FMO DATABASE

FMODB ID: VQ361

Calculation Name: 1GMV-A-Xray372

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: 2023-09-24

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1125928.42421
FMO2-HF: Nuclear repulsion	1072312.017708
FMO2-HF: Total energy	-53616.406502
FMO2-MP2: Total energy	-53771.491826

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.
-4.08	-3.652	5.931	-2.341	-4.017	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 : -0.037 / q_NPA : -0.034

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	-0.035	-0.029	2.038	-2.505	-2.153	5.932	-2.328	-3.955	0.004
4	A	4	LEU	0	0.029	0.029	6.138	0.120	0.120	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.058	-0.040	9.788	-0.035	-0.035	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.036	0.019	12.622	0.039	0.039	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.856	0.924	15.925	0.063	0.063	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.066	-0.005	17.993	0.001	0.001	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.918	-0.967	20.882	-0.054	-0.054	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.016	-0.014	23.429	0.013	0.013	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.002	-0.011	22.202	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.001	0.004	19.487	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.011	-0.004	17.893	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.031	0.025	17.880	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.044	-0.035	15.138	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.040	0.022	12.285	0.036	0.036	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.055	-0.053	13.182	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.087	0.060	12.869	0.037	0.037	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.032	0.030	14.803	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.033	-0.010	14.146	0.031	0.031	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.037	0.051	18.180	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.037	-0.027	20.820	-0.010	-0.010	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.921	-0.946	20.749	0.130	0.130	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.070	-0.005	15.517	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.802	0.897	17.529	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.034	0.016	19.308	-0.023	-0.023	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.921	0.984	16.261	-0.113	-0.113	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.118	-0.035	16.628	-0.024	-0.024	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.973	0.948	12.390	0.071	0.071	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.009	0.005	11.103	0.039	0.039	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.926	0.964	4.928	-2.432	-2.432	0.000	0.000	0.000	0.000
32	A	32	VAL	0	-0.004	0.005	9.073	0.088	0.088	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.019	-0.003	9.511	-0.050	-0.050	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.064	-0.021	8.750	-0.094	-0.094	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.016	-0.043	11.664	0.061	0.061	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.866	-0.915	9.991	0.236	0.236	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.007	-0.001	11.118	0.028	0.028	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.757	0.874	6.059	-0.241	-0.241	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.847	-0.928	5.519	1.008	1.008	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.008	-0.004	4.533	-0.454	-0.378	-0.001	-0.013	-0.062	0.000
41	A	41	GLY	0	-0.021	-0.022	5.225	0.500	0.500	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.072	-0.018	6.784	-0.169	-0.169	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.045	-0.013	10.142	0.017	0.017	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.033	0.018	12.433	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.016	-0.010	16.001	0.019	0.019	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.968	0.969	17.655	0.155	0.155	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.016	0.013	21.670	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.003	0.008	19.066	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.008	0.003	22.348	0.012	0.012	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.031	-0.003	17.033	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.881	0.936	21.292	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.006	0.011	22.405	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.005	0.007	22.094	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.901	-0.960	20.883	-0.031	-0.031	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.007	0.015	17.672	0.004	0.004	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.045	-0.032	13.738	-0.018	-0.018	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.021	0.000	13.861	0.011	0.011	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.025	-0.020	9.960	0.070	0.070	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.902	-0.958	11.569	-0.397	-0.397	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.930	-0.969	9.085	-0.727	-0.727	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.011	0.004	13.210	0.068	0.068	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.071	-0.045	10.471	0.060	0.060	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.881	-0.928	9.789	0.200	0.200	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.004	-0.007	12.935	-0.064	-0.064	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.000	0.032	12.141	0.034	0.034	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.029	-0.004	14.262	-0.021	-0.021	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.020	0.009	16.397	0.024	0.024	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.037	-0.015	18.110	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.014	-0.004	20.175	0.014	0.014	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.007	-0.014	20.597	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.907	-0.956	22.525	0.101	0.101	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.861	-0.957	24.688	0.113	0.113	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.944	-0.966	27.178	0.102	0.102	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.044	-0.022	30.274	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.013	-0.013	32.788	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	0.000	-0.004	37.823	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.888	0.945	37.232	-0.049	-0.049	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.046	-0.011	42.880	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.906	-0.941	45.625	0.024	0.024	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.770	-0.922	48.049	0.017	0.017	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.020	-0.030	47.033	0.000	0.000	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.003	0.017	47.739	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.022	-0.015	49.038	0.000	0.000	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.030	0.024	43.046	0.001	0.001	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.001	0.008	44.657	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.916	0.954	45.909	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.030	0.023	43.556	0.000	0.000	0.000	0.000	0.000	0.000
89	A	89	CYS	0	0.004	-0.009	41.467	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.035	-0.002	41.945	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	HIS	0	-0.033	-0.039	43.844	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.020	0.023	39.025	0.001	0.001	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.069	0.041	39.026	0.001	0.001	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.071	-0.037	40.114	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.894	0.961	40.125	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.086	-0.042	35.948	0.000	0.000	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.019	0.018	35.209	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	PRO	0	-0.009	-0.003	30.710	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.051	0.017	32.849	0.004	0.004	0.000	0.000	0.000	0.000
100	A	100	GLN	0	0.015	0.027	30.909	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.006	-0.008	33.716	0.001	0.001	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.002	0.006	34.961	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.009	-0.002	37.907	0.000	0.000	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.017	0.009	40.927	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.837	-0.927	36.258	0.049	0.049	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.011	0.011	37.652	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.863	0.915	30.985	-0.053	-0.053	0.000	0.000	0.000	0.000
108	A	108	TYR	0	-0.001	-0.050	33.362	-0.005	-0.005	0.000	0.000	0.000	0.000
109	A	109	HIS	0	-0.013	0.003	27.228	-0.004	-0.004	0.000	0.000	0.000	0.000
110	A	110	ALA	0	0.003	0.004	32.368	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.850	-0.933	34.716	0.054	0.054	0.000	0.000	0.000	0.000
112	A	112	HIS	0	0.045	0.023	37.451	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.001	0.016	40.920	-0.003	-0.003	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.033	-0.023	37.612	-0.004	-0.004	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.728	-0.823	39.961	0.050	0.050	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.921	-0.971	42.604	0.039	0.039	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.110	-0.050	43.439	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.030	0.001	41.322	-0.003	-0.003	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.871	0.945	42.931	-0.047	-0.047	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.070	-0.010	48.012	-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	-0.035	-0.014	50.584	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.025	-0.005	45.181	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.005	-0.005	44.718	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.025	-0.006	40.559	0.000	0.000	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.054	-0.022	39.498	0.000	0.000	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.035	0.012	32.705	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	128	GLY	0	0.004	0.004	34.421	-0.001	-0.001	0.000	0.000	0.000	0.000
129	A	129	GLN	0	0.012	0.013	28.530	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	130	LEU	0	-0.005	-0.007	29.365	-0.001	-0.001	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.034	0.048	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	-0.843	-0.949	25.843	0.042	0.042	0.000	0.000	0.000	0.000
134	A	134	PRO	0	-0.032	-0.011	27.481	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.858	-0.943	30.039	0.008	0.008	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.070	-0.037	29.868	0.001	0.001	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.020	0.004	30.382	-0.004	-0.004	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.043	0.000	27.710	0.003	0.003	0.000	0.000	0.000	0.000

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