FMO DATABASE

FMODB ID: 521ZZ

Calculation Name: 1VJH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VJH

Chain ID: A

ChEMBL ID:

UniProt ID: P0C0B0

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	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	120
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-980975.012356
FMO2-HF: Nuclear repulsion	934014.117347
FMO2-HF: Total energy	-46960.895009
FMO2-MP2: Total energy	-47099.236819

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:SER)

Summations of interaction energy for fragment #1(A:1: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.
-24.48	-18.949	11.865	-7.572	-9.827	0.027

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.017

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

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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	LEU	0	-0.006	0.015	2.027	-7.860	-6.417	5.956	-3.413	-3.986	0.028
4	A	4	LYS	1	0.827	0.896	2.173	-4.691	-2.981	5.150	-2.656	-4.205	0.020
5	A	5	GLY	0	0.038	0.017	3.749	-0.711	-0.664	0.003	-0.020	-0.031	0.000
6	A	6	ALA	0	-0.032	-0.014	6.676	0.092	0.092	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.001	0.014	10.367	-0.031	-0.031	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.037	-0.030	13.770	0.030	0.030	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.012	0.011	16.964	0.002	0.002	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.968	0.984	20.701	0.119	0.119	0.000	0.000	0.000	0.000
11	A	11	PHE	0	-0.058	-0.029	23.928	0.004	0.004	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.766	-0.864	27.412	-0.087	-0.087	0.000	0.000	0.000	0.000
13	A	13	VAL	0	-0.058	-0.028	30.255	0.001	0.001	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.863	0.901	33.018	0.046	0.046	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.039	-0.005	35.002	0.003	0.003	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.030	0.019	35.219	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.041	0.021	32.156	0.001	0.001	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.810	-0.905	32.829	-0.053	-0.053	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.892	0.960	34.705	0.039	0.039	0.000	0.000	0.000	0.000
20	A	20	PHE	0	0.027	0.000	28.168	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	PHE	0	0.016	0.004	26.145	0.000	0.000	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.015	-0.025	30.445	0.000	0.000	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.006	0.015	32.933	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	PHE	0	0.020	0.002	23.489	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	VAL	0	-0.028	-0.022	28.118	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.874	-0.909	29.383	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.777	-0.851	29.663	-0.043	-0.043	0.000	0.000	0.000	0.000
28	A	28	THR	0	-0.090	-0.058	24.952	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.051	-0.029	26.741	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.810	0.889	29.078	0.040	0.040	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.025	-0.009	25.303	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.035	0.013	22.364	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.784	-0.873	20.828	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.898	0.939	24.842	0.003	0.003	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.052	-0.033	24.178	0.001	0.001	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.024	0.014	22.362	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.808	0.891	18.842	0.059	0.059	0.000	0.000	0.000	0.000
38	A	38	THR	0	0.029	0.009	20.875	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.822	-0.893	19.583	-0.060	-0.060	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.029	0.006	20.520	-0.014	-0.014	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.803	-0.860	16.273	-0.160	-0.160	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.019	-0.011	20.727	0.005	0.005	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.019	-0.001	22.594	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.813	-0.882	25.586	-0.058	-0.058	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.071	0.024	28.111	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.027	-0.002	31.079	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.865	0.904	26.955	0.066	0.066	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.777	0.906	28.355	0.054	0.054	0.000	0.000	0.000	0.000
49	A	49	THR	0	-0.012	-0.003	23.459	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.021	-0.012	23.185	0.010	0.010	0.000	0.000	0.000	0.000
51	A	51	THR	0	0.009	0.018	16.994	-0.014	-0.014	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.023	0.014	19.305	0.010	0.010	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.050	-0.032	14.891	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.035	-0.011	16.289	0.019	0.019	0.000	0.000	0.000	0.000
55	A	55	SER	0	-0.022	-0.010	16.141	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.049	0.014	17.802	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.064	-0.025	18.589	0.005	0.005	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.812	-0.898	20.004	0.031	0.031	0.000	0.000	0.000	0.000
59	A	59	ILE	0	0.021	0.010	15.238	0.011	0.011	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.027	-0.013	13.446	0.007	0.007	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.745	0.873	14.205	-0.009	-0.009	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.017	0.009	13.214	0.030	0.030	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.034	0.000	9.351	0.078	0.078	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.868	0.949	5.052	0.548	0.548	0.000	0.000	0.000	0.000
65	A	65	THR	0	-0.040	-0.025	9.124	-0.059	-0.059	0.000	0.000	0.000	0.000
66	A	66	LEU	0	-0.001	0.009	9.992	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.848	0.900	12.271	0.230	0.230	0.000	0.000	0.000	0.000
68	A	68	GLY	0	0.018	0.012	14.705	-0.015	-0.015	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.016	-0.022	17.120	0.005	0.005	0.000	0.000	0.000	0.000
70	A	70	ILE	0	-0.041	-0.015	18.742	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.006	-0.002	22.104	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.001	0.008	24.403	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.007	-0.006	28.043	0.003	0.003	0.000	0.000	0.000	0.000
74	A	74	PRO	0	0.019	0.005	30.576	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.078	-0.029	33.452	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	76	GLY	0	0.044	0.008	35.030	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.103	-0.044	38.342	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	GLY	0	0.024	0.010	40.090	0.002	0.002	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.890	-0.947	38.310	-0.050	-0.050	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.039	0.042	36.386	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	SER	0	-0.073	-0.073	31.831	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	HIS	1	0.792	0.888	28.463	0.081	0.081	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.001	0.003	25.107	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.023	-0.018	20.469	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	85	TRP	0	0.018	0.008	20.091	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	THR	0	0.028	0.012	14.200	-0.008	-0.008	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.038	0.032	13.846	0.012	0.012	0.000	0.000	0.000	0.000
88	A	88	HIS	0	0.013	-0.011	10.730	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	89	PHE	0	0.020	0.005	7.462	0.020	0.020	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.796	-0.891	2.393	-11.754	-9.423	0.756	-1.483	-1.605	-0.021
91	A	91	LYS	1	0.839	0.910	6.030	-0.170	-0.170	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.016	-0.019	6.638	0.049	0.049	0.000	0.000	0.000	0.000
93	A	93	HIS	0	0.008	-0.001	8.225	0.141	0.141	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.821	0.869	7.425	-0.259	-0.259	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.811	-0.876	8.266	0.118	0.118	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.055	-0.005	10.466	-0.086	-0.086	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.837	-0.912	11.171	0.026	0.026	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.824	-0.911	11.102	-0.186	-0.186	0.000	0.000	0.000	0.000
99	A	99	PRO	0	-0.008	0.012	12.409	0.009	0.009	0.000	0.000	0.000	0.000
100	A	100	HIS	0	-0.005	-0.025	14.949	0.005	0.005	0.000	0.000	0.000	0.000
101	A	101	SER	0	0.044	0.010	18.219	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	ILE	0	0.021	0.018	16.394	0.003	0.003	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.033	0.004	17.005	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.792	-0.877	20.134	-0.071	-0.071	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.833	-0.932	23.392	-0.045	-0.045	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.015	-0.008	21.508	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.032	-0.009	23.476	0.003	0.003	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.805	0.887	25.785	0.067	0.067	0.000	0.000	0.000	0.000
109	A	109	TYR	0	-0.103	-0.080	25.977	0.003	0.003	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.047	0.010	23.117	0.004	0.004	0.000	0.000	0.000	0.000
111	A	111	LYS	1	0.931	0.973	28.665	0.079	0.079	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.857	0.929	29.129	0.050	0.050	0.000	0.000	0.000	0.000
113	A	113	LEU	0	0.014	0.016	30.152	0.003	0.003	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.775	-0.888	32.718	-0.052	-0.052	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.791	-0.878	34.468	-0.041	-0.041	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.013	0.010	36.264	0.003	0.003	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.009	-0.015	34.366	0.002	0.002	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.046	-0.028	38.270	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	ASN	0	-0.085	-0.048	39.992	0.002	0.002	0.000	0.000	0.000	0.000
120	A	120	PHE	0	-0.035	0.007	41.252	0.002	0.002	0.000	0.000	0.000	0.000

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