FMO DATABASE

FMODB ID: GY7R1

Calculation Name: 3N3F-A-Xray540

Preferred Name: Collagen

Target Type: PROTEIN COMPLEX GROUP

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3N3F

Chain ID: A

ChEMBL ID: CHEMBL2364188

UniProt ID: P39059

Base Structure: X-ray

Registration Date: 2025-07-08

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	103
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-278690.171218
FMO2-HF: Nuclear repulsion	256885.566905
FMO2-HF: Total energy	-21804.604313
FMO2-MP2: Total energy	-21868.02082

3D Structure Molmil

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:ASN)

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

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.
-11.893	-14.951	15.687	-7.558	-5.07	0.042

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.166 / q_NPA : 0.075

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].
4	A	2	LEU	0	-0.108	0.057	3.181	-0.185	-0.139	0.006	0.303	-0.355	0.001
5	A	3	VAL	0	0.095	-0.108	3.804	0.053	1.939	-0.027	-1.075	-0.784	0.000
6	A	3	VAL	0	-0.083	0.113	7.838	-0.109	-0.109	0.000	0.000	0.000	0.000
7	A	4	THR	0	0.075	-0.030	6.787	-0.545	-0.545	0.000	0.000	0.000	0.000
8	A	4	THR	0	-0.048	0.045	7.223	-0.148	-0.148	0.000	0.000	0.000	0.000
9	A	5	ALA	0	0.097	-0.100	8.679	0.043	0.043	0.000	0.000	0.000	0.000
10	A	5	ALA	0	-0.093	0.079	12.605	-0.048	-0.048	0.000	0.000	0.000	0.000
11	A	6	PHE	0	-0.004	-0.115	12.112	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	6	PHE	0	-0.056	0.124	10.931	0.020	0.020	0.000	0.000	0.000	0.000
13	A	7	SER	0	0.046	-0.066	14.989	-0.012	-0.012	0.000	0.000	0.000	0.000
14	A	7	SER	0	0.011	0.077	19.864	-0.002	-0.002	0.000	0.000	0.000	0.000
15	A	8	ASN	0	0.088	-0.033	18.469	-0.014	-0.014	0.000	0.000	0.000	0.000
16	A	8	ASN	0	-0.105	0.050	20.727	0.013	0.013	0.000	0.000	0.000	0.000
17	A	9	MET	0	0.177	-0.077	17.378	0.068	0.068	0.000	0.000	0.000	0.000
18	A	9	MET	0	-0.068	0.111	17.569	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	10	ASP	0	0.073	-0.124	17.758	0.073	0.073	0.000	0.000	0.000	0.000
20	A	10	ASP	-1	-0.934	-0.822	21.583	0.323	0.323	0.000	0.000	0.000	0.000
21	A	11	ASP	0	0.100	-0.087	18.154	0.000	0.000	0.000	0.000	0.000	0.000
22	A	11	ASP	-1	-0.914	-0.819	17.286	0.496	0.496	0.000	0.000	0.000	0.000
23	A	12	MET	0	0.139	-0.097	14.187	0.015	0.015	0.000	0.000	0.000	0.000
24	A	12	MET	0	-0.128	0.079	12.493	0.064	0.064	0.000	0.000	0.000	0.000
25	A	13	LEU	0	-0.005	-0.134	14.370	0.105	0.105	0.000	0.000	0.000	0.000
26	A	13	LEU	0	-0.083	0.108	16.513	-0.011	-0.011	0.000	0.000	0.000	0.000
27	A	14	GLN	0	0.073	-0.082	16.790	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	14	GLN	0	-0.116	0.088	17.871	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	15	LYS	0	0.003	-0.112	14.056	-0.081	-0.081	0.000	0.000	0.000	0.000
30	A	15	LYS	1	0.778	1.008	13.188	-0.463	-0.463	0.000	0.000	0.000	0.000
31	A	16	ALA	0	0.201	-0.092	11.843	0.215	0.215	0.000	0.000	0.000	0.000
32	A	16	ALA	0	-0.051	0.117	12.958	-0.024	-0.024	0.000	0.000	0.000	0.000
33	A	17	HIS	0	-0.030	-0.099	10.461	0.217	0.217	0.000	0.000	0.000	0.000
34	A	17	HIS	0	-0.078	0.085	12.721	0.033	0.033	0.000	0.000	0.000	0.000
35	A	18	LEU	0	0.076	-0.099	10.074	-0.089	-0.089	0.000	0.000	0.000	0.000
36	A	18	LEU	0	-0.064	0.097	10.771	-0.019	-0.019	0.000	0.000	0.000	0.000
37	A	19	VAL	0	0.049	-0.108	6.465	0.085	0.085	0.000	0.000	0.000	0.000
38	A	19	VAL	0	-0.103	0.101	5.986	0.089	0.089	0.000	0.000	0.000	0.000
39	A	20	ILE	0	0.117	-0.113	3.775	-0.602	-0.544	0.001	-0.011	-0.048	0.000
40	A	20	ILE	0	-0.082	0.115	2.757	-0.644	-0.224	0.097	-0.191	-0.326	0.000
41	A	21	GLU	0	0.093	-0.107	4.461	1.572	1.683	-0.002	-0.011	-0.098	0.000
42	A	21	GLU	-1	-0.936	-0.827	7.209	0.482	0.482	0.000	0.000	0.000	0.000
43	A	22	GLY	0	-0.039	-0.138	4.246	-0.475	-0.280	-0.001	-0.036	-0.157	0.000
44	A	23	THR	0	-0.026	0.009	3.165	-2.037	-1.372	0.039	-0.207	-0.497	0.001
45	A	23	THR	0	-0.049	0.031	1.879	-6.718	-13.404	15.556	-6.175	-2.695	0.039
46	A	24	PHE	0	0.058	-0.088	3.738	-1.815	-1.568	0.018	-0.155	-0.110	0.001
47	A	24	PHE	0	-0.090	0.095	5.880	-0.161	-0.161	0.000	0.000	0.000	0.000
48	A	25	ILE	0	0.060	-0.113	7.062	0.507	0.507	0.000	0.000	0.000	0.000
49	A	25	ILE	0	-0.071	0.093	8.370	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	26	TYR	0	0.156	-0.055	9.842	-0.190	-0.190	0.000	0.000	0.000	0.000
51	A	26	TYR	0	-0.109	0.081	12.466	-0.033	-0.033	0.000	0.000	0.000	0.000
52	A	27	LEU	0	0.036	-0.110	13.001	0.057	0.057	0.000	0.000	0.000	0.000
53	A	27	LEU	0	-0.100	0.092	14.575	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	28	ARG	0	0.129	-0.078	16.200	-0.045	-0.045	0.000	0.000	0.000	0.000
55	A	28	ARG	1	0.812	1.004	15.509	-0.428	-0.428	0.000	0.000	0.000	0.000
56	A	29	ASP	0	0.091	-0.083	18.424	-0.033	-0.033	0.000	0.000	0.000	0.000
57	A	29	ASP	-1	-0.959	-0.847	21.505	0.294	0.294	0.000	0.000	0.000	0.000
58	A	30	SER	0	0.016	-0.065	20.336	-0.037	-0.037	0.000	0.000	0.000	0.000
59	A	30	SER	0	-0.073	0.020	20.043	0.015	0.015	0.000	0.000	0.000	0.000
60	A	31	THR	0	-0.052	-0.056	18.635	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	31	THR	0	-0.041	0.041	20.014	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	32	GLU	0	0.115	-0.108	17.527	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	32	GLU	-1	-0.895	-0.775	17.616	0.367	0.367	0.000	0.000	0.000	0.000
64	A	33	PHE	0	0.090	-0.099	13.533	0.047	0.047	0.000	0.000	0.000	0.000
65	A	33	PHE	0	-0.095	0.099	10.467	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	34	PHE	0	0.054	-0.078	12.070	-0.136	-0.136	0.000	0.000	0.000	0.000
67	A	34	PHE	0	-0.028	0.085	12.331	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	35	ILE	0	0.097	-0.098	8.515	0.242	0.242	0.000	0.000	0.000	0.000
69	A	35	ILE	0	-0.092	0.116	8.390	-0.055	-0.055	0.000	0.000	0.000	0.000
70	A	36	ARG	0	0.155	-0.090	7.350	-0.533	-0.533	0.000	0.000	0.000	0.000
71	A	36	ARG	1	0.716	1.018	6.493	-1.151	-1.151	0.000	0.000	0.000	0.000
72	A	37	VAL	0	0.020	-0.075	7.298	0.201	0.201	0.000	0.000	0.000	0.000
73	A	37	VAL	0	-0.103	0.060	9.357	-0.052	-0.052	0.000	0.000	0.000	0.000
74	A	38	ARG	0	0.179	-0.091	9.745	0.077	0.077	0.000	0.000	0.000	0.000
75	A	38	ARG	1	0.743	1.025	12.159	-0.314	-0.314	0.000	0.000	0.000	0.000
76	A	39	ASP	0	-0.060	-0.121	12.104	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	39	ASP	-1	-0.892	-0.807	15.740	0.334	0.334	0.000	0.000	0.000	0.000
78	A	40	GLY	0	0.063	-0.102	12.773	-0.071	-0.071	0.000	0.000	0.000	0.000
79	A	41	TRP	0	0.041	-0.007	11.661	0.171	0.171	0.000	0.000	0.000	0.000
80	A	41	TRP	0	-0.016	0.119	10.809	-0.069	-0.069	0.000	0.000	0.000	0.000
81	A	42	LYS	0	0.067	-0.085	12.339	-0.122	-0.122	0.000	0.000	0.000	0.000
82	A	42	LYS	1	0.889	1.068	12.986	-0.415	-0.415	0.000	0.000	0.000	0.000
83	A	43	LYS	0	0.123	-0.099	13.126	0.124	0.124	0.000	0.000	0.000	0.000
84	A	43	LYS	1	0.798	1.046	16.889	-0.362	-0.362	0.000	0.000	0.000	0.000
85	A	44	LEU	0	0.037	-0.118	14.245	-0.058	-0.058	0.000	0.000	0.000	0.000
86	A	44	LEU	0	-0.082	0.106	12.030	0.007	0.007	0.000	0.000	0.000	0.000
87	A	45	GLN	0	0.074	-0.098	15.260	0.001	0.001	0.000	0.000	0.000	0.000
88	A	45	GLN	0	-0.111	0.086	18.860	0.010	0.010	0.000	0.000	0.000	0.000
89	A	46	LEU	0	0.048	-0.145	18.812	-0.018	-0.018	0.000	0.000	0.000	0.000
90	A	46	LEU	0	-0.039	0.124	16.001	0.006	0.006	0.000	0.000	0.000	0.000
91	A	47	GLY	0	-0.035	-0.092	19.874	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	48	GLU	0	0.155	0.003	23.161	0.021	0.021	0.000	0.000	0.000	0.000
93	A	48	GLU	-1	-1.033	-0.854	27.434	0.145	0.145	0.000	0.000	0.000	0.000
94	A	49	LEU	0	0.103	-0.107	24.573	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	49	LEU	0	-0.103	0.111	23.756	0.001	0.001	0.000	0.000	0.000	0.000
96	A	50	ILE	0	0.067	-0.110	25.093	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	50	ILE	0	-0.092	0.108	24.841	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	51	PRO	0	-0.047	-0.128	26.482	0.000	0.000	0.000	0.000	0.000	0.000
99	A	52	ILE	0	0.087	0.004	28.523	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	52	ILE	0	-0.063	0.103	25.505	0.000	0.000	0.000	0.000	0.000	0.000
101	A	53	PRO	0	-0.047	-0.116	29.110	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	54	ALA	0	-0.024	-0.019	32.317	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	54	ALA	0	0.043	0.040	36.364	0.000	0.000	0.000	0.000	0.000	0.000

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