FMO DATABASE

FMODB ID: 1N13Z

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	OptHSide
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	-1125748.311778
FMO2-HF: Nuclear repulsion	1072130.79356
FMO2-HF: Total energy	-53617.518218
FMO2-MP2: Total energy	-53772.465531

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.
-5.939	-2.607	1.459	-1.706	-3.085	0.008

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 : 0.000 / q_NPA : -0.004

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	-0.012	-0.026	2.252	-1.908	1.254	1.461	-1.680	-2.943	0.008
4	A	4	LEU	0	0.008	0.022	6.050	0.025	0.025	0.000	0.000	0.000	0.000
5	A	5	THR	0	-0.073	-0.059	9.708	0.056	0.056	0.000	0.000	0.000	0.000
6	A	6	GLN	0	0.017	0.008	12.528	0.235	0.235	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.848	0.913	15.843	0.198	0.198	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.066	-0.013	18.017	0.024	0.024	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.922	-0.965	20.871	-0.214	-0.214	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.008	-0.013	23.489	0.023	0.023	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.002	-0.002	22.203	-0.035	-0.035	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.005	-0.004	19.564	0.014	0.014	0.000	0.000	0.000	0.000
13	A	13	ALA	0	-0.011	0.000	18.008	0.032	0.032	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.025	0.019	17.876	-0.033	-0.033	0.000	0.000	0.000	0.000
15	A	15	THR	0	-0.023	-0.023	15.184	0.049	0.049	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.001	-0.003	12.241	0.024	0.024	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.052	-0.046	13.171	0.062	0.062	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.082	0.050	12.669	0.032	0.032	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.019	0.033	14.799	-0.041	-0.041	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.016	0.004	14.057	0.060	0.060	0.000	0.000	0.000	0.000
21	A	21	PRO	0	0.050	0.043	18.161	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	22	ILE	0	-0.025	-0.017	20.787	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.837	-0.914	20.765	0.161	0.161	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.029	0.001	15.560	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	ARG	1	0.745	0.860	17.480	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	26	VAL	0	0.031	0.015	19.258	-0.035	-0.035	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.816	0.903	16.296	-0.147	-0.147	0.000	0.000	0.000	0.000
28	A	28	SER	0	-0.103	-0.031	16.552	-0.015	-0.015	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.965	0.965	11.767	0.001	0.001	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.004	-0.004	11.200	0.082	0.082	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.864	0.915	5.108	-3.783	-3.686	-0.001	-0.012	-0.084	0.000
32	A	32	VAL	0	-0.008	-0.002	9.047	0.156	0.156	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.035	-0.021	9.538	-0.080	-0.080	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.046	-0.018	8.897	-0.112	-0.112	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.043	-0.064	11.682	0.111	0.111	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.826	-0.869	10.261	-0.467	-0.467	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.002	0.006	11.122	-0.026	-0.026	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.677	0.798	6.067	0.994	0.994	0.000	0.000	0.000	0.000
39	A	39	ASP	-1	-0.754	-0.851	5.566	1.760	1.760	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.003	0.001	4.511	-0.783	-0.710	-0.001	-0.014	-0.058	0.000
41	A	41	GLY	0	-0.021	-0.016	5.152	0.686	0.686	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.044	-0.023	6.721	-0.269	-0.269	0.000	0.000	0.000	0.000
43	A	43	LEU	0	-0.062	-0.026	10.063	0.078	0.078	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.057	0.035	12.339	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.025	-0.017	15.911	0.052	0.052	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.937	0.962	17.165	0.229	0.229	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.027	0.016	21.583	-0.010	-0.010	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.008	0.004	19.353	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.019	0.011	22.277	0.020	0.020	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.016	0.011	17.022	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	51	ARG	1	0.850	0.903	21.231	0.085	0.085	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.005	0.005	22.355	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.002	0.008	22.057	0.005	0.005	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.877	-0.936	20.744	-0.195	-0.195	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.038	-0.012	17.875	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	56	LEU	0	-0.042	-0.032	13.858	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.000	-0.023	13.814	-0.019	-0.019	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.025	-0.018	9.502	0.222	0.222	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.823	-0.896	11.687	-0.785	-0.785	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.916	-0.963	8.754	-2.128	-2.128	0.000	0.000	0.000	0.000
61	A	61	GLY	0	-0.003	0.013	13.107	0.133	0.133	0.000	0.000	0.000	0.000
62	A	62	THR	0	-0.076	-0.040	9.932	0.077	0.077	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.809	-0.879	9.828	-0.768	-0.768	0.000	0.000	0.000	0.000
64	A	64	PHE	0	0.004	0.001	12.898	-0.022	-0.022	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.008	0.023	12.094	0.078	0.078	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.043	0.001	14.267	0.037	0.037	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.011	0.012	16.210	0.031	0.031	0.000	0.000	0.000	0.000
68	A	68	ILE	0	-0.015	-0.010	18.073	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.004	0.000	20.155	0.028	0.028	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.010	-0.012	20.533	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	ASP	-1	-0.904	-0.962	22.516	0.065	0.065	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.827	-0.925	24.599	0.106	0.106	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.940	-0.969	27.172	0.126	0.126	0.000	0.000	0.000	0.000
74	A	74	VAL	0	-0.047	-0.027	30.165	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.014	-0.025	32.777	0.004	0.004	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.034	-0.032	35.250	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.001	-0.005	37.807	0.001	0.001	0.000	0.000	0.000	0.000
78	A	78	ARG	1	0.848	0.900	37.194	-0.020	-0.020	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.047	-0.014	42.859	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.881	-0.937	45.597	0.000	0.000	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.769	-0.911	48.020	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	PRO	0	-0.012	-0.022	46.998	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	PHE	0	0.028	0.022	47.697	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	MET	0	-0.019	-0.030	48.908	0.002	0.002	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.029	0.028	43.052	0.002	0.002	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.006	0.013	44.617	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.864	0.949	45.864	-0.005	-0.005	0.000	0.000	0.000	0.000
88	A	88	ALA	0	0.040	0.032	43.551	0.001	0.001	0.000	0.000	0.000	0.000
89	A	89	CYS	0	-0.005	-0.019	41.426	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	TYR	0	-0.026	0.001	41.899	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	HIS	0	-0.038	-0.048	43.796	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.001	0.014	39.132	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.074	0.043	38.977	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.081	-0.035	40.065	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	ARG	1	0.903	0.960	40.136	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.088	-0.046	35.962	0.003	0.003	0.000	0.000	0.000	0.000
97	A	97	VAL	0	0.028	0.022	35.163	0.004	0.004	0.000	0.000	0.000	0.000
98	A	98	PRO	0	-0.011	-0.003	30.680	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.034	0.012	32.805	0.006	0.006	0.000	0.000	0.000	0.000
100	A	100	GLN	0	0.023	0.005	31.066	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.008	-0.015	33.676	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.007	0.018	34.525	-0.009	-0.009	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.023	0.005	37.867	0.004	0.004	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.014	0.008	40.895	0.001	0.001	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.772	-0.864	36.010	0.015	0.015	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.012	0.004	37.621	-0.004	-0.004	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.841	0.903	30.945	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	108	TYR	0	0.002	-0.010	33.317	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	109	HIS	0	-0.026	-0.019	27.082	-0.003	-0.003	0.000	0.000	0.000	0.000
110	A	110	ALA	0	-0.007	0.002	32.348	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.823	-0.923	34.704	0.068	0.068	0.000	0.000	0.000	0.000
112	A	112	HIS	0	0.015	0.006	37.437	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	113	VAL	0	-0.001	0.011	40.911	-0.005	-0.005	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.032	-0.019	37.659	-0.006	-0.006	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.743	-0.840	39.866	0.049	0.049	0.000	0.000	0.000	0.000
116	A	116	ASP	-1	-0.869	-0.931	42.588	0.044	0.044	0.000	0.000	0.000	0.000
117	A	117	MET	0	-0.089	-0.035	43.204	-0.005	-0.005	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.040	0.004	41.390	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.851	0.924	42.616	-0.050	-0.050	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.090	-0.025	47.994	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	121	PHE	0	-0.072	-0.044	46.569	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	GLY	0	-0.024	-0.006	50.558	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.033	-0.007	45.311	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.002	-0.006	44.731	0.003	0.003	0.000	0.000	0.000	0.000
125	A	125	VAL	0	-0.032	-0.012	40.530	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	THR	0	-0.023	-0.014	39.532	0.003	0.003	0.000	0.000	0.000	0.000
127	A	127	PHE	0	0.011	0.008	32.856	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	128	GLY	0	-0.006	-0.002	34.421	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	129	GLN	0	-0.009	0.007	28.709	0.005	0.005	0.000	0.000	0.000	0.000
130	A	130	LEU	0	0.008	0.002	29.400	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.031	0.047	26.022	0.007	0.007	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.044	-0.027	26.446	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	133	GLU	-1	-0.775	-0.877	25.299	-0.043	-0.043	0.000	0.000	0.000	0.000
134	A	134	PRO	0	-0.035	-0.017	27.491	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.832	-0.933	29.988	-0.048	-0.048	0.000	0.000	0.000	0.000
136	A	136	ALA	0	-0.080	-0.028	29.809	0.003	0.003	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.032	0.005	30.293	-0.003	-0.003	0.000	0.000	0.000	0.000
138	A	138	ALA	0	-0.067	-0.012	27.607	0.008	0.008	0.000	0.000	0.000	0.000

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