FMO DATABASE

FMODB ID: 14K2Z

Calculation Name: 1VMO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VMO

Chain ID: A

ChEMBL ID:

UniProt ID: P41366

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	159
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1621741.113438
FMO2-HF: Nuclear repulsion	1557781.367505
FMO2-HF: Total energy	-63959.745933
FMO2-MP2: Total energy	-64143.67794

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:ARG)

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

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.
50.794	57.378	4.261	-3.583	-7.264	-0.026

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.961 / q_NPA : 0.971

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	3	ARG	1	0.842	0.925	3.179	21.492	24.029	0.133	-1.226	-1.445	-0.003
4	A	4	GLU	-1	-0.939	-0.963	2.596	-50.821	-48.948	2.191	-1.385	-2.679	-0.016
5	A	5	TYR	0	-0.008	-0.038	2.211	5.212	6.408	1.848	-0.660	-2.385	-0.005
6	A	6	THR	0	0.010	-0.015	5.523	-2.074	-2.074	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.007	0.002	8.414	1.458	1.458	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.029	-0.015	8.126	-1.439	-1.439	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.013	0.003	10.446	1.066	1.066	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.002	-0.027	13.848	-0.327	-0.327	0.000	0.000	0.000	0.000
11	A	11	VAL	0	0.015	-0.003	16.193	0.254	0.254	0.000	0.000	0.000	0.000
12	A	12	PRO	0	-0.031	-0.021	19.794	-0.233	-0.233	0.000	0.000	0.000	0.000
13	A	13	ASN	0	-0.015	0.026	22.337	-0.043	-0.043	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.028	0.006	21.945	-0.457	-0.457	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.046	0.040	22.601	-0.055	-0.055	0.000	0.000	0.000	0.000
16	A	16	HIS	0	-0.130	-0.072	20.392	-1.106	-1.106	0.000	0.000	0.000	0.000
17	A	17	TRP	0	0.012	0.014	20.939	-0.636	-0.636	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.061	0.027	20.138	-0.044	-0.044	0.000	0.000	0.000	0.000
19	A	19	LYN	0	-0.029	-0.001	14.483	-0.574	-0.574	0.000	0.000	0.000	0.000
20	A	20	TRP	0	-0.069	-0.055	11.644	-0.323	-0.323	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.058	0.041	12.341	0.020	0.020	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.002	0.004	7.763	-1.581	-1.581	0.000	0.000	0.000	0.000
23	A	23	ARG	1	0.827	0.916	4.674	31.284	31.449	-0.001	-0.016	-0.147	0.000
24	A	24	GLN	0	0.076	0.050	6.025	-1.214	-1.214	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.005	-0.033	3.095	-1.881	-1.068	0.090	-0.296	-0.608	-0.002
26	A	26	CYS	0	0.014	0.036	7.847	0.457	0.457	0.000	0.000	0.000	0.000
27	A	27	HIS	0	0.053	0.031	9.666	-3.297	-3.297	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.029	-0.043	10.548	-1.319	-1.319	0.000	0.000	0.000	0.000
29	A	29	GLY	0	-0.020	-0.009	12.718	0.806	0.806	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.029	-0.044	12.291	-1.180	-1.180	0.000	0.000	0.000	0.000
31	A	31	ALA	0	0.090	0.042	14.337	0.473	0.473	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.002	-0.007	15.870	-0.262	-0.262	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.050	0.029	18.831	0.758	0.758	0.000	0.000	0.000	0.000
34	A	34	PHE	0	-0.026	-0.025	18.767	-0.888	-0.888	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.028	0.027	20.355	0.541	0.541	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.013	-0.019	21.101	-0.648	-0.648	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.871	0.967	22.714	11.727	11.727	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.066	0.032	24.344	-0.147	-0.147	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.813	-0.922	27.481	-8.940	-8.940	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.056	-0.017	30.956	0.103	0.103	0.000	0.000	0.000	0.000
41	A	41	SER	0	0.079	0.048	33.738	0.045	0.045	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.064	-0.045	35.823	0.082	0.082	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.061	0.014	38.139	-0.118	-0.118	0.000	0.000	0.000	0.000
44	A	44	GLY	0	-0.029	-0.001	40.756	0.066	0.066	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.839	0.916	35.300	7.942	7.942	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.863	-0.922	36.686	-7.537	-7.537	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.951	-0.973	33.742	-8.379	-8.379	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.015	0.000	30.053	-0.136	-0.136	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.023	0.006	26.149	-0.116	-0.116	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.049	-0.004	22.731	-0.037	-0.037	0.000	0.000	0.000	0.000
51	A	51	ASN	0	0.032	0.001	23.056	-0.264	-0.264	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.016	-0.018	19.460	-0.470	-0.470	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.012	0.022	17.001	0.388	0.388	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.884	0.955	16.607	12.749	12.749	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.013	-0.006	13.079	0.549	0.549	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.958	0.990	16.525	12.057	12.057	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.013	-0.009	16.421	0.426	0.426	0.000	0.000	0.000	0.000
58	A	59	ASP	-1	-0.759	-0.853	14.877	-17.714	-17.714	0.000	0.000	0.000	0.000
59	A	60	GLY	0	-0.008	-0.006	18.342	-0.054	-0.054	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.083	-0.047	14.608	-0.063	-0.063	0.000	0.000	0.000	0.000
61	A	62	VAL	0	-0.002	-0.023	16.429	0.115	0.115	0.000	0.000	0.000	0.000
62	A	63	ILE	0	-0.046	-0.009	10.678	-0.594	-0.594	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.851	-0.941	13.297	-13.757	-13.757	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.014	-0.028	10.719	-1.250	-1.250	0.000	0.000	0.000	0.000
65	A	66	LEU	0	-0.025	0.000	12.940	0.122	0.122	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.042	-0.016	15.445	0.193	0.193	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.069	0.029	18.980	0.028	0.028	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.875	0.932	22.391	9.678	9.678	0.000	0.000	0.000	0.000
69	A	70	TRP	0	-0.020	-0.008	25.000	0.448	0.448	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.062	0.037	26.340	-0.347	-0.347	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.049	-0.042	27.840	0.040	0.040	0.000	0.000	0.000	0.000
72	A	73	TRP	0	-0.051	-0.026	19.438	-0.157	-0.157	0.000	0.000	0.000	0.000
73	A	74	THR	0	0.039	0.037	25.822	0.179	0.179	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.022	-0.007	25.825	-0.328	-0.328	0.000	0.000	0.000	0.000
75	A	76	PHE	0	-0.052	-0.043	19.650	-0.122	-0.122	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.061	0.056	24.187	0.311	0.311	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.072	-0.070	23.058	-0.574	-0.574	0.000	0.000	0.000	0.000
78	A	79	CYS	0	-0.059	-0.020	21.388	-0.525	-0.525	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.001	0.009	24.742	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	81	THR	0	0.001	-0.006	26.124	0.083	0.083	0.000	0.000	0.000	0.000
81	A	82	GLY	0	-0.032	-0.004	23.027	-0.327	-0.327	0.000	0.000	0.000	0.000
82	A	83	TYR	0	-0.018	-0.031	17.624	-0.380	-0.380	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.015	0.007	17.243	0.428	0.428	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.044	-0.034	17.111	-0.794	-0.794	0.000	0.000	0.000	0.000
85	A	86	SER	0	-0.051	-0.025	17.727	-0.210	-0.210	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.050	0.023	16.431	0.182	0.182	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.008	0.017	20.602	0.135	0.135	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.069	0.014	20.587	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.894	0.964	23.888	9.250	9.250	0.000	0.000	0.000	0.000
90	A	91	SER	0	0.020	0.009	25.981	-0.131	-0.131	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.824	-0.913	28.096	-8.830	-8.830	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.863	0.928	29.736	9.132	9.132	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.047	0.044	30.125	0.034	0.034	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.010	-0.018	32.138	0.190	0.190	0.000	0.000	0.000	0.000
95	A	96	GLY	0	-0.028	-0.009	32.071	-0.216	-0.216	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.021	0.023	31.614	-0.178	-0.178	0.000	0.000	0.000	0.000
97	A	98	GLY	0	0.091	0.048	31.311	-0.216	-0.216	0.000	0.000	0.000	0.000
98	A	99	ASP	-1	-0.833	-0.926	27.696	-9.889	-9.889	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.863	-0.933	28.113	-9.202	-9.202	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.075	-0.057	25.515	0.072	0.072	0.000	0.000	0.000	0.000
101	A	102	ALA	0	0.012	0.022	24.473	-0.549	-0.549	0.000	0.000	0.000	0.000
102	A	103	ALA	0	-0.049	-0.040	22.184	0.159	0.159	0.000	0.000	0.000	0.000
103	A	104	ASN	0	0.023	0.003	24.274	-0.038	-0.038	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.018	-0.023	25.806	-0.119	-0.119	0.000	0.000	0.000	0.000
105	A	106	ILE	0	-0.053	-0.017	19.217	-0.306	-0.306	0.000	0.000	0.000	0.000
106	A	107	GLN	0	-0.002	0.012	23.649	0.443	0.443	0.000	0.000	0.000	0.000
107	A	108	PHE	0	0.012	-0.007	17.098	-0.575	-0.575	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.950	0.989	21.856	11.441	11.441	0.000	0.000	0.000	0.000
109	A	111	SER	0	-0.006	0.004	20.939	0.303	0.303	0.000	0.000	0.000	0.000
110	A	112	ASP	-1	-0.820	-0.919	22.724	-10.692	-10.692	0.000	0.000	0.000	0.000
111	A	113	GLU	-1	-0.854	-0.914	25.507	-10.518	-10.518	0.000	0.000	0.000	0.000
112	A	114	ALA	0	-0.011	0.021	26.981	0.266	0.266	0.000	0.000	0.000	0.000
113	A	115	VAL	0	-0.026	-0.032	26.200	-0.464	-0.464	0.000	0.000	0.000	0.000
114	A	116	LEU	0	-0.015	-0.013	23.289	0.258	0.258	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.025	-0.028	25.519	-0.427	-0.427	0.000	0.000	0.000	0.000
116	A	118	GLY	0	0.028	0.026	25.717	0.102	0.102	0.000	0.000	0.000	0.000
117	A	119	ASP	-1	-0.876	-0.947	26.531	-9.082	-9.082	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.039	-0.019	28.090	-0.066	-0.066	0.000	0.000	0.000	0.000
119	A	121	LEU	0	0.017	0.030	28.714	0.294	0.294	0.000	0.000	0.000	0.000
120	A	122	SER	0	-0.120	-0.079	30.443	-0.226	-0.226	0.000	0.000	0.000	0.000
121	A	123	TRP	0	0.114	0.073	32.314	0.089	0.089	0.000	0.000	0.000	0.000
122	A	124	GLY	0	0.083	0.040	31.420	-0.283	-0.283	0.000	0.000	0.000	0.000
123	A	125	ARG	1	0.838	0.894	30.958	8.584	8.584	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.025	0.017	26.174	-0.192	-0.192	0.000	0.000	0.000	0.000
125	A	127	GLY	0	-0.019	-0.001	26.526	0.249	0.249	0.000	0.000	0.000	0.000
126	A	128	PRO	0	-0.016	-0.024	24.750	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	129	TRP	0	0.002	0.008	22.559	-0.372	-0.372	0.000	0.000	0.000	0.000
128	A	130	SER	0	0.014	0.018	17.871	0.012	0.012	0.000	0.000	0.000	0.000
129	A	131	LYS	1	0.936	0.962	17.273	14.840	14.840	0.000	0.000	0.000	0.000
130	A	132	ARG	1	0.899	0.921	17.936	11.782	11.782	0.000	0.000	0.000	0.000
131	A	133	CYS	0	-0.043	-0.007	8.711	1.158	1.158	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.931	0.984	13.484	17.893	17.893	0.000	0.000	0.000	0.000
133	A	135	ILE	0	0.042	0.025	12.167	-1.868	-1.868	0.000	0.000	0.000	0.000
134	A	136	CYS	0	-0.030	-0.005	8.177	-3.599	-3.599	0.000	0.000	0.000	0.000
135	A	137	GLY	0	0.075	0.042	7.967	-1.188	-1.188	0.000	0.000	0.000	0.000
136	A	138	LEU	0	-0.029	0.000	9.004	1.015	1.015	0.000	0.000	0.000	0.000
137	A	139	GLN	0	0.030	0.013	8.577	-2.189	-2.189	0.000	0.000	0.000	0.000
138	A	140	THR	0	0.025	0.013	10.657	0.311	0.311	0.000	0.000	0.000	0.000
139	A	141	LYS	1	0.906	0.967	14.271	14.390	14.390	0.000	0.000	0.000	0.000
140	A	142	VAL	0	-0.001	-0.008	16.427	0.514	0.514	0.000	0.000	0.000	0.000
141	A	143	GLU	-1	-0.856	-0.950	19.401	-11.642	-11.642	0.000	0.000	0.000	0.000
142	A	144	SER	0	0.029	0.048	22.454	0.275	0.275	0.000	0.000	0.000	0.000
143	A	145	PRO	0	-0.004	0.019	19.353	0.295	0.295	0.000	0.000	0.000	0.000
144	A	146	GLN	0	0.001	-0.026	22.111	0.079	0.079	0.000	0.000	0.000	0.000
145	A	147	GLY	0	0.019	0.024	24.398	0.343	0.343	0.000	0.000	0.000	0.000
146	A	148	LEU	0	0.023	-0.002	27.240	0.067	0.067	0.000	0.000	0.000	0.000
147	A	149	ARG	1	0.874	0.927	29.372	8.324	8.324	0.000	0.000	0.000	0.000
148	A	150	ASP	-1	-0.953	-0.985	30.547	-8.503	-8.503	0.000	0.000	0.000	0.000
149	A	151	ASP	-1	-0.816	-0.897	28.502	-9.545	-9.545	0.000	0.000	0.000	0.000
150	A	152	THR	0	-0.116	-0.047	23.958	-0.316	-0.316	0.000	0.000	0.000	0.000
151	A	153	ALA	0	0.030	0.001	24.231	0.195	0.195	0.000	0.000	0.000	0.000
152	A	154	LEU	0	-0.051	-0.004	18.107	-0.582	-0.582	0.000	0.000	0.000	0.000
153	A	155	ASN	0	0.031	0.002	20.311	0.491	0.491	0.000	0.000	0.000	0.000
154	A	156	ASN	0	0.001	-0.016	16.960	-0.093	-0.093	0.000	0.000	0.000	0.000
155	A	157	VAL	0	-0.005	0.000	14.229	-0.363	-0.363	0.000	0.000	0.000	0.000
156	A	158	ARG	1	0.822	0.941	10.124	20.969	20.969	0.000	0.000	0.000	0.000
157	A	159	PHE	0	0.047	0.022	11.081	-0.692	-0.692	0.000	0.000	0.000	0.000
158	A	160	PHE	0	-0.033	-0.014	6.561	-1.003	-1.003	0.000	0.000	0.000	0.000
159	A	163	LYS	1	1.012	1.024	8.312	33.012	33.012	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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