FMO DATABASE

FMODB ID: V21V1

Calculation Name: 1GMV-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GMV

Chain ID: A

ChEMBL ID:

UniProt ID: P18317

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	139
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1127679.153835
FMO2-HF: Nuclear repulsion	1074043.618191
FMO2-HF: Total energy	-53635.535644
FMO2-MP2: Total energy	-53790.716845

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:MET )

Summations of interaction energy for fragment #1(A:1: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.
-4.023	-3.519	5.942	-2.435	-4.011	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.032

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	TYR	0	-0.027	-0.025	2.039	-2.497	-2.075	5.942	-2.423	-3.941	0.004
4	A	4	LEU	0	0.023	0.027	6.139	0.133	0.133	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.057	-0.041	9.789	-0.039	-0.039	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.030	0.017	12.623	0.041	0.041	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.853	0.924	15.926	0.065	0.065	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.068	-0.008	17.991	0.001	0.001	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.919	-0.968	20.882	-0.052	-0.052	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.015	-0.013	23.429	0.013	0.013	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.004	-0.011	22.201	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.003	0.004	19.486	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.015	-0.008	17.894	0.014	0.014	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.037	0.028	17.879	-0.003	-0.003	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.043	-0.034	15.083	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.036	0.019	12.285	0.039	0.039	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.057	-0.052	13.182	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.082	0.058	12.867	0.043	0.043	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.030	0.030	14.803	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.026	-0.010	14.145	0.032	0.032	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.032	0.050	18.180	-0.021	-0.021	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.019	-0.026	20.820	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.928	-0.944	20.750	0.135	0.135	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.070	-0.007	15.517	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.799	0.898	17.530	-0.085	-0.085	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.031	0.015	19.308	-0.024	-0.024	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.920	0.984	16.263	-0.117	-0.117	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.119	-0.035	16.629	-0.027	-0.027	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.973	0.948	12.391	0.086	0.086	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.011	0.007	11.104	0.043	0.043	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.926	0.965	4.928	-2.549	-2.549	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.003	0.004	9.073	0.089	0.089	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.017	-0.003	9.511	-0.048	-0.048	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.064	-0.021	8.751	-0.106	-0.106	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.012	-0.042	11.664	0.062	0.062	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.865	-0.915	9.990	0.281	0.281	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.004	0.000	11.118	0.030	0.030	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.755	0.873	6.058	-0.270	-0.270	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.844	-0.927	5.520	1.085	1.085	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.009	-0.004	4.533	-0.426	-0.344	0.000	-0.012	-0.070	0.000
41	A	41	GLY	0	-0.032	-0.025	5.227	0.478	0.478	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.064	-0.016	6.784	-0.170	-0.170	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.047	-0.014	10.142	0.010	0.010	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.033	0.019	12.434	0.000	0.000	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.019	-0.012	16.002	0.018	0.018	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.967	0.969	17.655	0.165	0.165	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.019	0.016	21.672	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.003	0.008	19.065	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.011	0.003	22.349	0.013	0.013	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.029	-0.001	17.026	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.875	0.932	21.293	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.005	0.011	22.405	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.004	0.008	22.094	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.904	-0.962	20.884	-0.027	-0.027	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.002	0.018	17.672	0.005	0.005	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.045	-0.032	13.738	-0.022	-0.022	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.027	0.001	13.861	0.010	0.010	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.025	-0.019	9.958	0.067	0.067	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.904	-0.960	11.567	-0.406	-0.406	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.928	-0.967	9.083	-0.732	-0.732	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.006	0.006	13.208	0.071	0.071	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.077	-0.046	10.469	0.063	0.063	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.882	-0.930	9.788	0.227	0.227	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.006	-0.006	12.934	-0.065	-0.065	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.007	0.028	12.140	0.036	0.036	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.038	-0.001	14.261	-0.024	-0.024	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.011	0.007	16.398	0.027	0.027	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.033	-0.015	18.110	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.009	-0.005	20.176	0.015	0.015	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.011	-0.012	20.600	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.901	-0.953	22.524	0.108	0.108	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.867	-0.961	24.687	0.120	0.120	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.943	-0.966	27.178	0.107	0.107	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.048	-0.023	30.273	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.009	-0.014	32.789	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.028	-0.025	35.317	-0.002	-0.002	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.004	-0.002	37.823	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.878	0.943	37.232	-0.052	-0.052	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.047	-0.012	42.880	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.902	-0.940	45.625	0.026	0.026	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.771	-0.923	48.049	0.019	0.019	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.018	-0.031	47.032	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.003	0.019	47.739	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.022	-0.017	49.038	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.026	0.022	43.046	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.006	0.010	44.657	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.918	0.957	45.910	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.029	0.024	43.555	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	CYS	0	0.000	-0.012	41.467	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.031	0.000	41.947	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	HIS	0	-0.037	-0.040	43.844	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.023	0.021	39.025	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.070	0.042	39.026	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.069	-0.034	40.115	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.893	0.960	40.125	-0.032	-0.032	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.092	-0.045	35.948	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.021	0.017	35.208	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	PRO	0	-0.010	-0.003	30.710	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.050	0.017	32.849	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	GLN	0	0.007	0.022	30.909	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.013	-0.003	33.716	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.007	0.001	34.960	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.010	0.001	37.906	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.015	0.010	40.928	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.839	-0.929	36.258	0.053	0.053	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.012	0.011	37.652	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.869	0.916	30.986	-0.057	-0.057	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.011	-0.044	33.362	-0.006	-0.006	0.000	0.000	0.000	0.000
109	A	109	HIS	0	-0.010	0.003	27.228	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.002	0.004	32.368	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.847	-0.935	34.717	0.056	0.056	0.000	0.000	0.000	0.000
112	A	112	HIS	0	0.042	0.020	37.451	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.002	0.016	40.921	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.028	-0.020	37.612	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.726	-0.819	39.961	0.053	0.053	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.923	-0.971	42.604	0.041	0.041	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.113	-0.052	43.440	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.022	-0.004	41.323	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.874	0.945	42.932	-0.049	-0.049	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.068	-0.008	48.013	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	121	PHE	0	-0.078	-0.046	46.707	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.032	-0.011	50.585	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.026	-0.003	45.181	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.007	-0.005	44.718	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.032	-0.008	40.559	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.051	-0.022	39.498	0.001	0.001	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.036	0.012	32.705	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.003	0.005	34.422	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	GLN	0	0.014	0.014	28.530	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.003	-0.006	29.365	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.029	0.047	26.037	0.001	0.001	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.027	-0.017	26.476	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.845	-0.951	25.843	0.048	0.048	0.000	0.000	0.000	0.000
134	A	134	PRO	0	-0.025	-0.008	27.481	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.865	-0.944	30.039	0.010	0.010	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.063	-0.034	29.869	0.001	0.001	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.030	0.004	30.385	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.065	-0.012	27.705	0.005	0.005	0.000	0.000	0.000	0.000
139	A	139	NME	0	0.004	0.009	29.665	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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