FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 8NKYY

Calculation Name: 1GPQ-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1GPQ

Chain ID: A

ChEMBL ID:

UniProt ID: P0AD59

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 239
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1047174.803743
FMO2-HF: Nuclear repulsion 997515.313923
FMO2-HF: Total energy -49659.48982
FMO2-MP2: Total energy -49800.16282


3D Structure Molmil
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:2:ASP)


Summations of interaction energy for fragment #1(A:2:ASP)
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.
3.2924.959-0.012-0.875-0.7790.005
Interaction energy analysis for fragmet #1(A:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.113 / q_NPA : 0.013
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].
4A3ASP-1-0.897-0.7784.5454.8025.1530.000-0.133-0.2170.000
5A4LEU00.111-0.0943.787-2.532-1.216-0.012-0.742-0.5620.005
6A4LEU0-0.0960.1097.1600.0490.0490.0000.0000.0000.000
7A5THR0-0.034-0.1016.4940.6620.6620.0000.0000.0000.000
8A5THR0-0.0340.0766.1450.0390.0390.0000.0000.0000.000
9A6ILE00.206-0.0588.511-0.281-0.2810.0000.0000.0000.000
10A6ILE0-0.0840.10512.7690.0120.0120.0000.0000.0000.000
11A7SER00.041-0.07910.059-0.113-0.1130.0000.0000.0000.000
12A7SER0-0.0530.0559.0520.0330.0330.0000.0000.0000.000
13A8SER00.007-0.0946.5910.2150.2150.0000.0000.0000.000
14A8SER00.0100.1035.6460.1730.1730.0000.0000.0000.000
15A9LEU00.038-0.1238.013-0.292-0.2920.0000.0000.0000.000
16A9LEU0-0.0720.11710.2700.0420.0420.0000.0000.0000.000
17A10ALA00.132-0.07210.833-0.024-0.0240.0000.0000.0000.000
18A10ALA0-0.0920.09212.9700.0320.0320.0000.0000.0000.000
19A11LYS0-0.012-0.13610.9210.1310.1310.0000.0000.0000.000
20A11LYS10.8231.0469.6550.4010.4010.0000.0000.0000.000
21A12GLY00.036-0.0679.785-0.073-0.0730.0000.0000.0000.000
22A13GLU00.081-0.01110.5170.2260.2260.0000.0000.0000.000
23A13GLU-1-0.908-0.79012.673-0.873-0.8730.0000.0000.0000.000
24A14THR0-0.042-0.13012.3310.1720.1720.0000.0000.0000.000
25A14THR0-0.0280.07212.295-0.064-0.0640.0000.0000.0000.000
26A15THR00.030-0.08612.8050.1430.1430.0000.0000.0000.000
27A15THR0-0.0270.07711.720-0.104-0.1040.0000.0000.0000.000
28A16LYS00.171-0.03913.9900.1090.1090.0000.0000.0000.000
29A16LYS10.7010.99713.9230.8800.8800.0000.0000.0000.000
30A17ALA00.089-0.11415.3740.0790.0790.0000.0000.0000.000
31A17ALA0-0.0530.10819.0100.0020.0020.0000.0000.0000.000
32A18ALA00.142-0.11617.6270.0790.0790.0000.0000.0000.000
33A18ALA0-0.0680.14516.872-0.009-0.0090.0000.0000.0000.000
34A19PHE00.130-0.07916.3410.0710.0710.0000.0000.0000.000
35A19PHE0-0.1130.08115.4540.0090.0090.0000.0000.0000.000
36A20ASN00.053-0.09617.5850.0620.0620.0000.0000.0000.000
37A20ASN0-0.1080.05419.062-0.012-0.0120.0000.0000.0000.000
38A21GLN00.067-0.11820.4860.0450.0450.0000.0000.0000.000
39A21GLN0-0.0780.10821.912-0.020-0.0200.0000.0000.0000.000
40A22MET00.162-0.07120.6320.0400.0400.0000.0000.0000.000
41A22MET0-0.1640.09417.359-0.001-0.0010.0000.0000.0000.000
42A23VAL0-0.043-0.12321.3680.0370.0370.0000.0000.0000.000
43A23VAL0-0.1000.08819.7160.0040.0040.0000.0000.0000.000
44A24GLN00.171-0.08922.6100.0250.0250.0000.0000.0000.000
45A24GLN0-0.0860.12725.232-0.013-0.0130.0000.0000.0000.000
46A25GLY0-0.067-0.13725.6530.0110.0110.0000.0000.0000.000
47A26HIS00.026-0.00625.7640.0190.0190.0000.0000.0000.000
48A26HIS0-0.0400.11624.8010.0150.0150.0000.0000.0000.000
49A27LYS00.145-0.09225.235-0.018-0.0180.0000.0000.0000.000
50A27LYS10.8041.06423.8560.0820.0820.0000.0000.0000.000
51A28LEU00.010-0.14921.7080.0240.0240.0000.0000.0000.000
52A28LEU0-0.0090.14420.042-0.001-0.0010.0000.0000.0000.000
53A29PRO00.000-0.10121.304-0.007-0.0070.0000.0000.0000.000
54A30ALA00.1520.01519.868-0.019-0.0190.0000.0000.0000.000
55A30ALA0-0.0730.10819.9440.0020.0020.0000.0000.0000.000
56A31TRP0-0.033-0.13817.252-0.026-0.0260.0000.0000.0000.000
57A31TRP0-0.0680.09716.3090.0050.0050.0000.0000.0000.000
58A32VAL00.082-0.08815.5080.0500.0500.0000.0000.0000.000
59A32VAL0-0.0620.10816.007-0.005-0.0050.0000.0000.0000.000
60A33MET00.143-0.09614.0420.0010.0010.0000.0000.0000.000
61A33MET0-0.0760.12215.2130.0170.0170.0000.0000.0000.000
62A34LYS00.072-0.07212.817-0.086-0.0860.0000.0000.0000.000
63A34LYS10.8671.05714.061-0.156-0.1560.0000.0000.0000.000
64A35GLY0-0.011-0.09910.8540.0270.0270.0000.0000.0000.000
65A36GLY0-0.054-0.02511.8010.0830.0830.0000.0000.0000.000
66A37THR00.0770.02612.1360.1070.1070.0000.0000.0000.000
67A37THR0-0.0360.06914.7860.0030.0030.0000.0000.0000.000
68A38TYR00.004-0.07811.199-0.136-0.1360.0000.0000.0000.000
69A38TYR0-0.1600.0016.216-0.294-0.2940.0000.0000.0000.000
70A39THR0-0.001-0.09812.2900.1940.1940.0000.0000.0000.000
71A39THR0-0.0080.07614.094-0.016-0.0160.0000.0000.0000.000
72A40PRO00.011-0.10910.053-0.077-0.0770.0000.0000.0000.000
73A41ALA00.1490.04310.194-0.016-0.0160.0000.0000.0000.000
74A41ALA0-0.0790.06310.459-0.057-0.0570.0000.0000.0000.000
75A42GLN0-0.002-0.11912.0070.0690.0690.0000.0000.0000.000
76A42GLN0-0.0590.10015.3500.0480.0480.0000.0000.0000.000
77A43THR00.085-0.07915.190-0.067-0.0670.0000.0000.0000.000
78A43THR0-0.0840.05315.4370.0170.0170.0000.0000.0000.000
79A44VAL00.018-0.09117.1370.0480.0480.0000.0000.0000.000
80A44VAL0-0.0730.09219.1130.0020.0020.0000.0000.0000.000
81A45THR00.031-0.07920.545-0.044-0.0440.0000.0000.0000.000
82A45THR0-0.0600.07022.412-0.011-0.0110.0000.0000.0000.000
83A46LEU00.119-0.08423.2270.0280.0280.0000.0000.0000.000
84A46LEU0-0.1060.09424.0440.0000.0000.0000.0000.0000.000
85A47GLY00.011-0.09525.968-0.017-0.0170.0000.0000.0000.000
86A48ASP00.007-0.00827.1760.0100.0100.0000.0000.0000.000
87A48ASP-1-0.925-0.87027.971-0.185-0.1850.0000.0000.0000.000
88A49GLU00.041-0.14623.798-0.021-0.0210.0000.0000.0000.000
89A49GLU-1-0.881-0.79823.230-0.285-0.2850.0000.0000.0000.000
90A50THR00.046-0.05220.2350.0330.0330.0000.0000.0000.000
91A50THR0-0.0520.06518.232-0.004-0.0040.0000.0000.0000.000
92A51TYR0-0.012-0.12218.129-0.055-0.0550.0000.0000.0000.000
93A51TYR0-0.0830.08318.694-0.001-0.0010.0000.0000.0000.000
94A52GLN00.160-0.04813.7430.0720.0720.0000.0000.0000.000
95A52GLN0-0.0510.12511.6510.0390.0390.0000.0000.0000.000
96A53VAL00.058-0.12815.096-0.062-0.0620.0000.0000.0000.000
97A53VAL0-0.0700.11317.5600.0050.0050.0000.0000.0000.000
98A54MET00.078-0.11713.0420.0620.0620.0000.0000.0000.000
99A54MET0-0.0650.11311.324-0.084-0.0840.0000.0000.0000.000
100A55SER00.042-0.04514.146-0.072-0.0720.0000.0000.0000.000
101A55SER00.0030.08116.6280.0200.0200.0000.0000.0000.000
102A56ALA00.104-0.07513.7510.0710.0710.0000.0000.0000.000
103A56ALA0-0.1210.07913.242-0.009-0.0090.0000.0000.0000.000
104A57CYS00.056-0.11015.145-0.071-0.0710.0000.0000.0000.000
105A57CYS0-0.2100.23918.2460.0270.0270.0000.0000.0000.000
106A58LYS00.145-0.10916.9140.0470.0470.0000.0000.0000.000
107A58LYS10.7251.02320.826-0.129-0.1290.0000.0000.0000.000
108A59PRO0-0.014-0.12115.7680.0110.0110.0000.0000.0000.000
109A60HIS00.0010.02318.365-0.034-0.0340.0000.0000.0000.000
110A60HIS0-0.0820.07718.892-0.005-0.0050.0000.0000.0000.000
111A61ASP00.213-0.06421.336-0.010-0.0100.0000.0000.0000.000
112A61ASP-1-0.914-0.77423.1960.1380.1380.0000.0000.0000.000
113A62CYS00.071-0.14220.843-0.033-0.0330.0000.0000.0000.000
114A63GLY00.045-0.09521.592-0.013-0.0130.0000.0000.0000.000
115A64SER00.0270.00624.495-0.016-0.0160.0000.0000.0000.000
116A64SER0-0.0550.05625.422-0.003-0.0030.0000.0000.0000.000
117A65GLN00.151-0.06723.393-0.023-0.0230.0000.0000.0000.000
118A65GLN0-0.1210.06522.6800.0050.0050.0000.0000.0000.000
119A66ARG00.008-0.12319.8440.0300.0300.0000.0000.0000.000
120A66ARG10.8131.02119.863-0.100-0.1000.0000.0000.0000.000
121A67ILE00.037-0.09118.712-0.017-0.0170.0000.0000.0000.000
122A67ILE0-0.1110.05216.679-0.005-0.0050.0000.0000.0000.000
123A68ALA00.148-0.08217.6940.0360.0360.0000.0000.0000.000
124A68ALA0-0.0460.12219.5410.0040.0040.0000.0000.0000.000
125A69VAL00.033-0.11316.5250.0050.0050.0000.0000.0000.000
126A69VAL0-0.0890.07615.566-0.008-0.0080.0000.0000.0000.000
127A70MET00.146-0.06116.8340.0080.0080.0000.0000.0000.000
128A70MET0-0.1320.09419.4520.0170.0170.0000.0000.0000.000
129A71TRP00.062-0.12015.2380.0280.0280.0000.0000.0000.000
130A71TRP0-0.0820.08911.012-0.043-0.0430.0000.0000.0000.000
131A72SER00.151-0.04216.585-0.013-0.0130.0000.0000.0000.000
132A72SER0-0.0220.08119.893-0.002-0.0020.0000.0000.0000.000
133A73GLU00.058-0.12215.9010.0100.0100.0000.0000.0000.000
134A73GLU-1-0.968-0.84112.959-1.010-1.0100.0000.0000.0000.000
135A74LYS00.050-0.07916.759-0.015-0.0150.0000.0000.0000.000
136A74LYS10.7180.99520.6120.2590.2590.0000.0000.0000.000
137A75SER00.005-0.07120.3130.0080.0080.0000.0000.0000.000
138A75SER0-0.0370.06121.7330.0130.0130.0000.0000.0000.000
139A76ASN00.036-0.08017.7010.0230.0230.0000.0000.0000.000
140A76ASN0-0.1030.05716.4650.0380.0380.0000.0000.0000.000
141A77GLN00.113-0.13017.983-0.052-0.0520.0000.0000.0000.000
142A77GLN0-0.0860.09021.6880.0300.0300.0000.0000.0000.000
143A78MET00.131-0.05418.094-0.013-0.0130.0000.0000.0000.000
144A78MET0-0.1530.09914.5790.0090.0090.0000.0000.0000.000
145A79THR00.020-0.09219.1300.0160.0160.0000.0000.0000.000
146A79THR0-0.0640.08422.206-0.002-0.0020.0000.0000.0000.000
147A80GLY00.059-0.10320.115-0.010-0.0100.0000.0000.0000.000
148A81LEU00.053-0.02321.069-0.001-0.0010.0000.0000.0000.000
149A81LEU0-0.0850.12822.5600.0010.0010.0000.0000.0000.000
150A82PHE00.168-0.05521.6740.0130.0130.0000.0000.0000.000
151A82PHE0-0.1250.06920.5200.0000.0000.0000.0000.0000.000
152A83SER00.004-0.11823.300-0.011-0.0110.0000.0000.0000.000
153A83SER0-0.0460.05724.0470.0070.0070.0000.0000.0000.000
154A84THR00.062-0.05424.5810.0160.0160.0000.0000.0000.000
155A84THR0-0.0660.04626.544-0.001-0.0010.0000.0000.0000.000
156A85ILE00.021-0.12627.139-0.016-0.0160.0000.0000.0000.000
157A85ILE0-0.0310.14026.6310.0000.0000.0000.0000.0000.000
158A86ASP00.105-0.05529.2630.0080.0080.0000.0000.0000.000
159A86ASP-1-0.926-0.82333.2390.0570.0570.0000.0000.0000.000
160A87GLU00.145-0.10232.263-0.008-0.0080.0000.0000.0000.000
161A87GLU-1-0.986-0.84731.9140.0970.0970.0000.0000.0000.000
162A88LYS00.130-0.08033.569-0.001-0.0010.0000.0000.0000.000
163A88LYS10.7521.00535.058-0.066-0.0660.0000.0000.0000.000
164A89THR0-0.077-0.06936.265-0.002-0.0020.0000.0000.0000.000
165A89THR0-0.1020.01836.532-0.003-0.0030.0000.0000.0000.000
166A90SER00.062-0.07735.160-0.006-0.0060.0000.0000.0000.000
167A90SER0-0.0080.09436.7310.0010.0010.0000.0000.0000.000
168A91GLN00.037-0.11934.607-0.003-0.0030.0000.0000.0000.000
169A91GLN0-0.1120.04634.809-0.008-0.0080.0000.0000.0000.000
170A92GLU00.111-0.08230.6110.0080.0080.0000.0000.0000.000
171A92GLU-1-0.813-0.71527.2530.0560.0560.0000.0000.0000.000
172A93LYS00.050-0.08130.148-0.007-0.0070.0000.0000.0000.000
173A93LYS10.8051.03030.555-0.018-0.0180.0000.0000.0000.000
174A94LEU00.041-0.13227.7940.0060.0060.0000.0000.0000.000
175A94LEU0-0.0660.12826.839-0.002-0.0020.0000.0000.0000.000
176A95THR00.015-0.08526.796-0.002-0.0020.0000.0000.0000.000
177A95THR0-0.0240.06926.2280.0000.0000.0000.0000.0000.000
178A96TRP00.094-0.08625.721-0.001-0.0010.0000.0000.0000.000
179A96TRP0-0.1060.08825.686-0.003-0.0030.0000.0000.0000.000
180A97LEU00.019-0.13123.3180.0060.0060.0000.0000.0000.000
181A97LEU0-0.0930.10221.201-0.001-0.0010.0000.0000.0000.000
182A98ASN00.154-0.03423.846-0.008-0.0080.0000.0000.0000.000
183A98ASN0-0.1260.07222.7630.0100.0100.0000.0000.0000.000
184A99VAL00.115-0.10325.173-0.024-0.0240.0000.0000.0000.000
185A99VAL0-0.0820.08125.8490.0040.0040.0000.0000.0000.000
186A100ASN00.076-0.03226.6420.0150.0150.0000.0000.0000.000
187A100ASN0-0.0490.05025.3670.0140.0140.0000.0000.0000.000
188A101ASP00.120-0.12228.5460.0050.0050.0000.0000.0000.000
189A101ASP-1-0.980-0.83232.353-0.111-0.1110.0000.0000.0000.000
190A102ALA00.113-0.07128.8080.0170.0170.0000.0000.0000.000
191A102ALA0-0.0710.09927.893-0.004-0.0040.0000.0000.0000.000
192A103LEU00.023-0.11426.3070.0100.0100.0000.0000.0000.000
193A103LEU0-0.0760.10023.3430.0010.0010.0000.0000.0000.000
194A104SER00.030-0.12927.6750.0090.0090.0000.0000.0000.000
195A104SER0-0.0460.08131.5450.0050.0050.0000.0000.0000.000
196A105ILE00.030-0.08630.5840.0080.0080.0000.0000.0000.000
197A105ILE0-0.0740.10532.5260.0010.0010.0000.0000.0000.000
198A106ASP00.141-0.15329.1220.0090.0090.0000.0000.0000.000
199A106ASP-1-0.923-0.79828.354-0.065-0.0650.0000.0000.0000.000
200A107GLY00.024-0.07725.2690.0040.0040.0000.0000.0000.000
201A108LYS00.077-0.00825.0660.0010.0010.0000.0000.0000.000
202A108LYS10.8381.06327.9730.0740.0740.0000.0000.0000.000
203A109THR0-0.002-0.09426.6940.0110.0110.0000.0000.0000.000
204A109THR0-0.0360.08228.3020.0040.0040.0000.0000.0000.000
205A110VAL00.074-0.09423.7540.0250.0250.0000.0000.0000.000
206A110VAL0-0.0510.12521.670-0.002-0.0020.0000.0000.0000.000
207A111LEU00.124-0.07621.7780.0210.0210.0000.0000.0000.000
208A111LEU0-0.1170.07320.3990.0010.0010.0000.0000.0000.000
209A112PHE00.123-0.09322.6330.0180.0180.0000.0000.0000.000
210A112PHE0-0.1080.09026.8080.0000.0000.0000.0000.0000.000
211A113ALA00.044-0.13224.6120.0230.0230.0000.0000.0000.000
212A113ALA0-0.0460.12424.193-0.001-0.0010.0000.0000.0000.000
213A114ALA00.080-0.09519.9940.0350.0350.0000.0000.0000.000
214A114ALA0-0.0610.09618.955-0.007-0.0070.0000.0000.0000.000
215A115LEU00.015-0.11220.3630.0380.0380.0000.0000.0000.000
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