FMO DATABASE

FMODB ID: 431VN

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	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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1674006.086131
FMO2-HF: Nuclear repulsion	1609707.673919
FMO2-HF: Total energy	-64298.412211
FMO2-MP2: Total energy	-64488.240289

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.
-53.565	-52.992	20.734	-10.643	-10.663	-0.126

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 : -0.141 / q_NPA : -0.091

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	0.030	0.026	3.839	-1.179	0.092	-0.011	-0.472	-0.788	0.002
4	A	3	ALA	0	-0.006	-0.010	6.128	0.919	0.919	0.000	0.000	0.000	0.000
5	A	4	LEU	0	0.007	0.018	8.508	-0.544	-0.544	0.000	0.000	0.000	0.000
6	A	5	THR	0	-0.032	-0.023	11.198	0.284	0.284	0.000	0.000	0.000	0.000
7	A	6	LEU	0	0.004	0.005	13.734	0.015	0.015	0.000	0.000	0.000	0.000
8	A	7	PRO	0	0.030	0.017	15.291	0.141	0.141	0.000	0.000	0.000	0.000
9	A	8	GLU	-1	-0.853	-0.915	18.027	-0.483	-0.483	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.868	-0.946	21.417	-0.604	-0.604	0.000	0.000	0.000	0.000
11	A	10	ILE	0	0.043	0.031	18.065	0.033	0.033	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.753	0.854	22.458	0.497	0.497	0.000	0.000	0.000	0.000
13	A	12	GLN	0	-0.074	-0.041	25.558	0.071	0.071	0.000	0.000	0.000	0.000
14	A	13	GLN	0	0.054	0.063	21.778	0.031	0.031	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.880	-0.945	27.220	-0.350	-0.350	0.000	0.000	0.000	0.000
16	A	15	PRO	0	-0.022	-0.016	28.705	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.031	-0.028	28.489	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	17	ALA	0	0.046	0.044	25.917	-0.021	-0.021	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.025	0.026	23.774	-0.053	-0.053	0.000	0.000	0.000	0.000
20	A	19	LEU	0	-0.047	-0.036	23.537	-0.048	-0.048	0.000	0.000	0.000	0.000
21	A	20	TYR	0	-0.037	-0.038	22.324	-0.049	-0.049	0.000	0.000	0.000	0.000
22	A	21	THR	0	0.059	0.008	19.033	-0.087	-0.087	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.056	-0.020	18.812	-0.107	-0.107	0.000	0.000	0.000	0.000
24	A	23	VAL	0	-0.035	-0.027	19.018	-0.069	-0.069	0.000	0.000	0.000	0.000
25	A	24	SER	0	-0.004	-0.003	17.755	-0.026	-0.026	0.000	0.000	0.000	0.000
26	A	25	ALA	0	0.013	0.010	14.708	-0.144	-0.144	0.000	0.000	0.000	0.000
27	A	26	TYR	0	-0.035	-0.024	14.374	-0.105	-0.105	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.004	0.017	15.840	-0.025	-0.025	0.000	0.000	0.000	0.000
29	A	28	GLU	-1	-0.761	-0.892	10.471	-2.468	-2.468	0.000	0.000	0.000	0.000
30	A	29	HIS	0	-0.087	-0.041	10.118	0.107	0.107	0.000	0.000	0.000	0.000
31	A	30	THR	0	-0.051	-0.048	11.465	0.018	0.018	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.028	-0.008	13.429	0.112	0.112	0.000	0.000	0.000	0.000
33	A	32	GLN	0	-0.040	-0.039	7.250	0.238	0.238	0.000	0.000	0.000	0.000
34	A	33	THR	0	-0.035	-0.014	7.544	-0.389	-0.389	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.028	-0.004	8.924	0.321	0.321	0.000	0.000	0.000	0.000
36	A	35	ASP	-1	-0.757	-0.848	12.420	-0.260	-0.260	0.000	0.000	0.000	0.000
37	A	36	GLU	-1	-0.892	-0.937	8.145	0.538	0.538	0.000	0.000	0.000	0.000
38	A	37	SER	0	-0.105	-0.064	11.568	0.171	0.171	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.085	-0.027	14.278	0.087	0.087	0.000	0.000	0.000	0.000
40	A	39	SER	0	-0.063	-0.041	16.738	0.084	0.084	0.000	0.000	0.000	0.000
41	A	40	CYS	0	-0.072	-0.052	18.442	0.025	0.025	0.000	0.000	0.000	0.000
42	A	41	LEU	0	-0.008	-0.001	17.631	0.008	0.008	0.000	0.000	0.000	0.000
43	A	42	SER	0	0.015	0.007	18.773	0.003	0.003	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.862	-0.944	15.717	-0.571	-0.571	0.000	0.000	0.000	0.000
45	A	44	ASP	-1	-0.807	-0.904	17.810	-0.523	-0.523	0.000	0.000	0.000	0.000
46	A	45	GLN	0	-0.011	-0.031	20.222	-0.074	-0.074	0.000	0.000	0.000	0.000
47	A	46	HIS	0	-0.024	0.000	13.549	-0.207	-0.207	0.000	0.000	0.000	0.000
48	A	47	THR	0	-0.047	-0.027	15.587	-0.182	-0.182	0.000	0.000	0.000	0.000
49	A	48	LEU	0	-0.035	-0.015	16.876	-0.067	-0.067	0.000	0.000	0.000	0.000
50	A	49	THR	0	-0.032	-0.010	15.068	0.012	0.012	0.000	0.000	0.000	0.000
51	A	50	ALA	0	0.046	0.024	13.151	-0.065	-0.065	0.000	0.000	0.000	0.000
52	A	51	PHE	0	-0.037	-0.023	14.516	-0.070	-0.070	0.000	0.000	0.000	0.000
53	A	52	CYS	0	0.003	0.001	17.762	0.035	0.035	0.000	0.000	0.000	0.000
54	A	53	TYR	0	-0.017	-0.007	11.341	0.160	0.160	0.000	0.000	0.000	0.000
55	A	54	LEU	0	-0.009	-0.021	15.346	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	55	ASP	-1	-0.791	-0.856	16.348	-0.699	-0.699	0.000	0.000	0.000	0.000
57	A	56	SER	0	-0.016	-0.030	18.804	0.019	0.019	0.000	0.000	0.000	0.000
58	A	57	GLN	0	-0.019	0.001	14.978	0.071	0.071	0.000	0.000	0.000	0.000
59	A	58	VAL	0	-0.061	-0.030	17.615	0.054	0.054	0.000	0.000	0.000	0.000
60	A	59	GLU	-1	-0.845	-0.937	19.889	-0.566	-0.566	0.000	0.000	0.000	0.000
61	A	60	GLU	-1	-0.959	-0.975	22.256	-0.546	-0.546	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.025	0.010	20.977	0.050	0.050	0.000	0.000	0.000	0.000
63	A	62	GLY	0	-0.049	-0.020	19.937	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	63	PHE	0	-0.011	-0.041	15.319	-0.132	-0.132	0.000	0.000	0.000	0.000
65	A	64	VAL	0	-0.022	-0.008	14.706	-0.194	-0.194	0.000	0.000	0.000	0.000
66	A	65	GLN	0	0.012	0.003	15.097	-0.010	-0.010	0.000	0.000	0.000	0.000
67	A	66	LEU	0	0.008	0.035	11.499	-0.125	-0.125	0.000	0.000	0.000	0.000
68	A	67	ILE	0	-0.052	-0.040	9.540	-0.336	-0.336	0.000	0.000	0.000	0.000
69	A	68	ALA	0	-0.035	-0.021	10.183	-0.237	-0.237	0.000	0.000	0.000	0.000
70	A	69	SER	0	-0.025	-0.009	12.328	0.112	0.112	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.041	0.016	8.516	-0.057	-0.057	0.000	0.000	0.000	0.000
72	A	71	TYR	0	0.011	-0.026	6.196	0.106	0.106	0.000	0.000	0.000	0.000
73	A	72	GLY	0	0.043	0.030	7.272	0.117	0.117	0.000	0.000	0.000	0.000
74	A	73	GLU	-1	-0.848	-0.903	1.790	-45.759	-48.598	20.162	-9.245	-8.078	-0.119
75	A	74	TYR	0	0.012	-0.010	2.817	-3.099	-1.127	0.585	-0.922	-1.635	-0.009
76	A	75	ILE	0	-0.007	0.001	7.087	1.037	1.037	0.000	0.000	0.000	0.000
77	A	76	PHE	0	0.002	0.002	9.256	0.645	0.645	0.000	0.000	0.000	0.000
78	A	77	ARG	1	0.810	0.889	4.550	5.401	5.521	-0.001	-0.003	-0.116	0.000
79	A	78	ASN	0	0.052	0.045	7.148	0.204	0.204	0.000	0.000	0.000	0.000
80	A	79	PRO	0	0.000	0.006	9.149	0.031	0.031	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.042	0.029	12.511	0.180	0.180	0.000	0.000	0.000	0.000
82	A	81	ALA	0	0.053	0.014	14.448	0.143	0.143	0.000	0.000	0.000	0.000
83	A	82	ASP	-1	-0.890	-0.946	15.553	-0.464	-0.464	0.000	0.000	0.000	0.000
84	A	83	SER	0	-0.004	-0.013	16.521	0.124	0.124	0.000	0.000	0.000	0.000
85	A	84	LEU	0	0.056	0.038	18.209	0.075	0.075	0.000	0.000	0.000	0.000
86	A	85	ARG	1	0.762	0.846	18.086	0.629	0.629	0.000	0.000	0.000	0.000
87	A	86	ARG	1	0.889	0.945	19.379	0.292	0.292	0.000	0.000	0.000	0.000
88	A	87	TRP	0	-0.033	-0.016	20.665	0.030	0.030	0.000	0.000	0.000	0.000
89	A	88	LYS	1	0.905	0.953	24.836	0.258	0.258	0.000	0.000	0.000	0.000
90	A	89	ILE	0	0.103	0.071	23.049	0.022	0.022	0.000	0.000	0.000	0.000
91	A	90	LYS	1	0.717	0.844	24.264	0.379	0.379	0.000	0.000	0.000	0.000
92	A	91	ALA	0	-0.026	0.010	24.274	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	92	VAL	0	0.105	0.044	19.871	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	93	PRO	0	-0.034	-0.020	19.269	-0.062	-0.062	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.903	0.953	19.559	0.381	0.381	0.000	0.000	0.000	0.000
96	A	95	VAL	0	-0.006	0.021	20.007	0.016	0.016	0.000	0.000	0.000	0.000
97	A	96	LEU	0	0.029	0.011	14.917	-0.041	-0.041	0.000	0.000	0.000	0.000
98	A	97	ASP	-1	-0.857	-0.909	16.171	-0.709	-0.709	0.000	0.000	0.000	0.000
99	A	98	LYS	1	0.796	0.905	17.173	0.481	0.481	0.000	0.000	0.000	0.000
100	A	99	ALA	0	0.051	0.029	16.526	0.004	0.004	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.839	0.902	10.013	1.383	1.383	0.000	0.000	0.000	0.000
102	A	101	ALA	0	-0.053	-0.023	13.645	-0.069	-0.069	0.000	0.000	0.000	0.000
103	A	102	LEU	0	0.000	0.010	15.857	0.042	0.042	0.000	0.000	0.000	0.000
104	A	103	TYR	0	-0.039	-0.031	6.103	-0.173	-0.173	0.000	0.000	0.000	0.000
105	A	104	GLU	-1	-0.817	-0.895	9.390	-2.231	-2.231	0.000	0.000	0.000	0.000
106	A	105	GLN	0	-0.105	-0.035	12.145	0.227	0.227	0.000	0.000	0.000	0.000
107	A	106	HIS	0	-0.046	-0.046	13.886	0.098	0.098	0.000	0.000	0.000	0.000
108	A	107	GLY	0	0.038	0.018	9.864	0.042	0.042	0.000	0.000	0.000	0.000
109	A	108	LYS	1	0.872	0.941	4.528	1.504	1.553	-0.001	-0.001	-0.046	0.000
110	A	109	THR	0	0.003	0.008	8.996	0.185	0.185	0.000	0.000	0.000	0.000
111	A	110	ILE	0	0.039	0.019	12.014	0.090	0.090	0.000	0.000	0.000	0.000
112	A	111	GLU	-1	-0.785	-0.875	5.550	-4.278	-4.278	0.000	0.000	0.000	0.000
113	A	112	THR	0	-0.057	-0.045	9.529	0.248	0.248	0.000	0.000	0.000	0.000
114	A	113	LEU	0	-0.050	-0.025	11.099	0.127	0.127	0.000	0.000	0.000	0.000
115	A	114	ALA	0	0.001	0.016	12.071	0.083	0.083	0.000	0.000	0.000	0.000
116	A	115	ASP	-1	-0.957	-0.966	10.594	-0.674	-0.674	0.000	0.000	0.000	0.000
117	A	116	GLY	0	-0.056	-0.027	12.742	0.119	0.119	0.000	0.000	0.000	0.000
118	A	117	GLY	0	-0.043	-0.023	15.782	0.077	0.077	0.000	0.000	0.000	0.000
119	A	118	ALA	0	-0.070	-0.033	17.082	0.038	0.038	0.000	0.000	0.000	0.000
120	A	119	ASP	-1	-0.803	-0.873	17.874	-0.581	-0.581	0.000	0.000	0.000	0.000
121	A	120	ILE	0	0.060	0.026	17.057	-0.016	-0.016	0.000	0.000	0.000	0.000
122	A	121	PRO	0	0.013	0.002	20.283	0.006	0.006	0.000	0.000	0.000	0.000
123	A	122	SER	0	-0.081	-0.070	21.549	0.037	0.037	0.000	0.000	0.000	0.000
124	A	123	LEU	0	-0.004	-0.007	15.634	0.017	0.017	0.000	0.000	0.000	0.000
125	A	124	ARG	1	0.746	0.846	19.297	0.687	0.687	0.000	0.000	0.000	0.000
126	A	125	LYS	1	0.899	0.952	21.392	0.370	0.370	0.000	0.000	0.000	0.000
127	A	126	GLN	0	-0.074	-0.029	19.138	0.034	0.034	0.000	0.000	0.000	0.000
128	A	127	PHE	0	-0.028	-0.012	16.711	0.020	0.020	0.000	0.000	0.000	0.000
129	A	128	PRO	0	0.067	0.030	19.934	-0.058	-0.058	0.000	0.000	0.000	0.000
130	A	129	GLU	-1	-0.839	-0.912	20.361	-0.542	-0.542	0.000	0.000	0.000	0.000
131	A	130	PHE	0	-0.001	-0.022	14.362	-0.019	-0.019	0.000	0.000	0.000	0.000
132	A	131	GLU	-1	-0.863	-0.910	20.136	-0.540	-0.540	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.920	-0.951	23.521	-0.431	-0.431	0.000	0.000	0.000	0.000
134	A	133	TRP	0	-0.031	-0.045	20.486	0.026	0.026	0.000	0.000	0.000	0.000
135	A	134	ASP	-1	-0.669	-0.824	20.284	-0.884	-0.884	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.000	0.007	22.641	0.018	0.018	0.000	0.000	0.000	0.000
137	A	136	ALA	0	0.013	0.001	24.425	0.016	0.016	0.000	0.000	0.000	0.000
138	A	137	TYR	0	-0.089	-0.073	20.180	-0.026	-0.026	0.000	0.000	0.000	0.000
139	A	138	TYR	0	-0.010	-0.007	23.753	0.020	0.020	0.000	0.000	0.000	0.000
140	A	139	GLU	-1	-0.959	-0.986	26.808	-0.363	-0.363	0.000	0.000	0.000	0.000
141	A	140	ALA	0	-0.080	-0.047	24.791	0.026	0.026	0.000	0.000	0.000	0.000
142	A	141	ALA	0	0.033	0.014	24.891	0.019	0.019	0.000	0.000	0.000	0.000
143	A	142	GLU	-1	-0.858	-0.909	26.484	-0.354	-0.354	0.000	0.000	0.000	0.000
144	A	143	GLN	0	-0.119	-0.055	28.775	0.052	0.052	0.000	0.000	0.000	0.000
145	A	144	ASP	-1	-0.759	-0.911	25.177	-0.473	-0.473	0.000	0.000	0.000	0.000
146	A	145	LEU	0	0.011	0.021	24.391	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	146	PRO	0	-0.028	-0.010	27.511	0.015	0.015	0.000	0.000	0.000	0.000
148	A	147	LEU	0	-0.013	0.001	28.339	0.015	0.015	0.000	0.000	0.000	0.000
149	A	148	LEU	0	-0.003	0.006	23.192	0.016	0.016	0.000	0.000	0.000	0.000
150	A	149	ALA	0	0.010	0.011	26.779	0.008	0.008	0.000	0.000	0.000	0.000
151	A	150	GLU	-1	-0.959	-0.978	29.623	-0.248	-0.248	0.000	0.000	0.000	0.000
152	A	151	HIS	0	-0.025	-0.005	24.675	0.046	0.046	0.000	0.000	0.000	0.000
153	A	152	ILE	0	0.018	0.005	24.964	0.023	0.023	0.000	0.000	0.000	0.000
154	A	153	GLN	0	-0.065	-0.046	28.626	0.010	0.010	0.000	0.000	0.000	0.000
155	A	154	SER	0	-0.094	-0.054	31.558	0.028	0.028	0.000	0.000	0.000	0.000
156	A	155	ASN	0	-0.094	-0.043	28.587	0.038	0.038	0.000	0.000	0.000	0.000
157	A	156	TRP	0	0.043	0.036	29.462	-0.018	-0.018	0.000	0.000	0.000	0.000
158	A	157	GLU	-1	-0.910	-0.968	30.338	-0.224	-0.224	0.000	0.000	0.000	0.000
159	A	158	THR	0	-0.034	-0.023	25.009	0.008	0.008	0.000	0.000	0.000	0.000
160	A	159	PHE	0	-0.022	-0.006	22.802	-0.034	-0.034	0.000	0.000	0.000	0.000
161	A	160	ALA	0	-0.024	0.008	26.745	-0.019	-0.019	0.000	0.000	0.000	0.000
162	A	161	HIS	0	-0.057	-0.018	27.154	0.010	0.010	0.000	0.000	0.000	0.000
163	A	162	ILE	0	0.030	0.013	23.731	-0.024	-0.024	0.000	0.000	0.000	0.000
164	A	163	GLY	0	-0.070	-0.026	23.067	0.033	0.033	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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