FMO DATABASE

FMODB ID: LZGJ9

Calculation Name: 1VHS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VHS

Chain ID: A

ChEMBL ID:

UniProt ID: P71043

Base Structure: X-ray

Registration Date: 2023-06-22

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	165
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1661366.853895
FMO2-HF: Nuclear repulsion	1596376.855489
FMO2-HF: Total energy	-64989.998406
FMO2-MP2: Total energy	-65180.182545

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:SER)

Summations of interaction energy for fragment #1(A:0: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.
-40.194	-41.038	18.153	-10.382	-6.927	-0.082

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.075 / q_NPA : -0.053

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	0.013	0.022	3.792	-1.319	1.703	-0.028	-1.605	-1.389	0.004
4	A	3	LEU	0	-0.042	-0.024	5.993	-0.594	-0.594	0.000	0.000	0.000	0.000
5	A	4	ARG	1	0.771	0.849	9.724	0.467	0.467	0.000	0.000	0.000	0.000
6	A	5	LEU	0	-0.020	-0.011	12.694	-0.023	-0.023	0.000	0.000	0.000	0.000
7	A	6	ALA	0	-0.010	-0.002	16.151	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	7	GLU	-1	-0.869	-0.931	17.013	-0.265	-0.265	0.000	0.000	0.000	0.000
9	A	8	HIS	0	0.019	-0.006	19.691	-0.027	-0.027	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.883	0.933	15.546	0.435	0.435	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.740	-0.839	16.324	-0.379	-0.379	0.000	0.000	0.000	0.000
12	A	11	LEU	0	-0.039	-0.008	18.289	-0.007	-0.007	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.909	-0.974	18.596	-0.362	-0.362	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.082	0.051	14.918	0.010	0.010	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.031	-0.021	16.490	0.009	0.009	0.000	0.000	0.000	0.000
16	A	15	VAL	0	0.021	0.005	17.691	0.028	0.028	0.000	0.000	0.000	0.000
17	A	16	ALA	0	0.023	0.030	17.509	0.023	0.023	0.000	0.000	0.000	0.000
18	A	17	ILE	0	-0.033	-0.010	12.717	0.030	0.030	0.000	0.000	0.000	0.000
19	A	18	TYR	0	-0.068	-0.039	16.461	0.041	0.041	0.000	0.000	0.000	0.000
20	A	19	ASN	0	0.056	-0.003	19.565	0.039	0.039	0.000	0.000	0.000	0.000
21	A	20	SER	0	-0.089	-0.040	16.753	0.016	0.016	0.000	0.000	0.000	0.000
22	A	21	THR	0	-0.068	-0.052	17.364	0.028	0.028	0.000	0.000	0.000	0.000
23	A	22	ILE	0	-0.017	0.010	19.891	0.021	0.021	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.005	0.002	22.836	0.013	0.013	0.000	0.000	0.000	0.000
25	A	24	SER	0	-0.041	-0.020	20.555	0.012	0.012	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.815	0.895	23.540	0.027	0.027	0.000	0.000	0.000	0.000
27	A	26	MET	0	-0.045	-0.007	21.486	0.013	0.013	0.000	0.000	0.000	0.000
28	A	27	VAL	0	-0.024	-0.033	19.360	0.019	0.019	0.000	0.000	0.000	0.000
29	A	28	THR	0	0.042	0.041	22.648	0.004	0.004	0.000	0.000	0.000	0.000
30	A	29	ALA	0	0.003	0.003	24.546	0.006	0.006	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.842	-0.877	26.552	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.037	-0.065	27.381	0.003	0.003	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.867	-0.926	29.200	-0.042	-0.042	0.000	0.000	0.000	0.000
34	A	33	PRO	0	-0.048	-0.023	25.284	0.000	0.000	0.000	0.000	0.000	0.000
35	A	34	VAL	0	0.022	0.015	25.036	0.003	0.003	0.000	0.000	0.000	0.000
36	A	35	THR	0	-0.035	-0.053	25.878	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	36	PRO	0	0.016	-0.019	23.917	0.008	0.008	0.000	0.000	0.000	0.000
38	A	37	GLU	-1	-0.890	-0.948	25.935	-0.102	-0.102	0.000	0.000	0.000	0.000
39	A	38	ASP	-1	-0.861	-0.886	28.835	-0.070	-0.070	0.000	0.000	0.000	0.000
40	A	39	ARG	1	0.859	0.927	24.182	0.063	0.063	0.000	0.000	0.000	0.000
41	A	40	MET	0	0.044	0.038	26.541	-0.004	-0.004	0.000	0.000	0.000	0.000
42	A	41	GLU	-1	-0.916	-0.958	28.111	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	42	TRP	0	-0.057	-0.048	20.618	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	43	PHE	0	-0.029	-0.018	20.119	0.009	0.009	0.000	0.000	0.000	0.000
45	A	44	SER	0	0.003	-0.012	24.988	0.002	0.002	0.000	0.000	0.000	0.000
46	A	45	GLY	0	-0.013	0.015	27.358	0.007	0.007	0.000	0.000	0.000	0.000
47	A	46	HIS	1	0.754	0.888	22.791	0.037	0.037	0.000	0.000	0.000	0.000
48	A	47	THR	0	0.001	-0.009	25.465	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	48	GLU	-1	-0.927	-0.969	24.048	0.021	0.021	0.000	0.000	0.000	0.000
50	A	49	SER	0	-0.010	-0.001	23.778	0.012	0.012	0.000	0.000	0.000	0.000
51	A	50	ARG	1	0.767	0.869	23.934	-0.053	-0.053	0.000	0.000	0.000	0.000
52	A	51	PRO	0	0.067	0.043	19.822	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	52	LEU	0	0.040	0.024	18.233	0.017	0.017	0.000	0.000	0.000	0.000
54	A	53	TYR	0	-0.008	-0.012	13.946	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	54	VAL	0	0.029	0.012	12.617	0.002	0.002	0.000	0.000	0.000	0.000
56	A	55	ALA	0	-0.023	-0.022	7.843	0.121	0.121	0.000	0.000	0.000	0.000
57	A	56	GLU	-1	-0.829	-0.900	7.783	-0.903	-0.903	0.000	0.000	0.000	0.000
58	A	57	ASP	-1	-0.755	-0.879	4.054	-2.767	-2.600	-0.001	-0.056	-0.110	0.000
59	A	58	GLU	-1	-0.893	-0.934	1.614	-36.968	-41.227	18.182	-8.685	-5.238	-0.086
60	A	59	ASN	0	-0.140	-0.086	4.243	1.369	1.595	0.000	-0.036	-0.190	0.000
61	A	60	GLY	0	0.008	0.017	7.227	0.576	0.576	0.000	0.000	0.000	0.000
62	A	61	ASN	0	-0.069	-0.025	8.753	0.610	0.610	0.000	0.000	0.000	0.000
63	A	62	VAL	0	0.002	-0.005	8.695	-0.236	-0.236	0.000	0.000	0.000	0.000
64	A	63	ALA	0	0.033	0.019	7.336	0.062	0.062	0.000	0.000	0.000	0.000
65	A	64	ALA	0	-0.053	-0.043	9.346	0.200	0.200	0.000	0.000	0.000	0.000
66	A	65	TRP	0	-0.010	0.002	11.385	-0.018	-0.018	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.036	-0.015	12.131	0.049	0.049	0.000	0.000	0.000	0.000
68	A	67	SER	0	-0.043	-0.037	15.851	-0.021	-0.021	0.000	0.000	0.000	0.000
69	A	68	PHE	0	-0.006	0.002	17.861	0.023	0.023	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.751	-0.838	22.064	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	70	THR	0	-0.008	-0.012	25.595	0.010	0.010	0.000	0.000	0.000	0.000
72	A	71	PHE	0	-0.012	0.017	29.076	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	72	TYR	0	0.022	-0.012	30.887	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	73	GLY	0	0.041	0.046	34.335	0.002	0.002	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.930	0.947	35.640	-0.036	-0.036	0.000	0.000	0.000	0.000
76	A	75	PRO	0	0.075	0.024	36.341	0.004	0.004	0.000	0.000	0.000	0.000
77	A	76	ALA	0	-0.070	-0.029	36.725	0.004	0.004	0.000	0.000	0.000	0.000
78	A	77	TYR	0	0.022	-0.004	33.721	0.002	0.002	0.000	0.000	0.000	0.000
79	A	78	ASN	0	0.047	0.026	32.502	0.002	0.002	0.000	0.000	0.000	0.000
80	A	79	LYS	1	0.909	0.967	30.201	-0.067	-0.067	0.000	0.000	0.000	0.000
81	A	80	THR	0	0.010	0.016	29.308	0.010	0.010	0.000	0.000	0.000	0.000
82	A	81	ALA	0	-0.025	-0.008	25.445	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.857	-0.929	25.047	0.066	0.066	0.000	0.000	0.000	0.000
84	A	83	VAL	0	-0.012	-0.014	18.487	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.020	-0.007	20.034	0.002	0.002	0.000	0.000	0.000	0.000
86	A	85	ILE	0	-0.010	-0.016	13.684	0.002	0.002	0.000	0.000	0.000	0.000
87	A	86	TYR	0	0.004	0.017	15.669	0.015	0.015	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.022	-0.027	10.346	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	88	ASP	-1	-0.711	-0.845	10.903	-0.373	-0.373	0.000	0.000	0.000	0.000
90	A	89	GLU	-1	-0.813	-0.894	12.357	0.058	0.058	0.000	0.000	0.000	0.000
91	A	90	ALA	0	-0.004	0.008	12.334	0.069	0.069	0.000	0.000	0.000	0.000
92	A	91	CYS	0	-0.106	-0.072	8.420	-0.040	-0.040	0.000	0.000	0.000	0.000
93	A	92	ARG	1	0.756	0.872	10.008	0.152	0.152	0.000	0.000	0.000	0.000
94	A	93	GLY	0	-0.028	-0.011	12.651	0.012	0.012	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.924	0.937	7.492	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	95	GLY	0	-0.001	0.007	7.944	0.336	0.336	0.000	0.000	0.000	0.000
97	A	96	VAL	0	0.043	0.025	6.481	0.132	0.132	0.000	0.000	0.000	0.000
98	A	97	GLY	0	0.029	0.011	8.327	-0.034	-0.034	0.000	0.000	0.000	0.000
99	A	98	SER	0	-0.006	-0.018	10.737	-0.050	-0.050	0.000	0.000	0.000	0.000
100	A	99	TYR	0	0.000	0.017	6.243	0.072	0.072	0.000	0.000	0.000	0.000
101	A	100	LEU	0	0.068	0.026	8.945	-0.053	-0.053	0.000	0.000	0.000	0.000
102	A	101	LEU	0	-0.006	0.006	10.885	-0.048	-0.048	0.000	0.000	0.000	0.000
103	A	102	GLN	0	-0.047	-0.025	10.272	-0.050	-0.050	0.000	0.000	0.000	0.000
104	A	103	GLU	-1	-0.774	-0.876	9.509	0.716	0.716	0.000	0.000	0.000	0.000
105	A	104	ALA	0	-0.003	0.003	12.793	-0.061	-0.061	0.000	0.000	0.000	0.000
106	A	105	LEU	0	-0.040	-0.035	15.856	-0.041	-0.041	0.000	0.000	0.000	0.000
107	A	106	ARG	1	0.830	0.913	11.905	-0.523	-0.523	0.000	0.000	0.000	0.000
108	A	107	ILE	0	-0.012	-0.010	13.908	-0.031	-0.031	0.000	0.000	0.000	0.000
109	A	108	ALA	0	0.027	0.011	17.850	-0.030	-0.030	0.000	0.000	0.000	0.000
110	A	109	PRO	0	0.029	0.012	20.330	-0.026	-0.026	0.000	0.000	0.000	0.000
111	A	110	ASN	0	-0.054	-0.021	20.198	0.001	0.001	0.000	0.000	0.000	0.000
112	A	111	LEU	0	-0.022	0.011	20.470	-0.018	-0.018	0.000	0.000	0.000	0.000
113	A	112	GLY	0	-0.019	-0.001	23.995	-0.017	-0.017	0.000	0.000	0.000	0.000
114	A	113	ILE	0	-0.100	-0.040	22.990	-0.010	-0.010	0.000	0.000	0.000	0.000
115	A	114	ARG	1	0.908	0.967	26.181	-0.079	-0.079	0.000	0.000	0.000	0.000
116	A	115	SER	0	-0.059	-0.053	28.079	0.007	0.007	0.000	0.000	0.000	0.000
117	A	116	LEU	0	-0.013	0.000	20.673	-0.008	-0.008	0.000	0.000	0.000	0.000
118	A	117	MET	0	-0.023	-0.019	25.304	0.006	0.006	0.000	0.000	0.000	0.000
119	A	118	ALA	0	0.037	0.020	22.183	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	119	PHE	0	0.015	0.009	23.968	0.000	0.000	0.000	0.000	0.000	0.000
121	A	120	ILE	0	0.008	0.004	21.544	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	121	PHE	0	0.046	0.030	24.903	0.002	0.002	0.000	0.000	0.000	0.000
123	A	122	GLY	0	0.035	0.010	26.375	0.013	0.013	0.000	0.000	0.000	0.000
124	A	123	HIS	0	-0.027	-0.019	26.791	0.016	0.016	0.000	0.000	0.000	0.000
125	A	124	ASN	0	0.054	0.030	20.454	0.029	0.029	0.000	0.000	0.000	0.000
126	A	125	LYS	1	0.901	0.929	23.323	-0.104	-0.104	0.000	0.000	0.000	0.000
127	A	126	PRO	0	-0.012	-0.007	18.829	0.015	0.015	0.000	0.000	0.000	0.000
128	A	127	SER	0	0.027	-0.004	18.727	0.031	0.031	0.000	0.000	0.000	0.000
129	A	128	LEU	0	0.004	0.012	19.763	0.013	0.013	0.000	0.000	0.000	0.000
130	A	129	LYS	1	0.969	0.975	21.308	-0.217	-0.217	0.000	0.000	0.000	0.000
131	A	130	LEU	0	-0.049	-0.006	14.723	0.019	0.019	0.000	0.000	0.000	0.000
132	A	131	PHE	0	0.080	0.019	17.812	0.023	0.023	0.000	0.000	0.000	0.000
133	A	132	GLU	-1	-0.914	-0.949	20.378	0.180	0.180	0.000	0.000	0.000	0.000
134	A	133	LYS	1	0.863	0.945	18.245	-0.391	-0.391	0.000	0.000	0.000	0.000
135	A	134	HIS	0	-0.078	-0.047	15.627	0.054	0.054	0.000	0.000	0.000	0.000
136	A	135	GLY	0	0.017	0.007	20.331	-0.008	-0.008	0.000	0.000	0.000	0.000
137	A	136	PHE	0	-0.030	-0.003	20.182	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	137	ALA	0	0.025	0.016	24.806	0.004	0.004	0.000	0.000	0.000	0.000
139	A	138	GLU	-1	-0.811	-0.897	28.205	0.102	0.102	0.000	0.000	0.000	0.000
140	A	139	TRP	0	-0.030	-0.026	29.871	-0.006	-0.006	0.000	0.000	0.000	0.000
141	A	140	GLY	0	0.009	0.004	31.623	-0.008	-0.008	0.000	0.000	0.000	0.000
142	A	141	LEU	0	-0.017	0.006	31.855	0.006	0.006	0.000	0.000	0.000	0.000
143	A	142	PHE	0	-0.020	-0.004	33.034	-0.004	-0.004	0.000	0.000	0.000	0.000
144	A	143	PRO	0	0.006	-0.011	34.730	-0.001	-0.001	0.000	0.000	0.000	0.000
145	A	144	GLY	0	0.023	-0.005	35.953	-0.004	-0.004	0.000	0.000	0.000	0.000
146	A	145	ILE	0	-0.036	-0.006	33.432	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	146	ALA	0	0.016	0.030	31.920	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	147	GLU	-1	-0.946	-0.976	34.006	0.015	0.015	0.000	0.000	0.000	0.000
149	A	148	MET	0	0.020	0.017	28.391	-0.006	-0.006	0.000	0.000	0.000	0.000
150	A	149	ASP	-1	-0.802	-0.870	31.762	0.001	0.001	0.000	0.000	0.000	0.000
151	A	150	GLY	0	0.001	0.004	34.919	0.002	0.002	0.000	0.000	0.000	0.000
152	A	151	LYS	1	0.874	0.941	34.523	-0.022	-0.022	0.000	0.000	0.000	0.000
153	A	152	ARG	1	0.904	0.939	35.382	-0.030	-0.030	0.000	0.000	0.000	0.000
154	A	153	TYR	0	-0.031	-0.019	30.484	0.007	0.007	0.000	0.000	0.000	0.000
155	A	154	ASP	-1	-0.842	-0.912	32.142	0.058	0.058	0.000	0.000	0.000	0.000
156	A	155	LEU	0	-0.010	-0.001	27.916	0.004	0.004	0.000	0.000	0.000	0.000
157	A	156	LYS	1	0.822	0.889	27.997	-0.109	-0.109	0.000	0.000	0.000	0.000
158	A	157	ILE	0	-0.021	0.003	27.906	0.001	0.001	0.000	0.000	0.000	0.000
159	A	158	LEU	0	-0.005	-0.001	24.056	0.003	0.003	0.000	0.000	0.000	0.000
160	A	159	GLY	0	0.034	0.002	26.283	-0.004	-0.004	0.000	0.000	0.000	0.000
161	A	160	ARG	1	0.907	0.953	20.843	-0.234	-0.234	0.000	0.000	0.000	0.000
162	A	161	GLU	-1	-0.827	-0.895	26.425	0.104	0.104	0.000	0.000	0.000	0.000
163	A	162	LEU	0	-0.071	-0.047	22.575	0.011	0.011	0.000	0.000	0.000	0.000
164	A	163	SER	0	-0.047	-0.037	26.102	0.001	0.001	0.000	0.000	0.000	0.000
165	A	164	GLU	-1	-0.941	-0.949	28.759	0.139	0.139	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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