FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

tag_button

FMODB ID: RY3Z8

Calculation Name: 3N7C-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 3N7C

Chain ID: A

ChEMBL ID:

UniProt ID: Q75DJ0

Base Structure: X-ray

Registration Date: 2025-07-11

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 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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -898053.267567
FMO2-HF: Nuclear repulsion 853736.637159
FMO2-HF: Total energy -44316.630408
FMO2-MP2: Total energy -44445.334587


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:503:GLU)


Summations of interaction energy for fragment #1(A:503:GLU)
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.
-4.835-1.8949.387-6.39-5.9380.003
Interaction energy analysis for fragmet #1(A:503:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.102 / q_NPA : 0.003
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   
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].
4A504GLU-1-0.876-0.7934.0192.2952.6830.000-0.139-0.2490.000
5A505VAL00.069-0.1383.851-2.320-1.094-0.009-0.740-0.4780.003
6A505VAL0-0.0950.1076.037-0.010-0.0100.0000.0000.0000.000
7A506LEU00.041-0.1176.7100.6640.6640.0000.0000.0000.000
8A506LEU0-0.0340.1187.1450.0600.0600.0000.0000.0000.000
9A507PHE00.107-0.1059.3000.3050.3050.0000.0000.0000.000
10A507PHE0-0.0850.09811.5910.0310.0310.0000.0000.0000.000
11A508CYS00.126-0.12510.331-0.381-0.3810.0000.0000.0000.000
12A508CYS0-0.1450.09710.998-0.063-0.0630.0000.0000.0000.000
13A509GLU00.016-0.12512.6170.1170.1170.0000.0000.0000.000
14A509GLU-1-0.855-0.79416.521-0.553-0.5530.0000.0000.0000.000
15A510LYS00.110-0.03415.811-0.112-0.1120.0000.0000.0000.000
16A510LYS10.7200.97319.2500.6410.6410.0000.0000.0000.000
17A511ALA00.055-0.12118.2980.0610.0610.0000.0000.0000.000
18A511ALA0-0.0730.10517.605-0.011-0.0110.0000.0000.0000.000
19A512LYS00.114-0.06519.281-0.028-0.0280.0000.0000.0000.000
20A512LYS10.8241.03523.2400.3890.3890.0000.0000.0000.000
21A513LEU00.124-0.11420.3190.0070.0070.0000.0000.0000.000
22A513LEU0-0.1070.14318.414-0.013-0.0130.0000.0000.0000.000
23A514LEU00.037-0.13221.2600.0130.0130.0000.0000.0000.000
24A514LEU0-0.1160.11824.8560.0080.0080.0000.0000.0000.000
25A515ILE00.089-0.11423.963-0.017-0.0170.0000.0000.0000.000
26A515ILE0-0.0590.10821.911-0.004-0.0040.0000.0000.0000.000
27A516PHE00.055-0.09125.5850.0080.0080.0000.0000.0000.000
28A516PHE0-0.0540.10129.0590.0030.0030.0000.0000.0000.000
29A517ASP00.029-0.11029.068-0.012-0.0120.0000.0000.0000.000
30A517ASP-1-0.986-0.87430.780-0.237-0.2370.0000.0000.0000.000
31A518SER00.028-0.07831.6140.0060.0060.0000.0000.0000.000
32A518SER0-0.0150.05234.537-0.004-0.0040.0000.0000.0000.000
33A519ASP00.043-0.04735.016-0.002-0.0020.0000.0000.0000.000
34A519ASP-1-0.884-0.79737.692-0.171-0.1710.0000.0000.0000.000
35A520THR00.011-0.14338.0020.0130.0130.0000.0000.0000.000
36A520THR0-0.0260.08636.703-0.002-0.0020.0000.0000.0000.000
37A521LYS00.037-0.06435.3470.0080.0080.0000.0000.0000.000
38A521LYS10.7210.98936.4820.1610.1610.0000.0000.0000.000
39A522GLY00.099-0.08233.8130.0090.0090.0000.0000.0000.000
40A523TYR00.0350.01229.415-0.004-0.0040.0000.0000.0000.000
41A523TYR0-0.1200.06426.4180.0060.0060.0000.0000.0000.000
42A524THR00.057-0.10328.8690.0070.0070.0000.0000.0000.000
43A524THR00.0000.12529.838-0.008-0.0080.0000.0000.0000.000
44A525SER00.113-0.07025.799-0.021-0.0210.0000.0000.0000.000
45A525SER0-0.0500.05525.714-0.007-0.0070.0000.0000.0000.000
46A526ARG00.003-0.13923.6230.0310.0310.0000.0000.0000.000
47A526ARG10.8761.10622.6950.3490.3490.0000.0000.0000.000
48A527GLY00.027-0.10021.953-0.012-0.0120.0000.0000.0000.000
49A528VAL00.016-0.07120.963-0.012-0.0120.0000.0000.0000.000
50A528VAL0-0.0890.13320.9820.0090.0090.0000.0000.0000.000
51A529GLY00.059-0.08817.1660.0140.0140.0000.0000.0000.000
52A530GLU00.0730.04114.2070.1010.1010.0000.0000.0000.000
53A530GLU-1-0.920-0.85013.455-0.815-0.8150.0000.0000.0000.000
54A531LEU00.125-0.12512.880-0.191-0.1910.0000.0000.0000.000
55A531LEU0-0.1170.12012.5760.0350.0350.0000.0000.0000.000
56A532LYS00.066-0.1428.7280.2360.2360.0000.0000.0000.000
57A532LYS10.8941.0967.8522.3292.3290.0000.0000.0000.000
58A533LEU00.146-0.0948.810-0.125-0.1250.0000.0000.0000.000
59A533LEU0-0.1540.1219.2880.0630.0630.0000.0000.0000.000
60A534LEU00.031-0.1804.4920.5230.519-0.001-0.0030.0080.000
61A534LEU0-0.1120.1283.3790.2260.0880.0340.299-0.1950.001
62A535ARG00.184-0.0314.0840.1140.326-0.001-0.086-0.1250.000
63A535ARG10.7781.0535.184-0.179-0.1790.0000.0000.0000.000
64A536LYS00.077-0.0822.1920.669-0.7627.560-3.779-2.349-0.024
65A536LYS10.8171.0293.834-2.468-2.3260.000-0.055-0.0870.000
66A537LYS00.055-0.0952.761-3.480-2.8440.257-0.277-0.6160.002
67A537LYS10.9041.0702.687-9.622-7.7821.548-1.551-1.8370.021
68A538ASP00.003-0.0984.429-1.543-1.5470.000-0.0270.0310.000
69A538ASP-1-0.878-0.7986.1834.1644.1640.0000.0000.0000.000
70A539ASP00.056-0.1376.324-0.580-0.5800.0000.0000.0000.000
71A539ASP-1-0.978-0.8587.7580.7440.7440.0000.0000.0000.000
72A540LYS00.049-0.1467.271-0.151-0.1510.0000.0000.0000.000
73A540LYS10.8881.0716.138-2.400-2.4000.0000.0000.0000.000
74A541GLY00.038-0.0678.722-0.302-0.3020.0000.0000.0000.000
75A542LYS00.0480.0027.921-0.182-0.1820.0000.0000.0000.000
76A542LYS10.8571.0507.0130.8410.8410.0000.0000.0000.000
77A543VAL00.100-0.1276.437-0.169-0.1690.0000.0000.0000.000
78A543VAL0-0.0630.1387.8730.0040.0040.0000.0000.0000.000
79A544ARG00.053-0.0957.3200.3800.3800.0000.0000.0000.000
80A544ARG10.6930.9564.6984.5424.616-0.001-0.032-0.0410.000
81A545VAL00.095-0.0918.192-0.460-0.4600.0000.0000.0000.000
82A545VAL0-0.0520.10811.7110.0510.0510.0000.0000.0000.000
83A546LEU00.143-0.1089.0520.2310.2310.0000.0000.0000.000
84A546LEU0-0.1680.0837.971-0.094-0.0940.0000.0000.0000.000
85A547CYS00.111-0.10210.233-0.090-0.0900.0000.0000.0000.000
86A547CYS0-0.1470.10314.2420.0410.0410.0000.0000.0000.000
87A548ARG00.148-0.06613.3030.1020.1020.0000.0000.0000.000
88A548ARG10.7971.04110.2441.4631.4630.0000.0000.0000.000
89A549SER0-0.004-0.04614.444-0.021-0.0210.0000.0000.0000.000
90A549SER00.0420.03819.2550.0080.0080.0000.0000.0000.000
91A550GLU00.158-0.05918.029-0.025-0.0250.0000.0000.0000.000
92A550GLU-1-1.053-0.81820.732-0.554-0.5540.0000.0000.0000.000
93A551GLY00.009-0.11419.8730.0550.0550.0000.0000.0000.000
94A552MET00.1210.01920.8970.0320.0320.0000.0000.0000.000
95A552MET0-0.0700.11721.2660.0150.0150.0000.0000.0000.000
96A553GLY0-0.089-0.14516.506-0.024-0.0240.0000.0000.0000.000
97A554HIS00.1800.01916.251-0.082-0.0820.0000.0000.0000.000
98A554HIS0-0.1060.09819.414-0.014-0.0140.0000.0000.0000.000
99A555VAL00.048-0.10814.701-0.048-0.0480.0000.0000.0000.000
100A555VAL0-0.0890.08112.994-0.035-0.0350.0000.0000.0000.000
101A556LEU00.064-0.07015.4790.0780.0780.0000.0000.0000.000
102A556LEU0-0.0790.08317.0840.0120.0120.0000.0000.0000.000
103A557LEU00.136-0.11214.9550.0980.0980.0000.0000.0000.000
104A557LEU0-0.1120.11114.6430.0080.0080.0000.0000.0000.000
105A558ASN00.108-0.06011.641-0.177-0.1770.0000.0000.0000.000
106A558ASN0-0.1000.06110.260-0.255-0.2550.0000.0000.0000.000
107A559THR00.005-0.06611.8920.0940.0940.0000.0000.0000.000
108A559THR0-0.0060.06814.2040.0260.0260.0000.0000.0000.000
109A560SER00.144-0.06511.252-0.248-0.2480.0000.0000.0000.000
110A560SER0-0.0410.08912.1330.0190.0190.0000.0000.0000.000
111A561VAL00.039-0.13011.6630.0620.0620.0000.0000.0000.000
112A561VAL0-0.0930.12711.521-0.008-0.0080.0000.0000.0000.000
113A562VAL00.077-0.10113.5090.0440.0440.0000.0000.0000.000
114A562VAL0-0.0950.10516.6700.0070.0070.0000.0000.0000.000
115A563LYS00.159-0.10216.736-0.021-0.0210.0000.0000.0000.000
116A563LYS10.7811.01816.9560.0190.0190.0000.0000.0000.000
117A564SER0-0.006-0.09417.9370.0130.0130.0000.0000.0000.000
118A564SER0-0.0210.08421.6620.0040.0040.0000.0000.0000.000
119A565PHE00.032-0.10319.9530.0310.0310.0000.0000.0000.000
120A565PHE0-0.0350.12019.4220.0010.0010.0000.0000.0000.000
121A566LYS00.077-0.12320.204-0.009-0.0090.0000.0000.0000.000
122A566LYS10.9211.09023.3750.1770.1770.0000.0000.0000.000
123A567TYR00.020-0.06518.8410.0140.0140.0000.0000.0000.000
124A567TYR0-0.0570.13716.915-0.011-0.0110.0000.0000.0000.000
125A568GLN00.093-0.08920.378-0.008-0.0080.0000.0000.0000.000
126A568GLN0-0.0970.05823.7150.0040.0040.0000.0000.0000.000
127A569PRO00.054-0.07723.056-0.019-0.0190.0000.0000.0000.000
128A570ILE00.098-0.04025.1740.0140.0140.0000.0000.0000.000
129A570ILE0-0.1230.11826.648-0.004-0.0040.0000.0000.0000.000
130A571ASP00.007-0.13227.9720.0080.0080.0000.0000.0000.000
131A571ASP-1-0.839-0.78031.667-0.200-0.2000.0000.0000.0000.000
132A572ALA00.063-0.09729.393-0.020-0.0200.0000.0000.0000.000
133A572ALA0-0.0020.10932.3010.0030.0030.0000.0000.0000.000
134A573ASP00.053-0.13231.206-0.004-0.0040.0000.0000.0000.000
135A573ASP-1-0.937-0.79933.525-0.159-0.1590.0000.0000.0000.000
136A574ASN0-0.044-0.12329.4240.0010.0010.0000.0000.0000.000
137A574ASN0-0.1080.05328.719-0.008-0.0080.0000.0000.0000.000
138A575GLU00.199-0.09726.395-0.020-0.0200.0000.0000.0000.000
139A575GLU-1-0.890-0.81925.034-0.227-0.2270.0000.0000.0000.000
140A576ASN00.072-0.09923.942-0.027-0.0270.0000.0000.0000.000
141A576ASN0-0.0920.08424.8360.0190.0190.0000.0000.0000.000
142A577LEU00.065-0.11223.897-0.039-0.0390.0000.0000.0000.000
143A577LEU0-0.1060.10325.3890.0010.0010.0000.0000.0000.000
144A578ILE00.087-0.08920.8510.0490.0490.0000.0000.0000.000
145A578ILE0-0.0980.10119.357-0.011-0.0110.0000.0000.0000.000
146A579LYS00.156-0.08922.116-0.033-0.0330.0000.0000.0000.000
147A579LYS10.8411.07524.1340.2620.2620.0000.0000.0000.000
148A580TRP00.063-0.09319.2130.0120.0120.0000.0000.0000.000
149A580TRP0-0.0900.08613.948-0.014-0.0140.0000.0000.0000.000
150A581PRO00.011-0.11120.217-0.004-0.0040.0000.0000.0000.000
151A582ILE00.0700.00819.583-0.037-0.0370.0000.0000.0000.000
152A582ILE0-0.0930.10317.355-0.027-0.0270.0000.0000.0000.000
153A583ILE00.163-0.10620.2120.0300.0300.0000.0000.0000.000
154A583ILE0-0.1310.11021.2280.0020.0020.0000.0000.0000.000
155A584THR0-0.014-0.09621.028-0.042-0.0420.0000.0000.0000.000
156A584THR0-0.0580.03722.449-0.009-0.0090.0000.0000.0000.000
157A585ASP00.023-0.07123.4830.0210.0210.0000.0000.0000.000
158A585ASP-1-0.864-0.81725.874-0.285-0.2850.0000.0000.0000.000
159A586GLY00.043-0.10424.9660.0200.0200.0000.0000.0000.000
160A587LYS00.0660.01526.5830.0190.0190.0000.0000.0000.000
161A587LYS10.7680.97527.2330.2610.2610.0000.0000.0000.000
162A588LEU00.098-0.08725.081-0.027-0.0270.0000.0000.0000.000
163A588LEU0-0.1060.09723.7720.0030.0030.0000.0000.0000.000
164A589GLU00.020-0.11724.3560.0250.0250.0000.0000.0000.000
165A589GLU-1-0.879-0.77323.570-0.363-0.3630.0000.0000.0000.000
166A590THR00.027-0.10523.562-0.026-0.0260.0000.0000.0000.000
167A590THR0-0.0330.08223.8550.0090.0090.0000.0000.0000.000
168A591PHE00.089-0.08121.2990.0370.0370.0000.0000.0000.000
169A591PHE0-0.0650.09819.323-0.026-0.0260.0000.0000.0000.000
170A592ILE00.083-0.13922.6450.0020.0020.0000.0000.0000.000
171A592ILE0-0.0990.12924.2490.0040.0040.0000.0000.0000.000
172A593ILE00.097-0.09019.288-0.004-0.0040.0000.0000.0000.000
173A593ILE0-0.0890.11616.735-0.017-0.0170.0000.0000.0000.000
174A594LYS00.112-0.07620.7060.0220.0220.0000.0000.0000.000
175A594LYS10.8651.04123.8620.3180.3180.0000.0000.0000.000
176A595VAL00.055-0.07921.036-0.035-0.0350.0000.0000.0000.000
177A595VAL0-0.0550.13018.947-0.004-0.0040.0000.0000.0000.000
178A596LYS00.005-0.11822.0530.0370.0370.0000.0000.0000.000
179A596LYS10.7510.97120.5500.4780.4780.0000.0000.0000.000
180A597GLN00.113-0.10423.8060.0280.0280.0000.0000.0000.000
181A597GLN0-0.0630.12024.2590.0110.0110.0000.0000.0000.000
182A598LYS00.100-0.09523.913-0.040-0.0400.0000.0000.0000.000
183A598LYS10.7811.06927.4790.2180.2180.0000.0000.0000.000
184A599ALA00.078-0.08124.270-0.003-0.0030.0000.0000.0000.000
185A599ALA0-0.0480.08524.2590.0050.0050.0000.0000.0000.000
186A600ASP00.038-0.14420.2840.0070.0070.0000.0000.0000.000
187A600ASP-1-0.887-0.80020.033-0.429-0.4290.0000.0000.0000.000
188A601GLY0-0.008-0.08219.416-0.054-0.0540.0000.0000.0000.000
189A602ARG00.1380.02920.670-0.027-0.0270.0000.0000.0000.000
190A602ARG10.7701.01023.1340.2260.2260.0000.0000.0000.000
191A603ARG00.094-0.08518.8600.0240.0240.0000.0000.0000.000
192A603ARG10.8621.06416.9730.3630.3630.0000.0000.0000.000
193A604LEU00.063-0.10115.882-0.011-0.0110.0000.0000.0000.000
194A604LEU0-0.0810.10914.505-0.007-0.0070.0000.0000.0000.000
195A605VAL00.059-0.10116.326-0.061-0.0610.0000.0000.0000.000
196A605VAL0-0.0640.10720.4680.0080.0080.0000.0000.0000.000
197A606GLY0-0.009-0.11618.2700.0200.0200.0000.0000.0000.000
198A607ALA00.1390.03614.1300.0820.0820.0000.0000.0000.000
199A607ALA0-0.1040.09613.057-0.032-0.0320.0000.0000.0000.000
200A608VAL00.060-0.10713.581-0.004-0.0040.0000.0000.0000.000
201A608VAL0-0.1000.08813.568-0.016-0.0160.0000.0000.0000.000
202A609ALA00.104-0.07414.7310.0160.0160.0000.0000.0000.000
203A609ALA0-0.0340.07218.7460.0080.0080.0000.0000.0000.000
204A610ASP0-0.015-0.10315.3890.0580.0580.0000.0000.0000.000
205A610ASP-1-0.944-0.86013.432-0.102-0.1020.0000.0000.0000.000
206A611ALA00.130-0.07811.4780.1460.1460.0000.0000.0000.000
207A611ALA0-0.0970.09010.665-0.051-0.0510.0000.0000.0000.000
208A612GLN00.035-0.14612.3690.0760.0760.0000.0000.0000.000
209A612GLN0-0.1290.06815.2880.0120.0120.0000.0000.0000.000
210A613GLN00.036-0.08915.0330.0510.0510.0000.0000.0000.000
211A613GLN0-0.0930.07317.2120.0230.0230.0000.0000.0000.000
212A614ALA00.095-0.08112.9720.0350.0350.0000.0000.0000.000
213A614ALA0-0.0770.10212.3080.0120.0120.0000.0000.0000.000
214A615MET0-0.106-0.13212.8860.1200.1200.0000.0000.0000.000
215A615MET0-0.0260.02311.782-0.013-0.0130.0000.0000.0000.000