FMO DATABASE

FMODB ID: VRVG1

Calculation Name: 1DVK-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DVK

Chain ID: A

ChEMBL ID:

UniProt ID: P33411

Base Structure: X-ray

Registration Date: 2023-03-13

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	149
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1508777.645081
FMO2-HF: Nuclear repulsion	1448918.901571
FMO2-HF: Total energy	-59858.74351
FMO2-MP2: Total energy	-60034.640578

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:79:MET)

Summations of interaction energy for fragment #1(A:79:MET)

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.
-4.462	-5.18	8.223	-1.834	-5.672	0.01

Interaction energy analysis for fragmet #1(A:79:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.016

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	81	ILE	0	0.115	0.037	2.538	-1.859	-2.411	8.154	-2.438	-5.165	0.010
4	A	82	GLN	0	-0.024	-0.016	3.956	-1.324	-1.701	0.064	0.647	-0.334	0.000
5	A	83	GLU	-1	-0.932	-0.966	5.873	1.313	1.313	0.000	0.000	0.000	0.000
6	A	84	ALA	0	0.011	0.007	3.474	-0.591	-0.380	0.005	-0.043	-0.173	0.000
7	A	85	ILE	0	0.002	0.003	5.626	-0.196	-0.196	0.000	0.000	0.000	0.000
8	A	86	ALA	0	-0.001	-0.015	8.537	-0.142	-0.142	0.000	0.000	0.000	0.000
9	A	87	GLN	0	-0.087	-0.041	8.843	-0.203	-0.203	0.000	0.000	0.000	0.000
10	A	88	ASP	-1	-0.805	-0.899	9.508	-0.012	-0.012	0.000	0.000	0.000	0.000
11	A	89	LYS	1	0.846	0.930	11.196	-0.091	-0.091	0.000	0.000	0.000	0.000
12	A	90	THR	0	0.009	0.010	13.393	-0.022	-0.022	0.000	0.000	0.000	0.000
13	A	91	ILE	0	-0.049	-0.008	11.678	0.004	0.004	0.000	0.000	0.000	0.000
14	A	92	SER	0	-0.005	-0.003	15.917	0.007	0.007	0.000	0.000	0.000	0.000
15	A	93	VAL	0	0.054	0.004	19.106	0.020	0.020	0.000	0.000	0.000	0.000
16	A	94	ILE	0	0.012	0.018	21.592	0.005	0.005	0.000	0.000	0.000	0.000
17	A	95	ILE	0	-0.009	0.001	21.780	0.010	0.010	0.000	0.000	0.000	0.000
18	A	96	ASP	-1	-0.814	-0.862	22.239	0.033	0.033	0.000	0.000	0.000	0.000
19	A	97	PRO	0	0.042	0.000	23.337	0.009	0.009	0.000	0.000	0.000	0.000
20	A	98	SER	0	-0.071	-0.057	24.580	0.000	0.000	0.000	0.000	0.000	0.000
21	A	99	GLN	0	-0.020	-0.026	18.318	0.016	0.016	0.000	0.000	0.000	0.000
22	A	100	ILE	0	-0.048	-0.012	20.537	0.014	0.014	0.000	0.000	0.000	0.000
23	A	101	GLY	0	0.009	-0.003	21.763	0.011	0.011	0.000	0.000	0.000	0.000
24	A	102	SER	0	-0.036	0.003	18.322	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	103	THR	0	0.028	-0.006	15.979	0.021	0.021	0.000	0.000	0.000	0.000
26	A	104	GLU	-1	-0.948	-0.969	13.416	0.005	0.005	0.000	0.000	0.000	0.000
27	A	105	GLY	0	0.029	0.021	13.306	0.058	0.058	0.000	0.000	0.000	0.000
28	A	106	LYS	1	0.860	0.940	14.026	-0.230	-0.230	0.000	0.000	0.000	0.000
29	A	107	PRO	0	-0.011	-0.026	9.844	0.022	0.022	0.000	0.000	0.000	0.000
30	A	108	LEU	0	0.058	0.035	11.992	0.037	0.037	0.000	0.000	0.000	0.000
31	A	109	LEU	0	0.043	0.021	13.558	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	110	SER	0	-0.016	-0.024	14.233	-0.027	-0.027	0.000	0.000	0.000	0.000
33	A	111	MET	0	0.000	0.017	12.646	0.016	0.016	0.000	0.000	0.000	0.000
34	A	112	LYS	1	0.886	0.929	15.019	-0.160	-0.160	0.000	0.000	0.000	0.000
35	A	113	CYS	0	-0.006	0.012	17.943	-0.029	-0.029	0.000	0.000	0.000	0.000
36	A	114	ASN	0	0.048	0.019	16.918	0.013	0.013	0.000	0.000	0.000	0.000
37	A	115	LEU	0	-0.044	-0.039	15.631	-0.014	-0.014	0.000	0.000	0.000	0.000
38	A	116	TYR	0	0.036	0.023	19.464	-0.017	-0.017	0.000	0.000	0.000	0.000
39	A	117	ILE	0	0.031	0.024	22.571	-0.012	-0.012	0.000	0.000	0.000	0.000
40	A	118	HIS	0	-0.049	-0.041	19.713	0.016	0.016	0.000	0.000	0.000	0.000
41	A	119	GLU	-1	-0.833	-0.896	23.538	0.086	0.086	0.000	0.000	0.000	0.000
42	A	120	ILE	0	0.055	0.037	25.281	-0.009	-0.009	0.000	0.000	0.000	0.000
43	A	121	LEU	0	-0.072	-0.046	25.449	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	122	SER	0	-0.053	-0.019	26.419	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	123	ARG	1	0.842	0.905	28.459	-0.090	-0.090	0.000	0.000	0.000	0.000
46	A	124	TRP	0	-0.002	0.000	31.356	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	125	LYS	1	0.882	0.932	30.711	-0.100	-0.100	0.000	0.000	0.000	0.000
48	A	126	ALA	0	-0.022	-0.015	32.534	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	127	SER	0	0.018	0.017	34.263	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	128	LEU	0	-0.035	-0.015	35.214	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	129	GLU	-1	-0.971	-0.992	37.519	0.057	0.057	0.000	0.000	0.000	0.000
52	A	130	ALA	0	0.003	0.012	40.491	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	131	TYR	0	-0.022	-0.009	37.215	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	132	HIS	1	0.872	0.936	38.858	-0.063	-0.063	0.000	0.000	0.000	0.000
55	A	133	PRO	0	0.070	0.020	38.486	0.006	0.006	0.000	0.000	0.000	0.000
56	A	134	GLU	-1	-0.858	-0.944	38.444	0.080	0.080	0.000	0.000	0.000	0.000
57	A	135	LEU	0	0.022	0.029	37.372	0.004	0.004	0.000	0.000	0.000	0.000
58	A	136	PHE	0	0.003	0.025	30.445	0.010	0.010	0.000	0.000	0.000	0.000
59	A	137	LEU	0	-0.011	-0.019	32.063	0.010	0.010	0.000	0.000	0.000	0.000
60	A	138	ASP	-1	-0.829	-0.926	32.290	0.123	0.123	0.000	0.000	0.000	0.000
61	A	139	THR	0	-0.043	-0.029	30.506	0.006	0.006	0.000	0.000	0.000	0.000
62	A	140	LYS	1	0.906	0.966	28.339	-0.131	-0.131	0.000	0.000	0.000	0.000
63	A	141	LYS	1	0.928	0.963	27.513	-0.123	-0.123	0.000	0.000	0.000	0.000
64	A	142	ALA	0	0.005	0.013	28.139	0.014	0.014	0.000	0.000	0.000	0.000
65	A	143	LEU	0	0.015	-0.002	25.571	0.009	0.009	0.000	0.000	0.000	0.000
66	A	144	PHE	0	-0.023	0.008	21.913	0.021	0.021	0.000	0.000	0.000	0.000
67	A	145	PRO	0	-0.011	-0.016	21.877	0.031	0.031	0.000	0.000	0.000	0.000
68	A	146	LEU	0	0.044	0.036	20.735	0.029	0.029	0.000	0.000	0.000	0.000
69	A	147	LEU	0	0.021	0.004	20.018	0.027	0.027	0.000	0.000	0.000	0.000
70	A	148	LEU	0	-0.017	0.003	16.291	0.051	0.051	0.000	0.000	0.000	0.000
71	A	149	GLN	0	0.000	-0.010	16.045	0.053	0.053	0.000	0.000	0.000	0.000
72	A	150	LEU	0	-0.033	0.000	15.669	0.044	0.044	0.000	0.000	0.000	0.000
73	A	151	ARG	1	0.881	0.956	12.958	-0.366	-0.366	0.000	0.000	0.000	0.000
74	A	152	ARG	1	0.904	0.947	11.470	-0.594	-0.594	0.000	0.000	0.000	0.000
75	A	153	ASN	0	0.050	0.032	10.463	-0.014	-0.014	0.000	0.000	0.000	0.000
76	A	154	GLN	0	-0.028	-0.031	12.753	-0.070	-0.070	0.000	0.000	0.000	0.000
77	A	155	LEU	0	0.008	0.023	14.793	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	156	ALA	0	0.033	0.018	17.292	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	157	PRO	0	0.044	-0.007	17.727	0.008	0.008	0.000	0.000	0.000	0.000
80	A	158	ASP	-1	-0.814	-0.899	19.815	0.085	0.085	0.000	0.000	0.000	0.000
81	A	159	LEU	0	-0.021	-0.009	22.059	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	160	LEU	0	-0.034	-0.014	17.329	0.003	0.003	0.000	0.000	0.000	0.000
83	A	161	ILE	0	0.031	0.021	21.392	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	162	SER	0	0.015	0.002	23.640	-0.010	-0.010	0.000	0.000	0.000	0.000
85	A	163	LEU	0	-0.028	-0.008	22.166	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	164	ALA	0	0.044	0.008	22.107	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	165	THR	0	-0.009	-0.016	24.132	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	166	VAL	0	-0.042	-0.015	27.530	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	167	LEU	0	-0.043	-0.036	23.806	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	168	TYR	0	0.044	0.022	26.367	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	169	HIS	0	-0.009	-0.021	27.727	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	170	LEU	0	-0.031	-0.005	29.633	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	171	GLN	0	-0.044	-0.021	24.415	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	172	GLN	0	-0.010	0.014	29.653	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	173	PRO	0	0.060	0.028	33.370	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	174	LYS	1	0.911	0.948	36.414	-0.028	-0.028	0.000	0.000	0.000	0.000
97	A	175	GLU	-1	-0.871	-0.933	34.040	0.043	0.043	0.000	0.000	0.000	0.000
98	A	176	ILE	0	0.098	0.051	35.751	0.004	0.004	0.000	0.000	0.000	0.000
99	A	177	ASN	0	0.002	-0.019	37.155	0.004	0.004	0.000	0.000	0.000	0.000
100	A	178	LEU	0	0.010	0.019	35.444	0.001	0.001	0.000	0.000	0.000	0.000
101	A	179	ALA	0	0.036	0.040	32.952	0.003	0.003	0.000	0.000	0.000	0.000
102	A	180	VAL	0	0.024	0.010	33.863	0.006	0.006	0.000	0.000	0.000	0.000
103	A	181	GLN	0	0.016	0.005	36.487	0.001	0.001	0.000	0.000	0.000	0.000
104	A	182	SER	0	-0.046	-0.043	31.444	0.000	0.000	0.000	0.000	0.000	0.000
105	A	183	TYR	0	-0.056	-0.041	31.894	0.002	0.002	0.000	0.000	0.000	0.000
106	A	184	MET	0	0.026	0.004	33.369	0.003	0.003	0.000	0.000	0.000	0.000
107	A	185	LYS	1	0.952	1.000	33.096	-0.054	-0.054	0.000	0.000	0.000	0.000
108	A	186	LEU	0	0.049	0.035	27.873	0.002	0.002	0.000	0.000	0.000	0.000
109	A	187	SER	0	-0.110	-0.063	31.346	0.003	0.003	0.000	0.000	0.000	0.000
110	A	188	ILE	0	-0.026	-0.020	33.780	0.000	0.000	0.000	0.000	0.000	0.000
111	A	189	GLY	0	-0.029	0.002	31.283	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	190	ASN	0	-0.008	-0.009	31.470	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	191	VAL	0	0.009	0.003	27.097	0.006	0.006	0.000	0.000	0.000	0.000
114	A	192	ALA	0	-0.063	-0.021	28.929	-0.008	-0.008	0.000	0.000	0.000	0.000
115	A	193	TRP	0	0.043	0.026	24.868	0.008	0.008	0.000	0.000	0.000	0.000
116	A	194	PRO	0	-0.017	-0.022	27.724	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	195	ILE	0	-0.013	-0.011	30.647	-0.004	-0.004	0.000	0.000	0.000	0.000
118	A	196	GLY	0	-0.010	0.005	34.071	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	197	VAL	0	0.001	0.009	29.701	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	218	ALA	0	0.003	-0.001	29.132	0.000	0.000	0.000	0.000	0.000	0.000
121	A	219	ASN	0	-0.026	-0.031	29.896	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	220	ILE	0	0.013	0.021	26.159	0.004	0.004	0.000	0.000	0.000	0.000
123	A	221	MET	0	-0.016	-0.005	26.092	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	222	ILE	0	-0.044	-0.023	27.210	0.010	0.010	0.000	0.000	0.000	0.000
125	A	223	ASP	-1	-0.852	-0.927	26.395	0.162	0.162	0.000	0.000	0.000	0.000
126	A	224	GLU	-1	-0.891	-0.948	28.400	0.122	0.122	0.000	0.000	0.000	0.000
127	A	225	ARG	1	0.981	0.981	23.996	-0.214	-0.214	0.000	0.000	0.000	0.000
128	A	226	THR	0	-0.021	-0.030	25.258	0.010	0.010	0.000	0.000	0.000	0.000
129	A	227	ARG	1	0.991	1.000	26.919	-0.106	-0.106	0.000	0.000	0.000	0.000
130	A	228	LEU	0	0.000	0.001	29.063	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	229	TRP	0	0.033	0.019	24.218	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	230	ILE	0	0.042	0.015	28.396	-0.005	-0.005	0.000	0.000	0.000	0.000
133	A	231	THR	0	-0.009	0.005	30.184	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	232	SER	0	-0.009	-0.029	30.208	-0.009	-0.009	0.000	0.000	0.000	0.000
135	A	233	ILE	0	0.016	0.020	26.658	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	234	LYS	1	1.006	1.007	30.634	-0.090	-0.090	0.000	0.000	0.000	0.000
137	A	235	ARG	1	0.847	0.911	33.435	-0.114	-0.114	0.000	0.000	0.000	0.000
138	A	236	LEU	0	0.019	0.015	27.717	-0.003	-0.003	0.000	0.000	0.000	0.000
139	A	237	ILE	0	0.010	0.014	32.076	-0.004	-0.004	0.000	0.000	0.000	0.000
140	A	238	THR	0	-0.042	-0.012	34.129	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	239	PHE	0	0.012	0.022	32.563	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	240	GLU	-1	-0.786	-0.898	32.353	0.073	0.073	0.000	0.000	0.000	0.000
143	A	241	GLU	-1	-0.956	-0.973	34.771	0.051	0.051	0.000	0.000	0.000	0.000
144	A	242	TRP	0	0.008	0.012	38.064	-0.003	-0.003	0.000	0.000	0.000	0.000
145	A	243	TYR	0	0.002	-0.017	34.633	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	244	THR	0	-0.071	-0.049	35.559	-0.005	-0.005	0.000	0.000	0.000	0.000
147	A	245	SER	0	-0.038	-0.015	38.143	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	246	ASN	0	-0.075	-0.028	40.997	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	247	HIS	0	-0.021	-0.003	38.051	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:79:MET)