FMO DATABASE

FMODB ID: G5341

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1128211.812636
FMO2-HF: Nuclear repulsion	1074593.657667
FMO2-HF: Total energy	-53618.154969
FMO2-MP2: Total energy	-53773.038213

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.
-8.457	-4.482	1.201	-1.705	-3.473	0.005

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 : -0.002 / q_NPA : -0.007

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	-0.028	-0.030	2.522	-2.163	1.187	1.193	-1.565	-2.979	0.005
4	A	4	LEU	0	-0.003	0.015	5.949	-0.048	-0.048	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.056	-0.073	9.599	0.166	0.166	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.012	-0.020	12.564	0.236	0.236	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.799	0.882	15.633	0.169	0.169	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.063	-0.030	17.796	0.008	0.008	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.928	-0.966	20.986	-0.216	-0.216	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.008	-0.002	23.448	0.021	0.021	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.005	0.005	22.338	-0.033	-0.033	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.018	-0.012	19.603	0.011	0.011	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.006	-0.009	18.569	0.026	0.026	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.038	0.031	17.716	-0.048	-0.048	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.070	-0.048	14.592	0.071	0.071	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.003	0.013	11.964	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.045	-0.023	13.312	0.070	0.070	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.042	0.015	12.315	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.036	0.042	14.694	-0.034	-0.034	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.004	0.005	13.812	0.070	0.070	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.056	0.041	17.945	-0.037	-0.037	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.025	-0.033	20.246	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.844	-0.911	20.442	0.233	0.233	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.014	0.001	15.142	0.012	0.012	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.739	0.856	17.233	-0.041	-0.041	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.050	0.029	19.026	-0.038	-0.038	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.798	0.889	16.085	-0.240	-0.240	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.075	-0.015	16.345	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.942	0.963	10.840	-0.220	-0.220	0.000	0.000	0.000	0.000
30	A	30	VAL	0	0.018	0.007	10.950	0.069	0.069	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.871	0.918	4.192	-5.581	-5.281	0.008	-0.068	-0.240	0.000
32	A	32	VAL	0	-0.027	-0.003	8.384	0.168	0.168	0.000	0.000	0.000	0.000
33	A	33	THR	0	0.011	-0.015	8.527	-0.130	-0.130	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.042	-0.003	8.374	-0.080	-0.080	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.008	-0.038	11.100	0.115	0.115	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.795	-0.880	10.556	-0.604	-0.604	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.003	-0.001	10.709	-0.075	-0.075	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.707	0.822	6.328	1.201	1.201	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.831	-0.902	5.039	1.908	1.908	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.002	0.020	4.001	-1.055	-0.730	0.000	-0.072	-0.254	0.000
41	A	41	GLY	0	-0.001	-0.014	4.916	1.017	1.017	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.040	-0.007	6.470	-0.572	-0.572	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.069	-0.039	9.831	0.181	0.181	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.075	0.055	12.095	-0.054	-0.054	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.002	-0.008	15.545	0.058	0.058	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.873	0.915	16.835	0.136	0.136	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.029	0.011	21.026	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.032	0.000	19.138	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.032	0.025	21.170	0.017	0.017	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.017	0.000	16.839	-0.034	-0.034	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.826	0.885	21.081	0.065	0.065	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.003	-0.014	21.823	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.009	0.007	21.741	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.811	-0.881	19.674	-0.200	-0.200	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.013	0.005	17.713	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.018	-0.020	13.437	0.017	0.017	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.005	-0.017	13.430	-0.039	-0.039	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.010	-0.011	9.432	0.243	0.243	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.810	-0.865	11.944	-0.723	-0.723	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.924	-0.969	8.981	-2.246	-2.246	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.034	-0.005	13.426	0.100	0.100	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.057	-0.032	10.608	0.090	0.090	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.784	-0.873	10.144	-0.906	-0.906	0.000	0.000	0.000	0.000
64	A	64	PHE	0	-0.003	0.007	13.075	-0.009	-0.009	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.001	0.020	11.995	0.087	0.087	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.027	0.005	14.230	0.056	0.056	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.003	-0.006	16.000	0.033	0.033	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.016	-0.002	17.818	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.003	-0.004	19.701	0.030	0.030	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.001	-0.024	20.220	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.908	-0.959	22.134	0.067	0.067	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.809	-0.906	24.243	0.139	0.139	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.913	-0.962	26.643	0.151	0.151	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.038	-0.022	29.777	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.018	-0.027	32.339	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.035	-0.025	34.737	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.005	0.002	37.273	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.845	0.890	37.255	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.070	-0.012	42.577	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.843	-0.925	45.332	0.004	0.004	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.772	-0.894	47.926	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.006	-0.016	46.606	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.032	0.014	47.236	0.002	0.002	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.027	-0.043	48.244	0.002	0.002	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.038	0.038	42.627	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.021	0.016	43.805	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.839	0.936	45.348	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.047	0.030	42.769	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	CYS	0	-0.013	-0.015	40.850	0.002	0.002	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.031	-0.002	41.428	0.000	0.000	0.000	0.000	0.000	0.000
91	A	91	HIS	0	-0.041	-0.041	43.325	0.002	0.002	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.001	0.010	38.623	0.004	0.004	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.070	0.042	38.842	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.093	-0.056	39.921	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.912	0.963	39.767	-0.046	-0.046	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.078	-0.040	35.749	0.005	0.005	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.023	0.021	34.755	0.005	0.005	0.000	0.000	0.000	0.000
98	A	98	PRO	0	-0.003	-0.003	30.132	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.032	0.016	32.314	0.005	0.005	0.000	0.000	0.000	0.000
100	A	100	GLN	0	0.029	0.017	30.900	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.013	-0.011	33.428	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.013	0.012	34.205	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.003	-0.016	37.633	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.038	0.034	40.810	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.771	-0.859	35.698	0.021	0.021	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.017	-0.004	37.132	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.809	0.890	30.645	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.006	-0.021	32.754	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	109	HIS	0	-0.024	-0.023	26.417	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.007	-0.004	31.652	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.823	-0.912	34.248	0.091	0.091	0.000	0.000	0.000	0.000
112	A	112	HIS	0	0.007	-0.002	37.109	-0.007	-0.007	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.024	-0.010	40.444	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.048	-0.021	37.189	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.740	-0.840	39.471	0.061	0.061	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.831	-0.906	42.156	0.055	0.055	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.076	-0.022	42.681	-0.006	-0.006	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.027	0.009	41.095	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.801	0.888	41.936	-0.061	-0.061	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.073	-0.026	47.705	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	121	PHE	0	-0.074	-0.038	46.234	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.010	-0.006	50.161	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.048	-0.018	44.575	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.001	-0.001	44.153	0.003	0.003	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.026	-0.015	40.323	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.030	-0.009	38.820	0.003	0.003	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.030	0.020	32.347	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	128	GLY	0	-0.004	-0.009	34.001	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	129	GLN	0	-0.006	0.009	27.951	0.004	0.004	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.014	0.003	29.326	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	131	PRO	0	-0.001	0.029	25.763	0.008	0.008	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.041	-0.011	26.167	-0.013	-0.013	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.763	-0.878	24.996	-0.022	-0.022	0.000	0.000	0.000	0.000
134	A	134	PRO	0	-0.023	-0.005	27.258	-0.008	-0.008	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.809	-0.911	29.496	-0.034	-0.034	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.058	-0.018	29.512	0.006	0.006	0.000	0.000	0.000	0.000
137	A	137	GLY	0	-0.019	-0.006	30.571	-0.006	-0.006	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.071	-0.034	27.122	0.011	0.011	0.000	0.000	0.000	0.000

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