A	109	THR	0	-0.022	-0.006	9.057	0.077	0.077	0.000	0.000	0.000	0.000
111	A	110	ILE	0	0.036	0.014	12.360	0.041	0.041	0.000	0.000	0.000	0.000
112	A	111	GLU	-1	-0.818	-0.879	6.132	-3.953	-3.953	0.000	0.000	0.000	0.000
113	A	112	THR	0	-0.057	-0.033	9.511	0.198	0.198	0.000	0.000	0.000	0.000
114	A	113	LEU	0	-0.049	-0.032	10.819	0.105	0.105	0.000	0.000	0.000	0.000
115	A	114	ALA	0	0.010	0.010	12.278	0.083	0.083	0.000	0.000	0.000	0.000
116	A	115	ASP	-1	-0.973	-0.977	10.420	-0.695	-0.695	0.000	0.000	0.000	0.000
117	A	116	GLY	0	-0.049	-0.020	12.551	0.117	0.117	0.000	0.000	0.000	0.000
118	A	117	GLY	0	-0.038	-0.021	15.571	0.081	0.081	0.000	0.000	0.000	0.000
119	A	118	ALA	0	-0.082	-0.028	17.045	0.043	0.043	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.850	-0.925	18.128	-0.572	-0.572	0.000	0.000	0.000	0.000
121	A	120	ILE	0	0.074	0.015	17.404	0.006	0.006	0.000	0.000	0.000	0.000
122	A	121	PRO	0	0.003	0.003	20.469	0.018	0.018	0.000	0.000	0.000	0.000
123	A	122	SER	0	-0.039	-0.025	22.053	0.048	0.048	0.000	0.000	0.000	0.000
124	A	123	LEU	0	-0.021	-0.009	15.845	0.032	0.032	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.933	0.966	19.717	0.639	0.639	0.000	0.000	0.000	0.000
126	A	125	LYS	1	0.920	0.961	21.848	0.341	0.341	0.000	0.000	0.000	0.000
127	A	126	GLN	0	-0.081	-0.034	19.948	0.035	0.035	0.000	0.000	0.000	0.000
128	A	127	PHE	0	-0.028	-0.017	17.078	0.025	0.025	0.000	0.000	0.000	0.000
129	A	128	PRO	0	0.044	0.017	20.619	-0.056	-0.056	0.000	0.000	0.000	0.000
130	A	129	GLU	-1	-0.850	-0.928	20.514	-0.458	-0.458	0.000	0.000	0.000	0.000
131	A	130	PHE	0	-0.039	-0.039	15.533	-0.019	-0.019	0.000	0.000	0.000	0.000
132	A	131	GLU	-1	-0.921	-0.951	21.299	-0.468	-0.468	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.966	-0.974	24.541	-0.352	-0.352	0.000	0.000	0.000	0.000
134	A	133	TRP	0	-0.007	-0.033	21.278	0.019	0.019	0.000	0.000	0.000	0.000
135	A	134	ASP	-1	-0.740	-0.866	21.202	-0.816	-0.816	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.007	0.009	23.389	0.005	0.005	0.000	0.000	0.000	0.000
137	A	136	ALA	0	0.007	-0.005	24.757	0.012	0.012	0.000	0.000	0.000	0.000
138	A	137	TYR	0	-0.125	-0.096	20.387	-0.026	-0.026	0.000	0.000	0.000	0.000
139	A	138	TYR	0	0.015	0.030	23.768	0.010	0.010	0.000	0.000	0.000	0.000
140	A	139	GLU	-1	-0.947	-0.975	26.495	-0.343	-0.343	0.000	0.000	0.000	0.000
141	A	140	ALA	0	-0.082	-0.047	24.583	0.021	0.021	0.000	0.000	0.000	0.000
142	A	141	ALA	0	0.045	0.013	24.247	0.017	0.017	0.000	0.000	0.000	0.000
143	A	142	GLU	-1	-0.901	-0.940	25.963	-0.373	-0.373	0.000	0.000	0.000	0.000
144	A	143	GLN	0	-0.112	-0.045	28.549	0.051	0.051	0.000	0.000	0.000	0.000
145	A	144	ASP	-1	-0.806	-0.948	24.791	-0.480	-0.480	0.000	0.000	0.000	0.000
146	A	145	LEU	0	0.022	0.032	24.268	-0.010	-0.010	0.000	0.000	0.000	0.000
147	A	146	PRO	0	-0.040	-0.026	26.943	0.008	0.008	0.000	0.000	0.000	0.000
148	A	147	LEU	0	-0.009	0.013	27.687	0.016	0.016	0.000	0.000	0.000	0.000
149	A	148	LEU	0	0.002	-0.004	22.510	0.011	0.011	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.002	0.002	26.038	0.003	0.003	0.000	0.000	0.000	0.000
151	A	150	GLU	-1	-0.954	-0.973	28.710	-0.281	-0.281	0.000	0.000	0.000	0.000
152	A	151	HIS	0	-0.005	-0.014	24.050	0.043	0.043	0.000	0.000	0.000	0.000
153	A	152	ILE	0	0.010	-0.003	24.450	0.020	0.020	0.000	0.000	0.000	0.000
154	A	153	GLN	0	-0.064	-0.044	27.709	0.005	0.005	0.000	0.000	0.000	0.000
155	A	154	SER	0	-0.073	-0.024	30.580	0.031	0.031	0.000	0.000	0.000	0.000
156	A	155	ASN	0	-0.100	-0.044	27.412	0.040	0.040	0.000	0.000	0.000	0.000
157	A	156	TRP	0	0.021	0.028	28.132	-0.030	-0.030	0.000	0.000	0.000	0.000
158	A	157	GLU	-1	-0.892	-0.968	29.010	-0.297	-0.297	0.000	0.000	0.000	0.000
159	A	158	THR	0	-0.046	-0.016	23.555	0.007	0.007	0.000	0.000	0.000	0.000
160	A	159	PHE	0	-0.022	-0.023	21.752	-0.039	-0.039	0.000	0.000	0.000	0.000
161	A	160	ALA	0	-0.028	0.005	25.736	-0.025	-0.025	0.000	0.000	0.000	0.000
162	A	161	HIS	0	-0.065	-0.025	26.767	0.013	0.013	0.000	0.000	0.000	0.000
163	A	162	ILE	0	0.047	0.030	23.566	-0.028	-0.028	0.000	0.000	0.000	0.000
164	A	163	GLY	0	-0.034	-0.008	24.315	0.030	0.030	0.000	0.000	0.000	0.000

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